WO2017120285A1

WO2017120285A1 - METHODS OF USING miRNA FROM BODILY FLUIDS FOR DIAGNOSIS AND MONITORING OF NEURODEVELOPMENTAL DISORDERS

Info

Publication number: WO2017120285A1
Application number: PCT/US2017/012258
Authority: WO
Inventors: Samuil R. Umansky; Kira S. Sheinerman; Vladimir G. TSIVINSKY
Original assignee: DiamiR LLC
Current assignee: DiamiR LLC
Priority date: 2016-01-05
Filing date: 2017-01-05
Publication date: 2017-07-13
Anticipated expiration: 2018-07-05

Abstract

The invention provides methods for diagnosis and monitoring of Rett syndrome and other neurodevelopmental disorders by quantitative analysis of miRNAs in bodily fluids.

Description

METHODS OF USING miRNA FROM BODILY FLUIDS FOR DIAGNOSIS AND MONITORING OF NEURODEVELOPMENTAL DISORDERS

CROSS REFERENCE TO RELATED APPLICATIONS

The present application claims priority to U.S. Provisional Patent Application Serial No. 62/274,999, filed on January 5, 2016, and U.S. Provisional Patent Application Serial No. 62/396,577, filed on September 19, 2016, both of which are hereby incorporated by reference in their entirety.

TECHNICAL FIELD OF THE INVENTION

BACKGROUND OF THE INVENTION

Neurodevelopmental disorders (NDDs) include pathologies caused by disturbances of the nervous system development. Some of NDDs, such as Rett syndrome, Tourette syndrome and others are rare, but some, for example Autism Spectrum Disorders, are much more common. Early minimally invasive tests for early detection of NDDs are very important for the following reasons. First, although there is no effective treatment for most of NDDs, early symptomatic treatment may significantly improve patient health. Second, due to variability of mutations causing particular NDDs and other factors these disorders are characterized by the wide phenotypical and clinical heterogeneity, and biomarkers capable of predicting disease development and outcome would be very useful. Finally and maybe most importantly, such biomarkers would be extremely helpful on all stages of drug/treatment development, including use of animal models in preclinical studies, patient involvement and stratification for clinical studies and treatment monitoring.

Rett syndrome (RTT) is a monogenic X-linked disorder caused by mutations in MECP2 gene, which encodes the methyl-CpG binding protein 2 (Renieri A et al. Rett syndrome: the complex nature of a monogenic disease. J Mol Med (Berl). 2003; 81(6):346-54). Due to severe encephalopathy caused by a mutation in the single copy of MECP2 male fetuses usually die before birth, so the disease affects females almost exclusively (~1 in 10,000). An advantage of using RTT as an example for developing diagnostic tests for NDDs in general is the existence of several mouse models of RTT (see below). Of course, potential biomarkers should be evolutionary conservative to be applicable for both human and animals.

MicroRNAs (miRNAs) are a class of non-coding RNAs whose final product is an approximately 22 nt functional RNA molecule. They play important roles in the regulation of target genes by binding to complementary regions of messenger transcripts to repress their translation or regulate degradation (Griffiths-Jones Nucleic Acids Research. 2006; 34, Database issue: D140-D144; Jin and Xiao, Frontiers in Genetics. 2015; 6:328). Frequently, one miRNA can target multiple mRNAs and one mRNA can be regulated by multiple miRNAs targeting different regions of the 3' UTR. Once bound to an mRNA, miRNA can modulate gene expression and protein production by affecting, e.g., mRNA translation and stability (Baek et al. Nature. 2008; 455:64; Selbach et al. Nature. 2008; 455:58; Ambros. Nature. 2004; 431 : 350-355; Bartel. Cell. 2004; 116: 281-297; Cullen. Virus Research. 2004; 102: 3-9; He et al. Nat. Rev. Genet. 2004; 5: 522-531; and Ying et al. Gene. 2004; 342: 25-28). There are other classes of less characterized small RNAs (reviewed in Kim. Mol. Cells. 2005; 19: 1-15).

Many of miRNAs are specific to or over-expressed in certain organs / tissues / cells (see, e.g., Hua et al. BMC Genomics. 2009; 10:214; Liang et al. BMC Genomics. 2007; 8: 166; Landgraf et al. Cell. 2007; 129: 1401-1414; Lee et al. RNA. 2008; 14:35-42) and in different brain areas, such as hippocampus, midbrain, frontal cortex, pituitary gland, and in different cell types, such as neurons and glial cells (Sempere et al. Genome Biol. 2004; 5: R13; Deo et al. Dev. Din. 2006; 235:2538-2548; Bak et al. RNA. 2008; 14: 432-444; Trivedi and Ramakrishna Int.J.Neurosci. 2009; 119: 1995-2016; Weng et al. Biomed. Res. 2011; 32: 135-141; He et al. Neuron. 2012; 73 : 35-48).

Some miRNAs, including those that are cell-specific, are enriched in certain cellular compartments, particularly in axons, dendrites and synapses (see, e.g., Schratt et al. Nature. 2006; 439:283-289; Lugli et al. J. Neurochem. 2008; 106:650-661; Bicker and Schratt. J. Cell. Mol. Med. 2008; 12: 1466-1476; Smalheiser and Lugli. Neuromolecular Med. 2009; 11 : 133-140; Rajasethupathy. Neuron. 2009; 63 :714-716; Kye. RNA. 2007; 13 : 1224-1234; Yu et al. Exp Cell Res. 2008; 314:2618-2633; Cougot et al. J. Neurosci. 2008; 28: 13793-13804; Kawahara. Brain Nerve. 2008. 60: 1437-1444; Schratt G. Rev Neurosci. 2009; 10:842-849; Pichardo-Casas et al. Brain Research. 2012; 1436:20-33). Expression and concentrations of miRNAs are regulated by various physiological and pathological signals. Changes in expression of some miRNAs were found in neurons of Parkinson's, Alzheimer's and other neurodegenerative disease patients (Hebert and De Strooper. Trends Neurosci. 2009; 32: 199-206; Saba et al. PLoS One. 2008; 3 :e3652; Kocerha et al. Neuromolecular Med. 2009; 11 : 162-172; Sethi and Lukiw. Neurosci Lett. 2009; 459: 100-104; Zeng; Mol Pharmacol. 2009; 75:259-264; Cogswell et al. Journal of Alzheimer' s disease. 2008; 14: 27-41; Schaefer et al. J. Exp. Med. 2007; 204: 1553-1558; Hebert. Proc. Natl. Acad. Sci. USA. 2008; 105:6415-6420; Wanget al. J. Neurosci. 2008; 28: 1213-1223; Nelson et al. Brain Pathol. 2008; 18: 130-138; Lukiw. Neuroreport. 2007; 18:297-300) as well as in subjects with NDDs (Im, Kenny. Trends Neurosci. 2012; 35:325-334; Sun, Shi. Exp. Neurol. 2015; 268: 46- 53).

For the use of miRNA in diagnostics, it is also important that miRNA secretion varies depending on cellular physiology (Palma et al. Nucleic Acids Res. 2012; 40:9125-9138; Pigati et al. PLoS One. 2010; 5: el3515). In addition to miRNA release into extracellular space and subsequent appearance in the bodily fluids due to cell death, miRNA appear in circulation due to blebbing of apoptotic bodies, budding and shedding of microvesicles, active secretion in the form of exosomes and of miRNA complexes with proteins (AG02, NPMl and others) and high density lipoproteins (HDL) (reviews: Sun et al. Clin. Chem. Lab. Med. 2012; 50: 2121-2126; Zandberga et al. Genes Chromosomes Cancer. 2013; 52: 356-369). All these forms of cell-free miRNA are highly stable in the bloodstream and other bodily fluids. The secretion of miRNA is selective and can be significantly changed by various pathological processes. For example, changes in the spectrum of miRNA secreted in exosomes from prion-infected neuronal cells, as compared to uninfected cells, have been demonstrated (Belingham et al. Nucleic Acids Res. 2012; 40: 10937-10949).

Two approaches are widely used for searching miRNA biomarkers of various diseases in bodily fluids:

1. Measurement of hundreds of different miRNA in a bodily fluid from patients with a pathology of interest and from control subjects using miRNA array or next generation sequencing (NGS) (Qin et al. Cancer Inform. 2013; 12: 83-101). While this approach allows to analyze a huge numbers of various miRNA, currently the miRNA array-based and sequencing techniques are not sufficiently sensitive to detect many miRNA whose concentration in bodily fluids is relatively low. As a consequence, most of the miRNA detectable in bodily fluids by arrays and NGS are ubiquitous miRNA expressed in all or many tissues, and many of them derive from blood cells (Pritchard et al. Cancer Prev. Res. (Phila). 2012; 5:492-497; Leidner and Thompson. PLoS One. 2013; 8: 57841). The detection of changes in the concentrations of such ubiquitous miRNA in patients with one pathology does not mean that the same miRNA cannot be involved in other diseases of different organs. Many miRNA are associated with a particular pathology type, such as cancer, inflammation, hypoxia, etc., and changes in their concentration in bodily fluids can be associated with diseases of different organs. For example, changes of miR-155 concentrations were found in the bloodstream of patients with breast, esophageal, lung, pancreatic cancers and lymphomas (Blair and Yan. DNA Cell Biol. 2012; 31 Suppl. 1 : S49-61; Xie et al. Bioinformatics. 2013; 29: 638-644). Level of miR-21 increases in plasma/serum of patients with osteosarcoma, bladder, esophageal, gastric, lung, breast, colorectal cancers, neck squamous cell carcinoma and other tumors (Blair and Yan. DNA Cell Biol. 2012; 31 Suppl. 1 : S49-61; Farazi et al. J. Pathol. 2011; 223 : 102-115; Xie et al, Bioinformatics. 2013; 29: 638- 644). It follows that the potential biomarkers found by miRNA arrays should be also tested in other pathologies, not only in healthy control subjects.

2. The second approach is based on analysis of disease-specific miRNAs identified by comparison of miRNAs isolated from pathologic and normal tissue, organ or cell type. Here, subsequent to identification of disease-specific miRNAs (e.g., by an array followed by RT-PCR), their presence in bodily fluids is analyzed. In this strategy, since a limited number of circulating miRNAs is tested, the use of individual RT-PCR is possible which allows to increase sensitivity and reproducibility of the analysis. However, in many cases when this method was applied, no correlation was detected between miRNA concentration and pathology-induced changes in the tissue and in bodily fluids (Boeri et al., Proc. Natl. Acad. Sci. USA. 2011; 108: 3713-3718; Cuk et al. Int. J. Cancer. 2013; 132: 1602-1612). This phenomenon can be explained by several factors: (i) if pathology is caused by, or associated with, the change in concentration of a ubiquitous miRNA, the effect of the pathology on the concentration of this miRNA in circulation could be very limited, since only a small fraction of the miRNA in circulation comes from the affected organ or tissue; (ii) changes in miRNA concentration due to pathology development can be accompanied by much more prominent opposite changes in miRNA secretion/excretion, which neutralizes or even overcomes the effect of changed miRNA expression. SUMMARY OF THE INVENTION

There is a great need in the art in sensitive methods of early detection of neurodevelopmental disorders such as Rett Syndrome (RTT). The present invention addresses this and other needs by providing methods for early diagnosis, progression and treatment monitoring of RTT and its differentiation from other pathologies by quantifying brain-enriched miRNAs in bodily fluids.

In one aspect, the invention provides a method for detecting a neurodevelopmental disorder in a subject, which method comprises:

a) measuring the level of a first brain-enriched miRNA (e.g., synapse and/or neurite miRNA) in a bodily fluid sample collected from the subject, wherein said first brain-enriched miRNA is enriched in a brain area(s) affected by the neurodevelopmental disorder;

b) measuring the level of a second brain-enriched miRNA in the same bodily fluid sample collected from the subject, wherein said second brain-enriched miRNA (i) is enriched in a brain area(s) which is not affected by the neurodevelopmental disorder, or (ii) is enriched in a brain cell type which is not affected by the neurodevelopmental disorder, or (iii) is enriched in the same brain area as the first miRNA, but its expression and/or secretion change differently than expression and/or secretion of the first miRNA during development of the neurodevelopmental disorder;

c) calculating the ratio of the levels of the miRNAs measured in steps (a) and (b);

d) comparing the ratio of the levels of the miRNAs calculated in step (c) with a corresponding control ratio, and

e) (i) identifying the subject as being afflicted with the neurodevelopmental disorder when the ratio of the levels of the miRNAs calculated in step (c) is higher than the corresponding control ratio or (ii) identifying the subject as not being afflicted with the neurodevelopmental disorder when the ratio of the levels of the miRNA calculated in step (c) is not higher than the corresponding control ratio.

