Gene Reports最新文献

{"title":"HAVCR1 in cancer: A systematic review of its dual-faceted role as a biomarker and therapeutic target","authors":"Amirali Soltaninegar ,&nbsp;Fatemeh Sadat Jalilzadeh Ghahi ,&nbsp;Sepideh Hosseini ,&nbsp;Najaf Allahyari Fard","doi":"10.1016/j.genrep.2025.102178","DOIUrl":"10.1016/j.genrep.2025.102178","url":null,"abstract":"<div><div>Hepatitis A virus cellular receptor 1 (HAVCR1), also known as KIM-1 in kidney diseases and TIM-1 or CD365 in immunology, is a class 1 integral membrane glycoprotein member that plays a pivotal role in cancer progression, diagnosis, and potential treatment. This review study aims to explore the various aspects of the HAVCR1 protein, focusing on its role as a potential biomarker and therapeutic target in different types of cancers and analyze the correlation of HAVCR1 with prognosis, underlying molecular mechanisms, and its clinical potential in cancer diagnosis and treatment. In cancers such as RCC, ESCA, LIHC, PAAD, LUAD, and OV, HAVCR1 is associated with poor prognosis, whereas in others like COAD, RB, SKCM, and BLCA, it correlates with improved outcomes. HAVCR1 contributes to cancer progression through the MAPK/ERK and PI3K/AKT pathways, which regulate immune suppression, cell growth, survival, migration, and angiogenesis. Its expression level, shedding, and localization significantly influence its role in cancer in the plasma or internal membranes. The release of the HAVCR1 ectodomain during shedding and its detectability in urine, blood, and cerebrospinal fluid highlight its potential as a biomarker for diagnosing specific cancers. Furthermore, HAVCR1 represents a promising target for therapeutic interventions in oncology.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"39 ","pages":"Article 102178"},"PeriodicalIF":1.0,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143489001","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":"Expression of recombinant canine perilipin3 (PLIN3) and its assessment for immunoreactivity","authors":"Amrita Behera ,&nbsp;Ghanshyam Sahu ,&nbsp;Vineet Kumar Pandey ,&nbsp;Franco PS ,&nbsp;Pawan Kumar ,&nbsp;Mukesh Kumar ,&nbsp;Mohini Saini ,&nbsp;Karuna Irungbam","doi":"10.1016/j.genrep.2025.102157","DOIUrl":"10.1016/j.genrep.2025.102157","url":null,"abstract":"<div><div>Perilipins are the lipid droplet associated proteins (LDAPs) involved in the biogenesis and stabilization of lipid droplets. LDAPs contribute significantly to the pathogenesis of several diseases stemming from dysregulated lipid metabolism including cancers. Several studies indicate lipid droplet (LD) accumulation in cancer cells, emphasizing the critical importance of comprehending the role of perilipins in cancers. This study seeks to generate hyperimmune sera directed against canine perilipin3 (PLIN3), with the aim of investigating the expression of perilipin3 in canine mammary tumors (CMT). The limited availability of canine specific commercial perilipin antibodies substantiate the necessity of developing canine specific antibodies to better understand the role of perilipins in CMT pathogenesis. A fragment of the canine perilipin3 gene was amplified effectively from total RNA extracted from canine mammary tumor samples and it was cloned and expressed as a recombinant protein in pET32a+ prokaryotic system. The recombinant canine PLIN3 protein was purified using Ni- NTA (Nickel-nitroacetic acid) affinity chromatography and used to generate hyperimmune sera in chickens. The generated antisera showed strong reactivity to the recombinant canine PLIN3 protein in dot blot assays. Immunohistochemistry analysis revealed specific immunoreactivity to PLIN3 in CMT tissue samples, with elevated expression levels compared to control tissues. These data indicate that PLIN3 may be differentially expressed in canine mammary tumors, highlighting its potential role in tumor progression. The study provides a valuable tool for advancing the investigation of lipid droplet-associated proteins in canine cancers, particularly CMT, and offers insights into lipid metabolism as a possible therapeutic target in veterinary oncology.