A Machine Learning Computational Framework Develops a Multiple Programmed Cell Death Index for Improving Clinical Outcomes in Bladder Cancer
In conclusion, the MPCDI developed and verified in this study is not only an emerging clinical classifier for BLCA patients, but it also serves as a reliable forecaster for both chemotherapy and immunotherapy, which can guide clinical management and clinical decision-making for BLCA patients.PMID:38353892 | DOI:10.1007/s10528-024-10683-y (Source: Biochemical Genetics)
Source: Biochemical Genetics - February 14, 2024 Category: Genetics & Stem Cells Authors: Chunhong Li Wangshang Qin Jiahua Hu Jinxia Lin Yiming Mao Source Type: research
Gut Microbiota Disorders in Obesity-Associated Benign Prostatic Hyperplasia in Rats
CONCLUSION: The findings of our study indicated that there was a notable variation in the microbiota abundance within the intestinal tract of obese rats suffering from prostate hyperplasia. It is plausible that these differentially abundant bacteria played a role in the development of pathological alterations in the prostate through the facilitation of inflammatory responses; however, additional research is required to validate the findings.PMID:38349437 | DOI:10.1007/s10528-023-10634-z (Source: Biochemical Genetics)
Source: Biochemical Genetics - February 13, 2024 Category: Genetics & Stem Cells Authors: Lijiang Gu Akehu Alemasi Yuhang Chen Xing Li Yibo Mei Jinlai Zhou Dalin He Jin Zeng Source Type: research
The Association Between Genetic Variants in ACE1and ACE2 Genes with Susceptibility to COVID-19 Infection
Biochem Genet. 2024 Feb 13. doi: 10.1007/s10528-024-10722-8. Online ahead of print.ABSTRACTAngiotensin-converting enzyme 2 (ACE2) receptors facilitate the entry of the causative virus severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) into target cells. Some ACE gene variants have been suggested to be involved in COVID-19 pathogenesis. So, the aim was to assess the association between ACE1 rs4646994 and ACE2 rs2285666 genes polymorphisms and the susceptibility and severity of COVID-19. This case-control study was conducted on 197 patients with COVID-19 and 197 healthy controls. ACE-1 insertion/deletion (I/D) ...
Source: Biochemical Genetics - February 13, 2024 Category: Genetics & Stem Cells Authors: Hamid Abbaszadeh Hamid Kabiri-Rad Fariba Mohammadi Soheila Zangoie Mahdieh Rajabi-Moghaddam Shokouh Ghafari Masood Ziaee Davod Javanmard Ebrahim Miri-Moghaddam Source Type: research
Comprehensive Analysis of the SUMO-related Signature: Implication for Diagnosis, Prognosis, and Immune Therapeutic Approaches in Cervical Cancer
In conclusion, this study presents diagnostic and prognostic models based on SRGs, accompanied by a comprehensive index derived from SRGs expression patterns. These findings offer valuable insights for CC diagnosis, prognosis, treatment, and immune-related analysis.PMID:38349439 | DOI:10.1007/s10528-024-10728-2 (Source: Biochemical Genetics)
Source: Biochemical Genetics - February 13, 2024 Category: Genetics & Stem Cells Authors: Xing Zhang Jian Cao Xiuting Li Yan Zhang Wenjing Yan Bo Ding Jing Hu Haohan Liu Xue Chen Yamei Nie Fengying Liu Ning Lin Shizhi Wang Source Type: research
Identification of Central Genes and Regulatory Pathways Associated with Hyperlipidemia in Rats
Biochem Genet. 2024 Feb 13. doi: 10.1007/s10528-024-10685-w. Online ahead of print.ABSTRACTHyperlipidemia is an independent risk factor for cardiovascular and cerebrovascular diseases. The transcriptomic data and the gene regulatory networks of hyperlipidemia are largely unclear. We analyzed the changes in liver gene expression and the serum levels of biochemical indicators in rats with hyperlipidemia induced by high-fat diet (HFD). The body weight, liver weight, and the serum levels of TG, TC, HDL-C, LDL-C, ALT, and AST were significantly higher in the hyperlipidemic rats compared to the healthy controls (P < 0.05). In...
Source: Biochemical Genetics - February 13, 2024 Category: Genetics & Stem Cells Authors: Xinyue Fu Xinni Song Shufang Niu Jiali Liu Songli Shi Hong Chang Chuanming Zhang Jun Qi Peng Wang Yingchun Bai Wanfu Bai Source Type: research
Metformin Protects Against Acute Kidney Injury Induced by Lipopolysaccharide via Up-Regulating the MCPIP1/SIRT1 Pathway
Biochem Genet. 2024 Feb 12. doi: 10.1007/s10528-024-10692-x. Online ahead of print.ABSTRACTIn the present study, we aimed to explore the effect and underlying mechanism of metformin on lipopolysaccharide (LPS)-induced acute kidney injury (AKI). A total of 24 BALB/C mice were randomly divided into four groups: control group, LPS group and metformin group (50 or 100 mg/kg). The histological changes and cell apoptosis in kidney tissues were detected by hematoxylin-eosin staining and terminal-deoxynucleotidyl transferase-mediated nick end labeling assay, respectively. Enzyme-linked immunosorbent assay was applied to determine ...