In one embodiment, the method further comprises the following steps, which steps can be performed simultaneously or sequentially with each other and/or with the steps (d)-(e) of the above method: f) comparing the ratio of the levels of the miRNAs calculated in step (c) with the standard range of ratios of said miRNAs characteristic of another pathology ("a second pathology"), and g) (i) excluding the diagnosis of the second pathology in the subject if the ratio of the levels of the miRNAs calculated in step (c) does not fall within the standard range of ratios of said miRNAs characteristic of the second pathology, or (ii) not excluding the diagnosis of the second pathology in the subject if the ratio of the levels of the miRNAs calculated in step (c) falls within the standard range of ratios of said miRNAs characteristic of the second pathology.

In another embodiment, the method further comprises the following steps, which steps can be performed simultaneously or sequentially with each other and/or with the steps (a)-(e) of the above method:

f) measuring the level of a third brain-enriched miRNA (e.g., synapse and/or neurite miRNA) in the same bodily fluid sample collected from the subject, wherein said third brain- enriched miRNA is enriched in a brain area(s) affected by another pathology ("a second pathology");

g) measuring the level of a fourth brain-enriched miRNA in the same bodily fluid sample collected from the subject, wherein said fourth brain-enriched miRNA is (i) enriched in a brain area(s) which is not affected by the second pathology, or (ii) is enriched in a brain cell type which is not affected by the second pathology, or (iii) is enriched in the same brain area as the third miRNA, but its expression and/or secretion change differently than expression and/or secretion of the third miRNA during development of the second pathology;

h) calculating the ratio of the levels of the miRNAs measured in steps (f) and (g);

i) comparing the ratio of the levels of the miRNAs calculated in step (h) with the standard range of ratios of said miRNAs characteristic of the second pathology;

j) (i) identifying the subject as being afflicted with the second pathology in addition to the neurodevelopmental disorder if the ratio of the levels of the miRNAs calculated in step (h) falls within the standard range of ratios of said miRNAs characteristic of the second pathology, or (ii) excluding the diagnosis of the second pathology in the subject if the ratio of the levels of the miRNAs calculated in step (h) does not fall within the standard range of ratios of said miRNAs characteristic of the second pathology.

In a related aspect, the invention provides a method for detecting a neurodevelopmental disorder in a subject, which method comprises: a) measuring the level of a first brain-enriched miRNA (e.g., synapse and/or neurite miRNA) in a bodily fluid sample collected from the subject, wherein said first brain-enriched miRNA is enriched in a brain area(s) affected by the neurodevelopmental disorder;

b) measuring the level of a second brain-enriched miRNA in the same bodily fluid sample collected from the subject, wherein said second brain-enriched miRNA (i) is enriched in a brain area(s) which is not affected by the neurodevelopmental disorder, or (ii) is enriched in a brain cell type which is not affected by the neurodevelopmental disorder , or (iii) is enriched in the same brain area as the first miRNA, but its expression and/or secretion change differently than expression and/or secretion of the first miRNA during development of the neurodevelopmental disorder, and

c) calculating the ratio of the levels of the miRNAs measured in steps (a) and (b).

The invention also provides a computer-implemented method of assigning a subject into a category of being afflicted with a neurodevelopmental disorder, which method comprises: a. measuring the level of a first brain-enriched miRNA (e.g., synapse and/or neurite miRNA) in a bodily fluid sample collected from the subject, wherein said first brain-enriched miRNA is enriched in a brain area(s) affected by the neurodevelopmental disorder;

b. measuring the level of a second brain-enriched miRNA in the same bodily fluid sample collected from the subject, wherein said second brain-enriched miRNA (i) is enriched in a brain area(s) which is not affected by the neurodevelopmental disorder, or (ii) is enriched in a brain cell type which is not affected by the neurodevelopmental disorder , or (iii) is enriched in the same brain area as the first miRNA, but its expression and/or secretion change differently than expression and/or secretion of the first miRNA during development of the neurodevelopmental disorder;

c. calculating using a suitably programmed processor, the ratio of the levels of the miRNAs measured in steps (a) and (b);

d. calculating, by the processor and based on the ratio determined in step (c), a first probability based on a first predefined probability distribution curve, wherein the first predefined probability distribution curve corresponds to the neurodevelopmental disorder;

e. calculating, by the processor and based on the ratio determined in step (c), a second probability based on a second predefined probability distribution curve, wherein the second predefined probability distribution curve corresponds to a matched control (e.g., matched by gender and/or age and/or race, etc.) or another pathology;

f. determining, by the processor, a difference between the first probability calculated in step (d) and the second probability calculated in step (e), and

g. (i) identifying, by the processor, the subject as being afflicted with the neurodevelopmental disorder when the difference between the first probability and the second probability calculated in step (f) is positive or (ii) identifying the subject as not being afflicted with the neurodevelopmental disorder when the difference between the first probability and the second probability calculated in step (f) is negative.

In another aspect, the invention provides a method for treating a neurodevelopmental disorder in a subject in need thereof, which method comprises:

b) measuring the level of a second brain-enriched miRNA in the same bodily fluid sample collected from the subject, wherein said second brain-enriched miRNA (i) is enriched in a brain area(s) which is not affected by the neurodevelopmental disorder, or (ii) is enriched in a brain cell type which is not affected by the neurodevelopmental disorder , or (iii) is enriched in the same brain area as the first miRNA, but its expression and/or secretion change differently than expression and/or secretion of the first miRNA during development of the neurodevelopmental disorder;

c) optionally calculating the ratio of the levels of the miRNAs measured in steps (a) and (b); d) optionally comparing the ratio of the levels of the miRNAs calculated in step (c) with a corresponding control ratio;

e) optionally (i) identifying the subject as being afflicted with the neurodevelopmental disorder when the ratio of the levels of the miRNAs calculated in step (c) is higher than the corresponding control ratio or (ii) identifying the subject as not being afflicted with the neurodevelopmental disorder when the ratio of the levels of the miRNA calculated in step (c) is not higher than the corresponding control ratio, and

f) administering a therapeutic or preventive treatment to the subject. In yet another aspect, the invention provides a method for selecting subjects for enrollment in a clinical trial involving treatment of a neurodevelopmental disorder, which method comprises:

f) recruiting the subject in a clinical trial.

In one embodiment of any of the above methods, the neurodevelopmental disorder is Rett Syndrome (RTT). In another embodiment of any of the above methods, the neurodevelopmental disorder is selected from the group consisting of Landau-Kleffner Syndrome, Alexander Disease, Alpers' Disease, Alternating Hemiplegia, Angelman Syndrome, Ataxias and Cerebellar or Spinocerebellar Degeneration, Ataxia Telangiectasia, Attention Deficit-Hyperactivity Disorder, Autism Spectrum Disorders including Asperger Syndrome, Batten Disease, Canavan Disease, and Tourette Syndrome.

In one embodiment of any of the above methods, the control ratio is a predetermined value which represents a statistically validated threshold ratio of the levels of said first and second miRNAs (a single "cut-off value) equal to the highest possible value within the range of corresponding values in matched healthy subjects (e.g., matched by gender and/or age and/or race, etc.). In another embodiment of any of the above methods of disease detection, the control ratio is the ratio of the levels of said first and second miRNAs in a similarly processed bodily fluid sample from the same subject collected in the past.

In one embodiment of any of the above methods of disease differentiation, the standard range of ratios of miRNAs characteristic of the second pathology is a statistically validated predetermined range of values established by determining the ratios of the same miRNAs in a cohort of subjects diagnosed with the second pathology. In one specific embodiment, the cohort of subjects diagnosed with the second pathology represents a full range of development stages of said second pathology. In another specific embodiment, the cohort of subjects diagnosed with the second pathology represents one or more development stages of said second pathology.

In one embodiment of any of the above methods of disease differentiation, the neurodevelopmental disorder is Rett Syndrome and the second pathology is selected from the group consisting of Landau-Kleffner Syndrome, Alexander Disease, Alpers' Disease, Alternating Hemiplegia, Angelman Syndrome, Ataxias and Cerebellar or Spinocerebellar Degeneration, Ataxia Telangiectasia, Attention Deficit-Hyperactivity Disorder, Autism Spectrum Disorders including Asperger Syndrome, Batten Disease, Canavan Disease, and Tourette Syndrome.

In one embodiment of any of the above methods of disease differentiation, the second pathology is selected from the group consisting of Landau-Kleffner Syndrome, Alexander Disease, Alpers' Disease, Alternating Hemiplegia, Angelman Syndrome, Ataxias and Cerebellar or Spinocerebellar Degeneration, Ataxia Telangiectasia, Attention Deficit-Hyperactivity Disorder, Autism Spectrum Disorders including Asperger Syndrome, Batten Disease, Canavan Disease, and Tourette Syndrome.

In one embodiment of any of the above methods, said neurodevelopmental disorder is Rett Syndrome (RTT) and the method further comprises determining the underlying MECP2 mutation (e.g., for predicting disease severity).

In another aspect, the invention provides a method for monitoring changes in development of a neurodevelopmental disorder in a subject (e.g., a subject who had been previously diagnosed with said neurodevelopmental disorder), which method comprises: a) measuring the level of a first brain-enriched miRNA (e.g., synapse and/or neurite miRNA) in two or more bodily fluid samples collected from the subject, wherein said first brain- enriched miRNA is enriched in a brain area(s) affected by the neurodevelopmental disorder; b) measuring the level of a second brain-enriched miRNA in the same bodily fluids samples as in step (a), wherein said second brain-enriched miRNA (i) is enriched in a brain area(s) which is not affected by the neurodevelopmental disorder, or (ii) is enriched in a brain cell type which is not affected by the neurodevelopmental disorder, or (iii) is enriched in the same brain area as the first miRNA, but its expression and/or secretion change differently than expression and/or secretion of the first miRNA during development of the neurodevelopmental disorder;

c) calculating the ratio of the levels of the miRNA measured in steps (a) and (b) for each bodily fluid sample;

d) comparing the ratios of the levels of the miRNA calculated in step (c) between the earlier collected and later collected bodily fluid sample(s), and

e) (i) determining that the neurodevelopmental disorder in the subject has progressed if the ratio of the levels of the miRNA calculated in step (c) is increased in the later collected bodily fluid sample(s) as compared to the earlier collected sample(s), or (ii) determining that the neurodevelopmental disorder in the subject has not progressed if the ratio of the levels of the miRNA calculated in step (c) is not changed in the later collected bodily fluid sample(s) as compared to the earlier collected sample(s).

In a separate aspect, the invention provides a method for monitoring the effect of a treatment on development of a neurodevelopmental disorder in a subject (e.g., a subject who had been previously diagnosed with said neurodevelopmental disorder), which method comprises: a) measuring the level of a first brain-enriched miRNA (e.g., synapse and/or neurite miRNA) in a bodily fluid sample collected from the subject prior to initiation of the treatment, wherein said first brain-enriched miRNA is enriched in a brain area(s) affected by the neurodevelopmental disorder;

c) calculating the ratio of the levels of the miRNA measured in steps (a) and (b);

d) measuring the level of the same first miRNA as in step (a) in one or more bodily fluid sample(s) collected from the subject in the course of or following the treatment;

e) measuring the level of the same second miRNA as in step (b) in the same bodily fluid sample(s) as in step (d);

f) calculating the ratio of the levels of the miRNA measured in steps (d) and (e) for each bodily fluid sample;

g) comparing the ratios of the levels of the miRNA calculated in steps (c) and (f), and optionally comparing the ratios of the levels of the miRNA calculated in step (f) between different samples in step (d), and

h) (i) determining that the treatment is effective for said neurodevelopmental disorder if the ratio of the levels of the miRNA calculated in step (c) is higher than the corresponding ratio(s) calculated in step (f), or (ii) determining that the treatment is not effective for said neurodevelopmental disorder if the ratio of the levels of the miRNA calculated in step (c) is not higher than the corresponding ratio(s) calculated in step (f).

In a separate aspect, the invention provides a method for identifying a compound useful for slowing down the progression or treating a neurodevelopmental disorder in a subject (e.g., a subject who had been previously diagnosed with said neurodevelopmental disorder), which method comprises:

a) measuring the level of a first brain-enriched miRNA (e.g., synapse and/or neurite miRNA) in a bodily fluid sample, wherein said bodily fluid sample(s) is collected from the subject prior to test compound administration, and wherein said first brain-enriched miRNA is enriched in a brain area(s) affected by the neurodevelopmental disorder;

d) measuring the level of the same first miRNA as in step (a) in one or more bodily fluid samples collected from the subject following administration of a test compound;

f) calculating the ratio of the levels of the miRNAs measured in steps (d) and (e) for each of the bodily fluid samples collected from the subject following administration of the test compound;

g) comparing the ratio of the levels of the miRNA calculated in steps (c) and (f), and h) (i) identifying that the test compound is useful for slowing down the progression or treating the neurodevelopmental disorder if the ratio of the levels of the miRNA calculated in step (f) is lower than the ratio of the levels of the miRNA calculated in step (c); (ii) identifying that the test compound is not useful for slowing down the progression or treating the neurodevelopmental disorder if the ratio of the levels of the miRNA calculated in step (f) is not lower than the ratio of the levels of the miRNAs calculated in step (c).

