With the exacerbation of aging population in China, the number of patients with Alzheimer's disease (AD) is increasing rapidly. AD is a chronic but irreversible neurodegenerative disease, which cannot be cured radically at present. In recent years, in order to intervene in the course of AD in advance, many researchers have explored how to detect AD as early as possible, which may be helpful for effective treatment of AD. Imaging genomics is a kind of diagnosis method developed in recent years, which combines the medical imaging and high-throughput genetic omics together. It studies changes in cognitive function in patients with AD by extracting effective information from high-throughput medical imaging data and genomic data, providing effective guidance for early detection and treatment of AD patients. In this paper, the association analysis of magnetic resonance image (MRI) with genetic variation are summarized, as well as the research progress on AD with this method. According to complexity, the objects in the association analysis are classified as candidate brain phenotype, candidate genetic variation, genome-wide genetic variation and whole brain voxel. Then we briefly describe the specific methods corresponding to phenotypic of the brain and genetic variation respectively. Finally, some unsolved problems such as phenotype selection and limited polymorphism of candidate genes are put forward.
Healthcare-associated infection outbreaks are a serious threat to patient safety and often cause serious consequences. The use of genotyping methods to identify the source of infection and the route of transmission in outbreaks is a critical point in controlling outbreaks. Recently, the use of whole-genome sequencing (WGS) makes it faster and much more accurate. Compared with traditional methods, WGS can distinguish highly correlated pathogen lineages, track infection source accurately and help researchers understanding the propagation dynamics model, and even provide more target intervention information. The application of WGS technology in healthcare-associated infection outbreak investigation and control is reviewed in this paper, and its advantages and challenges are also evaluated.
ObjectiveTo explore the differential expressed lncRNA genes associated with formation of cholesterol gallstone, and analyze the biological functions of differential expressed lncRNA through bioinformatics.MethodsA total of 24 C57BL/6 mice were randomly divided into normal control group (n=8) and lithogenic group (n=16), which were treated with chow diets and lithogenic diets respectively for 5 weeks. After 5 weeks, mice of the lithogenic group were randomly divided into model control group (n=8) and ursodeoxycholic acid treatment group (n=8). Afterwards, mice of the normal control group were still fed with chow diets, mice of the model control group were fed with lithogenic diets, mice of the ursodeoxycholic acid treatment group were fed with ursodeoxycholic acid. After 2 weeks, collected liver tissues and gallbladder bile from the three groups, and observed gallbladder gross sample and analyzed lipids component of gallbladder bile, meanwhile detected the differential expressed lncRNA and analyzed the biological functions of differential expressed lncRNA through bioinformatics, including Gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) pathway analysis.ResultsWe successfully constructed the mice model of cholesterol gallstone. Total cholesterol level of gallbladder in the model control group had significantly higher than those of the normal control group and ursodeoxycholic acid treatment group (P<0.05), yet there was no significant difference between the normal control group and ursodeoxycholic acid treatment group (P=0.59). The levels of total bile acid, total bilirubin, and direct bilirubin had no significant difference among the three groups (P>0.05). There were 49 kinds of common overlapped difference lncRNA between the ursodeoxycholic acid treatment group and the model control group through differential expression analysis of lncRNA in liver tissues of the mice in three groups. GO and KEGG path analysis were performed separately by differential expressed lncRNA, and 88 kinds of GO terms and 18 kinds of pathways were significantly enriched from the model control group and the normal control group, 205 kinds of GO terms and 20 kinds of pathways were significantly enriched from the ursodeoxycholic acid treatment group and the normal control group.ConclusionsUrsodeoxycholic acid has therapeutic effect for cholesterol gallstone. Differential expressed lncRNAs play an important regulatory role in the formation of cholesterol gallstone and the prevention of gallstone formation by ursodeoxycholic acid treatment, which further lay the foundation in discussing specific mechanism regulated by lncRNA.
