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Yuan M, Zheng X, Jing J, Li Y, Liu N, Song Y. Genetic associations between gene polymorphisms on 3p25 and oral squamous cell carcinoma. Oral Dis 2024; 30:1018-1031. [PMID: 36680374 DOI: 10.1111/odi.14514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/14/2022] [Accepted: 01/17/2023] [Indexed: 01/22/2023]
Abstract
OBJECTIVES To evaluate the association of SYN2, PPARG, RAF1, TIMP4, and IQSEC1 polymorphisms in 3p25 with oral squamous cell carcinoma (OSCC) in the Chinese Han population. SUBJECTS AND METHODS Genomic DNA was extracted from 494 subjects with or without OSCC. Basic information on the subjects, clinical data, and prognoses were collected. Fifteen candidate single nucleotide polymorphisms (SNPs) were selected and genotyped. The statistical analyses included descriptive statistics, logistic regression, survival, and functional annotation was performed. RESULTS IQSEC1-rs2686742 correlated with OSCC occurrence. In addition, RAF1-rs1051208, PPARG-rs10865710, PPARG-rs3856806, IQSEC1-rs2686742, PPARG-rs1175544, IQSEC1-rs9211, and IQSEC1-rs2600322 were significantly associated with the clinical characteristics of patients with OSCC. The log-rank test showed that IQSEC1-rs2600322 may play an important role in the survival of patients with OSCC. The Cox regression analysis suggested that PPARG-rs10865710, PPARG-rs7649970, IQSEC1-rs9211, IQSEC1-rs2600322, and IQSEC1-rs12487715 influenced survival outcomes. The functional annotation indicated that the transcript levels of IQSEC1 were upregulated in head and neck squamous cell carcinoma tissues, whereas PPARG gene transcription was downregulated. CONCLUSIONS IQSEC1-rs2686742 may be closely associated with OSCC onset. Multiple SNPs in IQSEC1 and PPARG genes correlated with the clinical characteristics of OSCC, among which PPARG-rs10865710, IQSEC1-rs9211, and IQSEC1-rs2600322 were associated with cancer prognosis.
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Affiliation(s)
- Minyan Yuan
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Xueqing Zheng
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Jiaojiao Jing
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
- Department of Pediatric Dentistry, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Yang Li
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Nianke Liu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Yaling Song
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
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2
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Huang X, Su B, Li M, Zhou Y, He X. Multiomics characterization of fatty acid metabolism for the clinical management of hepatocellular carcinoma. Sci Rep 2023; 13:22472. [PMID: 38110715 PMCID: PMC10728109 DOI: 10.1038/s41598-023-50156-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/15/2023] [Indexed: 12/20/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a prevalent malignancy and there is a lack of effective biomarkers for HCC diagnosis. Living organisms are complex, and different omics molecules interact with each other to implement various biological functions. Genomics and metabolomics, which are the top and bottom of systems biology, play an important role in HCC clinical management. Fatty acid metabolism is associated with malignancy, prognosis, and immune phenotype in cancer, which is a potential hallmark in malignant tumors. In this study, the genes and metabolites related to fatty acid metabolism were thoroughly investigated by a dynamic network construction algorithm named EWS-DDA for the early diagnosis and prognosis of HCC. Three gene ratios and eight metabolite ratios were identified by EWS-DDA as potential biomarkers for HCC clinical management. Further analysis using biological analysis, statistical analysis and document validation in the discovery and validation sets suggested that the selected potential biomarkers had great clinical prognostic value and helped to achieve effective early diagnosis of HCC. Experimental results suggested that in-depth evaluation of fatty acid metabolism from different omics viewpoints can facilitate the further understanding of pathological alterations associated with HCC characteristics, improving the performance of early diagnosis and clinical prognosis.
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Affiliation(s)
- Xin Huang
- School of Artificial Intelligence, Anshan Normal University, Pingan Street, Anshan, 114007, Liaoning, China.
- Biomedical Engineering Postdoctoral Research Station, Dalian University of Technology, Dalian, Liaoning, China.
