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Sehgal M, Ramu S, Vaz JM, Ganapathy YR, Muralidharan S, Venkatraghavan S, Jolly MK. Characterizing heterogeneity along EMT and metabolic axes in colorectal cancer reveals underlying consensus molecular subtype-specific trends. Transl Oncol 2024; 40:101845. [PMID: 38029508 PMCID: PMC10698572 DOI: 10.1016/j.tranon.2023.101845] [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: 08/06/2023] [Revised: 11/01/2023] [Accepted: 11/21/2023] [Indexed: 12/01/2023] Open
Abstract
Colorectal cancer (CRC) is highly heterogeneous with variable survival outcomes and therapeutic vulnerabilities. A commonly used classification system in CRC is the Consensus Molecular Subtypes (CMS) based on gene expression patterns. However, how these CMS categories connect to axes of phenotypic plasticity and heterogeneity remains unclear. Here, in our analysis of CMS-specific TCGA data and 101 bulk transcriptomic datasets, we found the epithelial phenotype score to be consistently positively correlated with scores of glycolysis, OXPHOS and FAO pathways, while PD-L1 activity scores positively correlated with mesenchymal phenotype scoring, revealing possible interconnections among plasticity axes. Single-cell RNA-sequencing analysis of patient samples revealed that that CMS2 and CMS3 subtype samples were relatively more epithelial as compared to CMS1 and CMS4. CMS1 revealed two subpopulations: one close to CMS4 (more mesenchymal) and the other closer to CMS2 or CMS3 (more epithelial), indicating a partial EMT-like behavior. Consistent observations were made in single-cell analysis of metabolic axes and PD-L1 activity scores. Together, our results quantify the patterns of two functional interconnected axes of phenotypic heterogeneity - EMT and metabolic reprogramming - in a CMS-specific manner in CRC.
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Affiliation(s)
- Manas Sehgal
- Department of Bioengineering, Indian Institute of Science, Bangalore 560012, India
| | - Soundharya Ramu
- Department of Bioengineering, Indian Institute of Science, Bangalore 560012, India
| | - Joel Markus Vaz
- Department of Bioengineering, Indian Institute of Science, Bangalore 560012, India; School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332, United States
| | | | - Srinath Muralidharan
- Department of Bioengineering, Indian Institute of Science, Bangalore 560012, India
| | | | - Mohit Kumar Jolly
- Department of Bioengineering, Indian Institute of Science, Bangalore 560012, India.
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morsi RM, Mansour DS, Mousa AM. Ameliorative potential role of Rosmarinus officinalis extract on toxicity induced by etoposide in male albino rats. BRAZ J BIOL 2024; 84:e258234. [DOI: 10.1590/1519-6984.258234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 06/17/2022] [Indexed: 11/21/2022] Open
Abstract
Abstract The present work was showed to assess the effect of administration of rosemary extract on etoposide-induced toxicity, injury and proliferation in male rats were investigated. Forty male albino rats were arranged into four equal groups. 1st group, control; 2nd group, etoposide; 3rd group, co-treated rosemary & etoposide; 4th group, rosemary alone. In comparison to the control group, etoposide administration resulted in a significant increase in serum ALT, AST, ALP, total bilirubin, total protein, and gamma GT. In contrast; a significant decrease in albumin level in etoposide group as compared to G1. G3 revealed a significant decrease in AST, ALT, ALP, total protein and total bilirubin levels and a significant rise in albumin level when compared with G2. Serum levels of urea, creatinine, potassium ions, and chloride ions significantly increased; while sodium ions were significantly decreased in G2 when compared with G1. Also, there was an increase of MDA level for etoposide treated group with corresponding control rats. However, there was a remarkable significant decrease in SOD, GPX and CAT levels in G2 as compared to G1. There was a significant increase in serum hydrogen peroxide (H2O2) and Nitric oxide (NO) levels in group treated with etoposide when compared to control group. It was noticeable that administrated by rosemary alone either with etoposide had not any effect on the levels of H2O2 and Nitric oxide. Serum level of T3 and T4 was significantly increased in etoposide-administered rats in comparison with G1. The administration of rosemary, either alone or with etoposide, increased the serum levels of T3 and T4 significantly when compared to control rats. The gene expression analysis showed significant downregulation of hepatic SOD and GPx in (G2) when compared with (G1). The treatment with rosemary extract produced significant upregulation of the antioxidant enzymes mRNA SOD and GPx. MDA gene was increased in (G2) when contrasted with (G1). Treatment of the etoposide- induced rats with rosemary extract delivered significant decrease in MDA gene expression when compared with etoposide group. Rats treated with etoposide showed significant decline in hepatic Nrf2 protein expression, when compared with G1. While, supplementation of Etoposide- administered rats with the rosemary produced a significant elevation in hepatic Nrf2 protein levels. Additionally, the liver histological structure displayed noticeable degeneration and cellular infiltration in liver cells. It is possible to infer that rosemary has a potential role and that it should be researched as a natural component for etoposide-induced toxicity protection.
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Men X, Zhu W. Silencing of Perilipin 3 Inhibits Lung Adenocarcinoma Cell Immune Resistance by Regulating the Transcription of PD-L1 Through c-Myc. Immunol Invest 2023; 52:815-831. [PMID: 37578465 DOI: 10.1080/08820139.2023.2244976] [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] [Indexed: 08/15/2023]
Abstract
BACKGROUND Perilipin 3 (PLIN3), a lipid droplet-associated protein, is found to be highly expressed in human cancers. This study aimed to investigate the biological functions and underlying mechanism of PLIN3 in lung adenocarcinoma (LUAD). METHODS To analyse PLIN3 expression in normal and cancerous tissues, relevance between PLIN3 expression and survival prognosis, and to predict the pathways related to PLIN3, bioinformatic analysis was performed. In A549 and H1299 cells, qRT-PCR or western blotting was used to determine mRNA/protein expression of PLIN3, PD-L1, and c-Myc. In A549 and H1299 cells, CCK-8 assay, EdU, and flow cytometry were used to assess cell viability, proliferation, and apoptosis. Chip and luciferase reporter assays were performed to verify the binding of PD-L1 with c-Myc. The functions of PLIN3 were examined in vivo in a xenograft tumor model. RESULTS In LUAD tissues and cells, PLIN3 expression was downregulated. A shorter survival time was observed in patients with high PLIN3 expression than in patients with low PLIN3 expression. Silencing of PLIN3 inhibited cell proliferation, PD-L1 expression, and Myc pathway, as well as induced apoptosis in LUAD cells. c-Myc acts as a transcription factor of PD-L1. Moreover, the inhibitory actions of PLIN3 silencing on c-Myc and PD-L1 expression as well as cell proliferation and stimulatory action of PLIN3 silencing on cell apoptosis were reversed by c-Myc overexpression. In vivo, PLIN3 silencing inhibited the growth of xenograft tumour and reduced PLIN3, PD-L1, and c-Myc protein expression. CONCLUSION Silencing of PLIN3 inhibited tumour growth by regulating the Myc/PD-L1 pathway.
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Affiliation(s)
- Xuelin Men
- Department of Respiratory and Critical Care II, The Fourth People's Hospital of Jinan, Jinan, Shandong, P.R. China
| | - Wei Zhu
- Department of Respiratory and Critical Care II, The Fourth People's Hospital of Jinan, Jinan, Shandong, P.R. China
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Zhang K, Dong Y, Li M, Zhang W, Ding Y, Wang X, Chen D, Liu T, Wang B, Cao H, Zhong W. Clostridium butyricum inhibits epithelial-mesenchymal transition of intestinal carcinogenesis through downregulating METTL3. Cancer Sci 2023. [PMID: 37243376 PMCID: PMC10394142 DOI: 10.1111/cas.15839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 03/10/2023] [Accepted: 03/30/2023] [Indexed: 05/28/2023] Open
Abstract
Colorectal cancer (CRC) is related to gut microbiota dysbiosis, especially butyrate-producing bacteria reduction. Our previous study suggested that administration of Clostridium butyricum, a butyrate-producing bacterium, exerts a crucial effect against CRC, however the potential mechanism is not clear. We first found that methyltransferase-like 3 (METTL3) showed a positive correlation with proliferation, epithelial-mesenchymal transition (EMT), DNA repair, metastasis, and invasion in a database analysis. The expression of METTL3 gradually increased from human normal colon tissue, to adenoma, and carcinoma, and was positively correlated with E-cadherin and CD34 levels. Overexpression of METTL3 promoted the proliferation, migration, and invasion of CRC cells and induced vasculogenic mimicry (VM) formation. Clostridium butyricum could downregulate METTL3 expression in CRC cells and decrease the expression of vimentin and vascular endothelial growth factor receptor 2 to reduce EMT and VM formation. Clostridium butyricum alleviated the pro-oncogenic effect of METTL3 overexpressing plasmid in CRC cells. The anti-EMT effect on METTL3 reduction of C. butyricum could be blunted by knocking down G-protein coupled receptor 43. Moreover, C. butyricum prevented EMT and VM and inhibited tumor metastasis in nude mice. Accordingly, C. butyricum could inhibit EMT and VM formation of intestinal carcinogenesis through downregulating METTL3. These findings broaden our understanding of probiotics supplement in CRC prevention and treatment.
