Genes & genomics最新文献

{"title":"Association between PDCD6-VNTR polymorphism and urinary cancer susceptibility.","authors":"Gi-Eun Yang, Min-Hye Kim, Mi-So Jeong, Sang-Yeop Lee, Yung Hyun Choi, Jong-Kil Nam, Tae Nam Kim, Sun-Hee Leem","doi":"10.1007/s13258-024-01523-9","DOIUrl":"10.1007/s13258-024-01523-9","url":null,"abstract":"<p><strong>Background: </strong>Programmed cell death 6 (PDCD6) is known to be involved in apoptosis and tumorigenesis. Given the reported association with urinary cancer susceptibility through SNP analysis, we further analyzed the entire genomic structure of PDCD6.</p><p><strong>Methods: </strong>Three VNTR regions (MS1-MS3) were identified through the analysis of the genomic structure of PDCD6. To investigate the association between these VNTR regions and urinary cancer susceptibility, genomic DNA was extracted from 413 cancer-free male controls, 267 bladder cancer patients, and 331 prostate cancer patients. Polymerase chain reaction (PCR) was performed to analyze the PDCD6-MS regions. Statistical analysis was performed to determine the association between specific genotypes and cancer risk. In addition, the effect of specific VNTRs on PDCD6 expression was also confirmed using a reporter vector.</p><p><strong>Results: </strong>Among the three VNTR regions, MS1 and MS2 exhibited monomorphism, while the MS3 region represented polymorphism, with its transmission to subsequent generations through meiosis substantiating its utility as a DNA typing marker. In a case-control study, the presence of rare alleles within PDCD6-MS3 exhibited significant associations with both bladder cancer (OR = 2.37, 95% CI: 1.33-4.95, P = 0.019) and prostate cancer (OR = 2.11, 95% CI: 1.03-4.36, P = 0.038). Furthermore, through luciferase assays, we validated the impact of the MS3 region on modulating PDCD6 expression.</p><p><strong>Conclusions: </strong>This study suggests that the PDCD6-MS3 region could serve as a prognostic marker for urinary cancers, specifically bladder cancer and prostate cancer. Moreover, the subdued influence exerted by PDCD6-MS3 on the expression of PDCD6 offers another insight concerning the progression of urinary cancer.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"1281-1291"},"PeriodicalIF":1.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141293334","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Epigenetic regulation of HERVs: Implications for cancer immunotherapy.","authors":"Joo Mi Yi","doi":"10.1007/s13258-024-01546-2","DOIUrl":"10.1007/s13258-024-01546-2","url":null,"abstract":"<p><strong>Background: </strong>Human endogenous retroviruses (HERVs), integrated into the human genome during primate evolution, constitute approximately 8% of the human genome. Although most HERVs are non-protein-coding owing to mutations, insertions, deletions, and truncations, recent research has revealed their diverse roles in biological processes, including disease pathogenesis.</p><p><strong>Objective: </strong>Although many HERVs remain inactive, they have been implicated in various diseases, particularly cancer, prompting an increased interest in harnessing HERVs for therapeutic purposes. This review explores the recent advancements in our understanding of the biological roles of HERVs, emphasizing their clinical relevance in cancer treatment.</p><p><strong>Methods: </strong>Here, we discuss how the detection of transposable elements (TEs), including HERVs, by the immune system triggers innate immune responses in human cancers.</p><p><strong>Conclusion: </strong>Additionally, we outline recent progress in elucidating the implications of HERV activation in cancer and how targeting HERVs holds promise for anti-cancer treatments by modulating epigenetic plasticity and disrupting cancer initiation and progression.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"1303-1312"},"PeriodicalIF":1.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141859515","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A novel frameshift TBX4 variant in a family with ischio-coxo-podo-patellar syndrome and variable severity.","authors":"Giada Moresco, Ornella Rondinone, Alessia Mauri, Rita Gorgoglione, Daniela Maria Grazia Graziani, Michal Dziuback, Monica Rosa Miozzo, Silvia Maria Sirchia, Luca Pietrogrande, Angela Peron, Laura Fontana","doi":"10.1007/s13258-024-01589-5","DOIUrl":"10.1007/s13258-024-01589-5","url":null,"abstract":"<p><strong>Background: </strong>Congenital anomalies of the knee are a spectrum of rare disorders with wide clinical and genetic variability, which are mainly due to the complex processes underlying knee development. Despite progresses in understanding pathomechanisms and associated genes, many patients remain undiagnosed.</p><p><strong>Objective: </strong>To uncover the genetic bases of a congenital patellar dislocation affecting multiple family members with variable severity.