Underage drinking has become a global public health concern. One of the major causes of underage drinking is stress. The orexin system has been reported to be involved in both alcohol addiction and stress. However, few studies have examined this system, especially among adolescents. Therefore, we constructed protein-protein interaction (PPI) networks to confirm that orexin receptors are connected to stress- and alcohol dependence-related genes, providing a theoretical basis for our experimental approach. Animal experiments employed the conditioned place preference (CPP), the foot-shock stress model and the enzyme-linked immunosorbent assay (ELISA), to elucidate the role of the orexin system in the stress-induced alcohol addiction-related behaviour among adolescent mice. Our results revealed that there were interactions among orexin system, chronic/acute stress and alcohol dependence related proteins. Otherwise, chronic stress can increase the animals' vulnerability to alcohol addition-related behaviour. Additionally, acute foot-shock can promote alcohol-seeking behaviour reinstatement and facilitate orexin concentrations in brain regions that have been shown to be associated with reward and addiction. Moreover, the inhibition of orexin receptors can attenuate the formation and reinstatement of alcohol addiction-like behaviour among adolescent mice. Collectively, our findings indicate that orexin system may be a pivotal target for preventing stress-induced alcohol addiction and reinstatement among the adolescents.

Background:Genome-wide association studies (GWAS) have identified numerous lung cancer susceptibility loci based on single nucleotide polymorphisms (SNPs), yet a substantial proportion of heritability remains unexplained. We therefore evaluated germline copy number variants (CNVs) as an underexplored source of genetic susceptibility and potential contributors to genomic instability in lung cancer. Methods:We conducted a genome-wide analysis of germline CNVs using 19,342 cases and 15,917 controls from the Transdisciplinary Research in Cancer of the Lung (TRICL) consortium, with replication in two independent cohorts. High-confidence CNVs were identified by integrating two CNV callers including PennCNV and modSaRa2. Association analyses were performed using both gene-based and CNV region-based approaches. Polygenic risk scores (PRS) were constructed from top loci, and functional validation was conducted using siRNA-mediated knockdown in lung fibroblast cells. Results:We identified CNVs in four genomic regions (1p36.22, 2q31.2, 6p21.32, and 19q13.32) significantly associated with lung cancer risk. Two loci (1p36.22 and 2q31.2) were consistently supported across both analytical strategies. A CNV-based PRS constructed from key genes (CLCN6, NFE2L2, OPA3, and PSMB8) was significantly associated with lung cancer risk and replicated across independent datasets. Functional assays demonstrated that knockdown of NFE2L2 and OPA3 increased endogenous DNA damage, supporting a role in genomic stability. Conclusions:Germline CNVs contribute to lung cancer susceptibility and may influence carcinogenesis through mechanisms related to genomic instability. Impact:These findings expand the genetic architecture of lung cancer and highlight CNVs as potential biomarkers for improving risk stratification and informing precision prevention strategies.

Heterozygosity at human leukocyte antigen (HLA) loci may improve lung cancer immunosurveillance by increasing recognition of the tumor by the immune system. Previous studies utilizing data from population-level biobanks, such as the United Kingdom Biobank and FinnGen, have identified an association between germline HLA class II (HLA-II) heterozygosity and reduced lung cancer risk in smokers. In the present study, we evaluate the association between HLA heterozygosity and lung cancer in a large case-control study (15,302 cases and 14,580 controls) with imputed HLA allele-type information, comparing differences in HLA heterozygosity between smokers and non-smokers, among lung cancer subtypes, and at 2- and 4-digit HLA allele resolution. We identify a strong protective association of HLA-II heterozygosity in smokers compared to non-smokers, particularly at the HLA-DPB1 and HLA-DPA1 loci, and provide subtype-specific resolution. Finally, analysis of the additive effects of HLA allele heterozygosity in smokers identified significant associations with several 4-digit HLA alleles, including HLA-B∗08:01, HLA-A∗01:01, HLA-C∗07:01, HLA-DQA1∗05:01, HLA-DRB1∗03:01, and HLA-C∗03:04. Our study provides additional evidence, with added histologic subtype information, that germline HLA-II heterozygosity is inversely associated with lung cancer risk.

