The journey to implement cancer genomic medicine(CGM)in oncology practice began in the 1980s,which is considered the dawn of genetic and genomic cancer research.At the time,a variety of activating oncogenic alteration...The journey to implement cancer genomic medicine(CGM)in oncology practice began in the 1980s,which is considered the dawn of genetic and genomic cancer research.At the time,a variety of activating oncogenic alterations and their functional significance were unveiled in cancer cells,which led to the development of molecular targeted therapies in the 2000s and beyond.Although CGM is still a relatively new discipline and it is difficult to predict to what extent CGM will benefit the diverse pool of cancer patients,the National Cancer Center(NCC)of Japan has already contributed considerably to CGM advancement for the conquest of cancer.Looking back at these past achievements of the NCC,we predict that the future of CGM will involve the following:1)A biobank of paired cancerous and non-cancerous tissues and cells from various cancer types and stages will be developed.The quantity and quality of these samples will be compatible with omics analyses.All biobank samples will be linked to longitudinal clinical information.2)New technologies,such as whole-genome sequencing and artificial intelligence,will be introduced and new bioresources for functional and pharmacologic analyses(e.g.,a patient-derived xenograft library)will be systematically deployed.3)Fast and bidirectional translational research(bench-to-bedside and bedside-to-bench)performed by basic researchers and clinical investigators,preferably working alongside each other at the same institution,will be implemented;4)Close collaborations between academia,industry,regulatory bodies,and funding agencies will be established.5)There will be an investment in the other branch of CGM,personalized preventive medicine,based on the individual's genetic predisposition to cancer.展开更多
In the past decade, the remarkable development of high-throughput sequencing technology accelerates the generation of large amount of multiple dimensional data such as genomic, epigenomic, transcriptomic and proteomic...In the past decade, the remarkable development of high-throughput sequencing technology accelerates the generation of large amount of multiple dimensional data such as genomic, epigenomic, transcriptomic and proteomic data. The comprehensive data make it possible to understand the underlying mechanisms of biology and disease such as cancer systematically. It also provides great challenges for computa- tional cancer genomics due to the complexity, scale and noise of data. In this article, we aim to review the recent develop- ments and progresses of computational models, algorithms and analysis of complex data in cancer genomics. These topics of this paper include the identification of driver mutations, the genetic heterogeneity analysis, genomic markers discovery of drug response, pan-cancer scale analysis and so on.展开更多
Publicly-accessible resources have promoted the advance of scientific discovery. The era of genomics and big data has brought the need for collaboration and data sharing in order to make effective use of this new know...Publicly-accessible resources have promoted the advance of scientific discovery. The era of genomics and big data has brought the need for collaboration and data sharing in order to make effective use of this new knowledge. Here, we describe the web resources for cancer genomics research and rate them on the basis of the diversity of cancer types, sample size, omics data comprehensiveness, and user experience. The resources reviewed include data repository and analysis tools; and we hope such introduction will promote the awareness and facilitate the usage of these resources in the cancer research community.展开更多
Background:The past decade has witnessed a rapid progress in our understanding of the genetics of cancer and its progression.Probabilistic and statistical modeling played a pivotal role in the discovery of general pat...Background:The past decade has witnessed a rapid progress in our understanding of the genetics of cancer and its progression.Probabilistic and statistical modeling played a pivotal role in the discovery of general patterns from cancer genomics datasets and continue to be of central importance for personalized medicine.Results:In this review we introduce cancer genomics from a probabilistic and statistical perspective.We start from(1)functional classification of genes into oncogenes and tumor suppressor genes,then(2)demonstrate the importance of comprehensive analysis of different mutation types for individual cancer genomes,followed by(3)tumor purity analysis,which in turn leads to(4)the concept of ploidy and clonality,that is next connected to(5)tumor evolution under treatment pressure,which yields insights into cancer drug resistance.We also discuss future challenges including the non-coding genomic regions,integrative analysis of genomics and epigenomics,as well as early cancer detection.Conclusion:We believe probabilistic and statistical modeling will continue to play important roles for novel discoveries in the field o f cancer genomics and personalized medicine.展开更多
Gastric cancer(GC) is a highly heterogenic disease,and it is the second leading cause of cancer death in the world.Common chemotherapies are not very effective for GC,which often presents as an advanced or metastatic ...Gastric cancer(GC) is a highly heterogenic disease,and it is the second leading cause of cancer death in the world.Common chemotherapies are not very effective for GC,which often presents as an advanced or metastatic disease at diagnosis.Treatment options are limited,and the prognosis for advanced GCs is poor.The landscape of genomic alterations in GCs has recently been characterized by several international cancer genome programs,including studies that focused exclusively on GCs in Asians.These studies identified major recurrent driver mutations and provided new insights into the mutational heterogeneity and genetic profiles of GCs.An analysis of gene expression data by the Asian Cancer Research Group(ACRG) further uncovered four distinct molecular subtypes with well-defined clinical features and their intersections with actionable genetic alterations to which targeted therapeutic agents are either already available or under clinical development.In this article,we review the ACRG GC project.We also discuss the implications of the genetic and molecular findings from various GC genomic studies with respect to developing more precise diagnoses and treatment approaches for GCs.展开更多
All cancers arise as a result of abnormalities occurring in the DNA sequence of cancer cells, and we are now stepping into an era in which it is feasible to obtain the complete DNA sequence of large cohorts of cancer ...All cancers arise as a result of abnormalities occurring in the DNA sequence of cancer cells, and we are now stepping into an era in which it is feasible to obtain the complete DNA sequence of large cohorts of cancer patients. The International Cancer Genome Consortium （ICGC） launched in 2007 is devoted to coordinate large-scale cancer genome studies in tumors from 50 different cancer types and/or subtypes and systematic studies of more than 25,000 cancer genomes. Several participant groups have summa- rized and published their data for various cancers. As the active members of ICGC, Chinese cancer genome investi- gators have contributed research for 13 tumor types and released some research articles about esophageal, liver, bladder, and kidney cancers. As genetic alterations in thousands of tumors have now been catalogued, the pan- cancer analysis has become ICGC at present. The ICGC the most significant role of research network will reveal the repertoire of oncogenic mutations, uncover traces of the mutagenic influences, define molecular subtypes for clinicalimplication, and enable the development of individual therapeutics for human cancers.展开更多
Endometrial cancer is the most common gynecologic cancer diagnosed in the United States and mortality is on the rise.Advanced and recurrent endometrial cancer represents a treatment challenge as historically there hav...Endometrial cancer is the most common gynecologic cancer diagnosed in the United States and mortality is on the rise.Advanced and recurrent endometrial cancer represents a treatment challenge as historically there have been limited therapeutic options for patients.In the last several years,multiple practice-changing clinical trials have led to significant improvements in the treatment landscape.This review will cover updates in the treatment and management of advanced and recurrent endometrial cancer with a focus on novel therapeutics,such as anti-PD-L1 and PD-1 inhibitors,poly ADP-ribose polymerase(PARP)inhibitors,antibody-drug conjugates,and hormonal therapy.展开更多
