PTBP1 promotes the progression of hepatocellular carcinoma by enhancing the oncogenic splicing switch of FGFR2.

Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer accounting for 90% of cases. It is a highly invasive and deadly cancer with a gradual onset. Polypyrimidine tract-binding protein 1 (PTBP1) is an important RNA-binding protein involved in RNA metabolism and has been linked to oncogenic splicing events. While the oncogenic role of PTBP1 in HCC cells has been established, the exact mechanism of action remains unclear. This study aimed to investigate the functional connection between PTBP1 and dysregulated splicing events in HCC. Through immunoprecipitation-mass spectrometry analyses, we discovered that the proteins bound to PTBP1 were significantly enriched in the complex responsible for the alternative splicing of FGFR2 (fibroblast growth factor receptor 2). Further RNA immunoprecipitation and quantitative PCR assays confirmed that PTBP1 down-regulated the FGFR2-IIIb isoform levels and up-regulated the FGFR2-IIIc isoform levels in HCC cells, leading to a switch from FGFR2-IIIb to FGFR2-IIIc isoforms. Subsequent functional evaluations using CCK-8, transwell, and plate clone formation assays in HCC cell lines HepG2 and Huh7 demonstrated that FGFR2-IIIb exhibited tumor-suppressive effects, while FGFR2-IIIc displayed tumor-promoting effects. In conclusion, this study provides insights into the PTBP1-mediated alternative splicing mechanism in HCC progression, offering a new theoretical basis for the prevention and treatment of this malignancy. Mechanistically, the isoform switch from FGFR2-IIIb to FGFR2-IIIc promoted epithelial-mesenchymal transformation (EMT) of HCC cells and activated the FGFR cascades ERK and AKT pathways.

The application of CRISPR genome editing technologies in the pathogenesis studies, diagnosis, prevention and treatment of infectious diseases.

The CRISPR genome editing technology shows great application prospects in gene manipulation and infectious disease research, and is of great value for effective control and cure of infectious diseases. It has been utilized to generate specific disease models in cells, organoids and animals, which provide great convenience for research into the molecular mechanisms associated with infectious diseases. CRISPR screening technology enables high-throughput identification of risk factors. New molecular diagnostic tools based on CRISPR offer a more sensitive and faster method for detecting pathogens. The use of CRISPR tools to introduce resistance genes or to specifically destroy risk genes and virus genomes is intended to help prevent or treat infectious diseases. This review discusses the application of CRISPR genome editing technologies in the construction of disease models, screening of risk factors, pathogen diagnosis, and prevention and treatment of infectious diseases, thereby providing a reference for follow-up research in pathogenesis, diagnosis, prevention and treatment of infectious diseases.

Progresses on genetic susceptibility of COVID-19.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection causes a broad clinical spectrum of coronavirus disease 2019 (COVID-19). Genetic factors might influence susceptibility to the SARS-CoV-2 infection or disease severity. Genome-wide association studies (GWASs) have identified multiple susceptible genes related to COVID-19 phenotypes, providing the scientific basis for the COVID-19 prevention and treatment. In this review, we summarize the recent progresses of COVID-19 susceptible genes, including the GWASs on multiple phenotypes of COVID-19, GWASs of COVID-19 in multiple ethnic populations, GWASs of COVID-19 based on multiple types of genetic variations, and the fine-mapping of the regions surrounding the susceptible genes.