Background:Ependymoma is a malignancy of the neuroepithelium-derived ependyma that lines the spinal cord and ventricles of the brain, occurring most frequently in young children and older adults. Genetic susceptibility to ependymoma has proven difficult to assess due to disease rarity. Methods:We performed genome-wide association studies (GWAS) of 478 ependymoma patients and 4,841 disease-free controls of European ancestry. Ependymoma patients consisted of 117 children (<18 years old) with whole-genome sequencing (WGS), 142 children with genotyping, and 219 adults (≥18 years old) with genotyping. Genotyped samples were imputed using the 1,000 Genomes Project as the reference panel and underwent quality control filtering. The GWAS was performed separately by age group and technology (genotyped or WGS). GWAS variants were considered significant at P < 5 × 10-8. Results:Among pediatric subjects with WGS data, we identified a significant intronic variant in EDIL3 (rs149378, P = 1.9 × 10-8) and a nearly significant intronic variant in LHX4 (rs79008224, P = 7.2 × 10-8). In pediatric subjects with genotyped data, two significant intronic variants were detected: FAM149A (rs6852180, P = 1.8 × 10-8) and CYS1 (rs61052588, P = 3.0 × 10-8). Additionally, an intergenic variant near C1orf94 (rs1404350, P = 1.2 × 10-14) was highly significant. In genotyped adult subjects, a single variant was observed in KCNQ3 (rs79089725, P = 2.0 × 10-8). Conclusion:Our analysis represents one of the most extensive ependymoma-specific GWAS conducted to date. Several significant intronic variants were harbored in genes associated with cancer and neurological disease. Future studies are needed to investigate the role of these age-specific alterations in ependymoma pathogenesis.

Genotype imputation is a cornerstone of modern genetic studies, enhancing the resolution of genome-wide association studies (GWAS), fine mapping, and polygenic risk score estimation by inferring untyped variants using reference panels. The output of imputation is a set of probabilistic genotypes, each associated with an inherent degree of uncertainty. However, conventional downstream analyses often overlook this uncertainty, relying instead on allelic dosages-expected allele counts computed from probabilistic genotypes-as proxies. This practice can be misleading, as distinct genotype probability distributions may produce identical dosages despite vastly different confidence levels, potentially introducing bias and inflating false discoveries. To address this limitation, we introduce an entropy-weighted association method that explicitly quantifies imputation uncertainty using Shannon entropy. These entropy values are integrated as observation-level weights within the association model, allowing the method to dynamically account for the reliability of each imputed genotype. Through simulation studies, we demonstrate that this approach substantially reduces false positives, especially when genotypic uncertainty is pronounced. Our findings highlight the importance of modeling imputation uncertainty and offer a framework that improves the robustness of GWAS and other genotype imputation-dependent analyses.

