Analysis and prediction of traumatic brain injury and concusion symptoms

Patent metadata

Field	Value
Publication number	US-2020277676-A1
Application number	US-201816496154-A
Country	US
Kind code	A1
Filing date	Mar 23, 2018
Priority date	Mar 23, 2017
Publication date	Sep 3, 2020
Grant date	—

Abstract

Provided are methods for detecting or diagnosing a traumatic brain injury or TBI by detecting concentration levels miRNAs associated with TBI in saliva. Methods for controlled and normalized comparisons of salivary miRNA concentration levels are further provided. Assay kits comprising salivary miRNAs, probes and/or primers for detecting salivary miRNAs are also provided.

First claim

1 . A method for detecting or diagnosing a concussion, mild traumatic brain injury (“mTBI”), or other traumatic brain injury (“TBI”) comprising:
(a) determining abundance or concentration level(s) of one or more micro RNAs (“miRNAs”) in a saliva sample taken from a human subject, and
(b) comparing the determined abundance or concentration level(s) of the one or more miRNAs against normal level(s) of the same one or more miRNAs, wherein the normal level is that found in a subject, or an average from two of more subjects, not having a concussion or mild traumatic brain injury; or is an abundance or concentration level(s) determined in the subject prior to an event that produces a concussion, mTBI or other TBI, and
(c) selecting a subject having an abnormal level of said one or more miRNAs as having, or as being at higher risk for having, a concussion, mild traumatic brain injury or other traumatic brain injury;
wherein the one or more miRNA is selected from the group consisting hsa-let-7f-5p, hsa-let-7i, hsa-miR-10a-5p, hsa-miR-10b-5p, hsa-miR-23a-3p, hsa-mir-23b, hsa-mir-25, hsa-miR-25-3p, hsa-mir-26a-1, hsa-mir-26a-2, hsa-miR-26a-5p, hsa-mir-26b, hsa-miR-26b-5p, hsa-mir-28, hsa-miR-28-3p, hsa-miR-28-5p, hsa-miR-29c-3p, hsa-mir-30b, hsa-miR-30e-3p, hsa-miR-30e-5p, hsa-mir-92a-1, hsa-mir-92a-2, hsa-mir-103a-1, hsa-mir-103a-2, hsa-miR-125b-1-3p, hsa-miR-125b-2-3p, hsa-miR-141-3p, hsa-miR-148b-3p, hsa-mir-151a, hsa-miR-151a-3p, hsa-miR-151a-5p, hsa-miR-155-5p, hsa-mir-181a-2, hsa-miR-181a-5p, hsa-miR-182-5p, hsa-miR-193a-3p, hsa-miR-203a-3p, hsa-miR-205-5p, hsa-mir-218-2, hsa-miR-221-3p, hsa-miR-320c, hsa-miR-338-3p, hsa-miR-338-5p, hsa-miR-342-5p, hsa-miR-374a-5p, hsa-miR-378d, hsa-miR-378f, hsa-miR-378g, hsa-miR-378i, hsa-miR-454-3p, hsa-miR-501-3p, hsa-miR-532-5p, hsa-miR-577, hsa-miR-625-3p, hsa-miR-744-5p, hsa-miR-944, hsa-miR-1273g-5p, hsa-miR-1285-3p, hsa-miR-1303, hsa-miR-1307-3p, hsa-miR-3074-5p, hsa-mir-3160-1, hsa-mir-3613, hsa-miR-3613-5p, hsa-miR-3916, hsa-mir-4532, hsa-mir-5091, hsa-miR-6770-5p and those miRNAs which share the seed sequences thereof; and/or are selected from the group consisting of at least one of miR-769, miR-769-3p, miR-769-5p, miR-320c-1, miR-320c-1-3p, miR-320c-1-5p, miR-4792, miR-4792-3p, miR-4792-5p, miR-140, miR-140-3p, miR-140-5p, miR-629, miR-629-3p, miR-629-5p, miR-192, miR-192-3p, miR-192-5p, miR-145, miR-145-3p, miR-145-5p, let-7a, let-7a-3p, let-7s-5p, miR-133a, miR-133a-3p, miR-133a-5p, miR-1307, miR-1307-3p, miR-1307-5p, miR-200b, miR-200b-3p, miR-200b-5p, let-7a, let-7a-3p, let-7a-5p, miR-4508, miR-4508-3p, miR-4508-5p, miR-30e, miR-30e-3p, miR-30e-5p, let-7b, let-7b-3p, let-7b-5p, miR-194, miR-194-3p, miR-194-5p, miR-199a, miR-199a-3p, miR-199a-5p, let-7f, let-7f-3p, let-7f-5p, miR-128, miR-128-3p, miR-128-5p, miR-215, miR-215-3p, miR-215-5p, miR-149, miR-149-3p, miR-149-5p, miR-421, miR-421-3p, and miR-421-5p; and those miRNA which share the seed sequences thereof.

2 . The method of claim 1 , wherein said miRNA expression levels are normalized to an expression level, or average expression level, of one or more housekeeping genes whose RNA expression level is substantially invariant; and/or wherein said miRNA levels are normalized to compensate for diurnal or circadian fluctuations in the expression of the one or more miRNA levels, controlled or normalized to compensate for fluctuations in the expression of the one or more miRNA levels due to food intake, or exercise that raises the heart rate; or adjusted to compensate for differences in age, sex or genetic background.

