Anahit Hovhannisyan, Pierpaolo Maisano Delser, Anna Hakobyan, Eppie R Jones, Joshua G Schraiber, Mariya Antonosyan, Ashot Margaryan, Zhe Xue, Sungwon Jeon, Jong Bhak, Peter Hrechdakian, Hovhannes Sahakyan, Lehti Saag, Zaruhi Khachatryan, Levon Yepiskoposyan, Andrea Manica
{"title":"Demographic history and genetic variation of the Armenian population.","authors":"Anahit Hovhannisyan, Pierpaolo Maisano Delser, Anna Hakobyan, Eppie R Jones, Joshua G Schraiber, Mariya Antonosyan, Ashot Margaryan, Zhe Xue, Sungwon Jeon, Jong Bhak, Peter Hrechdakian, Hovhannes Sahakyan, Lehti Saag, Zaruhi Khachatryan, Levon Yepiskoposyan, Andrea Manica","doi":"10.1016/j.ajhg.2024.10.022","DOIUrl":"https://doi.org/10.1016/j.ajhg.2024.10.022","url":null,"abstract":"<p><p>We introduce a sizable (n = 34) whole-genome dataset on Armenians, a population inhabiting the region in West Asia known as the Armenian highlands. Equipped with this genetic data, we conducted a whole-genome study of Armenians and deciphered their fine-scale population structure and complex demographic history. We demonstrated that the Armenian populations from western, central, and eastern parts of the highlands are relatively homogeneous. The Sasun, a population in the south that had been argued to have received a major genetic contribution from Assyrians, was instead shown to have derived its slightly divergent genetic profile from a bottleneck that occurred in the recent past. We also investigated the debated question on the genetic origin of Armenians and failed to find any significant support for historical suggestions by Herodotus of their Balkan-related ancestry. We checked the degree of continuity of modern Armenians with ancient inhabitants of the eastern Armenian highlands and detected a genetic input into the region from a source linked to Neolithic Levantine Farmers at some point after the Early Bronze Age. Additionally, we cataloged an abundance of new mutations unique to the population, including a missense mutation predicted to cause familial Mediterranean fever, an autoinflammatory disorder highly prevalent in Armenians. Thus, we highlight the importance of further genetic and medical studies of this population.</p>","PeriodicalId":7659,"journal":{"name":"American journal of human genetics","volume":" ","pages":""},"PeriodicalIF":8.1,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142724766","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Georgia Katsoula, John E G Lawrence, Ana Luiza Arruda, Mauro Tutino, Petra Balogh, Lorraine Southam, Diane Swift, Sam Behjati, Sarah A Teichmann, J Mark Wilkinson, Eleftheria Zeggini
{"title":"Primary cartilage transcriptional signatures reflect cell-type-specific molecular pathways underpinning osteoarthritis.","authors":"Georgia Katsoula, John E G Lawrence, Ana Luiza Arruda, Mauro Tutino, Petra Balogh, Lorraine Southam, Diane Swift, Sam Behjati, Sarah A Teichmann, J Mark Wilkinson, Eleftheria Zeggini","doi":"10.1016/j.ajhg.2024.10.019","DOIUrl":"https://doi.org/10.1016/j.ajhg.2024.10.019","url":null,"abstract":"<p><p>Translational efforts in osteoarthritis are hampered by a gap in our understanding of disease processes at the molecular level. Here, we present evidence of pronounced transcriptional changes in high- and low-disease-grade cartilage tissue, pointing to embryonic processes involved in disease progression. We identify shared transcriptional programs between osteoarthritis cartilage and cell populations in the human embryonic and fetal limb, pointing to increases in pre-hypertrophic chondrocytes' transcriptional programs in low-grade cartilage and increases in osteoblastic signatures in high-grade disease tissue. We find that osteoarthritis genetic risk signals are enriched in six gene co-expression modules and show that these transcriptional signatures reflect cell-type-specific expression along the endochondral ossification developmental trajectory. Using this network approach in combination with causal inference analysis, we present evidence of a causal effect on osteoarthritis risk for variants associated with the expression of ten genes that have not been previously reported as effector genes in genome-wide association studies in osteoarthritis. Our findings point to key molecular pathways as drivers of cartilage degeneration and identify high-value drug targets and repurposing opportunities.</p>","PeriodicalId":7659,"journal":{"name":"American journal of human genetics","volume":" ","pages":""},"PeriodicalIF":8.1,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142695100","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Iftikhar J Kullo, Matthew P Conomos, Sarah C Nelson, Sally N Adebamowo, Ananyo Choudhury, David Conti, Stephanie M Fullerton, Stephanie M Gogarten, Ben Heavner, Whitney E Hornsby, Eimear E Kenny, Alyna Khan, Amit V Khera, Yun Li, Iman Martin, Josep M Mercader, Maggie Ng, Laura M Raffield, Alex Reiner, Robb Rowley, Daniel Schaid, Adrienne Stilp, Ken Wiley, Riley Wilson, John S Witte, Pradeep Natarajan
