Biochemical Genetics最新文献_第9页

A New Differential Gene Expression Based Simulated Annealing for Solving Gene Selection Problem: A Case Study on Eosinophilic Esophagitis and Few Other Gastro-intestinal Diseases. 一种新的基于差异基因表达的模拟退火方法用于解决基因选择问题：以嗜酸性粒细胞性食管炎和少数其他胃肠道疾病为例

IF 2.1 4区生物学

Biochemical Genetics Pub Date : 2024-12-06 DOI: 10.1007/s10528-024-10987-z

Koushiki Sinha, Sanchari Chakraborty, Arohit Bardhan, Riju Saha, Srijan Chakraborty, Surama Biswas

{"title":"A New Differential Gene Expression Based Simulated Annealing for Solving Gene Selection Problem: A Case Study on Eosinophilic Esophagitis and Few Other Gastro-intestinal Diseases.","authors":"Koushiki Sinha, Sanchari Chakraborty, Arohit Bardhan, Riju Saha, Srijan Chakraborty, Surama Biswas","doi":"10.1007/s10528-024-10987-z","DOIUrl":"https://doi.org/10.1007/s10528-024-10987-z","url":null,"abstract":"Identifying the set of genes collectively responsible for causing a disease from differential gene expression data is called gene selection problem. Though many complex methodologies have been applied to solve gene selection, formulated as an optimization problem, this study introduces a new simple, efficient, and biologically plausible solution procedure where the collective power of the targeted gene set to discriminate between diseased and normal gene expression profiles was focused. It uses Simulated Annealing to solve the underlying optimization problem and termed here as Differential Gene Expression Based Simulated Annealing (DGESA). The Ranked Variance (RV) method has been applied to prioritize genes to form reference set to compare with the outcome of DGESA. In a case study on Eosinophilic Esophagitis (EoE) and other gastrointestinal diseases, RV identified the top 40 high-variance genes, overlapping with disease-causing genes from DGESA. DGESA identified 40 gene pathways each for EoE, Crohn's Disease (CD), and Ulcerative Colitis (UC), with 10 genes for EoE, 8 for CD, and 7 for UC confirmed in literature. For EoE, confirmed genes include KRT79, CRISP2, IL36G, SPRR2B, SPRR2D, and SPRR2E. For CD, validated genes are NPDC1, SLC2A4RG, LGALS8, CDKN1A, XAF1, and CYBA. For UC, confirmed genes include TRAF3, BAG6, CCDC80, CDC42SE2, and HSPA9. RV and DGESA effectively elucidate molecular signatures in gastrointestinal diseases. Validating genes like SPRR2B, SPRR2D, SPRR2E, and STAT6 for EoE demonstrates DGESA's efficacy, highlighting potential targets for future research.","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142790634","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Mitochondrial Genome of Melipona fasciculata (Apidae, Meliponini): Genome Organization and Comparative Analyses, Phylogenetic Implications and Divergence Time Estimations. 束状棘足鼠线粒体基因组（蜜蜂科，棘足鼠）：基因组组织和比较分析，系统发育意义和分化时间估计。

IF 2.1 4区生物学

Biochemical Genetics Pub Date : 2024-12-06 DOI: 10.1007/s10528-024-10991-3

Geice Ribeiro da Silva, Isis Gomes de Brito Souza, Fábia de Mello Pereira, Bruno de Almeida Souza, Maria Teresa do Rêgo Lopes, Francisco Prosdocimi, Paul Bentzen, Fábio Mendonça Diniz