- Postdoctoral Workstation of Dalian Yongjia Electronic Technology Co., Ltd, Dalian, Liaoning, China.
| | - Benzhe Su
- School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning, China
| | - Mengjun Li
- School of Artificial Intelligence, Anshan Normal University, Pingan Street, Anshan, 114007, Liaoning, China
| | - Yang Zhou
- Ningbo Institute of Innovation for Combined Medicine and Engineering, Ningbo Medical Center Li Huili Hospital, Ningbo, Zhejiang, China
| | - Xinyu He
- School of Computer and Information Technology, Liaoning Normal University, Dalian, Liaoning, China
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3
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Zhan K, Yang X, Li S, Bai Y. Correlation of endoplasmic reticulum stress patterns with the immune microenvironment in hepatocellular carcinoma: a prognostic signature analysis. Front Immunol 2023; 14:1270774. [PMID: 38143739 PMCID: PMC10748430 DOI: 10.3389/fimmu.2023.1270774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/23/2023] [Indexed: 12/26/2023] Open
Abstract
Backgrounds The extended duration of endoplasmic reticulum stress (ERS) can impact the progression of hepatocellular carcinoma (HCC) and the efficacy of immunotherapies by interacting with immune cells that have infiltrated the tumor microenvironment (TME). Methods and results The study utilized a training cohort of 364 HCC patients with complete information from The Cancer Genome Atlas Program (TCGA) database, and a validation cohort of 231 HCC patients from the International Cancer Genome Consortium (ICGC) database. The genes related to ERS exhibiting a strong correlation with overall survival (OS) were identified using univariate Cox regression analysis. A 13-gene predictive signature was then produced through the least absolute shrinkage and selection operator (LASSO) regression approach. The data revealed that the ERS-associated gene signature effectively stratified patients into high- or low-risk groups regarding OS in both the training and validation cohorts (P < 0.0001 and P = 0.00029, respectively). Using the multivariate method, it is still an independent prognostic factor in both the training and validation cohorts (P < 0.001 and P = 0.008, respectively). Moreover, several metabolic pathways were identified to be enriched among the 13 genes in the predictive signature. When the ERS-associated gene signature was combined with the tumor-node-metastasis (TNM) stage, the ERS nomogram performed better than either the gene signature or the TNM stage alone (C-index values: 0.731, 0.729, and 0.573, respectively). Further analysis revealed that patients in the high-risk group exhibited increased infiltration of immune cells. Additionally, GP6 was downregulated in HCC tissues among these signature genes (P < 0.05), which was related to poor OS. Conclusions The data suggest that this novel ERS-associated gene signature could contribute to personalized cancer management for HCC. Moreover, targeting GP6 inhibition might be a potential method for HCC therapy.
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Affiliation(s)
- Ke Zhan
- Department of Gastroenterology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xin Yang
- Department of Gastroenterology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Shuang Li
- Department of Gastrointestinal Surgery, Jinshan Hospital, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yang Bai
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Tanouti IA, Fellah H, El Fihry R, Zerrad C, Abounouh K, Tahiri M, Belkouchi A, Badre W, Pineau P, Benjelloun S, Ezzikouri S. Association of Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1 Alpha Coding Variants with Hepatocellular Carcinoma Risk in the Moroccan Population: A Case-Control Study. Asian Pac J Cancer Prev 2023; 24:3689-3696. [PMID: 38019226 PMCID: PMC10772742 DOI: 10.31557/apjcp.2023.24.11.3689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 11/17/2023] [Indexed: 11/30/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is the most common primary malignancy. Peroxisome proliferator-activated receptor gamma coactivator 1 alpha (PPARGC1A) plays a crucial role in regulating the biogenesis of mitochondria. We aimed to assess the association between PPARGC1A polymorphisms and HCC risk in a Moroccan population. METHODS In this case-control study, 147 patients with HCC and 147 controls without pre-existing liver disease were matched for ethnicity. TaqMan SNP allelic discrimination assays were used for genotyping of PPARGC1A rs8192678 and rs12640088 polymorphisms. RESULTS The result revealed that individuals with the GA/AA genotypes for rs8192678 had a significantly higher risk of HCC compared to those with the GG genotype (OR=6.68; P<0.0001, and OR=9.78; P<0.0001, respectively). In particular, the A allele of rs8192678 was over-represented in HCC patients compared to controls (40% versus 12%, P<0.0001, respectively). With respect to PPARGC1A rs12640088 variant, two genetic models (codominant and dominant) were tested to explore any potential variations in the distribution of SNP A>C among HCC cases and control subjects group. Overall, no significant association between rs12640088 and HCC was found (P>0.05). Interestingly, a significantly higher level of aspartate aminotransferase was observed in HCC patients with GG-GA genotypes (280 IU/L) compared to those with GG genotype (164 IU/L) at rs8192678 (P=0.0019). CONCLUSION Our results suggest that the PPARGC1A rs8192678 polymorphism is associated with an increased risk of HCC in Moroccan population and may serve as a prognostic marker for liver cancer.