Source: Biochemical Genetics - February 12, 2024 Category: Genetics & Stem Cells Authors: Wen-Long Zhang Long-Jun Zhang Piao Liang Hui-Long Fang Xiao-Li Wang Yan-Juan Liu Hua-Fei Deng Source Type: research
Role of the Neanderthal Genome in Genetic Susceptibility to COVID-19: 3p21.31 Locus in the Spotlight
Biochem Genet. 2024 Feb 12. doi: 10.1007/s10528-024-10669-w. Online ahead of print.ABSTRACTSince the outbreak of COVID-19, genome-wide association studies have tried to discover the role of genetic predisposition in the clinical variability of this viral infection. The findings of various investigations have led to several loci for COVID-19 genetic susceptibility. Among candidate regions, the 3p21.31 locus has been in the spotlight among scientists, as it can increase the risk of severe COVID-19 by almost two fold. In addition to its substantial association with COVID-19 severity, this locus is related to some common disea...
Source: Biochemical Genetics - February 12, 2024 Category: Genetics & Stem Cells Authors: Mohammad Yaghmouri Pantea Izadi Source Type: research
Identifying an AML Prognostic Model Using 10 Marker Genes from Single-Cell Transcriptome and Bulk Transcriptome Analysis
The objective of this study is to examine the involvement of the FANC core complex in BMF and ascertain nucleolar homeostasis-related genes by conducting transcriptome analysis on primary hematopoietic stem cells obtained from FA patients with FANCA and FANCC variants. In the present study, we analyzed scRNA-seq data obtained from both healthy donors and individuals diagnosed with FA in order to investigate the phenomenon of cell-cell communication. Through the implementation of trajectory analysis, the differentiation pathways of several progenitor cell types, such as HSC cells transitioning into LMPP, N, M, B-prog, and E...
Source: Biochemical Genetics - February 12, 2024 Category: Genetics & Stem Cells Authors: Fangyuan Zhang Xiaohua Guo Lihong Ye Shicheng Yu Source Type: research
In Silico Identification and Characterization of Rare Cold Inducible 2 (RCI2) Gene Family in Cotton
Biochem Genet. 2024 Feb 12. doi: 10.1007/s10528-023-10663-8. Online ahead of print.ABSTRACTRCI2/PMP3s are involved in biotic and abiotic stresses and have an influence on the regulation of many genes. RCI2/PMP3 genes, which particularly encode small membrane proteins of the PMP3 family, are involved in abiotic stress responses in plants. In this work, in silico studies were used to investigate RCI2's potential function in stress tolerance and organogenesis. We conducted an extensive study of the RCI2 gene family and revealed 36 RCI2 genes from cotton species that were distributed over 36 chromosomes of the cotton genome. F...
Source: Biochemical Genetics - February 12, 2024 Category: Genetics & Stem Cells Authors: Muhammad Fahad Leeza Tariq Muhammad Tanveer Altaf Muhammad Shahnawaz Mudassir Aslam Waqas Liaqat Inayat Ullah Izhar Ullah Heba I Mohamed Abdul Basit Source Type: research
Aberrant DNA Methylation Profile of Dickkopf-1 in Ankylosing Spondylitis
Biochem Genet. 2024 Feb 12. doi: 10.1007/s10528-024-10675-y. Online ahead of print.ABSTRACTIn recent years, the impact of methylation modifications on Dickkopf-1 (DKK1) in relation to ankylosing spondylitis (AS) has remained elusive. Our objective was to investigate the potential link between DKK1 methylation patterns and transcript levels and AS susceptibility. DNA methylation level of DKK1 was measured in 82 AS and 82 healthy controls (HCs) using targeted bisulfite sequencing. In addition, the transcript level of DKK1 in peripheral blood mononuclear cells from 35 AS patients and 35 HCs was detected using real-time quanti...