{"title":"The Mitochondrial Genome of Melipona fasciculata (Apidae, Meliponini): Genome Organization and Comparative Analyses, Phylogenetic Implications and Divergence Time Estimations.","authors":"Geice Ribeiro da Silva, Isis Gomes de Brito Souza, Fábia de Mello Pereira, Bruno de Almeida Souza, Maria Teresa do Rêgo Lopes, Francisco Prosdocimi, Paul Bentzen, Fábio Mendonça Diniz","doi":"10.1007/s10528-024-10991-3","DOIUrl":"https://doi.org/10.1007/s10528-024-10991-3","url":null,"abstract":"The native stingless bee Melipona fasciculata is economically and ecologically important to the Brazilian Northeast, providing a sustainable source of income to family farmers and being considered an effective pollinator in most ecosystems and crops. This study describes, for the first time, the mitogenome of the species and its phylogenetic position. The mitochondrial genome was sequenced using a MiSeq Sequencer (Illumina Inc.) and compared with other GenBank bee mitogenomes. The length of the mitochondrial DNA, excluding most of the control region, is 14,753 bp, and contains 13 protein-coding genes (PCGs), 21 transfer RNAs, 2 ribosomal RNAs (16S and 12S), and 1 AT-rich region. The GC-content of the M. fasciculata mitogenome was 13.4%. Of the 36 coding regions, 12 tRNAs and 9 PCGs were encoded in the heavy strand, and 9 tRNAs, 4 PCGs and 2 rRNAs were encoded in the light strand. The relative orientation and gene order was the same as other stingless bee mitogenomes. Phylogenetic inference produced well-resolved relationships with high statistical support for concordant branch topologies, under different optimization schemes and model parameters, within and among Melipona, Bombus, Apis, and related clades of Hymenoptera. In general, our divergence time estimates, which were based on the concatenated gene sequences (PCGs + rRNAs) from various groups, overlapped estimations captured by Bayesian analysis from different studies. The divergence time among Melipona species was estimated to occur during the Oligocene, approximately 24 Mya (95% HPD 14-36 Mya). Our results represent a valuable addition to help understanding not only the taxonomy and evolution of Brazilian stingless bee species, but also to uncover historical dispersal and isolation patterns in Meliponinae.","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142790692","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Exploring the Role of the TGF-β Signaling Pathway in Colorectal Precancerous Polyps Biochemical Genetics. TGF-β信号通路在结直肠癌前息肉生化遗传学中的作用

IF 2.1 4区生物学

Biochemical Genetics Pub Date : 2024-12-05 DOI: 10.1007/s10528-024-10988-y

Shadi Sadri, Ali Aghajani, Hiva Soleimani, Sourena Ghorbani Kalkhajeh, Haniyeh Nazari, Peiman Brouki Milan, Noshad Peyravian, Zahra Pezeshkian, Maziar Malekzadeh Kebria, Fatemeh Shirazi, Elahe Shams, Fatemeh Naderi Noukabadi, Ehsan Nazemalhosseini-Mojarad, Zahra Salehi

{"title":"Exploring the Role of the TGF-β Signaling Pathway in Colorectal Precancerous Polyps Biochemical Genetics.","authors":"Shadi Sadri, Ali Aghajani, Hiva Soleimani, Sourena Ghorbani Kalkhajeh, Haniyeh Nazari, Peiman Brouki Milan, Noshad Peyravian, Zahra Pezeshkian, Maziar Malekzadeh Kebria, Fatemeh Shirazi, Elahe Shams, Fatemeh Naderi Noukabadi, Ehsan Nazemalhosseini-Mojarad, Zahra Salehi","doi":"10.1007/s10528-024-10988-y","DOIUrl":"https://doi.org/10.1007/s10528-024-10988-y","url":null,"abstract":"Colorectal cancer (CRC) is an important public health issue and is the third most common cancer, accounting for approximately 10% of all cancer cases worldwide. CRC results from the accumulation of multiple genetic and epigenetic alterations in the normal epithelial cells of the colon and rectum, leading to the development of colorectal polyps and invasive carcinomas. The transforming growth factor-beta (TGF-β) pathway is regulated in many diseases, such as cancer. This factor can show tumor suppressant function in the early stages in healthy and cancer cells. It can be regulated and affected by different factors, including noncoding RNAs, which are the remarkable regulators for this pathway. The most prominent functions of this factor are cell cycle arrest and apoptosis in cancer cells. However, activating at the final stages of the cell cycle can cause tumor metastasis. Thus, the dual function of TGF-β and the pleiotropic nature of this signaling make it a crucial challenge for cancer treatment. Accurately studying the TGF-β signaling pathway is critical to determine its role. One of the roles of TGF-β signaling is its significant effect on colorectal polyp malignancy and cancer. In this article, we review the published scientific papers regarding the TGF-β signaling pathway, its related genes, and their contribution to precancerous conditions and colorectal cancer progression. The complex interaction of the TGF-β signaling pathway with noncoding RNAs, such as lncRNA TUG1 and miR-21, significantly influences colorectal polyp and cancer progression. Identifying dysregulated TGF-β-related noncoding RNAs offers promising therapeutic avenues for colorectal cancer. Comprehending TGF-β's connection to other molecular mechanisms is crucial for advancing effective therapeutic strategies.","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142783643","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

