Gene Reports最新文献

{"title":"Antimicrobial resistance and bioactive metabolites of Serratia marcescens CAB03 from a Palk Bay coral reef","authors":"S. Hari Krishna Kumar ,&nbsp;Ragothaman Prathiviraj ,&nbsp;Muregesan Sobanaa ,&nbsp;George Seghal Kiran ,&nbsp;Joseph Selvin","doi":"10.1016/j.genrep.2025.102339","DOIUrl":"10.1016/j.genrep.2025.102339","url":null,"abstract":"<div><div>Antimicrobial-resistant pathogens are poorly understood and pose emerging threats to coral reef ecosystems. Coral-associated microbial diversity is crucial for reef resilience; however, there is a limited understanding of opportunistic pathogens from Indian reefs. Here, we report the identification of <em>Serratia marcescens</em> CAB03, which may be associated with coral disease, isolated from <em>Acropora cythera</em> of Palk Bay coral reef, India. Whole genome sequencing of <em>S. marcescens</em> CAB03 produced 24 contigs (total G + C 59.7 %) and 4713 predicted genes. Identification of functional annotation revealed 17 antimicrobial resistance (AMR) genes, including three copies of the <em>adeF</em> gene, which encapsulates a resistance-nodulation-division (RND) efflux system that provides resistance to tetracyclines and fluoroquinolones. At the same time, related genes were also associated with resistance to β-lactams, aminoglycosides, macrolides, glycopeptides, and disinfectants, suggesting that this strain may have multidrug resistance potential. Further secondary metabolite prediction revealed biosynthetic gene clusters for ririwpeptide, a cyclic lipopetide with membrane-disrupting antibacterial and anticancer activity, and prodigiosin, which has gained notoriety for its antimicrobial, anticancer, and immunosuppressant activities as a red-colored pigment. Genome-based evidence clearly indicates that <em>S. marcescens</em> CAB03 is a contributor to coral health degradation through the proliferation of AMR bacteria and also a potential repository of bioactive compounds for pharmaceutical purposes. We used whole-genome sequencing here to address a long-standing knowledge gap regarding AMR bacteria associated with coral from Indian reefs. This study illustrates the need for genomic surveillance and conservation for AMR bacteria, ideally and more generally advances the study of microbial metabolites for drug discovery. Linking pathogen genomic profiles to reef health and advances in applied biotechnology reveal new reasons for coral reef conservation and provide new sources of data for potential drug development.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"41 ","pages":"Article 102339"},"PeriodicalIF":0.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145216396","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogenomic insights into a psychrotolerant, plant growth-promoting strain of Pseudomonas marginalis isolated from Xinantécatl volcano","authors":"José Germán Serrano-Gamboa ,&nbsp;José Tomás Tavarez-Arriaga ,&nbsp;Mario L. Iza-Arteaga ,&nbsp;Martín Romualdo Ide-Pérez ,&nbsp;Irán Tapia-Vázquez ,&nbsp;Jorge L. Folch-Mallol","doi":"10.1016/j.genrep.2025.102356","DOIUrl":"10.1016/j.genrep.2025.102356","url":null,"abstract":"<div><div>A novel strain of the genus <em>Pseudomonas</em> was isolated from a high-altitude volcano in Toluca, Mexico. This isolate, designed as <em>Pseudomonas marginalis</em> BMH-2007, could grow at 4 °C, whereas other microbes usually stop growth at this temperature. The fact of its isolation from snow implies that the population was big enough to thrive at low temperature, making it a psychrotolerant bacterium.</div><div>Previous characterization of BMH-2007 revealed interesting characteristics related to plant growth promotion, including auxin production, siderophore production, and phosphate solubilization capacity. In this work, the ability of BMH-2007 to stimulate the early development of <em>Capsicum annuum</em> plants without signs of phytopathogenicity was proven. A thorough whole-genome analysis revealed that isolate BMH-2007 belongs to the <em>Pseudomonas fluorescens</em> species complex, specifically to the species <em>P. marginalis</em>, with a Mash distance of 0.0118927 from the closest reference genome (RefSeq: GCF_007858175.1).