Prognostic and predictive value of the hypoxia-associated long non-coding RNA signature in hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) is a common cancer worldwide. Hypoxia is an important feature of solid tumors, including HCC, and is also an important factor involved in malignancy progression. However, the identification of hypoxia-related long non-coding RNA (lncRNAs) and their prognostic value in HCC have not been systematically investigated. The aim of this study is to identify the features based on the hypoxia-related lncRNAs and evaluate their predictive value for HCC prognosis. Based on the integrated analysis of HCC transcriptome data from The Cancer Genome Atlas (TCGA), we had identified 233 potential hypoxia-related lncRNAs. We further evaluated the prognostic value of these lncRNAs and optimally established a 12-lncRNA (AC012676.1, PRR7-AS1, AC020915.2, AC008622.2, AC026401.3, MAPKAPK5-AS1, MYG1-AS1, AC015908.3, AC009275.1, MIR210HG, CYTOR and SNHG3) prognostic risk model. The Cox proportional hazards regression analysis revealed that the hypoxia risk score is a novel independent prognostic predictor for HCC patients, which outperforms the traditional clinical pathological factors. Gene set enrichment analysis (GSEA) showed that the hypoxia risk score reflects the activation of biological features related to cell proliferation and the inactivation of lipid metabolism processes. In summary, we had constructed a risk score model based on 12 hypoxia-related lncRNAs, which might be a promising prognostic predictor for HCC patients and highlight their potential roles in the prevention and treatment of this malignancy.

MCM2 promotes the proliferation, migration and invasion of cholangiocarcinoma cells by reducing the p53 signaling pathway.

The abnormal expressions of minichromosome maintenance protein 2 (MCM2) are closely related to the development of various kinds of cancers. We aimed to explore the functions and potential molecular mechanisms of MCM2 gene in cholangiocarcinoma (CCA) cell lines (Huh28 and RBE). First, the cell counting kit-8 (CCK-8), plate clone formation, transwell and invasion assays showed that MCM2 promotes the proliferation, migration and invasion of CCA cells. Flow cytometry assays showed that MCM2 significantly promotes the cell cycle, and inhibits the apoptosis of CCA cells. Further, by analyzing the RNA sequencing data of cholangiocarcinoma, we found that MCM2 gene is significantly negatively correlated with p53 signaling pathway. Quantitative real time polymerase chain reaction (qRT-PCR) and Western blotting (WB) assays confirmed that MCM2 in CCA cells significantly down-regulated the mRNA and protein expression levels of p53 and BAX, and up-regulated the mRNA and protein expression levels of BCL2 and CCND1. Flow cytometry, qRT-PCR and WB assays confirmed that MCM2 promotes CCA through p53 pathway. Finally, we found that MCM2 is up-regulated in CCA tissues compared to the matched non-tumor cholangiocarcinoma tissues, and the high expressions of MCM2 are significantly associated with the poor clinical outcomes of CCA patients. In conclusion, this study revealed that MCM2 promotes the development of CCA by reducing the p53 pathway, and its high expression levels predict poor prognosis in CCA patients. These results provide a theoretical basis for the development of new clinical diagnosis and treatment of cholangiocarcinoma in the future.

Prognostic and predictive value of a DNA methylation-driven transcriptional signature in hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide. DNA methylation alterations are frequently observed in malignant tumours and play critical roles in the development of cancers, including HCC. To provide novel clinical prognosis biomarkers for HCC patients, we first performed a comprehensive analysis and identified a collection of prognosis-associated genes with DNA methylation-driven expression dysregulation in HCCs. Then, we optimally established a 10-gene prognostic risk score model using the least absolute shrinkage and selection operator (LASSO) analysis. Cox's proportional hazards regression analysis revealed that the high-risk score is significantly associated with poor prognosis after being adjusted by clinical parameters, indicating its potential prognostic value. The receiver operating characteristic curve (ROC) analysis showed that this 10-gene prognostic risk score model outperformed several other publicly available models in predicting both short- and long-term prognosis. Gene set enrichment analysis revealed that the high-risk score is relevantly associated with pathways involved in cell cycle and DNA damage repair. The above results indicate that we have constructed a 10-DNA-methylation-driven-gene prognostic risk score model, which might serve as a potential prognostic biomarker for HCC patients and guide treatment decisions for patients at high risk of tumour progression.

[Genetic association of MKL1 gene polymorphisms with the high-altitude adaptation].