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"39 ","pages":"Article 102157"},"PeriodicalIF":1.0,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143563256","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":"Diagnosis of diabetes and hypertension: A performance comparison between transcriptome data and clinical data","authors":"Pratheeba Jeyananthan,&nbsp;T.A.P. Dharmasena,&nbsp;W.D.A. Nuwansiri","doi":"10.1016/j.genrep.2025.102176","DOIUrl":"10.1016/j.genrep.2025.102176","url":null,"abstract":"<div><div>Diabetes and hypertension are two related diseases common among most of the people all over the word. The impact of these diseases can elevate the risk of developing additional health issues, including cardiovascular disease, kidney disease, and other related conditions. Numerous research initiatives are underway to uncover the underlying mechanisms of these diseases. This study compares the roles of clinical data and transcriptome data in the diagnosis of patients with diabetes or hypertension. This study utilizes two distinct datasets, each containing unique clinical features along with a third dataset that includes transcriptome characteristics, all analyzed through machine learning algorithms. In both diseases, there is a marked difference in the accuracies of the models based on various clinical features. This highlights the importance of selecting appropriate clinical features to develop an optimal diagnostic model for these conditions. In comparing the best clinical model with the transcriptome model for diagnosing diabetic patients, it has been found that the transcriptome data yields superior results. Conversely, for diagnosing hypertension patients, the clinical data proves to be more effective. Hence, identifying the appropriate set of clinical features, clinical data could become more effective for diagnosing both diabetes and hypertension.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"39 ","pages":"Article 102176"},"PeriodicalIF":1.0,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143480347","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":"Genome-wide characterization of DREB transcription factors in Medicago truncatula: Insights into their roles in development and abiotic stress response","authors":"Loua Haddoudi ,&nbsp;Mariem Ayadi ,&nbsp;Sabrine Hdira ,&nbsp;Mohsen Hanana ,&nbsp;Irene Romero ,&nbsp;Hatem Ben Jouira ,&nbsp;Naceur Djébali ,&nbsp;Ludidi Ndiko ,&nbsp;Maria Teresa Sanchez Ballesta ,&nbsp;Chedly Abdelly ,&nbsp;Mounawer Badri","doi":"10.1016/j.genrep.2025.102170","DOIUrl":"10.1016/j.genrep.2025.102170","url":null,"abstract":"<div><div>Dehydration-responsive-element binding (<em>DREB</em>) proteins play a crucial role in drought, salt, and environmental stress tolerance. In this study, we identified and annotated fifty-four <em>DREB</em> genes from the <em>Medicago truncatula</em> genome. These genes were analyzed at the molecular level, focusing on gene classification, genomic organization, phylogeny, synteny, structural features, and expression profiles. Phylogenetic analysis revealed that <em>MtDREB</em> proteins are categorized into six subgroups (A1–A6), with highly conserved motif compositions among them. Expression profiling showed that <em>MtDREB</em> genes are differentially expressed in various plant organs and under abiotic stresses (cold, salinity, and dehydration), with 30 % exhibiting high expression during flowering and development. Data from RNA-seq and microarrays demonstrated that 76 % of <em>MtDREB</em> genes are differentially expressed under at least one stress condition, indicating their involvement in various signaling pathways activated by abiotic stresses. Notably, <em>MtDREB05</em>, primarily induced under osmotic stress, appears to be a promising candidate for improving abiotic stress tolerance. These findings will enhance our understanding of the <em>DREB</em> family and aid in functional validation of <em>DREB</em>genes in <em>M. truncatula</em> and related forage species.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"39 ","pages":"Article 102170"},"PeriodicalIF":1.0,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143510735","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":"Somatic mutation profiles in non-tobacco smoking and non-alcohol drinking South African female esophageal squamous cell carcinoma patients of African ancestry","authors":"Lucien Ferndale ,&nbsp;Wenlong Carl Chen ,&nbsp;Phelelani Thokozani Mpangase ,&nbsp;Jean-Tristan Brandenburg ,&nbsp;Lamantha Nerija Ngundu ,&nbsp;Mishalan Moodley ,&nbsp;Reubina Wadee ,&nbsp;Colleen A. Wright ,&nbsp;M. Iqbal Parker ,&nbsp;Pascale Willem ,&nbsp;Colleen Aldous ,&nbsp;Christopher G. Mathew","doi":"10.1016/j.genrep.2025.102174","DOIUrl":"10.1016/j.genrep.2025.102174","url":null,"abstract":"<div><h3>Background</h3><div>Esophageal squamous cell carcinoma (ESCC) accounts for 85 % of the global esophageal cancer incidence, with a high disease burden in Eastern and Southern Africa. The etiology of ESCC is complex, with several factors such as tobacco smoking and alcohol consumption contributing to disease risk. Somatic mutations involved in the development of ESCC have been described but are under-studied in Africa. Our study reports the first whole-exome sequencing analysis of ESCC in a South African population who were not exposed to tobacco or alcohol.