OBJECTIVE:Idiopathic inflammatory myopathies (IIMs, myositis) are rare systemic autoimmune disorders that lead to muscle inflammation, weakness, and extramuscular manifestations, with a strong genetic component influencing disease development and progression. Previous genome-wide association studies identified loci associated with IIMs. In this study, we imputed data from two prior genome-wide myositis studies and analyzed the largest myositis data set to date to identify novel risk loci and susceptibility genes associated with IIMs and its clinical subtypes. METHODS:We performed association analyses on 14,903 individuals (3,206 patients and 11,697 controls) with genotypes and imputed data from the Trans-Omics for Precision Medicine reference panel. Fine-mapping and expression quantitative trait locus colocalization analyses in myositis-relevant tissues indicated potential causal variants. Functional annotation and network analyses using the random walk with restart (RWR) algorithm explored underlying genetic networks and drug repurposing opportunities. RESULTS:Our analyses identified novel risk loci and susceptibility genes, such as FCRLA, NFKB1, IRF4, DCAKD, and ATXN2 in overall IIMs; NEMP2 in polymyositis; ACBC11 in dermatomyositis; and PSD3 in myositis with anti-histidyl-transfer RNA synthetase autoantibodies (anti-Jo-1). We also characterized effects of HLA region variants and the role of C4. Colocalization analyses suggested putative causal variants in DCAKD in skin and muscle, HCP5 in lung, and IRF4 in Epstein-Barr virus (EBV)-transformed lymphocytes, lung, and whole blood. RWR further prioritized additional candidate genes, including APP, CD74, CIITA, NR1H4, and TXNIP, for future investigation. CONCLUSION:Our study uncovers novel genetic regions contributing to IIMs, advancing our understanding of myositis pathogenesis and offering new insights for future research.

INTRODUCTION:Rare, deleterious germline variants are key contributors to inherited lung cancer (LC) risk. The Genetic Epidemiology of LC Consortium (GELCC) has curated valuable high-risk LC families and is uniquely positioned to uncover rare, high-penetrance variants underlying familial LC (FLC). METHODS:We performed whole-genome and exome sequencing on germline DNA from 120 high-risk LC families (177 FLC cases, 309 unaffected relatives). We prioritized rare (allele frequency <1% in the genome aggregation database), potentially deleterious variants present in two or more FLC cases. These variants were then validated in 10,085 sporadic LC (SLC) cases and 612,970 controls. RESULTS:We identified 118 candidate variants, 28 of which were validated in SLC with strong statistical support. We discovered a novel pathogenic axis of three truncating variants in GALNT6, MUC4, and ERBB3 genes, which are critical regulators of mucin-type O-glycosylation. Nine top hits were mapped to the known 6q23-25 linkage region (ROS1, LAMA2, PRKN, SYNE1). Other candidates were clustered in DNA repair (ATM, BRCA2, MLH1), oncogenic signaling (ERBB3, JAK1, PIM1), and extracellular matrix genes (COL6A3, FLG). Carriers of two or more variant alleles had a strong dose-dependent risk. Furthermore, gene-based burden tests revealed strong associations between RARB, MGMT, and EBF1 with FLC susceptibility. CONCLUSION:Our findings underscore the important role of rare, high-penetrance genetic variants in FLC susceptibility, particularly in mucin glycosylation and DNA repair genes. These findings offer promising targets for early detection and personalized therapies.

Despite lung cancer affecting all races and ethnicities, disparities are observed in incidence and mortality rates among different ethnic groups in the United States. Non-Hispanic African Americans had a high incidence rate of lung cancer at 55.8 per 100 000 people, as well as the highest death rate at 37.2 per 100 000 people from 2016 to 2020. While previous genome-wide association studies (GWAS) have identified over 45 susceptibility risk loci that influence lung cancer development, few GWAS have investigated the etiology of lung cancer in African Americans. To address this gap in knowledge, we conducted GWAS of lung cancer focused on studying African Americans, comprising 2267 lung cancer cases and 4264 controls. We identified three loci associated with lung cancer, one with lung adenocarcinoma, and four with lung squamous cell carcinoma in this population at the genomic-wide significance level. Among them, three novel loci were identified near VWF at 12p13.31 for overall lung cancer and GACAT3 at 2p24.3 and LMAN1L at 15q24.1 for lung squamous cell carcinoma. In addition, we confirmed previously reported risk loci with known or new lead variants near CHRNA5 at 15q25.1 and CYP2A6 at 19q13.2 associated with lung cancer and TRIP13 at 5p15.33 and ERC1 at 12p13.33 associated with lung squamous cell carcinoma. Further multi-step functional analyses shed light on biological mechanisms underlying these associations of lung cancer in this population. Our study highlights the importance of ancestry-specific studies for the potential alleviation of lung cancer burden in African Americans.