ObjectiveTo explore the expression of genes related to hepatocellular carcinoma (HCC) stem cells and their prognostic correlation by using weighted gene co-expression network analysis (WGCNA).MethodsFirstly, the transcriptome sequencing (RNA-seq) and clinical data of HCC were downloaded from the public database the Cancer Genome Atlas (TCGA), and the mRNA expression-based stiffness index (mRNAsi) table of cancer stem cells was downloaded and sorted out to analyze the relationship between mRNAsi and pathological grade and prognosis of HCC. The mRNAsi of HCC was downloaded and the prognostic value of mRNAsi was discussed. Then we used WGCNA to screen the key modules related to liver cancer stem cells (LSCS). Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes were used for the functional and pathway enrichment analysis. The online database STRING was used to construct hub genes coding proteins interaction (PPI) network and screen key genes. Finally, the key genes were analyzed for expression differences and expression correlations. The online database Kaplan-Meier plotter was used for survival analysis and verified.ResultsmRNAsi was significantly upregulated in cancer tissues (P<0.001), and increased with the increase of pathological grade of HCC (P=0.001). The mortality rate of the higher mRNAsi group was higher than that of the lower mRNAsi group (P=0.006). GO analysis found that hub genes were mainly involved in biological processes, such as mitosis and DNA replication, and KEGG showed that hub genes were enriched in cell cycle, DNA mismatch repair, oocyte meiosis, and other signaling pathways. We screened 10 key genes (included CCNB1, CDC20, CDCA8, NDC80, KIF20A, TTK, CDC45, KIF15, MCM2, and NCAPG) related to mRNAsi of HCC based on WGCNA. The key genes were highly expressed in the tumor samples compared to the normal samples. In addition, there was a strong interaction between proteins of these key genes (P<0.05), a strong co-expression relationship at the transcriptional level, and all related to prognosis of HCC.ConclusionsmRNAsi plays an important role in the occurrence and development of HCC. Ten key genes related to LSCS were screened, which may act as therapeutic targets for inhibiting the stem cell characteristics of HCC.
Epigenetics refers to the modification effect of external and internal environmental factors on genes under the premise of the unaltered genetic sequence, leading to changes in gene expression level or function, and thereby affecting various phenotypes or disease outcomes. In recent years, epigenetics has attracted increasing attention. Among them, DNA methylation has been shown to be closely related to human development and the development of disease. However, the high-dimensional omics data generated by genome-wide methylation detection can comprehensively reflect the overall and local epigenetic modifications at the genome level, which has become one of the main research contents in this field. Based on genome-wide methylation chip data, this paper summarized the quality control process of this omics data, common epigenetic omics correlation statistical analysis methods and ideas, and visualization realization of main results based on SAS JMP Genomics 10 software, so as to provide reference for similar studies.
Objective To detecting the genetic etiology of a family with idiopathic pulmonary arterial hypertension and make gene diagnosis for the patient, so as to guide the targeted treatment and early intervention for the patient and her families. Methods The phenotype information of the family members was reviewed and their peripheral blood was collected for genomic DNA extraction. Exome sequencing was used to screen the mutations and proving the selected mutations by PCR-Sanger sequencing method. The pathogenicity of candidate mutation sites were searched through PubMed and related databases, and analyzed by protein function software. The judgement of pathogenicity was considered by clinical presentations and sequencing results of the patients based on Standards and guidelines for the interpretation of sequence variants revised by ACMG. Results At present, there was only one patient with pulmonary hypertension in this family, and other family members had no clinical manifestations of pulmonary hypertension. The female patient had BMPR2 gene c.1748dupA(p.Asn583Lysfs*6) heterozygous mutant. Her father and second son had BMPR2 gene c.1748dupA(p.Asn583Lysfs*6) heterozygous mutant, but none of the other members of the family had the mutation. Conclusions The heterozygous mutation of c.1748dupA (p.Asn583Lysfs*6) of BMPR2 gene is the genetic cause of the idiopathic pulmonary arterial hypertension patient, and the clinical significance of c.1748dupA(p.Asn583Lysfs*6) is pathogenic. The patient can be further diagnosed as pulmonary hypertension, primary 1 (PPH1) by gene diagnosis, and the mutant is novel and pathogenic for PPH1.