Source: Biochemical Genetics - February 12, 2024 Category: Genetics & Stem Cells Authors: Xiaoya Sun Yujie Deng Man Ni Tao Zhang Xinqi Wang Ye Wu Zongwen Shuai Faming Pan Source Type: research
Expression Analysis of Nitrogen Metabolism Genes in Lelliottia amnigena PTJIIT1005, Comparison with Escherichia coli K12 and Validation of Nitrogen Metabolism Genes
This study showed that E. coli K12 and L. amnigena PTJIIT1005 have common nitrogen metabolism genes involved in the same functional role, like the denitrification pathway. Additionally, operon arrangement study and PPI network revealed that E. coli K12 has only a denitrification pathway, while L. amnigena PTJIIT1005 has both an assimilation and denitrification pathway. PCR successfully amplified selected N-metabolizing genes, and the expression level of N-genes was high in strain L. amnigena PTJIIT1005. Our previous experimental study exhibited a better nitrate remediation rate in L. amnigena PTJIIT1005 over E. coli K12. T...
Source: Biochemical Genetics - February 10, 2024 Category: Genetics & Stem Cells Authors: Preeti Thakur Pammi Gauba Source Type: research
Identification of Hub Genes and Prediction of Targeted Drugs for Rheumatoid Arthritis and Idiopathic Pulmonary Fibrosis
Biochem Genet. 2024 Feb 9. doi: 10.1007/s10528-023-10650-z. Online ahead of print.ABSTRACTThere is a potential link between rheumatoid arthritis (RA) and idiopathic pulmonary fibrosis (IPF). The aim of this study is to investigate the molecular processes that underlie the development of these two conditions by bioinformatics methods. The gene expression samples for RA (GSE77298) and IPF (GSE24206) were retrieved from the Gene Expression Omnibus (GEO) database. After identifying the overlapping differentially expressed genes (DEGs) for RA and IPF, we conducted functional annotation, protein-protein interaction (PPI) network...
Source: Biochemical Genetics - February 9, 2024 Category: Genetics & Stem Cells Authors: Ting Cui Zhican Huang Kun Luo Jingwei Nie Yimei Xv Zhu Zeng Linghan Liao Xin Yang Haiyan Zhou Source Type: research
SPARC Controls Migration and Invasion of Hepatocellular Carcinoma Cells Via Regulating GPD2-Mediated Mitochondrial Respiration
In this study, we aimed to explore the potential influence of glycoprotein SPARC on mitochondrial respiration and its subsequent influence on the migration and invasion of hepatocellular carcinoma (HCC) cells. Lentivirus-mediated shRNA delivery was employed to deplete SPARC in HCC cell lines. The mitochondria localization of SPARC was validated using cellular fractionation followed by Western blot analysis, as well as immunofluorescence staining and Proteinase K protection assay. Co-immunoprecipitation was employed to investigate the interaction between SPARC and GPD2. Seahorse XF Cell Mito Stress Test was conducted to ass...
Source: Biochemical Genetics - February 9, 2024 Category: Genetics & Stem Cells Authors: Lei Liu Huawei Xiao Guiqing Yang Source Type: research
Bioinformatics Analysis and Experimental Validation of Differential Genes and Pathways in Bone Nonunions
This study integrates bioinformatics analysis and experimental validation to unravel key genes and pathways associated with non-union fractures. We identified differentially expressed genes (DEGs) between non-union and fracture healing tissues using bioinformatics techniques. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were employed to elucidate the biological processes and pathways involved. Common DEGs were identified, and a protein-protein interaction (PPI) network was constructed. Fibronectin-1 (FN1), Thrombospondin-1 (THBS1), and Biglycan (BGN) were pinpointed as critical target gene...
Source: Biochemical Genetics - February 7, 2024 Category: Genetics & Stem Cells Authors: Wei Xiong Xing-Li Shu Lv Huang Su-Qi He Lang-Hui Liu Song Li Zi-Chen Shao Jun Wang Ling Cheng Source Type: research
Novel Pathogenic Mutation of P209L in TRPC6 Gene Causes Adult Focal Segmental Glomerulosclerosis
We describe a single affected family member who presented with FSGS. We used high-throughput sequencing, sanger sequencing to identify the pathogenic mutations, and a systems genetics analysis in the BXD mice was conducted to explore the genetic regulatory mechanisms of pathogenic genes in the development of FSGS. We identified high urinary protein (++++) and creatinine levels (149 μmol/L) in a 29-year-old male diagnosed with a 5-year history of grade 2 hypertension. Histopathology of the kidney biopsy showed stromal hyperplasia at the glomerular segmental sclerosis and endothelial cell vacuolation degeneration. Whole-exo...
Source: Biochemical Genetics - February 5, 2024 Category: Genetics & Stem Cells Authors: Tianxi Yu Yongqiang Ji Xin Cui Ning Liang Shuang Wu Chongjun Xiang Yue Li Huiying Tao Yaqi Xie Hongwei Zuo Wenting Wang Nauman Khan Kamran Ullah Fuyi Xu Yan Zhang Chunhua Lin Source Type: research
