Frontiers in GeneticsPub Date : 2025-03-05eCollection Date: 2025-01-01DOI: 10.3389/fgene.2025.1533424
Felipe André Oliveira Freitas, Luiz F Brito, Bárbara Silva-Vignato, Fernanda Nery Ciconello, Vivian Vezzoni de Almeida, Aline Silva Mello Cesar
{"title":"Expression quantitative trait loci associated with performance traits, blood biochemical parameters, and cytokine profile in pigs.","authors":"Felipe André Oliveira Freitas, Luiz F Brito, Bárbara Silva-Vignato, Fernanda Nery Ciconello, Vivian Vezzoni de Almeida, Aline Silva Mello Cesar","doi":"10.3389/fgene.2025.1533424","DOIUrl":"10.3389/fgene.2025.1533424","url":null,"abstract":"<p><p>Identifying expression Quantitative Trait Loci (eQTL) and functional candidate variants associated with blood biochemical parameters can contribute to the understanding of genetic mechanisms underlying phenotypic variation in complex traits in pigs. We identified eQTLs through gene expression levels in muscle and liver tissues of Large White pigs. The identified eQTL were then tested for association with biochemical parameters, cytokine profiles, and performance traits of pigs. A total of 41,759 SNPs and 15,093 and 15,516 expression gene levels from muscle and liver tissues, respectively, enabled the identification of 1,199 eQTL. The eQTL identified related the SNP rs345667860 as significantly associated with interleukin-6 and interleukin-18 in liver tissue, while the rs695637860 SNP was associated with aspartate aminotransferase and interleukin-6, and rs337362164 was associated with high-density lipoprotein of the blood serum. In conclusion, the identification of three eQTL significantly associated with aspartate aminotransferase and cytokine levels in both serum and liver tissues suggests a potential role for these variants in modulating immune function and overall health in production pigs. Further research is needed to validate these findings and explore their potential for improving pig health and productivity.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1533424"},"PeriodicalIF":2.8,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11919875/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143663315","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Frontiers in GeneticsPub Date : 2025-03-05eCollection Date: 2025-01-01DOI: 10.3389/fgene.2025.1481863
Manuela Reveiz, Sarah Bouhouita-Guermech, Kristina M Blackmore, Jocelyne Chiquette, Éric Demers, Michel Dorval, Laurence Lambert-Côté, Hermann Nabi, Nora Pashayan, Penny Soucy, Annie Turgeon, Meghan J Walker, Bartha M Knoppers, Anna M Chiarelli, Jacques Simard, Yann Joly
{"title":"Genetic discrimination in insurance and employment based on personalized risk stratification for breast cancer screening.","authors":"Manuela Reveiz, Sarah Bouhouita-Guermech, Kristina M Blackmore, Jocelyne Chiquette, Éric Demers, Michel Dorval, Laurence Lambert-Côté, Hermann Nabi, Nora Pashayan, Penny Soucy, Annie Turgeon, Meghan J Walker, Bartha M Knoppers, Anna M Chiarelli, Jacques Simard, Yann Joly","doi":"10.3389/fgene.2025.1481863","DOIUrl":"10.3389/fgene.2025.1481863","url":null,"abstract":"<p><strong>Background: </strong>The Breast and Ovarian Analysis of Disease Incidence and Carrier Estimation Algorithm (BOADICEA) incorporates the effects of common genetic variants, from polygenic risk scores, pathogenic variants in major breast cancer (BC) susceptibility genes, lifestyle/hormonal risk factors, mammographic density, and cancer family history to predict risk levels of developing breast and ovarian cancer. While offering multifactorial risk assessment to the population could be a promising avenue for early detection of BC, obstacles to its implementation including fear of genetic discrimination (GD), could prevent individuals from undergoing screening.</p><p><strong>Methods: </strong>The aim of our study was two-fold: determine the extent of legal protection in Canada available to protect information generated by risk prediction models such as the BOADICEA algorithm through a literature review, and then, assess individuals' knowledge of and concerns about GD in this context by collecting data through surveys.