In one embodiment of any of the above methods, the first brain-enriched miRNA is a synapse and/or neurite miRNA.

In one embodiment of any of the above methods, the second miRNA is a brain-enriched miRNA, which (1) is enriched in a brain area(s) which is not affected by the neurodevelopmental disorder (e.g., RTT) or (2) is enriched in a brain cell type which is not affected by the neurodevelopmental disorder (e.g., RTT). In one embodiment of any of the above methods, the second miRNA is a brain-enriched miRNA selected from the group consisting of miRNAs which are mainly expressed in brain areas not involved in RTT, miRNAs which are mainly expressed in glial cells, and brain-enriched miRNAs downregulated in RTT.

In one embodiment of any of the above methods involving the first and second miRNAs which are brain-enriched, the first brain-enriched miRNA is enriched in neurons and the second brain-enriched miRNA is enriched in glial cells.

In one embodiment of any of the above methods, the pair of the first miRNA and the second miRNA is selected from the group consisting of: miR-107/miR-323-3p, miR-107/miR- 335-5p, miR-491-5p/miR-323-3p, miR-491-5p/miR-335-5p, miR-491-5p/miR-132, miR-491- 5p/miR-411, miR-41 l/miR-335-5p, miR-41 l/miR-132, miR-107/miR-132, miR-323-3p/miR- 335-5p, and miR-323-3p/miR-132. In another embodiment of any of the above methods, the pair of the first miRNA and the second miRNA is selected from the pairs provided in Tables 3-5, below.

In one embodiment of any of the above methods, the method comprises measuring the level and calculating the ratios of the levels for two or more different pairs of miRNA. In one specific embodiment, the method comprises measuring the level and calculating the ratios of the levels for one or more pair combinations selected from the group consisting of:

(a) miR-107/miR-323-3p and miR-107/miR-335-5p;

(b) miR-491-5p/miR-323-3p, miR-491-5p/miR-335-5p, miR-491-5p/miR-132, and miR-491- 5p/miR-411;

(c) miR-411/miR-132, miR-107/miR-132 and miR-107/miR-335-5p;

(d) miR-323-3p/miR-335-5p and miR-323-3p/miR-132;

(e) miR-323-3p/miR-335-5p, miR-491-5p/miR-335-5p and miR-41 l/miR-335 -5p;

(f) miR-491-5p/miR-335-5p and miR-491-5p/miR-132.

In one embodiment of any of the above disease detection or differentiation methods, the method comprises measuring the levels of the miRNAs in two or more bodily fluid samples collected from the subject, wherein the samples have been collected at spaced apart time points.

In one embodiment of any of the above methods involving bodily fluid samples which have been collected at spaced apart time points, the bodily fluid samples are obtained several months apart (e.g., 3-6 months apart).

In one embodiment of any of the above methods, the method further comprises normalizing the levels of the first and second miRNAs to the level of a normalizer miRNA. In one specific embodiment, the normalizer miRNA is miRNA which is expressed in numerous tissues but is not significantly expressed in brain.

In one embodiment of any of the above methods, the subject does not have clinical symptoms of the neurological disorder.

In one embodiment of any of the above methods, the subject is human. In one specific embodiment, the human subject is an infant or a child. In another embodiment of any of the above methods, the subject is an experimental animal (e.g., an animal model of a neurodevelopmental disorder such as, e.g., RTT).

In one embodiment of any of the above methods, the bodily fluid is selected from the group consisting of blood plasma, serum, urine, and saliva. Any other bodily fluid can also be used, preferably, those bodily fluids that allow low cost non-invasive or minimally invasive collection and analysis.

In one embodiment of any of the above methods, the method comprises the step of collecting the bodily fluid sample(s) from the subject (e.g., prior to step (a)).

In one embodiment of any of the above methods, the level of the miRNAs is determined using a method selected from the group consisting of hybridization, polymerase chain reaction (PCR)-based detection (for example, RT-PCR), sequencing, and microfluidic technologies. Non-limiting examples of useful methods for measuring miRNA level in bodily fluids include hybridization with selective probes (e.g., using Northern blotting, bead-based flow-cytometry, oligonucleotide microchip [microarray], or solution hybridization assays such as Ambion mirVana miRNA Detection Kit), polymerase chain reaction (PCR)-based detection (e.g., stem- loop reverse transcription-polymerase chain reaction [RT-PCR], quantitative RT-PCR based array method [qPCR-array]), direct sequencing by one of the next generation sequencing technologies (e.g., Helicos small RNA sequencing, miRNA BeadArray (Ulumina), Roche 454 (FLX-Titanium), and ABI SOLiD), or various microfluidic technologies. For review of additional applicable techniques see, e.g., Chen et al., BMC Genomics, 2009, 10:407; Kong et al., J Cell Physiol. 2009; 218:22-25. One of the preferred types of techniques are RT-PCR-based techniques as such techniques allow to achieve good sensitivity and specificity.

In one embodiment of any of the above methods, prior to measuring miRNA level, the miRNA is purified from the bodily fluid sample. miRNAs can be isolated and purified from bodily fluids by various methods, including, without limitation, the use of commercial kits (e.g., miRNeasy kit [Qiagen], MirVana RNA isolation kit [Ambion/ABI], miRACLE [Agilent], High Pure miRNA isolation kit [Roche], and miRNA Purification kit [Norgen Biotek Corp.]), Trizol extraction, concentration and purification on anion-exchangers, magnetic beads covered by RNA-binding substances, or adsorption of certain miRNA on complementary oligonucleotides.

In one embodiment of any of the above methods, the method further comprises reducing or eliminating degradation of the miRNAs. Useful methods for reducing or eliminating miRNA degradation include, without limitation, adding RNase inhibitors (e.g., RNasin Plus [Promega], SUPERase-In [ABI], etc.), use of guanidine chloride, guanidine isothiocyanate, N- lauroylsarcosine, sodium dodecyl sulphate (SDS), or a combination thereof. Reducing miRNA degradation in bodily fluid samples is particularly important when sample storage and transportation is required prior to miRNA quantification.

To account for possible losses of a given miRNA during purification, and potentially RT- PCR inhibition, miRNA contaminants derived from dying or damaged blood or urine cells during sample isolation and treatment, variations in kidney filtration, etc., various additional methods of experimental data normalization can be employed. For example, the following quality control (QC) and/or normalization methods can be used in the present invention:

a) Ubiquitous miRNAs can be used for QC by comparing their concentrations in subject's bodily fluid with pre-established normal values.

b) Synthetic small RNA (e.g., non-human miRNA) oligonucleotides can be synthesized and used as controls for losses during purification and/or RT-PCR inhibition (e.g., by adding them to bodily fluid samples before RNA purification).

c) To account for variations in kidney filtration (when working with urine samples), miRNA concentration in urine can be normalized on creatinine and/or albumin level.

In one embodiment of any of the above methods, neurodevelopmental disorder detection based on miRNA levels is combined with additional methods of detection. Non-limiting examples of such additional methods include, e.g., genetic testing (e.g., MECP2 mutation determination for RTT), hearing test, eye and/or vision exam, positron emission tomography (PET), computed tomography (CT), magnetic resonance imaging (MRI), multiphoton imaging, magnetoencephalography (MEG), and electroencephalography (EEG).

In one embodiment of any of the above disease detection or disease monitoring methods, the method further comprises administering a therapeutic or preventive treatment to the subject. Non-limiting examples of useful symptomatic and prophylactic treatments include, for example, physical therapies, occupational therapies and/or speech-language therapies, nutritional support, controlling seizures, controlling muscle stiffness, GI treatments, heart treatments, and treatments for breathing problems. The therapeutic or preventative treatment may be administered prior the appearance of one or more clinical symptoms of the neurodevelopmental disorder. In the case of when the neurodevelopmental disorder is RTT, effective treatment can mean RTT improvement (decrease of a monitored biomarker miRNA ratio) or prevention/inhibition of further development of RTT (monitored biomarker miRNA ratio stays the same or increases slower).

In one embodiment of any of the above disease detection or disease progression monitoring methods, the method further comprises recruiting the subject in a clinical trial.

In conjunction with the above methods of the invention, the invention also provides various kits. Non-limiting examples of the kits of the invention include:

1. A kit for detecting a neurodevelopmental disorder (e.g., RTT) comprising primers and/or probes specific for one or more pairs of miRNAs selected from the group consisting of: miR- 107/miR-323-3p, miR-107/miR-335-5p, miR-491-5p/miR-323-3p, miR-491-5p/miR-335-5p, miR-491-5p/miR-132, miR-491-5p/miR-411, miR-41 l/miR-335-5p, miR-41 l/miR-132; miR- 107/miR-132, miR-323-3p/miR-335-5p, and miR-323-3p/miR-132.

2. A kit for detecting a neurodevelopmental disorder (e.g., RTT) comprising primers and/or probes specific for one or more pairs of miRNAs selected from the pairs provided in Tables 3-5, below.

3. A kit for detecting a neurodevelopmental disorder comprising primers and/or probes specific for one or more combinations of pairs of miRNAs selected from the group consisting of:

(a) miR-107/miR-323-3p and miR-107/miR-335-5p;

(c) miR-41 l/miR-132, miR-107/miR-132 and miR-107/miR-132;

(d) miR-323-3p/miR-335-5p and miR-323-3p/miR-132;

(e) miR-323-3p/miR-335-5p, miR-491-5p/miR-335-5p and miR-41 l/miR-335 -5p;

(f) miR-491-5p/miR-335-5p and miR-491-5p/miR-132.

Any of the above kits can further comprise miRNA isolation means and/or miRNA purification means and/or instructions for use. These and other aspects of the present invention will be apparent to those of ordinary skill in the art in the following description, claims and drawings.

BRIEF DESCRIPTION OF THE DRAWINGS

Figures 1A-1E are graphs showing ratios of miRNA levels (biomarker miRNA pairs) in plasma of wild type and Mecp2^{tml lJae} Null mice. miRNA ratios are presented as log 10 of 2 Average for each pair is indicated.

Figures 2A-2B are graphs presenting ROC curves for differentiation between wild type and Mecp2^{tml lJae}Null mice with miRNA pairs.

Figures 3A-3E are graphs showing ratios of miRNA levels (biomarker miRNA pairs identified in Example 3 for differentiating Mecp2^{tml lJae} Null and wild type mice) in plasma of wild type and Mecp2^{tml lBird} mice. miRNA ratios are presented as loglO of 2ACt. Average for each pair is indicated.

Figures 4A-4H are graphs showing additional biomarker miRNA pairs effectively distinguishing wild type and Mecp2^{tml 1Bird} Null mice. miRNA ratios are presented as loglO of 2 . Average for each pair is indicated.

Figures 5A-5B are graphs presenting ROC curves for differentiation between wild type and Mecp2^{tml lBird}Null mice with miRNA pairs.

Figures 6A-6F are graphs showing ratios of miRNA levels (biomarker miRNA pairs) in plasma of wild type and Mecp2^{tml lJae} Het mice. miRNA ratios are presented as loglO of 2 Average for each pair is indicated.

Figures 7A-7B are graphs presenting ROC curves for differentiation between wild type and Mecp2^{tol 1Jae}Het mice with miRNA pairs.

Figures 8A-8E are graphs showing biomarker miRNA pairs effectively distinguishing wild type and Mecp2^{tml lBird} Het mice. miRNA ratios are presented as loglO of 2^ACt. Average for each pair is indicated.