{"title":"The PRIMED Consortium: Reducing disparities in polygenic risk assessment.","authors":"Iftikhar J Kullo, Matthew P Conomos, Sarah C Nelson, Sally N Adebamowo, Ananyo Choudhury, David Conti, Stephanie M Fullerton, Stephanie M Gogarten, Ben Heavner, Whitney E Hornsby, Eimear E Kenny, Alyna Khan, Amit V Khera, Yun Li, Iman Martin, Josep M Mercader, Maggie Ng, Laura M Raffield, Alex Reiner, Robb Rowley, Daniel Schaid, Adrienne Stilp, Ken Wiley, Riley Wilson, John S Witte, Pradeep Natarajan","doi":"10.1016/j.ajhg.2024.10.010","DOIUrl":"https://doi.org/10.1016/j.ajhg.2024.10.010","url":null,"abstract":"<p><p>By improving disease risk prediction, polygenic risk scores (PRSs) could have a significant impact on health promotion and disease prevention. Due to the historical oversampling of populations with European ancestry for genome-wide association studies, PRSs perform less well in other, understudied populations, leading to concerns that clinical use in their current forms could widen health care disparities. The PRIMED Consortium was established to develop methods to improve the performance of PRSs in global populations and individuals of diverse genetic ancestry. To this end, PRIMED is aggregating and harmonizing multiple phenotype and genotype datasets on AnVIL, an interoperable secure cloud-based platform, to perform individual- and summary-level analyses using population and statistical genetics approaches. Study sites, the coordinating center, and representatives from the NIH work alongside other NHGRI and global consortia to achieve these goals. PRIMED is also evaluating ethical and social implications of PRS implementation and investigating the joint modeling of social determinants of health and PRS in computing disease risk. The phenotypes of interest are primarily cardiometabolic diseases and cancer, the leading causes of death and disability worldwide. Early deliverables of the consortium include methods for data sharing on AnVIL, development of a common data model to harmonize phenotype and genotype data from cohort studies as well as electronic health records, adaptation of recent guidelines for population descriptors to global cohorts, and sharing of PRS methods/tools. As a multisite collaboration, PRIMED aims to foster equity in the development and use of polygenic risk assessment.</p>","PeriodicalId":7659,"journal":{"name":"American journal of human genetics","volume":" ","pages":""},"PeriodicalIF":8.1,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142674908","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Euan McDonnell, Sarah E Orr, Matthew J Barter, Danielle Rux, Abby Brumwell, Nicola Wrobel, Lee Murphy, Lynne M Overman, Antony K Sorial, David A Young, Jamie Soul, Sarah J Rice
{"title":"The methylomic landscape of human articular cartilage development contains epigenetic signatures of osteoarthritis risk.","authors":"Euan McDonnell, Sarah E Orr, Matthew J Barter, Danielle Rux, Abby Brumwell, Nicola Wrobel, Lee Murphy, Lynne M Overman, Antony K Sorial, David A Young, Jamie Soul, Sarah J Rice","doi":"10.1016/j.ajhg.2024.10.017","DOIUrl":"https://doi.org/10.1016/j.ajhg.2024.10.017","url":null,"abstract":"<p><p>Increasing evidence is emerging to link age-associated complex musculoskeletal diseases, including osteoarthritis (OA), to developmental factors. Multiple studies have shown a functional role for DNA methylation in the genetic mechanisms of OA risk using articular cartilage samples taken from aged individuals, yet knowledge of temporal changes to the methylome during human cartilage development is limited. We quantified DNA methylation at ∼700,000 individual CpGs across the epigenome of developing human chondrocytes in 72 samples ranging from 7 to 21 post-conception weeks. We identified significant changes in 3% of all CpGs and >8,200 developmental differentially methylated regions. We further identified 24 loci at which OA genetic variants colocalize with methylation quantitative trait loci. Through integrating developmental and mature human chondrocyte datasets, we find evidence for functional effects exerted solely in development or throughout the life course. This will have profound impacts on future approaches to translating genetic pathways for therapeutic intervention.</p>","PeriodicalId":7659,"journal":{"name":"American journal of human genetics","volume":" ","pages":""},"PeriodicalIF":8.1,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142695101","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mafalda Dias, Rose Orenbuch, Debora S Marks, Jonathan Frazer