</p><p><strong>Results: </strong>Our legal analysis highlighted that while Canadian employment and privacy laws provide a good level of protection against GD, it remains uncertain whether the Genetic Non-Discrimination Act (GNDA) would provide protection for BC risk levels generated by a risk prediction model. The survey results of 3,055 participants who consented to risk assessment in the PERSPECTIVE I&I project showed divergent perspectives of how the law would protect BC risk level in the context of employment and that a high number of participants did not feel that their risk level was protected from access and use by life insurers. Indeed, 49,1% of participants reckon that the level of breast cancer risk could have an impact on a woman's ability to buy insurance and 58,9% of participants reckon that a woman's insurance might be cancelled if important health information (including level of breast cancer risk) is not given when buying or renewing life or health insurance.</p><p><strong>Conclusion: </strong>The results indicate that much work needs to be done to improve and clarify the extent of protection against GD in Canada and to inform the population of how the legal framework applies to risk levels generated by risk prediction models.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1481863"},"PeriodicalIF":2.8,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11919849/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143663317","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Frontiers in GeneticsPub Date : 2025-03-05eCollection Date: 2025-01-01DOI: 10.3389/fgene.2025.1560276
Bichen Peng, Weiyi Ye, Shuai Liu, Yue Jiang, Ziang Meng, Miao Guo, Lili Zhi, Xiao Chang, Lei Shao
{"title":"Sex differences in asthma: omics evidence and future directions.","authors":"Bichen Peng, Weiyi Ye, Shuai Liu, Yue Jiang, Ziang Meng, Miao Guo, Lili Zhi, Xiao Chang, Lei Shao","doi":"10.3389/fgene.2025.1560276","DOIUrl":"10.3389/fgene.2025.1560276","url":null,"abstract":"<p><p>Asthma is a common and complex heterogeneous disease, with prevalence and severity varying across different age groups and sexes. Over the past few decades, with the development of high-throughput technologies, various \"omics\" analyses have emerged and been applied to asthma research, providing us with significant opportunities to study the genetic mechanisms underlying asthma. However, despite these advancements, the differences and specificities in the genetic mechanisms of asthma between sexes remain to be fully explored. Moreover, clinical guidelines have yet to incorporate or recommend sex-specific asthma management based on high-quality omics evidence. In this article, we review recent omics-level findings on sex differ-ences in asthma and discuss how to better integrate these multidimensional findings to generate further insights and advance the precision and effectiveness of asthma treatment.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1560276"},"PeriodicalIF":2.8,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11920188/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143663327","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Frontiers in GeneticsPub Date : 2025-03-05eCollection Date: 2025-01-01DOI: 10.3389/fgene.2025.1578094
Jingxin Mao
{"title":"Editorial: The role of genes and network pharmacology in new drug discovery.","authors":"Jingxin Mao","doi":"10.3389/fgene.2025.1578094","DOIUrl":"10.3389/fgene.2025.1578094","url":null,"abstract":"","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1578094"},"PeriodicalIF":2.8,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11920149/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143663223","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Frontiers in GeneticsPub Date : 2025-03-04eCollection Date: 2025-01-01DOI: 10.3389/fgene.2025.1294105
Rongfang Xie, Shiyu Chen, Xiaojian Li, Zhihui Lan
{"title":"Assessment of the causal association between obstructive sleep apnea and telomere length: a bidirectional mendelian randomization study.","authors":"Rongfang Xie, Shiyu Chen, Xiaojian Li, Zhihui Lan","doi":"10.3389/fgene.2025.1294105","DOIUrl":"10.3389/fgene.2025.1294105","url":null,"abstract":"<p><strong>Background: </strong>A plethora of observational studies has established a significant correlation between Obstructive Sleep Apnea (OSA) and Telomere Length (TL). Nevertheless, a universal consensus on precise causal association and its directionality has not yet been achieved. To shed light on this, we employed Mendelian Randomization (MR) to investigate the bidirectional causal association between OSA and TL.</p><p><strong>Method: </strong>Utilizing publicly accessible Genome-Wide Association Studies (GWAS) datasets, we procured genetic data pertinent to MR analysis. The study incorporated samples from both the OSA (n = 217,955) and TL (n = 472,174) cohorts. In the forward MR analysis, OSA served as the exposure variable and TL as the outcome. Conversely, the reverse MR analysis treated TL as the exposure and OSA as the outcome. We employed the Inverse variance weighted (IVW) as the primary methodology for MR analysis. To ensure the robustness of our MR findings, multiple sensitivity analyses were performed.