Gene Reports最新文献

{"title":"Genetic interactions and co-operating effects of non-HSA21 genes on the phenotypic variability in Down syndrome","authors":"Bani Bandana Ganguly,&nbsp;Nitin N. Kadam","doi":"10.1016/j.genrep.2024.102106","DOIUrl":"10.1016/j.genrep.2024.102106","url":null,"abstract":"<div><div>Trisomy 21 (T21) defines the complex characteristics of Down syndrome (DS). However, enormous variation has been documented in the multifarious features of the syndrome, regardless of full or partial T21 among individuals with DS. Individual variability exists in degree of manifestation for each subset of the DS-features, especially intellectual disability, characteristic facial/physical dysmorphology, a hypocellular brain, and Alzheimer's disease (AD), though constitutively present in all DS. A small segment in the chromosome 21 (HSA21) was designated as the Down Syndrome Critical Region (DSCR) responsible for defining DS characteristics; however, DSCR dogma has been challenged due to variability in penetrance and expressivity of DS-phenotypes. Characterization of genes identified in human DS and recombinant mouse models of DS have postulated that DS-features are not the sole contribution of DSCR genes but the possibility of interaction among non-contiguous genes might exist. Several studies suggested that DSCR region is necessary for some of the DS-phenotypes but not sufficient to produce most of the DS-specific features such as congenital heart defect (DS-CHD) and leukemia. Further, allelic variation, epigenetic and environmental impact and small effects of modifier genes might result in perturbation of genetic homeostasis in subjects with DS. Collectively, the solitary effect of a triplicated gene was demonstrated to be inconspicuous; however, its contribution to trisomic phenotypes was predicted likely in antagonistic or synergistic association with other specific genes. Nevertheless, gene-phenotype association has remained unanswered for complex expression of the DS-phenotypes at the backdrop of trisomic HSA21.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"38 ","pages":"Article 102106"},"PeriodicalIF":1.0,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143134909","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":"Corrigendum to “Upregulated long non-coding RNAs TMPO-AS1, DDX11-AS1, and POLE gene expression predict poor prognosis in head and neck squamous cell carcinoma (HNSCC)” [Gene Rep. Volume 36, September 2024/101942]","authors":"Mahnoosh Mokhtarinejad ,&nbsp;Maryam Pirhoushiaran ,&nbsp;Roozbeh Heidarzadehpilehrood ,&nbsp;Sara Hesami ,&nbsp;Farid Azmoudeh-Ardalan ,&nbsp;Abbas Shakoori Farahani","doi":"10.1016/j.genrep.2024.102095","DOIUrl":"10.1016/j.genrep.2024.102095","url":null,"abstract":"","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"37 ","pages":"Article 102095"},"PeriodicalIF":1.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143175070","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 uniqueness and phylogenetic study of Magnaporthe oryzae isolates from Bangladesh","authors":"Muhammad Mahmudul Hasan ,&nbsp;Md. Dheeman Tanvir Swakshar ,&nbsp;Atiqur Rahman ,&nbsp;M.A. Malek ,&nbsp;M.A.K. Azad ,&nbsp;Most. Maliha Parvin ,&nbsp;Md. Hasin Raiyan ,&nbsp;Ujjal Kumar Nath ,&nbsp;Md. Amirul Alam","doi":"10.1016/j.genrep.2024.102103","DOIUrl":"10.1016/j.genrep.2024.102103","url":null,"abstract":"<div><div>Rice blast, induced by the hemibiotrophic fungus <em>Magnaporthe oryzae</em>, poses a significant threat to global rice production, causing substantial yield losses and being particularly prevalent in Bangladesh. This study aimed to explore the mutational dynamics of the rice blast pathogen, influencing the development of disease epidemics, by conducting a phylogenetic analysis. To achieve this, 19 <em>M. oryzae</em> isolates were gathered from four districts in the Sylhet division of