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Affiliation(s)
- Kexin Zhang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Yue Dong
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Mengfan Li
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Wanru Zhang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Yiyun Ding
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Xin Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Danfeng Chen
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Tianyu Liu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Bangmao Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Hailong Cao
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Weilong Zhong
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
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Zhan T, Cheng X, Zhu Q, Han Z, Zhu K, Tan J, Liu M, Chen W, Chen X, Chen X, Tian X, Huang X. LncRNA LOC105369504 inhibits tumor proliferation and metastasis in colorectal cancer by regulating PSPC1. Cell Death Discov 2023; 9:89. [PMID: 36894530 PMCID: PMC9998613 DOI: 10.1038/s41420-023-01384-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 02/21/2023] [Accepted: 02/27/2023] [Indexed: 03/11/2023] Open
Abstract
There is growing evidence that long non-coding RNAs (lncRNAs) are significant contributors to the epigenetic mechanisms implicated in the emergence, progression and metastasis of the colorectal cancer (CRC), but many remain underexplored. A novel lncRNA LOC105369504, was identified to be a potential functional lncRNA by microarray analysis. In CRC, the expression of LOC105369504 was markedly decreased and resulted in distinct variations in proliferation, invasion, migration and epithelial-mesenchymal transition (EMT) in vivo and in vitro. This study showed that LOC105369504 bound to the protein of paraspeckles compound 1 (PSPC1) directly and regulated its stability using the ubiquitin-proteasome pathway in CRC cells. The suppression of CRC by LOC105369504 could be reversed through PSPC1 overexpression.This study showed that in CRC, LOC105369504 was under-regulated and as a novel lncRNA, LOC105369504 exerted tumor suppressive activity to suppress the proliferation together with metastasis in CRC cells through the regulation of PSPC1. These results offer new perspectives on the lncRNA effect on the progression of CRC.
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Affiliation(s)
- Ting Zhan
- Department of Gastroenterology, WuHan Third Hospital (Tongren hospital of WuHan University), 430060, Wuhan, China
| | - Xueting Cheng
- Department of Gastroenterology, WuHan Third Hospital (Tongren hospital of WuHan University), 430060, Wuhan, China
| | - Qingxi Zhu
- Department of Gastroenterology, WuHan Third Hospital (Tongren hospital of WuHan University), 430060, Wuhan, China
| | - Zheng Han
- Department of Gastroenterology, WuHan Third Hospital (Tongren hospital of WuHan University), 430060, Wuhan, China
| | - Kejing Zhu
- Department of Pharmacy, WuHan Third Hospital (Tongren hospital of WuHan University), 430060, Wuhan, China
| | - Jie Tan
- Department of Gastroenterology, WuHan Third Hospital (Tongren hospital of WuHan University), 430060, Wuhan, China
| | - Men Liu
- Department of Gastroenterology, WuHan Third Hospital (Tongren hospital of WuHan University), 430060, Wuhan, China
| | - Wei Chen
- Department of Gastroenterology, WuHan Third Hospital (Tongren hospital of WuHan University), 430060, Wuhan, China
| | - Xiaoli Chen
- Department of Gastroenterology, WuHan Third Hospital (Tongren hospital of WuHan University), 430060, Wuhan, China
| | - Xiaohong Chen
- Department of Gastroenterology, WuHan Third Hospital (Tongren hospital of WuHan University), 430060, Wuhan, China
| | - Xia Tian
- Department of Gastroenterology, WuHan Third Hospital (Tongren hospital of WuHan University), 430060, Wuhan, China.
| | - Xiaodong Huang
- Department of Gastroenterology, WuHan Third Hospital (Tongren hospital of WuHan University), 430060, Wuhan, China.
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Cai D, Wang W, Zhong ME, Fan D, Liu X, Li CH, Huang ZP, Zhu Q, Lv MY, Hu C, Duan X, Wu XJ, Gao F. An immune, stroma, and epithelial-mesenchymal transition-related signature for predicting recurrence and chemotherapy benefit in stage II-III colorectal cancer. Cancer Med 2023; 12:8924-8936. [PMID: 36629124 PMCID: PMC10134284 DOI: 10.1002/cam4.5534] [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: 04/28/2022] [Revised: 10/27/2022] [Accepted: 12/02/2022] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Debates exist on the treatment decision of the stage II/III colorectal cancer (CRC) due to the insufficiency of the current TNM stage-based risk stratification system. Epithelial-mesenchymal transition (EMT) and tumor microenvironment (TME) have both been linked to CRC progression in recent studies. We propose to improve the prognosis prediction of CRC by integrating TME and EMT. METHODS In total, 2382 CRC patients from seven datasets and one in-house cohort were collected, and 1640 stage II/III CRC patients with complete survival information and gene expression profiles were retained and divided into a training cohort and three independent validation cohorts. Integrated analysis of 398 immune, stroma, and epithelial-mesenchymal transition (ISE)-related genes identified an ISE signature independently associated with the recurrence of CRC. The underlying biological mechanism of the ISE signature and its influence on adjuvant chemotherapy was further explored. RESULTS We constructed a 26-gene signature which was significantly associated with poor outcome in Training cohort (p < 0.001, HR [95%CI] = 4.42 [3.25-6.01]) and three independent validation cohorts (Validation cohort-1: p < 0.01, HR [95%CI] = 1.70 [1.15-2.51]; Validation cohort-2: p < 0.001, HR [95% CI] = 2.30 [1.67-3.16]; Validation cohort-3: p < 0.01, HR [95% CI] = 2.42 [1.25-4.70]). After adjusting for known clinicopathological factors, multivariate cox analysis confirmed the ISE signature's independent prognostic value. Subgroup analysis found that stage III patients with low ISE score might benefit from adjuvant chemotherapy (p < 0.001, HR [95%CI] = 0.15 [0.04-0.55]). Hypergeometric test and enrichment analysis revealed that low-risk group was enriched in thr immune pathway while high-risk group was associated with the EMT pathway and CMS4 subtype. CONCLUSION We proposed an ISE signature for robustly predicting the recurrence of stage II/III CRC and help treatment decision by identifying patients who will not benefit from current standard treatment.
