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US-12618112-B2 - Epigenetic moderators of naltrexone efficacy in reducing heavy drinking in individuals diagnosed with alcohol use disorder

US12618112B2US 12618112 B2US12618112 B2US 12618112B2US-12618112-B2

Abstract

Disclosed are method for predicting naltrexone response in subjects with AUD. In some embodiments, the methods include performing or having performed one or more methylation assays on a genomic DNA sample isolated from the subject to determine the methylation status of one or more regions of the isolated genomic DNA, wherein the one or more regions are subsequences of a gene selected from a mu opioid receptor (OPRM1) gene, a catechol-O-methyltransferase (COMT) gene, and a dopamine transporter (SLC6A3) gene, wherein the methylation status of the one or more regions of the isolated genomic DNA determined is predictive of naltrexone response in the subject. Also provided are method for treating patients diagnosed with AUD with the medication naltrexone based on a methylation status of a combination of specific methylation sites located associated with an OPRM1 gene, a COMT gene, and/or an SLC6A3 gene in obtained from each AUD patient.

Inventors

  • Raymond F. Anton
  • Joseph P. Schacht

Assignees

  • MUSC FOUNDATION FOR RESEARCH DEVELOPMENT
  • THE REGENTS OF THE UNIVERSITY OF COLORADO, A BODY CORPORATE

Dates

Publication Date
20260505
Application Date
20220525

Claims (8)

  1. 1 . A method for treating an individual with an alcohol use disorder (AUD), the method comprising, consisting essentially of, or consisting of: (a) performing or having performed: (i) a first methylation assay on a genomic DNA sample isolated from the individual to determine the methylation status of one or more regions of a mu opioid receptor (OPRM1) gene sequence comprising, consisting essentially of, or consisting of SEQ ID NO: 1 in the isolated genomic DNA; and (ii) at least one additional methylation assay on a genomic DNA sample isolated from the individual to determine the methylation status(es) of a subsequence of a catechol-O-methyltransferase (COMT) gene corresponding to SEQ ID NO: 27, a subsequence of a dopamine transporter (SLC6A3) gene corresponding to SEQ ID NO: 11, and/or a subsequence of an SLC6A3 40-base-pair variable number tandem repeat (VNTR) in the 3′ untranslated region of the SLC6A3 gene corresponding to SEQ ID NO: 21; and (b) treating the individual with an effective amount of naltrexone if the methylation status of the one or more regions of the OPRM1 gene sequence corresponding to SEQ ID NO: 1 is low, defined as lower than 0.126 with respect to nucleotide position 357 of the OPRM1 gene sequence corresponding to SEQ ID NO: 1; lower than 0.147 with respect to nucleotide position 274 of the OPRM1 gene sequence corresponding to SEQ ID NO: 1; lower than 0.157 with respect to nucleotide position 277 of the OPRM1 gene sequence corresponding to SEQ ID NO: 1; and/or lower than 0.488 with respect to nucleotide position 419 of the OPRM1 gene sequence corresponding to SEQ ID NO: 1, and in addition: (1) the methylation status of the subsequence of the COMT gene corresponding to SEQ ID NO: 27 is low, defined as lower than 0.587 with respect to nucleotide position 46 of the COMT gene corresponding to SEQ ID NO: 27 and/or lower than 0.546 with respect to position 107 of the COMT gene corresponding to SEQ ID NO: 27; or (2) the methylation status of the subsequence of the SLC6A3 gene corresponding to SEQ ID NO: 11 is low, defined as lower than 0.651 with respect to nucleotide position 576 of the SLC6A3 gene corresponding to SEQ ID NO: 11 and/or lower than 0.648 with respect to nucleotide position 1102 of the SLC6A3 gene corresponding to SEQ ID NO: 11; or (3) the methylation status of the subsequence of the SLC6A3 40-base-pair VNTR in the 3′ untranslated region of the SLC6A3 gene sequence corresponding to SEQ ID NO: 21 is low, defined as lower than 0.089 with respect to nucleotide position 46 of the SLC6A3 40-base-pair VNTR in the 3′ untranslated region of SLC6A3 gene corresponding to SEQ ID NO: 21, wherein the individual with a low methylation status with respect to the OPRM1 gene sequence corresponding to SEQ ID NO: 1 in combination with one or more low methylation statuses of the COMT gene corresponding to SEQ ID NO: 27, the SLC6A3 gene corresponding to SEQ ID NO: 11, and/or the SLC6A3 40-base-pair VNTR in the 3′ untranslated region of the SLC6A3 gene sequence corresponding to SEQ ID NO: 21 is predicted to respond positively to naltrexone.
  2. 2 . The method of claim 1 , wherein the one or more regions of the OPRM1 gene sequence corresponding to SEQ ID NO: 1 include 130 nucleotides upstream and 600 nucleotides downstream of the OPRM1 transcription start site (TSS); optionally comprising one or more of SEQ ID NOs: 2-10.
  3. 3 . The method of claim 1 , wherein the subsequence of the SLC6A3 gene corresponding to SEQ ID NO: 11 comprises one or more of SEQ ID NOs: 12-20.
  4. 4 . The method of claim 1 , wherein the subsequence of the COMT gene corresponding to SEQ ID NO: 27 comprises one or more of SEQ ID NOs: 28-38.
  5. 5 . The method of claim 1 , wherein the subsequence of the SLC6A3 VNTR corresponding to SEQ ID NO: 21 comprises one or more of SEQ ID NOs: 22-25.
  6. 6 . The method of claim 1 , wherein the methylation statuses of at least one nucleotide position of each of the OPRM1 gene corresponding to SEQ ID NO: 1, the COMT gene corresponding to SEQ ID NO: 27, the dopamine transporter (SLC6A3) gene corresponding to SEQ ID NO: 11, and the 40-base-pair VNTR in the 3′ untranslated region of SLC6A3 gene corresponding to SEQ ID NO: 21 are determined.
  7. 7 . The method of claim 1 , wherein the genomic DNA is isolated from a cell selected from the group consisting of blood cells, optionally peripheral blood mononuclear cells, and buccal cells, and/or from a biological sample containing cells, optionally, blood, saliva, cerebrospinal fluid, and/or any fraction or component thereof.
  8. 8 . The method of claim 1 , further comprising converting the isolated genomic DNA with bisulfite prior to performing or having performed the methylation assays.