BACKGROUNDGastric cancer(GC)has a high prevalence and mortality overall.GEN1 is associatedwith abnormal centrosome amplification,DNA damage and increasedapoptosis.To date,little is known about the function and mechani...BACKGROUNDGastric cancer(GC)has a high prevalence and mortality overall.GEN1 is associatedwith abnormal centrosome amplification,DNA damage and increasedapoptosis.To date,little is known about the function and mechanism of GEN1 inGC.AIMTo explore the cellular processes associated with GC will help to elucidate themechanism of the occurrence and development of GC and discover potentialtherapeutic targets.METHODSThe detection of GEN1 expression at mRNA and protein levels was done by realtimequantitative polymerase chain reaction and western blotting.The function ofGEN1 was verified by loss-of-function experiments in AGS cells.The genes coexpressedwith GEN1 were searched from the stomach adenocarcinomas(STAD)data in The Cancer Genome Atlas database.Kyoto Encyclopedia of Genes andGenomes(KEGG)enrichment analysis of the genes co-expressed with GEN1 tofurther identify the pathways involved in GEN1.Rescue experiments usingferroptosis inhibitor ferrostatin-1 and chemotherapeutic sensitivity assays withcisplatin were also performed.RESULTSSignificant up-regulation of GEN1 was observed in GC cell lines AGS and MGC-803.Inhibition of GEN1 induced cell apoptosis and decreased cell proliferation,cycle progression,migration in AGS cells.There were 264 genes co-expressedwith GEN1 in STAD cohort(r>0.4,P<0.001).KEGG enrichment analysis showed that GEN1 might be associated with the cell cycle,Fanconi anemia pathway,homologous recombination,oocytemeiosis and cellular senescence in GC.Furthermore,CCNA2,CCNB1,CCNB2,cyclin-dependent kinase(CDK)1,CDK2 and polo-like kinase 1 protein levels were lower in GEN1-knockdown AGS cells,manifesting that GEN1 wasassociated with the cell cycle pathway in AGS cells.Downregulation of GEN1 decreased adenosine triphosphatecontent and elevated reactive oxygen species in AGS cells,suggesting that GEN1 silencing led to mitochondrialdysfunction in AGS cells.In addition,GEN1 silencing caused an overt decrease in FTH1 and GPX4 protein levelsand a significant elevation in ACSL4 protein levels,implying that GEN1 silencing promoted AGS cell ferroptosis.Treatment with ferrostatin-1 rescued cell viability loss induced by GEN1 knockdown,confirming ferroptosis as akey death mechanism.Additionally,GEN1-deficient AGS cells showed enhanced sensitivity to cisplatin,with asignificantly reduced half-maximal inhibitory concentration compared to control cells.CONCLUSIONGEN1 promotes GC cell proliferation and migration while suppressing apoptosis and ferroptosis.Targeting GEN1not only disrupts mitochondrial function and cell cycle progression but also sensitizes GC cells to ferroptosis andchemotherapy.These findings highlight GEN1 as a potential therapeutic target for enhancing treatment efficacy ingastric cancer.展开更多
Objectives:Colorectal cancer(CRC)remains a major contributor to global cancer mortality,ranking second worldwide for cancer-related deaths in 2022,and is characterized by marked heterogeneity in prognosis and therapeu...Objectives:Colorectal cancer(CRC)remains a major contributor to global cancer mortality,ranking second worldwide for cancer-related deaths in 2022,and is characterized by marked heterogeneity in prognosis and therapeutic response.We sought to construct a machine-learning prognosticmodel based on a complement-related risk signature(CRRS)and to situate this signature within the CRC immune microenvironment.Methods:Transcriptomic profiles with matched clinical annotations from TCGA and GEO CRC cohorts were analyzed.Prognostic CRRS genes were screened using Cox proportional hazards modeling alongside machine-learning procedures.A random survival forest(RSF)predictor was trained and externally validated.Comparisons of immune infiltration,mutational burden,pathway enrichment,and drug sensitivity were made between risk groups.The function of FAM84A,a key model gene,was examined in CRC cell lines.Results:The six-gene CRRS model accurately stratified patients by survival outcomes.Low-risk patients exhibited greater immune cell infiltration and higher predicted response to immunotherapy and chemotherapy,while high-risk patients showed enrichment of complement activation and matrix remodeling pathways.FAM84A was shown to promote CRC cell proliferation,migration,and epithelial–mesenchymal transition.Conclusion:CRRS is a critical modulator of the CRC immune microenvironment.The developed model enables precise risk prediction and supports individualized therapeutic decisions in CRC.展开更多
Background:Published clinical trials have yielded controversial findings regarding the effects of sex on the benefits of immune checkpoint inhibitors(ICIs).Sex-associated differences in the efficacy of immunotherapy r...Background:Published clinical trials have yielded controversial findings regarding the effects of sex on the benefits of immune checkpoint inhibitors(ICIs).Sex-associated differences in the efficacy of immunotherapy remain an important,unresolved question.Methods:We investigated sex-biased molecular profiles across a multitude of biomarkers linked to immunotherapy responses.Multiomics data from major solid tumors in The Cancer Genome Atlas,with sufficient sample sizes(≥50 patients of each sex),were analyzed.Ninety-five molecular markers characterizing 4 distinct aspects of the tumor immune system were summarized and compared.The inverse probability of weights algorithm was used to generate well-balanced sex subgroups.Results:Our results showed that lung squamous cell carcinoma(LUSC),pancreatic adenocarcinoma,and liver hepatocellular carcinoma were the top 3 cancer types with extensive sex-biased biomarker profiles(31/95,15/95,and 14/95,respectively).Notably,although both were categorized as non–small cell lung carcinoma,LUSC harbored significantly more sex-biased immunological features than those of lung adenocarcinoma(p<0.01).We further explored the validity of this finding by analyzing ICI-responsive signatures and individual patient-level data for non–small cell lung carcinoma and found that sex had significant interaction effects on immunotherapy outcomes in LUSC(p_(interaction)<0.05),with women tending to derive greater benefits from ICIs than men.However,this difference was not apparent in the lung adenocarcinoma group(p_(interaction)=0.66),with men and women deriving comparable benefits.Conclusions:We systematically characterized sex-biased profiles of key molecular biomarkers predicting immunotherapy responses across solid tumors,which could pave the way for individualized therapeutic approaches for men and women.展开更多
BACKGROUND Gastrointestinal tumors are among the most common cancer types,and early detection is paramount to improve their management.Cell-free DNA(cfDNA)liquid biopsy raises significant hopes for non-invasive early ...BACKGROUND Gastrointestinal tumors are among the most common cancer types,and early detection is paramount to improve their management.Cell-free DNA(cfDNA)liquid biopsy raises significant hopes for non-invasive early detection.AIM To describe current applications of this technology for gastrointestinal cancer detection and screening.METHODS A systematic review of the literature was performed across the PubMed database.Articles reporting the use of cfDNA liquid biopsy in the screening or diagnosis of gastrointestinal cancers were included in the analysis.RESULTS A total of 263 articles were screened for eligibility,of which 13 articles were included.Studies investigated colorectal cancer(5 studies),pancreatic cancer(2 studies),hepatocellular carcinoma(3 studies),and multi-cancer detection(3 studies),including gastric,oesophageal,or bile duct cancer,representing a total of 4824 patients.Test sensitivities ranged from 71% to 100%,and specificities ranged from 67.4% to 100%.Pre-cancerous lesions detection was less performant with a sensitivity of 16.9% and a 100% specificity in one study.Another study using a large biobank demonstrated a 94.9% sensitivity in detecting cancer up to 4 years before clinical symptoms,with a 61% accuracy in tissue-of-origin identification.CONCLUSION cfDNA liquid biopsy seems capable of detecting gastrointestinal cancers at an early stage of development in a non-invasive and repeatable manner and screening simultaneously for multiple cancer types in a single blood sample.Further trials in clinically relevant settings are required to determine the exact place of this technology in gastrointestinal cancer screening and diagnosis strategies.展开更多