</div><div>The phylogenomic evidence allowed us to confirm the new strain designation. Notably, its genomic features were consistent with those of plant growth-promoting traits, and we observed coding sequences for IAA biosynthesis and iron and phosphate transport, among others. As it is a species associated with phytopathogenicity, the virulence factors encoded by the genome were analyzed, which revealed the presence of a type VI secretion system associated with both biological control and plant growth promotion.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"41 ","pages":"Article 102356"},"PeriodicalIF":0.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145358385","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular characterization of current field isolates of zoonotic parapoxviruses and their growth characteristics","authors":"Gizem Aytoğu ,&nbsp;Mevlüt Yaşar ,&nbsp;Nilay Aybey ,&nbsp;Zafer Mecitoğlu ,&nbsp;Kadir Yeşilbağ","doi":"10.1016/j.genrep.2025.102328","DOIUrl":"10.1016/j.genrep.2025.102328","url":null,"abstract":"<div><div>Parapoxviruses (PPVs), including Bovine papular stomatitis virus (BPSV), Pseudocowpox virus (PCPV), and ORF virus (ORFV), are zoonotic pathogens affecting wild and domesticated ruminants. Between 2023 and 2024, erosive papules and ulcers on the lips, nose, and tongue of calves, as well as proliferative oral lesions in lambs, were reported in various Turkish regions. In two geographically distant beef herds, nodular hand lesions in animal handlers indicated zoonotic transmission. Suspected samples were confirmed by PCR using B2L gene-specific primers. Three isolates representing BPSV, PCPV, and ORFV were sequenced and compared to global data. PCPV showed closest similarity to strains from Bangladesh and Finland, while BPSV was most similar to strains from China and Iran. Virus isolation was attempted on four cell lines: primary fetal lamb kidney (PLK), Madin-Darby bovine kidney (MDBK), sheep fetal thymus (SFT-R), and African green monkey kidney (VERO). PLK cells showed 100 % isolation success for all three viruses. In serial passages, ORFV replicated best in PLK cells, consistently yielding the highest viral titers. This study provides molecular and phylogenetic characterization of currently circulating zoonotic PPVs in Türkiye and compares their in vitro replication efficiency. PLK cells were identified as the most sensitive and productive system, particularly for ORFV, which is of interest due to its immunomodulatory potential.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"41 ","pages":"Article 102328"},"PeriodicalIF":0.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144911586","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In silico exploration of the metabolic and biosynthetic potential of Brevibacillus borstelensis UE10 through whole genome analysis","authors":"Hassan Ghayas ,&nbsp;Uroosa Ejaz ,&nbsp;Ayaz Taj ,&nbsp;Sabiha Yousuf ,&nbsp;Muhammad Sohail","doi":"10.1016/j.genrep.2025.102355","DOIUrl":"10.1016/j.genrep.2025.102355","url":null,"abstract":"<div><div>Thermophilic microorganisms produce heat-stable metabolites with significant importance in industrial applications. In this study, we present the whole genome sequence of a thermophilic bacterium, <em>Brevibacillus borstelensis</em> UE10, isolated from a crocodile pond in Manghopir, Pakistan. In silico functional annotation and comparative genomic analyses provided valuable insights into the biosynthetic capabilities and metabolic potential of this strain. The draft genome of UE10 was assembled into 132 contigs with a total size of 5,322,029 bp and a GC content of 52 %. The genome contained 5080 coding sequences (CDSs), 116 tRNAs, and 4 rRNAs. Whole genome and 16S rRNA gene sequence comparisons confirmed the identification of the strain as <em>B. borstelensis</em>. Furthermore, seven putative biosynthetic gene clusters (BGCs) involved in the production of potentially antimicrobial and metal-chelating agents were identified. In addition to other metabolic pathways, the presence of a 13-gene xenobiotic degradation pathway, including benzoate degradation, demonstrates the strain's strong potential for bioremediation. Overall, in silico genomic evidence highlights the potential of <em>B. borstelensis</em> UE10 in biotechnological applications and environmental remediation.