PFKP Lactylation Promotes the Ovarian Cancer Progression Through Targeting PTEN. PFKP乳酸化通过靶向PTEN促进卵巢癌进展。

IF 2.1 4区生物学

Biochemical Genetics Pub Date : 2024-12-05 DOI: 10.1007/s10528-024-10990-4

Jianfeng Mi, Ling Zhao, Yonglong Shen, Shien Mo, Yan Kuang

{"title":"PFKP Lactylation Promotes the Ovarian Cancer Progression Through Targeting PTEN.","authors":"Jianfeng Mi, Ling Zhao, Yonglong Shen, Shien Mo, Yan Kuang","doi":"10.1007/s10528-024-10990-4","DOIUrl":"https://doi.org/10.1007/s10528-024-10990-4","url":null,"abstract":"Ovarian cancer (OC) ranks among the most prevalent malignancies affecting females globally and is a leading cause of cancer-related mortality in women. This study sought to elucidate the influence of phosphofructokinase P (PFKP) on the progression of OC. A cohort of sixty OC patients was enrolled. OC cells were exposed to both normoxic and hypoxic conditions. Expression levels of PFKP and phosphatase and tensin homolog (PTEN) were quantified using real time quantitative polymerase chain reaction (RT-qPCR) and Western blot analyses. Immunofluorescence confirmed these protein expression patterns. Glycolysis-related parameters, encompassing glucose uptake, extracellular lactate levels, extracellular acidification rates, and oxygen consumption rates, were assessed using commercially available kits. Lactylation status of PFKP was evaluated via immunoprecipitation followed by Western blot analysis. An OC xenograft mouse model was also established. Findings indicated elevated PFKP expression in OC tissues and cells. Additionally, PFKP knockdown attenuated glycolysis and counteracted the hypoxia-induced enhancement of glycolytic activity in OC cells. Mutation of the lysine (K) residue at position 392 diminished PFKP lactylation. Further investigations revealed that PFKP depletion upregulated PTEN expression in hypoxia-treated OC cells. Besides, PTEN suppression increased the glycolysis in hypoxia-treated OC cells. Animal study results demonstrated that PFKP inhibition curtailed OC tumor growth by modulating PTEN expression. Collectively, these results suggested that lactylation of PFKP at the K392 residue promoted glycolysis in OC cells by regulating PTEN, thereby facilitating the disease's progression.","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142783658","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Prevalence of SPOP and IDH Gene Mutations in Prostate Cancer in a Jordanian Population. 约旦人群前列腺癌中SPOP和IDH基因突变的患病率

IF 2.1 4区生物学

Biochemical Genetics Pub Date : 2024-12-04 DOI: 10.1007/s10528-024-10974-4

Mohammed S Alorjani, Samir Al Bashir, Basmah Al-Zaareer, Sohaib Al-Khatib, Raed M Al-Zoubi, Bahaa Al-Trad, Manal AbuAlarja, Ayman Alzu'bi, Mohammad Al-Hamad, Khalid Al-Batayneh, Mazhar S Al-Zoubi

{"title":"Prevalence of SPOP and IDH Gene Mutations in Prostate Cancer in a Jordanian Population.","authors":"Mohammed S Alorjani, Samir Al Bashir, Basmah Al-Zaareer, Sohaib Al-Khatib, Raed M Al-Zoubi, Bahaa Al-Trad, Manal AbuAlarja, Ayman Alzu'bi, Mohammad Al-Hamad, Khalid Al-Batayneh, Mazhar S Al-Zoubi","doi":"10.1007/s10528-024-10974-4","DOIUrl":"https://doi.org/10.1007/s10528-024-10974-4","url":null,"abstract":"Speckle-type POZ (SPOP) is described as an essential tumor suppressor factor in gastric cancer, colorectal cancer, and prostate cancer (PCa). SPOP gene mutations were reported in primary human PCa. Isocitrate dehydrogenase-1 (IDH1) oncogene mutations were detected in gliomas, acute myeloid leukemia, some benign and malignant cartilaginous tumors, and only 1% of PCa. This study aimed to investigate the prevalence of mutations of SPOP and IDH1 genes in PCa in the Jordanian population. One hundred formalin-fixed paraffin-embedded tissue samples were collected from patients diagnosed with prostate adenocarcinoma. The obtained specimens were subjected to genomic DNA extraction, PCR amplification, and direct sequencing of exons 4, 5, 6, and 7 of the SPOP gene and exon 6 of the IDH1 gene. SPOP gene mutations were found in 17% of PCa cases, while no mutation was detected in the screened exon 6 of the IDH1 gene. Clinicopathological data demonstrated a strong correlation between prostate-specific antigen (PSA) levels and both Gleason score (GS) and the International Society of Urological Pathology (ISUP) grade group (GG). There was no significant correlation between PSA levels and age (p = 0.816) nor there were significant associations for SPOP mutational status with age (p = 0.659), PSA levels (p = 0.395), GS (p = 0.259), and ISUP GG (p = 0.424) in the tested population. The study found a strong correlation between PSA levels and both GS and ISUP GG. It also identified a high frequency (17%) of SPOP gene mutations in Jordanian Arab PCa patients, mainly in exon 7. No IDH1 mutations were detected in exon 6.","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142765354","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