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Affiliation(s)
- Du Cai
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Institute of Gastroenterology, Guangzhou, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Wei Wang
- Department of Clinical Laboratory, Haining People's Hospital, Jiaxing, China
| | - Min-Er Zhong
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Institute of Gastroenterology, Guangzhou, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Dejun Fan
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Institute of Gastroenterology, Guangzhou, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Department of Gastrointestinal Endoscopy, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xuanhui Liu
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Institute of Gastroenterology, Guangzhou, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Cheng-Hang Li
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Institute of Gastroenterology, Guangzhou, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ze-Ping Huang
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Institute of Gastroenterology, Guangzhou, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Qiqi Zhu
- Department of Colorectal Surgery, Ningbo Medical Center Lihuili Hospital, Ningbo, China
| | - Min-Yi Lv
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Institute of Gastroenterology, Guangzhou, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Chuling Hu
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Institute of Gastroenterology, Guangzhou, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xin Duan
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Institute of Gastroenterology, Guangzhou, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiao-Jian Wu
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Institute of Gastroenterology, Guangzhou, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Feng Gao
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Institute of Gastroenterology, Guangzhou, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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Wang Z, Fu L, Zhang J, Ge Y, Guo C, Wang R, Deng M, Wang Q, Wang Z. A comprehensive analysis of potential gastric cancer prognostic biomarker ITGBL1 associated with immune infiltration and epithelial-mesenchymal transition. Biomed Eng Online 2022; 21:30. [PMID: 35596183 PMCID: PMC9123716 DOI: 10.1186/s12938-022-00998-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 04/27/2022] [Indexed: 11/17/2022] Open
Abstract
Background Integrin, beta-like 1 (ITGBL1) is involved in a variety of human malignancies. However, the information on the involvement of ITGBL1 in gastric carcinoma (GC) is limited. Hence, this study aimed further to explore the functions and mechanisms of ITGBL1 in GC. Methods First, multiple bioinformatics databases, including Oncomine, Tumor Immune Estimation Resource, UALCAN, and Kaplan–Meier Plotter, were used to predict the expression level and prognostic value of ITGBL1, as well as its association with immune infiltration and epithelial–mesenchymal transition (EMT) in GC. Quantitative reverse transcription–polymerase chain reaction and immunohistochemical analysis were used to detect the expression of ITGBL1 in both GC tissues and cells. Then, targeted silencing of ITGBL1 in GC cells was further used to examine the biological functions of ITGBL1. Results These databases revealed that ITGBL1 was overexpressed and affected the overall survival in GC. Besides, the expression of ITGBL1 positively correlated with immune-infiltrating cells and EMT-related markers. Subsequently, molecular biology experiments verified these predictions. In GC tissues and cells, ITGBL1 was notably overexpressed. Loss-of-function studies showed that the knockdown of ITGBL1 significantly suppressed migration and invasion but promoted apoptosis in MGC803 GC cells. Furthermore, the inhibition of ITGBL1 resulted in remarkably increased protein expression levels of cadherin 1, while the expression of Vimentin, Snail, and transforming growth factor-β1 was downregulated, indicating the initiation and progression of GC caused by ITGBL1 partly via inducing EMT. Conclusions To sum up, the findings indicated that ITGBL1 acted as a valuable oncogenic factor in GC.
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Affiliation(s)
- Zhe Wang
- Department of Gastroenterology, Tongji Hospital, Tongji University School of Medicine, 389 Xincun Road, Putuo District, Shanghai, 200065, People's Republic of China
| | - Liu Fu
- Department of Gastroenterology, Putuo People's Hospital, Tongji University, Shanghai, 200060, People's Republic of China
| | - Junjie Zhang
- Department of Gastroenterology, Tongji Hospital, Tongji University School of Medicine, 389 Xincun Road, Putuo District, Shanghai, 200065, People's Republic of China
| | - Yanli Ge
- Department of Gastroenterology, Tongji Hospital, Tongji University School of Medicine, 389 Xincun Road, Putuo District, Shanghai, 200065, People's Republic of China
| | - Cheng Guo
- Department of Gastroenterology, Tongji Hospital, Tongji University School of Medicine, 389 Xincun Road, Putuo District, Shanghai, 200065, People's Republic of China
| | - Rui Wang
- Department of Gastroenterology, Tongji Hospital, Tongji University School of Medicine, 389 Xincun Road, Putuo District, Shanghai, 200065, People's Republic of China
| | - Min Deng
- Department of Gastroenterology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, 233004, People's Republic of China
| | - Qizhi Wang
- Department of Gastroenterology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, 233004, People's Republic of China
| | - Zhirong Wang
- Department of Gastroenterology, Tongji Hospital, Tongji University School of Medicine, 389 Xincun Road, Putuo District, Shanghai, 200065, People's Republic of China.
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8
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Yu J, Yang K, Zheng J, Sun X, Zhao W. Establishment of a novel prognostic signature based on an identified expression profile of integrin superfamily to predict overall survival of patients with colorectal adenocarcinoma. Gene 2022; 808:145990. [PMID: 34624456 DOI: 10.1016/j.gene.2021.145990] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/14/2021] [Accepted: 10/01/2021] [Indexed: 12/02/2022]
Abstract
The abnormal expression of integrin superfamily members commonly related to kinds of malignancies. However, the role of integrins in predicting the prognosis of cancers is still little known, especially for colorectal cancer that is one of the leading causes of cancer-related death. RNA-seq data and clinical features of colorectal adenocarcinoma (COAD) patients were derived from The Cancer Genome Atlas (TCGA), used to analyze the expression pattern and genomic alterations of integrin genes in the COAD cohort. Unsupervised hierarchical clustering divided COAD patients into two clusters (clusters 1 & 2), and we observed that patients in cluster 2 with high expressions of most integrin genes had worse clinical features and shorter overall survival (a median OS: 67.25 months vs 99.93 months, p = 0.012), compared to those in cluster 1. Combined with univariate Cox regression analysis, Pearson Correlation Coefficients (PCC), and Principal Component Analysis (PCA), an integrin-related signature was established, including ITGA1, ITGA5, ITGA7, ITGA11, ITGAX, ITGAM, ITGB1, and ITGB5. And the AUC values for OS at 1, 3, and 5 years was 0.61, 0.59, and 0.56, further demonstrating the predicting capacity of our signature. Furthermore, overexpression of which also significantly correlated with poorer prognosis of colon cancer patients in a separate validation cohort, GSE17536 (p < 0.05). Meanwhile, the AUC values for OS in the validation cohort at 1, 3, and 5 years was 0.62, 0.59, and 0.59. Additionally, enrichment analysis indicated significant differences between cluster 1 and cluster 2 in the biological processes of cell adhesion, signal transduction, extracellular matrix, immune system, and in tumor microenvironment (TME), which were crucial to the progression of tumor. The findings supplied compelling evidence that our signature could be a novel prognostic biomarker for COAD patients, and these genes had the potential to be therapeutic targets.
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Affiliation(s)
- Junhui Yu
- Department of General Surgery, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi Province, People's Republic of China.
| | - Kui Yang
- Department of General Surgery, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi Province, People's Republic of China.
| | - Jianbao Zheng
- Department of General Surgery, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi Province, People's Republic of China.
| | - Xuejun Sun
- Department of General Surgery, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi Province, People's Republic of China.
| | - Wei Zhao
- Department of General Surgery, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi Province, People's Republic of China.
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Integrative analysis from multi-center studies identities a consensus machine learning-derived lncRNA signature for stage II/III colorectal cancer. EBioMedicine 2021; 75:103750. [PMID: 34922323 PMCID: PMC8686027 DOI: 10.1016/j.ebiom.2021.103750] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 11/30/2021] [Accepted: 11/30/2021] [Indexed: 02/07/2023] Open
Abstract
Background Long non-coding RNAs (lncRNAs) have recently emerged as essential biomarkers of cancer progression. However, studies are limited regarding lncRNAs correlated with recurrence and fluorouracil-based adjuvant chemotherapy (ACT) in stage II/III colorectal cancer (CRC). Methods 1640 stage II/III CRC patients were enrolled from 15 independent datasets and a clinical in-house cohort. 10 prevalent machine learning algorithms were collected and then combined into 76 combinations. 109 published transcriptome signatures were also retrieved. qRT-PCR assay was performed to verify our model. Findings We comprehensively identified 27 stably recurrence-related lncRNAs from multi-center cohorts. According to these lncRNAs, a consensus machine learning-derived lncRNA signature (CMDLncS) that exhibited best power for predicting recurrence risk was determined from 76 kinds of algorithm combinations. A high CMDLncS indicated unfavorable recurrence and mortality rates. CMDLncS not only could work independently of common clinical traits (e.g., AJCC stage) and molecular features (e.g., microsatellite state, KRAS mutation), but also presented dramatically better performance than these variables. qRT-PCR results from 173 patients further verified our in-silico findings and assessed its feasible in different centers. Comparisons of CMDLncS with 109 published transcriptome signatures further demonstrated its predictive superiority. Additionally, patients with high CMDLncS benefited more from fluorouracil-based ACT and were characterized by activation of stromal and epithelial-mesenchymal transition, while patients with low CMDLncS suggested the sensitivity to bevacizumab and displayed enhanced immune activation. Interpretation CMDLncS provides an attractive platform for identifying patient at high risk of recurrence and could optimize precision treatment to improve the clinical outcomes in stage II/III CRC. Funding This study was supported by the National Natural Science Foundation of China (81,972,663); Henan Province Young and Middle‐Aged Health Science and Technology Innovation Talent Project (YXKC2020037); and Henan Provincial Health Commission Joint Youth Project (SB201902014).