Figure 9 is a graph presenting ROC curves for differentiation between wild type and Mecp2^{tml 1 Bird}Het mice with miRNA pairs. DETAILED DESCRIPTION OF THE INVENTION

DDs differ from neurodegenerative diseases by no or very limited neuronal death [Armstrong et al. Selective Dendritic Alterations in the Cortex of Rett Syndrome. J. Neuropathol. Exp. Neurol. 54, 195 (1995); Katz DM et al. Preclinical research in Rett syndrome: setting the foundation for translational success. Dis. Models and Mechanisms, 5, 733-745 (2012)]. NDDs are characterized by synapse and/or neurite dysfunction in particular brain areas. The present inventors have hypothesized that such synapse and/or neurite dysfunction can be accompanied by changes in miRNA expression and secretion, leading to increased or decreased levels of particular miRNAs in plasma/serum or other bodily fluids, such as, e.g., urine or saliva. The present inventors have hypothesized that, since miRNAs are evolutionary conserved, one can expect that same miRNAs may be used as biomarkers of RTT in human, mouse and other animals. Data on miRNA expression in brain of RTT subjects are limited and obtained mainly in various mouse models with mutant MECP2 [Wu et al. Genome-wide analysis reveals methyl- CpG-binding protein 2-dependent regulation of microRNAs in a mouse model of Rett syndrome. Proc. Natl. Acad. Sci. 107, 18161-18166 (2010); Urdinguio et al. Disrupted microRNA expression caused by Mecp2 loss in a mouse model of RTT. Epigenetics, 5, 656-663 (2010)]. Several factors cause changes in miRNA expression due to inactivation of Mecp2. First, being involved in transcription regulation Mecp2 affects synthesis of some miRNAs [Leon- Guerrero et al. In sickness and in health: the role of methyl-CpG binding protein 2 in the central nervous system. Europ. J. Neurosci. 33, 1563-1574, (2011)] and its inactivation changes transcription of those miRNAs. Second, expression of some miRNAs can be changed indirectly due to other cellular effects of Mecp2 inactivity. Since the presently proposed approach for developing RTT diagnostics is based on analysis of brain-enriched miRNAs circulating in bodily fluids, changes in miRNA secretion/excretion caused by inactivity of Mecp2 are also very important. Several brain areas, such as substantia nigra/midbrain (Gantz et al. J. Neurosci. 2011; 31 : 12629-12637; Panayotis et al. Neurobiol. Dis. 2011, 41 : 385-397), frontal cortex (Gibson et al. BMC Neurosci. 2010; 11 :53), hippocampus (Toloe et al. Mol. Cell Neurosci. 2014; 59: 47- 56), and hypothalamus (Sakai et al. Eur. J. Med. Genet. 2013; 56: 475-483) are affected in RTT.

Taken together, the present invention is based on the following ideas and findings made by the present inventors: (1) changes in concentrations of circulating miRNAs enriched in the brain, and more specifically in brain areas involved in a particular pathology, are more likely to reflect associated pathologic processes in the brain than ubiquitous or other brain-enriched miRNAs;

(2) miRNAs present in neurites and synapses should be analyzed, because dysfunction and destruction of neurites and synapses is characteristic of NDDs, and therefore, can affect expression and secretion of these miRNAs;

(3) to compensate for processes unrelated directly to a particular pathology, e.g., changes in blood supply or blood-brain barrier permeability, the present inventors used the "biomarker miRNA pair" approach normalizing miRNAs enriched in neurons of damaged brain area(s) by other brain-enriched miRNAs, such as, e.g., (i) miRNAs enriched in a brain area(s) which is not affected by the NDD which is being diagnosed, or (ii) miRNAs enriched in a brain cell type which is not affected by the NDD which is being diagnosed, or (iii) miRNAs enriched in the same brain area as the biomarker miRNA, but its expression and/or secretion change differently than expression and/or secretion of the biomarker miRNA during development of the NDD which is being diagnosed;

(4) high correlation of plasma concentrations of miRNAs used as numerator and denominator in a biomarker miRNA pair is very important for its sensitivity and specificity.

The present invention is based on analysis of the ratios of the levels for pairs of circulating cell-free miRNA in bodily fluids, wherein both miRNA in the pair are brain-enriched, and either (i) are enriched in certain brain areas, which are (for one miRNA in the pair) or are not (for the other miRNA in the pair) affected by the NDD (e.g., by being involved in NDD development), or (ii) are enriched in different cell types (e.g., neurons and glial cells), or (iii) are enriched in the same brain area but whose expression and/or secretion change differently due to NDD development. Brain-enriched miRNAs which are particularly useful as numerators in the biomarker miRNA pairs of the invention include neuronal miRNAs present in neurites and synapses (i.e., synapse and/or neurite miRNAs), whose normal functioning suffers in RTT or other NDDs. Since various NDDs are characterized by neuronal pathology in different brain areas such biomarker miRNA pairs can be used for differentiating those pathologies from each other independent of their clinical symptoms, if any. In addition, discovered biomarker miRNA pairs, reflecting important events in pathology development, could be used for patient selection and stratification for clinical trials, early patient treatment, disease and treatment monitoring as well as for drug screening. Due to evolutionary conservation of miRNAs the same biomarker miRNA pairs may be also used in animal models for preclinical phase of drug development.

Use of brain-enriched miRNA in the methods of the invention significantly increases chances that changes of their levels in bodily fluids are caused by brain pathology, and changes in bodily fluid concentration of miRNA enriched in a particular brain area should be indicative of pathology in that brain part. For example, changes in levels of midbrain- or cortex-enriched miRNA would be associated with RTT, reflecting synapse and neuronal dysfunctions in these brain areas. In addition, concentrations of brain-enriched miRNA in blood cells are low, which decreases contamination of plasma and serum by miRNA leakage during purification of these bodily fluids.

The concentrations of miRNAs detected in bodily fluids depend on many biological and technical factors. Biological factors include miRNA levels in various tissues, intensity of secretion and excretion into extracellular space, forms of circulating miRNAs (exosomes and other vesicles, complexes with proteins and lipids) affecting their ability to cross various barriers, e.g. blood-brain, placental, and kidney barriers, and miRNA stability and half-life in the bloodstream. Technical factors include variability in methods of bodily fluid collection and storage, methods used for miRNA extraction, and presence in bodily fluids of various factors affecting miRNA purification and quantitation. As a consequence, the importance of miRNA normalization is broadly recognized (Meyer et al., Biotechnol. Lett. 2010; 32: 1777-1788). At the same time, no single normalization method is commonly accepted.

The present invention is based on the use of brain-enriched biomarker miRNA pairs instead of (or in addition to) normalization per ubiquitous RNA or an average of numerous miRNAs. The use of brain-enriched biomarker miRNA pairs (one as a numerator and another one as a denominator in a ratio) has several advantages. First, any pathology is usually associated with up-regulation of some miRNAs and down-regulation of other miRNAs, thus considering miRNA pairs of up- and down-regulated miRNAs may increase test sensitivity and specificity. Second, the use of a pair of brain-enriched miRNAs, rather than one brain-enriched miRNA, decreases potential overlap with pathologies of other organs. Third, one can expect that changes unrelated to or non-specific for a pathology of interest, such as, e.g., changes in blood supply, blood-brain permeability and others, will be better compensated for by using the pair of miRNAs enriched in the same organ. In addition, changes in relative concentrations of miRNAs enriched in different brain areas or different cell types (e.g., neurons and glial cells) may be an indicator of disease progression.

Another innovative aspect of the present invention is the use of probabilistic approach in addition to or instead of calculating ratios of miRNA concentrations in plasma. The use of integral distribution curves, which characterize probabilities of a subject belonging to control or having a pathology has such advantages as better definition of diagnostic uncertainty zone, simplicity of combining biomarkers of different nature (e.g., protein levels, imaging techniques and miRNA levels) and others.

In the present invention, since various miRNA are involved in regulation of different processes, combination of several miRNA pairs were also tested to find out the groups of miRNA pairs providing the highest test accuracy. Non-limiting examples of such groups for RTT detection include:

(a) miR-107/miR-323-3p and miR-107/miR-335-5p;

(c) miR-411/miR-132, miR-107/miR-132 and miR-107/miR-335-5p;

(d) miR-323-3p/miR-335-5p and miR-323-3p/miR-132;

(e) miR-323-3p/miR-335-5p, miR-491-5p/miR-335-5p and miR-41 l/miR-335-5p.

Definitions

As used herein, the term "brain-enriched" means that miRNA concentration in brain is at least 4-5 times higher than in other organs.

As used herein in connection with miRNA enrichment in a certain area of the brain, the term "enriched" means that miRNA concentration in said area of the brain is higher (preferably, at least 2-fold higher, more preferably at least 5-fold higher, most preferably at least 10-fold higher) than in brain in general. The term refers to the difference in concentrations within the brain areas (e.g., as measured using qRT-PCR).

Within the meaning of the present invention, the term "synapse and/or neurite miRNA" refers to miRNA which (i) is "brain-enriched" and (ii) is present in a synapse and/or neurite (i.e., axon and/or dendrite and/or spine). To be useful in the methods of the present invention, synapse and/or neurite miRNAs should be detectable in bodily fluids as a result of their release from neurons (e.g., due to secretion, neurite/synapse destruction or neuronal death).

The term "neurite" as used herein refers to any projection from the cell body of a neuron. This projection can be an axon, a dendrite, or a spine.

The term "axon" refers to a long, slender projection of a neuron that conducts electrical impulses away from the neuron's cell body or soma. Axons are distinguished from dendrites by several features, including shape (dendrites often taper while axons usually maintain a constant radius), length (dendrites are restricted to a small region around the cell body while axons can be much longer), and function (dendrites usually receive signals while axons usually transmit them). Axons and dendrites make contact with other cells (usually other neurons but sometimes muscle or gland cells) at junctions called synapses.

The term "dendrite" refers to a branched projection of a neuron that acts to conduct the electrochemical stimulation received from other neural cells to the cell body of the neuron from which the dendrites project.

The term "synapse" refers to specialized junctions, through which neurons signal to each other and to non-neuronal cells such as those in muscles or glands. A typical neuron gives rise to several thousand synapses. Most synapses connect axons to dendrites, but there are also other types of connections, including axon-to-cell-body, axon-to-axon, and dendrite-to-dendrite. In the brain, each neuron forms synapses with many others, and, likewise, each receives synaptic inputs from many others. As a result, the output of a neuron may depend on the input of many others, each of which may have a different degree of influence, depending on the strength of its synapse with that neuron. There are two major types of synapses, chemical synapses and electrical synapses. In electrical synapses, cells approach within about 3.5 nm of each other, rather than the 20 to 40 nm distance that separates cells at chemical synapses. In chemical synapses, the postsynaptic potential is caused by the opening of ion channels by chemical transmitters, while in electrical synapses it is caused by direct electrical coupling between both neurons. Electrical synapses are therefore faster than chemical synapses.

The term "normalizer miRNA" as used herein refers to miRNA which is used for normalization of biomarker miRNA concentration to account for factors that affect appearance and/or stability of miRNA in bodily fluids but are not related to a target pathology. The terms "neurodevelopmental disorders", "neurodevelopmental diseases" and " DDs" refer to pathologies caused by disturbances of the nervous system development such as, e.g., Rett Syndrome, Landau-Kleffner Syndrome, Alexander Disease, Alpers' Disease, Alternating Hemiplegia, Angelman Syndrome, Ataxias and Cerebellar or Spinocerebellar Degeneration, Ataxia Telangiectasia, Attention Deficit-Hyperactivity Disorder, Autism Spectrum Disorders including Asperger Syndrome, Batten Disease, Canavan Disease, and Tourette Syndrome.

The term "development of a neurodevelopmental disorder" is used herein to refer to any negative change in the extent/severity of a metabolic and/or structural change in individual neurons and/or any increase in the number of neurons affected. The phrase "improvement of a neurodevelopmental disorder" and similar terms refer to any positive change in the extent/severity of a metabolic and/or structural change in individual neurons and/or any decrease in the number of neurons affected.

The term "associated with" is used to encompass any correlation, co-occurrence and any cause-and-effect relationship.

The terms "microRNA" or "miRNA" as used herein refer to a class of small approximately 22 nt long non-coding RNA molecules. They play important roles in the regulation of target genes by binding to complementary regions of messenger transcripts (mRNA) to repress their translation or regulate degradation (Griffiths- Jones Nucleic Acids Research, 2006, 34, Database issue: D140-D144). Frequently, one miRNA can target multiple mRNAs and one mRNA can be regulated by multiple miRNAs targeting different regions of the 3' UTR. Once bound to an mRNA, miRNA can modulate gene expression and protein production by affecting, e.g., mRNA translation and stability (Baek et al., Nature 455(7209):64 (2008); Selbach et al., Nature 455(7209):58 (2008); Ambros, 2004, Nature, 431, 350-355; B artel, 2004, Cell, 116, 281-297; Cullen, 2004, Virus Research., 102, 3-9; He et al., 2004, Nat. Rev. Genet., 5, 522-531; and Ying et al., 2004, Gene, 342, 25-28). Unless otherwise noted, the name of a specific miRNA refers to a mature miRNA sequence. Under current nomenclature rules, human miRNAs are preceded with the prefix "hsa-" (i.e., an abbreviation for Homo sapiens). Throughout the specification and figures the hsa- prefix may be dropped for purposes of abbreviation, thus, for example, "hsa-miR-155" and "miR-155" would represent the same RNA sequence. Examples of miRNAs useful in the methods of the present invention include, without limitation, miR-107, miR-323-3p, miR-491-5p, miR-335-5p, miR-132, and miR-411. Information on most currently known miRNAs can be found in the miRNA database miRBase (available at the world wide web at mirbase.org). See also Burside et al., BMC Genomics 9: 185 (2008); Williams et al., BMC Genomics 8: 172 (2007); Landgraf et al., Cell 129: 1401 (2007).