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Affiliation(s)
- Ikram-Allah Tanouti
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco.
- Laboratory of Cellular and Molecular Pathology Infectious Diseases and Systemic Immunology Team, Faculty of Medicine and Pharmacy, University Hassan II of Casablanca, Morocco.
| | - Hassan Fellah
- Laboratory of Cellular and Molecular Pathology Infectious Diseases and Systemic Immunology Team, Faculty of Medicine and Pharmacy, University Hassan II of Casablanca, Morocco.
| | - Raouia El Fihry
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco.
| | - Chaimaa Zerrad
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco.
| | - Karima Abounouh
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco.
| | | | | | | | | | - Soumaya Benjelloun
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco.
| | - Sayeh Ezzikouri
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco.
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Sproule TJ, Philip VM, Chaudhry NA, Roopenian DC, Sundberg JP. Seven naturally variant loci serve as genetic modifiers of Lamc2jeb induced non-Herlitz junctional Epidermolysis Bullosa in mice. PLoS One 2023; 18:e0288263. [PMID: 37437067 DOI: 10.1371/journal.pone.0288263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 06/22/2023] [Indexed: 07/14/2023] Open
Abstract
Epidermolysis Bullosa (EB) is a group of rare genetic disorders that compromise the structural integrity of the skin such that blisters and subsequent erosions occur after minor trauma. While primary genetic risk of all subforms of EB adhere to Mendelian patterns of inheritance, their clinical presentations and severities can vary greatly, implying genetic modifiers. The Lamc2jeb mouse model of non-Herlitz junctional EB (JEB-nH) demonstrated that genetic modifiers can contribute substantially to the phenotypic variability of JEB and likely other forms of EB. The innocuous changes in an 'EB related gene', Col17a1, have shown it to be a dominant modifier of Lamc2jeb. This work identifies six additional Quantitative Trait Loci (QTL) that modify disease in Lamc2jeb/jeb mice. Three QTL include other known 'EB related genes', with the strongest modifier effect mapping to a region including the epidermal hemi-desmosomal structural gene dystonin (Dst-e/Bpag1-e). Three other QTL map to intervals devoid of known EB-associated genes. Of these, one contains the nuclear receptor coactivator Ppargc1a as its primary candidate and the others contain related genes Pparg and Igf1, suggesting modifier pathways. These results, demonstrating the potent disease modifying effects of normally innocuous genetic variants, greatly expand the landscape of genetic modifiers of EB and therapeutic approaches that may be applied.
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Affiliation(s)
- Thomas J Sproule
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Vivek M Philip
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Nabig A Chaudhry
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | | | - John P Sundberg
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
- Department of Dermatology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
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Jiang JK, Chen HS, Tang WF, Chen Y, Lin J. Rs3746444 T>C locus in miR-499 increases the susceptibility to hepatocellular carcinoma: A meta-analysis 14812 subjects. World J Gastrointest Oncol 2023; 15:171-185. [PMID: 36684045 PMCID: PMC9850759 DOI: 10.4251/wjgo.v15.i1.171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 10/26/2022] [Accepted: 11/28/2022] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Recently, many investigations have suggested that the rs3746444 T>C locus in the microRNA (miR)-499 gene may contribute to the occurrence of cancer. However, reports on the association between rs3746444 and hepatocellular carcinoma (HCC) are conflicting.
AIM To further understand and explore the potential correlation between the single-nucleotide polymorphism of rs3746444 and the incidence of HCC.
METHODS In this meta-analysis, we obtained electronic literature by searching the PubMed, Embase and Chinese BioMedical Disc databases (through May 20, 2022). All eligible case-control, prospective cohort or nested case-control studies with sufficient data for calculating the odds ratios with their 95% confidence intervals were included.
RESULTS Ultimately, a total of 17 independent studies were included. We identified that rs3746444 was associated with the development of HCC (C vs T: P = 0.019 and CC/CT vs TT: P = 0.016). In Asian individuals, rs3746444 was associated with susceptibility to HCC (C vs T: P = 0.013 and CC/CT vs TT: P = 0.016). In addition, this study identified that the miR-499 rs3746444 locus was associated with susceptibility to HCC in the normal/healthy control subgroup (C vs T: P = 0.034 and CC/CT vs TT: P = 0.024).