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"41 ","pages":"Article 102355"},"PeriodicalIF":0.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145324273","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single-nucleotide polymorphisms (SNPs) in sperm adhesion molecule 1 (SPAM1) gene are associated with egg production in Yangzhou geese","authors":"Murtada Alsiddig ,&nbsp;Tarig Badri ,&nbsp;Hind Widaa ,&nbsp;Bojiang Li ,&nbsp;Honglin Liu","doi":"10.1016/j.genrep.2025.102311","DOIUrl":"10.1016/j.genrep.2025.102311","url":null,"abstract":"<div><div>Sperm adhesion molecule 1(SPAM1) is a vital candidate gene that plays an important role in fertilization and hatchability of geese. In this study, we investigated for the first time the genetic variation of the SPAM1 gene and its association with egg production trait in Yangzhou geese. By using the direct sequencing technique, we detected three single nucleotide polymorphisms, g206 G&gt;C, c123 T&gt;A, and c159 T&gt;C, located in the promoter and exon one regions, respectively. Six alleles and nine genotypes (GG, CC, GC, TT, TA, AA, TT, TC and CC) were obtained, respectively. The results indicated that the GG (g206 G&gt;C) genotype had a significantly higher egg production rate during the 34-week egg-laying period. In the case of the SNPs c123 T &gt; A and c159 T &gt; C individuals with the AA and TT genotypes produced more eggs number, respectively. The SPAM 1 gene was highly expressed in the oviduct, abdominal fat, ovary and small intestine tissues. The mRNA expression level in the oviduct and ovary indicated that the geese with GG genotype recorded significantly lower expression levels (0.72 ± 0.02; 0.93 ± 0.02) compared to the geese with CC genotype (1.27 ± 0.19, 1.11 ± 0.06), respectively. Transcriptional activity results showed that both constructed vectors (pGL3-328G and pGL3-333C) had higher and more significant luciferase activity than the pGL3-basic vector. Future studies in Yangzhou and other native breeds of geese may be required to validate the association between these polymorphisms and egg production traits.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"41 ","pages":"Article 102311"},"PeriodicalIF":0.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144771853","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Carrier frequency of spinal muscular atrophy: a large-scale study in Iranian population","authors":"Shahram Savad ,&nbsp;Mohammad-Hossein Modarressi ,&nbsp;Mahnaz Seifi-Alan ,&nbsp;Niusha Samadaian ,&nbsp;Saloomeh Amidi ,&nbsp;Mona Masoomy ,&nbsp;Shima Norouzi ,&nbsp;Sanaz Seifi-Alan ,&nbsp;Alireza Ronagh ,&nbsp;Shahab Nourian ,&nbsp;Sarang Younesi ,&nbsp;Mohammad Mahdi Taheri Amin ,&nbsp;Maryam Eslami ,&nbsp;Mostafa Iranpour ,&nbsp;Asyeh Mohammadi ,&nbsp;Bahar Parastooei ,&nbsp;Mahdi Heydari ,&nbsp;Amirreza Boroumand ,&nbsp;Mahmoud Reza Ashrafi ,&nbsp;Donya Jahedi ,&nbsp;Soudeh Ghafouri-Fard","doi":"10.1016/j.genrep.2025.102378","DOIUrl":"10.1016/j.genrep.2025.102378","url":null,"abstract":"<div><div>Copy number variation in the <em>SMN1</em> gene is the main cause of Spinal Muscular Atrophy (SMA). We assessed the carrier frequency of SMA, which is the second most common genetic disease, in the Iranian population. This paper demonstrates the largest population including unrelated subjects and also provides an evaluation with variant analysis of <em>SMN1</em> in <em>cis</em>. To acquire inclusive molecular data about the carrier frequency of SMA and the frequency of <em>SMN1</em> polymorphisms g.27134T&gt;G (c.*3+80T&gt;G) among Iranian population, we analyzed data from 2157 individuals referred to the Pars-Genome and Genome-Nilou laboratories for SMA carrier detection between 2018 and 2024. A total of 2003 unrelated non-consanguineous healthy individuals were selected from 2157 individuals underwent MLPA using kit P460 or P021. We also assessed available whole exome sequencing (WES) data of another cohort of patients for the presence of the c.*3+80T&gt;G variant in the <em>SMN1</em>. The results indicated that 3.5 % (<em>n</em> = 70) were carriers of the disease, possessing only one copy of the <em>SMN1</em> gene. Totally, 89 % (<em>n</em> = 1783) of all participants exhibited two copies of <em>SMN1</em>. Among 526 cases underwent assessment by P460 kit and 2211 cases underwent WES, c.