Bangladesh. All isolates underwent confirmation as <em>M. oryzae</em> through internal transcribed spacer (ITS) sequence analysis. The phylogenetic analysis revealed a consistent distribution of the 19 blast isolates into three clusters, highlighting substantial genetic variation among isolates from the same location and genetic similarities among isolates from diverse geographical origins. Notably, cluster-B comprised 18 noble blast isolates out of the total 19, suggesting a common origin for these isolates. In contrast, isolates from cluster A and cluster C, specifically W30216962_BN10_ITS5_F12, did not exhibit any noble blast isolates. This finding indicates that all the noble isolates in cluster B shared the same source or originated from the same ancestor. The insights gained from this study hold promise for shaping strategies to enhance disease management against rice blast. These strategies may involve resistance breeding, genetic studies, and a deeper understanding of host-pathogen interactions.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"38 ","pages":"Article 102103"},"PeriodicalIF":1.0,"publicationDate":"2024-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143134959","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":"Human papillomavirus as a potential etiological factor and biomarker in bladder carcinogenesis: A molecular epidemiological study","authors":"Mouna Aqerrout ,&nbsp;Abdelilah Laraqui ,&nbsp;Khalid Ennibi ,&nbsp;Ahmed Ameur ,&nbsp;Larbi Hamedoun ,&nbsp;Mohammed Alami ,&nbsp;Anouar El Ghazzaly ,&nbsp;Moulay Mustapha Ennaji","doi":"10.1016/j.genrep.2024.102104","DOIUrl":"10.1016/j.genrep.2024.102104","url":null,"abstract":"<div><div>Bladder cancer is a major public health concern, and the identification of novel biomarkers is crucial for improving its diagnosis and treatment. Human Papillomavirus (HPV) has been linked to various neoplasms, though its relevance to bladder cancer (BC) is hardly known. In this study, we aimed at evaluating the presence of HPV in bladder cancer tissues and determine its utility as a potential biomarker. Nested PCR, using consensus primers MY09/11, GP5+/6+ and reference plasmids targeting HPVs 16, 18, 33, 11, 6 and 31 were employed on 50 samples from patients with bladder carcinoma. Among the 50 bladder cancer patients analyzed, 23 (46 %) tested positive for HPV, while 27 (54 %) tested negative and significant association was identified between HPV infection and key clinical parameters including tumor stage (<em>P</em> = 0.031**), tumor grade (<em>P</em> = 0.007**) and muscle invasion (<em>P</em> = 0.046*). High-risk HPV genotypes, specifically type 16 was the most prevalent and was detected in 11 (47.8 %) of bladder cancer cases. Single HPV infection 18 (78.2 %) was more common than co-infection cases 5 (21.7 %), though no statistical significance was observed between infection type and patients' clinicopathological parameters. Our findings revealed a significant association between HPV infection and advanced tumor characteristics, particularly with higher tumor grade and pathological T-stage. High-risk HPV genotypes, notably types 16 and 18, were the most frequently observed, suggesting a potential role for high-risk HPV subtypes in bladder tumor progression. These findings underscore the possible contribution of HPV in bladder carcinogenesis and suggest that infection with the virus, particularly with high-risk strains, could serve as a valuable biomarker for early bladder cancer diagnosis and risk assessment. Targeting HPV in bladder cancer tissues may thus pave the way for HPV-based diagnostic and prognostic tools and tailored therapeutic approaches.