Genetic factors are closely related to the high-altitude adaptation. Several candidate genes have been reported to be significantly associated with high-altitude adaptation. Megakaryocytic leukemia 1 (MKL1) is a transcriptional regulator, which plays crucial roles in the phenotypic modulation of smooth muscle cells. To explore whether MKL1 gene is involved in high-altitude adaptation, we performed genetic association study between MKL1 gene polymorphisms and high-altitude adaptation. We recruited 595 Tibetans from the Qinghai-Tibet plateau and 442 Hans living at low altitude. The SNP rs59098711 locus in the MKL1 gene was genotyped using the MassARRAY assays. We compared the genotypes and allele frequency distributions of rs59098711 between the Hans and Tibetans. The results showed that the genotypes of rs59098711 are significantly different between these two populations (P<0.05). We further compared the genotypes of rs59098711 between Tibetans and other ethnic groups using data from various public databases. We also observed that the genotypes of rs59098711 are significantly different between Tibetans and these other populations (P<0.05). Bioinformatics analyses suggested that rs59098711 could be located at the enhancer region and regulate the expression of the MKL1 gene. Additional study of gene expression data from available public datasets showed that MKL1 gene was up-regulated in a hypobaric hypoxic environment. Our results suggested that the genetic polymorphism rs59098711 locus of the MKL1 gene is associated with high-altitude adaption.

The critical roles of TBC proteins in human diseases.

The Tre-2/Bub2/Cdc16 (TBC) domain is a conserved protein motif consisting of approximately 200 amino acids, and is present in many eukaryotic proteins. TBC domain-containing proteins (TBC proteins) function as GTPase activating proteins (GAPs) for the small GTPase Rab, which can promote the hydrolysis of Rab-GTP to Rab-GDP in regulation of specific intracellular trafficking pathways. Several TBC proteins play important roles in cellular functions in mammals, and defects of which are closely associated with numerous disease processes. In this review, we summarize the structures and functions of the mammalian TBC proteins and recent advances in understanding their critical roles in the development of human diseases. This review serves as a reference for further investigations on the functions of TBC proteins in disease pathogeneses.

[Research advances on medical genetics in China in 2015].

Steady progress has been achieved in the medical genetics in China in 2015, as numerous original researches were published in the world's leading journals. Chinese scientists have made significant contributions to various fields of medical genetics, such as pathogenicity of rare diseases, predisposition of common diseases, somatic mutations of cancer, new technologies and methods, disease-related microRNAs (miRNAs), disease-related long non-coding RNAs (lncRNAs), disease-related competing endogenous RNAs (ceRNAs), disease-related RNA splicing and molecular evolution. In these fields, Chinese scientists have gradually formed the tendency, from common variants to rare variants, from single omic analyses to multipleomics integration analyses, from genetic discovery to functional confirmation, from basic research to clinical application. Meanwhile, the findings of Chinese scientists have been drawn great attentions of international peers. This review aims to provide an overall picture of the front in Chinese medical genetics, and highlights the important findings and their research strategy.

Recombinant Neorudin for the Prevention of Deep-Vein Thrombosis After Spinal-Cord Injury.

Background: Whether anticoagulant therapy should be used after spinal-cord injury (SCI) surgery was controversial. The anticoagulation characteristics of a newly developed anticoagulant, recombinant neorudin (EPR-hirudin (EH)), were explored using a rat model of SCI to provide a basis for clinical anticoagulation therapy of SCI. Methods: A rat model of SCI was developed by Allen's method. Then, thrombosis in the inferior vena cava was induced by ligation. The low-bleeding characteristics of EH were explored by investigating dose-response and time-effect relationships, as well as multiple administration of EH, on thrombus formation complicated with SCI. Results: EH inhibited thrombosis in a dose-dependent manner by reducing the wet weight and dry weight of the thrombus. An inhibiting action of EH on thrombosis was most evident in the group given EH 2 h after SCI. After multiple intravenous doses of EH, thrombosis inhibition was improved to that observed with low molecular weight heparin (LMWH) (87% vs 90%). EH administration after SCI neither increased bleeding in the injured spine nor damaged to nerve function. Bleeding duration and activated partial thromboplastin time were increased in the high-dose EH group compared with that in the normal-saline group, but were lower than those in the LMWH group. Conclusion: EH can reduce thrombus formation in a rat model of SCI, and bleeding is decreased significantly compared with that using LMWH. EH may prevent thrombosis after SCI or spinal surgery.