</div></div><div><h3>Methods</h3><div>Fifteen female patients of African ancestry with ESCC who had never smoked or consumed alcohol were enrolled. Demographic and epidemiological data were obtained. DNA was extracted from matched blood and tumor tissue and subjected to whole exome sequencing. Bioinformatic analysis was used to identify somatic mutations, somatic copy number variations, and identify mutation signatures.</div></div><div><h3>Results</h3><div>The genes <em>TP53</em>, <em>MUC2</em>, <em>KMT2D</em>, and <em>KMT2C</em> were the most commonly mutated among genes previously reported to be mutated in ESCC tumors from other populations. The most common copy number variations detected were amplifications of chromosome 11q13, containing the <em>CCND1</em> gene; 3q26, containing <em>PIK3CA</em> and <em>SOX2</em>; and 8q24, containing <em>MYC</em>. The most common mutation signature detected in the tumors was SBS5, associated with aging.</div></div><div><h3>Conclusions</h3><div>Despite the lack of two major risk factors for ESCC in our patients, DNA sequencing detected somatic mutation profiles comparable to those found in patients from other populations, suggesting similar molecular pathways. This may stimulate their access to new therapeutic approaches developed in high-income countries.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"39 ","pages":"Article 102174"},"PeriodicalIF":1.0,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143510627","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic diversity analysis of wild population based on SNP developed from transcriptome sequencing of spot-fin porcupine fish (Diodon hystrix)","authors":"Jun Ma ,&nbsp;Yanfeng Yue ,&nbsp;Yuanhao Ren ,&nbsp;Liu Cao ,&nbsp;Haishan Wang ,&nbsp;Yan Chen ,&nbsp;Wenqi Zhuo ,&nbsp;Zhou Wang ,&nbsp;Tingting Dang ,&nbsp;Xueyi Wang ,&nbsp;Pan Chen ,&nbsp;Xingrong Hou ,&nbsp;Hai Huang ,&nbsp;Keji Jiang ,&nbsp;Tingting Lin","doi":"10.1016/j.genrep.2025.102171","DOIUrl":"10.1016/j.genrep.2025.102171","url":null,"abstract":"<div><div><em>Diodon hystrix</em> is widely distributed in tropical and subtropical coastal waters. Owing to its delicious taste, the annual catch of this fish in the South China Sea has been on the rise. It is urgent to assess the population status of <em>D. hystrix</em>. Molecular markers are often used to evaluate the population status of the important and rare fishery resource, however, there was still no suitable markers of <em>D. hystrix</em> with overfishing in recent years. This study totally obtained 7.2 Mb clean reads with 94.92 % of Q20 bases and 4179 variants of 2276 unigenes by Illumina sequencing platform. Additionally, 64 amplifiable variants of 36 unigenes were obtained by PCR amplification, and 25 available SNPs showing polymorphism were confirmed from these amplifiable variants. By assessing the index of association, we ultimately identified 14 SNPs after removing 10 SNPs with linkage disequilibrium and 1 SNP with Hardy-Weinberg disequilibrium. Using these 14 SNPs, we can evaluate the wild population of <em>D. hystrix</em> as a sexually reproducing population and speculate that this population was relatively stable (HWE. <em>p</em> = 0.525) with moderate genetic diversity (PIC = 0.328). In conclusion, transcriptomic sequencing can quickly obtain the SNPs as molecular markers which can be used for population genetic diversity. It provides necessary help for the conservation biology and resource evaluation of <em>D. hystrix</em>.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"39 ","pages":"Article 102171"},"PeriodicalIF":1.0,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143464533","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":"miRNAs involved in the TGFB signaling as possible markers of steroid-resistant nephrotic syndrome in children","authors":"Ahmedz Widiasta ,&nbsp;Yunia Sribudiani ,&nbsp;Husna Nugrahapraja ,&nbsp;Dedi Rachmadi","doi":"10.1016/j.genrep.2025.102173","DOIUrl":"10.1016/j.genrep.2025.102173","url":null,"abstract":"<div><h3>Introduction</h3><div>Steroid-resistant nephrotic syndrome (SRNS) and subsequent chronic kidney disease (CKD) cause morbidity and mortality in children. Transforming growth factor-β (TGFB) participates in the development of focal segmental glomerulosclerosis (FSGS), the most common histopathological form of SRNS. This study demonstrated a correlation between the levels of blood TGFB and its related microRNAs (miRNAs) in children with SRNS.