</p><p><strong>Methods: </strong>We performed ES in the proband and his father, both showing bilateral patellar dislocation, his sister with a milder similar condition, and his unaffected mother. Sanger sequencing was then performed in the proband's brother and paternal aunt, both affected as well.</p><p><strong>Results: </strong>ES and Sanger sequencing identified the presence of the novel heterozygous frameshift mutation c.735delT in the TBX4 gene in all affected family members. TBX4 is associated with autosomal dominant ischio-coxo-podo-patellar syndrome with/without pulmonary arterial hypertension (ICPPS, #147891), reaching a diagnosis in the family. Intrafamilial clinical heterogeneity suggests that other factors might be involved, such as additional variants in TBX4 or in other modifier genes. Interestingly, we identified three additional variants in the TBX4 gene in the proband only, whose phenotype is more severe. Despite being classified as benign, one of these variants is predicted to disrupt a splicing protein binding site, and may therefore affect TBX4 alternative splicing, accounting for the more severe phenotype of the proband.</p><p><strong>Conclusion: </strong>We expand and further delineate the genotypic and phenotypic spectrum of ICPPS. Further studies are necessary to shed light on the potential effect of this variant and on the variable phenotypic expressivity of TBX4-related phenotypes.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":""},"PeriodicalIF":1.6,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142521713","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A novel CLRN2 variant: expanding the mutation spectrum and its critical role in isolated hearing impairment.","authors":"Farooq Ahmad, Arif Mahmood, Ibrahim Abdullah Almazni, Afnan Mohammed Shakoori, Fatemah Alhakami, Qamre Alam, Muhammad Ismail, Muhammad Umair","doi":"10.1007/s13258-024-01590-y","DOIUrl":"https://doi.org/10.1007/s13258-024-01590-y","url":null,"abstract":"<p><strong>Background: </strong>Biallelic variants in the CLRN2 gene have been reported to cause autosomal recessive profound hearing impairment in humans. CLRN2 belongs to the clarin gene family that encodes a tetraspan protein that contains a cytosolic N-terminus, multiple helical transmembrane domains, and an endoplasmic reticulum membrane retention signal, TKGH, in the C-terminus. The encoded protein may be important in development and homeostasis of the inner ear and retina.</p><p><strong>Methods: </strong>Here, we present a consanguineous family suffering from autosomal recessive non-syndromic profound hearing impairment (HI). We employed state of the art Whole exome sequencing (WES), Sanger sequencing followed by routine bioinformatics filtration steps and homology modeling to elucidate the effect of mutation at the protein level.</p><p><strong>Results: </strong>ES followed by Sanger sequencing revealed a novel homozygous nonsense variant in the CLRN2 gene [c.414 C > A; p.Cys138*]. Furthermore, insilico protein modeling of the wildtype and mutated version of the CLRN2 protein revealed large-scale changes that predict to compromise the routine normal function of the protein.</p><p><strong>Conclusion: </strong>Our finding further extends the mutations spectrum of CLRN2 gene and confirms its important role in hearing homeostasis and with developmental disorder in humans.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":""},"PeriodicalIF":1.6,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142498909","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Insights into ACO genes across Rosaceae: evolution, expression, and regulatory networks in fruit development.","authors":"Yuxin Zhang, Yirong Zhang, Ze Yu, Hanyu Wang, Boya Ping, Yunxiao Liu, Jiakai Liang, Fengwang Ma, Yangjun Zou, Tao Zhao","doi":"10.1007/s13258-024-01551-5","DOIUrl":"10.1007/s13258-024-01551-5","url":null,"abstract":"<p><strong>Background: </strong>ACO (1-aminocyclopropane-1-carboxylic acid) serves as a pivotal enzyme within the plant ethylene synthesis pathway, exerting influence over critical facets of plant biology such as flowering, fruit ripening, and seed development.</p><p><strong>Objective: </strong>This study aims to identify ACO genes from representative Rosaceae genomes, reconstruct their phylogenetic relationships by integrating synteny information, and investigate their expression patterns and networks during fruit development.</p><p><strong>Methods: </strong>we utilize a specialized Hidden Markov Model (HMM), crafted on the sequence attributes of ACO gene-encoded proteins, to systematically identify and analyze ACO gene family members across 12 representative species within the Rosaceae botanical family. Through transcriptome analysis, we delineate the expression patterns of ACO genes in six distinct Rosaceae fruits.