HLA-A, HLA-B, HLA-DRB1 Polymorphisms and Risk of Cervical Squamous Epithelial Cell Carcinoma: A Population Study in China

Xiao, Xu; Liu, Li; Li, Weijie; Liu, Juan; Chen, Dunjin

doi:10.7314/apjcp.2013.14.7.4427

Cited by 15 publications

(10 citation statements)

References 19 publications

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“…indicating that loss of function due to HLA mutations is tightly correlated with the immune escape of cancer cells (Xiao et al 2013). In summary, we demonstrated that the immune-related scores on the basis of ESTIMATE algorithm were the most proper immune scoring method for CSCC.…”

Section: Csccmentioning

confidence: 65%

Peer Review #1 of "Mining of prognosis-related genes in cervical squamous cell carcinoma immune microenvironment (v0.1)"

2020

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The aim of this study was to explore the effective immune scoring method and mine the novel and potential immune microenvironment-related diagnostic and prognostic markers for cervical squamous cell carcinoma (CSSC). Materials and Methods: The Cancer Genome Atlas (TCGA) data was downloaded and multiple data analysis approaches were initially used to search for the immune-related scoring system on the basis of Estimation of STromal and Immune cells in MAlignant Tumour tissues using Expression data (ESTIMATE) algorithm. After-wards, the representative genes in the gene modules correlated with immune-related scores based on ESTIMATE algorithm were further screened using Weighted Gene Co-expression Network Analysis (WGCNA) and network topology analysis. Gene functions were mined through enrichment analysis, followed by exploration of the correlation between these genes and immune checkpoint genes. Finally, survival analysis was applied to search for genes with significant association with overall survival and external database was employed for further validation. Results: The immune-related scores based on ESTIMATE algorithm was closely associated with other categories of scores, the HPV infection status, prognosis and the mutation levels of multiple CSCC-related genes (HLA and TP53). 18 new representative immune microenvironment-related genes were finally screened closely associated with patient prognosis and were further validated by the independent dataset GSE44001. Conclusion: Our present study suggested that the immune-related scores based on ESTIMATE algorithm can help to screen out novel immune-related diagnostic indicators, therapeutic targets and prognostic predictors in CSCC.

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Section: Csccmentioning

confidence: 65%

Peer Review #1 of "Mining of prognosis-related genes in cervical squamous cell carcinoma immune microenvironment (v0.1)"

2020

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“…A large number of somatic mutations of HLA genes have been reported in CSCC, strongly indicating that loss of function due to HLA mutations is tightly correlated with the immune escape of cancer cells ( Xiao et al, 2013 ). It is of great significance for us to analyze the changes of HLA gene sequence in tumor patients.…”

Section: Resultsmentioning

confidence: 99%

Mining of prognosis-related genes in cervical squamous cell carcinoma immune microenvironment

Cheng

Chen

et al. 2020

PeerJ

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Purpose The aim of this study was to explore the effective immune scoring method and mine the novel and potential immune microenvironment-related diagnostic and prognostic markers for cervical squamous cell carcinoma (CSSC). Materials and Methods The Cancer Genome Atlas (TCGA) data was downloaded and multiple data analysis approaches were initially used to search for the immune-related scoring system on the basis of Estimation of STromal and Immune cells in MAlignant Tumour tissues using Expression data (ESTIMATE) algorithm. Afterwards, the representative genes in the gene modules correlated with immune-related scores based on ESTIMATE algorithm were further screened using Weighted Gene Co-expression Network Analysis (WGCNA) and network topology analysis. Gene functions were mined through enrichment analysis, followed by exploration of the correlation between these genes and immune checkpoint genes. Finally, survival analysis was applied to search for genes with significant association with overall survival and external database was employed for further validation. Results The immune-related scores based on ESTIMATE algorithm was closely associated with other categories of scores, the HPV infection status, prognosis and the mutation levels of multiple CSCC-related genes (HLA and TP53). Eighteen new representative immune microenvironment-related genes were finally screened closely associated with patient prognosis and were further validated by the independent dataset GSE44001. Conclusion Our present study suggested that the immune-related scores based on ESTIMATE algorithm can help to screen out novel immune-related diagnostic indicators, therapeutic targets and prognostic predictors in CSCC.

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“…Previous reports have shown that different platform based studies like GWAS and SBT kit-based association-study from the same population might suggest association of different HLA alleles/SNPs. 37,40 Hence, instead of using SBT kit or genotyping of reported SNPs only, we resequenced the most polymorphic exons of HLA-A, HLA-B and HLA-C to identify all the single nucleotide variations (with 95% genotyping rate) within the study-group.…”

Section: Discussionmentioning

confidence: 99%

Impact of genetic variations and transcriptional alterations of HLA class I genes on cervical cancer pathogenesis

et al. 2017

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In a novel attempt to understand the variations in DNA sequences underlying HLA class I alleles associated with HPV16-related CaCx, we determined the alleles by reconstructing SNP-based haplotypes from resequencing of the most polymorphic exons 2 and 3 of HLA-A, HLA-B and HLA-C. We also determined the impact of SNPs and transcriptional alterations of the genes on CaCx. A high density of SNPs was identified from resequencing. HLA expression was determined by real-time PCR. We identified that even a single associated HLA allele had many underlying SNP-based haplotypes. Out of the most frequent (≥5%) HLA class I alleles, HLA-B*40:06 and HLA-B*15:02 respectively imparted significant risk towards and protection from CaCx as well as HPV16 infection. Employing median-joining networks to detect clusters of sequence-variations for specific HLA alleles, we found the protective SNP-based signature, GAATTTA, in all SNP-based haplotypes of HLA-B*15:02 allele. The signature was derived from seven SNPs within HLA-B which were newly associated with the disease. Contrarily, similarly derived risk-signature, TTGCGCC, mapped only to 52% of SNP-based haplotypes of HLA-B*40:06 allele. This indicated that all SNP-based haplotypes underlying a particular associated HLA allele might or might not have a single signature of risk/protection. HLA-A, HLA-B and HLA-C expressions were downregulated among CaCx cases compared to asymptomatic infections and HPV-negative controls. HLA-A and HLA-B were repressed in both cases harbouring episomal and integrated HPV16, whereas HLA-C in only the latter. Novel genetic variations and differential downregulation-patterns of HLA class I have a significant bearing on HPV16-related CaCx pathogenesis.

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HLA-A, HLA-B, HLA-DRB1 Polymorphisms and Risk of Cervical Squamous Epithelial Cell Carcinoma: A Population Study in China

Cited by 15 publications

References 19 publications

Peer Review #1 of "Mining of prognosis-related genes in cervical squamous cell carcinoma immune microenvironment (v0.1)"

Peer Review #1 of "Mining of prognosis-related genes in cervical squamous cell carcinoma immune microenvironment (v0.1)"

Mining of prognosis-related genes in cervical squamous cell carcinoma immune microenvironment

Impact of genetic variations and transcriptional alterations of HLA class I genes on cervical cancer pathogenesis

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