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Ye Y, Xu G. Construction of a new prognostic model for colorectal cancer based on bulk RNA-seq combined with The Cancer Genome Atlas data. Transl Cancer Res 2024; 13:2704-2720. [PMID: 38988915 PMCID: PMC11231782 DOI: 10.21037/tcr-23-2281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 05/08/2024] [Indexed: 07/12/2024]
Abstract
Background Colorectal cancer (CRC) is one of the leading causes of cancer-related deaths, and improving the prognosis of CRC patients is an urgent concern. The aim of this study was to explore new immunotherapy targets to improve survival in CRC patients. Methods We analyzed CRC-related single-cell data GSE201348 from the Gene Expression Omnibus (GEO) database, and identified differentially expressed genes (DEGs). Subsequently, we performed differential analysis on the rectum adenocarcinoma (READ) and colon adenocarcinoma (COAD) transcriptome sequencing data [The Cancer Genome Atlas (TCGA)-CRC queue] and clinical data downloaded from TCGA database. Subgroup analysis was performed using CIBERSORTx and cluster analysis. Finally, biomarkers were identified by one-way cox regression as well as least absolute shrinkage and selection operator (LASSO) analysis. Results In this study, we analyzed CRC-related single-cell data GSE201348, and identified 5,210 DEGs. Subsequently, we performed differential analysis on the TCGA-CRC queue database, and obtained 4,408 DEGs. Then, we categorized the cancer samples in the sequencing data into three groups (k1, k2, and k3), with significant differences observed between the k1 and k2 groups via survival analysis. Further differential analysis on the samples in the k1 and k2 groups identified 1,899 DEGs. A total of 77 DEGs were selected among those DEGs obtained from three differential analyses. Through subsequent Cox univariate analysis and LASSO analysis, seven biomarkers (RETNLB, CLCA4, UGT2A3, SULT1B1, CCL24, BMP5, and ATOH1) were identified and selected to establish a risk score (RS). Conclusions To sum up, this study demonstrates the potential of the seven-gene prognostic risk model as instrumental variables for predicting the prognosis of CRC.
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Affiliation(s)
- Yu Ye
- Department of General Surgery, Zhejiang Hospital of Integrated Traditional Chinese and Western Medicine, Hangzhou, China
| | - Gang Xu
- Department of General Surgery, Zhejiang Hospital, Hangzhou, China
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2
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Azizan S, Cheng KJ, Mejia Mohamed EH, Ibrahim K, Faruqu FN, Vellasamy KM, Khong TL, Syafruddin SE, Ibrahim ZA. Insights into the molecular mechanisms and signalling pathways of epithelial to mesenchymal transition (EMT) in colorectal cancer: A systematic review and bioinformatic analysis of gene expression. Gene 2024; 896:148057. [PMID: 38043836 DOI: 10.1016/j.gene.2023.148057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 11/19/2023] [Accepted: 11/29/2023] [Indexed: 12/05/2023]
Abstract
Colorectal cancer (CRC) is ranked as the second leading cause of mortality worldwide, mainly due to metastasis. Epithelial to mesenchymal transition (EMT) is a complex cellular process that drives CRC metastasis, regulated by changes in EMT-associated gene expression. However, while numerous genes have been identified as EMT regulators through various in vivo and in vitro studies, little is known about the genes that are differentially expressed in CRC tumour tissue and their signalling pathway in regulating EMT. Using an integration of systematic search and bioinformatic analysis, gene expression profiles of CRC tumour tissues were compared to non-tumour adjacent tissues to identify differentially expressed genes (DEGs), followed by performing systematic review on common identified DEGs. Fifty-eight common DEGs were identified from the analysis of 82 tumour tissue samples obtained from four gene expression datasets (NCBI GEO). These DEGS were then systematically searched for their roles in modulating EMT in CRC based on previously published studies. Following this, 10 common DEGs (CXCL1, CXCL8, MMP1, MMP3, MMP7, TACSTD2, VIP, HPGD, ABCG2, CLCA4) were included in this study and subsequently subjected to further bioinformatic analysis. Their roles and functions in modulating EMT in CRC were discussed in this review. This study enhances our understanding of the molecular mechanisms underlying EMT and uncovers potential candidate genes and pathways that could be targeted in CRC.