3 . The method of claim 1 , wherein (a) determining abundance or concentration of one or more miRNAs is done by RNA sequencing (“RNA-seq”), qPCR, a miRNA array, or multiplex miRNA profiling.

4 . The method of claim 1 , wherein the saliva sample is taken from a human subject suspected of having a mTBI and wherein the miRNAs are selected from the group consisting of at least one of miR-769, miR-769-3p, miR-769-5p, miR-320c-1, miR-320c-1-3p, miR-320c-1-5p, miR-4792, miR-4792-3p, miR-4792-5p, miR-140, miR-140-3p, miR-140-5p, miR-629, miR-629-3p, miR-629-5p, miR-192, miR-192-3p, miR-192-5p, miR-145, miR-145-3p, miR-145-5p, let-7a, let-7a-3p, let-7s-5p, miR-133a, miR-133a-3p, miR-133a-5p, miR-1307, miR-1307-3p, miR-1307-5p, miR-200b, miR-200b-3p, miR-200b-5p, let-7a, let-7a-3p, let-7a-5p, miR-4508, miR-4508-3p, miR-4508-5p, miR-30e, miR-30e-3p, miR-30e-5p, let-7b, let-7b-3p, let-7b-5p, miR-194, miR-194-3p, miR-194-5p, miR-199a, miR-199a-3p, miR-199a-5p, let-7f, let-7f-3p, let-7f-5p, miR-128, miR-128-3p, miR-128-5p, miR-215, miR-215-3p, miR-215-5p, miR-149, miR-149-3p, miR-149-5p, miR-421, miR-421-3p, and miR-421-5p; and those miRNAs which share the seed sequences thereof.

5 . The method of claim 1 , wherein the saliva sample is taken from a human subject suspected of having a concussion and wherein the miRNAs are selected from the group consisting of at least one of miR-29c-3p, miR-26b-5p, miR-30e-5p, miR-182-5p, miR-320c, and miR-221-3p; and those miRNAs which share the seed sequences thereof.

6 . The method of claim 1 , wherein the saliva sample is taken from the human subject at a particular time of day and abundance or the concentration level(s) of miRNAs in said sample are compared to normal miRNA values in saliva taken at the same time of day under otherwise identical conditions.

7 . The method of claim 1 , wherein the saliva sample is taken from the human subject at a different time of day than the time of day at which the normal level(s) of miRNAs were determined, further comprising adjusting or normalizing the value of the miRNA level(s) determined in the saliva sample to compensate for diurnal or circadian fluctuations in miRNA level(s).

8 . The method of claim 1 , wherein the saliva sample is taken from the human subject at a different time of day than the time of day at which the normal level(s) of miRNAs were determined, further comprising adjusting or normalizing the value of the miRNA level(s) determined in the saliva sample to compensate for diurnal or circadian fluctuations in miRNA level(s) using a regression model or other statistical analysis; or to compensate for age, sex, or genetic background.

9 . The method of claim 1 , wherein the saliva sample is taken within 1 hour of waking, before brushing or rinsing the mouth, before eating or drinking, and/or before exercise that elevates heart rate.

10 . The method of claim 1 , wherein said selecting comprises selecting a subject having abnormal levels of four or more of said miRNAs, and, optionally calculating a Pearson correlation coefficient of said abnormal miRNA levels with at least one symptom of a concussion, mTBI or TBI.

11 . The method of claim 1 , wherein said selecting comprises selecting a subject having abnormal levels of ten or more of said miRNAs, and, optionally calculating a Pearson correlation coefficient of said abnormal miRNA levels with at least one symptom of a concussion, mTBI or TBI.

12 . The method of claim 1 , wherein determining salivary miRNA levels is done by RNA sequencing (RNA-seq).

13 . The method of claim 12 , wherein the sequencing data raw read counts are quantile-normalized, mean-centered, and divided by the standard deviation of each variable; data are normalized to account for inter-sample count variations; and/or wherein data are normalized to expression of one or more invariant miRNAs to describe relative and/or absolute expression levels; and optionally further statistically analyzing the normalized data.

14 . The method of claim 1 , further comprising treating a subject having at least one abnormal level of miRNA with a regimen that redu

Assignees

• Quadrant Biosciences Inc
• Univ New York State Res Found
• Penn State Res Found

Inventors

• Hicks Steven D
• Middleton Frank A
• Uhlig Richard

Classifications

• A61B5/4064 Primary

  Evaluating the brain (for intracranial pressure A61B5/031; for cerebral blood gases A61B5/14553; using EEG A61B5/369) · CPC title

• C12Q2600/178

  miRNA, siRNA or ncRNA · CPC title

• C12Q1/6883 Primary

  for diseases caused by alterations of genetic material · CPC title

• C07K14/705

  Receptors; Cell surface antigens; Cell surface determinants {(tumour specific antigens C07K14/4748)} · CPC title

• A61B10/0051

  for taking saliva or sputum samples (devices for receiving spittle A61J9/00) · CPC title