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1. Multiomics analysis reveals metabolic subtypes and identifies diacylglycerol kinase α (DGKA) as a potential therapeutic target for intrahepatic cholangiocarcinoma

Author

Weiren Liu, Huqiang Wang, Qianfu Zhao, Chenyang Tao, Weifeng Qu, Yushan Hou, Run Huang, Zimei Sun, Guiqi Zhu, Xifei Jiang, Yuan Fang, Jun Gao, Xiaoling Wu, Zhixiang Yang, Rongyu Ping, Jiafeng Chen, Rui Yang, Tianhao Chu, Jian Zhou, Jia Fan, Zheng Tang, Dong Yang, and Yinghong Shi

Subjects
diacylglycerol kinase α, intrahepatic cholangiocarcinoma, MAPK signaling, metabolic classification, multiomics analysis, phosphatidic acid metabolism, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Abstract Background Intrahepatic cholangiocarcinoma (iCCA) is a highly heterogeneous and lethal hepatobiliary tumor with few therapeutic strategies. The metabolic reprogramming of tumor cells plays an essential role in the development of tumors, while the metabolic molecular classification of iCCA is largely unknown. Here, we performed an integrated multiomics analysis and metabolic classification to depict differences in metabolic characteristics of iCCA patients, hoping to provide a novel perspective to understand and treat iCCA. Methods We performed integrated multiomics analysis in 116 iCCA samples, including whole‐exome sequencing, bulk RNA‐sequencing and proteome analysis. Based on the non‐negative matrix factorization method and the protein abundance of metabolic genes in human genome‐scale metabolic models, the metabolic subtype of iCCA was determined. Survival and prognostic gene analyses were used to compare overall survival (OS) differences between metabolic subtypes. Cell proliferation analysis, 5‐ethynyl‐2'‐deoxyuridine (EdU) assay, colony formation assay, RNA‐sequencing and Western blotting were performed to investigate the molecular mechanisms of diacylglycerol kinase α (DGKA) in iCCA cells. Results Three metabolic subtypes (S1‐S3) with subtype‐specific biomarkers of iCCA were identified. These metabolic subtypes presented with distinct prognoses, metabolic features, immune microenvironments, and genetic alterations. The S2 subtype with the worst survival showed the activation of some special metabolic processes, immune‐suppressed microenvironment and Kirsten rat sarcoma viral oncogene homolog (KRAS)/AT‐rich interactive domain 1A (ARID1A) mutations. Among the S2 subtype‐specific upregulated proteins, DGKA was further identified as a potential drug target for iCCA, which promoted cell proliferation by enhancing phosphatidic acid (PA) metabolism and activating mitogen‐activated protein kinase (MAPK) signaling. Conclusion Via multiomics analyses, we identified three metabolic subtypes of iCCA, revealing that the S2 subtype exhibited the poorest survival outcomes. We further identified DGKA as a potential target for the S2 subtype.

Published
2024
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2. Combinatorial Analysis of AT-Rich Interaction Domain 1A and CD47 in Gastric Cancer Patients Reveals Markers of Prognosis

Author

Qianfu Zhao, Qu Cai, Shanhe Yu, Jun Ji, Zhenggang Zhu, Chao Yan, and Jun Zhang

Subjects
ARID1A, CD47, gastric cancer, prognosis, immunotherapy, Biology (General), QH301-705.5
Abstract