[Association of human microRNA related genetic variations with cancer].

microRNAs (miRNAs) are a highly conserved class of small noncoding RNAs that regulate gene expression by post-transcriptional degradation or translational repression. miRNAs are involved in the regulation of cell apoptosis, proliferation, differentiation and other physiological processes, and are closely related with the development of cancer. More recently, it has been proposed that the presence of genetic variations (e.g., single nucleotide polymorphism and copy number variation) in microRNA genes, their biogenesis pathway and target binding sites affect the miRNA processing machinery and targeting, and have a significant genetic effect. In this review, we focus on the miRNA-related genetic variations and cancer susceptibility and progression.

[Detection and controlling for population stratification in association studies of human complex disease].

Case-control studies, which serve as standard design for genetic association analysis, can be the most practical and powerful approach to detect genetic polymorphisms contributing to susceptibility to complex human diseases. However, considerable concern has been expressed that this approach is prone to population stratification, which can lead to biased or spurious results. We review several methods to detect and account for population stratification; these methods include nuclear family-based transmission/disequilibrium test (TDT), and genomic control (GC) and structured association (SA) based on unlinked genetic markers.

A GWAS Meta-analysis and Replication Study Identifies a Novel Locus within CLPTM1L/TERT Associated with Nasopharyngeal Carcinoma in Individuals of Chinese Ancestry.

BACKGROUND: Genetic loci within the major histocompatibility complex (MHC) have been associated with nasopharyngeal carcinoma (NPC), an Epstein-Barr virus (EBV)-associated cancer, in several GWAS. Results outside this region have varied. METHODS: We conducted a meta-analysis of four NPC GWAS among Chinese individuals (2,152 cases; 3,740 controls). Forty-three noteworthy findings outside the MHC region were identified and targeted for replication in a pooled analysis of four independent case-control studies across three regions in Asia (4,716 cases; 5,379 controls). A meta-analysis that combined results from the initial GWA and replication studies was performed. RESULTS: In the combined meta-analysis, rs31489, located within the CLPTM1L/TERT region on chromosome 5p15.33, was strongly associated with NPC (OR = 0.81; P value 6.3 × 10(-13)). Our results also provide support for associations reported from published NPC GWAS-rs6774494 (P = 1.5 × 10(-12); located in the MECOM gene region), rs9510787 (P = 5.0 × 10(-10); located in the TNFRSF19 gene region), and rs1412829/rs4977756/rs1063192 (P = 2.8 × 10(-8), P = 7.0 × 10(-7), and P = 8.4 × 10(-7), respectively; located in the CDKN2A/B gene region). CONCLUSIONS: We have identified a novel association between genetic variation in the CLPTM1L/TERT region and NPC. Supporting our finding, rs31489 and other SNPs in this region have been reported to be associated with multiple cancer sites, candidate-based studies have reported associations between polymorphisms in this region and NPC, the TERT gene has been shown to be important for telomere maintenance and has been reported to be overexpressed in NPC, and an EBV protein expressed in NPC (LMP1) has been reported to modulate TERT expression/telomerase activity. IMPACT: Our finding suggests that factors involved in telomere length maintenance are involved in NPC pathogenesis.

[Study on single nucleotide polymorphism of TLR4 in Chinese population].

OBJECTIVE: To identify the single nucleotide polymorphisms(SNPs) in the regulatory and coding regions of human Toll-like receptor 4(TLR4) gene and to search for its new genetic makers. METHODS: The 5' flank region, exons, parts of the introns, as well as 3' flank region of TLR4 gene were sequenced to identify and characterize the SNPs in Chinese population. SNP genotyping was performed by polymerase chain reaction-restriction fragment length polymorphism for 2 highly distributed SNPs. RESULTS: Five novel SNPs were identified through a 4.98 kb sequencing of TLR4 gene. Among them, three were in 5'flank region, two in 3'UTR. In the sample of Han population from Chongqing, the minor allele frequencies of two highly distributed SNPs were 0.266 and 0.404 respectively. CONCLUSION: Sampling analysis in Han population of Chongqing showed that the two highly distributed SNPs of TLR4 were common in Chinese population and could be used for genetic marker of TLR4 gene.