</p><p><strong>Results: </strong>In the forward MR analysis, a negative correlation was indicated between OSA and TL (IVW: odds ratio (OR) = 0.964, 95% confidence interval (CI): 0.939-0.980, P = 0.006 < 0.05). However, no significant association was identified between TL and the risk of OSA in the reverse MR analysis (IVW: OR = 0.965, 95% CI: 0.870-1.070, P = 0.499 > 0.05).</p><p><strong>Conclusion: </strong>Our study indicated a potential association between OSA and the increased risk of shorter TL, offering vital academic support for future clinical studies on this association.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1294105"},"PeriodicalIF":2.8,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11913802/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143656885","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Frontiers in GeneticsPub Date : 2025-03-04eCollection Date: 2025-01-01DOI: 10.3389/fgene.2025.1521663
Bin Zhao, Shi Fu, Yuanlong Shi, Jinye Yang, Chengwei Bi, Libo Yang, Yong Yang, Xin Li, Zhiyu Shi, Yuanpeng Duan, Zongyan Luo, Guoying Zhang, Jiansong Wang
{"title":"Development and validation of prognostic and diagnostic models utilizing immune checkpoint-related genes in public datasets for clear cell renal cell carcinoma.","authors":"Bin Zhao, Shi Fu, Yuanlong Shi, Jinye Yang, Chengwei Bi, Libo Yang, Yong Yang, Xin Li, Zhiyu Shi, Yuanpeng Duan, Zongyan Luo, Guoying Zhang, Jiansong Wang","doi":"10.3389/fgene.2025.1521663","DOIUrl":"10.3389/fgene.2025.1521663","url":null,"abstract":"<p><strong>Background: </strong>Clear cell renal cell carcinoma (ccRCC) is the most prevalent subtype of renal cell carcinoma, and immune checkpoint regulator-based immunotherapy has emerged as an effective treatment for advanced stages of the disease. However, the expression patterns, prognostic significance, and diagnostic value of immune checkpoint-related genes (ICRGs) in ccRCC remain underexplored. This study utilized large-scale ccRCC datasets from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), and the International Cancer Genome Consortium (ICGC) to analyze ICRGs and develop a prognostic and diagnostic model, which was validated using quantitative PCR in clinical samples from ccRCC patients.</p><p><strong>Methods: </strong>RNA-seq data and clinical information were retrieved from TCGA, ICGC, and GEO databases. Differentially expressed genes (DEGs) were identified, and immune checkpoint-related genes (DICRGs) were selected by intersecting DEGs with ICRGs, followed by validation in independent datasets. Univariate and multivariate Cox regression analyses were used to develop the prognostic model. Protein expression of key genes was validated through immunohistochemistry (IHC) using data from the Human Protein Atlas (HPA). qRT-PCR confirmed gene expression levels in ccRCC and normal kidney tissues. Diagnostic models were constructed using machine learning, and functional enrichment and immune infiltration analyses were performed.</p><p><strong>Results: </strong>Fourteen DICRGs were identified, with four (<i>EGFR</i>, <i>TRIB3</i>, <i>ZAP70</i>, and <i>CD4</i>) showing prognostic significance in Cox analyses. IHC revealed high expression of these genes in ccRCC tissues, and qRT-PCR confirmed increased expression of <i>EGFR</i>, <i>TRIB3</i>, and <i>CD4</i>, while <i>ZAP70</i> expression showed no significant change. A prognostic risk score was developed based on gene expression levels. Functional analysis identified enriched pathways related to organic anion transport and metabolism, while immune infiltration analysis revealed associations between <i>ZAP70</i>, <i>CD4</i>, and risk scores.</p><p><strong>Conclusion: </strong>This study establishes a prognostic model for ccRCC based on four ICRGs, providing valuable insights into the molecular mechanisms underlying prognosis and diagnosis in ccRCC.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1521663"},"PeriodicalIF":2.8,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11913831/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143656890","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Frontiers in GeneticsPub Date : 2025-03-03eCollection Date: 2025-01-01DOI: 10.3389/fgene.2025.1366743
Yongwei Du, Xiqiu Xiao, Fuping Liu, Wenqing Zhu, Jianwen Mo, Zhen Liu
