| Literature DB >> 34037083 |
José J Martínez-Magaña1,2, Alma D Genis-Mendoza2,3, Vanessa González-Covarrubias4, Isela E Juárez-Rojop1, Carlos A Tovilla-Zárate5, Xavier Soberón4, Nuria Lanzagorta6, Humberto Nicolini1,6.
Abstract
OBJECTIVE: Individuals with schizophrenia and substance use disorders have a poor prognosis and increased psychiatric symptoms. The present study aimed to explore the association of 106 genes in individuals with schizophrenia and comorbid substance use through a next-generation sequencing (NGS) analysis and different in silico algorithms.Entities:
Mesh:
Substances:
Year: 2022 PMID: 34037083 PMCID: PMC9041971 DOI: 10.1590/1516-4446-2020-1546
Source DB: PubMed Journal: Braz J Psychiatry ISSN: 1516-4446
Clinical characteristics of the sample
| Sample (n = 105) | |
|---|---|
| Sex | |
| Male | 62 (59.05) |
| Female | 43 (40.95) |
| Scale for the Assessment of Negative Symptoms | 36.85 (34.38) |
| Scale for the Assessment of Positive Symptoms | 16.05 (26.03) |
| Age (years), mean (SD) | 33.28 (9.09) |
| Schizophrenia onset (years), mean (SD) | 9.76 (13.75) |
| Substance comorbidity | 49 (46.67) |
| Alcohol abuse/dependence | 42 (40.00) |
| Tobacco abuse/dependence | 33 (31.43) |
| Cannabis abuse/dependence | 2 (1.90) |
| Cocaine abuse/dependence | 5 (4.76) |
| Stimulant abuse/dependence | 4 (3.81) |
Data presented as n (%), unless otherwise specified.
SD = standard deviation.
Missense variants associated with comorbid substance use
| Position (hg19) | Gene | Type | SNP | Ref/alt | Freq. com | Freq. no com | p-value | All freq | GnomAD | Effect | PolyPhen | SIFT |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| chr1:46870761 |
| SNV | rs324420 | C/A | 0.3936 | 0.2404 | 0.0222 | 0.3131 | 0.2405 | p.Pro129Thr (ENST00000243167.8) | Probable Damaging | Tolerated |
| chr1:171174531 |
| SNV | rs2020863 | A/G | 0.0889 | 0.2444 | 0.0085 | 0.1667 | 0.1313 | p.Glu314Gly (ENST00000441535.1) | Probable Damaging | Deleterious |
| chr22:19950263 |
| SNV | rs6267 | G/T | 0.0204 | 0.09804 | 0.0335 | 0.0600 | 0.0136 | p.Ala72Ser (ENST00000361682.6) | Possibly Damaging | Deleterious |
All freq = frequency in the overall sample; Freq. com = frequency on individuals with substance use comorbidity; Freq. no com = frequency on individuals without substance use comorbidity; GnomAD = Genome Aggregation Database; PolyPhen = Polymorphism Phenotyping tool; Ref/alt = reference and alternative alleles; SIFT = Sorting Intolerant from Tolerant algorithm; SNP = single nucleotide polymorphisms; SNV = single-nucleotide variants.
Regulatory variants associated with comorbid substance use
| Position (hg19) | Gene | Type | SNP | Ref/alt | Freq com | Freq no com | p-value | All freq | GnomAD | Transcript | Effect |
|---|---|---|---|---|---|---|---|---|---|---|---|
| chr1:171178257-171178258 |
| InDel | rs2234889 | C/CT | 0.0682 | 0.1979 | 0.0165 | 0.1359 | 0.0979 | 3-UTR (ENST00000441535.1) | hsa-miR-182-5p/hsa-miR-3613-3p/hsa-miR-4715-5p |
| chr1:171178490 |
| SNV | rs28369914 | C/T | 0.0851 | 0.2400 | 0.0038 | 0.1649 | 0.0986 | 3-UTR (ENST00000441535.1) | hsa-miR-3545-3p/hsa-miR-3688-3p |
| chr1:171179351 |
| SNV | rs16864194 | A/T | 0.0778 | 0.2447 | 0.0025 | 0.1630 | 0.0991 | 3-UTR (ENST00000441535.1) | hsa-miR-3942-3p |