Supplementary Figures S1-S3, corresponded figure legends, and legends of supplementary table S1-S3

Rare, functionally deleterious genetic variants have been implicated as having substantially larger effect sizes than common variants, potentially accounting for much of the missing heritability in lung cancer (LC). Over 25 years, the Genetic Epidemiology of LC Consortium (GELCC) has curated an invaluable resource of specimens and data from individuals with a strong family history of LC. Whole-genome and exome sequencing data were analyzed in 129 high-risk familial LC (FLC) families, defined as having two first-degree relatives or three or more second-degree relatives affected by LC (177 affected FLC and 309 unaffected relatives). The discovery focused on rare (allele frequency < 1% in gnomAD global population) and deleterious variations (missense, stop-gained, frameshift) enriched in FLC. Promising candidates were further external validated in 2,408 sporadic lung cancer (SLC) cases and 885 population controls from the International Lung Cancer Consortium. We identified 168 variants with moderate-to-large effects on FLC risk, 100 of which were validated for SLC risk (Table 1 Table 1. Top 20 candidates Gene Rare (MAF < 1%), deleterious variants No. of variant carrier counts Odds Ratio, LC vs Control FLC | Relative | SLC | Control FLC+SLC SLC Oncogene ERBB3 / HER3 p.A1131T 3 | 1 | 2 | 0 35 15 JAK p.V651M 2 | 3 | 7 | 0 62 51 NOTCH3 p.R1560P 3 | 1 | 4 | 0 48 29 ROS1 p.N785X 6 | 4 | 10 | 0 110 74 USP6 p.R522 fs del 3 | 6 | 6 | 0 62 45 Tumor suppressor gene ATM p.L2332P 3 | 2 | 8 | 0 76 59 LZTS2 p.K458R 4 | 4 | 18 | 0 152 133 NPIPB13 p.V270 fs del 13 | 14 | 10 | 0 159 74 PARK2 / PRKN p.P153R 3 | 3 | 8 | 0 76 59 RB1 p.A525G 3 | 0 | 6 | 0 62 45 SLX4 p.S1716T 3 | 2 | 9 | 0 83 66 SYNE1 p.M6566I 2 | 0 | 7 | 0 62 52 TGFBRAP1 p.T301R 5 | 0 | 11 | 0 110 82 WNK1 p.K583 fs del 4 | 0 | 23 | 0 187 171 Other cancer-associated gene CFTR p.R74W 4 | 2 | 4 | 0 55 30 FLG p.R3404 fs del 7 | 2 | 4 | 0 69 30 LTN1 p.R349H 6 | 1 | 10 | 0 110 74 MLNR p.Q334 fs del 3 | 2 | 19 | 0 152 134 SLC39A11 p.R38Q 4 | 2 | 13 | 0 117 96 TTYH2 p.R493C 5 | 4 | 14 | 0 131 104 Dose effect of the top candidates No. candidates 0 variant allele 67 | 194 | 1911 | 834 reference reference 1 variant allele 50 | 66 | 363 | 50 3.5 (2.6 - 4.7) 3.2 (2.3 - 4.3) 2 variant alleles 15 | 18 | 62 | 1 32 (4.5 - 230) 27 (3.8 - 195) 3+ variant alleles 45 | 31 | 72 | 0 98 (6 - 1506) 62 (3.9 -1012) lists 20 top hits). Among these, 15 variants mapped to our previously identified lung cancer linkage locus at 6q23-25 (ROS1, PARK2, SYNE1). Others were enriched in oncogenes (ERBB3, JAK1, MET), tumor suppressor genes (ATM, BRCA2, RB1), and genes involved in the extracellular matrix (COL6A3, FLG, MUC5B). Importantly, individuals carrying more than two combinations of these variants exhibited exceptionally strong dose effects, with odds ratios (OR) exceeding 27. Our findings underscore the significant role of rare, high-penetrance variants in FLC etiology and highlight promising targets for early detection and personalized treatment. Future in-depth mechanistic studies are planned to evaluate the pathogenic effects of these specific alleles. Yanhong Liu, Claudio Pikielny, Xiangjun Xiao, Bo Peng, Yafang Li, Jinyoung Byun, Chao Cheng, Dakai Zhu, Spiridon Tsavachidis, Colette Gaba, Elena Kupert, Ellen L. Goode, Erin L. Crawford, Kristen Purrington, Marshall Anderson, Michael Cole, Paul Brennan, Geoffrey Liu, James McKay, John K. Field, Rayjean J. Hung, David C. Christiani, Diptasri Mandal, James C. Willey, Ann Schwartz, Joan Bailey-Wilson, Susan M. Pinney, Christopher I. Amos. High-penetrance rare variants underlying familial lung cancer risk: Insights from the Genetic Epidemiology of Lung Cancer Consortium [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 3815.