{"title":"Causal effects of metabolites on malignant neoplasm of bone and articular cartilage: a mendelian randomization study.","authors":"Yongwei Du, Xiqiu Xiao, Fuping Liu, Wenqing Zhu, Jianwen Mo, Zhen Liu","doi":"10.3389/fgene.2025.1366743","DOIUrl":"10.3389/fgene.2025.1366743","url":null,"abstract":"<p><strong>Objective: </strong>Previous research has demonstrated that metabolites play a significant role in modulating disease phenotypes; nevertheless, the causal association between metabolites and malignant malignancies of bones and joint cartilage (MNBAC)has not been fully elucidated.</p><p><strong>Methods: </strong>This study used two-sample Mendelian randomization (MR) to explore the causal correlation between 1,400 metabolites and MNBAC. Data from recent genome-wide association studies (GWAS) involving 8,299 individuals were summarized. The GWAS summary data for metabolites were acquired from the IEU Open GWAS database, while those for MNBAC were contributed by the Finnish Consortium. We employed eight distinct MR methodologies: simple mode, maximum likelihood estimator, MR robust adjusted profile score, MR-Egger, weighted mode, weighted median, MR-PRESSO and inverse variance weighted to scrutinize the causal association between metabolites engendered by each gene and MNBAC. Consequently, we evaluated outliers, horizontal pleiotropy, heterogeneity, the impact of single nucleotide polymorphisms (SNPs), and adherence to the normal distribution assumption in the MR analysis.</p><p><strong>Results: </strong>Our findings suggested a plausible causative relationship between N-Formylmethionine (FMet) levels, lignoceroylcarnitine (C24) levels, and MNBAC. We observed a nearly significant causal association between FMet levels and MNBAC within the cohort of 1,400 metabolites (<i>P</i> = 0.024, odds ratio (OR) = 3.22; 95% CI [1.16-8.92]). Moreover, we ascertained a significant causal link between levels of C24 and MNBAC (<i>P</i> = 0.0009; OR = 0.420; 95%CI [0.25-0.70]). These results indicate a potential causative relationship between FMet, C24 level and MNBAC.</p><p><strong>Conclusion: </strong>The occurrence of MNBAC may be causally related to metabolites. This might unveil new possibilities for investigating early detection and treatment of MNBAC.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1366743"},"PeriodicalIF":2.8,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11911353/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143648374","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Frontiers in GeneticsPub Date : 2025-03-03eCollection Date: 2025-01-01DOI: 10.3389/fgene.2025.1504443
Emily Palmer, Austin Hammer, Thomas Sharpton, Yuan Jiang
{"title":"A group penalization framework for detecting time-lagged microbiota-host associations.","authors":"Emily Palmer, Austin Hammer, Thomas Sharpton, Yuan Jiang","doi":"10.3389/fgene.2025.1504443","DOIUrl":"10.3389/fgene.2025.1504443","url":null,"abstract":"<p><p>There is rising interest in using longitudinal microbiome data to understand how the past status of the microbiome impacts the current state of the host, referred to as \"time-lagged\" effects, as these effects may take time to occur. While existing works used previous states of the microbiome in their analysis, they did not use methods that identify both the time-lagged associations and their corresponding time lags. In this article, we present a framework to identify time-lagged associations between abundances of longitudinally sampled microbiota and a stationary response (final health outcome, disease status, etc.). We start with a definition of the time-lagged effect by imposing a particular structure on the association pattern of longitudinal microbial measurements. Using group penalization methods, we identify these time-lagged associations including their strengths, signs, and timespans. Through simulation studies, we demonstrate accurate identification of time lags and estimation of signal strengths by our approach. We further apply our approach to find specific gut microbial taxa and their time-lagged effects on increased parasite worm burden in zebrafish.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1504443"},"PeriodicalIF":2.8,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11911519/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143648422","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Identification of QTL for branch traits in soybean (<i>Glycine max</i> L.) and its application in genomic selection.","authors":"Qichao Yang, Jing Wang, Yajun Xiong, Alu Mao, Zhiqing Zhang, Yijie Chen, Shirui Teng, Zhiyu Liu, Jun Wang, Jian Song, Lijuan Qiu","doi":"10.3389/fgene.2025.1484146","DOIUrl":"10.3389/fgene.2025.1484146","url":null,"abstract":"<p><strong>Introduction: </strong>Branches are important for soybean yield, and previous studies examining branch traits have primarily focused on branch number (BN), while research assessing branch internode number (BIN), branch length (BL), and branch internode length (BIL) remains insufficient.