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Affiliation(s)
- Suha Azizan
- Department of Pharmacology, Faculty of Medicine, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kim Jun Cheng
- Department of Pharmacology, Faculty of Medicine, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | | | - Kamariah Ibrahim
- Department of Biomedical Science, Faculty of Medicine, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - Farid Nazer Faruqu
- Department of Pharmacology, Faculty of Medicine, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kumutha Malar Vellasamy
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - Tak Loon Khong
- Department of Surgery, Faculty of Medicine, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - Saiful Effendi Syafruddin
- UKM Medical Molecular Biology Institute (UMBI), UKM Medical Centre, 56000 Cheras, Kuala Lumpur, Malaysia
| | - Zaridatul Aini Ibrahim
- Department of Pharmacology, Faculty of Medicine, Universiti Malaya, 50603 Kuala Lumpur, Malaysia.
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3
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Xu Z, Wang J, Wang G. Weighted gene co-expression network analysis for hub genes in colorectal cancer. Pharmacol Rep 2024; 76:140-153. [PMID: 38150140 DOI: 10.1007/s43440-023-00561-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 12/28/2023]
Abstract
BACKGROUND This study is designed to explore hub genes participating in colorectal cancer (CRC) development through weighted gene co-expression network analysis (WGCNA). METHODS Expression profiles of CRC and normal samples were retrieved from the Gene Expression Omnibus (GEO) and the Cancer Genome Atlas (TCGA), and were subjected to WGCNA to filter differentially expressed genes with significant association with CRC. Functional enrichment analysis and protein-protein interaction (PPI) analysis were carried out to filter the candidate genes, further and survival analysis was performed for the candidate genes to obtain potential regulatory hub genes in CRC. Expression analysis was conducted for the candidate genes and a multifactor model was established. RESULTS After differential analysis and WGCNA, 289 candidate genes were filtered from the GEO and TCGA. Further functional enrichment analysis demonstrated possible regulatory pathways and functions. PPI analysis filtered 15 hub genes and survival analysis indicated a significant correlation of CLCA1, CLCA4, and CPT1A with prognosis of patients with CRC. The multifactor Cox risk model established based on the three genes revealed that if the three genes were a gene set, they had well predictive capacity for the prognosis of patients with CRC. CONCLUSIONS CLCA1, CLCA4, and CPT1A express at low levels in CRC and function as core anti-tumor genes. As a gene set, they can predict prognosis well.
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Affiliation(s)
- Zheng Xu
- Department of Oncology Surgery, Beidahuang Industry Group General Hospital, Harbin, 150088, Heilongjiang, People's Republic of China
| | - Jianing Wang
- Department of Gastrointestinal Surgery, Beidahuang Industry Group General Hospital, Harbin, 150088, Heilongjiang, People's Republic of China
| | - Guosheng Wang
- Department of Pancreaticobiliary Surgery, The First Affiliated Hospital of Harbin Medical University, No. 23, Post Street, Nangang District, Harbin, 150007, Heilongjiang, People's Republic of China.
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Yoshie S, Murono S, Hazama A. Approach for Elucidating the Molecular Mechanism of Epithelial to Mesenchymal Transition in Fibrosis of Asthmatic Airway Remodeling Focusing on Cl - Channels. Int J Mol Sci 2023; 25:289. [PMID: 38203460 PMCID: PMC10779031 DOI: 10.3390/ijms25010289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/15/2023] [Accepted: 12/16/2023] [Indexed: 01/12/2024] Open
Abstract
Airway remodeling caused by asthma is characterized by structural changes of subepithelial fibrosis, goblet cell metaplasia, submucosal gland hyperplasia, smooth muscle cell hyperplasia, and angiogenesis, leading to symptoms such as dyspnea, which cause marked quality of life deterioration. In particular, fibrosis exacerbated by asthma progression is reportedly mediated by epithelial-mesenchymal transition (EMT). It is well known that the molecular mechanism of EMT in fibrosis of asthmatic airway remodeling is closely associated with several signaling pathways, including the TGF-β1/Smad, TGF-β1/non-Smad, and Wnt/β-catenin signaling pathways. However, the molecular mechanism of EMT in fibrosis of asthmatic airway remodeling has not yet been fully clarified. Given that Cl- transport through Cl- channels causes passive water flow and consequent changes in cell volume, these channels may be considered to play a key role in EMT, which is characterized by significant morphological changes. In the present article, we highlight how EMT, which causes fibrosis and carcinogenesis in various tissues, is strongly associated with activation or inactivation of Cl- channels and discuss whether Cl- channels can lead to elucidation of the molecular mechanism of EMT in fibrosis of asthmatic airway remodeling.