BACKGROUND:Some studies have highlighted the crucial role of aversion in addiction treatment. The pathway from the anterior paraventricular thalamus (PVT) to the shell of the nucleus accumbens (NAc) has been reported as an essential regulatory pathway for processing aversion and is also closely associated with substance addiction. However, its impact on alcohol addiction has been relatively underexplored. Therefore, this study focused on the role of the PVT-NAc pathway in the formation and relapse of alcohol addiction-like behaviour, offering a new perspective on the mechanisms of alcohol addiction. RESULTS:The chemogenetic inhibition of the PVT-NAc pathway in male mice resulted in a notable decrease in the establishment of ethanol-induced conditioned place aversion (CPA), and NAc-projecting PVT neurons were recruited due to aversive effects. Conversely, activation of the PVT-NAc pathway considerably impeded the formation of ethanol-induced conditioned place preference (CPP). Furthermore, during the memory reconsolidation phase, activation of this pathway effectively disrupted the animals' preference for alcohol-associated contexts. Whether it was administered urgently 24 h later or after a long-term withdrawal of 10 days, a low dose of alcohol could still not induce the reinstatement of ethanol-induced CPP. CONCLUSIONS:Our results demonstrated PVT-NAc circuit processing aversion, which may be one of the neurobiological mechanisms underlying aversive counterconditioning, and highlighted potential targets for inhibiting the development of alcohol addiction-like behaviour and relapse after long-term withdrawal.

Background & Aims:Cirrhosis is a leading cause of liver-related mortality and a multifactorial disease. To date, the complex genetic architecture of non-viral cirrhosis has not been fully explored. Cross-trait genetic correlations can elucidate the common genetic etiology of genetically correlated phenotypes. This study aims to identify polygenic and pleiotropic traits associated with cirrhosis using the linkage disequilibrium score regression analysis. Methods:We conducted genome-wide association analysis of 9,622,842 imputed SNPs on 3,368 non-viral cirrhosis cases and 258,258 controls, and cross-trait analysis between non-viral cirrhosis and various polygenic and pleiotropic traits using the UK Biobank cohort study. We further performed sensitivity analyses by removing genomic regions of alcohol intake, smoking behaviors, and obesity. We observed multiple traits showing robust genetic correlations (rg) with non-viral cirrhosis. Results:We found strong genetic correlations between the genetic architectures of non-viral cirrhosis and clinical/physiologic factors, including BMI (rg=0.82), alanine aminotransferase (0.71), diabetes (0.70), number of cigarettes currently smoked daily (0.67), amount of alcohol drunk on a typical drinking day (0.60), insomnia (0.59), gout (0.57), depression (0.50), apoliprotein-A (-0.33), HDL cholesterol (-0.49). Exclusion of genomic regions associated with alcohol intake, smoking behaviors, and obesity demonstrated consistent directions and persistent associations in genetic patterns. The inheritability of cirrhosis on the observed scale showed 0.56%. Conclusions:This study provides a comprehensive assessment of the shared genetic architecture of non-viral cirrhosis predisposition and numerous polygenic and pleiotropic traits, most notably BMI, alanine aminotransferase, and diabetes. These findings provide new information on underlying comorbid conditions that can increase the non-viral cirrhosis risk.