</p><p><strong>Results: </strong>Our investigation reveals the presence of 62 ACO genes distributed among the surveyed Rosaceae species, characterized by hydrophilic proteins predominantly expressed within the cytoplasm. Phylogenetic analysis categorizes these ACO genes into three discernible classes, namely Class I, Class II, and Class III. Further scrutiny via collinearity assessment indicates a lack of collinearity relationships among these classes, highlighting variations in conserved motifs and promoter types within each class. Transcriptome analysis unveils significant disparities in both expression levels and trends of ACO genes in fruits exhibiting respiratory bursts compared to those that do not. Employing Weighted Gene Co-Expression Network Analysis (WGCNA), we discern that the co-expression correlation of ACO genes within loquat fruit notably differs from that observed in apples. Our findings, derived from Gene Ontology (GO) enrichment results, signify the involvement of ACO genes and their co-expressed counterparts in biological processes linked to terpenoid metabolism and carbohydrate synthesis in loquat. Moreover, our exploration of gene regulatory networks (GRN) highlights the potential pivotal role of the GNAT transcription factor (Ejapchr1G00010380) in governing the overexpression of the ACO gene (Ejapchr10G00001110) within loquat fruits.</p><p><strong>Conclusion: </strong>The constructed HMM of ACO proteins offers a precise and systematic method for identifying plant ACO proteins, facilitating phylogenetic reconstruction. ACO genes from representative Rosaceae fruits exhibit diverse expression and regulative patterns, warranting further function characterizations.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"1209-1223"},"PeriodicalIF":1.6,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141975521","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ADP-glucose pyrophosphorylase gene family in soybean and implications in drought stress tolerance.","authors":"Maoni Chao, Qiufang Zhang, Ling Huang, Li Wang, Jie Dong, Shibo Kou, Weifeng Song, Tiegu Wang","doi":"10.1007/s13258-024-01558-y","DOIUrl":"10.1007/s13258-024-01558-y","url":null,"abstract":"<p><strong>Background: </strong>ADP-glucose pyrophosphorylase (AGPase) is the key rate-limiting enzyme in starch biosynthesis pathway, and has been identified as a potential target for manipulation strategies aimed at improving crop yield and quality.</p><p><strong>Objective: </strong>To identify the AGPase gene family members in soybean, and explore the potential implications of GmAGPS2 in drought stress tolerance.</p><p><strong>Methods: </strong>The genome-wide identification and sequence analysis of soybean AGPase gene family was carried out by bioinformatics methods. The GmAGP gene expression was analyzed using transcriptome data and quantitative real-time PCR (qRT-PCR). Furthermore, transgenic yeast strains overexpressing GmAGPS2 were generated, and their growth was observed under drought stress.</p><p><strong>Results: </strong>In this study, we searched for AGPase genes (GmAGP) in the soybean genome and identified a total of 14 GmAGP genes. The GmAGP proteins had a unique conserved NTP_transferase domain and were mainly located in the chloroplast and cytosol. Evolutionarily, the GmAGP proteins can be clustered into two distinct subgroups; within the same subgroup, they displayed a similar distribution pattern of conserved motifs. The GmAGP genes exhibited an uneven distribution on 10 chromosomes, and segmental duplication contributed to AGPase gene family expansion in soybean. The GmAGP genes presented different tissue expression pattern, in which GmAGPL6, GmAGPL9, and GmAGPL10 mainly exhibited tissue-specific expression pattern. The promoter of GmAGP genes had multiple cis-acting elements related to phytohormones and stress responses, and 8 GmAGP genes contained drought-responsive cis-acting elements. qRT‒PCR analysis demonstrated a significant upregulation expression of GmAGPL6, GmAGPL10, and GmAGPS2 in response to drought stress. Further functional analysis indicated that GmAGPS2 gene could improve yeast growth under drought stress conditions and enhance the drought tolerance of yeast.</p><p><strong>Conclusion: </strong>These results will contribute to further elucidation of the function of GmAGP genes, and offer important candidate genes for the genetic improvement of starch and yield-related traits and the breeding of high drought stress tolerance varieties in soybean.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"1183-1199"},"PeriodicalIF":1.6,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142106589","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Purposive breeding strategies drive genetic differentiation in Thai fighting cock breeds.","authors":"Trifan Budi, Anh Huynh Luu, Worapong Singchat, Wongsathit Wongloet, Juniman Rey, Nichakorn Kumnan, Piangjai Chalermwong, Chien Phuoc Tran Nguyen, Thitipong Panthum, Nivit Tanglertpaibul, Thanyapat Thong, Hina Ali, Kanithaporn Vangnai, Aingorn Chaiyes, Chotika Yokthongwattana, Chomdao Sinthuvanich, Kyudong Han, Agostinho Antunes, Narongrit Muangmai, Prateep Duengkae, Kornsorn Srikulnath","doi":"10.1007/s13258-024-01561-3","DOIUrl":"10.1007/s13258-024-01561-3","url":null,"abstract":"<p><strong>Background: </strong>Fighting cock breeds have considerable historical and cultural place in Thailand. Breeds such as Lueng Hang Khao (LHK) and Pradu Hang Dam (PDH) are known for their impressive plumage and unique meat quality, suggesting selection for fighting and other purposes. However, information regarding the genetic diversity and clustering in indigenous and local Thai chickens used for cockfighting is unclear.