CONCLUSION In summary, this meta-analysis highlights that rs3746444 in the miR-499 gene is involved in the occurrence of HCC, especially in Asian individuals.
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Affiliation(s)
- Jia-Kai Jiang
- Department of General Surgery, Changzhou No. 3 People’s Hospital, Changzhou 213000, Jiangsu Province, China
| | - Han-Shen Chen
- Department of Anesthesiology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350000, Fujian Province, China
| | - Wei-Feng Tang
- Department of Cardiothoracic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210000, Jiangsu Province, China
| | - Yu Chen
- Department of Medical Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou 350000, Fujian Province, China
- Cancer Bio-Immunotherapy Center, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou 350000, Fujian Province, China
- College of Chemistry, Fuzhou University, Fuzhou 350000, Fujian Province, China
| | - Jing Lin
- Department of Medical Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou 350000, Fujian Province, China
- Cancer Bio-Immunotherapy Center, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou 350000, Fujian Province, China
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Chen B, Wang Y, Tang W, Chen Y, Liu C, Kang M, Xie J. Association between PPARγ, PPARGC1A, and PPARGC1B genetic variants and susceptibility of gastric cancer in an Eastern Chinese population. BMC Med Genomics 2022; 15:274. [PMID: 36587194 PMCID: PMC9805199 DOI: 10.1186/s12920-022-01428-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 12/26/2022] [Indexed: 01/01/2023] Open
Abstract
PURPOSE Previous studies showed that peroxisome proliferator-activated receptor gamma (PPARγ) and PPARγ coactivator1 family (PPARGC1A and PPARGC1B) gene single nucleotide variants (SNVs)were strongly associated with cancer susceptibility. The purpose of this study was to investigate the association of PPARγ, PPARGC1A, and PPARGC1B variants with the risk of gastric cancer (GC). PATIENTS AND METHODS We performed a case-control study of 490 GC cases and 1,476 healthy controls from eastern China. PPARγ rs1801282 C > G, rs3856806 C > T, PPARGC1A rs2970847 C > T, rs8192678 C > T and PPARGC1B rs7732671 G > C, rs17572019 G > A SNVs were selected to investigate the association between these SNVs and GC susceptibility. Genotypes of the SNVs were assessed by multiplex fluorescent PCR using a custom-by-design 48-Plex SNPscantm Kit. RESULTS The PPARγ rs1801282 SNV was associated with a decreased risk for GC (GC vs. CC: odds ratio (OR) = 0.62, 95% confidence interval (95%CI) = 0.42-0.93, adjusted P = 0.019; GC + GG vs. GG: OR = 0.63 95%CI = 0.42-0.93, adjusted P = 0.019; respectively). In addition, stratified analysis revealed that the PPARγ rs1801282 SNV was correlated with the risk of GC in subgroups of age ≥ 61, no smoking, and no alcohol consuming. We also confirmed that the PPARγ rs3856806 C > T SNV promoted the risk of GC in women. The PPARGC1A rs8192678 TT genotype decreased the susceptibility of GC in men. The PPARGC1A rs2970847 C > T SNV decreased the susceptibility of GC in the subgroup of BMI ≥ 24 kg/m2. The PPARGC1B rs7732671 G > C and rs17572019 G > A SNVs promoted the risk of GC in the subgroup of BMI ≥ 24 kg/m2. CONCLUSION This study indicates that the PPARγ, PPARGC1A, and PPARGC1B SNVs may be associated with the susceptibility of GC in eastern Chinese population. Future studies with larger populations, detailed H. pylori infection status for subgroup analysis, and functional study are needed to further clarify the relationship between these SNVs and GC risk.