</p><p><strong>Methods: </strong>A recombinant inbred line (RIL) population consisting of 364 lines was constructed by crossing ZD41 and ZYD02878. Based on the RIL population, we genetically analyzed four branch traits using four different GWAS methods including efficient mixed-model association expedited, restricted two-stage multi-locus genome-wide association analysis, trait analysis by association, evolution and linkage, and three-variance-component multi-locus random-SNP-effect mixed linear model analyses. Additionally, we screened candidate genes for the major QTL and constructed a genomic selection (GS) model to assess the prediction accuracy of the four branch traits.</p><p><strong>Results and discussion: </strong>In this study, four branch traits (BN, BIN, BL, and BIL) were phenotypically analyzed using the F<sub>6</sub>-F<sub>9</sub> generations of a RIL population consisting of 364 lines. Among these four traits, BL exhibited the strongest correlation with BIN (0.92), and BIN exhibited the strongest broad-sense heritability (0.89). Furthermore, 99, 43, 50, and 59 QTL were associated with BN, BIN, BL, and BIL, respectively, based on four different methods, and a major QTL region (Chr10:45,050,047..46,781,943) was strongly and simultaneously associated with all four branch traits. For the 207 genes within this region, nine genes were retained as candidates after SNP variation analysis, fixation index (<i>F</i> <sub><i>ST</i></sub> ), spatial and temporal expression analyses and functionality assessment that involved the regulation of phytohormones, transcription factors, cell wall and cell wall cellulose synthesis. Genomic selection (GS) prediction accuracies for BN, BIN, BL, and BIL in the different environments were 0.59, 0.49, 0.48, and 0.56, respectively, according to GBLUP. This study lays the genetic foundation for BN, BIN, BL, and BIL and provides a reference for functional validation of regulatory genes in the future.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1484146"},"PeriodicalIF":2.8,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11911462/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143648455","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Frontiers in GeneticsPub Date : 2025-03-03eCollection Date: 2025-01-01DOI: 10.3389/fgene.2025.1512435
Yinghao Fu, Leqi Tian, Weiwei Zhang
{"title":"STsisal: a reference-free deconvolution pipeline for spatial transcriptomics data.","authors":"Yinghao Fu, Leqi Tian, Weiwei Zhang","doi":"10.3389/fgene.2025.1512435","DOIUrl":"10.3389/fgene.2025.1512435","url":null,"abstract":"<p><p>Spatial transcriptomics has emerged as an invaluable tool, helping to reveal molecular status within complex tissues. Nonetheless, these techniques have a crucial challenge: the absence of single-cell resolution, resulting in the observation of multiple cells in each spatial spot. While reference-based deconvolution methods have aimed to solve the challenge, their effectiveness is contingent upon the quality and availability of single-cell RNA (scRNA) datasets, which may not always be accessible or comprehensive. In response to these constraints, our study introduces STsisal, a reference-free deconvolution method meticulously crafted for the intricacies of spatial transcriptomics (ST) data. STsisal leverages a novel approach that integrates marker gene selection, mixing ratio decomposition, and cell type characteristic matrix analysis to discern distinct cell types with precision and efficiency within complex tissues. The main idea of our method is its adaptation of the SISAL algorithm, which expertly disentangles the ratio matrix, facilitating the identification of simplices within the ST data. STsisal offers a robust means to unveil the intricate composition of cell types in spatially resolved transcriptomic data. To verify the efficacy of STsisal, we conducted extensive simulations and applied the method to real data, comparing its performance against existing techniques. Our findings highlight the superiority of STsisal, underscoring its utility in capturing the cell composition within complex tissues.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1512435"},"PeriodicalIF":2.8,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11911522/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143648456","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}