</p><p><strong>Objective: </strong>To investigates the genetic diversity and differentiation in Thai fighting cock breeds, including populations for cockfighting, ornamental aspects, and consumption.</p><p><strong>Methods: </strong>Thai fighting cook breeds, including LHK and PDH chickens were analyzed using genotyping with 28 microsatellite loci. Data were compared to a gene pool library from \"The Siam Chicken Bioresource Project\" to understand the impact of human selection on genetic differentiation. Fighting cock strains from different breeds may cluster owing to shared breeding goals.</p><p><strong>Result: </strong>The analysis of several chicken breeds showed subpopulation differentiation driven by artificial selection and genetic drift, affecting the genetic landscape and causing genetic hitchhiking. Eleven of 28 microsatellite loci showed hitchhiking selection, indicating directional selection in fighting cocks. Additionally, analyses revealed admixture with domestic chicken breeds and minimal influence of red junglefowl in the gene pool of Thai fighting chickens. These findings inform breed improvement, selection strategies, genetic resource management, and maintaining genetic diversity in fighting cocks.</p><p><strong>Conclusion: </strong>Analysis of Thai Fighting chicken breeds revealed a correlation between utilization and subpopulation differentiation. Specifically, selection for cockfighting and ornamental traits appears to explain the observed genetic structure within these breeds.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"1225-1237"},"PeriodicalIF":1.6,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142106601","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"MiR-122, miR-133a, and miR-206 as potential biomarkers for post-mortem interval estimation.","authors":"Eun Ju Lee, Mingyoung Jeong, Haneul Lee, Min-A Je, Kwangmin Park, Dong Geon Lee, Xianglan Xuan, Sunghyun Kim, Sunyoung Park, Jungho Kim","doi":"10.1007/s13258-024-01559-x","DOIUrl":"10.1007/s13258-024-01559-x","url":null,"abstract":"<p><strong>Backgroud: </strong>Accurate estimation of post-mortem interval (PMI) is crucial in forensic investigations. MicroRNAs (miRNAs or miRs) are small non-coding RNAs that remain relatively stable within the cell nucleus despite post-mortem changes.</p><p><strong>Objective: </strong>We assessed three target genes (miR-122, miR-133a, and miR-206) for PMI estimation using 72 healthy adult male BALB/c mice exposed to two different temperatures (4 and 21℃) at nine different time points over 10 days.</p><p><strong>Methods: </strong>Initially, the stability of the two reference genes (RNU6B and 5 srRNA) was evaluated using gene stability analysis tools (Delta Ct, Best Keeper, and Genorm) to select the optimal reference gene. RNU6B was found to be the most stable endogenous control. Subsequently, the expression patterns of miR-122, miR-133a, and miR-206 were analyzed within a 10-day PMI period using the heart, skeletal muscle, liver, and brain tissues.</p><p><strong>Results: </strong>At 4℃, miR-122 levels significantly decreased on days 8 and 10 in all tissues, with only the liver showing significant changes at 21℃. MiR-133a decreased over time in the heart, muscles, and brain, showing a dramatic decrease on days 8 and 10 in the heart and muscles at both temperatures. Although miR-206 levels decreased over time in muscles and liver at 4 ℃, these increased in the brain at 21 ℃, with no expression changes in other organs.</p><p><strong>Conclusion: </strong>In summary, miR-122, miR-133a, and miR-206 are potential PMI markers in heart and skeletal muscle tissues.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"1175-1182"},"PeriodicalIF":1.6,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142106600","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of an autophagy- and macropinocytosis-related prognostic signature for the prediction of prognosis and therapeutic response in gastric cancer.","authors":"Yuhua Shi, Aifeng Qiu, Hengfeng Cui, Heng Lv, Lei Zhou","doi":"10.1007/s13258-024-01557-z","DOIUrl":"10.1007/s13258-024-01557-z","url":null,"abstract":"<p><strong>Background: </strong>Traditional liquid biopsy markers show a low rate of positivity and accurate in gastric cancer. With the rapid advancement of sequencing technology, scientists have identified promising research avenues in this field. Autophagy and macropinocytosis utilize diverse pathways and mechanisms to supply resources and fuel for tumor growth. Nonetheless, their potential interplay introduces an untapped avenue for the discovery of novel tumor biomarkers.