Background:Doublecortin(DCX),a microtubule-associated protein,is best known for its critical role in neuronal migration during neural development,where it stabilizes microtubules and guides neurons to their proper pos...Background:Doublecortin(DCX),a microtubule-associated protein,is best known for its critical role in neuronal migration during neural development,where it stabilizes microtubules and guides neurons to their proper positions.Recently,DCX has been implicated in various cancer processes,suggesting it may influence tumor progression and the tumor microenvironment.Emerging evidence indicates that DCX can modulate cell migration,invasion,and interaction with immune cells,making it a potential player in oncogenesis.However,the role of DCX across different cancer types and its potential as a prognostic biomarker remain underexplored,necessitating a comprehensive analysis.Methods:We utilized The Cancer Genome Atlas to extract data on DCX expression in tumor and adjacent normal tissues across diverse cancer types.Differential expression analysis was conducted using differential expression sequencing 2.Survival analysis was performed with Kaplan-Meier estimates and Cox proportional hazards models.Correlations between DCX expression and tumor mutational burden,microsatellite instability,and immune infiltration were examined using Spearman’s correlation.Results:DCX showed variable expression across cancer types,with significant overexpression in certain tumors such as liver and lung cancer and downexpression in others like breast cancer.High DCX expression was correlated with poor prognosis in adrenocortical carcinoma but with better outcomes in low-grade glioma.Additionally,DCX expression was significantly associated with various immune markers and chemokines,suggesting a role in modulating the immune microenvironment.Conclusion:Our findings highlight the complex role of DCX in cancer,underlining its potential as a prognostic marker and its involvement in immune-related pathways.Targeting DCX could represent a novel approach to modulating tumor behavior and enhancing immune response in cancer therapy.展开更多
Gastric cancer(GC) is a highly aggressive and life-threatening malignancy.Even with radical surgical removal and front-line chemotherapy,more than half of GCs locally relapse and metastasize at a distant site.The dism...Gastric cancer(GC) is a highly aggressive and life-threatening malignancy.Even with radical surgical removal and front-line chemotherapy,more than half of GCs locally relapse and metastasize at a distant site.The dismal outcomes reflect the ineffectiveness of a one-size fits-all approach for a highly heterogeneous disease with diverse etiological causes and complex molecular underpinnings.The recent comprehensive genomic and molecular profiling has led to our deepened understanding of GC.The emerging molecular classification schemes based on the genetic,epigenetic,and molecular signatures are providing great promise for the development of more effective therapeutic strategies in a more personalized and precise manner.To this end,the Cancer Genome Atlas(TCGA) research network conducted a comprehensive molecular evaluation of primary GCs and proposed a new molecular classification dividing GCs into four subtypes:Epstein-Barr virus-associated tumors,microsatellite unstable tumors,genomically stable tumors,and tumors with chromosomal instability.This review primarily focuses on the TCGA molecular classification of GCs and discusses the implications on novel targeted therapy strategies.We believe that these fundamental findings will support the future application of targeted therapies and will guide our efforts to develop more efficacious drugs to treat human GCs.展开更多
BACKGROUND Self-renewal of gastric cancer stem cells(GCSCs)is considered to be the underlying cause of the metastasis,drug resistance,and recurrence of gastric cancer(GC).AIM To characterize the expression of stem cel...BACKGROUND Self-renewal of gastric cancer stem cells(GCSCs)is considered to be the underlying cause of the metastasis,drug resistance,and recurrence of gastric cancer(GC).AIM To characterize the expression of stem cell-related genes in GC.METHODS RNA sequencing results and clinical data for gastric adenoma and adenocarcinoma samples were obtained from The Cancer Genome Atlas database,and the results of the GC mRNA expression-based stemness index(mRNAsi)were analyzed.Weighted gene coexpression network analysis was then used to find modules of interest and their key genes.Survival analysis of key genes was performed using the online tool Kaplan-Meier Plotter,and the online database Oncomine was used to assess the expression of key genes in GC.RESULTS mRNAsi was significantly upregulated in GC tissues compared to normal gastric tissues(P<0.0001).A total of 16 modules were obtained from the gene coexpression network;the brown module was most positively correlated with mRNAsi.Sixteen key genes(BUB1,BUB1 B,NCAPH,KIF14,RACGAP1,RAD54 L,TPX2,KIF15,KIF18 B,CENPF,TTK,KIF4 A,SGOL2,PLK4,XRCC2,a n d C1 orf112)were identified in the brown module.The functional and pathway enrichment analyses showed that the key genes were significantly enriched in the spindle cellular component,the sister chromatid segregation biological process,the motor activity molecular function,and the cell cycle and homologous recombination pathways.Survival analysis and Oncomine analysis revealed that the prognosis of patients with GC and the expression of three genes(RAD54 L,TPX2,and XRCC2)were consistently related.CONCLUSION Sixteen key genes are primarily associated with stem cell self-renewal and cell proliferation characteristics.RAD54 L,TPX2,and XRCC2 are the most likely therapeutic targets for inhibiting the stemness characteristics of GC cells.展开更多
Human tongue cancer （TC） is an aggressive malignancy with a very poor prognosis. There is an urgent need to elucidate the underlying molecular mechanisms involved in TC progression, mRNA expression profiles play a v...Human tongue cancer （TC） is an aggressive malignancy with a very poor prognosis. There is an urgent need to elucidate the underlying molecular mechanisms involved in TC progression, mRNA expression profiles play a vital role in the exploration of cancer-related genes. Therefore, the purpose of our study was to identify the progression associated candidate genes of TC by bioinformatics analysis. Five microarray datasets of TC samples were downloaded from the Gene Expression Onmibus （GEO） database and the data of 133 TC patients were screened from The Cancer Genome Atlas （TCGA） head and neck squamous cell carcinoma （HNSC） database. The integrated analysis of five microarray datasets and the RNA sequencing data of TC samples in TCGA-HNSC was performed to obtain 1023 overlapping differentially expressed genes （DEGs） in TC and adjacent normal tissue （ANT） samples. Next, Kyoto Encyclopedia of Genes and Genomes （KEGG） pathway analysis was conducted to enrich the significant pathways of the 1023 DEGs and PI3K- Akt signaling pathway （P=0.011） was selected to be the candidate pathway. A total of 23 DEGs with ｜log2 fold change （FC）｜ ≥1.0 in phosphatidylinositol 3-kinase-serine/threonine kinase （PI3K-Akt） signaling pathway were subjected to survival analysis of 125 eligible TC samples in TCGA database, indicating increased integrin-α3 gene （ITGA3） expression was significantly associated with poorer prognosis. Taken together, our study suggested ITGA3 may facilitate the development of TC via activating PI3K-Akt signaling pathway.展开更多
Esophageal cancer is a common malignant tumor, whose pathogenesis and prognosis factors are not fully understood. This study aimed to discover the gene clusters that have similar functions and can be used to predict t...Esophageal cancer is a common malignant tumor, whose pathogenesis and prognosis factors are not fully understood. This study aimed to discover the gene clusters that have similar functions and can be used to predict the prognosis of esophageal cancer. The matched microarray and RNA sequencing data of 185 patients with esophageal cancer were downloaded from The Cancer Genome Atlas(TCGA), and gene co-expression networks were built without distinguishing between squamous carcinoma and adenocarcinoma. The result showed that 12 modules were associated with one or more survival data such as recurrence status, recurrence time, vital status or vital time. Furthermore, survival analysis showed that 5 out of the 12 modules were related to progression-free survival(PFS) or overall survival(OS). As the most important module, the midnight blue module with 82 genes was related to PFS, apart from the patient age, tumor grade, primary treatment success, and duration of smoking and tumor histological type. Gene ontology enrichment analysis revealed that 'glycoprotein binding' was the top enriched function of midnight blue module genes. Additionally, the blue module was the exclusive gene clusters related to OS. Platelet activating factor receptor(PTAFR) and feline Gardner-Rasheed(FGR) were the top hub genes in both modeling datasets and the STRING protein interaction database. In conclusion, our study provides novel insights into the prognosis-associated genes and screens out candidate biomarkers for esophageal cancer.展开更多