[An investigation of polymorphism in IL-1R1 gene in Chinese population and the functional prediction of a variation in the transmembrane region of IL-1R1].

OBJECTIVE: To identify the single nucleotide polymorphisms (SNPs) in the regulatory and coding regions of human interleukin-1 receptor type I (IL-1R1) gene and to assess their potential effect on the function of IL-1R1. METHODS: The 5' flank region, exons, parts of the introns, as well as 3' flank region of IL-1R1 gene were sequenced to identify and characterize the SNPs in Chinese population. Effects of the SNP on the structure and function of IL-1R1 were analyzed by computational methods. RESULTS: Sixteen SNPs were identified through a 9643 bp sequencing of IL-1R1 gene. Among them, four were in 5' flank region, four in intron region, one in coding region, and seven in 3' untranslated region. A novel SNP in Chinese population was involved in a structural change in IL-1R1, which may influence the signal transduction of IL-1R1. CONCLUSION: The SNP in the IL-1R1 gene might influence its function as an important receptor of IL-1 family.

Functional polymorphism in exon 5 and variant haplotype of the interleukin-1 receptor-associated kinase 1 gene are associated with susceptibility to and severity of sepsis in the Chinese population.

BACKGROUND: The interleukin-1 (IL-1) receptor-associated kinase 1 (IRAK1) is believed to play an important role in the pathogenesis of sepsis. Recent studies have suggested that the IRAK1 functional genetic variant could affect the severity of sepsis in Caucasians. In this report, we have investigated whether polymorphisms at the IRAK1 gene are associated with the susceptibility to and severity of sepsis among the Chinese population. METHODS: Haplotype-tagging single nucleotide polymorphisms (htSNPs) were selected from the HapMap database. They were genotyped in 255 patients with sepsis and 260 control subjects by PCR/restriction fragment length polymorphism (RFLP) analysis. The association between the selected htSNPs and the susceptibility to and severity of sepsis were estimated by Logistic regression with adjustments for age, sex, smoking, drinking, chronic disease status, Acute Physiology and Chronic Health Evaluation (APACHE) II score and primary diseases. RESULTS: rs1059702 was selected to represent the six linked htSNPs for IRAK1. Genotype frequencies of the htSNPs were in Hardy-Weinberg equilibrium for females, as were allele frequencies for both sex groups. Associations were observed in females between the htSNPs C/C genotype and increased susceptibility to sepsis (odds ratio (OR), 5.46; 95% confidence interval (CI), 1.12 - 26.67; P = 0.018), and such associations were also observed between the IRAK1 variant haplotype (CC/C-allele) and increased susceptibility to sepsis (OR, 1.68; 95% CI, 1.05 - 2.70; P = 0.031) when compared with the T/T + T/C genotype and the wild-type haplotype (TC + TT/T-allele). In the multiple organ dysfunction syndrome (MODS) subgroup, the variant haplotype was also associated with increased severity of sepsis (OR, 2.37; 95% CI, 1.13 - 4.94; P = 0.02) when compared with the wild haplotype. This association was not significant in male patients. CONCLUSIONS: The functional polymorphism in exon 5 and the variant haplotype of IRAK1 gene mediate susceptibility to and severity of sepsis. IRAK1 might be a genetic risk factor for the occurrence and development of sepsis in the Chinese population.

TRAF6 polymorphisms not associated with the susceptibility to and severity of sepsis in a Chinese population.