Supplementary Table S7 shows the signals from interaction with smoking status for the identified variants in lung cancer.

Supplementary Table S8 displays the sample size from independent Asian studies.

Lung cancer remains the leading cause of cancer mortality, despite declines in smoking rates. Previous lung cancer genome-wide association studies (GWAS) have identified numerous loci, but separating the genetic risks of lung cancer and smoking behavioral susceptibility remains challenging. We performed multi-ancestry GWAS meta-analyses of lung cancer using the Million Veteran Program (MVP) cohort and a previous study of European-ancestry individuals, comprising 42,102 cases and 181,270 controls, followed by replication in an independent cohort of 19,404 cases and 17,378 controls. We further performed conditional meta-analyses on cigarettes per day and identified two novel, replicated loci, including the 19p13.11 pleiotropic cancer locus in LUSC. Overall, we report twelve novel risk loci for overall lung cancer, lung adenocarcinoma (LUAD), and squamous cell lung carcinoma (LUSC), nine of which were externally replicated. Finally, we performed phenome-wide association studies (PheWAS) on polygenic risk scores (PRS) for lung cancer, with and without conditioning on smoking. The unconditioned lung cancer PRS was associated with smoking status in controls, illustrating reduced predictive utility in non-smokers. Additionally, our PRS demonstrates smoking-independent pleiotropy of lung cancer risk across neoplasms and metabolic traits.### Competing Interest StatementS.-G.J. is an employee and shareholder of BridgeBio Pharma. The other authors declare no competing interests.### Funding StatementThis work was supported by award #MVP000 from the United States Department of Veterans Affairs (VA) Million Veteran Program.### Author DeclarationsI confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.YesThe details of the IRB/oversight body that provided approval or exemption for the research described are given below:Central IRB of the VA Office of Research & Development gave ethical approval for this work.I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals.YesI understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).YesI have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable.YesThe full summary level association data from the individual population analyses in MVP will be available upon publication via the dbGaP study accession number phs001672.

Supplementary Table S1 displays the number of ever- and never-smokers from each of the ten studies.

Lung cancer remains the leading cause of cancer mortality, despite declining smoking rates. Previous lung cancer GWAS have identified numerous loci, but separating the genetic risks of lung cancer and smoking behavioral susceptibility remains challenging. Here, we perform multi-ancestry GWAS meta-analyses of lung cancer using the Million Veteran Program cohort (approximately 95% male cases) and a previous study of European-ancestry individuals, jointly comprising 42,102 cases and 181,270 controls, followed by replication in an independent cohort of 19,404 cases and 17,378 controls. We then carry out conditional meta-analyses on cigarettes per day and identify two novel, replicated loci, including the 19p13.11 pleiotropic cancer locus in squamous cell lung carcinoma. Overall, we report twelve novel risk loci for overall lung cancer, lung adenocarcinoma, and squamous cell lung carcinoma, nine of which are externally replicated. Finally, we perform PheWAS on polygenic risk scores for lung cancer, with and without conditioning on smoking. The unconditioned lung cancer polygenic risk score is associated with smoking status in controls, illustrating a reduced predictive utility in non-smokers. Additionally, our polygenic risk score demonstrates smoking-independent pleiotropy of lung cancer risk across neoplasms and metabolic traits.

Supplementary Figure S4 shows the results of eQTL analysis of rs968516 in GTEx.

Supplementary Table S4 shows the imputation quality score of identified variants in different studies.