BACKGROUND Breast cancer(BC)is the most common malignant tumor in women.AIM To investigate BC-associated hub genes to obtain a better understanding of BC tumorigenesis.METHODS In total,1203 BC samples were downloaded ...BACKGROUND Breast cancer(BC)is the most common malignant tumor in women.AIM To investigate BC-associated hub genes to obtain a better understanding of BC tumorigenesis.METHODS In total,1203 BC samples were downloaded from The Cancer Genome Atlas database,which included 113 normal samples and 1090 tumor samples.The limma package of R software was used to analyze the differentially expressed genes(DEGs)in tumor tissues compared with normal tissues.The cluster Profiler package was used to perform Kyoto Encyclopedia of Genes and Genomes(KEGG)enrichment analysis of upregulated and downregulated genes.Univariate Cox regression was conducted to explore the DEGs with statistical significance.Protein-protein interaction(PPI)network analysis was employed to investigate the hub genes using the CytoHubba plug-in of Cytoscape software.Survival analyses of the hub genes were carried out using the Kaplan-Meier method.The expression level of these hub genes was validated in the Gene Expression Profiling Interactive Analysis database and Human Protein Atlas database.RESULTS A total of 1317 DEGs(fold change>2;P<0.01)were confirmed through bioinformatics analysis,which included 744 upregulated and 573 downregulated genes in BC samples.KEGG enrichment analysis indicated that the upregulated genes were mainly enriched in the cytokine-cytokine receptor interaction,cell cycle,and the p53 signaling pathway(P<0.01);and the downregulated genes were mainly enriched in the cytokine-cytokine receptor interaction,peroxisome proliferator-activated receptor signaling pathway,and AMP-activated protein kinase signaling pathway(P<0.01).CONCLUSION In view of the results of PPI analysis,which were verified by survival and expression analyses,we conclude that MAD2L1,PLK1,SAA1,CCNB1,SHCBP1,KIF4A,ANLN,and ERCC6L may act as biomarkers for the diagnosis and prognosis in BC patients.展开更多
BACKGROUND Breast cancer is regarded as a highly malignant neoplasm in the female population,posing a significant risk to women’s overall well-being.The prevalence of breast cancer has been observed to rise in China,...BACKGROUND Breast cancer is regarded as a highly malignant neoplasm in the female population,posing a significant risk to women’s overall well-being.The prevalence of breast cancer has been observed to rise in China,accompanied by an earlier age of onset when compared to Western countries.Breast cancer continues to be a prominent contributor to cancer-related mortality and morbidity among women,primarily due to its limited responsiveness to conventional treatment modalities.The diagnostic process is challenging due to the presence of non-specific clinical manifestations and the suboptimal precision of conventional diagnostic tests.There is a prevailing uncertainty regarding the most effective screening method and target populations,as well as the specificities and execution of screening programs.AIM To identify diagnostic and prognostic biomarkers for breast cancer.METHODS Overlapping differentially expressed genes were screened based on Gene Expression Omnibus(GSE36765,GSE10810,and GSE20086)and The Cancer Genome Atlas datasets.A protein-protein interaction network was applied to excavate the hub genes among these differentially expressed genes.Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses,as well as gene set enrichment analyses,were conducted to examine the functions of these genes and their potential mechanisms in the development of breast cancer.For clarification of the diagnostic and prognostic roles of these genes,Kaplan–Mei-er and Cox proportional hazards analyses were conducted.RESULTS This study demonstrated that calreticulin,heat shock protein family B member 1,insulin-like growth Factor 1,interleukin-1 receptor 1,Krüppel-like factor 4,suppressor of cytokine signaling 3,and triosephosphate isomerase 1 are potential diagnostic biomarkers of breast cancer as well as potential treatment targets with clinical implications.CONCLUSION The screening of biomarkers is of guiding significance for the diagnosis and prognosis of the diseases.展开更多
BACKGROUND Gastric cancer(GC) ranks as the third leading cause of cancer-related death worldwide. Epigenetic alterations contribute to tumor heterogeneity in early stages.AIM To identify the specific deoxyribonucleic ...BACKGROUND Gastric cancer(GC) ranks as the third leading cause of cancer-related death worldwide. Epigenetic alterations contribute to tumor heterogeneity in early stages.AIM To identify the specific deoxyribonucleic acid(DNA) methylation sites that influence the prognosis of GC patients and explore the prognostic value of a model based on subtypes of DNA methylation.METHODS Patients were randomly classified into training and test sets. Prognostic DNA methylation sites were identified by integrating DNA methylation profiles and clinical data from The Cancer Genome Atlas GC cohort. In the training set, unsupervised consensus clustering was performed to identify distinct subgroups based on methylation status. A risk score model was built based on Kaplan-Meier, least absolute shrinkage and selector operation, and multivariate Cox regression analyses. A test set was used to validate this model.RESULTS Three subgroups based on DNA methylation profiles in the training set were identified using 1061 methylation sites that were significantly associated with survival. These methylation subtypes reflected differences in T, N, and M category, age, stage, and prognosis. Forty-one methylation sites were screened as specific hyper-or hypomethylation sites for each specific subgroup. Enrichment analysis revealed that they were mainly involved in pathways related to carcinogenesis, tumor growth, and progression. Finally, two methylation sites were chosen to generate a prognostic model. The high-risk group showed a markedly poor prognosis compared to the low-risk group in both the training [hazard ratio(HR) = 2.24, 95% confidence interval(CI): 1.28-3.92, P < 0.001] and test(HR = 2.12, 95%CI: 1.19-3.78, P = 0.002) datasets.CONCLUSION DNA methylation-based classification reflects the epigenetic heterogeneity of GC and may contribute to predicting prognosis and offer novel insights for individualized treatment of patients with GC.展开更多
BACKGROUND The distal-less homeobox(DLX)gene family plays an important role in the development of several tumors.However,the expression pattern,prognostic and diagnostic value,possible regulatory mechanisms,and the re...BACKGROUND The distal-less homeobox(DLX)gene family plays an important role in the development of several tumors.However,the expression pattern,prognostic and diagnostic value,possible regulatory mechanisms,and the relationship between DLX family genes and immune infiltration in colon cancer have not been systematically reported.AIM We aimed to comprehensively analyze the biological role of the DLX gene family in the pathogenesis of colon cancer.METHODS Colon cancer tissue and normal colon tissue samples were collected from the Cancer Genome Atlas and Gene Expression Omnibus databases.Wilcoxon rank sum test and t-test were used to assess DLX gene family expression between colon cancer tissue and unpaired normal colon tissue.cBioPortal was used to analyze DLX gene family variants.R software was used to analyze DLX gene expression in colon cancer and the relationship between DLX gene family expression and clinical features and correlation heat map.The survival package and Cox regression module were used to assess the prognostic value of the DLX gene family.The pROC package was used to analyze the diagnostic value of the DLX gene family.R software was used to analyze the possible regulatory mechanisms of DLX gene family members and related genes.The GSVA package was used to analyze the relationship between the DLX gene family and immune infiltration.The ggplot2,the survminer package,and the clusterProfiler package were used for visualization.RESULTS DLX1/2/3/4/5 were significantly aberrantly expressed in colon cancer patients.The expression of DLX genes were associated with M stage,pathologic stage,primary therapy outcome,residual tumor,lymphatic invasion,T stage,N stage,age,perineural invasion,and history of colon polyps.DLX5 was independently correlated with the prognosis of colon cancer in multivariate analysis.DLX1/2/3/4/5/6 were involved in the development and progression of colon cancer by participating in immune infiltration and associated pathways,including the Hippo signaling pathway,the Wnt signaling pathway,several signaling pathways regulating the pluripotency of stem cells,and Staphylococcus aureus infection.CONCLUSION The results of this study suggest a possible role for the DLX gene family as potential diagnostic or prognostic biomarkers and therapeutic targets in colon cancer.展开更多