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Affiliation(s)
- Susumu Yoshie
- Department of Cellular and Integrative Physiology, Graduate School of Medicine, Fukushima Medical University, Fukushima 960-1295, Japan
| | - Shigeyuki Murono
- Department of Otolaryngology Head and Neck Surgery, Graduate School of Medicine, Fukushima Medical University, Fukushima 960-1295, Japan
| | - Akihiro Hazama
- Department of Cellular and Integrative Physiology, Graduate School of Medicine, Fukushima Medical University, Fukushima 960-1295, Japan
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5
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Hosseini ST, Nemati F. Identification of GUCA2A and COL3A1 as prognostic biomarkers in colorectal cancer by integrating analysis of RNA-Seq data and qRT-PCR validation. Sci Rep 2023; 13:17086. [PMID: 37816854 PMCID: PMC10564945 DOI: 10.1038/s41598-023-44459-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 10/09/2023] [Indexed: 10/12/2023] Open
Abstract
By 2030, it is anticipated that there will be 2.2 million new instances of colorectal cancer worldwide, along with 1.1 million yearly deaths. Therefore, it is critical to develop novel biomarkers that could help in CRC early detection. We performed an integrated analysis of four RNA-Seq data sets and TCGA datasets in this study to find novel biomarkers for diagnostic, prediction, and as potential therapeutic for this malignancy, as well as to determine the molecular mechanisms of CRC carcinogenesis. Four RNA-Seq datasets of colorectal cancer were downloaded from the Sequence Read Archive (SRA) database. The metaSeq package was used to integrate differentially expressed genes (DEGs). The protein-protein interaction (PPI) network of the DEGs was constructed using the string platform, and hub genes were identified using the cytoscape software. The gene ontology and KEGG pathway enrichment analysis were performed using enrichR package. Gene diagnostic sensitivity and its association to clinicopathological characteristics were demonstrated by statistical approaches. By using qRT-PCR, GUCA2A and COL3A1 were examined in colon cancer and rectal cancer. We identified 5037 differentially expressed genes, including (4752 upregulated, 285 downregulated) across the studies between CRC and normal tissues. Gene ontology and KEGG pathway analyses showed that the highest proportion of up-regulated DEGs was involved in RNA binding and RNA transport. Integral component of plasma membrane and mineral absorption pathways were identified as containing down-regulated DEGs. Similar expression patterns for GUCA2A and COL3A1 were seen in qRT-PCR and integrated RNA-Seq analysis. Additionally, this study demonstrated that GUCA2A and COL3A1 may play a significant role in the development of CRC.
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Affiliation(s)
- Seyed Taleb Hosseini
- Department of Biology, Faculty of Basic Sciences, Qaemshahr Branch, Islamic Azad University, Mazandaran, Iran
- Young Researchers and Elite Club, Qaemshahr Branch, Islamic Azad University, Mazandaran, Iran
| | - Farkhondeh Nemati
- Department of Biology, Faculty of Basic Sciences, Qaemshahr Branch, Islamic Azad University, Mazandaran, Iran.