{"title":"Toward trustable use of machine learning models of variant effects in the clinic.","authors":"Mafalda Dias, Rose Orenbuch, Debora S Marks, Jonathan Frazer","doi":"10.1016/j.ajhg.2024.10.011","DOIUrl":"https://doi.org/10.1016/j.ajhg.2024.10.011","url":null,"abstract":"<p><p>There has been considerable progress in building models to predict the effect of missense substitutions in protein-coding genes, fueled in large part by progress in applying deep learning methods to sequence data. These models have the potential to enable clinical variant annotation on a large scale and hence increase the impact of patient sequencing in guiding diagnosis and treatment. To realize this potential, it is essential to provide reliable assessments of model performance, scope of applicability, and robustness. As a response to this need, the ClinGen Sequence Variant Interpretation Working Group, Pejaver et al., recently proposed a strategy for validation and calibration of in-silico predictions in the context of guidelines for variant annotation. While this work marks an important step forward, the strategy presented still has important limitations. We propose core principles and recommendations to overcome these limitations that can enable both more reliable and more impactful use of variant effect prediction models in the future.</p>","PeriodicalId":7659,"journal":{"name":"American journal of human genetics","volume":" ","pages":""},"PeriodicalIF":8.1,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142674909","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Comparative analysis of predicted DNA secondary structures infers complex human centromere topology.","authors":"Sai Swaroop Chittoor, Simona Giunta","doi":"10.1016/j.ajhg.2024.10.016","DOIUrl":"https://doi.org/10.1016/j.ajhg.2024.10.016","url":null,"abstract":"<p><p>Secondary structures are non-canonical arrangements of nucleic acids due to intra-strand interactions, including base pairing, stacking, or other higher-order features that deviate from the standard double-helical conformation. While these structures are extensively studied in RNA, they can also form when DNA becomes single stranded, creating topological roadblocks that can impact essential DNA-based processes such as replication, transcription, and repair, ultimately affecting genome stability. The availability of a complete linear sequence of human genomes, including repetitive loci, enables the prediction of DNA secondary structures comparing across various regions. Here, we evaluate the intrinsic properties of linear single-stranded DNA sequences derived from sampling specialized human loci such as centromeres, pericentromeres, ribosomal DNA (rDNA), and coding regions from the CHM13 genome. Our comparative analysis of predicted secondary structures across human chromosomes revealed the heightened presence, complexity, and instability of secondary structures within the centromere, which gradually decreased toward the pericentromere onto chromosomes' arms, on average lowest in coding regions. Notably, centromeric repeats exhibited the highest level of topological complexity within both the active and divergent domains, even when compared to other repetitive tandem satellites, such as rDNA in acrocentric chromosomes. Our findings provide evidence of the intrinsic self-hybridizing properties of centromere repeats, which are capable of generating complex topological structures that may functionally correlate with chromosome missegregation, especially when centromeric chromatin is disrupted. Processes such as long non-coding RNA transcription, recombination, and other mechanisms that dechromatinize and unwind stretches of linear DNA in these regions create in vivo opportunities for the DNA acrobatics hereby predicted.</p>","PeriodicalId":7659,"journal":{"name":"American journal of human genetics","volume":" ","pages":""},"PeriodicalIF":8.1,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142674906","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Allele frequency impacts the cross-ancestry portability of gene expression prediction in lymphoblastoid cell lines.","authors":"Marie Saitou, Andy Dahl, Qingbo Wang, Xuanyao Liu","doi":"10.1016/j.ajhg.2024.10.009","DOIUrl":"https://doi.org/10.1016/j.ajhg.2024.10.009","url":null,"abstract":"<p><p>Population-level genetic studies are overwhelmingly biased toward European ancestries. Transferring genetic predictions from European ancestries to other ancestries results in a substantial loss of accuracy. Yet, it remains unclear how much various genetic factors, such as causal effect differences, linkage disequilibrium (LD) differences, or allele frequency differences, contribute to the loss of prediction accuracy across ancestries. In this study, we used gene expression levels in lymphoblastoid cell lines to understand how much each genetic factor contributes to lowered portability of gene expression prediction from European to African ancestries. We found that cis-genetic effects on gene expression are highly similar between European and African