Background: The AT-rich interaction domain 1A (ARID1A) is thought to be a tumor suppressive gene, and most of its mutations result in loss of expression of ARID1A protein. Combined with SIRPα on the surface of macrophages, CD47 on the surface of cancer cells can send an antiphagocytic “Don’t eat me” signal to the immune system that helps to avoid immune surveillance. However, the relationship between ARID1A and CD47 expression and their prognostic value in gastric cancer (GC) are still unknown.Methods: In this study, we evaluated ARID1A and CD47 expression in 154 GC patients’ tissues using tissue microarray. Expressions of ARID1A and CD47 in GC cell lines were determined by western blot and quantitative reverse transcriptase–polymerase chain reaction (qRT-PCR) techniques, and cell membranous CD47 expression was quantified by flow cytometry. In addition, chromatin immunoprecipitation (ChIP)–qPCR was used to determine the aspects of regulation of CD47 by ARID1A. The proportions of tumor-infiltrating immune cells were estimated on The Cancer Genome Atlas (TCGA) data set by using quanTIseq and EPIC algorithms. The infiltration of M1-polarized macrophages, M2-polarized macrophages, and regulatory T cells (Tregs) in GC tissues was determined by multispectral immunofluorescence.Results: A significant correlation was found between loss of ARID1A and high expression of CD47 at protein level in GC. By integrating 375 bulk RNA sequencing samples from TCGA data set, we found that mutated ARID1A correlated with high CD47 expression. In GC cell lines, knockdown of ARID1A significantly increased CD47 expression both at protein and mRNA levels as measured by western blot, qRT-PCR, and flow cytometry. Moreover, ChIP-qPCR revealed that CD47 was a direct downstream target gene of ARID1A in GC. Utilizing univariate and multivariate survival analyses, we found that patients with ARID1AlossCD47high expression had a worse prognosis. Estimation of infiltrating immune cells on TCGA data set showed that a higher infiltration proportion of M2 macrophages and Tregs was found in ARID1AmutatedCD47high expression subgroup. Furthermore, application of multispectral immunofluorescence revealed a higher infiltration proportion of M2 macrophages and Tregs in ARID1AlossCD47high GC tissues.Conclusion: Loss of ARID1A is strongly correlated with high CD47 expression in GC, and combination of ARID1A and CD47 is a promising prognosis factor in GC.

Published
2021
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3. Stearoyl-CoA desaturase 1 (SCD1) facilitates the growth and anti-ferroptosis of gastric cancer cells and predicts poor prognosis of gastric cancer

Author

Jinling Jiang, Huan Zhang, Jun Zhang, Jing Liu, Qianfu Zhao, Jun Ji, Min Shi, Chao Wang, Zhenggang Zhu, and Qu Cai

Subjects
Male, Aging, In silico, proliferation, Cell, medicine.disease_cause, In vivo, Stomach Neoplasms, lipid metabolism, medicine, Tumor Cells, Cultured, Humans, Aged, business.industry, gastric cancer, Cancer, Cell Biology, Middle Aged, medicine.disease, Prognosis, ferroptosis, medicine.anatomical_structure, Cancer cell, Cancer research, Biomarker (medicine), lipids (amino acids, peptides, and proteins), Female, Carcinogenesis, business, Stearoyl-CoA desaturase-1, SCD1, Stearoyl-CoA Desaturase, Research Paper
Abstract

Cancer cells are characterized by metabolic alterations. Thereinto, Stearoyl-CoA Desaturase 1 (SCD1), an enzymatic node located in the conversion of saturated fatty acids into monounsaturated fatty acids (MUFAs), has been reported to accelerate the tumorigenesis of multiple cancers. However, its role in the metabolic process of gastric cancer remains largely unexplored. In this study, by in vitro, in vivo and in silico assessments, our results revealed that SCD1 exhibited the ability to promote tumor growth, migration and anti-ferroptosis of gastric cancer. The underlying mechanism might involve the alteration of cancer stemness and modulation of cell cycle-related proteins. Moreover, based on our findings, high expression of SCD1 might predict poor prognosis in gastric cancer patients. Our study provided new insights into the potential of SCD1 as a biomarker as well as a therapeutic target in the treatment of gastric cancer.

Published
2020

4. The prognostic value of HGF-c-MET signaling pathway in Gastric Cancer: a study based on TCGA and GEO databases

Author

Zhenggang Zhu, Wenqi Xi, Min Shi, Jun Zhang, Jinling Jiang, Chao Wang, Jun Ji, Qianfu Zhao, Qu Cai, Huan Zhang, and Chenfei Zhou

Subjects
Adult, Male, C-Met, T cell, Biology, 03 medical and health sciences, chemistry.chemical_compound, Growth factor receptor binding, 0302 clinical medicine, Cell Movement, Stomach Neoplasms, Databases, Genetic, medicine, Humans, HGF, Phosphorylation, KEGG, Aged, Cell Proliferation, c-MET, Hepatocyte Growth Factor, gastric cancer, Cancer, General Medicine, Methylation, Middle Aged, Proto-Oncogene Proteins c-met, TCGA, GEO, medicine.disease, Gene Expression Regulation, Neoplastic, medicine.anatomical_structure, chemistry, Cancer research, Female, 030211 gastroenterology & hepatology, prognosis, Signal transduction, CD8, Signal Transduction, Research Paper
Abstract