LncRNA H19 Promotes Angiogenesis in Mouse Pulmonary Artery Endothelial Cells by Regulating the HIF-1α/VEGF Signaling Pathway. LncRNA H19通过调控HIF-1α/VEGF信号通路促进小鼠肺动脉内皮细胞血管生成

IF 2.1 4区生物学

Biochemical Genetics Pub Date : 2024-12-04 DOI: 10.1007/s10528-024-10983-3

Lei Dou, Wei You, Yannan Chai, Huiju Shi, Qing Liu, Qiaoli Jiang, Huiling Li

{"title":"LncRNA H19 Promotes Angiogenesis in Mouse Pulmonary Artery Endothelial Cells by Regulating the HIF-1α/VEGF Signaling Pathway.","authors":"Lei Dou, Wei You, Yannan Chai, Huiju Shi, Qing Liu, Qiaoli Jiang, Huiling Li","doi":"10.1007/s10528-024-10983-3","DOIUrl":"https://doi.org/10.1007/s10528-024-10983-3","url":null,"abstract":"Persistent pulmonary hypertension of the newborn (PPHN) is a syndrome of acute respiratory failure characterized by systemic hypoxemia and elevated pulmonary arterial pressure, which leads to pathological changes in pulmonary vascular remodeling and endothelial cell function. Long non-coding RNA (lncRNA) H19 has been shown to be involved in the regulation of arterial endothelial cell function, but its regulatory role in PPHN is not fully understood. In the present study, mouse pulmonary artery endothelial cells (MPAECs) were cultured in a hypoxic conditions. Subsequently, the regulatory function of lncRNA H19 on MPAECs was explored by constructing adenoviruses knocking down and overexpressing lncRNA H19. The results revealed that the hypoxic conditions could induce the proliferation and migration of MPAECs, as well as the high expression of lncRNA H19 in MPAECs. Knockdown of lncRNA H19 expression in MPAECs reversed hypoxic environment-induced functional changes in endothelial cells, whereas overexpression of lncRNA H19 further enhanced the proliferation and migration of MPAECs. In addition, lncRNA H19 upregulated the hypoxia-inducible factor-1α (HIF-1α)/vascular endothelial growth factor (VEGF) pathway through sponge of miNA-20a-5p, which in turn promoted changes in endothelial cell function. LncRNA H19 may interfere with vascular remodeling in hypoxia-induced pulmonary hypertension by upregulating the expression of HIF-1α and VEGF in vascular endothelial cells.","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142779152","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Novel Efficient Genome-Wide STR Panels for the Conservation of the Endemic Catfishes of Western Ghats: Critically Endangered Hemibagrus punctatus Jerdon (1849) and Vulnerable Horabagrus brachysoma (Günther, 1864). 保护西高加斯特有鲶鱼的新型高效全基因组STR图谱：极度濒危的半斑鲶鱼（1849）和脆弱的短尾鲶鱼（g<s:1> nther, 1864）。