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Affiliation(s)
- Boyang Chen
- grid.440618.f0000 0004 1757 7156Department of Cardiothoracic Surgery, The Affiliated Hospital of Putian University, Putian, 351100 Fujian Province China
| | - Yafeng Wang
- Department of Cardiology, The People’s Hospital of Xishuangbanna Dai Autonomous Prefecture, Jinghong, Yunnan Province China
| | - Weifeng Tang
- grid.428392.60000 0004 1800 1685Department of Cardiothoracic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu Province China
| | - Yu Chen
- grid.415110.00000 0004 0605 1140Department of Medical Oncology, Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, Fuzhou, Fujian Province China
| | - Chao Liu
- grid.452247.2Department of Cardiothoracic Surgery, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu Province China
| | - Mingqiang Kang
- grid.440618.f0000 0004 1757 7156Department of Cardiothoracic Surgery, The Affiliated Hospital of Putian University, Putian, 351100 Fujian Province China ,grid.411176.40000 0004 1758 0478Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001 Fujian Province China
| | - Jinbiao Xie
- grid.440618.f0000 0004 1757 7156Department of Cardiothoracic Surgery, The Affiliated Hospital of Putian University, Putian, 351100 Fujian Province China
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A Novel Hypoxic-Angiogenesis-Immune-Related Gene Model for Prognostic and Therapeutic Effect Prediction in Hepatocellular Carcinoma Patients. DISEASE MARKERS 2022; 2022:9428660. [PMID: 35069936 PMCID: PMC8769836 DOI: 10.1155/2022/9428660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 12/07/2021] [Indexed: 12/04/2022]
Abstract
Background Hepatocellular carcinoma (HCC) is one of the most heterogeneous malignant tumors that have been discovered so far, which makes the prognostic prediction difficult. The hypoxia, angiogenesis, and immunity-related genes (HAIRGs) are closely related to the development of liver cancer. However, the prognostic and treatment effect of hypoxia, angiogenesis, and immunity-related genes in HCC continues to be further clarified. Methods The gene expression quantification data and clinical information in patients with liver cancer were downloaded from the TCGA database, and HAIRG signature was built by using the least absolute shrinkage and selection operator (LASSO) technique. Patient from the ICGC database validated the model. Then, tumor immune dysfunction and exclusion (TIDE) algorithm was applied to estimate the clinical response to immunotherapy and the sensitivity of drugs was evaluated by the half-maximal inhibitory concentration (IC50). Result The HAIRGs were identified between the HCC patients and normal patients in the TCGA database. In univariate Cox regression analysis, seventeen differentially expressed genes (DEGs) were associated with overall survival (OS). An eight HAIRG signature model was constructed and was used to divide the patients into two groups according to the median value of the risk score base on the TCGA dataset. Patients in the high-risk group had a significant reduction in OS compared to those in the low-risk group (P < 0.001 in the TCGA, P < 0.001 in the ICGC). For TCGA and ICGC databases of univariate Cox regression analyses, the risk score was used as an independent predictor of OS (HR > 1, P < 0.001). Functional analysis showed that the relevant immune pathways and immune responses were enriched, cellular component analysis showed that the immunoglobulin complex and other related substances were enriched, and immune status existed a difference in the high- and low-risk groups. Then, the tumor immune dysfunction and exclusion (TIDE) algorithm presented differences in immune response in the high- and low-risk groups (P < 0.05), and based on drug sensitivity prediction, patients in the high-risk group were more sensitive to cisplatin compared to those in the low-risk group in both the TCGA and ICGC cohorts (P < 0.05). Conclusions HAIRG signature can be utilized for prognostic prediction in HCC, while it can be considered a prediction model for clinical evaluation of immunotherapy response and chemotherapy sensitivity in HCC.
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Dou M, Zhou X, Li L, Zhang M, Wang W, Wang M, Jing Y, Ma R, Zhao J, Zhu L. Illumination of Molecular Pathways in Multiple Sclerosis Lesions and the Immune Mechanism of Matrine Treatment in EAE, a Mouse Model of MS. Front Immunol 2021; 12:640778. [PMID: 33912166 PMCID: PMC8072148 DOI: 10.3389/fimmu.2021.640778] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 03/22/2021] [Indexed: 12/20/2022] Open
Abstract
The etiology of multiple sclerosis (MS) is not clear, and the treatment of MS presents a great challenge. This study aimed to investigate the pathogenesis and potential therapeutic targets of MS and to define target genes of matrine, a quinolizidine alkaloid component derived from the root of Sophorae flavescens that effectively suppressed experimental autoimmune encephalomyelitis (EAE), an animal model of MS. To this end, the GSE108000 gene data set in the Gene Expression Omnibus Database, which included 7 chronic active MS lesions and 10 control samples of white matter, was analyzed for differentially expressed genes (DEGs). X cell was used to analyze the microenvironmental differences in brain tissue samples of MS patients, including 64 types of immune cells and stromal cells. The biological functions and enriched signaling pathways of DEGs were analyzed by multiple approaches, including GO, KEGG, GSEA, and GSVA. The results by X cell showed significantly increased numbers of immune cell populations in the MS lesions, with decreased erythrocytes, megakaryocytes, adipocytes, keratinocytes, endothelial cells, Th1 cells and Tregs. In GSE108000, there were 637 DEGs, including 428 up-regulated and 209 down-regulated genes. Potential target genes of matrine were then predicted by the network pharmacology method of Traditional Chinese medicine, and 12 key genes were obtained by cross analysis of the target genes of matrine and DEGs in MS lesions. Finally, we confirmed by RT-PCR the predicted expression of these genes in brain tissues of matrine-treated EAE mice. Among these genes, 2 were significantly downregulated and 6 upregulated by matrine treatment, and the significance of this gene regulation was further investigated. In conclusion, our study defined several possible matrine target genes, which can be further elucidated as mechanism(s) of matrine action, and novel targets in the treatment of MS.