文摘The journey to implement cancer genomic medicine(CGM)in oncology practice began in the 1980s,which is considered the dawn of genetic and genomic cancer research.At the time,a variety of activating oncogenic alterations and their functional significance were unveiled in cancer cells,which led to the development of molecular targeted therapies in the 2000s and beyond.Although CGM is still a relatively new discipline and it is difficult to predict to what extent CGM will benefit the diverse pool of cancer patients,the National Cancer Center(NCC)of Japan has already contributed considerably to CGM advancement for the conquest of cancer.Looking back at these past achievements of the NCC,we predict that the future of CGM will involve the following:1)A biobank of paired cancerous and non-cancerous tissues and cells from various cancer types and stages will be developed.The quantity and quality of these samples will be compatible with omics analyses.All biobank samples will be linked to longitudinal clinical information.2)New technologies,such as whole-genome sequencing and artificial intelligence,will be introduced and new bioresources for functional and pharmacologic analyses(e.g.,a patient-derived xenograft library)will be systematically deployed.3)Fast and bidirectional translational research(bench-to-bedside and bedside-to-bench)performed by basic researchers and clinical investigators,preferably working alongside each other at the same institution,will be implemented;4)Close collaborations between academia,industry,regulatory bodies,and funding agencies will be established.5)There will be an investment in the other branch of CGM,personalized preventive medicine,based on the individual's genetic predisposition to cancer.
文摘In the past decade, the remarkable development of high-throughput sequencing technology accelerates the generation of large amount of multiple dimensional data such as genomic, epigenomic, transcriptomic and proteomic data. The comprehensive data make it possible to understand the underlying mechanisms of biology and disease such as cancer systematically. It also provides great challenges for computa- tional cancer genomics due to the complexity, scale and noise of data. In this article, we aim to review the recent develop- ments and progresses of computational models, algorithms and analysis of complex data in cancer genomics. These topics of this paper include the identification of driver mutations, the genetic heterogeneity analysis, genomic markers discovery of drug response, pan-cancer scale analysis and so on.
基金supported by the Strategic Priority Research Program of the Chinese Academy of Sciences,Stem Cell and Regenerative Medicine Research(Grant No.XDA01040405)the National High-tech R&D Program of China(863Program,2012AA022502)+1 种基金the National‘‘Twelfth FiveYear’’Plan for Science&Technology Support of China(2013BAI01B09) awarded to XFthe National Natural Science Foundation of China(Grant No.31471236)awarded to YL
文摘Publicly-accessible resources have promoted the advance of scientific discovery. The era of genomics and big data has brought the need for collaboration and data sharing in order to make effective use of this new knowledge. Here, we describe the web resources for cancer genomics research and rate them on the basis of the diversity of cancer types, sample size, omics data comprehensiveness, and user experience. The resources reviewed include data repository and analysis tools; and we hope such introduction will promote the awareness and facilitate the usage of these resources in the cancer research community.
文摘Background:The past decade has witnessed a rapid progress in our understanding of the genetics of cancer and its progression.Probabilistic and statistical modeling played a pivotal role in the discovery of general patterns from cancer genomics datasets and continue to be of central importance for personalized medicine.Results:In this review we introduce cancer genomics from a probabilistic and statistical perspective.We start from(1)functional classification of genes into oncogenes and tumor suppressor genes,then(2)demonstrate the importance of comprehensive analysis of different mutation types for individual cancer genomes,followed by(3)tumor purity analysis,which in turn leads to(4)the concept of ploidy and clonality,that is next connected to(5)tumor evolution under treatment pressure,which yields insights into cancer drug resistance.We also discuss future challenges including the non-coding genomic regions,integrative analysis of genomics and epigenomics,as well as early cancer detection.Conclusion:We believe probabilistic and statistical modeling will continue to play important roles for novel discoveries in the field o f cancer genomics and personalized medicine.
文摘Gastric cancer(GC) is a highly heterogenic disease,and it is the second leading cause of cancer death in the world.Common chemotherapies are not very effective for GC,which often presents as an advanced or metastatic disease at diagnosis.Treatment options are limited,and the prognosis for advanced GCs is poor.The landscape of genomic alterations in GCs has recently been characterized by several international cancer genome programs,including studies that focused exclusively on GCs in Asians.These studies identified major recurrent driver mutations and provided new insights into the mutational heterogeneity and genetic profiles of GCs.An analysis of gene expression data by the Asian Cancer Research Group(ACRG) further uncovered four distinct molecular subtypes with well-defined clinical features and their intersections with actionable genetic alterations to which targeted therapeutic agents are either already available or under clinical development.In this article,we review the ACRG GC project.We also discuss the implications of the genetic and molecular findings from various GC genomic studies with respect to developing more precise diagnoses and treatment approaches for GCs.
基金supported by the National NaturalScience Foundation of China(81402300)
文摘All cancers arise as a result of abnormalities occurring in the DNA sequence of cancer cells, and we are now stepping into an era in which it is feasible to obtain the complete DNA sequence of large cohorts of cancer patients. The International Cancer Genome Consortium （ICGC） launched in 2007 is devoted to coordinate large-scale cancer genome studies in tumors from 50 different cancer types and/or subtypes and systematic studies of more than 25,000 cancer genomes. Several participant groups have summa- rized and published their data for various cancers. As the active members of ICGC, Chinese cancer genome investi- gators have contributed research for 13 tumor types and released some research articles about esophageal, liver, bladder, and kidney cancers. As genetic alterations in thousands of tumors have now been catalogued, the pan- cancer analysis has become ICGC at present. The ICGC the most significant role of research network will reveal the repertoire of oncogenic mutations, uncover traces of the mutagenic influences, define molecular subtypes for clinicalimplication, and enable the development of individual therapeutics for human cancers.
文摘Endometrial cancer is the most common gynecologic cancer diagnosed in the United States and mortality is on the rise.Advanced and recurrent endometrial cancer represents a treatment challenge as historically there have been limited therapeutic options for patients.In the last several years,multiple practice-changing clinical trials have led to significant improvements in the treatment landscape.This review will cover updates in the treatment and management of advanced and recurrent endometrial cancer with a focus on novel therapeutics,such as anti-PD-L1 and PD-1 inhibitors,poly ADP-ribose polymerase(PARP)inhibitors,antibody-drug conjugates,and hormonal therapy.