Gastric cancer is a heterogeneous tumor that underlying molecular mechanisms are largely unclear. This study aimed to elucidate the expression level of HGF-c-MET in gastric cancer patients and to investigate the prognostic and diagnostic value of HGF-c-MET. In silico analysis of the TCGA and GEO database found that HGF and c-MET mRNA expression are significantly higher in gastric cancer tissues than those in peritumor tissues. Both higher mRNA expression of HGF and c-MET were associated with a poorer prognosis. c-MET expression was modulated by methylation in the promoter regions. HGF was positively correlated with CD8+ T cell, CD4+ T cell, macrophage, neutrophil and dendritic cell. Furthermore, functional enrichment analysis and protein-protein interaction networks further shown that HGF-c-MET and related proteins mainly participated in growth factor receptor binding, protein tyrosine kinase activity and signaling receptor binding. Finally, outcome of GSEA analysis showed 13 shared KEGG pathways enriched in high expressed group of HGF and c-MET.

Published
2020

5. CRISPR/Cas9-mediated knockout of SGLT1 inhibits proliferation and alters metabolism of gastric cancer cells

Author

Wenqi Xi, Qianfu Zhao, Jun Zhang, Qu Cai, Min Shi, Jun Ji, and Chao Wang

Subjects
digestive, oral, and skin physiology, Cancer, Cell Biology, Metabolism, Biology, medicine.disease, Glucose, Stomach Neoplasms, Transcription (biology), Apoptosis, Cancer cell, Extracellular, medicine, Cancer research, Transcriptional regulation, Humans, CRISPR, CRISPR-Cas Systems, Cell Proliferation
Abstract

Background The roles played by sodium/glucose cotransporters 1 (SGLT1) that transport glucose in cells independent of extracellular glucose concentration in gastric cancer are unknown. Methods The expression of SGLT1 in 75 primary gastric cancer and paired adjacent normal tissue specimens was determined. Also, the underlying mechanism of the altered SGLT1 expression and its impact on the proliferation of the gastric cancer cells and their metabolism were investigated. Results SGLT1 expression was found to be positively associated with pT, pN, TNM staging, histological differentiation, and a worse overall survival. CRISPR/Cas9 mediated knockout of SGLT1 could inhibit proliferation of gastric cancer cells, promote their apoptosis, and could also alter the metabolism of gastric cancer cells. Mechanistically, the transcription activity of SGLT1 could be negatively regulated by p53. Conclusions Besides identifying the important role of SGLT1 in gastric cancer, the underlying regulation mechanism in play was also elucidated. These make SGLT1 a promising new molecular target for the design of novel therapeutic modalities to control gastric cancer.

Published
2022

6. Low expression of transferrin receptor 2 predict poor prognosis in gastric cancer patients

Author

Jun Zhang, Zhenggang Zhu, Chenfei Zhou, Chao Wang, Qu Cai, Jun Ji, Min Shi, and Qianfu Zhao

Subjects
Male, Messenger RNA, medicine.medical_specialty, business.industry, Cancer, Transferrin receptor, General Medicine, Middle Aged, medicine.disease, Prognosis, Gastroenterology, Survival Analysis, Blot, Gene Expression Regulation, Neoplastic, Stomach Neoplasms, Internal medicine, Receptors, Transferrin, medicine, T-stage, Immunohistochemistry, Humans, Female, Stage (cooking), business, Survival analysis
Abstract

This study was to detect the expression level of transferrin receptor 2 (TfR2) in gastric cancer and to analyze its value in predicting the prognosis of gastric cancer patients. Real-time PCR (RT-qPCR) was applied to detect the mRNA expression of TfR2 in gastric cancer tissues and paired adjacent nontumorous tissues. Immunohistochemistry (IHC) and western blotting were used to determine the protein expression of TfR2 in gastric cancer, and the relationship with the prognosis of gastric cancer patients was analyzed. The results were: (1) The mRNA and protein levels of TfR2 in gastric cancer tissues were remarkably lower than those in adjacent nontumorous gastric tissue (P < .05). (2) Clinicopathological analysis showed that the expression level of TfR2 was significantly correlated with TNM stage of patients (P = .047). (3) The results of univariate survival analysis showed that histological grade, T stage, N stage, M stage, Lauren's classification, and TfR2 expression level influenced the overall survival of gastric cancer patients. Multivariate survival analysis showed that low TfR2 expression (HR = 1.671, 95%CI: 1.006-2.774, P = .047), poor differentiation (HR = 2.123, 95%CI: 1.188-3.795, P = .011), and M1 stage (HR = 8.541, 95%CI: 3.416-21.353, P < .001) were independent risk factors affecting the overall survival of gastric cancer patients. In conclusion, TfR2 exhibited low expression in gastric cancer tissue, and is an independent prognostic factor of gastric cancer patients.