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TMEM100 Modulates TGF- β Signaling Pathway to Inhibit Colorectal Cancer Progression. Gastroenterol Res Pract 2021; 2021:5552324. [PMID: 34422038 PMCID: PMC8373494 DOI: 10.1155/2021/5552324] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 07/02/2021] [Accepted: 07/13/2021] [Indexed: 02/08/2023] Open
Abstract
Objectives This study investigated the functional mechanism of transmembrane protein 100 (TMEM100) as a tumor inhibitor gene in CRC cells and offered a reference for the treatment of CRC. Methods The mRNA expression data of CRC were acquired from the TCGA database to mine differentially expressed mRNAs. The role of TMEM100 in the progression of CRC cells was evaluated by MTT, colony formation, scratch healing, and Transwell assays. The influence of TMEM100 on the TGF-β signaling pathway was detected by western blot. Results TMEM100 was markedly lowly expressed in CRC. CRC cell growth was significantly suppressed by overexpressing TMEM100 but noticeably facilitated by silencing TMEM100. Overexpression of TMEM100 inhibited the activation of the TGF-β signaling pathway, thus inhibiting malignant progression of CRC. Conclusion TMEM100 is lowly expressed in CRC, which can suppress CRC cell growth by regulating the TGF-β signaling pathway.
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11
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Liu Y, Feng Z, Chen H. Integrated analysis of the expression, involved functions, and regulatory network of RUNX3 in melanoma. Comb Chem High Throughput Screen 2021; 25:1552-1564. [PMID: 34397327 DOI: 10.2174/1386207324666210816121833] [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: 01/20/2021] [Revised: 05/31/2021] [Accepted: 06/02/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND As a tumor suppressor or oncogenic gene, abnormal expression of RUNX family transcription factor 3 (RUNX3) has been reported in various cancers. <p> Introduction: This study aimed to investigate the role of RUNX3 in melanoma. <p> Methods: The expression level of RUNX3 in melanoma tissues was analyzed by immunohistochemistry and the Oncomine database. Based on microarray datasets GSE3189 and GSE7553, differentially expressed genes (DEGs) in melanoma samples were screened, followed by functional enrichment analysis. Gene Set Enrichment Analysis (GSEA) was performed for RUNX3. DEGs that co-expressed with RUNX3 were analyzed, and the transcription factors (TFs) of RUNX3 and its co-expressed genes were predicted. The protein-protein interactions (PPIs) for RUNX3 were analyzed utilizing the GeneMANIA database. MicroRNAs (miRNAs) that could target RUNX3 expression, were predicted. <p> Results: RUNX3 expression was significantly up-regulated in melanoma tissues. GSEA showed that RUNX3 expression was positively correlated with melanogenesis and melanoma pathways. Eleven DEGs showed significant co-expression with RUNX3 in melanoma, for example, TLE4 was negatively co-expressed with RUNX3. RUNX3 was identified as a TF that regulated the expression of both itself and its co-expressed genes. PPI analysis showed that 20 protein-encoding genes interacted with RUNX3, among which 9 genes were differentially expressed in melanoma, such as CBFB and SMAD3. These genes were significantly enriched in transcriptional regulation by RUNX3, RUNX3 regulates BCL2L11 (BIM) transcription, regulation of I-kappaB kinase/NF-kappaB signaling, and signaling by NOTCH. A total of 31 miRNAs could target RUNX3, such as miR-326, miR-330-5p, and miR-373-3p. <p> Conclusion: RUNX3 expression was up-regulated in melanoma and was implicated in the development of melanoma.
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Affiliation(s)
- Yanxin Liu
- Department of Burn and Plastic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, China
| | - Zhang Feng
- Department of Burn and Plastic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, China
| | - Huaxia Chen
- Department of Burn and Plastic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, China
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12
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Wu Y, Liang X, Ni J, Zhao R, Shao S, Lu S, Han W, Yu L. Effect of ISM1 on the Immune Microenvironment and Epithelial-Mesenchymal Transition in Colorectal Cancer. Front Cell Dev Biol 2021; 9:681240. [PMID: 34350177 PMCID: PMC8326811 DOI: 10.3389/fcell.2021.681240] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 06/28/2021] [Indexed: 12/21/2022] Open
Abstract
Background: An increasing number of studies have shown that Isthmin 1 (ISM1), a secreted protein, is important in tumorigenesis and invasion, including in colorectal cancer (CRC). However, the mechanisms are still unclear. This study aims to explore the function and prognosis capacity of ISM1 in CRC. Methods: We investigated the expression of ISM1 in 18 CRC tissues vs. adjacent normal tissues from GSE50760, 473 CRC tissues vs. 41 normal tissues from The Cancer Genome Atlas (TCGA), and across gastrointestinal cancer types. Differences were further confirmed in CRC tissues via quantitative real-time polymerase chain reaction (qRT-PCR). Then, we analyzed correlations between clinicopathologic features and ISM1 expression, including prognostic prediction value, using the Kaplan–Meier method and multivariate Cox regression. Gene set enrichment analysis (GSEA) was performed to identify ISM1-related pathways. In vitro experiments were performed to verify the role of ISM1 in epithelial-mesenchymal transition (EMT) and CRC progression. Results: Multiple datasets showed that ISM1 is upregulated in CRC tissues, which was validated. Patients with higher ISM1 expression had shorter overall survival (OS), and ISM1 expression served as an independent prognostic factor. Enrichment analysis showed that ISM1 upregulation was positively correlated with cancer-related pathways, such as EMT, hypoxia, and the Notch and KRAS signaling pathways. We were exclusively interested in the connection between ISM1 and EMT because 71% of genes in this pathway were significantly positively co-expressed with ISM1, which may account for why patients with higher ISM1 expression are prone to regional lymph node involvement and progression to advanced stages. In addition, we found that ISM1 was positively correlated with multiple immunosuppressive pathways such as IL2/STAT5, TNF-α/NF-κB, and TGF-β, and immune checkpoints, including PD-L1, PD-1, CTLA-4, and LAG3, which may account for upregulation of ISM1 in immunotherapy-resistant patients. Notably, through in vitro experiments, we found that ISM1 promoted EMT and colon cancer cell migration and proliferation. Conclusion: ISM1 is critical for CRC development and progression, which enhances our understanding of the low response rate of CRC to immunotherapy via immunosuppressive signaling pathways.
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Affiliation(s)
- Yuhui Wu
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaojing Liang
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Junjie Ni
- Department of Breast and Thyroid Surgery, Jinhua Municipal Central Hospital, Jinhua, China
| | - Rongjie Zhao
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Shengpeng Shao
- Department of Urinary Surgery, The First People's Hospital of Fuyang, Hangzhou, China
| | - Si Lu
- Institute of Translational Medicine, Zhejiang University, Hangzhou, China
| | - Weidong Han
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Liangliang Yu
- Department of Gastroenterology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China
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13
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Ma YS, Liu JB, Yang XL, Xin R, Shi Y, Zhang DD, Wang HM, Wang PY, Lin QL, Li W, Fu D. Basic approaches, challenges and opportunities for the discovery of small molecule anti-tumor drugs. Am J Cancer Res 2021; 11:2386-2400. [PMID: 34249406 PMCID: PMC8263657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 05/15/2021] [Indexed: 06/13/2023] Open
Abstract
Chemotherapy is one of the main treatments for cancer, especially for advanced cancer patients. In the past decade, significant progress has been made with the research into the molecular mechanisms of cancer cells and the precision medicine. The treatment on cancer patients has gradually changed from cytotoxic chemotherapy to precise treatment strategy. Research into anticancer drugs has also changed from killing effects on all cells to targeting drugs for target genes. Besides, researchers have developed the understanding of the abnormal physiological function, related genomics, epigenetics, and proteomics of cancer cells with cancer genome sequencing, epigenetic research, and proteomic research. These technologies and related research have accelerated the development of related cancer drugs. In this review, we summarize the research progress of anticancer drugs, the current challenges, and future opportunities.