individuals. However, we found that allele frequency differences of causal variants have a striking impact on prediction portability. For example, portability is reduced by more than 32% when the causal cis-variant is common (minor allele frequency, MAF >5%) in European samples (training population) but is rarer (MAF <5%) in African samples (prediction population). While large allele frequency differences can decrease portability through increasing LD differences, we also determined that causal allele frequency can significantly impact portability when the impact from LD is substantially controlled. This observation suggests that improving statistical fine-mapping alone does not overcome the loss of portability resulting from differences in causal allele frequency. We conclude that causal cis-eQTL effects are highly similar in European and African individuals, and allele frequency differences have a large impact on the accuracy of gene expression prediction.</p>","PeriodicalId":7659,"journal":{"name":"American journal of human genetics","volume":" ","pages":""},"PeriodicalIF":8.1,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142643243","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Sanni Ruotsalainen, Juha Karjalainen, Mitja Kurki, Elisa Lahtela, Matti Pirinen, Juha Riikonen, Jarmo Ritari, Silja Tammi, Jukka Partanen, Hannele Laivuori, Aarno Palotie, Henrike Heyne, Mark Daly, Elisabeth Widen
{"title":"Inherited infertility: Mapping loci associated with impaired female reproduction.","authors":"Sanni Ruotsalainen, Juha Karjalainen, Mitja Kurki, Elisa Lahtela, Matti Pirinen, Juha Riikonen, Jarmo Ritari, Silja Tammi, Jukka Partanen, Hannele Laivuori, Aarno Palotie, Henrike Heyne, Mark Daly, Elisabeth Widen","doi":"10.1016/j.ajhg.2024.10.018","DOIUrl":"https://doi.org/10.1016/j.ajhg.2024.10.018","url":null,"abstract":"<p><p>Female infertility is a common and complex health problem affecting millions of women worldwide. While multiple factors can contribute to this condition, the underlying cause remains elusive in up to 15%-30% of affected individuals. In our large genome-wide association study (GWAS) of 22,849 women with infertility and 198,989 control individuals from the Finnish population cohort FinnGen, we unveil a landscape of genetic factors associated with the disorder. Our recessive analysis identified a low-frequency stop-gained mutation in TATA-box binding protein-like 2 (TBPL2; c.895A>T [p.Arg299Ter]; minor-allele frequency [MAF] = 1.2%) with an impact comparable to highly penetrant monogenic mutations (odds ratio [OR] = 650, p = 4.1 × 10<sup>-25</sup>). While previous studies have linked the orthologous gene to anovulation and sterility in knockout mice, the severe consequence of the p.Arg299Ter variant was evidenced by individuals carrying two copies of that variant having significantly fewer offspring (average of 0.16) compared to women belonging to the other genotype groups (average of 1.75 offspring, p = 1.4 × 10<sup>-15</sup>). Notably, all homozygous women who had given birth had received infertility therapy. Moreover, our age-stratified analyses identified three additional genome-wide significant loci. Two loci were associated with early-onset infertility (diagnosed before age 30), located near CHEK2 and within the major histocompatibility complex (MHC) region. The third locus, associated with late-onset infertility, had its lead SNP located in an intron of a long non-coding RNA (lncRNA) gene. Taken together, our data highlight the significance of rare recessive alleles in shaping female infertility risk. The results further provide evidence supporting specific age-dependent mechanisms underlying this complex disorder.</p>","PeriodicalId":7659,"journal":{"name":"American journal of human genetics","volume":" ","pages":""},"PeriodicalIF":8.1,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142680622","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Michelle A Ramos, Katherine E Bonini, Laura Scarimbolo, Nicole R Kelly, Beverly Insel, Sabrina A Suckiel, Kaitlyn Brown, Miranda Di Biase, Katie M Gallagher, Jessenia Lopez, Karla López Aguiñiga, Priya N Marathe, Estefany Maria, Jacqueline A Odgis, Jessica E Rodriguez, Michelle A Rodriguez, Nairovylex Ruiz, Monisha Sebastin, Nicole M Yelton, Charlotte Cunningham-Rundles, Melvin Gertner, Irma Laguerre, Thomas V McDonald, Patricia E McGoldrick, Mimsie Robinson, Arye Rubinstein, Lisa H Shulman, Trinisha Williams, Steven M Wolf, Elissa G Yozawitz, Randi E Zinberg, Noura S Abul-Husn, Laurie J Bauman, George A Diaz, Bart S Ferket, John M Greally, Vaidehi Jobanputra, Bruce D Gelb, Eimear E Kenny, Melissa P Wasserstein, Carol R Horowitz