*3+80T&gt;G variant was detected in 28 (1 %) cases. This data can be used in the genetic counseling, carrier screening, and prenatal diagnosis of SMA in Iran.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"41 ","pages":"Article 102378"},"PeriodicalIF":0.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145462419","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Investigation of NT-3 as a diagnostic indicator in beta thalassemia with emphasis on relationship with hemoglobin electrophoresis patterns","authors":"Duaa K. Mohammed ,&nbsp;Layla O. Farhan","doi":"10.1016/j.genrep.2025.102313","DOIUrl":"10.1016/j.genrep.2025.102313","url":null,"abstract":"<div><div>Beta-thalassemia (β-TH) is a hereditary hemoglobinopathy that presents in various clinical forms, including major and intermedia. Emerging evidence suggests that neurotrophin-3 (NT-3), which is a key neurotrophic factor, may play a role in hematological and systemic responses to chronic anemia. This study quantified serum neurotrophin-3 (NT-3) levels in 120 subjects: 55 with (β-TH) major, 25 with β-TH intermedia, and 40 healthy control, using enzyme-linked immunosorbent assay (ELISA). NT-3 levels were significantly decreased in β-TH patients compared to controls (p &lt; 0.001), with a progressive decline from controls to intermedia and major groups. The lower NT-3 levels in the intermedia group are attributed to irregular blood transfusions and inconsistent treatment adherence. Multivariate regression revealed no significant correlation between NT-3 and hemoglobin A2 or fetal hemoglobin. The receiver operating characteristic (ROC) curve analysis demonstrated a high diagnostic accuracy for NT-3 in distinguishing β-TH patients from controls (AUC = 0.998) with a cut-off value ≤1921.84 pg/mL. These findings highlight the potential role of NT-3 as a novel, non-invasive biomarker reflecting disease severity and hypoxia-related oxidative stress in β-TH.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"41 ","pages":"Article 102313"},"PeriodicalIF":0.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144757412","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrating machine learning with OMICs data for early detection in breast cancer","authors":"Jiaqi Mu ,&nbsp;Aquib Nazar ,&nbsp;Muhammad Asim Ali ,&nbsp;Athar Hussain","doi":"10.1016/j.genrep.2025.102325","DOIUrl":"10.1016/j.genrep.2025.102325","url":null,"abstract":"<div><div>Breast cancer is one of the most common cancers that significantly affects a large population of women, emphasizing its importance in early detection for effective treatments. The advancement in technologies, especially in machine learning and its integration with multi-omics data, such as genomics, transcriptomics, proteomics, metabolomics, and imaging, is not only revolutionizing the diagnosis and prognosis of breast cancer at its early stages but also providing a door for personalized treatment plans to improve patient outcomes. However, achieving truly personalized treatment requires integration of causal inference methods into machine learning frameworks, as correlational models alone may not ensure effective or safe decision-making. The current study revisits the progress made in this research area, providing a comprehensive insight into the challenges of breast cancer early detection, machine learning (ML) in cancer detection, ML-Omics integration, clinical applications, case studies, and future directions and innovations.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"41 ","pages":"Article 102325"},"PeriodicalIF":0.