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Affiliation(s)
- Mengmeng Dou
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Department of Neurology, the Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Xueliang Zhou
- Department of Interventional Radiology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lifeng Li
- Department of Oncology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Internet Medical and System Applications of National Engineering Laboratory, Zhengzhou, China
| | - Mingliang Zhang
- Department of Pharmacy, the first Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, China
| | - Wenbin Wang
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Department of Neurology, the Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Mengru Wang
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Yilei Jing
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Rui Ma
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jie Zhao
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Internet Medical and System Applications of National Engineering Laboratory, Zhengzhou, China
| | - Lin Zhu
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Huang Y, Chen S, Qin W, Wang Y, Li L, Li Q, Yuan X. A Novel RNA Binding Protein-Related Prognostic Signature for Hepatocellular Carcinoma. Front Oncol 2020; 10:580513. [PMID: 33251144 PMCID: PMC7673432 DOI: 10.3389/fonc.2020.580513] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 08/24/2020] [Indexed: 12/24/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a highly malignant and aggressive cancer with high recurrence rates and mortality. Some studies have illustrated that RNA binding proteins (RBPs) were involved in the carcinogenesis and development of multiple cancers, but the roles in HCC were still unclear. We downloaded the RNA-seq and corresponding clinical information of HCC from The Cancer Genome Atlas (TCGA) database, and 330 differentially expressed RBPs were identified between normal and HCC tissues. Through series of the univariate, the least absolute shrinkage selection operator (LASSO), and the stepwise multivariate Cox regression analyses, six prognosis-related key RBPs (CNOT6, UPF3B, MRPL54, ZC3H13, IFIT5, and PPARGC1A) were screened out from DE RBPs, and a six-RBP gene risk score signature was constructed in training set. Survival analysis indicated that HCC patients with high-risk scores had significantly worse overall survival than low-risk patients, and furthermore, the signature can be used as an independent prognostic indicator. The good accuracy of this prognostic signature was confirmed by the ROC curve analysis and was further validated in the International Cancer Genome Consortium (ICGC) HCC cohort. Besides, a nomogram based on six RBP genes was established and internally validated in the TCGA cohort. Gene set enrichment analysis demonstrated some cancer-related phenotypes were significantly gathered in the high-risk group. Overall, our study first identified an RBP-related six-gene prognostic signature, which could serve as a promising prognostic biomarker and provide some potential therapeutic targets for HCC.
