Gene Reports最新文献

{"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}

{"title":"Biocomputational identification of microRNAs from indigenous Gaddi dog genome","authors":"Kanwaljit Rana ,&nbsp;S.S. Randhawa ,&nbsp;J. Mohindroo ,&nbsp;R.S. Sethi ,&nbsp;C.S. Mukhopadhyay","doi":"10.1016/j.genrep.2025.102167","DOIUrl":"10.1016/j.genrep.2025.102167","url":null,"abstract":"<div><div>MicroRNAs (miRNAs) are non-coding RNAs that regulate post-transcriptional gene expression in eukaryotes and play a key role in a variety of biological and metabolic functions. Through target-specific cleavage of mRNAs, miRNAs affect the activity of mRNAs important for diverse cellular functions such as signal transduction, cell proliferation, differentiation, and disease control, among others. Bioinformatics algorithms for predicting putative miRNAs from genomic sequence data using typical properties of previously found miRNAs like secondary structures, GC content, and minimum free energy index (MFEI), among others, enable cost-effective identification of putative miRNAs. The goal of this study is to uncover putative miRNAs utilizing a comparative biocomputational technique from an indigenous dog breed, the Gaddi, in which miRNAs have yet to be discovered. Individually, the five contig level whole-genome assemblies of Gaddi dogs in our lab (Bio Project: PRJNA843534) were blasted against miRbase's known non-redundant miRNAs dataset of mammalian origin. Minimum E-value, maximum percent identity, and pre-miRNA sequences were filtered out of the results. Furthermore, protein-coding sequences were removed from these pre-miRNA sequences using BLASTX, and the remaining sequences were screened for secondary structure, GC content, and MFEI value. In total, 22 putative miRNAs were detected in individual five samples, ranging from 03 to 06 in number, which were then compared to previously reported mature miRNAs from <em>Canis lupus familiaris</em> and 39 other mammalian species and novel miRNAs were identified. In the genome of the local Gaddi dog, miRNAs have been computationally predicted for the first time. Six miRNAs were selected based on the miRNA with the lowest E value, and they were then validated using real-time PCR, SYBR green chemistry, and U6 as an internal control. Three of the six miRNAs selected (Bta-mir 1277, Mmu-mir-466 m-5p, and Mmu-mir-669f) show no discernible expression in Gaddi dog PBMCs, according to the results of quantitative PCR (qPCR). This study is the first to use whole genome sequencing data to estimate native Gaddi dog miRNAs, followed by empirical validation. These results may serve as a springboard for further research elucidating the regulatory functions of miRNAs in native dog populations.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"39 ","pages":"Article 102167"},"PeriodicalIF":1.0,"publicationDate":"2025-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143421460","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":"Discovery of a novel missense mutation in the RIMS1 gene potentially enhances the severity of retinitis pigmentosa (RP) caused by RP1 mutation in humans","authors":"José M. Lazaro-Guevara ,&nbsp;Karen M. Garrido-Lopez ,&nbsp;Laura Sofía Reyna Soberanis ,&nbsp;Maria A. Sandoval-Vargas ,&nbsp;Bryan-Josué Flores-Robles ,&nbsp;José Luis Téllez-Arreola","doi":"10.1016/j.genrep.2025.102156","DOIUrl":"10.1016/j.genrep.2025.102156","url":null,"abstract":"<div><div>Retinitis pigmentosa (RP) is a genetically diverse disorder characterized by the progressive degeneration of photoreceptors, ultimately leading to vision impairment and potential blindness. Understanding the disease progression and developing effective therapies is challenging due to its complex genetic landscape. This study unveils a di-genic complexity in RP involving a novel missense mutation in the RIMS1 and RP1 genes, traditionally associated with Cone-Rod Dystrophy. This mutation potentially enhances the RP phenotype, particularly in cases caused by RP1 mutations. We conducted a comprehensive genetic analysis on a family with a severe form of RP, focusing on the combined effects of RIMS1 and RP1. Using a targeted gene panel of 322 inherited retinal dystrophy (IRD) genes, we discovered a significant interaction between the RIMS1 variant and RP1 mutation within the cohort. Interestingly, patients with identical mutations exhibited substantial disease severity and progression differences. This discrepancy was particularly apparent in Patient E_1, who experienced rapid vision decline, emphasizing the impact of the mutation when combined with RP1. Biological network analysis shed light on the intricate genetic interplay, indicating a complex mechanism of disease modulation. Our findings contribute to a more nuanced understanding of RP's genetic heterogeneity. The RIMS1 variant may serve as a modifier of the disease phenotype. This discovery expands our comprehension of the genetic factors influencing RP and underscores the importance of considering digenic interactions in future research and therapy development for retinal dystrophies.