Objective To summarize the progress in related basic research of molecular targeted therapy in pancreatic cancer. Method The relevant literatures on oncogenes, epigenome, tumour microenvironment and immunotherapy in recent years at home and abroad were reviewed. ResultsIn basic research, molecularly targeted drugs had shown some efficacy in the treatment of progression of pancreatic cancer, however, in clinical trials, more satisfactory results were not achieved. Conclusion Molecularly targeted therapies for pancreatic cancer are still at a preliminary stage of exploration, and basic research has not yet been effectively translated clinically, which requires further exploration efforts in subsequent studies to provide a more solid and reliable basis for precise treatment of pancreatic cancer and achieve better clinical benefits.
ObjectiveTo analyze the single nucleotide polymorphism (SNP) and the copy number variation (CNV) of cardiac tumors to find the SNP sites and CNV events that may play important roles in the occurrence of tumors. MethodsThe patients with myxoma admitted to our hospital from 2015 to 2019 were randomly selected. The SNP analysis and the CNV test in gene level were performed through whole exome sequencing (WES). The samples were divided into two groups according to the mean size of the tumor: a diameter≤5.7 cm group and a dimeter>5.7 cm group. The analysis results were compared between the two groups. ResultsA total of 14 patients were enrolled, including 8 females and 6 males with a mean age of 61.4 (41-79) years. Thirty-seven cancer-genes with SNP were detected, among which 18 mutated sites had a mutation rate of>10%; and TP53, EP300 and CREBBP played a core binding role in protein-protein interaction-network. The GO enrichment results showed significant differences in the regulation of cell secretion of the mutated genes, and the KEGG enrichment results showed significant differences in the PI3K-AKT and JAK-STAT signaling pathways in the occurrence of myxoma. In addition, 17 new mutation sites of tumor genes with high mutation effect were found in SNP detection. The WES results of 14 samples showed that the CNV events were detected in 120 tumor genes of the samples, 10 of which were included in two tumor databases. The GO enrichment results showed significant differences in the tube development and regulation of cell proliferation, and the KEGG enrichment results showed significant differences in the comprehensive tumor signaling pathway. Statistical differences of ERCC6L and INTS6L in CNV test were found (P<0.05). ConclusionThere may be multiple tumor gene site mutations in the process of tumor generation, among which there are multiple core tumor genes such as TP53, EP300 and CREB, which regulate tumor cells through PI3K-AKT and JAK-STAT signaling pathways and play an important role in tumor generation. The CNV of ERCC6L and INTS6L genes may be related to tumor growth.
Objective To analyze the drug resistance genes, virulence genes and homologies of carbapenem-resistant Klebsiella pneumoniae (CRKP) colonized and infected patients in surgical intensive care unit based on whole genome sequencing. Methods Whole genome sequencing analysis was performed on CRKP infected strains isolated from the Department of General Surgery Intensive Care Unit and the Department of Liver Surgery Intensive Care Unit of Zhongshan Hospital, Fudan University in March 2021 and CRKP colonized strains isolated from the above departments between January and March 2021. The drug resistance genes, virulence genes and homologies of the strains were analyzed. ResultsA total of 16 CRKP strains were included, including 10 colonized strains and 6 infected strains. Except for the β-lactamase drug resistance gene CTX (16.7% vs. 100.0%, P<0.05), there was no significant difference in the detection rate of other drug resistance genes between CRKP infected strains and colonized strains (P>0.05). The cluster analysis of drug resistance genes of some strains was relatively close. Whole genome sequencing analysis showed that CRKP strains carried a variety of virulence genes, and the detection rates of entB, irp2, iroN, and rmpA genes were 100.0%, 87.5%, 37.5%, and 62.5%, respectively. There was no significant difference in the detection rate of virulence genes between CRKP infected strains and colonized strains (P>0.05). Homology analysis showed that some strains had close homologous relationships, and there was the possibility of cross transmission. Conclusions Some of CRKP infection strains and colonization strains in surgical intensive care unit patients have the risk of cross transmission. In the future, we should strengthen the prevention and control of nosocomial infection to reduce the incidence of infection.