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144886620","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"MeX_Docker: An integrated application for transposon identification and annotation based on the Docker platform","authors":"P. Preeti ,&nbsp;Mihir Nakul ,&nbsp;Chhavi Dudeja ,&nbsp;Abhishek Singh ,&nbsp;Arushi Gupta ,&nbsp;Yuktika Malhotra ,&nbsp;Deepika Yadav ,&nbsp;Kamal Rawal","doi":"10.1016/j.genrep.2025.102364","DOIUrl":"10.1016/j.genrep.2025.102364","url":null,"abstract":"<div><div>Transposable elements (TEs) are mobile genetic elements that can disrupt genomic integrity, influencing gene regulation and contributing to various diseases, including cancer. The accurate identification and characterization of TEs in high-throughput sequencing data is essential for understanding their role in genomic instability and tumorigenesis. To streamline this process, we developed MeX_Docker, a pipeline that utilizes Docker containerization to overcome software dependency issues and ensure reproducibility across different computing environments. Docker provides a standardized, portable solution that allows researchers to deploy and run the pipeline seamlessly, eliminating common obstacles in bioinformatics workflows. MeX_Docker integrates widely-used tools such as FastQC, Fastp, SAMtools, TEfinder, and Ensembl Variant Effect Predictor (VEP) for efficient data preprocessing, alignment, TE calling, and annotation. The pipeline was applied to human paired end whole-genome sequencing cancer datasets (breast, lung, and colorectal cancers), successfully identifying reference and non-reference Alu and L1 elements. In a lung cancer sample, an in-frame insertion in the CATSPERD gene was detected, which was classified as benign polymorphism. These findings highlight the use of MeX_Docker as an efficient tool for studying the impact of transposable elements on genomic instability and their potential role in cancer biology.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"41 ","pages":"Article 102364"},"PeriodicalIF":0.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145412788","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Survey of long non-coding RNA HOTTIP expression level in endometriosis","authors":"Parisa Vesal ,&nbsp;Amirhossein Rezvani Rezvandeh ,&nbsp;Namdar Razmavar ,&nbsp;Zivar Salehi ,&nbsp;Farhad Mashayekhi ,&nbsp;Kiana Sojoudi ,&nbsp;Ziba Zahiri ,&nbsp;Zakieh Siahpoosh","doi":"10.1016/j.genrep.2025.102338","DOIUrl":"10.1016/j.genrep.2025.102338","url":null,"abstract":"<div><h3>Background</h3><div>Recent researches have highlighted the promising potential of long non-coding RNA (lncRNAs) as an important regulator in endometriosis. Accumulating shreds of evidence has shown an important role of HOTTIP (HOXA transcript at the distal tip) in cell proliferation, differentiation, and migration. The function of HOTTIP in relation to endometriosis is still not well understood.</div></div><div><h3>Materials and methods</h3><div>The goal of this research was to examine the expression profile of HOTTIP and HOXA genes in 70 matched eutopic endometrium (EU) and ectopic endometrium (EC) samples from women with endometriosis, with 85 normal endometrium control samples (C) from healthy women. Quantitative real-time PCR (qRT-PCR) assay was performed to measure the level of gene expression. Cell viability was assessed using the CCK-8 assay. Two endometriotic cell lines were transfected with siRNA against HOTTIP (si-HOTTIP) and then used to monitor the effect of HOTTIP on the expression of HOXA13. Bioinformatic tools and the Cytoscape platform were utilized to perform network analysis and gene enrichment analysis.</div></div><div><h3>Results</h3><div>Results indicated that the expression of HOXA13 and HOTTIP was elevated in EC and EU samples in comparison to the C group (<em>p</em> &lt; 0.05). However, HOXA9, HOXA10, and HOXA11 showed decreased expression in EC samples compared to their levels in the C and EU samples. The expression levels of HOTTIP RNA showed a positive correlation with HOXA13 in patients with endometriosis. qRT-PCR data exhibited that si-HOTTIP triggered the reduction of both HOTTIP and HOXA13 expression levels and cell viability, and bioinformatics analysis in the Cytoscape platform helped us to make our laboratory results more reliable. In conclusion, the dysregulation of <em>HOXA</em> genes by HOTTIP lncRNA, characterized by the upregulation of <em>HOXA13</em> and the downregulation of <em>HOXA9</em>, <em>HOXA10</em> and <em>HOXA11</em>, suggests its significant role in the development of endometriosis and its potential as a therapeutic target.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"41 ","pages":"Article 102338"},"PeriodicalIF":0.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145060422","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}