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"39 ","pages":"Article 102156"},"PeriodicalIF":1.0,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143436707","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":"Genetic analysis of Vibrio alginolyticus challenged by Scutellaria baicalensis reveals the mechanism of virulence genes","authors":"Genhuang Xu ,&nbsp;Xiaojin Xu ,&nbsp;Rui Lai ,&nbsp;Zhixing Zhang ,&nbsp;Yongqi Lai ,&nbsp;Kejin Dai ,&nbsp;Xin Yi ,&nbsp;Minglan Guo","doi":"10.1016/j.genrep.2025.102159","DOIUrl":"10.1016/j.genrep.2025.102159","url":null,"abstract":"<div><div><em>Scutellaria baicalensis</em> can be used to treat bacterial infections caused by <em>Vibrio alginolyticus</em>, with marked inhibition at 1200 μg/mL. <em>S. baicalensis</em> significantly impacts the motility and biofilm formation capabilities of <em>V. alginolyticus</em>. <em>V. alginolyticus</em> exhibits a discerning sensitivity profile to antibiotics, demonstrating resistance against beta-lactam antibiotics such as penicillins and oxacillins, while showing susceptibility to a broader spectrum of antibiotic classes, including tetracyclines, aminoglycosides, and others. Under <em>S. baicalensis</em> stress, flagellar biogenesis genes (<em>fliP</em>, <em>fliQ</em>, <em>fliR</em>) exhibit concentration-dependent expression changes, declining at higher concentrations. The expression profiles of <em>rpoD</em> and <em>rpoS</em> initially show an upregulation but subsequently decline under higher stress levels. Conversely, <em>glpD</em> presents a continuously declining expression pattern regardless of the intensity of the stress condition. After treating <em>V. alginolyticus</em> with 8 mg/mL of <em>S. baicalensis</em> for 2 h and 4 h, transcriptome analysis identified 2350 differentially expressed genes (DEGs). These DEGs are enriched in 29 distinct secondary Gene Ontology (GO) categories, among which metabolic processes are the most significantly represented. KEGG analysis indicated that amino acid metabolism pathways and two-component system pathways play important roles. Chemotaxis pathways related to bacterial movement and response to external stimuli have also been notably affected<em>.</em></div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"39 ","pages":"Article 102159"},"PeriodicalIF":1.0,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143446050","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 mechanism of angiogenesis in colorectal cancer","authors":"P.P. Raphela-Choma,&nbsp;M.S. Choene,&nbsp;L.R. Motadi","doi":"10.1016/j.genrep.2025.102163","DOIUrl":"10.1016/j.genrep.2025.102163","url":null,"abstract":"<div><div>Colorectal cancer (CRC) is one of the healthcare burdens in South Africa with a high probability of cancer relapse. Colorectal cancer has been demonstrated to be caused by oncogene activation and deactivation of tumor suppressor genes in the system. Human diseases such as cancer have been reported to be associated with vascular dysfunction which contributes to malignancy, tumor evasion, and metastasis. Vascular dysfunction in most tumors has led to treatment resistance and cancer relapses. The expression of vascular endothelial growth factor is mediated by HIF-1 during oxidative stress, hypoxic conditions, or mediated by epidermal growth factor receptor as an oncogene in the development of new abnormal blood vessels in tumors, as well as metastasis in CRC. Angiogenic targeted therapies that are developed thus far against colorectal cancer have been shown to improve the survival rate of patients, nonetheless, poor prognosis is still a major issue for metastatic CRC. Angiogenesis is a critical and promising target for the inhibition of tumor growth, progression, and metastatic CRC therapies. In this review, we report some of the molecular mechanisms of angiogenesis in colorectal cancer. The roles of epidermal growth factor receptor (EGFR), Hypoxia-induced factor-1 (HIF-1), and miRNAs as factors that contribute to the induction of VEGF activity to elicit tumor angiogenic pathway in colorectal cancer. Despite the limitations of CRC therapies, several studies have shown that the combination of conventional therapies and pro-angiogenic agents has slightly improved the survival rate of patients. Moreover, studies have shown several ways to target the pro-angiogenic factors in combating tumor angiogenesis and more research is still required to understand the molecular mechanism and pathogenesis of CRC.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"39 ","pages":"Article 102163"},"PeriodicalIF":1.0,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143436706","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}