| chr5:1420306 |
| SNV | rs28382248 | G/A | 0.1809 | 0.3039 | 0.0481 | 0.2449 | 0.2112 | Intron (ENST00000270349.9) | CTCF BS (ENSR00000402282) |
| chr5:1420346 |
| SNV | rs28382247 | G/T | 0.1809 | 0.3039 | 0.0481 | 0.2449 | 0.2152 | Intron (ENST00000270349.9) | CTCF BS (ENSR00000402282) |
| chr5:1420476 |
| SNV | rs28382245 | C/T | 0.1915 | 0.0769 | 0.0206 | 0.1313 | 0.2732 | Intron (ENST00000270349.9) | CTCF BS (ENSR00000402282) |
| chr6:18128659 |
| SNV | rs7886 | T/A | 0.2447 | 0.1154 | 0.0244 | 0.1768 | 0.2114 | 3'-UTR (ENST00000309983.4) | hsa-miR-4789-3p/hsa-miR-642a-3p/hsa-miR-642b-3p |
| chr6:18128999 |
| SNV | rs1142378 | T/G | 0.2553 | 0.1100 | 0.0093 | 0.1804 | 0.2091 | 3'-UTR (ENST00000309983.4) | - |
| chr7:150645682 |
| SNV | rs2968860 | G/A | 0.2889 | 0.4796 | 0.0107 | 0.3883 | 0.3765 | Intron (ENST00000262186.5) | TF and CTCF BS (ENSR00000219754, ENSR00000414356) |
| chr7:150647569 |
| SNV | rs4725983 | T/C | 0.3205 | 0.5333 | 0.0078 | 0.4345 | 0.3179 | Intron (ENST00000262186.5) | Open Chromatin (ENSR00000219755) |
| chr7:150649603 |
| SNV | rs740852 | G/A | 0.4333 | 0.2900 | 0.04891 | 0.3579 | 0.2988 | Synonymous (ENST00000262186.5) | CTCF BS (ENSR00000414357) |
| chr7:150655624 |
| SNV | rs758891 | T/C | 0.4318 | 0.2692 | 0.0223 | 0.3438 | 0.3899 | Intron (ENST00000262186.5) | TF BS (ENSR00000219757) |
| chr7:150655643 |
| SNV | rs758890 | G/A | 0.4872 | 0.3182 | 0.0385 | 0.3976 | 0.4172 | Intron (ENST00000262186.5) | TF BS (ENSR00000219757) |
| chr7:150657095 |
| SNV | rs56282717 | G/A | 0.1477 | 0.0556 | 0.0487 | 0.1011 | 0.1534 | Intron (ENST00000262186.5) | CTCF BS (ENSR00000414361) |
| chr7:150657201 |
| SNV | rs12668582 | A/C | 0.4886 | 0.2708 | 0.0036 | 0.3750 | 0.4222 | Intron (ENST00000262186.5) | CTCF BS (ENSR00000414361) |
| chr8:32406148 |
| SNV | rs7834206 | C/A | 0.5319 | 0.3700 | 0.0302 | 0.4485 | 0.3948 | 5’-UTR (ENST00000356819.4) | Promoter (ENSR00000330589) |
| chr8:32406382 |
| SNV | rs73234136 | T/C | 0.5426 | 0.3600 | 0.0139 | 0.4485 | 0.4295 | 5’-UTR (ENST00000356819.4) | Promoter (ENSR00000330589) |
| chr15:92715167 |
| SNV | rs2270060 | C/T | 0.5532 | 0.3679 | 0.0105 | 0.4550 | 0.3928 | 3’-UTR (ENST00000424469.2) | hsa-miR-1321, hsa-miR-4270, hsa-miR-765 |
| chr15:92715131 |
| SNV | rs2270061 | A/T | 0.5761 | 0.4000 | 0.0205 | 0.4844 | 0.4035 | 3’-UTR (ENST00000424469.2) | hsa-miR-1293, hsa-miR-1587, hsa-miR-4417, hsa-miR-4446-3p, hsa-miR-4483, hsa-miR-4721,hsa-miR-541-3p, hsa-miR-654-5p |
| chrX:43626085 |
| rs3027438 | G/A | 0.0106 | 0.1078 | 0.0054 | 0.0612 | 0.0207 | 3’-UTR (ENST00000378069.4) | hsa-miR-181c-3p | |
| chrX:43626136 |
| rs3027439 | G/A | 0.0106 | 0.1346 | 0.0008 | 0.0758 | 0.0488 | 3’-UTR (ENST00000378069.4) | hsa-miR-3173-3p, hsa-miR-3689d, hsa-miR-4668-5p, hsa-miR-583 | |
| chrX:43626329 |
| rs2072745 | T/A | 0.0104 | 0.1300 | 0.0013 | 0.0714 | 0.0509 | 3’-UTR (ENST00000378069.4) | hsa-miR-4511 |
All freq = frequency in the overall sample; Freq com = frequency in individuals with substance use comorbidity; Freq no com = frequency in individuals without comorbid substance use; GnomAD = Genome Aggregation Database; Ref/alt = reference and alternative alleles; SNP = single nucleotide polymorphisms; SNV = single-nucleotide variants.