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Affiliation(s)
- Yu-Shui Ma
- National Engineering Laboratory for Deep Process of Rice and Byproducts, College of Food Science and Engineering, Central South University of Forestry and TechnologyChangsha 410004, Hunan, China
- Cancer Institute, Nantong Tumor HospitalNantong 226631, China
- Central Laboratory for Medical Research, Shanghai Tenth People’s Hospital, Tongji University School of MedicineShanghai 200072, China
| | - Ji-Bin Liu
- Cancer Institute, Nantong Tumor HospitalNantong 226631, China
| | - Xiao-Li Yang
- Central Laboratory for Medical Research, Shanghai Tenth People’s Hospital, Tongji University School of MedicineShanghai 200072, China
| | - Rui Xin
- Central Laboratory for Medical Research, Shanghai Tenth People’s Hospital, Tongji University School of MedicineShanghai 200072, China
| | - Yi Shi
- National Engineering Laboratory for Deep Process of Rice and Byproducts, College of Food Science and Engineering, Central South University of Forestry and TechnologyChangsha 410004, Hunan, China
- Cancer Institute, Nantong Tumor HospitalNantong 226631, China
| | - Dan-Dan Zhang
- Central Laboratory for Medical Research, Shanghai Tenth People’s Hospital, Tongji University School of MedicineShanghai 200072, China
| | - Hui-Min Wang
- Central Laboratory for Medical Research, Shanghai Tenth People’s Hospital, Tongji University School of MedicineShanghai 200072, China
| | - Pei-Yao Wang
- Central Laboratory for Medical Research, Shanghai Tenth People’s Hospital, Tongji University School of MedicineShanghai 200072, China
| | - Qin-Lu Lin
- National Engineering Laboratory for Deep Process of Rice and Byproducts, College of Food Science and Engineering, Central South University of Forestry and TechnologyChangsha 410004, Hunan, China
| | - Wen Li
- National Engineering Laboratory for Deep Process of Rice and Byproducts, College of Food Science and Engineering, Central South University of Forestry and TechnologyChangsha 410004, Hunan, China
| | - Da Fu
- National Engineering Laboratory for Deep Process of Rice and Byproducts, College of Food Science and Engineering, Central South University of Forestry and TechnologyChangsha 410004, Hunan, China
- Central Laboratory for Medical Research, Shanghai Tenth People’s Hospital, Tongji University School of MedicineShanghai 200072, China
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Ye F, Huang W, Xue Y, Tang E, Wang M, Shi F, Wei D, Han Y, Chen P, Zhang X, Yu D. Serum Levels of ITGBL1 as an Early Diagnostic Biomarker for Hepatocellular Carcinoma with Hepatitis B Virus Infection. J Hepatocell Carcinoma 2021; 8:285-300. [PMID: 33948441 PMCID: PMC8088298 DOI: 10.2147/jhc.s306966] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/07/2021] [Indexed: 12/24/2022] Open
Abstract
Purpose Early diagnostic biomarkers of hepatocellular carcinoma (HCC) are needed to distinguish hepatitis B virus (HBV) associated HCC (HBV-HCC) patients from at-risk patients. We assessed the diagnostic values of serum Integrin beta-like 1 (ITGBL1) for early-stage HBV-HCC. Patients and Methods We recruited 716 participators including 299 in the training and 417 in the validation stage, (HBV-HCC, chronic hepatitis B (CHB), HBV‐related liver cirrhosis (HBV-LC), and healthy controls) between 2017 and 2020 from three centers. Serum ITGBL1 was measured by ELISA. Receiver operating characteristic (ROC) was used to calculate diagnostic accuracy. Results The serum levels of ITGBL1 in HBV-HCC patients were significantly lower than those in CHB and HBV-LC patients. This result was confirmed in the follow-up patients who progressed from HBV-LC to HCC. The optimum diagnostic cutoff value of serum ITGBL1 was 47.93ng/mL for detection of early-stage HBV-HCC. The serum ITGBL1 has higher diagnostic accuracy than AFP20 in differentiating the early-stage HBV-HCC from the at-risk patients (area under curve [AUC] 0.787 vs 0.638, p<0.05). For AFP-negative (<20ng/mL) HBV-HCC patients, serum ITGBL1 maintained diagnostic accuracy (training cohort: AUC 0.756, 95% confidence interval [CI] 0.683–0.819, sensitivity 68.18%, and specificity 68.85%; validation cohort: 0.744, 0.686–0.796, 81.13%, and 55.88%). Combination ITGBL1 with AFP20 significantly increased diagnostic accuracy in differentiating the HBV-HCC from at-risk patients (AUC 0.840; 0.868) than ITGBL1 (AUC 0.773, p<0.05; 0.732, p<0.0001) or AFP20 (AUC 0.705, p<0.0001; 0.773, p<0.0001) alone. Conclusion The serum level of ITGBL1 improved identification of AFP-negative HBV-HCC patients, and increased diagnostic accuracy with AFP20 together in the early detection of HBV-HCC.
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Affiliation(s)
- Fei Ye
- Department of Infectious Diseases, Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 200025, People's Republic of China
| | - Wei Huang
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong, 226000, People's Republic of China
| | - Yuan Xue
- Institute of Hepatology, The Third People's Hospital of Changzhou, Changzhou, 213000, People's Republic of China
| | - Erjiang Tang
- Center for Clinical Research and Translational Medicine, Yangpu Hospital, Tongji University School of Medicine, Shanghai, 200090, People's Republic of China.,Institute of Gastrointestinal Surgery and Translational Medicine, Tongji University School of Medicine, Shanghai, 200090, People's Republic of China
| | - Mingjie Wang
- Department of Gastroenterology & Hepatology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 201821, People's Republic of China
| | - Fengchun Shi
- Department of Infectious Diseases, Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 200025, People's Republic of China
| | - Dong Wei
- Department of Infectious Diseases, Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 200025, People's Republic of China
| | - Yue Han
- Department of Infectious Diseases, Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 200025, People's Republic of China
| | - Peizhan Chen
- Clinical Research Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201821, People's Republic of China
| | - Xinxin Zhang
- Department of Infectious Diseases, Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 200025, People's Republic of China
| | - Demin Yu
- Department of Infectious Diseases, Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 200025, People's Republic of China
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15
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Wu TM, Liu JB, Liu Y, Shi Y, Li W, Wang GR, Ma YS, Fu D. Power and Promise of Next-Generation Sequencing in Liquid Biopsies and Cancer Control. Cancer Control 2021; 27:1073274820934805. [PMID: 32806937 PMCID: PMC7791471 DOI: 10.1177/1073274820934805] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Traditional methods of cancer treatment are usually based on the morphological
and histological diagnosis of tumors, and they are not optimized according to
the specific situation. Precision medicine adjusts the existing treatment
regimen based on the patient’s genomic information to make it most suitable for
patients. Detection of genetic mutations in tumors is the basis of precise
cancer medicine. Through the analysis of genetic mutations in patients with
cancer, we can tailor the treatment plan for each patient with cancer to
maximize the curative effect, minimize damage to healthy tissues, and optimize
resources. In recent years, next-generation sequencing technology has developed
rapidly and has become the core technology of precise targeted therapy and
immunotherapy for cancer. From early cancer screening to treatment guidance for
patients with advanced cancer, liquid biopsy is increasingly used in cancer
management. This is as a result of the development of better noninvasive,
repeatable, sensitive, and accurate tools used in early screening, diagnosis,
evaluation, and monitoring of patients. Cell-free DNA, which is a new
noninvasive molecular pathological detection method, often carries
tumor-specific gene changes. It plays an important role in optimizing treatment
and evaluating the efficacy of different treatment options in clinical trials,
and it has broad clinical applications.
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Affiliation(s)
- Ting-Miao Wu
- Department of Radiology, 12485The Fourth Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Ji-Bin Liu
- Cancer Institute, 377323Nantong Tumor Hospital, Nantong, China
| | - Yu Liu
- National Engineering Laboratory for Rice and By-product Deep Processing, College of Food Science and Engineering, 12571Central South University of Forestry and Technology, Chaha, China
| | - Yi Shi
- National Engineering Laboratory for Rice and By-product Deep Processing, College of Food Science and Engineering, 12571Central South University of Forestry and Technology, Chaha, China
| | - Wen Li
- National Engineering Laboratory for Rice and By-product Deep Processing, College of Food Science and Engineering, 12571Central South University of Forestry and Technology, Chaha, China
| | - Gao-Ren Wang
- Cancer Institute, 377323Nantong Tumor Hospital, Nantong, China
| | - Yu-Shui Ma
- Cancer Institute, 377323Nantong Tumor Hospital, Nantong, China.,Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, 12476Tongji University School of Medicine, Shanghai, China
| | - Da Fu
- Department of Radiology, 12485The Fourth Affiliated Hospital of Anhui Medical University, Hefei, China.,Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, 12476Tongji University School of Medicine, Shanghai, China
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16
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Zhang S, Chen H, Yue D, Blackwell TS, Lv C, Song X. Long non-coding RNAs: Promising new targets in pulmonary fibrosis. J Gene Med 2021; 23:e3318. [PMID: 33533071 PMCID: PMC7988597 DOI: 10.1002/jgm.3318] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 01/09/2021] [Accepted: 01/15/2021] [Indexed: 12/11/2022] Open
Abstract
Pulmonary fibrosis is characterized by progressive and irreversible scarring in the lungs with poor prognosis and treatment. It is caused by various factors, including environmental and occupational exposures, and some rheumatic immune diseases. Even the rapid global spread of the COVID‐19 pandemic can also cause pulmonary fibrosis with a high probability. Functions attributed to long non‐coding RNAs (lncRNAs) make them highly attractive diagnostic and therapeutic targets in fibroproliferative diseases. Therefore, an understanding of the specific mechanisms by which lncRNAs regulate pulmonary fibrotic pathogenesis is urgently needed to identify new possibilities for therapy. In this review, we focus on the molecular mechanisms and implications of lncRNAs targeted protein‐coding and non‐coding genes during pulmonary fibrogenesis, and systematically analyze the communication of lncRNAs with various types of RNAs, including microRNA, circular RNA and mRNA. Finally, we propose the potential approach of lncRNA‐based diagnosis and therapy for pulmonary fibrosis. We hope that understanding these interactions between protein‐coding and non‐coding genes will contribute to the development of lncRNA‐based clinical applications for pulmonary fibrosis.