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"38 ","pages":"Article 102104"},"PeriodicalIF":1.0,"publicationDate":"2024-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143134896","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":"Phylogenetic annotation and expression analysis of heat shock protein 70 genes in two Henosepilachna species","authors":"Yu-Xing Zhang ,&nbsp;Hai-Hui Liu ,&nbsp;Jia-Qing Yu ,&nbsp;Lin Jin ,&nbsp;Kai-Yun Fu ,&nbsp;Wen-Chao Guo ,&nbsp;Guo-Qing Li","doi":"10.1016/j.genrep.2024.102098","DOIUrl":"10.1016/j.genrep.2024.102098","url":null,"abstract":"<div><div>Two <em>Henosepilachna</em> beetles are notorious defoliators mainly attacking potatoes. In China, <em>H. vigintioctopunctata</em> is predominantly distributed in the southern region of the Yangtze River, while <em>H. vigintioctomaculata</em> is found in northern area. In the current paper, we uncovered <em>H. vigintioctopunctata</em> displayed a higher thermotolerance than <em>H. vigintioctomaculata</em>. We identified 15 and 20 full-length heat shock protein 70 (<em>hsp70</em>) genes from <em>H. vigintioctopunctata</em> and <em>H. vigintioctomaculata</em> transcriptomes. A total of 8, 3, 2 and 2 <em>Hvphsp70</em>s in <em>H. vigintioctopunctata</em>, and 6, 9, 2 and 3 <em>Hvmhsp70</em>s in <em>H. vigintioctomaculata</em> fell into cytosolic A (<em>hsp70ca</em>), cytosolic B (<em>hsp70cb</em>), endoplasmic reticulum (<em>hsp70era</em>) and mitochondria (<em>hsp70ma</em>) subfamilies, respectively. Compared with <em>H. vigintioctopunctata</em>, two <em>hspca</em> genes (<em>hspca6</em> and <em>7</em>) were absent, whereas <em>hsp70cb</em> subfamily underwent independent expansion, resulting in the generation of 6 new <em>hsp70cb</em> members (<em>Hvmhsp70cb4</em> to <em>Hvmhsp70cb9</em>) during evolution in <em>H. vigintioctomaculata</em>. Nine <em>H. vigintioctopunctata hsp70</em>s (<em>Hvphsp70ca1-Hvphsp70ca7, Hvphsp70cb1</em> and <em>Hvphsp70cb2</em>) and 13<em>H. vigintioctomaculata hsp70</em>s (<em>Hvmhsp70ca1-Hvmhsp70ca5</em>, <em>Hvmhsp70cb2</em>, <em>Hvmhsp70cb4</em>-<em>Hvmhsp70cb9</em> and <em>Hvmhsp70era1</em>) expressionally responded to heat shock, in a species-specific and temperature-dependent manner. Our findings raise a possibility that different members and/or specific compositions of <em>hsp70</em>s may cause thermoresistant disparity between the two <em>Henosepilachna</em> beetles.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"38 ","pages":"Article 102098"},"PeriodicalIF":1.0,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143134895","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":"Characterization and regulatory analysis of betaine homocysteine S-methyltransferase gene 1 (BHMT1) in mud crab: A gene responsive to salinity and feeding behavior","authors":"Jinju Yin ,&nbsp;Zhiqiang Liu ,&nbsp;Xin Jin ,&nbsp;Wei Wang ,&nbsp;Lingbo Ma ,&nbsp;Ming Zhao","doi":"10.1016/j.genrep.2024.102102","DOIUrl":"10.1016/j.genrep.2024.102102","url":null,"abstract":"<div><div>Betaine homocysteine <em>S</em>-methyltransferase gene 1 (<em>BHMT1</em>) encoded betaine homocysteine <em>S</em>-methyltransferase (BHMT) catalyzes the homocysteine-to-methionine reaction using betaine as a methyl donor. Previously, we found that <em>BHMT</em> was lost in the genome of the insect clade of arthropods, but was highly expressed in the mandibular organ (MO) of the mud crab <em>Scylla paramamosain (Sp)</em>. To further explore its significance, we performed a primary regulatory analysis of <em>BHMT</em> in mud crabs. The open reading frame (ORF) length of <em>Sp-BHMT1</em> was 1203 bp, encoding 400 amino acids. Sequence alignment revealed that <em>BHMT1</em> was highly conserved in different animals, and its identity was higher in more closely related species. <em>Sp-BHMT1</em> had the highest expression in the MO of both sexes, while its expression in the MO was 1.6-fold higher in males than in females; similar results were also found in the cerebral ganglion, hepatopancreas, and thoracic ganglia tissues. During larval development, <em>Sp-BHMT1</em> was weakly