The term "miRNA array" refers to a multiplex technology used in molecular biology and in medicine. It consists of an arrayed series of multiple (e.g., thousands) microscopic spots of oligonucleotides, each containing a specific sequence (probe) complementary to a particular target miRNA. After probe-target hybridization under high-stringency conditions the resulting hybrids are usually detected and quantified by quantifying fluorophore-, silver-, or chemiluminescence-labeled targets to determine relative abundance of miRNA. In the methods of the present invention, both custom-made and commercially available miRNA arrays can be used. Examples of useful commercially available miRNA arrays (based on various methods of target labeling, hybrid detection and analysis) include arrays produced by Agilent, Illumina, Invitrogen, Febit, and LC Sciences.

The term "next generation sequencing technologies" broadly refers to sequencing methods which generate multiple sequencing reactions in parallel. This allows vastly increased throughput and yield of data. Non-limiting examples of commonly used next generation sequencing platforms include Helicos small RNA sequencing, miRNA BeadArray (Illumina), Roche 454 (FLX-Titanium), and ABI SOLiD.

An "individual" or "subject" or "animal", as used herein, refers to humans, veterinary animals (e.g., cats, dogs, cows, horses, sheep, pigs, etc.) and experimental animal models of neurodevelopmental diseases. In a preferred embodiment, the subject is a human.

The term "purified" as used herein refers to material that has been isolated under conditions that reduce or eliminate the presence of unrelated materials, i.e., contaminants, including native materials from which the material is obtained. For example, RNA purification includes elimination of proteins, lipids, salts and other unrelated compounds present in bodily fluids. Besides, for some methods of analysis a purified miRNA is preferably substantially free of other RNA oligonucleotides contained in bodily fluid samples (e.g., rRNA and mRNA fragments, ubiquitous miRNAs, which are expressed at high levels in almost all tissues [e.g., miR-16], etc.). As used herein, the term "substantially free" is used operationally, in the context of analytical testing of the material. Preferably, purified material substantially free of contaminants is at least 50% pure; more preferably, at least 90% pure, and still more preferably at least 99% pure. Purity can be evaluated by chromatography, gel electrophoresis, composition analysis, biological assay, and other methods known in the art.

As used herein, the term "similarly processed" refers to samples (e.g., bodily fluid samples or purified miRNAs) which have been obtained using the same protocol.

In the context of the present invention insofar as it relates to any of the disease conditions recited herein, the terms "treat", "treatment", and the like mean to relieve or alleviate at least one symptom associated with such condition, or to slow or reverse the progression of such condition, or to arrest, delay the onset (i.e., the period prior to clinical manifestation of a disease) and/or reduce the risk of developing or worsening a disease. Within the meaning of the present invention, the term "treat" also encompasses preventing and/or reducing a positive symptom associated with neurodevelopmental disorders, such as, e.g., seizures, muscle stiffness, GI, heart, and breathing problems.

The term "about" or "approximately" means within a statistically meaningful range of a value. Such a range can be within an order of magnitude, preferably within 50%, more preferably within 20%, still more preferably within 10%, and even more preferably within 5% of a given value or range. The allowable variation encompassed by the term "about" or "approximately" depends on the particular system under study, and can be readily appreciated by one of ordinary skill in the art.

In accordance with the present invention there may be employed conventional molecular biology, microbiology, and recombinant DNA techniques within the skill of the art. Such techniques are explained fully in the literature. See, e.g., Sambrook, Fritsch & Maniatis, Molecular Cloning: A Laboratory Manual, Second Edition. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 1989 (herein "Sambrook et al., 1989"); DNA Cloning: A Practical Approach, Volumes I and II (D.N. Glover ed. 1985); Oligonucleotide Synthesis (M.J. Gait ed. 1984); Nucleic Acid Hybridization [B.D. Hames & S.J. Higgins eds. (1985)]; Transcription And Translation [B.D. Hames & S.J. Higgins, eds. (1984)]; Animal Cell Culture [R.I. Freshney, ed. (1986)]; Immobilized Cells And Enzymes [IRL Press, (1986)]; B. Perbal, A Practical Guide To Molecular Cloning (1984); Ausubel, F.M. et al. (eds.). Current Protocols in Molecular Biology. John Wiley & Sons, Inc., 1994. These techniques include site directed mutagenesis as described in Kunkel, Proc. Natl. Acad. Sci. USA 82: 488- 492 (1985), U. S. Patent No. 5,071, 743, Fukuoka et al., Biochem. Biophys. Res. Commun. 263 : 357-360 (1999); Kim and Maas, BioTech. 28: 196-198 (2000); Parikh and Guengerich, BioTech. 24: 4 28-431

(1998) ; Ray and Nickoloff, BioTech. 13 : 342-346 (1992); Wang et al., BioTech. 19: 556-559

(1995) ; Wang and Malcolm, BioTech. 26: 680-682 (1999); Xu and Gong, BioTech. 26: 639-641

(1999) , U.S. Patents Nos. 5,789, 166 and 5,932, 419, Hogrefe, Strategies 14. 3 : 74-75 (2001), U. S. Patents Nos. 5,702,931, 5,780,270, and 6,242,222, Angag and Schutz, Biotech. 30: 486-488 (2001), Wang and Wilkinson, Biotech. 29: 976-978 (2000), Kang et al., Biotech. 20: 44-46

(1996) , Ogel and McPherson, Protein Engineer. 5: 467-468 (1992), Kirsch and Joly, Nucl. Acids. Res. 26: 1848-1850 (1998), Rhem and Hancock, J. Bacterid. 178: 3346-3349 (1996), Boles and Miogsa, Curr. Genet. 28: 197-198 (1995), Barrenttino et al., Nuc. Acids. Res. 22: 541-542 (1993), Tessier and Thomas, Meths. Molec. Biol. 57: 229-237, and Pons et al., Meth. Molec. Biol. 67: 209-218.

Methods for Identification of Diagnostic miRNA Pairs

To identify the most promising biomarker miRNA pairs, the present inventors used the following approach: selection of a numerator and a denominator for each pair from those circulating miRNAs, which significantly correlate (Spearman's rank correlation coefficient r>0.8) in a respective bodily fluid of different individuals. Concentrations of miRNAs in plasma depend on numerous factors, including (i) levels of miRNA expression in various organs and tissues; (ii) levels of miRNA secretion from different cell types; (iii) stability of miRNAs in extracellular space and their appearance in plasma in different forms, such as exosomes and other microvesicles, complexes with proteins, lipids and, possibly, other molecules; and (iv) blood-brain barrier permeability for brain-enriched miRNAs. A pathological process may affect some or all of these factors. The present inventors suggest that a nominator and a denominator of an effective biomarker miRNA pair should share some of these basic common factors (e.g., both are brain-enriched and secreted in exosomes) and would change differently in response to a pathology. This does not mean that any correlated miRNA will form a good biomarker pair, since if they are similarly changed by pathology their ratio will mask those changes.

The present invention provides a method of "promising" miRNA pair selection, which method comprises the following steps: 1. Concentrations of miRNAs pre-selected on the basis of their enrichment in an organ of interest (e.g., brain) are measured in a bodily fluid (e.g., plasma, serum, saliva, urine) of at least two comparative cohorts (e.g., a disease and control for a diagnostic test, two diseases for a test capable of differentiating two pathologies, a disease at different stages of pathologic process development, or a disease before and after treatment for monitoring tests).

2. Means of each miRNA concentrations are calculated for comparative cohorts.

3. The difference between the means for each miRNA from two comparative cohorts is calculated and miRNAs are divided in two groups: (i) with high difference values; and (ii) with low or with opposite sign difference values.

4. miRNAs from different groups are combined as potential biomarker pairs if parameters determined in step 3 differ at least 1.5 times. One miRNA is used as a numerator and another miRNA is used as a denominator in a potential "promising" miRNA pair.

5. To further reduce an impact of individual variations of each particular miRNA concentration in plasma or other bodily fluid, miRNA with high positive correlation (Spearman's rank correlation coefficient r calculated for all samples in compared groups is >0.8) are selected as a numerator and a denominator for the biomarker pair. This step significantly decreases the number of potential biomarker miRNA pairs, reduces variance of selected biomarkers caused by factors unrelated to processes differentiating two comparative cohorts and significantly increases test sensitivity and specificity.

The order of steps 3-4 and step 5 can be switched as follows:

After step 1, calculate Spearman's rank correlation coefficient (r) for all possible pairs of individual miRNA measured in step 1 in all bodily fluid samples. Then select as potential biomarker pairs of miRNA with a high positive correlation (r>0.8), compare a ratio of miRNA concentrations in two subject cohorts for each selected miRNA pair and determine a miRNA pair as a suitable biomarker if this pair differentiates two subject cohorts with a statistically significant P-value.

Selection of miRNAs for biomarker pairs is an important step in developing screening, diagnostic and monitoring tests based on analysis of cell-free circulating miRNAs in bodily fluids. The present invention addresses this issue by providing the following methods for selection of effective biomarker pairs. In one embodiment, the invention provides a method for selecting a biomarker miRNA pair for diagnosis and/or monitoring of a pathology, said method comprising the following steps:

(a) selecting at least four miRNAs known to be enriched in an organ affected by the pathology;

(b) measuring the level of each miRNA selected in step (a) in bodily fluid samples from two subject cohorts;

(c) calculating the mean level of each miRNA measured in step (b);

(d) calculating the difference between the mean miRNA levels calculated in step (c);

(e) comparing the differences between the mean miRNA levels calculated in step (d) between all studied miRNAs and selecting as potential biomarker pairs those miRNA pairs for which the difference calculated in step (d) for one miRNA is at least 1.5 times the difference calculated for the other miRNA;

(f) calculating Spearman's rank correlation coefficient (r) for each potential biomarker miRNA pair selected in step (e), and

(g) identifying the miRNA pair as a suitable biomarker pair for diagnosis and/or monitoring of said pathology if its (r) value calculated in step (f) is at least 0.8.

In another embodiment, the invention provides a method for selecting a biomarker miRNA pair for diagnosis and/or monitoring of a pathology, said method comprising the following steps:

(c) calculating Spearman's rank correlation coefficient (r) for all possible pairs of individual miRNAs measured in step (b);

(d) selecting as potential biomarker pairs those miRNA pairs which have the (r) value calculated in step (c) of at least 0.8;

(e) calculating the mean level of each miRNA selected in step (d);

(f) calculating the difference between the mean miRNA levels calculated in step (e); (g) identifying a miRNA pair as a suitable biomarker pair for diagnosis and/or monitoring of said pathology if the difference calculated in step (f) for one miRNA is at least 1.5 times the difference calculated for the other miRNA.

In a further embodiment, the invention provides a method for selecting a biomarker miRNA pair for diagnosis and/or monitoring of a pathology, said method comprising the following steps:

(e) calculating P-value of two subject cohorts separation for each miRNA pair selected in step (d), and

(f) identifying a miRNA pair as a suitable biomarker pair for diagnosis and/or monitoring of said pathology if this pair differentiates two subject cohorts with a statistically significant P-value.

In another embodiment, the invention provides a computer-implemented method for selecting a biomarker miRNA pair for diagnosis and/or monitoring of a pathology, said method comprising the following steps:

(a) selecting a group of miRNAs known to be enriched in an organ affected by the pathology;

(c) electronically calculating the mean level of each miRNA measured in step (b);

(d) electronically calculating a difference between the mean miRNA levels calculated in step (c);

(e) selecting from the group of measured miRNAs a set of potential miRNA pairs each comprising a first miRNA and a second miRNA, wherein the calculated difference in the mean level in step (d) of the first miRNA is at least 1.5 times the calculated difference in the mean level of the second miRNA;

(f) electronically calculating the Spearman's rank correlation coefficient (r) for each potential miRNA pair selected in (e);

(g) selecting from the set of potential miRNA pairs those miRNA pairs, which are suitable for the diagnosis and/or monitoring of the pathology, wherein the (r) value calculated in step (f) is at least 0.8, and

(h) displaying all or part of the miRNA pairs selected in step (g).