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Affiliation(s)
- Yongbiao Huang
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Sheng Chen
- Department of Hepatobiliary Surgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Wan Qin
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Yali Wang
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Long Li
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Qianxia Li
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Xianglin Yuan
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
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11
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Wu M, Zhao H. Analysis of key genes and pathways in breast ductal carcinoma in situ. Oncol Lett 2020; 20:217. [PMID: 32963623 PMCID: PMC7491034 DOI: 10.3892/ol.2020.12080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 09/17/2019] [Indexed: 12/12/2022] Open
Abstract
Breast cancer (BC) remains the most common cancer in females. Therefore, the present study aimed to identify key genes involved in the carcinogenesis of BC and to explore their prognostic values by integrating bioinformatics tools. The gene expression profiles of 46 ductal carcinoma in situ (DCIS) and three normal breast tissues from the GSE59248 dataset were downloaded. Differentially expressed genes (DEGs) were subsequently identified using the online tool GEO2R and a functional enrichment analysis was performed. In addition, a protein-protein interaction (PPI) network was constructed and the top eight hub genes were identified. The prognostic values of the hub genes were further investigated. A total of 316 DEGs, including 32 upregulated and 284 downregulated genes, were identified. Furthermore, eight hub genes, including lipase E hormone sensitive type, patatin like phospholipase domain containing 2, adiponectin C1Q and collagen domain containing (ADIPOQ), peroxisome proliferator activated receptor γ (PPARG), fatty acid binding protein 4 (FABP4), diacylglycerol O-acyltransferase 2, lipoprotein lipase (LPL) and leptin (LEP), were identified from the PPI network. The downregulated expression of ADIPOQ, PPARG, FABP4, LPL and LEP was significantly associated with poor overall survival in patients with DCIS. Therefore, these genes may serve as potential biomarkers for prognosis prediction. However, further investigation is required to validate the results obtained in the present study.
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Affiliation(s)
- Min Wu
- Department of General Surgery, Beijing Youan Hospital, Capital Medical University, Beijing 100069, P.R. China
| | - Hongmei Zhao
- Department of General Surgery, Peking University Third Hospital, Beijing 100191, P.R. China
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12
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Chen Z, Wang Y, Wang J, Kang M, Tang W, Chen S. Assessment of PPARGC1A, PPARGC1B, and PON1 Genetic Polymorphisms in Esophageal Squamous Cell Carcinoma Susceptibility in the Eastern Chinese Han Population: A Case-Control Study Involving 2351 Subjects. DNA Cell Biol 2020; 39:1521-1531. [PMID: 32721231 DOI: 10.1089/dna.2020.5416] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Previous studies suggested that alterations in the energy metabolism might be underlying cancer initiation and progression. Polymorphisms of genes involved in energy metabolism regulation, such as peroxisome proliferator-activated receptor gamma coactivator 1α (PPARGC1A), -β (PPARGC1B), and paraoxonase 1 (PON1), might confer susceptibility to esophageal squamous cell carcinoma (ESCC) and partially explain its pathogenesis. We investigated the effects of several single nucleotide polymorphisms (SNPs) in three metabolic-related genes (e.g., PPARGC1A, PPARGC1B, and PON1) on ESCC susceptibility. In total, 829 patients with sporadic ESCC and 1522 nontumor controls were enrolled in the study. SNPs were genotyped using PCR-ligase detection reaction. Our study revealed that the PPARGC1A rs3736265 G/A SNP significantly increased the risk for ESCC (GA vs. GG: adjusted odds ratio [OR] = 1.25, 95% confidence interval [95% CI] = 1.02-1.54, p = 0.034; GA+AA vs. GG: adjusted OR = 1.25, 95% CI = 1.03-1.52, p = 0.027]. In addition, a stratified analysis revealed that the PPARGC1A rs3736265 SNP was correlated with the development of ESCC in male and nondrinking subgroups. We also confirmed that the PPARGC1B rs17572019 G/A SNP promoted the risk of ESCC in subgroup with high alcohol intake. The PPARGC1A rs8192678 C/T polymorphism decreased the susceptibility of ESCC in men. These findings highlight that polymorphisms in PPARGC1A and PPARGC1B may contribute to ESCC susceptibility. In the future, further well-designed epidemiological studies are needed to confirm our findings.