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Affiliation(s)
- Songzi Zhang
- Department of Cellular and Genetic Medicine, School of Pharmaceutical Sciences, Binzhou Medical University, Yantai, China.,Department of Respiratory Medicine, Affiliated Hospital to Binzhou Medical University, Binzhou Medical University, Binzhou, China
| | - Hongbin Chen
- Department of Cellular and Genetic Medicine, School of Pharmaceutical Sciences, Binzhou Medical University, Yantai, China
| | - Dayong Yue
- Department of Cellular and Genetic Medicine, School of Pharmaceutical Sciences, Binzhou Medical University, Yantai, China
| | | | - Changjun Lv
- Department of Cellular and Genetic Medicine, School of Pharmaceutical Sciences, Binzhou Medical University, Yantai, China.,Department of Respiratory Medicine, Affiliated Hospital to Binzhou Medical University, Binzhou Medical University, Binzhou, China
| | - Xiaodong Song
- Department of Cellular and Genetic Medicine, School of Pharmaceutical Sciences, Binzhou Medical University, Yantai, China.,Department of Respiratory Medicine, Affiliated Hospital to Binzhou Medical University, Binzhou Medical University, Binzhou, China
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17
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Ahluwalia P, Kolhe R, Gahlay GK. The clinical relevance of gene expression based prognostic signatures in colorectal cancer. Biochim Biophys Acta Rev Cancer 2021; 1875:188513. [PMID: 33493614 DOI: 10.1016/j.bbcan.2021.188513] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 01/14/2021] [Accepted: 01/14/2021] [Indexed: 12/24/2022]
Abstract
Colorectal cancer (CRC) is one of the most prevalent cancers, with more than one million new cases every year. In the last few decades, several advancements in therapeutic and preventative levels have reduced the mortality rate, but new biomarkers are required for improved prognosis. The alterations at the genetic and epigenetic level have been recognized as major players in tumorigenesis. The products of gene expression in the form of mRNA, microRNA, and long-noncoding RNA, have started to emerge as important regulatory molecules, playing an important role in cancer. Gene-expression based prognostic risk scores, which quantify and compare their expression, have emerged as promising biomarkers with enormous clinical value. These composite multi-gene models in which more than one gene is used to predict prognosis have been shown to be significantly effective in identifying patients with multiple clinico-pathological risks like overall mortality, response to chemotherapy, risk of metastasis, etc. The advent of microarray and advanced sequencing technologies have led to the generation of large datasets like TCGA (The Cancer Genome Atlas) and GEO (Gene Expression Omnibus), which have fueled the search for new biomarkers. Continuous evaluation of these candidate biomarkers in clinical settings is promising to improve the management of CRC. These composite gene signatures provide potential in identifying high-risk patients, which might help clinicians to better manage these patients and design appropriate personalized therapeutic interventions. In this review, we emphasize on composite prognostic scores from diverse resources with clinical utility in CRC.
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Affiliation(s)
- Pankaj Ahluwalia
- Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar, India; Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Gagandeep K Gahlay
- Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar, India.
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Cui Y, Yang J, Bai Y, Li Q, Yao Y, Liu C, Wu F, Zhang J, Zhang Y. ENC1 Facilitates Colorectal Carcinoma Tumorigenesis and Metastasis via JAK2/STAT5/AKT Axis-Mediated Epithelial Mesenchymal Transition and Stemness. Front Cell Dev Biol 2021; 9:616887. [PMID: 33816464 PMCID: PMC8010667 DOI: 10.3389/fcell.2021.616887] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 02/05/2021] [Indexed: 01/08/2023] Open
Abstract
Ectodermal neural cortex 1 (ENC1) is an actin-binding protein and has been known to be upregulated in several cancers, but the molecular mechanisms through which it contributes to the pathology of CRC have largely been elusive. We utilized data mining and validated the aberrant expression of ENC1, following which phenotypic traits of malignancy were assessed in vitro. Ruxolitinib was used as a surrogate to compare the effects of ENC1 expression and silencing on the JAK-STAT-AKT pathway. In vivo models were employed to confirm the in vitro observations. Computation analysis, strengthened by in situ and in vitro data, confirmed the overexpression of ENC1 in CRC and predicted a poor prognosis, while enhanced cell proliferation, invasion, migration, EMT, and stemness were associated with ENC1 overexpression. Silencing of ENC1 downregulated the phenotypes. Additionally, silencing of ENC1 significantly reduced the activation of JAK2 and consequent activation of STAT5 and AKT comparable to ruxolitinib inhibition of JAK2. Silencing of ENC1 resulted in lesser tumor volumes and fewer numbers of tumors, in vivo. These data suggest that ENC1 induces CRC through the JAK2-STAT5-AKT axis. ENC1 is a suitable diagnostic marker for CRC detection, and ENC1 targeting therapies may suppress CRC progression.
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Affiliation(s)
- Ying Cui
- Department of Radiation Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Jiani Yang
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yibing Bai
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - QingWei Li
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yuanfei Yao
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Chao Liu
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Feng Wu
- Department of Gastroenterology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jingchun Zhang
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yanqiao Zhang
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
- *Correspondence: Yanqiao Zhang,
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Cortez AJ, Kujawa KA, Wilk AM, Sojka DR, Syrkis JP, Olbryt M, Lisowska KM. Evaluation of the Role of ITGBL1 in Ovarian Cancer. Cancers (Basel) 2020; 12:E2676. [PMID: 32961775 PMCID: PMC7563769 DOI: 10.3390/cancers12092676] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 12/27/2022] Open
Abstract
In our previous microarray study we identified two subgroups of high-grade serous ovarian cancers with distinct gene expression and survival. Among differentially expressed genes was an Integrin beta-like 1 (ITGBL1), coding for a poorly characterized protein comprised of ten EGF-like repeats. Here, we have analyzed the influence of ITGBL1 on the phenotype of ovarian cancer (OC) cells. We analyzed expression of four putative ITGBL1 mRNA isoforms in five OC cell lines. OAW42 and SKOV3, having the lowest level of any ITGBL1 mRNA, were chosen to produce ITGBL1-overexpressing variants. In these cells, abundant ITGBL1 mRNA expression could be detected by RT-PCR. Immunodetection was successful only in the culture media, suggesting that ITGBL1 is efficiently secreted. We found that ITGBL1 overexpression affected cellular adhesion, migration and invasiveness, while it had no effect on proliferation rate and the cell cycle. ITGBL1-overexpressing cells were significantly more resistant to cisplatin and paclitaxel, major drugs used in OC treatment. Global gene expression analysis revealed that signaling pathways affected by ITGBL1 overexpression were mostly those related to extracellular matrix organization and function, integrin signaling, focal adhesion, cellular communication and motility; these results were consistent with the findings of our functional studies. Overall, our results indicate that higher expression of ITGBL1 in OC is associated with features that may worsen clinical course of the disease.
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Affiliation(s)
- Alexander Jorge Cortez
- Department of Biostatistics and Bioinformatics, Maria Skłodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-102 Gliwice, Poland; (A.J.C.); (A.M.W.)