</div></div><div><h3>Materials and methods</h3><div>This was an open-prospective cohort study conducted at Hasan Sadikin General Hospital, Bandung, Indonesia. Of 188 children with nephrotic syndrome (NS), 24 (aged 1–18 years) were enrolled, only those who had never received steroids. Blood samples were collected before treatment with steroids or other immunosuppressants. Steroid resistance was diagnosed after four weeks of follow-up. SRNS was defined as persistent proteinuria after treatment with prednisolone or methylprednisolone. Blood levels of miRNAs of interest and the expression were measured using qRT-PCR (TaqMan miRNA Assay).</div></div><div><h3>Results</h3><div>There was a significant increase in miR-433 and <em>TGFB2</em> expression in SRNS (p = 0.030 and p = 0.001, respectively). Meanwhile, there were no significant correlations between miR-21, miR-29, miR-200, miR-205, and miR-433 and <em>TGFB1</em> and <em>TGFB2</em>.</div></div><div><h3>Conclusions</h3><div>MiR-433 is potentially involved in SRNS, <em>TGFB2</em> baseline is a promising biomarker for predicting steroid resistance in SRNS, and antimiR-433 is promising as the next proposed study to discover novel SRNS therapies.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"39 ","pages":"Article 102173"},"PeriodicalIF":1.0,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143529445","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":"Upregulation of TNF-α and IL-6 in palindromic rheumatism: A biomarker link to rheumatoid arthritis progression and therapeutic implications","authors":"Kamran Javidi-Aghdam ,&nbsp;Mostafa Akbarzadeh-Khiavi ,&nbsp;Sepideh Parvizpour ,&nbsp;Shima Rahmani ,&nbsp;Faranak Sheikhmonazzah ,&nbsp;Ata Khodaparast ,&nbsp;Aida Malek Mahdavi ,&nbsp;Azam Safary ,&nbsp;Alireza Khabbazi","doi":"10.1016/j.genrep.2025.102175","DOIUrl":"10.1016/j.genrep.2025.102175","url":null,"abstract":"<div><h3>Background</h3><div>Palindromic rheumatism (PR) is a rare autoimmune disease characterized by episodic joint inflammation, often progressing to rheumatoid arthritis (RA). However, the molecular mechanisms driving this transition remain unclear. This study aimed to investigate the roles of tumor necrosis factor-alpha (TNF-α) and interleukin-6 (IL-6) in the PR progression toward RA by examining their serum levels and gene expression in patients with PR and RA, compared to healthy controls (HCs).</div></div><div><h3>Methods</h3><div>This cross-sectional study was conducted on peripheral blood mononuclear cells (PBMCs) obtained from patients with PR (<em>n</em> = 17), RA (<em>n</em> = 35), and age-sex-matched HCs (<em>n</em> = 38). TNF-α and IL-6 serum levels were quantified using enzyme-linked immunosorbent assay, and mRNA levels were analyzed through real-time PCR. Classification and regression tree (CART) models were employed to determine the relevance of these cytokines in RA.</div></div><div><h3>Results</h3><div>TNF-α serum levels in PR, RA, and HCs were measured at 10.5 ± 1.3, 8.9 ± 1.1, and 6.3 ± 0.8 pg/mL, respectively. IL-6 levels were 6.84 ± 2.6, 6.65 ± 2.5, and 1.10 ± 0.5 pg/mL for the same groups. Both cytokines were significantly elevated in PR and RA patients compared to HCs (<em>p</em> &lt; 0.05). Gene expression analysis confirmed the upregulation of TNF-α and IL-6 in both the PR and RA groups.</div></div><div><h3>Conclusions</h3><div>These findings suggest that the upregulation of TNF-α and IL-6 may be key factors driving the progression of PR to RA. Targeting these cytokines could represent a novel therapeutic strategy to prevent disease advancement.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"39 ","pages":"Article 102175"},"PeriodicalIF":1.0,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143445940","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":"A decline in taxonomic diversity of milk microbiome is linked to clinical mastitis and physiological states of cow","authors":"I.L. Maslennikova ,&nbsp;Y.I. Nechaeva ,&nbsp;L.A. Ilina ,&nbsp;G.Y. Laptev ,&nbsp;E.S. Ponomareva ,&nbsp;I.N. Zhdanova ,&nbsp;M.V. Kuznetsova","doi":"10.1016/j.genrep.2025.102169","DOIUrl":"10.1016/j.genrep.2025.102169","url":null,"abstract":"<div><div>Using 16S rRNA gene amplicon sequencing, longitudinal shifts in the microbial composition during dry-off, calving, the early, middle and late lactation state of healthy and mastitis cows were examined. Compared