In yet another embodiment, the invention provides a computer-implemented method for selecting a biomarker miRNA pair for diagnosis and/or monitoring of a pathology, said method comprising the following steps:

(c) electronically calculating the Spearman's rank correlation coefficient (r) for all possible pairs of individual miRNAs measured in step (b);

(d) selecting from the group of measured miRNAs a set of potential biomarker miRNA pairs, wherein the (r) value calculated in step (c) is at least 0.8;

(e) electronically calculating the mean level of each miRNA selected in step (d);

(f) electronically calculating the difference between the mean miRNA levels calculated in step (e);

(g) selecting from the group of measured miRNAs a set of suitable miRNA biomarker pairs each comprising a first miRNA and a second miRNA, wherein for each suitable biomarker miRNA pair, the calculated difference in the mean level in step (f) of the first miRNA is at least 1.5 times the calculated difference in the mean level of the second miRNA, and

(h) displaying all or part of the suitable biomarker miRNA pairs selected in step (g). In a further embodiment, the invention provides a computer-implemented method for selecting a biomarker miRNA pair for diagnosis and/or monitoring of a pathology, said method comprising the following steps: (a) selecting a group of miRNAs known to be enriched in an organ affected by the pathology;

(c) electronically calculating the Spearman's rank correlation coefficient (r) of the levels measured in step (b) for all possible pairs of individual miRNAs;

(e) electronically calculating P-value of two subject cohorts separation for each miRNA pair selected in step (d);

(f) selecting a miRNA pair as a suitable biomarker pair for diagnosis and/or monitoring of said pathology if this miRNA pair differentiates two subject cohorts with a statistically significant P-value, and

(g) displaying all or part of the suitable biomarker miRNA pairs selected in step (f).

Non-limiting examples of the methods which can be used to measure miRNA level in any of the above methods of the invention include, e.g., RT-PCR-based methods, miRNA array- based methods, new generation sequencing, and hybridization.

Non-limiting examples of the bodily fluid samples which can be used in any of the above methods of the invention include, e.g., plasma, serum, urine, and saliva.

In any of the above methods of the invention, the subjects can be, e.g., humans or experimental animals.

In any of the above methods of the invention, any two cohorts can be compared. Non- limiting examples of such cohorts include, e.g., pathology versus control [e.g., age, gender, and/or race/ethni city-matched healthy subjects], one pathology of the organ versus another pathology of the same organ, two age groups, males versus females [e.g., age and/or race/ethnicity-matched], two different ethnic or racial groups [e.g., age and/or gender-matched], etc.).

Spearman's correlation algorithm used in the methods of the invention (Graham J. Borradaile. Statistics of Earth Science Data, Springer, 2003, p.159). A minimal number of samples sufficient for obtaining a statistically significant difference between two cohorts in the above methods of the invention can be calculated by a standard formula for case-control study (see, e.g. Eng J. Radiology 2003, 227:309-313).

In the methods of the invention, a statistically significant P-value can be calculated using any method known in the art. Non-limiting examples of such methods are Student's t-test (for samples with normal distribution) and Mann-Whitney test (for samples with non-random distribution) (Mann and Whitney, Annals Math Stat. 1947, 18: 50-60). P-value >0.05 is usually accepted as statistically significant. If numerous potential biomarkers are tested Bonferroni correction can be applied.

Kits of the Invention

In conjunction with the above diagnostic, monitoring and screening methods, the present invention provides various kits comprising one or more primer and/or probe sets specific for the detection of the biomarker miRNA pairs.

Such kits can further include primer and/or probe sets specific for the detection of additional normalizer miRNAs.

Such kits can be useful for direct miRNA detection in bodily fluid samples isolated from patients or can be used on purified total RNA or miRNA samples.

A kit of the invention can also provide reagents for primer extension and amplification reactions. For example, in some embodiments, the kit may further include one or more of the following components: a reverse transcriptase enzyme, a DNA polymerase enzyme (such as, e.g., a thermostable DNA polymerase), a polymerase chain reaction buffer, a reverse transcription buffer, and deoxynucleoside triphosphates (dNTPs). Alternatively (or in addition), a kit can include reagents for performing a hybridization assay. The detecting agents can include nucleotide analogs and/or a labeling moiety, e.g., directly detectable moiety such as a fluorophore (fluorochrome) or a radioactive isotope, or indirectly detectable moiety, such as a member of a binding pair, such as biotin, or an enzyme capable of catalyzing a non-soluble colorimetric or luminometric reaction. In addition, the kit may further include at least one container containing reagents for detection of electrophoresed nucleic acids. Such reagents include those which directly detect nucleic acids, such as fluorescent intercalating agent or silver staining reagents, or those reagents directed at detecting labeled nucleic acids, such as, but not limited to, ECL reagents. A kit can further include miRNA isolation or purification means as well as positive and negative controls. A kit can also include a notice associated therewith in a form prescribed by a governmental agency regulating the manufacture, use or sale of diagnostic kits. Detailed instructions for use, storage and troubleshooting may also be provided with the kit. A kit can also be optionally provided in a suitable housing that is preferably useful for robotic handling in a high throughput setting.

The components of the kit may be provided as dried powder(s). When reagents and/or components are provided as a dry powder, the powder can be reconstituted by the addition of a suitable solvent. It is envisioned that the solvent may also be provided in another container. The container will generally include at least one vial, test tube, flask, bottle, syringe, and/or other container means, into which the solvent is placed, optionally aliquoted. The kits may also comprise a second container means for containing a sterile, pharmaceutically acceptable buffer and/or other solvent.

Where there is more than one component in the kit, the kit also will generally contain a second, third, or other additional container into which the additional components may be separately placed. However, various combinations of components may be comprised in a container.

Such kits may also include components that preserve or maintain DNA or RNA, such as reagents that protect against nucleic acid degradation. Such components may be nuclease or RNase-free or protect against RNases, for example. Any of the compositions or reagents described herein may be components in a kit.

EXAMPLES

The present invention is also described and demonstrated by way of the following examples. However, the use of these and other examples anywhere in the specification is illustrative only and in no way limits the scope and meaning of the invention or of any exemplified term. Likewise, the invention is not limited to any particular preferred embodiments described here. Indeed, many modifications and variations of the invention may be apparent to those skilled in the art upon reading this specification, and such variations can be made without departing from the invention in spirit or in scope. The invention is therefore to be limited only by the terms of the appended claims along with the full scope of equivalents to which those claims are entitled.

Example 1: Selection of miRNAs for testing

The methods of the instant invention are based on the use of miRNAs enriched in different brain areas as numerators and denominators, which significantly improves test sensitivity and specificity. Table 1 below presents lists of brain-enriched miRNAs, miRNAs enriched in synapses, axons, dendrites and spines ("synapse and/or neurite miRNAs") and miRNAs enriched in different brain areas.

Table 1. miRNAs enriched in brain, different brain areas and neuronal compartments

Brain areas and

Enriched miRNAs

compartments

dendrites, spines 337, 342-3p, 369-3p, 369-5p, 370, 381, 382, 409-3p, 425, 433- 5p, 483-3p, 485-5p, 487b, 491-5p, 494, 495, 496, 541, 543, 656, 668, 874, 889, 935, 939, 9*, 181a-l * (axon)

Cortex 9, 98, 103, 107, 124a, 125a, 125b, 126 (?), 128a, 129, 132, 134,

138, 149, 154, 181a,b,c,d, 197, 212, 213, 222, 323, 330-3p, 338- 3p,-5p, 342, 370, 381, 382, 411, 425, 433, 491-5p, 539, 885

Hippocampus 9, 96, 99a, 103, 107, 124a, 125b, 126 (?), 128a, 132, 134, 137,

138, 153, 181a, 181b,c, 184, 197, 212 (?), 218, 219, 221, 222, 324-5p, 328, 330 (?), 331, 335-5p, 338, 369-3p, 379, 381, 382, 383, 411, 425, 433-5p, 485-5p, 488, 491-5p, 574, 874, 885 (?)

Hypothalamus Let-7a,b,c, 103, 124a, 125a, 128a, 132, 136, 138, 212, 338, 451

Cerebellum 9, 98, 103, 124a, 125b, 128 (?), 132, 134, 137, 138, 181a, 181b,

181c, 204, 212, 213, 218, 338, 381, 382 (?), 425, 432, 489, 592, 874, 885

Amygdala 103, 134, 138, 182, 183, 222, 323-3p, 369, 381, 382

Spinal cord 218, 219, 338, 451, 486

Pituitary gland Let-7c, 7, 9, 92a,b, 96, 99a,b, 103, 107, 125a,b, 127, 128, 132,

134, 135a, 154, 181a-c, 182, 183, 184, 195, 197, 200a,b,c (?), 204, 212, 213, 218, 322 (?), 323, 324, 328, 329, 335-5p, 369, 370, 375, 377, 379, 381, 410, 411, 432, 433, 487b, 491, 494, 508, 514, 539, 542 (?), 603 (?), 618, 628, 652, 663 (?), 665, 885, 890

(?)

Midbrain, Substantia Let-7a,b,c,d,e, 9, 98, 99a,b, 100, 107, 125a,b (?), 126, 127-3p, nigra 129-3p, 134, 138, 149, 181a, 197, 204, 323, 329, 338, 340, 340*,

379, 383, 410, 424, 425, 432, 433, 487a,b, 539, 744 (?), 760, 9*, 99b*, 129*;

Medulla oblongata 10a,b, 34a, 451 (all not brain-enriched), 219, 338

Insufficient or contradictory data. Tested miRNAs were initially selected by the present inventors based on literature data on their enrichment in brain compartments and presence in neurites (i.e., axons and/or dendrites and/or spines) and/or synapses (Hua et al. BMC Genomics. 2009; 10: 214; Liang et al. BMC Genomics. 2007; 8: 166; Landgraf et al. Cell. 2007; 129: 1401-1414; Lee et al. RNA. 2008; 14: 35-42; Schratt et al. Nature. 2006; 439: 283-289; Lugli et al. J. Neurochem. 2008; 106: 650-661 ; Bicker and Schratt. J. Cell Mol. Med. 2008; 12: 1466-1476; Smalheiser and Lugli. Neuromolecular Med. 2009; 1 1 : 133-140; Rajasethupathy. Neuron. 2009; 63 : 714-716; Kye. RNA. 2007; 13 : 1224-1234; Yu et al. Exp. Cell Res. 2008; 314: 2618-2633; Cougot et al. J. Neurosci. 2008; 28: 13793-13804; Kawahara. Brain Nerve. 2008; 60: 1437-1444; Schratt. Rev. Neurosci. 2009; 10: 842-849; Pichardo-Casas et al. Brain Research. 2012; 1436: 20-33) as well as on their suggested involvement in neurite- and synapse-associated processes (the miR- Ontology Data Base: ferrolab.dmi.unict.it/miro/ ; Landgraf et al., Cell, 2007, 129: 1401-1414; Liang et al., BMC Genomics, 2007, 8: 166; Jovicic, J. Neurosci., 2013, 33 :5127-5137; Ludwig et al., Nucleic Acids Res., 2016, 44:3865-3877; Martini et al., PLoS One, 2014, 9:e89755; Penso- Dolfin et al., PLoS One, 2016, l l :e0153453). Ubiquitous miR-16 was also tested as a potential denominator. Then the present inventors analyzed literature and their own data to find out which miRNAs are detectable in plasma. 8 miRNAs were analyzed in the study (Table 2).

Table 2. miRNAs used in the mouse study of RETT syndrome models

Cer - Cerebel um; FC - Frontal Cortex; Hip - Hippocampus; MB - Midbrain; PG - Pituitary Gland Example 2: Quantitative Analysis

Mann-Whitney U-test was used to evaluate significance of differentiation of any two patient groups by various biomarker miRNA pairs. Bonferroni correction was applied for estimating significant P-values. In all experiments (differentiation of RTT mouse model from wild type control) 8 miRNAs were tested, thus P-value<0.002 (calculated as 0.05/28; 28 here indicates the total number of miRNA pairs examined) was considered significant. A standard formula for a case-control study (Eng J. Radiology. 2003; 227:309-313) was applied for estimating the sample size required to produce statistical power 0.90. Two approaches for comparison of two cohorts, namely ratios of two miRNA concentrations and described above probability-based method, were used and gave similar results, although the latter is much more convenient for combining several miRNA pairs or other biomarkers.

Example 3: Differentiation of Mecp2^{tml lJae} mouse RTT model from wild type controls

Two mouse models were used, namely Mecp2^{tml lJae} and Mecp2^{tml lBird}. Both models are male mice (Null) with nonfunctional Mecp2 due to deletion of exon 3 in Mecp2^{tml lJae} (Guy, J., Hendrich, B., Holmes, M., Martin, J. E. and Bird, A. (2001). A mouse Mecp2-null mutation causes neurological symptoms that mimic Rett syndrome. Nat. Genet. 27, 322-326) or exon 3-4 in Mecp^{2tml lBird} (Chen, R. Z., Akbarian, S., Tudor, M. and Jaenisch, R. (2001). Deficiency of methyl-CpG binding protein-2 in CNS neurons results in a Rett-like phenotype in mice. Nat. Genet. 27, 327-331), respectively. Since the total amount of plasma that can be obtained from a mouse is relatively low, 8 miRNAs expressed in different brain regions were tested (see Table 2, above).