- Center for Translational Research and Molecular Biology of Cancer, Maria Skłodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-102 Gliwice, Poland; (K.A.K.); (D.R.S.); (J.P.S.); (M.O.)
| | - Katarzyna Aleksandra Kujawa
- Center for Translational Research and Molecular Biology of Cancer, Maria Skłodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-102 Gliwice, Poland; (K.A.K.); (D.R.S.); (J.P.S.); (M.O.)
| | - Agata Małgorzata Wilk
- Department of Biostatistics and Bioinformatics, Maria Skłodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-102 Gliwice, Poland; (A.J.C.); (A.M.W.)
| | - Damian Robert Sojka
- Center for Translational Research and Molecular Biology of Cancer, Maria Skłodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-102 Gliwice, Poland; (K.A.K.); (D.R.S.); (J.P.S.); (M.O.)
| | - Joanna Patrycja Syrkis
- Center for Translational Research and Molecular Biology of Cancer, Maria Skłodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-102 Gliwice, Poland; (K.A.K.); (D.R.S.); (J.P.S.); (M.O.)
| | - Magdalena Olbryt
- Center for Translational Research and Molecular Biology of Cancer, Maria Skłodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-102 Gliwice, Poland; (K.A.K.); (D.R.S.); (J.P.S.); (M.O.)
| | - Katarzyna Marta Lisowska
- Center for Translational Research and Molecular Biology of Cancer, Maria Skłodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-102 Gliwice, Poland; (K.A.K.); (D.R.S.); (J.P.S.); (M.O.)
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Ma YS, Li W, Liu Y, Shi Y, Lin QL, Fu D. Targeting Colorectal Cancer Stem Cells as an Effective Treatment for Colorectal Cancer. Technol Cancer Res Treat 2020; 19:1533033819892261. [PMID: 32748700 PMCID: PMC7785997 DOI: 10.1177/1533033819892261] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
As one of the common cancers that threaten human life, the recurrence and metastasis of colorectal cancer seriously affect the prognosis of patients. Although new drugs and comprehensive treatments have been adopted, the current treatment effect on this tumor, especially in advanced colorectal cancer, is still not satisfactory. More and more evidence shows that tumors are likely to be a stem cell disease. In recent years, the rise of cancer stem cell theory has provided a new way for cancer treatment. Studies have found that a small number of special cells in colorectal cancer tissues that induce tumorigenesis, proliferation, and promote tumor migration and metastasis, namely, colorectal cancer stem cells. Colorectal cancer stem cells are defined with a group of cell-surface markers, such as CD44, CD133, CD24, epithelial cell adhesion factor molecule, LGR5, and acetaldehyde dehydrogenase. They are highly tumorigenic, aggressive, and chemoresistant and thus are critical in the metastasis and recurrence of colorectal cancer. Therefore, targeting colorectal cancer stem cells may become an important research direction for the future cure of colorectal cancer.
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Affiliation(s)
- Yu-Shui Ma
- National Engineering Laboratory for Rice and By-Product Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, China.,Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wen Li
- National Engineering Laboratory for Rice and By-Product Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, China
| | - Yu Liu
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yi Shi
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qin-Lu Lin
- National Engineering Laboratory for Rice and By-Product Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, China
| | - Da Fu
- National Engineering Laboratory for Rice and By-Product Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, China.,Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
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21
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Huang W, Yu D, Wang M, Han Y, Lin J, Wei D, Cai J, Li B, Chen P, Zhang X. ITGBL1 promotes cell migration and invasion through stimulating the TGF-β signalling pathway in hepatocellular carcinoma. Cell Prolif 2020; 53:e12836. [PMID: 32537856 PMCID: PMC7377936 DOI: 10.1111/cpr.12836] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 04/24/2020] [Accepted: 05/07/2020] [Indexed: 12/12/2022] Open
Abstract
Objectives Integrin beta‐like 1 (ITGBL1) is involved in the migration and invasion of several cancers; however, its roles in the development and progression of hepatocellular carcinoma (HCC) remain largely unknown. Materials and methods Immunohistochemistry staining was used to investigate the expression pattern of ITGBL1 and its prognostic values in HCC patients. The transwell, wound‐healing assays, xenograft and orthotopic mouse models were employed to determine the effects of ITGBL1 on HCC cell migration and invasion in vitro and in vivo. The biological mechanisms involved in cell migration and invasion caused by ITGBL1 were determined with Western blotting and RT‐PCR methods. Results ITGBL1 expression was significantly increased in HCC tissues compared to adjacent normal tissues. Patients with higher ITGBL1 expression were associated with more reduced overall survival. ITGBL1 overexpression promoted migration and invasion in SMMC‐7721 and HepG2 cells in vitro and in vivo, whereas knockdown or knockout ITGBL1 in CSQT‐2 cells significantly reduced cell migration and invasion abilities. In SMMC‐7721 cells, ITGBL1 overexpression stimulated TGF‐β/Smads signalling pathway, along with the KRT17 and genes involved in the epithelial‐mesenchymal transition (EMT). In contrast, ITGBL1 knockout inhibited the TGF‐β/Smads signalling pathway in CSQT‐2 cells. Conclusions These findings suggested that ITGBL1 promoted migration and invasion in HCC cells by stimulating the TGF‐β/Smads signalling pathway. ITGBL1 could be a promising prognostic biomarker, as well as a potential therapeutic target in HCC.
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Affiliation(s)
- Wei Huang
- Research Laboratory of Clinical Virology, Ruijin Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Demin Yu
- Research Laboratory of Clinical Virology, Ruijin Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Mingjie Wang
- Research Laboratory of Clinical Virology, Ruijin Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Yue Han
- Research Laboratory of Clinical Virology, Ruijin Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Junyu Lin
- Research Laboratory of Clinical Virology, Ruijin Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Dong Wei
- Research Laboratory of Clinical Virology, Ruijin Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Jialin Cai
- Clinical Research Center, Ruijin Hospital North, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Bin Li
- Biliary Tract Surgery Department I, Eastern Hepatobiliary Surgery Hospital, Secondary Military Medical University, Shanghai, China
| | - Peizhan Chen
- Clinical Research Center, Ruijin Hospital North, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xinxin Zhang
- Research Laboratory of Clinical Virology, Ruijin Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China.,Clinical Research Center, Ruijin Hospital North, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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22
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Al-Mustanjid M, Mahmud SMH, Royel MRI, Rahman MH, Islam T, Rahman MR, Moni MA. Detection of molecular signatures and pathways shared in inflammatory bowel disease and colorectal cancer: A bioinformatics and systems biology approach. Genomics 2020; 112:3416-3426. [PMID: 32535071 DOI: 10.1016/j.ygeno.2020.06.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 05/03/2020] [Accepted: 06/02/2020] [Indexed: 02/07/2023]
Abstract
Emerging evidence indicates IBD is a risk factor for the increasing incidence of colorectal cancer (CRC) development. We used a system biology approach to identify common molecular signatures and pathways that interact between IBD and CRC and the indispensable pathological mechanisms. First, we identified 177 common differentially expressed genes (DEGs) between IBD and CRC. Gene set enrichment, protein-protein, DEGs-transcription factors, DEGs-microRNAs, protein-drug interaction, gene-disease association, Gene Ontology, pathway enrichment analyses were conducted to these common genes. The inclusion of common DEGs with bimolecular networks disclosed hub proteins (LYN, PLCB1, NPSR1, WNT5A, CDC25B, CD44, RIPK2, ASAP1), transcription factors (SCD, SLC7A5, IKZF3, SLC16A1, SLC7A11) and miRNAs (mir-335-5p, mir-26b-5p, mir-124-3p, mir-16-5p, mir-192-5p, mir-548c-3p, mir-29b-3p, mir-155-5p, mir-21-5p, mir-15a-5p). Analysis of the interaction between protein and drug discovered ASAP1 interacts with cysteine sulfonic acid and double oxidized cysteine drug compounds. Gene-disease association analysis retrieved ASAP1 also associated with pulmonary and bladder neoplasm diseases.
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Affiliation(s)
- Md Al-Mustanjid
- Department of Software Engineering, Faculty of Science and Information Technology, Daffodil International University, Dhaka 1207, Bangladesh
| | - S M Hasan Mahmud
- School of Computer Science and Engineering, University of Electronic Science and Technology of China, Chengdu 611731, China.
| | - Md Rejaul Islam Royel
- Department of Software Engineering, Faculty of Science and Information Technology, Daffodil International University, Dhaka 1207, Bangladesh
| | - Md Habibur Rahman
- Department of Information and Communication Technology, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Tania Islam
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia 7003, Bangladesh
| | - Md Rezanur Rahman
- Department of Biochemistry and Biotechnology, School of Biomedical Science, Khwaja Yunus Ali, University, Enayetpur, Sirajganj 6751, Bangladesh
| | - Mohammad Ali Moni
- WHO Collaborating Centre on eHealth, UNSW Digital Health, School of Public Health and Community Medicine, Faculty of Medicine, UNSW Sydney, Australia.