</p><p><strong>Objective: </strong>To develop an innovative prognostic signature based on autophagy- and micropinocytosis-related genes, with the aim to predict the outcome and therapeutic response of gastric cancer patients. Additionally, to validate the prognostic impact of this signature, and elucidate the role of representative molecules in gastric cancer.</p><p><strong>Methods: </strong>To construct and validate a prognostic signature for gastric cancer, bioinformatics methods such as COX regression, LASSO regression, survival analysis, ROC curve, and nomogram were utilized based on the sequencing and clinical data of gastric cancer patients retrieved from the TCGA and GEO databases. GSEA functional enrichment analyses were employed to predict the biological functions. Meanwhile, qRT-PCR and Western blot experiments were utilized to quantify the mRNA and protein expression levels. Furthermore, the EdU assay and colony formation assay were utilized to examine the cell proliferation ability while the Transwell assays were conducted to assess the migration and invasion abilities of gastric cancer cells.</p><p><strong>Results: </strong>Through consistency clustering and univariate COX analyses, potential prognostic genes involved in both autophagy and macropinocytosis were identified. Based on these genes, a 9-gene signature was constructed, which demonstrated high accuracy in predicting gastric cancer patients' survival period, immunotherapeutic response, and chemotherapy drug tolerance. Furthermore, qRT-PCR analyses of gastric cancer tissue samples showed that the representative genes of this signature were aberrantly overexpressed in gastric cancer, with MATN3, as the most notable molecule, exhibiting significant carcinogenic effects on cancer cells by actively regulating their proliferation, migration, and invasion abilities.</p><p><strong>Conclusion: </strong>Our newly created prognostic signature possesses significant potential as a biomarker for gastric cancer, while MATN3 is identified as an oncogenic factor in gastric cancer. This brings to light new perspectives, which can contribute to enhancing the diagnosis and treatment of gastric cancer.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"1149-1164"},"PeriodicalIF":1.6,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141987777","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prognostic significance of HS2ST1 expression in patients with hepatocellular carcinoma.","authors":"Ting Ting Chung, Sang Kyum Kim, Seung Jin Lee","doi":"10.1007/s13258-024-01556-0","DOIUrl":"10.1007/s13258-024-01556-0","url":null,"abstract":"<p><strong>Background: </strong>Heparan sulfate 2-O-sulfotransferase 1 (HS2ST1) catalyzes the sulfation of glucuronic acid residues in heparan sulfate proteoglycans, enabling these proteoglycans to interact with numerous ligands within tumor microenvironments. However, the prognostic role of HS2ST1 expression in cancer remains unclear.</p><p><strong>Objective: </strong>This investigated HS2ST1 expression levels and their prognostic significance in various cancer types, demonstrated the prognostic value of HS2ST1 expression in hepatocellular carcinoma (HCC) patients, and identified molecular signatures associated with HS2ST1 expression.</p><p><strong>Methods: </strong>HS2ST1 expression and patient survival data from The Cancer Genome Atlas (TCGA) datasets were analyzed using the Gene Expression Profiling Interactive Analysis (GEPIA) portal. We obtained gene expression and clinicopathological information on HCC patients from the TCGA and the Japan and France International Cancer Genome Consortium (ICGC) databases and performed survival analyses. We also examined relevant protein networks, differentially expressed genes, gene set enrichments, and tumor immune microenvironment features associated with HS2ST1 expression.</p><p><strong>Results: </strong>HS2ST1 exhibited higher expression in eight tumor types compared with normal tissues and was associated with poor prognoses in five tumors, including HCC. HS2ST1 status correlated with poor prognosis in two ICGC HCC cohorts. Elevated HS2ST1 expression in HCC tumors was associated with signaling pathways involved in cell cycle progression, protein secretion, and mTORC1 signaling. Moreover, HS2ST1 expression levels were inversely correlated with immune cell infiltration in the tumor microenvironment.</p><p><strong>Conclusion: </strong>Our study elucidates the prognostic significance of HS2ST1 expression in HCC patients and provides insights into the potential roles of HS2ST1 in signaling pathways and the tumor microenvironment.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"1165-1174"},"PeriodicalIF":1.6,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11410915/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141995644","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}