0.2 ml plasma samples were obtained from 11 Mecp2^{tml lJae} mice and 9 wild type controls of the same age. Concentrations of miRNAs in plasma were analyzed using RT-qPCR with primers and probes for each individual miRNA (Life Technologies). The amount of RNA equivalent to 25 μΐ. of plasma were taken in each RT reaction, and the amount of miRNA (cDNA) equivalent to 2 μΐ. plasma was taken into final PCR. The results obtained for each miRNA were converted into Relative Concentration (RC) of miRNA according to the ABI protocol (2^" ), normalized per potential normalizer miRNA, and this ratio was compared with respective control values. The biomarker miRNA pairs were selected as described above. Comparison of brain-enriched miRNA pair ratios in mutant and control mice are presented in Figure 1. P-values for differentiation of RTT mice model from wild type controls and AUC (Area under ROC curve) for best miRNA pairs are presented in Table 3 and in Figure 2. miR-107 and miR-491-5p enriched in midbrain and frontal cortex and present in synapses behave as the best numerators, which is in a good agreement with known involvement of these brain regions in the RTT pathology. Hippocampus-enriched miR-132 and miR-335-5p are good denominators. Interestingly, miR-323-3p, whose presence in midbrain and cortex has been described in literature behaves as a good denominator. Most likely miR-323-3p is present in different brain regions and its plasma concentration depends on involvement of these areas in pathology and respective changes in miR-323-3p expression and secretion. Although accuracy for individual miRNA pairs is sufficiently high (up to 0.89), their combination gives even higher accuracy (0.95).

Table 3. Differentiation of Mecp2^{tml 1Jae} Null and control mice by miRNA pairs and their combinations

Example 4: Differentiation of Mecp2 ^m " ^,r Null mouse RTT model from wild type controls

0.2 ml plasma samples were obtained from 8 Mecp2^{tml lBird} mouse and 10 wild type controls of the same age. Same 8 miRNAs were tested and experiments were performed as described above in Example 3. Data obtained are presented in Figures 3-5 and Table 4. Again miR-107 and miR-491-5p are very good numerators, while miR-132 and miR-335-5p, enriched in hippocampus are among the best denominators. miR-323-3p is still a good denominator for miR-491-5p but also behaves as a numerator being combined with miR-132 and miR-335-5p, which again agrees with its expression in various brain areas.

Table 4. Differentiation of Mecp2^{tml lBird}Null and control mice by miRNA pairs and their combinations (Grey rows indicate miRNA pairs common for two RTT mice models).

Example 5. Differentiation of Mecp2^{tml lJae} Het and Mecp2^{tmi imra} Het mouse RTT models from wild type controls

The levels of the eight miRNA in two cohorts of female heterozygous (Het) and wild type (Wt) mice: Mecp2^tmUJae Het n=6, Wt n=7 (6 months old), and Mecp2^tmL1Bird Het n=10, Wt n=10 (18 weeks old) were compared. The two pairs of mutant and Wt cohorts were tested at different ages, and therefore were analyzed independently. Same 8 miRNAs were tested and experiments were performed as described above in Example 3. Fig. 6 and Fig. 8, respectively, present the data from these two experiments as dot-plots and Fig. 5 and Fig. 7 demonstrate the associated ROC curves. As expected, in Het, the AUC and its associated accuracy representing the ability of miRNA pairs to distinguish mutant from wild type mice, were lower than in Null mice, since female heterozygotes retain some normal MeCP2 expression. However, signatures consisting of combined miRNA pairs provide >90% overall accuracy in female heterozygous Mecp2^{tml lJae} md Mecp2^tmUB,rd mouse models.

The AUC for all four experiments are summarized in Table 5. Notably, certain miRNA pairs effectively distinguish between mutant and wild type mice consistently in all four animal models (Jae Null and Het and Bird ^'Null and Het).

Table 5. Data summary for effective miRNA pairs. The table lists miRNA pairs identified in the study oiMecp2^tmL1Bird, Null and Wt (shown in Italic if also identified in female models). The miRNA pairs also identified in the study of Mecp2^{tml lJae} , Null and Wt, are shown in bold. miRNA pairs identified in all four studies Mecp2^tmL1Bird, Mecp2^tmL1Ja Null and Wt, Het and Wt, are shown in bold Italic.

miRNA pair AUC Sensitivity Specificity Accuracy P-value miR-411 / miR-132 0.93 0.88 0.9 0.89 <0.0032 miR-107 /miR-132 0.98 0.88 0.9 0.89 <0.0002 miR-107/ miR-335-5p 0.99 1 0.9 0.94 <0.0001

Combined 1 0.88 1 0.94 miR-491-5p / miR-335-5p 0.98 0.88 1 0.94 <0.0003 miR-491-5p / miR-132 0.99 0.88 1 0.94 <0.0001

Combined 0.99 0.88 1 0.94 miR-323-3p / miR-335-5p 0.98 0.75 1 0.89 <0.0002 miR-323-3p / miR-132 0.91 0.88 0.9 0.89 <0.0078

Combined 0.95 0.88 0.9 0.89 miR-323-3p / miR-335-5p 0.98 0.75 1 0.89 <0.0002 miR-491-5p / miR-335-5p 0.98 0.88 1 0.94 <0.0003 miR-41 1 / miR-335-5p 0.98 0.88 1 0.94 <0.0003

Combined 1 1 1 1 miR-491-5p / miR-323-3p 0.81 0.88 0.7 0.78 0.06

* * *

The present invention is not to be limited in scope by the specific embodiments described herein. Indeed, various modifications of the invention in addition to those described herein will become apparent to those skilled in the art from the foregoing description. Such modifications are intended to fall within the scope of the appended claims.

All patents, applications, publications, test methods, literature, and other materials cited herein are hereby incorporated by reference in their entirety as if physically present in this specification.

Claims

WHAT IS CLAIMED IS:

1. A method for detecting a neurodevelopmental disorder in a subject, which method comprises:

a) measuring the level of a first brain-enriched miRNA in a bodily fluid sample collected from the subject, wherein said first brain-enriched miRNA is enriched in a brain area(s) affected by the neurodevelopmental disorder;

b) measuring the level of a second brain-enriched miRNA in the bodily fluid sample collected from the subject, wherein said second brain-enriched miRNA (i) is enriched in a brain area(s) which is not affected by the neurodevelopmental disorder, or (ii) is enriched in a brain cell type which is not affected by the neurodevelopmental disorder, or (iii) is enriched in the same brain area as the first miRNA, but its expression and/or secretion change differently than expression and/or secretion of the first miRNA during development of the neurodevelopmental disorder;

d) comparing the ratio of the levels of the miRNAs calculated in step (c) with a corresponding control ratio; and

2. The method of claim 1, further comprising the following steps, which steps can be performed simultaneously or sequentially with each other and/or with the steps (d)-(e) of claim 1 :

f) comparing the ratio of the levels of the miRNAs calculated in step (c) with the standard range of ratios of said miRNAs characteristic of a second pathology, and

g) (i) excluding the diagnosis of the second pathology in the subject if the ratio of the levels of the miRNAs calculated in step (c) does not fall within the standard range of ratios of said miRNAs characteristic of the second pathology, or (ii) not excluding the diagnosis of the second pathology in the subject if the ratio of the levels of the miRNAs calculated in step (c) falls within the standard range of ratios of said miRNAs characteristic of the second pathology.

3. The method of claim 1, further comprising the following steps, which steps can be performed simultaneously or sequentially with each other and/or with the steps (a)-(e) of claim 1 : f) measuring the level of a third brain-enriched miRNA in the bodily fluid sample collected from the subject, wherein said third brain-enriched miRNA is enriched in a brain area(s) affected by a second pathology;

g) measuring the level of a fourth brain-enriched miRNA in the bodily fluid sample collected from the subject, wherein said fourth brain-enriched miRNA is (i) enriched in a brain area(s) which is not affected by the second pathology, or (ii) is enriched in a brain cell type which is not affected by the second pathology, or (iii) is enriched in the same brain area as the third miRNA, but its expression and/or secretion change differently than expression and/or secretion of the third miRNA during development of the second pathology;

j) (i) not excluding the diagnosis of the second pathology in the subject if the ratio of the levels of the miRNAs calculated in step (h) falls within the standard range of ratios of said miRNAs characteristic of the second pathology, or (ii) excluding the diagnosis of the second pathology in the subject if the ratio of the levels of the miRNAs calculated in step (h) does not fall within the standard range of ratios of said miRNAs characteristic of the second pathology.

4. A method for detecting a neurodevelopmental disorder in a subject, which method comprises:

b) measuring the level of a second brain-enriched miRNA in the bodily fluid sample collected from the subject, wherein said second brain-enriched miRNA (i) is enriched in a brain area(s) which is not affected by the neurodevelopmental disorder, or (ii) is enriched in a brain cell type which is not affected by the neurodevelopmental disorder, or (iii) is enriched in the same brain area as the first miRNA, but its expression and/or secretion change differently than expression and/or secretion of the first miRNA during development of the neurodevelopmental disorder, and

5. A computer-implemented method of assigning a subject into a category of being afflicted with a neurodevelopmental disorder, which method comprises:

a. measuring the level of a first brain-enriched miRNA in a bodily fluid sample collected from the subject, wherein said first brain-enriched miRNA is enriched in a brain area(s) affected by the neurodevelopmental disorder;

b. measuring the level of a second brain-enriched miRNA in the bodily fluid sample collected from the subject, wherein said second brain-enriched miRNA (i) is enriched in a brain area(s) which is not affected by the neurodevelopmental disorder, or (ii) is enriched in a brain cell type which is not affected by the neurodevelopmental disorder, or (iii) is enriched in the same brain area as the first miRNA, but its expression and/or secretion change differently than expression and/or secretion of the first miRNA during development of the neurodevelopmental disorder;

e. calculating, by the processor and based on the ratio determined in step (c), a second probability based on a second predefined probability distribution curve, wherein the second predefined probability distribution curve corresponds to a matched control or another pathology; f. determining, by the processor, a difference between the first probability calculated in step (d) and the second probability calculated in step (e), and

6. A method for treating a neurodevelopmental disorder in a subject in need thereof, which method comprises:

f) administering a therapeutic or preventive treatment to the subject.

7. A method for selecting subjects for enrollment in a clinical trial involving treatment of a neurodevelopmental disorder, which method comprises:

a) measuring the level of a first brain-enriched miRNA in a bodily fluid sample collected from the subject, wherein said first brain-enriched miRNA is enriched in a brain area(s) affected by the neurodevelopmental disorder; b) measuring the level of a second brain-enriched miRNA in the bodily fluid sample collected from the subject, wherein said second brain-enriched miRNA (i) is enriched in a brain area(s) which is not affected by the neurodevelopmental disorder, or (ii) is enriched in a brain cell type which is not affected by the neurodevelopmental disorder, or (iii) is enriched in the same brain area as the first miRNA, but its expression and/or secretion change differently than expression and/or secretion of the first miRNA during development of the neurodevelopmental disorder;

f) recruiting the subject in a clinical trial.

8. The method of any one of claims 1-7, wherein the neurodevelopmental disorder is Rett Syndrome (RTT).

9. The method of any one of claims 1-7, the neurodevelopmental disorder is selected from the group consisting of Landau-Kleffner Syndrome, Alexander Disease, Alpers' Disease, Alternating Hemiplegia, Angelman Syndrome, Ataxias and Cerebellar or Spinocerebellar Degeneration, Ataxia Telangiectasia, Attention Deficit-Hyperactivity Disorder, Autism Spectrum Disorders including Asperger Syndrome, Batten Disease, Canavan Disease, and Tourette Syndrome.

10. The method of any one of claims 1-9, wherein the control ratio is a predetermined value which represents a statistically validated threshold ratio of the levels of said first and second miRNAs, wherein the statistically validated threshold ratio is equal to the highest possible value within the range of corresponding values in matched healthy subjects.

11. The method of claim 10, wherein the matched healthy subjects are matched by gender and/or age and/or race.

12. The method of any one of claims 1-11, wherein the control ratio is the ratio of the levels of said first and second miRNAs in a similarly processed bodily fluid sample from the same subject collected in the past.

13. The methods of claim 2 or claim 3, wherein the standard range of ratios of miRNAs characteristic of the second pathology is a statistically validated predetermined range of values established by determining the ratios of the same miRNAs in a cohort of subjects diagnosed with the second pathology.