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Ephraim R, Fraser S, Devereaux J, Stavely R, Feehan J, Eri R, Nurgali K, Apostolopoulos V. Differential Gene Expression of Checkpoint Markers and Cancer Markers in Mouse Models of Spontaneous Chronic Colitis. Cancers (Basel) 2023; 15:4793. [PMID: 37835487 PMCID: PMC10571700 DOI: 10.3390/cancers15194793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/17/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
The presence of checkpoint markers in cancer cells aids in immune escape. The identification of checkpoint markers and early cancer markers is of utmost importance to gain clarity regarding the relationship between colitis and progressive inflammation leading to cancer. Herein, the gene expression levels of checkpoint makers, cancer-related pathways, and cancer genes in colon tissues of mouse models of chronic colitis (Winnie and Winnie-Prolapse mice) using next-generation sequencing are determined. Winnie mice are a result of a Muc2 missense mutation. The identification of such genes and their subsequent expression and role at the protein level would enable novel markers for the early diagnosis of cancer in IBD patients. The differentially expressed genes in the colonic transcriptome were analysed based on the Kyoto Encyclopedia of Genes and Genomes pathway. The expression of several oncogenes is associated with the severity of IBD, with Winnie-Prolapse mice expressing a large number of key genes associated with development of cancer. This research presents a number of new targets to evaluate for the development of biomarkers and therapeutics.
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Affiliation(s)
- Ramya Ephraim
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (R.E.); (S.F.); (J.D.); (J.F.); (K.N.)
| | - Sarah Fraser
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (R.E.); (S.F.); (J.D.); (J.F.); (K.N.)
| | - Jeannie Devereaux
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (R.E.); (S.F.); (J.D.); (J.F.); (K.N.)
| | - Rhian Stavely
- Pediatric Surgery Research Laboratories, Department of Pediatric Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA;
| | - Jack Feehan
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (R.E.); (S.F.); (J.D.); (J.F.); (K.N.)
- Immunology Program, Australian Institute of Musculoskeletal Science (AIMSS), Melbourne, VIC 3021, Australia
| | - Rajaraman Eri
- STEM/School of Science, RMIT University, Melbourne, VIC 3001, Australia;
| | - Kulmira Nurgali
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (R.E.); (S.F.); (J.D.); (J.F.); (K.N.)
- Department of Medicine Western Health, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3010, Australia
- Regenerative Medicine and Stem Cells Program, Australian Institute of Musculoskeletal Science (AIMSS), Melbourne, VIC 3021, Australia
| | - Vasso Apostolopoulos
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (R.E.); (S.F.); (J.D.); (J.F.); (K.N.)
- Immunology Program, Australian Institute of Musculoskeletal Science (AIMSS), Melbourne, VIC 3021, Australia
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7
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Maharati A, Moghbeli M. PI3K/AKT signaling pathway as a critical regulator of epithelial-mesenchymal transition in colorectal tumor cells. Cell Commun Signal 2023; 21:201. [PMID: 37580737 PMCID: PMC10424373 DOI: 10.1186/s12964-023-01225-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 07/12/2023] [Indexed: 08/16/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most frequent gastrointestinal malignancies that are considered as a global health challenge. Despite many progresses in therapeutic methods, there is still a high rate of mortality rate among CRC patients that is associated with poor prognosis and distant metastasis. Therefore, investigating the molecular mechanisms involved in CRC metastasis can improve the prognosis. Epithelial-mesenchymal transition (EMT) process is considered as one of the main molecular mechanisms involved in CRC metastasis, which can be regulated by various signaling pathways. PI3K/AKT signaling pathway has a key role in CRC cell proliferation and migration. In the present review, we discussed the role of PI3K/AKT pathway CRC metastasis through the regulation of the EMT process. It has been shown that PI3K/AKT pathway can induce the EMT process by down regulation of epithelial markers, while up regulation of mesenchymal markers and EMT-specific transcription factors that promote CRC metastasis. This review can be an effective step toward introducing the PI3K/AKT/EMT axis to predict prognosis as well as a therapeutic target among CRC patients. Video Abstract.