文摘BACKGROUNDGastric cancer(GC)has a high prevalence and mortality overall.GEN1 is associatedwith abnormal centrosome amplification,DNA damage and increasedapoptosis.To date,little is known about the function and mechanism of GEN1 inGC.AIMTo explore the cellular processes associated with GC will help to elucidate themechanism of the occurrence and development of GC and discover potentialtherapeutic targets.METHODSThe detection of GEN1 expression at mRNA and protein levels was done by realtimequantitative polymerase chain reaction and western blotting.The function ofGEN1 was verified by loss-of-function experiments in AGS cells.The genes coexpressedwith GEN1 were searched from the stomach adenocarcinomas(STAD)data in The Cancer Genome Atlas database.Kyoto Encyclopedia of Genes andGenomes(KEGG)enrichment analysis of the genes co-expressed with GEN1 tofurther identify the pathways involved in GEN1.Rescue experiments usingferroptosis inhibitor ferrostatin-1 and chemotherapeutic sensitivity assays withcisplatin were also performed.RESULTSSignificant up-regulation of GEN1 was observed in GC cell lines AGS and MGC-803.Inhibition of GEN1 induced cell apoptosis and decreased cell proliferation,cycle progression,migration in AGS cells.There were 264 genes co-expressedwith GEN1 in STAD cohort(r>0.4,P<0.001).KEGG enrichment analysis showed that GEN1 might be associated with the cell cycle,Fanconi anemia pathway,homologous recombination,oocytemeiosis and cellular senescence in GC.Furthermore,CCNA2,CCNB1,CCNB2,cyclin-dependent kinase(CDK)1,CDK2 and polo-like kinase 1 protein levels were lower in GEN1-knockdown AGS cells,manifesting that GEN1 wasassociated with the cell cycle pathway in AGS cells.Downregulation of GEN1 decreased adenosine triphosphatecontent and elevated reactive oxygen species in AGS cells,suggesting that GEN1 silencing led to mitochondrialdysfunction in AGS cells.In addition,GEN1 silencing caused an overt decrease in FTH1 and GPX4 protein levelsand a significant elevation in ACSL4 protein levels,implying that GEN1 silencing promoted AGS cell ferroptosis.Treatment with ferrostatin-1 rescued cell viability loss induced by GEN1 knockdown,confirming ferroptosis as akey death mechanism.Additionally,GEN1-deficient AGS cells showed enhanced sensitivity to cisplatin,with asignificantly reduced half-maximal inhibitory concentration compared to control cells.CONCLUSIONGEN1 promotes GC cell proliferation and migration while suppressing apoptosis and ferroptosis.Targeting GEN1not only disrupts mitochondrial function and cell cycle progression but also sensitizes GC cells to ferroptosis andchemotherapy.These findings highlight GEN1 as a potential therapeutic target for enhancing treatment efficacy ingastric cancer.
文摘Objectives:Colorectal cancer(CRC)remains a major contributor to global cancer mortality,ranking second worldwide for cancer-related deaths in 2022,and is characterized by marked heterogeneity in prognosis and therapeutic response.We sought to construct a machine-learning prognosticmodel based on a complement-related risk signature(CRRS)and to situate this signature within the CRC immune microenvironment.Methods:Transcriptomic profiles with matched clinical annotations from TCGA and GEO CRC cohorts were analyzed.Prognostic CRRS genes were screened using Cox proportional hazards modeling alongside machine-learning procedures.A random survival forest(RSF)predictor was trained and externally validated.Comparisons of immune infiltration,mutational burden,pathway enrichment,and drug sensitivity were made between risk groups.The function of FAM84A,a key model gene,was examined in CRC cell lines.Results:The six-gene CRRS model accurately stratified patients by survival outcomes.Low-risk patients exhibited greater immune cell infiltration and higher predicted response to immunotherapy and chemotherapy,while high-risk patients showed enrichment of complement activation and matrix remodeling pathways.FAM84A was shown to promote CRC cell proliferation,migration,and epithelial–mesenchymal transition.Conclusion:CRRS is a critical modulator of the CRC immune microenvironment.The developed model enables precise risk prediction and supports individualized therapeutic decisions in CRC.
基金supported by grants from the Special Funding of China Postdoctoral Science Foundation(No.2022TQ0389)the National Natural Science Foundation of China(No.82303693)the National Postdoctoral Program for Innovative Talents(No.BX2021386)。
文摘Background:Published clinical trials have yielded controversial findings regarding the effects of sex on the benefits of immune checkpoint inhibitors(ICIs).Sex-associated differences in the efficacy of immunotherapy remain an important,unresolved question.Methods:We investigated sex-biased molecular profiles across a multitude of biomarkers linked to immunotherapy responses.Multiomics data from major solid tumors in The Cancer Genome Atlas,with sufficient sample sizes(≥50 patients of each sex),were analyzed.Ninety-five molecular markers characterizing 4 distinct aspects of the tumor immune system were summarized and compared.The inverse probability of weights algorithm was used to generate well-balanced sex subgroups.Results:Our results showed that lung squamous cell carcinoma(LUSC),pancreatic adenocarcinoma,and liver hepatocellular carcinoma were the top 3 cancer types with extensive sex-biased biomarker profiles(31/95,15/95,and 14/95,respectively).Notably,although both were categorized as non–small cell lung carcinoma,LUSC harbored significantly more sex-biased immunological features than those of lung adenocarcinoma(p<0.01).We further explored the validity of this finding by analyzing ICI-responsive signatures and individual patient-level data for non–small cell lung carcinoma and found that sex had significant interaction effects on immunotherapy outcomes in LUSC(p_(interaction)<0.05),with women tending to derive greater benefits from ICIs than men.However,this difference was not apparent in the lung adenocarcinoma group(p_(interaction)=0.66),with men and women deriving comparable benefits.Conclusions:We systematically characterized sex-biased profiles of key molecular biomarkers predicting immunotherapy responses across solid tumors,which could pave the way for individualized therapeutic approaches for men and women.
文摘BACKGROUND Gastrointestinal tumors are among the most common cancer types,and early detection is paramount to improve their management.Cell-free DNA(cfDNA)liquid biopsy raises significant hopes for non-invasive early detection.AIM To describe current applications of this technology for gastrointestinal cancer detection and screening.METHODS A systematic review of the literature was performed across the PubMed database.Articles reporting the use of cfDNA liquid biopsy in the screening or diagnosis of gastrointestinal cancers were included in the analysis.RESULTS A total of 263 articles were screened for eligibility,of which 13 articles were included.Studies investigated colorectal cancer(5 studies),pancreatic cancer(2 studies),hepatocellular carcinoma(3 studies),and multi-cancer detection(3 studies),including gastric,oesophageal,or bile duct cancer,representing a total of 4824 patients.Test sensitivities ranged from 71% to 100%,and specificities ranged from 67.4% to 100%.Pre-cancerous lesions detection was less performant with a sensitivity of 16.9% and a 100% specificity in one study.Another study using a large biobank demonstrated a 94.9% sensitivity in detecting cancer up to 4 years before clinical symptoms,with a 61% accuracy in tissue-of-origin identification.CONCLUSION cfDNA liquid biopsy seems capable of detecting gastrointestinal cancers at an early stage of development in a non-invasive and repeatable manner and screening simultaneously for multiple cancer types in a single blood sample.Further trials in clinically relevant settings are required to determine the exact place of this technology in gastrointestinal cancer screening and diagnosis strategies.
基金Tianjin Health Technology Project(Grant no.2022QN106).