Description

CROSS REFERENCE TO RELATED APPLICATION The presently disclosed subject matter claims the benefit of U.S. Provisional Patent Application Ser. No. 63/192,952, filed May 25, 2021, the disclosure of which incorporated herein by reference in its entirety. GRANT STATEMENT This invention was made with government support under Grant Numbers AA017435 and AA017633 awarded by The National Institute on Alcohol Abuse and Alcoholism of the National Institutes of Health. The government has certain rights in the invention. REFERENCE TO SEQUENCE LISTING SUBMITTED ELECTRONICALLY The content of the electronically submitted sequence listing in ASCII text file (Name: 1586_24_2_ST25.txt; Size: 285 kilobytes; and Date of Creation: May 25, 2022) filed with the instant application is incorporated herein by reference in its entirety. TECHNICAL FIELD The presently disclosed subject matter relates in some embodiments to methods for predicting naltrexone responses in patients diagnosed with alcohol use disorders. The presently disclosed subject matter also relates in some embodiments to methods for treating subjects with alcohol use disorders with a treatment strategy for the subject that is predicated at least in part on the methylation statuses of subsequences of the OPRM1, COMT, and/or SLC6A3 genomic loci in the subject. BACKGROUND The opioid antagonist naltrexone reduces heavy drinking among individuals with Alcohol Use Disorder (AUD; Jonas et al., 2014a), but is not effective for everyone. Genomic factors might account for variability in its efficacy. The most extensively studied genomic factor is the rs1799971 single nucleotide polymorphism (SNP) in the gene encoding the μ-opioid receptor (MOR) OPRM1, which is an A/G SNP that encodes an aspartic acid or an asparagine at amino acid 40 of the human OPRM1 polypeptide in the endorphin binding domain and is associated with increased MOR binding affinity for β-endorphin (Bond et al., 1998). This gain-of-function SNP could also increase MOR affinity for naltrexone (Weerts et al., 2013), increasing naltrexone effects. However, meta-analyses of randomized controlled trials (RCTs) of naltrexone for AUD have found only weak evidence in support of rs1799971 moderation of naltrexone response (Hartwell et al., 2020; Jonas et al., 2014b). Naltrexone is believed to reduce drinking through opioid-mediated downstream effects on alcohol-induced dopamine release (Benjamin et al., 1993; Gonzales & Weiss, 1998), so genomic factors associated with dopamine reuptake and inactivation might also moderate its effects. Accordingly, in a human laboratory study of short-term naltrexone dosing among non-treatment-seeking AUD individuals, it was previously reported that variation at OPRM1 rs1799971, and a 40-base-pair variable number tandem repeat (VNTR) polymorphism in the 3′ untranslated region of SLC6A3, the gene encoding the dopamine transporter (DAT), interacted to predict naltrexone effects on alcohol self-administration and alcohol cue-elicited activation of the ventral striatum (Anton et al., 2012; Schacht et al., 2013; see also U.S. Patent Application Publication No. 2018/0371542 A1, each of which is incorporated herein by reference in its entirety). The SLC6A3 VNTR 10-repeat (10R) allele, relative to the 9-repeat (9R) allele, has been associated with relatively greater striatal DAT expression in AUD (Heinz et al., 2000), presumably reducing synaptic dopamine accumulation, and naltrexone, relative to placebo, reduced self-administration and cue-elicited ventral striatal activation most among individuals who carried the rs1799971 G allele and were homozygous for the SLC6A3 10R allele. These findings suggested that the predisposition to greater MOR affinity for naltrexone putatively conferred by the rs1799971 G allele might be beneficial only in the presence of genetically influenced reductions in synaptic dopamine accumulation. This finding was subsequently replicated and extended in a secondary analysis of a 16-week naltrexone RCT among treatment-seeking AUD patients (Anton et al., 2020; see also U.S. Patent Application Publication No. 2018/0369238, each of which is incorporated herein by reference in its entirety). While OPRM1 rs1799971 genotype alone did not significantly moderate naltrexone effects on heavy drinking, there were epistatic interactions between rs1799971 and both the SLC6A3 VNTR and the rs4680 (va1158met) SNP in COMT, the gene encoding the dopamine-inactivating enzyme catechol-O-methyltransferase (COMT; Anton et al., 2020). The rs4680 val allele has been associated with a three- to four-fold increase in COMT efficacy (Chen et al., 2004; Lachman et al., 1996), presumably reducing synaptic dopamine accumulation in a manner similar to the SLC6A3 10-repeat allele (but possibly in different brain areas, since DAT and COMT expression vary across the brain). As disclosed herein, naltrexone, relative to placebo, most effectively reduced heavy drinking among individuals who carried the rs179997