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Affiliation(s)
- Amirhosein Maharati
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Meysam Moghbeli
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
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8
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Paskeh MDA, Ghadyani F, Hashemi M, Abbaspour A, Zabolian A, Javanshir S, Razzazan M, Mirzaei S, Entezari M, Goharrizi MASB, Salimimoghadam S, Aref AR, Kalbasi A, Rajabi R, Rashidi M, Taheriazam A, Sethi G. Biological impact and therapeutic perspective of targeting PI3K/Akt signaling in hepatocellular carcinoma: Promises and Challenges. Pharmacol Res 2023; 187:106553. [PMID: 36400343 DOI: 10.1016/j.phrs.2022.106553] [Citation(s) in RCA: 46] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/17/2022]
Abstract
Cancer progression results from activation of various signaling networks. Among these, PI3K/Akt signaling contributes to proliferation, invasion, and inhibition of apoptosis. Hepatocellular carcinoma (HCC) is a primary liver cancer with high incidence rate, especially in regions with high prevalence of viral hepatitis infection. Autoimmune disorders, diabetes mellitus, obesity, alcohol consumption, and inflammation can also lead to initiation and development of HCC. The treatment of HCC depends on the identification of oncogenic factors that lead tumor cells to develop resistance to therapy. The present review article focuses on the role of PI3K/Akt signaling in HCC progression. Activation of PI3K/Akt signaling promotes glucose uptake, favors glycolysis and increases tumor cell proliferation. It inhibits both apoptosis and autophagy while promoting HCC cell survival. PI3K/Akt stimulates epithelial-to-mesenchymal transition (EMT) and increases matrix-metalloproteinase (MMP) expression during HCC metastasis. In addition to increasing colony formation capacity and facilitating the spread of tumor cells, PI3K/Akt signaling stimulates angiogenesis. Therefore, silencing PI3K/Akt signaling prevents aggressive HCC cell behavior. Activation of PI3K/Akt signaling can confer drug resistance, particularly to sorafenib, and decreases the radio-sensitivity of HCC cells. Anti-cancer agents, like phytochemicals and small molecules can suppress PI3K/Akt signaling by limiting HCC progression. Being upregulated in tumor tissues and clinical samples, PI3K/Akt can also be used as a biomarker to predict patients' response to therapy.
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Affiliation(s)
- Mahshid Deldar Abad Paskeh
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Farhikhtegan Medical Convergence sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Fatemeh Ghadyani
- Farhikhtegan Medical Convergence sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Mehrdad Hashemi
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Farhikhtegan Medical Convergence sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Alireza Abbaspour
- Cellular and Molecular Research Center,Qazvin University of Medical Sciences, Qazvin, Iran
| | - Amirhossein Zabolian
- Resident of department of Orthopedics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Salar Javanshir
- Young Researchers and Elite Club, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Mehrnaz Razzazan
- Medical Student, Student Research Committee, Golestan University of Medical Sciences, Gorgan, Iran
| | - Sepideh Mirzaei
- Department of Biology, Faculty of Science, Islamic Azad University, Science and Research Branch, Tehran, Iran
| | - Maliheh Entezari
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Farhikhtegan Medical Convergence sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | | | - Shokooh Salimimoghadam
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Amir Reza Aref
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Translational Sciences, Xsphera Biosciences Inc. 6, Tide Street, Boston, MA 02210, USA
| | - Alireza Kalbasi
- Department of Pharmacy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Romina Rajabi
- Faculty of Veterinary Medicine, Islamic Azad University, Science and Research Branch, Tehran, Iran.
| | - Mohsen Rashidi
- Department Pharmacology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran; The Health of Plant and Livestock Products Research Center, Mazandaran University of Medical Sciences, Sari, Iran.
| | - Afshin Taheriazam
- Farhikhtegan Medical Convergence sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Orthopedics, Faculty of medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore; NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore.