expressed on most days but was significantly elevated on the first day of the Zoea 2nd (Z2) and Z3 stages. <em>Sp-BHMT1</em> exhibited the highest expression at a salinity of 10 ‰ and the lowest at a salinity of 30 ‰. With decreasing salinity, the expression of <em>Sp-BHMT1</em> increased significantly at 6 h and then returned to baseline at 8 h. After starvation treatment, the expression of <em>Sp-BHMT1</em> was significantly upregulated compared to that in the feed group at all examined time points, with a peak expression at 18:00 on the third day in the starvation group. Krüppel homolog 1 (<em>Kr-h1</em>), a methyl farnesoate (MF) signal gene, could increase <em>Sp-BHMT1</em> expression under low salinity and starvation, suggesting that a “salinity/starvation→<em>BHMT1</em> → MF biosynthesis” regulatory axis might exist in crabs. This study provides valuable insights into the functional study of <em>Sp-BHMT1</em> and MF biosynthetic regulation.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"38 ","pages":"Article 102102"},"PeriodicalIF":1.0,"publicationDate":"2024-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142748011","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":"Unraveling genetic similarities of Klebsiella pneumoniae from poultry and poultry handlers in Punjab, India","authors":"Neha Parmar ,&nbsp;Randhir Singh ,&nbsp;Simranpreet Kaur ,&nbsp;Anuj Tyagi ,&nbsp;Hina Malik ,&nbsp;Rabinder Singh Aulakh ,&nbsp;Jatinder Paul Singh Gill","doi":"10.1016/j.genrep.2024.102101","DOIUrl":"10.1016/j.genrep.2024.102101","url":null,"abstract":"<div><div>The study aimed to characterize <em>K. pneumoniae</em> isolates from poultry (broiler) farms of Ludhiana, Punjab, India. The Whole genome sequencing (WGS) of <em>K. pneumoniae</em> isolates (<em>K. pneumoniae</em> strain PF_L1_IN, <em>K. pneumoniae</em> strain PF_L2_IN, <em>K. pneumoniae</em> strain PHS_IN) using NovaSeq6000 (Illumina, USA) platform revealed the presence of several antimicrobial resistant genes (ARGs) on the genome of the isolates conferring potential resistance to antibiotics classified as critically important, highly important and important. The virulence factors (VFs) detected were Type I fimbriae, Type 3 fimbriae, AcrAB, Aerobactin, Enterobactin, Salmochelin, RcsAB, T6SS-I, II and III. The mobile genetic elements such as plasmid replicons (IncFIB and Col440I), integron elements (In0, CALIN), a unit transposon (Tn<em>512</em>) and insertion sequences (ISKpn<em>24</em>, ISEc<em>9</em>, ISKpn<em>1</em>, IS<em>102</em>, IS<em>903</em>, IS<em>5075</em> and ISKpn<em>38</em>) were detected in the isolates. The plasmids carried ARGs for the important antibiotic classes such as aminoglycoside, macrolides, quinolones, tetracyclines, carbapenems and sulphonamides. However, none of the insertion sequences and transposons in the isolates was associated with any antimicrobial resistant gene. In multilocus sequence typing (MLST) analysis, the isolates belonged to sequence type (ST) ST-147 and ST-147 with double locus variation, while, in core-genome multilocus sequence typing (cgMLST) the isolates belonged to ST-25590 and ST-1508. The isolates from broiler (<em>K. pneumoniae</em> strain PF_L1_IN) and its handler (<em>K. pneumoniae</em> strain PHS_IN) showed clonal relationship. The present study suggested that the food animal's production environment could act as a reservoir of multidrug resistant (MDR) and Extended spectrum β-lactamases (ESBL) producing <em>K. pneumoniae</em>. These resistant isolates could easily be disseminated to human through shared environment and food.