to healthy cow milk, fewer bacteria taxa were found for mastitis cow milk. Throughout the dry-off, calving, the early, middle, and late lactation phases, the taxonomic diversity of bacteria in both groups were declined. At dry-off, post-calving, early, middle, and late lactation periods, the percentage of bacteria species that were shared by milk samples of healthy and mastitis cows was 71.1, 65.8, 80.3, 52.6, and 44.3 %, respectively. From dry-off to late lactation periods, the core unique bacteria species of mastitis cow milk rose from 13 to 34 taxa, while the core unique species for healthy cow milk declined from 31 to 20 taxa. In the milk samples of healthy/mastitis cows the majority of microorganisms were represented by the phylum Proteobacteria as 52.9/9.1 %; 38.5/95.4 %; 24.0/19.2 %; 92.9/43.5 %; 46.8/57.1 %; the phylum Firmicutes as 16.5/50.7 %; 35.9/1.4 %; 28.6/11.3 %; 3.1/11.4 %; 7.0/2.7 % at dry-off, post-calving, early, middle and late lactation period, respectively. Taxonomic profile of 40 most abundant bacterial genera of milk samples were comparable in the both group of healthy and mastitis animals at all physiological states. There are prevalence of positive/negative correlation between the number of microorganisms of clinically important species in milk of healthy/mastitis cows, respectively, from dry-off to the late lactation periods.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"39 ","pages":"Article 102169"},"PeriodicalIF":1.0,"publicationDate":"2025-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143446051","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":"Development of a single-step SYBR green-based real-time PCR assay for detection and quantification of lumpy skin disease virus in cattle","authors":"Sanganagouda K. ,&nbsp;Sabha Kounin ,&nbsp;K. Nagaraja ,&nbsp;Basavaraj Sajjanar ,&nbsp;Amitha Rena Gomes ,&nbsp;B.H. Pavithra ,&nbsp;Shivaraj Murag ,&nbsp;B.R. Sumathi ,&nbsp;B.P. Shankar ,&nbsp;B.P. Shivashankar ,&nbsp;H.C. Indresh ,&nbsp;K.R. Anjan Kumar ,&nbsp;Raveendra Hegade ,&nbsp;D. Rathnamma","doi":"10.1016/j.genrep.2025.102172","DOIUrl":"10.1016/j.genrep.2025.102172","url":null,"abstract":"<div><h3>Background</h3><div>Lumpy skin disease (LSD) is a vector-borne viral disease of cattle and water buffalos. The disease causes substantial economic losses in cattle across the Indian subcontinent. Effective diagnosis and control are critical for managing this disease. The primary aim of the current study is to develop a single-step SYBR green-based real-time PCR assay for the detection and quantification of Lumpy Skin Disease Virus (LSDV) in clinical samples.</div></div><div><h3>Methods</h3><div>A total of 160 samples were collected and subsequently viral propagation was carried out in Madin Darby Bovine Kidney (MDBK) cell lines. Initial viral identification was performed via conventional PCR employing newly synthesized primers, which targeted both the envelope protein (P32) and the G protein-coupled chemokine receptor (GPCR) gene. For the quantification of LSDV within infected nodular tissues, two distinct real-time PCR assays (Assay-I and Assay-II) were implemented. These assays utilized standard curves generated from specific GPCR amplicons of 610 bp and 786 bp, enabling precise absolute quantification. This methodological enhancement greatly improves the accuracy of LSDV prevalence assessment and supports more effective disease management strategies.</div></div><div><h3>Results</h3><div>LSDV viral loads in infected nodular tissues were measured using Real-Time PCR Assay-I and Assay-II, with average log mean values of 7.36 ± 0.18 and 7.27 ± 0.17 (<em>n</em> = 37), respectively. The lower detection limits were 284 and 153 copies per microliter (μl), with corresponding threshold cycle values of 25.75 ± 0.27 and 32.10 ± 0.64. Negative controls showed Ct values of 33.01 ± 0.37 and 33.39 ± 1.37 (<em>n</em> = 6), respectively. Additionally, LSDV was isolated in MDBK cell lines, demonstrating that primary cells can be effectively replaced with MDBK cell lines for viral isolation.</div></div><div><h3>Conclusions</h3><div>The single-step SYBR Green-based real-time PCR assay targeting the GPCR gene proved to be highly sensitive, specific, and reproducible for the detection and quantification of LSDV, offering a robust tool for monitoring and managing LSD.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"39 ","pages":"Article 102172"},"PeriodicalIF":1.0,"publicationDate":"2025-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143464718","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}