IF 2.1 4区生物学

Biochemical Genetics Pub Date : 2024-12-04 DOI: 10.1007/s10528-024-10982-4

P R Divya, Divya Merin Jose, Magdeline Christo, Charan Ravi, Uttam Kumar Sarkar

{"title":"Novel Efficient Genome-Wide STR Panels for the Conservation of the Endemic Catfishes of Western Ghats: Critically Endangered Hemibagrus punctatus Jerdon (1849) and Vulnerable Horabagrus brachysoma (Günther, 1864).","authors":"P R Divya, Divya Merin Jose, Magdeline Christo, Charan Ravi, Uttam Kumar Sarkar","doi":"10.1007/s10528-024-10982-4","DOIUrl":"https://doi.org/10.1007/s10528-024-10982-4","url":null,"abstract":"The IUCN classifies two-endemic fishes of the Western Ghats in Peninsular India: Nilgiri mystus Hemibagrus punctatus is critically endangered, and Yellow catfish Horabagrus brachysoma is vulnerable. These are threatened by habitat degradation, excess fishing, and dam construction. ICAR-NBFGR, the premier research organisation in India for fish conservation, aims to conserve these two species through captive propagation, stock identification, and stock-specific ranching programs. The information on this species' genetic diversity and population structure is crucial for the successful rehabilitation of the species. Microsatellite markers are considered suitable markers for genetic stock structure analyses. An attempt was made to identify microsatellite markers in H. brachysoma (n = 27) and H. punctatus (n = 31) using Illumina Sequencing technology. The preliminary studies show that markers are efficient enough to differentiate the genetic stocks of these conservation-important species across their range of natural distribution. Three genetic stocks are identified in H. brachysoma and two in H.punctatus using the developed markers.","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142765351","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

AKR1B1 is Required for Maintaining Acute Leukemia Cell Survival by Epigenetic Silencing of Tumor Suppressor Genes. 通过表观遗传沉默肿瘤抑制基因，AKR1B1是维持急性白血病细胞存活所必需的

IF 2.1 4区生物学

Biochemical Genetics Pub Date : 2024-12-04 DOI: 10.1007/s10528-024-10984-2

Jingyu Chen, Lu Xu, Wangshi Li, Meiling Sun, Yao Chen, Ting Qiu, Yue Wu, Xingzhi Lv, Fukai Liu, Huitao Fan

{"title":"AKR1B1 is Required for Maintaining Acute Leukemia Cell Survival by Epigenetic Silencing of Tumor Suppressor Genes.","authors":"Jingyu Chen, Lu Xu, Wangshi Li, Meiling Sun, Yao Chen, Ting Qiu, Yue Wu, Xingzhi Lv, Fukai Liu, Huitao Fan","doi":"10.1007/s10528-024-10984-2","DOIUrl":"https://doi.org/10.1007/s10528-024-10984-2","url":null,"abstract":"AKR1B1 is a member of aldo-keto-reductase (AKR) superfamily which catalyze the reduction of carbonyl groups to hydroxyl groups in NADPH-dependent ways. Previous studies have shown that AKR1B1 promotes cancer progression, but its exact role in acute leukemia was unclear. Cell counting and Luminescent Cell Viability Assay were performed to measure the cell proliferation and viability. Soft-Agar Colony Formation (CFU) assay was conducted to measure the capacity of single cells to form colonies in vitro. Cell apoptosis, cell cycle, and cell differentiation were assessed by flow cytometry. Western blotting and RT-qPCR were utilized to examine AKR1B1 expression in acute leukemia cells. In vivo leukemia growth and mouse survival were evaluated using a model of xenotransplantation mice. We explored the AKR1B1 effect and mechanism in acute leukemia cells using RNA-sequencing technology and transcriptomic analysis. AKR1B1 is highly expressed in acute leukemia cells. Knockdown of AKR1B1 inhibited acute leukemia cell proliferation, colony-forming capability, and cell cycle and promoted apoptosis. Additionally, xenograft experiments proved that knockdown of AKR1B1 delayed the progression of acute leukemia cell in vivo. RNA-sequencing data analysis demonstrated that AKR1B1 was involved in the epigenetic silencing of H3K27me3-targeted genes. EZH2 inhibitor UNC1999 combined with knockdown of AKR1B1 showed synergistic inhibitory effect on acute leukemia cells. AKR1B1 is essential for the leukemogenesis and may serve as a potential therapeutic target to treat acute leukemia patients.","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142765319","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Circ_0000972 Inhibits Hepatocellular Carcinoma Cell Stemness by Targeting miR-96-5p/PFN1. Circ_0000972靶向miR-96-5p/PFN1抑制肝癌细胞干性