Published
2020

7. Using circular RNA hsa_circ_0000190 as a new biomarker in the diagnosis of gastric cancer

Author

Junming Guo, Tianwen Li, Qianfu Zhao, Shijun Chen, and Bingxiu Xiao

Subjects
0301 basic medicine, Microarray, Clinical Biochemistry, Down-Regulation, Biology, Biochemistry, Sensitivity and Specificity, 03 medical and health sciences, 0302 clinical medicine, Circular RNA, Stomach Neoplasms, medicine, Biomarkers, Tumor, Humans, Neoplasm Staging, Receiver operating characteristic, Plasma samples, Biochemistry (medical), Cancer, General Medicine, RNA, Circular, Middle Aged, medicine.disease, Molecular biology, digestive system diseases, 030104 developmental biology, 030220 oncology & carcinogenesis, Area Under Curve, Lymphatic Metastasis, Cancer research, Clinicopathological features, Biomarker (medicine), RNA
Abstract

Circular RNAs (circRNA) are an abundant class of non-coding RNAs in mammalian cells. However, their value in the diagnosis of cancers remains unknown. In this study, we focused on hsa_circ_0000190, which was found to be down-regulated in gastric cancer tissues in our previous microarray screening.The hsa_circ_0000190 levels in 104 paired gastric cancer tissues and adjacent non-tumor tissues, 104 plasma samples from patients with gastric cancer and 104 plasma samples from health controls were detected by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Then, the association between the expression level of hsa_circ_0000190 and the clinicopathological features of patients with gastric cancer was further analyzed. A receiver operating characteristic (ROC) curve was generated to evaluate the diagnostic value.Hsa_circ_0000190 was first found to be down-regulated in gastric cancer tissues (P0.001) and plasma samples from patients with gastric cancer (P0.001). Its expression levels were significantly correlated with tumor diameter (P=0.034), lymphatic metastasis (P=0.026), distal metastasis (P=0.001), TNM stage (P=0.001), and CA19-9 levels (P=0.019). The areas under the ROC curve (AUC) of hsa_circ_0000190 in tissues and plasma were up to 0.75 and 0.60, respectively. The sensitivity and specificity of the combination were 0.712 and 0.750; the AUC was increased to 0.775.These results indicated that hsa_circ_0000190 may be a novel non-invasive biomarker for the diagnosis of gastric cancer. Its AUC, sensitivity and specificity are better than commonly used biomarkers such as CEA and CA19-9.

Published
2016

8. Clinical values of circular RNA 0000181 in the screening of gastric cancer

Author

Xinjun Zhang, Shijun Chen, Qianfu Zhao, Tianwen Li, and Bingxiu Xiao

Subjects
Male, 0301 basic medicine, Microbiology (medical), Lymphatic metastasis, medicine.medical_specialty, Pathology, Clinical Biochemistry, Biology, Gastroenterology, Metastasis, 03 medical and health sciences, 0302 clinical medicine, Carcinoembryonic antigen, Stomach Neoplasms, Circular RNA, Internal medicine, Biomarkers, Tumor, medicine, Humans, Immunology and Allergy, Early Detection of Cancer, Research Articles, Tumor size, Receiver operating characteristic, Biochemistry (medical), Public Health, Environmental and Occupational Health, Cancer, RNA, Circular, Hematology, Middle Aged, medicine.disease, Medical Laboratory Technology, 030104 developmental biology, Molecular Diagnostic Techniques, 030220 oncology & carcinogenesis, biology.protein, RNA, Biomarker (medicine), Female
Abstract

Background Circular RNAs (circRNAs) are recently found involved in cancer occurrence and development. However, their values in the diagnosis of gastric cancers are largely unknown. In this study, we analyzed the values of hsa_circ_0000181 in the diagnosis of gastric cancer. Methods Using divergent primers, hsa_circ_0000181 expression levels in fresh gastric cancer tissues and paired adjacent non-tumorous tissues, and plasmas from patient with gastric cancer and health people were detected by real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR). The association between hsa_circ_0000181 levels and the clinicopathologic features of patients with gastric cancer was further analyzed. Finally, to evaluate the diagnostic value, receiver operating characteristic (ROC) curve was established. Results Hsa_circ_0000181 levels in gastric cancer tissues and plasma from gastric cancer patients were significantly decreased than those in paired adjacent non-tumorous tissues (P

Published
2017

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