14. The method of claim 13, wherein the cohort of subjects diagnosed with the second pathology represents a full range of development stages of said second pathology.

15. The method of claim 13, wherein the cohort of subjects diagnosed with the second pathology represents one or more development stages of said second pathology.

16. The method of claim 2 or claim 3, wherein said neurodevelopmental disorder is Rett Syndrome and said second pathology is selected from the group consisting of Landau-Kleffner Syndrome, Alexander Disease, Alpers' Disease, Alternating Hemiplegia, Angelman Syndrome, Ataxias and Cerebellar or Spinocerebellar Degeneration, Ataxia Telangiectasia, Attention Deficit-Hyperactivity Disorder, Autism Spectrum Disorders including Asperger Syndrome, Batten Disease, Canavan Disease, and Tourette Syndrome.

17. The method of claim 2 or claim 3, wherein said second pathology is selected from the group consisting of Rett Syndrome, Landau-Kleffner Syndrome, Alexander Disease, Alpers' Disease, Alternating Hemiplegia, Angelman Syndrome, Ataxias and Cerebellar or Spinocerebellar Degeneration, Ataxia Telangiectasia, Attention Deficit-Hyperactivity Disorder, Autism Spectrum Disorders including Asperger Syndrome, Batten Disease, Canavan Disease, and Tourette Syndrome.

18. The method of any one of claims 1-17, wherein said neurodevelopmental disorder is Rett Syndrome (RTT) and the method further comprises determining the underlying MECP2 mutation.

19. A method for monitoring changes in development of a neurodevelopmental disorder in a subject, which method comprises:

a) measuring the level of a first brain-enriched miRNA in two or more bodily fluid samples collected from the subject, wherein said first brain-enriched miRNA is enriched in a brain area(s) affected by the neurodevelopmental disorder;

b) measuring the level of a second brain-enriched miRNA in the same bodily fluids samples as in step (a), wherein said second brain-enriched miRNA (i) is enriched in a brain area(s) which is not affected by the neurodevelopmental disorder, or (ii) is enriched in a brain cell type which is not affected by the neurodevelopmental disorder, or (iii) is enriched in the same brain area as the first miRNA, but its expression and/or secretion change differently than expression and/or secretion of the first miRNA during development of the neurodevelopmental disorder;

20. The method of claim 19, wherein the subject has been previously diagnosed with said neurodevelopmental disorder.

21. A method for monitoring the effect of a treatment on development of a neurodevelopmental disorder in a subject, which method comprises:

a) measuring the level of a first brain-enriched miRNA in a bodily fluid sample collected from the subject prior to initiation of the treatment, wherein said first brain-enriched miRNA is enriched in a brain area(s) affected by the neurodevelopmental disorder;

22. The method of claim 21, wherein the subject has been previously diagnosed with said neurodevelopmental disorder.

23. A method for identifying a compound useful for slowing down the progression or treating a neurodevelopmental disorder in a subject, which method comprises:

a) measuring the level of a first brain-enriched miRNA in a bodily fluid sample, wherein said bodily fluid sample(s) is collected from the subject prior to test compound administration, and wherein said first brain-enriched miRNA is enriched in a brain area(s) affected by the neurodevelopmental disorder;

g) comparing the ratio of the levels of the miRNA calculated in steps (c) and (f), and

h) (i) identifying that the test compound is useful for slowing down the progression or treating the neurodevelopmental disorder if the ratio of the levels of the miRNA calculated in step (f) is lower than the ratio of the levels of the miRNA calculated in step (c); (ii) identifying that the test compound is not useful for slowing down the progression or treating the neurodevelopmental disorder if the ratio of the levels of the miRNA calculated in step (f) is not lower than the ratio of the levels of the miRNAs calculated in step (c).

24. The method of any one of claims 19-23, wherein the neurodevelopmental disorder is Rett Syndrome (RTT).

25. The method of any one of claims 19-23, the neurodevelopmental disorder is selected from the group consisting of Landau-Kleffner Syndrome, Alexander Disease, Alpers' Disease, Alternating Hemiplegia, Angelman Syndrome, Ataxias and Cerebellar or Spinocerebellar Degeneration, Ataxia Telangiectasia, Attention Deficit-Hyperactivity Disorder, Autism Spectrum Disorders including Asperger Syndrome, Batten Disease, Canavan Disease, and Tourette Syndrome.

26. The method of any one of claims 1-25, wherein the first brain-enriched miRNA is a synapse and/or neurite miRNA.

27. The method of any one of claims 1-26, wherein the second miRNA is a brain- enriched miRNA, which (1) is enriched in a brain area(s) which is not affected by the neurodevelopmental disorder or (2) is enriched in a brain cell type which is not affected by the neurodevelopmental disorder.

28. The method of claim 27, wherein the neurodevelopmental disorder is RTT.

29. The method of any one of claims 1-28, wherein the second miRNA is a brain- enriched miRNA selected from the group consisting of miRNAs which are mainly expressed in brain areas not involved in RTT, miRNAs which are mainly expressed in glial cells, and brain- enriched miRNAs downregulated in RTT.

30. The method of any one of claims 1-29, wherein the first brain-enriched miRNA is enriched in neurons and the second brain-enriched miRNA is enriched in glial cells.

31. The method of any one of claims 1-30, wherein the pair of the first miRNA and the second miRNA is selected from the group consisting of: miR-107/miR-323-3p, miR-107/miR- 335-5p, miR-491-5p/miR-323-3p, miR-491-5p/miR-335-5p, miR-491-5p/miR-132, miR-491- 5p/miR-411, miR-41 l/miR-335-5p, miR-411/miR-l 32, miR-107/miR-132, miR-323-3p/miR- 335-5p, and miR-323-3p/miR-132.

32. The method of any one of claims 1-30, wherein the pair of the first miRNA and the second miRNA is selected from the pairs provided in Tables 3-5.

33. The method of any one of claims 1-32, wherein the method comprises measuring the level and calculating the ratios of the levels for two or more different pairs of miRNA.

34. The method of claim 33, wherein the method comprises measuring the level and calculating the ratios of the levels for one or more pair combinations selected from the group consisting of:

(a) miR-107/miR-323-3p and miR-107/miR-335-5p;

(c) miR-411/miR-l 32, miR-107/miR-132 and miR-107/miR-335-5p;

(d) miR-323-3p/miR-335-5p and miR-323-3p/miR-132;

(e) miR-323-3p/miR-335-5p, miR-491-5p/miR-335-5p and miR-41 l/miR-335 -5p; and

(f) miR-491-5p/miR-335-5p and miR-491-5p/miR-132.

35. The method of any one of claims 1-34, wherein the method comprises measuring the levels of the miRNAs in two or more bodily fluid samples collected from the subject, and wherein the samples have been collected at spaced apart time points.

36. The method of claim 35, wherein the bodily fluid samples are obtained several months apart.

37. The method of claim 36, wherein the bodily fluid samples are obtained 3-6 months apart.

38. The method of any one of claims 1-37, wherein the method further comprises normalizing the levels of the first and second miRNAs to the level of a normalizer miRNA.

39. The method of claim 38, wherein the normalizer miRNA is expressed in numerous tissues but is not significantly expressed in brain.

40. The method of any one of claims 1-39, wherein the subject does not have clinical symptoms of said neurodevelopmental disorder.

41. The method of any one of claims 1-40, wherein the subject is human.

42. The method of claim 41, wherein the subject is an infant or a child.

43. The method of any one of claims 1-40, wherein the subject is an experimental animal.

44. The method of claim 43, wherein the experimental animal is an animal model of a neurodevelopmental disorder.

45. The method of claim 44, wherein the neurodevelopmental disorder is RTT.

46. The method of any one of claims 1-45, wherein the bodily fluid is selected from the group consisting of blood plasma, serum, urine, and saliva.

47. The method of any one of claims 1-46, wherein the bodily fluid allows low cost noninvasive or minimally invasive collection and analysis.

48. The method of any one of claims 1-47, wherein the method further comprises the step of collecting the bodily fluid sample(s) from the subject.

49. The method of claim 48, wherein the step of collecting the bodily fluid sample(s) from the subject is performed prior to step (a).

50. The method of any one of claims 1-49, wherein the level of the miRNAs is determined using a method selected from the group consisting of hybridization, polymerase chain reaction (PCR)-based detection, sequencing, and microfluidic technologies.

51. The method of any one of claims 1-50, wherein the level of the miRNAs is determined using RT-PCR.

52. The method of any one of claims 1-50, wherein the level of the miRNAs is determined using a method selected from the group consisting of Northern blotting, bead-based flow-cytometry, oligonucleotide microchip, oligonucleotide microarray, solution hybridization assays, stem-loop reverse transcription-polymerase chain reaction [RT-PCR], quantitative RT- PCR based array method, Helicos small RNA sequencing, miRNA BeadArray, Roche 454, and ABI SOLiD.

53. The method of any one of claims 1-52, wherein prior to measuring miRNA level, the miRNA is purified from the bodily fluid sample.

54. The method of claim 53, wherein prior to measuring miRNA level, the miRNA is isolated and purified from the bodily fluid sample by one or more of Trizol extraction, concentration and purification on anion-exchangers, magnetic beads covered by RNA-binding substances, and adsorption of certain miRNA on complementary oligonucleotides.

55. The method of any one of claims 1-54, wherein the method further comprises reducing or eliminating degradation of the miRNAs.

56. The method of claim 55, wherein the reducing or eliminating degradation of the miRNAs involves one or more of adding RNase inhibitors, use of guanidine chloride, guanidine isothiocyanate, N-lauroylsarcosine, sodium dodecyl sulphate (SDS), or a combination thereof.

57. The method of any one of claims 1-56, further comprising applying one or more quality control (QC) and/or normalization steps.

58. The method of claim 57, wherein one of the QC or normalization steps is selected from the group consisting of:

a) comparing the concentration of ubiquitous miRNAs in the bodily fluid of the subject with pre-established normal values,

b) synthesizing and using synthetic small RNA oligonucleotides as controls for losses during purification by adding them to bodily fluid samples before RNA purification, and c) normalizing miRNA concentration in urine on creatinine and/or albumin level to account for variations in kidney filtration.

59. The method of any one of claims 1-58, further comprising using one or more additional methods of detection of the neurodevelopmental disorder.

60. The method of claim 59, wherein the additional method of detection is selected from the group consisting of genetic testing, hearing test, eye exam, vision exam, positron emission tomography (PET), computed tomography (CT), magnetic resonance imaging (MRI), multiphoton imaging, magnetoencephalography (MEG), and electroencephalography (EEG).

61. The method of any one of claims 1-5 and 7-60, further comprising administering a therapeutic or preventive treatment to the subject.

62. The method of claim 6 or claim 61, wherein the therapeutic or preventive treatment is selected from the group consisting of physical therapies, occupational therapies, speech therapies, language therapies, nutritional support, controlling seizures, controlling muscle stiffness, GI treatments, heart treatments, and treatments for breathing problems.

63. The method of claim 6, 61 or 62, wherein the therapeutic or preventive treatment is administered prior to appearance of one or more clinical symptoms of the neurodevelopmental disorder.

64. The method of any one of claims 1-63, wherein the method further comprises recruiting the subject in a clinical trial.

65. A kit for detecting a neurodevelopmental disorder comprising primers and/or probes specific for one or more pairs of miRNAs selected from the group consisting of: miR-107/miR- 323-3p, miR-107/miR-335-5p, miR-491-5p/miR-323-3p, miR-491-5p/miR-335-5p, miR-491- 5p/miR-132, miR-491-5p/miR-411, miR-41 l/miR-335-5p, miR-411/miR- 132; miR-107/miR- 132, miR-323-3p/miR-335-5p, and miR-323-3p/miR-132.

66. A kit for detecting a neurodevelopmental disorder comprising primers and/or probes specific for one or more pairs of miRNAs selected from the pairs provided in Tables 3-5.

67. A kit for detecting a neurodevelopmental disorder comprising primers and/or probes specific for one or more combinations of pairs of miRNAs selected from the group consisting of:

(a) miR-107/miR-323-3p and miR-107/miR-335-5p;

(c) miR-41 l/miR-132, miR-107/miR-132 and miR-107/miR-132;

(d) miR-323-3p/miR-335-5p and miR-323-3p/miR-132;

(e) miR-323-3p/miR-335-5p, miR-491-5p/miR-335-5p and miR-41 l/miR-335 -5p; and

(f) miR-491-5p/miR-335-5p and miR-491-5p/miR-132.

68. The kit of any one of claims 65-67, further comprising miRNA isolation means and/or miRNA purification means and/or instructions for use.