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"38 ","pages":"Article 102101"},"PeriodicalIF":1.0,"publicationDate":"2024-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143134894","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":"Role of 1,25-dihydroxy vitamin D3 pathway in chronic urticaria: Findings from a hospital-based case-control study","authors":"Fizalah Kawoosa ,&nbsp;Tabasum Shafi ,&nbsp;Roohi Rasool,&nbsp;Shazia Nazir,&nbsp;Nusrat Kounsar","doi":"10.1016/j.genrep.2024.102093","DOIUrl":"10.1016/j.genrep.2024.102093","url":null,"abstract":"<div><h3>Background</h3><div>Previous research has linked dysregulation of the vitamin D pathway to skin diseases. In this study, we sought to explore the genetic variations in the vitamin D receptor (<em>VDR</em>) and vitamin D-binding protein (<em>VDBP</em>), alongside the estimation of serum vitamin D and VDBP levels in Chronic Urticaria (CU) patients.</div></div><div><h3>Methods</h3><div>Blood samples were obtained from all participants (<em>n</em> = 200) to assess serum vitamin D, VDBP, and total IgE levels using enzyme-linked immunosorbent assay (ELISA). Additionally, DNA was extracted from the blood samples for analysis of <em>VDR</em> (rs1544410, rs2228570) and <em>VDBP</em> (rs7041) polymorphisms using polymerase chain reaction (PCR) followed by restriction fragment length polymorphism (RFLP).</div></div><div><h3>Results</h3><div>CU patients exhibited elevated levels of total IgE (208.29 ± 151.293 vs. 125.91 ± 73.13 IU/ml) and VDBP (570.59 ± 158.74 vs. 314.408 ± 140.31 μg/ml) (<em>p</em>-value &lt; 0.0001), as compared to controls. Further, such patients also showed lower vitamin D levels (14.57 ± 8.71 vs. 20.022 ± 8.9 ng/ml, <em>p</em>-value &lt; 0.0001). Additionally, we observed that the ‘G’ and ‘C’ alleles of <em>VDBP</em> rs7041 and <em>VDR</em> rs2228570, respectively, might be a potential risk factor for the progression of CU.</div></div><div><h3>Conclusion</h3><div>This study provides valuable insights into the potential involvement of <em>VDR</em> and <em>VDBP</em> genetic variants in the pathogenesis of Chronic Urticaria (CU). While no significant associations were observed between these genetic variants and serum levels of vitamin D or VDBP, the identified genetic variations may play a role in increasing CU susceptibility within the Kashmiri population. Further research, including Mendelian randomization studies, is required to confirm any causal relationships.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"38 ","pages":"Article 102093"},"PeriodicalIF":1.0,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142719665","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":"Investigating the Rrelationship between polymorphisms pd1.9 and rs7421861 of PD1 gene with breast cancer","authors":"Mehdi Kakavandi ,&nbsp;Mahdi Hassani Bafrani ,&nbsp;Javad Amini Mahabadi ,&nbsp;Hassan Hassani Bafrani","doi":"10.1016/j.genrep.2024.102096","DOIUrl":"10.1016/j.genrep.2024.102096","url":null,"abstract":"<div><h3>Introduction</h3><div><em>PD1</em> molecule is a regulatory protein in the immune system that is responsible for the negative induction of active T cells. The <em>PD1</em> gene has many single nucleotide polymorphisms. In this study, the association of polymorphisms in the pd1.9 and rs7421861 positions of the <em>PD1</em> gene with breast cancer was investigated in women with breast cancer.</div></div><div><h3>Materials and methods</h3><div>This experimental study was done in healthy (<em>n</em> = 110) and breast cancer (n = 110) women. First, 2 ml of blood were taken from groups, and the genome of white blood cells (WBCs) was extracted using a DNA extraction kit. The genotype of samples was determined in pd1.9 and rs7421861 region of <em>PD1</em> gene with the help of PCR-RFLP technique. Data analysis was done by SPSS software version 19.