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9
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Bartenschlager F, Klymiuk N, Gruber AD, Mundhenk L. Genomic, biochemical and expressional properties reveal strong conservation of the CLCA2 gene in birds and mammals. PeerJ 2022; 10:e14202. [PMID: 36389428 PMCID: PMC9651043 DOI: 10.7717/peerj.14202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/19/2022] [Indexed: 11/11/2022] Open
Abstract
Recent studies have revealed the dynamic and complex evolution of CLCA1 gene homologues in and between mammals and birds with a particularly high diversity in mammals. In contrast, CLCA2 has only been found as a single copy gene in mammals, to date. Furthermore, CLCA2 has only been investigated in few mammalian species but not in birds. Here, we established core genomic, protein biochemical and expressional properties of CLCA2 in several bird species and compared them with mammalian CLCA2. Chicken, turkey, quail and ostrich CLCA2 were compared to their mammalian orthologues using in silico, biochemical and expressional analyses. CLCA2 was found highly conserved not only at the level of genomic and exon architecture but also in terms of the canonical CLCA2 protein domain organization. The putatively prototypical galline CLCA2 (gCLCA2) was cloned and immunoblotting as well as immunofluorescence analyses of heterologously expressed gCLCA2 revealed protein cleavage, glycosylation patterns and anchoring in the plasma membrane similar to those of most mammalian CLCA2 orthologues. Immunohistochemistry found highly conserved CLCA2 expression in epidermal keratinocytes in all birds and mammals investigated. Our results suggest a highly conserved and likely evolutionarily indispensable role of CLCA2 in keratinocyte function. Its high degree of conservation on the genomic, biochemical and expressional levels stands in contrast to the dynamic structural complexities and proposed functional diversifications between mammalian and avian CLCA1 homologues, insinuating a significant degree of negative selection of CLCA2 orthologues among birds and mammals. Finally, and again in contrast to CLCA1, the high conservation of CLCA2 makes it a strong candidate for studying basic properties of the functionally still widely unresolved CLCA gene family.
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Affiliation(s)
- Florian Bartenschlager
- Department of Veterinary Pathology, Faculty of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Nikolai Klymiuk
- Large Animal Models in Cardiovascular Research, Internal Medical Department I, Technische Universität München, Munich, Germany
- Center for Innovative Medical Models, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Achim D. Gruber
- Department of Veterinary Pathology, Faculty of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Lars Mundhenk
- Department of Veterinary Pathology, Faculty of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
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10
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Samadi P, Soleimani M, Nouri F, Rahbarizadeh F, Najafi R, Jalali A. An integrative transcriptome analysis reveals potential predictive, prognostic biomarkers and therapeutic targets in colorectal cancer. BMC Cancer 2022; 22:835. [PMID: 35907803 PMCID: PMC9339198 DOI: 10.1186/s12885-022-09931-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 07/25/2022] [Indexed: 12/09/2022] Open
Abstract
BACKGROUND A deep understanding of potential molecular biomarkers and therapeutic targets related to the progression of colorectal cancer (CRC) from early stages to metastasis remain mostly undone. Moreover, the regulation and crosstalk among different cancer-driving molecules including messenger RNAs (mRNAs), long non-coding RNAs (lncRNAs) and micro-RNAs (miRNAs) in the transition from stage I to stage IV remain to be clarified, which is the aim of this study. METHODS We carried out two separate differential expression analyses for two different sets of samples (stage-specific samples and tumor/normal samples). Then, by the means of robust dataset analysis we identified distinct lists of differently expressed genes (DEGs) for Robust Rank Aggregation (RRA) and weighted gene co-expression network analysis (WGCNA). Then, comprehensive computational systems biology analyses including mRNA-miRNA-lncRNA regulatory network, survival analysis and machine learning algorithms were also employed to achieve the aim of this study. Finally, we used clinical samples to carry out validation of a potential and novel target in CRC. RESULTS We have identified the most significant stage-specific DEGs by combining distinct results from RRA and WGCNA. After finding stage-specific DEGs, a total number of 37 DEGs were identified to be conserved across all stages of CRC (conserved DEGs). We also found DE-miRNAs and DE-lncRNAs highly associated to these conserved DEGs. Our systems biology approach led to the identification of several potential therapeutic targets, predictive and prognostic biomarkers, of which lncRNA LINC00974 shown as an important and novel biomarker. CONCLUSIONS Findings of the present study provide new insight into CRC pathogenesis across all stages, and suggests future assessment of the functional role of lncRNA LINC00974 in the development of CRC.
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Affiliation(s)
- Pouria Samadi
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Meysam Soleimani
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Fatemeh Nouri
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Fatemeh Rahbarizadeh
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Rezvan Najafi
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Akram Jalali
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran.