{"title":"Employing effective recruitment and retention strategies to engage a diverse pediatric population in genomics research.","authors":"Michelle A Ramos, Katherine E Bonini, Laura Scarimbolo, Nicole R Kelly, Beverly Insel, Sabrina A Suckiel, Kaitlyn Brown, Miranda Di Biase, Katie M Gallagher, Jessenia Lopez, Karla López Aguiñiga, Priya N Marathe, Estefany Maria, Jacqueline A Odgis, Jessica E Rodriguez, Michelle A Rodriguez, Nairovylex Ruiz, Monisha Sebastin, Nicole M Yelton, Charlotte Cunningham-Rundles, Melvin Gertner, Irma Laguerre, Thomas V McDonald, Patricia E McGoldrick, Mimsie Robinson, Arye Rubinstein, Lisa H Shulman, Trinisha Williams, Steven M Wolf, Elissa G Yozawitz, Randi E Zinberg, Noura S Abul-Husn, Laurie J Bauman, George A Diaz, Bart S Ferket, John M Greally, Vaidehi Jobanputra, Bruce D Gelb, Eimear E Kenny, Melissa P Wasserstein, Carol R Horowitz","doi":"10.1016/j.ajhg.2024.10.015","DOIUrl":"https://doi.org/10.1016/j.ajhg.2024.10.015","url":null,"abstract":"<p><p>Underrepresentation in clinical genomics research limits the generalizability of findings and the benefits of scientific discoveries. We describe the impact of patient-centered, data-driven recruitment and retention strategies in a pediatric genome sequencing study. We collaborated with a stakeholder board, conducted formative research with adults whose children had undergone genomic testing, and piloted and revised study approaches and materials. Our approaches included racially, ethnically, and linguistically congruent study staff, relational interactions, study visit flexibility, and data-informed quality improvement. Of 1,656 eligible children, only 6.5% declined. Their parents/legal guardians were 76.9% non-White, 65.6% had public health insurance for the child, 49.9% lived below the federal poverty level, and 52.8% resided in a medically underserved area. Among those enrolled, 87.3% completed all study procedures. There were no sociodemographic differences between those who enrolled and declined or between those retained and lost to follow-up. We outline stakeholder-engaged approaches that may have led to the successful enrollment and retention of diverse families. These approaches may inform future research initiatives aiming to engage and retain underrepresented populations in genomics medicine research.</p>","PeriodicalId":7659,"journal":{"name":"American journal of human genetics","volume":" ","pages":""},"PeriodicalIF":8.1,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142680668","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Proteome-wide Mendelian randomization and functional studies uncover therapeutic targets for polycystic ovarian syndrome.","authors":"Feida Ni, Feixia Wang, Jing Sun, Mixue Tu, Jianpeng Chen, Xiling Shen, Xiaohang Ye, Ruixue Chen, Yifeng Liu, Xiao Sun, Jianhua Chen, Xue Li, Dan Zhang","doi":"10.1016/j.ajhg.2024.10.008","DOIUrl":"10.1016/j.ajhg.2024.10.008","url":null,"abstract":"<p><p>Polycystic ovarian syndrome (PCOS) is an endocrine syndrome that affects a large portion of women worldwide. This proteogenomic and functional study aimed to uncover candidate therapeutic targets for PCOS. We comprehensively investigated the causal association between circulating proteins and PCOS using two-sample Mendelian randomization analysis. Cis-protein quantitative trait loci were derived from six genome-wide association studies (GWASs) on plasma proteome. Genetic associations with PCOS were obtained from a large-scale GWAS meta-analysis, FinnGen cohort, and UK Biobank. Colocalization analyses were performed to prioritize the causal role of candidate proteins. Protein-protein interaction (PPI) and druggability evaluation assessed the druggability of candidate proteins. We evaluated the enrichment of tier 1 and 2 candidate proteins in individuals with PCOS and a mouse model and explored the potential application of the identified drug target. Genetically predicted levels of 65 proteins exhibited associations with PCOS risk, with 30 proteins showing elevated levels and 35 proteins showing decreased levels linked to higher susceptibility. PPI analyses revealed that FSHB, POSTN, CCN2, and CXCL11 interacted with targets of current PCOS medications. Eighty medications targeting 20 proteins showed their potential for repurposing as therapeutic targets for PCOS. EGLN1 levels were elevated in granulosa cells and the plasma of individuals with PCOS and in the plasma and ovaries of dehydroepiandrosterone (DHEA)-induced PCOS mouse model. As an EGLN1 inhibitor, administration of roxadustat in the PCOS mouse model elucidated the EGLN1-HIF1α-ferroptosis axis in inducing PCOS and validated its therapeutic effect in PCOS. Our study identifies candidate proteins causally associated with PCOS risk and suggests that targeting EGLN1 provides a promising treatment strategy.</p>","PeriodicalId":7659,"journal":{"name":"American journal of human genetics","volume":" ","pages":""},"PeriodicalIF":8.1,"publicationDate":"2024-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142612266","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}