</div></div><div><h3>Results</h3><div>The analysis of the data about pd1.9 polymorphism genotypes demonstrated that the frequency of CC genotype in the control group was equal to 92.7 %; while this amount was reported as 80 % in the patient group. Regarding the CT genotype, its frequency was 19.1 % in the patient group, while this rate was 7.3 % in the control group. Also, the data showed that the frequency of TT allele is 0.9 % in the patient group and 0 % in healthy people. In the case of rs7421861, the frequency of TT genotype in the control group was equal to 56.4 %, while this rate was equal to 41.8 % in the patient group. Regarding the CT genotype, its frequency in the patient group was 48.2 %, while this rate was 36.4 % in the control group. The frequency of CC allele is 10 % in the patient group and 7.3 % in healthy people.</div></div><div><h3>Conclusion</h3><div>The results showed that polymorphism of pd1.9 and rs7421861 in <em>PD1</em> gene cannot be related to breast cancer. Therefore, determining the genotype of polymorphism in these gene regions will not be useful for screening affected people.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"38 ","pages":"Article 102096"},"PeriodicalIF":1.0,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142700813","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 analysis of XRCC5 non-synonymous single nucleotide polymorphisms (nsSNPs) in acute myeloid leukemia prognosis","authors":"Md. Arif Hossen ,&nbsp;Md. Arju Hossain ,&nbsp;Mohammad Kamruzzaman ,&nbsp;Fahim Alam Nobel ,&nbsp;Md. Moin Uddin ,&nbsp;Md. Tanvir Hossain ,&nbsp;Numan Bin Taz ,&nbsp;Shahidullah ,&nbsp;Tumpa Rani Sarker ,&nbsp;Rafia Tabassum Farin ,&nbsp;Abdullah Al Noman ,&nbsp;Mohammad Nasir Uddin ,&nbsp;Mohammod Johirul Islam","doi":"10.1016/j.genrep.2024.102090","DOIUrl":"10.1016/j.genrep.2024.102090","url":null,"abstract":"<div><div>The X-ray repair cross-complementing 5 (<em>XRCC5</em>) gene plays a pivotal role in the classical non-homologous end joining (NHEJ) pathway further responding to DNA double-strand breaks. Our study aims to explore harmful non-synonymous single nucleotide polymorphisms (nsSNPs) within the coding region of the <em>XRCC5</em> gene, potentially impacting protein function and influencing cancer progression. We utilized several computational methods to examine potential harmful nsSNPs within the human <em>XRCC5</em> gene to understand their influence on protein structure and function. Out of 412 missense variants, the 42 missense and somatic nsSNPs identified in the <em>XRCC5</em> gene, two (Y316C and R643W) were found to be potentially harmful. Analysis through Project HOPE highlighted significant differences in physicochemical properties, structural changes, and mutations within conserved domains between wild-type and mutant amino acids. Additionally, we identified a methylation site (R486) and phosphorylation sites (318S and 333Y) on the <em>XRCC5</em> protein using GPS-MSP 1.0 and NetPhos 3.1 servers, respectively. The four pharmacologically significant compounds, CID: 348883 (−9.1 kcal/mol), CID: 376106 (−8.9 kcal/mol), CID: 381764 (−8.8 kcal/mol) and CID: 402650 (−8.7 kcal/mol) demonstrate strong binding affinity to the mutant proteins. Decreased binding affinity to mutant <em>XRCC5</em> proteins compared to wild-type protein has been determined to influence drug resistance. Besides, molecular dynamics simulation studies demonstrated that the Y316C and R643W mutations are likely to affect the structural integrity of the XRCC5 protein, limiting its capacity to retain correct conformation. Ultimately, examination through the Kaplan-Meier plotter study demonstrated that alterations in <em>XRCC5</em> gene expression significantly impact the survival rates of patients across various cancer types. Finally, the study found two highly deleterious nsSNPs in the <em>XRCC5</em> protein that can be helpful for further proteomic and genomic studies for disease diagnosis and treatment.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"38 ","pages":"Article 102090"},"PeriodicalIF":1.0,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142719664","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}