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Affiliation(s)
- Zhan Chen
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Yafeng Wang
- Department of Cardiology, The People's Hospital of Xishuangbanna Dai Autonomous Prefecture, Jinghong, China
| | - Jusi Wang
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Mingqiang Kang
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, China.,Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China.,Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Weifeng Tang
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Shuchen Chen
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, China
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13
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ElFihry R, Elmessaoudi-Idrissi M, Jadid FZ, Zaidane I, Chihab H, Tahiri M, Kabine M, Badre W, Chemin I, Marchio A, Pineau P, Ezzikouri S, Benjelloun S. Effect of Peroxisome Proliferator-Activated Receptor-γ Coactivator-1 Alpha Variants on Spontaneous Clearance and Fibrosis Progression during Hepatitis C Virus Infection in Moroccan Patients. Virol Sin 2020; 35:566-574. [PMID: 32297157 DOI: 10.1007/s12250-020-00220-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 02/08/2020] [Indexed: 12/18/2022] Open
Abstract
Hepatitis C virus (HCV) is still one of the main causes of liver disease worldwide. Metabolic disorders, including non-alcoholic fatty liver disease (NAFLD), induced by HCV have been shown to accelerate the progression of fibrosis to cirrhosis and to increase the risk of hepatocellular carcinoma. An optimal peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PPARGC1A) activity is crucial to prevent NAFLD installation. The present study aims to investigate the associations between two common PPARGC1A polymorphisms (rs8192678 and rs12640088) and the outcomes of HCV infection in a North African context. A series of 592 consecutive Moroccan subjects, including 292 patients with chronic hepatitis C (CHC), 100 resolvers and 200 healthy controls were genotyped using a TaqMan allelic discrimination assay. PPARGC1A variations at rs8192678 and rs12640088 were not associated with spontaneous clearance of HCV infection (adjusted ORs = 0.76 and 0.79 respectively, P > 0.05, for both). Furthermore, multivariable logistic regression analysis showed that both SNPs were not associated with fibrosis progression (OR = 0.71; 95% CI 0.20-2.49; P = 0.739; OR = 1.28; 95% CI 0.25-6.54; P = 0.512, respectively). We conclude that, in the genetic context of South Mediterranean patients, rs8192678 and rs12640088 polymorphisms of PPARGC1A are neither associated with spontaneous clearance nor with disease progression in individuals infected with HCV.
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Affiliation(s)
- Raouia ElFihry
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, 20360, Casablanca, Morocco
- Laboratoire Santé et Environnement, département de Biologie, Faculté des Sciences Ain Chock, University Hassan II of Casablanca, 20360, Casablanca, Morocco
| | | | - Fatima-Zahra Jadid
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, 20360, Casablanca, Morocco
| | - Imane Zaidane
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, 20360, Casablanca, Morocco
| | - Hajar Chihab
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, 20360, Casablanca, Morocco
| | - Mohamed Tahiri
- Service d'Hépato-Gastro-Entérologie, CHU Ibn Rochd, 20360, Casablanca, Morocco
| | - Mostafa Kabine
- Laboratoire Santé et Environnement, département de Biologie, Faculté des Sciences Ain Chock, University Hassan II of Casablanca, 20360, Casablanca, Morocco
| | - Wafaa Badre
- Service d'Hépato-Gastro-Entérologie, CHU Ibn Rochd, 20360, Casablanca, Morocco
| | - Isabelle Chemin
- Centre de Recherche en Cancérologie de Lyon, UMR INSERM 1052, CNRS 5286, Lyon Cedex 03, France
| | - Agnes Marchio
- Unité "Organisation Nucléaire et Oncogenèse", INSERM U993, Institut Pasteur, 75015, Paris, France
| | - Pascal Pineau
- Unité "Organisation Nucléaire et Oncogenèse", INSERM U993, Institut Pasteur, 75015, Paris, France
| | - Sayeh Ezzikouri
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, 20360, Casablanca, Morocco.
| | - Soumaya Benjelloun
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, 20360, Casablanca, Morocco.
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Dhaini HR, Daher Z. Genetic polymorphisms of PPAR genes and human cancers: evidence for gene-environment interactions. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART C, ENVIRONMENTAL CARCINOGENESIS & ECOTOXICOLOGY REVIEWS 2019; 37:146-179. [PMID: 31045458 DOI: 10.1080/10590501.2019.1593011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Peroxisome proliferator-activated receptors (PPARs) are nuclear transcription factors that play a role in lipid metabolism, cell proliferation, terminal differentiation, apoptosis, and inflammation. Although several cancer models have been suggested to explain PPARs' involvement in tumorigenesis, however, their role is still unclear. In this review, we examined associations of the different PPARs, polymorphisms and various types of cancer with a focus on gene-environment interactions. Reviewed evidence suggests that functional genetic variants of the different PPARs may modulate the relationship between environmental exposure and cancer risk. In addition, this report unveils the scarcity of reliable quantitative environmental exposure data when examining these interactions, and the current gaps in studying gene-environment interactions in many types of cancer, particularly colorectal, prostate, and bladder cancers.
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Affiliation(s)
- Hassan R Dhaini
- a Department of Environmental Health, American University of Beirut , Lebanon
| | - Zeina Daher
- b Faculty of Public Health I, Lebanese University , Beirut , Lebanon
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