BACKGROUND: The tumor necrosis factor recepter associated factor (TRAF) 6 is an important intracellular adapter protein that plays a pivotal role in activating multiple inflammatory and immune related processes induced by cytokines. TRAF6 represents a strong candidate susceptibility factor for sepsis. We investigated whether polymorphisms at the TRAF6 gene are associated with the susceptibility to and severity of sepsis. METHODS: A hospital-based case-control study was conducted with 255 patients with sepsis and 260 controls who were recruited from Zhengzhou, China. Haplotype tagging single nucleotide polymorphisms (htSNPs) were selected from the HapMap database and genotyped using the SNPstream genotyping platform. The associations with the susceptibility and disease severity of sepsis were estimated by logistic regression, and adjusted for age, sex, smoking, drinking, chronic diseases status, APACHEII score and critical illness status. RESULTS: A total of 13 TRAF6 SNPs were tagged by 7 htSNPs. Five htSNPs (rs5030490, rs5030411, rs5030416, rs5030445 and rs3740961) were genotyped in the case control study. Genotype frequencies of the htSNPs were conformed to the Hardy-Weinberg equilibrium in both patients and controls. No significant association was found between the 5 htSNPs and the susceptibility to and severity of sepsis. Compared with the main haplotype -11120A/-10688T/-9423A/805G/12967G, no certain haplotype was associated with the significantly susceptibility to or severity of sepsis. CONCLUSION: TRAF6 gene polymorphisms might not play a major role in mediating the susceptibility to and severity of sepsis in the Chinese population. A larger population-based case-control study is warranted.

[Association of the T1270533G polymorphism in GSTM1 gene coding region with susceptibility to nasopharyngeal carcinoma in a Chinese population].

OBJECTIVE: To explore the association of T1270533G polymorphism in the glutathione S-transferase M1 (GSTM1) gene with the susceptibility to nasopharyngeal carcinoma (NPC) and clinical phenotype of NPC in Chinese population. METHDOS: The genomic DNAs were obtained from 27 Chinese subjects, and the single nucleotide polymorphism (SNP) in all the exons and relevant intron-exon boundaries of GSTM1 were determined by PCR and direct sequencing. A case-control study was performed to analyze the SNP site T1270533G (the rare allele frequency is 22.2% in Chinese population) in the coding region by means of tetra-primer amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) and sequencing. RESULT: Sequence analysis identified 29 SNPs in GSTM1 gene, among which 13 SNPs presented high linkage disequilibrium with each other. No obvious relations were found between the variation in the coding region T1270533G and the clinical phenotype of NPC (RR=0.170, 95% CI =0.95-0.306 for TT homozygotes). CONCLUSION: The missense mutation in the coding region T1270533G of GSTM1 gene that causes an amino acid change does not affect the detoxification function of GSTM1, and the T1270533G polymorphism does not have apparent relations to NPC susceptibility in Chinese subjects in Guangdong Province.

Correlation of polymorphism of the coding region of glutathione S- transferase M1 to susceptibility of nasopharyngeal carcinoma in South China population.

BACKGROUND AND OBJECTIVE: Glutathione S-transferase M1 (GSTM1) deficiency may increase the risk of nasopharyngeal carcinoma (NPC). This study was to evaluate the correlation of the single nucleotide polymorphism (SNP) in the coding region of GSTM1 gene to NPC susceptibility in southern China population. METHODS: In total 239 NPC patients and 286 age-matched healthy controls were entered into the study. Among them, 225 out of 239 NPC patients and 273 out of 286 controls were used for statistical analysis. SNP screening of all exons, relevant intron-exon boundaries, and the promoter region of GSTM1, in total 4739bp, was performed by PCR direct sequencing. The loci T1270533G and C1256088C were selected for the case-control study using the tetra-Primer ARMS-PCR, as well as the sequencing method. RESULTS: In total 29 SNPs of GSTM1 were identified by sequencing. Missense mutation occurred in the polymorphic loci of T1270533G and C1256088C. However, no evident relationships between the variants of T1270533G and clinical phenotypes of NPC were observed in the NPC group and healthy control group (OR = 0.170, 95%CI = 0.95-0.306 for homozygote TT). The deletion frequency of C1256088C was 45% (45/100) for NPC patients and 42% (42/100) for controls. CONCLUSIONS: The polymorphism of T1270533G does not affect the detoxification function of GSTM1. The T1270533G locus has no apparent association with genetic susceptibility to NPC in the southern China population. The loss rate of C1256088C is high in this study.