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Qi L, Song F, Ding Y. Regulatory Mechanism of ITGBL1 in the Metastasis of Colorectal Cancer. Front Oncol 2020; 10:259. [PMID: 32211321 PMCID: PMC7076154 DOI: 10.3389/fonc.2020.00259] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 02/14/2020] [Indexed: 12/14/2022] Open
Abstract
Integrin, beta-like 1 (ITGBL1) protein is located in the extracellular matrix (ECM) and involved in the development and metastasis of many tumors. However, the regulatory mechanism of ITGBL1 in colorectal cancer (CRC) remains unclear. This study was to analyze the expression profile of CRC and to identify the expression change of ITGBL1 gene at different stages of CRC. Survival analysis showed that ITGBL1 was related to the metastasis of CRC, and CRC patients with a high expression of ITGBL1 had earlier metastasis. Gene Set Enrichment Analysis (GSEA) indicated the relationship between ITGBL1 expression and molecular events of CRC. The results indicated that a high expression of ITGBL1 was linked to Wnt signaling pathway, cell polarity, and tissue development, while a low expression of ITGBL1 was related to cellular respiration, electron transfer chain, and oxidative phosphorylation. With the expression profiles from interstitial and parenchyma CRC tissues, a comparison was made to determine the difference between high/low expression of ITGBL1 and Wnt signaling pathway, respectively, and further confirmed the close relation between ITGBL1 and Wnt signaling pathway. To determine the relation, an interaction network of ITGBL1 and Wnt signaling proteins was constructed. It was found that β-catenin interacted with multiple extracellular Wnt signals and could bind to ITGBL1. As a result, the regulatory mechanism of ITGBL1 in CRC is related to extracellular Wnt signals and may affect extracellular Wnt signals via β-catenin.
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Affiliation(s)
- Lu Qi
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Molecular Oncologic Pathology, Guangzhou, China
| | - Fuyao Song
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Molecular Oncologic Pathology, Guangzhou, China
| | - Yanqing Ding
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Molecular Oncologic Pathology, Guangzhou, China
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Long noncoding RNA RHPN1-AS1 promotes colorectal cancer progression via targeting miR-7-5p/OGT axis. Cancer Cell Int 2020; 20:54. [PMID: 32099527 PMCID: PMC7029493 DOI: 10.1186/s12935-020-1110-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 01/16/2020] [Indexed: 02/08/2023] Open
Abstract
Background Rhophilin Rho GTPase binding protein 1 antisense RNA 1 (RHPN1-AS1) is a newly discovered oncogene in several diseases, such as breast cancer, non-small cell lung cancer and uveal melanoma. Nevertheless, its molecular role in colorectal cancer (CRC) remains unknown. This paper explored the role of RHPN1-AS1 in CRC progression. Methods qRT-PCR was used to detect relevant RNAs expression. CCK-8, EdU, flow cytometry, Transwell and western blot assays were performed to investigate the function of RHPN1-AS1 in CRC cells. Xenograft model was constructed to evaluate the effects of RHPN1-AS1 on tumor growth in vivo. Mechanical experiments were performed to investigate the relationship between relative genes. Results RHPN1-AS1 was significantly overexpressed in CRC cell lines. Knockdown of RHPN1-AS1 could inhibit cell proliferation, while stimulating cell apoptosis in vitro. Cell migration and invasion abilities were greatly suppressed after silencing RHPN1-AS1. Besides, signal transducer and activator of transcription 3 (STAT3) served as transcription factor of RHPN1-AS1. Moreover, miR-7-5p was identified as a target of RHPN1-AS1 and was negatively regulated by RHPN1-AS1 in CRC. MiR-7-5p inhibition rescued the oncogenic function of RHPN1-AS1. Additionally, O-GlcNAcylation transferase (OGT) was the downstream target of miR-7-5p. OGT overexpression could abrogate the anti-tumor effects of RHPN1-AS1 knockdown on CRC. Conclusion RHPN1-AS1 regulates CRC by mediating OGT through sponging miR-7-5p, suggesting that RHPN1-AS1 might be a potential therapeutic target for CRC.
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Wang YR, Meng LB, Su F, Qiu Y, Shi JH, Xu X, Luo QF. Insights regarding novel biomarkers and the pathogenesis of primary colorectal carcinoma based on bioinformatic analysis. Comput Biol Chem 2020; 85:107229. [PMID: 32058945 DOI: 10.1016/j.compbiolchem.2020.107229] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/29/2020] [Accepted: 02/02/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Biomarkers are important in the study of tumor processes for early detection and precise treatment. The biomarkers that have been previously detected are not useful for clinical application for primary colorectal carcinoma (PCRC). The aim of this study was to explore clinically valuable biomarkers of PCRC based on integrated bioinformatic analysis. MATERIAL AND METHODS Gene expression data were acquired from the GSE41258 dataset, and the differentially expressed genes were determined between PCRC and normal colorectal samples. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were implemented via Gene Set Enrichment Analysis. A protein-protein interaction (PPI) network was constructed. The significant modules and hub genes were screened and identified in the PPI network. RESULTS A total of 202 DEGs were identified, including 58 upregulated and 144 downregulated genes in PCRC samples compared to those in normal colorectal samples. Enrichment analysis demonstrated that the gene sets enriched in PCRC were significantly related to bicarbonate transport, regulation of sodium ion transport, potassium ion homeostasis, regulation of telomere maintenance, and other processes. A total of 10 hub genes was identified by cytoHubba: PYY, CXCL3, CXCL11, CXCL8, CXCL12, CCL20, MMP3, P2RY14, NPY1R, and CXCL1. CONCLUSION The hub genes, such as NPY1R, P2RY14, and CXCL12, and the electrolyte disequilibrium resulting from the differential expression of genes, especially bicarbonate imbalance, may provide novel insights and evidence for the future diagnosis and targeted therapy of PCRC.
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Affiliation(s)
- Yi-Ran Wang
- Department of Gastroenterology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China.
| | - Ling-Bing Meng
- Department of Neurology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China.
| | - Fei Su
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China.
| | - Yong Qiu
- Department of Anesthesia, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China.
| | - Ji-Hua Shi
- Department of Gastroenterology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China.
| | - Xue Xu
- Department of Gastroenterology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China.
| | - Qing-Feng Luo
- Department of Gastroenterology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China.
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Rodrigues D, Souza T, Jennen DG, Lemmens L, Kleinjans JC, de Kok TM. Drug-induced gene expression profile changes in relation to intestinal toxicity: State-of-the-art and new approaches. Cancer Treat Rev 2019; 77:57-66. [DOI: 10.1016/j.ctrv.2019.06.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 06/26/2019] [Indexed: 12/22/2022]
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Pinu FR, Goldansaz SA, Jaine J. Translational Metabolomics: Current Challenges and Future Opportunities. Metabolites 2019; 9:E108. [PMID: 31174372 PMCID: PMC6631405 DOI: 10.3390/metabo9060108] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 06/04/2019] [Accepted: 06/04/2019] [Indexed: 02/06/2023] Open
Abstract
Metabolomics is one of the latest omics technologies that has been applied successfully in many areas of life sciences. Despite being relatively new, a plethora of publications over the years have exploited the opportunities provided through this data and question driven approach. Most importantly, metabolomics studies have produced great breakthroughs in biomarker discovery, identification of novel metabolites and more detailed characterisation of biological pathways in many organisms. However, translation of the research outcomes into clinical tests and user-friendly interfaces has been hindered due to many factors, some of which have been outlined hereafter. This position paper is the summary of discussion on translational metabolomics undertaken during a peer session of the Australian and New Zealand Metabolomics Conference (ANZMET 2018) held in Auckland, New Zealand. Here, we discuss some of the key areas in translational metabolomics including existing challenges and suggested solutions, as well as how to expand the clinical and industrial application of metabolomics. In addition, we share our perspective on how full translational capability of metabolomics research can be explored.
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Affiliation(s)
- Farhana R Pinu
- The New Zealand Institute for Plant and Food Research, Private Bag 92169, Auckland 1142, New Zealand.
| | - Seyed Ali Goldansaz
- Department of Agriculture, Food and Nutritional Sciences, University of Alberta, Edmonton, AB T6G 2P5, Canada.
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
| | - Jacob Jaine
- Analytica Laboratories Ltd., Ruakura Research Centre, Hamilton 3216, New Zealand.
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