文摘Background:Doublecortin(DCX),a microtubule-associated protein,is best known for its critical role in neuronal migration during neural development,where it stabilizes microtubules and guides neurons to their proper positions.Recently,DCX has been implicated in various cancer processes,suggesting it may influence tumor progression and the tumor microenvironment.Emerging evidence indicates that DCX can modulate cell migration,invasion,and interaction with immune cells,making it a potential player in oncogenesis.However,the role of DCX across different cancer types and its potential as a prognostic biomarker remain underexplored,necessitating a comprehensive analysis.Methods:We utilized The Cancer Genome Atlas to extract data on DCX expression in tumor and adjacent normal tissues across diverse cancer types.Differential expression analysis was conducted using differential expression sequencing 2.Survival analysis was performed with Kaplan-Meier estimates and Cox proportional hazards models.Correlations between DCX expression and tumor mutational burden,microsatellite instability,and immune infiltration were examined using Spearman’s correlation.Results:DCX showed variable expression across cancer types,with significant overexpression in certain tumors such as liver and lung cancer and downexpression in others like breast cancer.High DCX expression was correlated with poor prognosis in adrenocortical carcinoma but with better outcomes in low-grade glioma.Additionally,DCX expression was significantly associated with various immune markers and chemokines,suggesting a role in modulating the immune microenvironment.Conclusion:Our findings highlight the complex role of DCX in cancer,underlining its potential as a prognostic marker and its involvement in immune-related pathways.Targeting DCX could represent a novel approach to modulating tumor behavior and enhancing immune response in cancer therapy.
基金supported by the National Natural Science Foundation of China(No.81502523)
文摘Gastric cancer(GC) is a highly aggressive and life-threatening malignancy.Even with radical surgical removal and front-line chemotherapy,more than half of GCs locally relapse and metastasize at a distant site.The dismal outcomes reflect the ineffectiveness of a one-size fits-all approach for a highly heterogeneous disease with diverse etiological causes and complex molecular underpinnings.The recent comprehensive genomic and molecular profiling has led to our deepened understanding of GC.The emerging molecular classification schemes based on the genetic,epigenetic,and molecular signatures are providing great promise for the development of more effective therapeutic strategies in a more personalized and precise manner.To this end,the Cancer Genome Atlas(TCGA) research network conducted a comprehensive molecular evaluation of primary GCs and proposed a new molecular classification dividing GCs into four subtypes:Epstein-Barr virus-associated tumors,microsatellite unstable tumors,genomically stable tumors,and tumors with chromosomal instability.This review primarily focuses on the TCGA molecular classification of GCs and discusses the implications on novel targeted therapy strategies.We believe that these fundamental findings will support the future application of targeted therapies and will guide our efforts to develop more efficacious drugs to treat human GCs.
基金the National Natural Science Foundation of China,No.81560389Key Research and Development Program of Jiangxi Province,No.20181BBG70015。
文摘BACKGROUND Self-renewal of gastric cancer stem cells(GCSCs)is considered to be the underlying cause of the metastasis,drug resistance,and recurrence of gastric cancer(GC).AIM To characterize the expression of stem cell-related genes in GC.METHODS RNA sequencing results and clinical data for gastric adenoma and adenocarcinoma samples were obtained from The Cancer Genome Atlas database,and the results of the GC mRNA expression-based stemness index(mRNAsi)were analyzed.Weighted gene coexpression network analysis was then used to find modules of interest and their key genes.Survival analysis of key genes was performed using the online tool Kaplan-Meier Plotter,and the online database Oncomine was used to assess the expression of key genes in GC.RESULTS mRNAsi was significantly upregulated in GC tissues compared to normal gastric tissues(P<0.0001).A total of 16 modules were obtained from the gene coexpression network;the brown module was most positively correlated with mRNAsi.Sixteen key genes(BUB1,BUB1 B,NCAPH,KIF14,RACGAP1,RAD54 L,TPX2,KIF15,KIF18 B,CENPF,TTK,KIF4 A,SGOL2,PLK4,XRCC2,a n d C1 orf112)were identified in the brown module.The functional and pathway enrichment analyses showed that the key genes were significantly enriched in the spindle cellular component,the sister chromatid segregation biological process,the motor activity molecular function,and the cell cycle and homologous recombination pathways.Survival analysis and Oncomine analysis revealed that the prognosis of patients with GC and the expression of three genes(RAD54 L,TPX2,and XRCC2)were consistently related.CONCLUSION Sixteen key genes are primarily associated with stem cell self-renewal and cell proliferation characteristics.RAD54 L,TPX2,and XRCC2 are the most likely therapeutic targets for inhibiting the stemness characteristics of GC cells.
文摘Human tongue cancer （TC） is an aggressive malignancy with a very poor prognosis. There is an urgent need to elucidate the underlying molecular mechanisms involved in TC progression, mRNA expression profiles play a vital role in the exploration of cancer-related genes. Therefore, the purpose of our study was to identify the progression associated candidate genes of TC by bioinformatics analysis. Five microarray datasets of TC samples were downloaded from the Gene Expression Onmibus （GEO） database and the data of 133 TC patients were screened from The Cancer Genome Atlas （TCGA） head and neck squamous cell carcinoma （HNSC） database. The integrated analysis of five microarray datasets and the RNA sequencing data of TC samples in TCGA-HNSC was performed to obtain 1023 overlapping differentially expressed genes （DEGs） in TC and adjacent normal tissue （ANT） samples. Next, Kyoto Encyclopedia of Genes and Genomes （KEGG） pathway analysis was conducted to enrich the significant pathways of the 1023 DEGs and PI3K- Akt signaling pathway （P=0.011） was selected to be the candidate pathway. A total of 23 DEGs with ｜log2 fold change （FC）｜ ≥1.0 in phosphatidylinositol 3-kinase-serine/threonine kinase （PI3K-Akt） signaling pathway were subjected to survival analysis of 125 eligible TC samples in TCGA database, indicating increased integrin-α3 gene （ITGA3） expression was significantly associated with poorer prognosis. Taken together, our study suggested ITGA3 may facilitate the development of TC via activating PI3K-Akt signaling pathway.
文摘Esophageal cancer is a common malignant tumor, whose pathogenesis and prognosis factors are not fully understood. This study aimed to discover the gene clusters that have similar functions and can be used to predict the prognosis of esophageal cancer. The matched microarray and RNA sequencing data of 185 patients with esophageal cancer were downloaded from The Cancer Genome Atlas(TCGA), and gene co-expression networks were built without distinguishing between squamous carcinoma and adenocarcinoma. The result showed that 12 modules were associated with one or more survival data such as recurrence status, recurrence time, vital status or vital time. Furthermore, survival analysis showed that 5 out of the 12 modules were related to progression-free survival(PFS) or overall survival(OS). As the most important module, the midnight blue module with 82 genes was related to PFS, apart from the patient age, tumor grade, primary treatment success, and duration of smoking and tumor histological type. Gene ontology enrichment analysis revealed that 'glycoprotein binding' was the top enriched function of midnight blue module genes. Additionally, the blue module was the exclusive gene clusters related to OS. Platelet activating factor receptor(PTAFR) and feline Gardner-Rasheed(FGR) were the top hub genes in both modeling datasets and the STRING protein interaction database. In conclusion, our study provides novel insights into the prognosis-associated genes and screens out candidate biomarkers for esophageal cancer.