IF 2.1 4区生物学

Biochemical Genetics Pub Date : 2024-12-02 DOI: 10.1007/s10528-024-10975-3

Jintian Tang, Runjuan Tang, Feng Xue, Peng Gu, Jing Han, Wukui Huang

{"title":"Circ_0000972 Inhibits Hepatocellular Carcinoma Cell Stemness by Targeting miR-96-5p/PFN1.","authors":"Jintian Tang, Runjuan Tang, Feng Xue, Peng Gu, Jing Han, Wukui Huang","doi":"10.1007/s10528-024-10975-3","DOIUrl":"https://doi.org/10.1007/s10528-024-10975-3","url":null,"abstract":"Previous study has identified circRNAs as an important factor in cancer stem cells (CSCs) progression, which contributes to tumor initiation and progression. This study aspired to uncover the mechanisms of circ_0000972 on hepatocellular carcinoma (HCC) CSCs. RT-qPCR was utilized to quantify circ_0000972, miR-96-5p, and profilin 1(PFN1) expression in HCC tissues and cells. To evaluate the in vivo functions of circ_0000972, HCC cells with circ_0000972 overexpression were utilized to establish xenograft model through subcutaneous injection. The cell colony and sphere formation assays were adopted to evaluate the impact of circ_0000972 on the stemness characteristics of HCC cells. Additionally, the interaction between circ_0000972, miR-96-5p, and PFN1 was determined through bioinformatics analysis, dual-luciferase reporter assays, and rescue experiments. Circ_0000972 and PFN1 expression was significantly downregulated in HCC tissues and cells, while miR-96-5p exhibited an increased expression level. The overexpression of circ_0000972 was observed to inhibit the cell colony, sphere formation, and EMT of HCC CSCs. In xenograft model, circ_0000972 overexpression restrained the tumor volume and weight. Mechanistically, circ_0000972 stimulated PFN1 expression through the inhibition of miR-96-5p. More importantly, circ_0000972 overexpression could promote PFN1 expression and inhibit the stemness of HCC CSCs. Interestingly, the effect of circ_0000972 overexpression on such progresses was reversed by PFN1 silencing. This study elucidates that circ_0000972, an antitumor factor, sponges miR-96-5p to inhibit oncogenic cellular process in HCC by mediating PFN1 expression.","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142765328","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genome-Wide Identification and In Silico Analysis of Annexins in Chickpea (Cicer arietinum L.). 鹰嘴豆（Cicer arietinum L.）膜联蛋白的全基因组鉴定和计算机分析。

IF 2.1 4区生物学

Biochemical Genetics Pub Date : 2024-12-02 DOI: 10.1007/s10528-024-10979-z

Bharati Swain, Prateek Gupta, Deepanker Yadav

{"title":"Genome-Wide Identification and In Silico Analysis of Annexins in Chickpea (Cicer arietinum L.).","authors":"Bharati Swain, Prateek Gupta, Deepanker Yadav","doi":"10.1007/s10528-024-10979-z","DOIUrl":"https://doi.org/10.1007/s10528-024-10979-z","url":null,"abstract":"Annexins are a ubiquitous, evolutionarily conserved group of Ca2+-dependent phospholipid-binding proteins. They are a family of less numerous and more varied proteins that form a unique monophyletic group. They play an important role in various abiotic and biotic stress responses through Ca2+-mediated signaling. Chickpea (Cicer arietinum L.) is one of the most widely grown legume crops in the world. In recent years, intensive research has been carried out to identify and elucidate genes and molecular pathways that control stress responses in plants. The availability of the chickpea genome has hastened the functional genomics of chickpea. In the current study, we attempted Genome-wide identification and in silico analysis of Annexins in chickpea. Thirteen annexin sequences have been identified in the chickpea genome. Four conserved annexin domains were found in ten annexin members, while three annexins CaAnn5, CaAnn12, and CaAnn13, showed three, two, and one conserved domain, respectively. The gene structure analysis showed the presence of multiple exons in all thirteen annexins. Most Annexin genes are composed of 3-5 introns. Their chromosomal locations showed that out of thirteen genes, ten could be mapped on four chromosomes. Three genes were placed on the scaffold regions. The promoter sequence analysis of all thirteen annexins showed the presence of various elements related to growth and development and response to different phytohormones and abiotic stress. The gene expression data of different annexins in various tissues like leaf, shoot, root, flower bud, and young pod showed their differential expression. Analysis of expression data of roots in drought stress showed their differential expression with the different stages of plant growth. Overall, the current findings show the possible role of CaAnns in different stages of plant growth and development in normal and stressful conditions. Moreover, these findings will be helpful in the further characterization of CaAnn genes and their promoters.","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142765376","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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