文摘BACKGROUND Breast cancer(BC)is the most common malignant tumor in women.AIM To investigate BC-associated hub genes to obtain a better understanding of BC tumorigenesis.METHODS In total,1203 BC samples were downloaded from The Cancer Genome Atlas database,which included 113 normal samples and 1090 tumor samples.The limma package of R software was used to analyze the differentially expressed genes(DEGs)in tumor tissues compared with normal tissues.The cluster Profiler package was used to perform Kyoto Encyclopedia of Genes and Genomes(KEGG)enrichment analysis of upregulated and downregulated genes.Univariate Cox regression was conducted to explore the DEGs with statistical significance.Protein-protein interaction(PPI)network analysis was employed to investigate the hub genes using the CytoHubba plug-in of Cytoscape software.Survival analyses of the hub genes were carried out using the Kaplan-Meier method.The expression level of these hub genes was validated in the Gene Expression Profiling Interactive Analysis database and Human Protein Atlas database.RESULTS A total of 1317 DEGs(fold change>2;P<0.01)were confirmed through bioinformatics analysis,which included 744 upregulated and 573 downregulated genes in BC samples.KEGG enrichment analysis indicated that the upregulated genes were mainly enriched in the cytokine-cytokine receptor interaction,cell cycle,and the p53 signaling pathway(P<0.01);and the downregulated genes were mainly enriched in the cytokine-cytokine receptor interaction,peroxisome proliferator-activated receptor signaling pathway,and AMP-activated protein kinase signaling pathway(P<0.01).CONCLUSION In view of the results of PPI analysis,which were verified by survival and expression analyses,we conclude that MAD2L1,PLK1,SAA1,CCNB1,SHCBP1,KIF4A,ANLN,and ERCC6L may act as biomarkers for the diagnosis and prognosis in BC patients.
基金Supported by the Natural Science Foundation of Inner Mongolia,No.2021GG0298.
文摘BACKGROUND Breast cancer is regarded as a highly malignant neoplasm in the female population,posing a significant risk to women’s overall well-being.The prevalence of breast cancer has been observed to rise in China,accompanied by an earlier age of onset when compared to Western countries.Breast cancer continues to be a prominent contributor to cancer-related mortality and morbidity among women,primarily due to its limited responsiveness to conventional treatment modalities.The diagnostic process is challenging due to the presence of non-specific clinical manifestations and the suboptimal precision of conventional diagnostic tests.There is a prevailing uncertainty regarding the most effective screening method and target populations,as well as the specificities and execution of screening programs.AIM To identify diagnostic and prognostic biomarkers for breast cancer.METHODS Overlapping differentially expressed genes were screened based on Gene Expression Omnibus(GSE36765,GSE10810,and GSE20086)and The Cancer Genome Atlas datasets.A protein-protein interaction network was applied to excavate the hub genes among these differentially expressed genes.Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses,as well as gene set enrichment analyses,were conducted to examine the functions of these genes and their potential mechanisms in the development of breast cancer.For clarification of the diagnostic and prognostic roles of these genes,Kaplan–Mei-er and Cox proportional hazards analyses were conducted.RESULTS This study demonstrated that calreticulin,heat shock protein family B member 1,insulin-like growth Factor 1,interleukin-1 receptor 1,Krüppel-like factor 4,suppressor of cytokine signaling 3,and triosephosphate isomerase 1 are potential diagnostic biomarkers of breast cancer as well as potential treatment targets with clinical implications.CONCLUSION The screening of biomarkers is of guiding significance for the diagnosis and prognosis of the diseases.
基金Supported by the International Science and Technology Cooperation Projects,No. 2016YFE0107100Capital Special Research Project for Health Development,No. 2014-2-4012+3 种基金Beijing Natural Science Foundation,No. L172055 and No. 7192158National Ten-thousand Talent Programthe Fundamental Research Funds for the Central Universities,No. 3332018032CAMS Innovation Fund for Medical Science (CIFMS),No. 2017-I2M-4-003 and No. 2018-I2M-3-001。
文摘BACKGROUND Gastric cancer(GC) ranks as the third leading cause of cancer-related death worldwide. Epigenetic alterations contribute to tumor heterogeneity in early stages.AIM To identify the specific deoxyribonucleic acid(DNA) methylation sites that influence the prognosis of GC patients and explore the prognostic value of a model based on subtypes of DNA methylation.METHODS Patients were randomly classified into training and test sets. Prognostic DNA methylation sites were identified by integrating DNA methylation profiles and clinical data from The Cancer Genome Atlas GC cohort. In the training set, unsupervised consensus clustering was performed to identify distinct subgroups based on methylation status. A risk score model was built based on Kaplan-Meier, least absolute shrinkage and selector operation, and multivariate Cox regression analyses. A test set was used to validate this model.RESULTS Three subgroups based on DNA methylation profiles in the training set were identified using 1061 methylation sites that were significantly associated with survival. These methylation subtypes reflected differences in T, N, and M category, age, stage, and prognosis. Forty-one methylation sites were screened as specific hyper-or hypomethylation sites for each specific subgroup. Enrichment analysis revealed that they were mainly involved in pathways related to carcinogenesis, tumor growth, and progression. Finally, two methylation sites were chosen to generate a prognostic model. The high-risk group showed a markedly poor prognosis compared to the low-risk group in both the training [hazard ratio(HR) = 2.24, 95% confidence interval(CI): 1.28-3.92, P < 0.001] and test(HR = 2.12, 95%CI: 1.19-3.78, P = 0.002) datasets.CONCLUSION DNA methylation-based classification reflects the epigenetic heterogeneity of GC and may contribute to predicting prognosis and offer novel insights for individualized treatment of patients with GC.
文摘BACKGROUND The distal-less homeobox(DLX)gene family plays an important role in the development of several tumors.However,the expression pattern,prognostic and diagnostic value,possible regulatory mechanisms,and the relationship between DLX family genes and immune infiltration in colon cancer have not been systematically reported.AIM We aimed to comprehensively analyze the biological role of the DLX gene family in the pathogenesis of colon cancer.METHODS Colon cancer tissue and normal colon tissue samples were collected from the Cancer Genome Atlas and Gene Expression Omnibus databases.Wilcoxon rank sum test and t-test were used to assess DLX gene family expression between colon cancer tissue and unpaired normal colon tissue.cBioPortal was used to analyze DLX gene family variants.R software was used to analyze DLX gene expression in colon cancer and the relationship between DLX gene family expression and clinical features and correlation heat map.The survival package and Cox regression module were used to assess the prognostic value of the DLX gene family.The pROC package was used to analyze the diagnostic value of the DLX gene family.R software was used to analyze the possible regulatory mechanisms of DLX gene family members and related genes.The GSVA package was used to analyze the relationship between the DLX gene family and immune infiltration.The ggplot2,the survminer package,and the clusterProfiler package were used for visualization.RESULTS DLX1/2/3/4/5 were significantly aberrantly expressed in colon cancer patients.The expression of DLX genes were associated with M stage,pathologic stage,primary therapy outcome,residual tumor,lymphatic invasion,T stage,N stage,age,perineural invasion,and history of colon polyps.DLX5 was independently correlated with the prognosis of colon cancer in multivariate analysis.DLX1/2/3/4/5/6 were involved in the development and progression of colon cancer by participating in immune infiltration and associated pathways,including the Hippo signaling pathway,the Wnt signaling pathway,several signaling pathways regulating the pluripotency of stem cells,and Staphylococcus aureus infection.CONCLUSION The results of this study suggest a possible role for the DLX gene family as potential diagnostic or prognostic biomarkers and therapeutic targets in colon cancer.