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11
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Liu Y, Chen L, Meng X, Ye S, Ma L. Identification of Hub Genes in Colorectal Adenocarcinoma by Integrated Bioinformatics. Front Cell Dev Biol 2022; 10:897568. [PMID: 35693937 PMCID: PMC9184445 DOI: 10.3389/fcell.2022.897568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/20/2022] [Indexed: 11/13/2022] Open
Abstract
An improved understanding of the molecular mechanism of colorectal adenocarcinoma is necessary to predict the prognosis and develop new target gene therapy strategies. This study aims to identify hub genes associated with colorectal adenocarcinoma and further analyze their prognostic significance. In this study, The Cancer Genome Atlas (TCGA) COAD-READ database and the gene expression profiles of GSE25070 from the Gene Expression Omnibus were collected to explore the differentially expressed genes between colorectal adenocarcinoma and normal tissues. The weighted gene co-expression network analysis (WGCNA) and differential expression analysis identified 82 differentially co-expressed genes in the collected datasets. Enrichment analysis was applied to explore the regulated signaling pathway in colorectal adenocarcinoma. In addition, 10 hub genes were identified in the protein–protein interaction (PPI) network by using the cytoHubba plug-in of Cytoscape, where five genes were further proven to be significantly related to the survival rate. Compared with normal tissues, the expressions of the five genes were both downregulated in the GSE110224 dataset. Subsequently, the expression of the five hub genes was confirmed by the Human Protein Atlas database. Finally, we used Cox regression analysis to identify genes associated with prognosis, and a 3-gene signature (CLCA1–CLCA4–GUCA2A) was constructed to predict the prognosis of patients with colorectal cancer. In conclusion, our study revealed that the five hub genes and CLCA1–CLCA4–GUCA2A signature are highly correlated with the development of colorectal adenocarcinoma and can serve as promising prognosis factors to predict the overall survival rate of patients.
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Affiliation(s)
- Yang Liu
- Endoscopy Center, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Lanlan Chen
- Department of Hepatobiliary and Pancreatic Surgery, The First Hospital of Jilin University, Changchun, China
| | - Xiangbo Meng
- Endoscopy Center, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Shujun Ye
- Endoscopy Center, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Lianjun Ma
- Endoscopy Center, China-Japan Union Hospital of Jilin University, Changchun, China
- *Correspondence: Lianjun Ma,
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12
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Bartenschlager F, Klymiuk N, Weise C, Kuropka B, Gruber AD, Mundhenk L. Evolutionarily conserved properties of CLCA proteins 1, 3 and 4, as revealed by phylogenetic and biochemical studies in avian homologues. PLoS One 2022; 17:e0266937. [PMID: 35417490 PMCID: PMC9007345 DOI: 10.1371/journal.pone.0266937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 03/30/2022] [Indexed: 12/21/2022] Open
Abstract
Species-specific diversities are particular features of mammalian chloride channel regulator, calcium activated (CLCA) genes. In contrast to four complex gene clusters in mammals, only two CLCA genes appear to exist in chickens. CLCA2 is conserved in both, while only the galline CLCA1 (gCLCA1) displays close genetic distance to mammalian clusters 1, 3 and 4. In this study, sequence analyses and biochemical characterizations revealed that gCLCA1 as a putative avian prototype shares common protein domains and processing features with all mammalian CLCA homologues. It has a transmembrane (TM) domain in the carboxy terminal region and its mRNA and protein were detected in the alimentary canal, where the protein was localized in the apical membrane of enterocytes, similar to CLCA4. Both mammals and birds seem to have at least one TM domain containing CLCA protein with complex glycosylation in the apical membrane of enterocytes. However, some characteristic features of mammalian CLCA1 and 3 including entire protein secretion and expression in cell types other than enterocytes seem to be dispensable for chicken. Phylogenetic analyses including twelve bird species revealed that avian CLCA1 and mammalian CLCA3 form clades separate from a major branch containing mammalian CLCA1 and 4. Overall, our data suggest that gCLCA1 and mammalian CLCA clusters 1, 3 and 4 stem from a common ancestor which underwent complex gene diversification in mammals but not in birds.
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Affiliation(s)
- Florian Bartenschlager
- Faculty of Veterinary Medicine, Department of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Nikolai Klymiuk
- Large Animal Models in Cardiovascular Research, Internal Medical Department I, Technical University of Munich, Munich, Germany
- Center for Innovative Medical Models, Ludwig-Maximilians University Munich, Munich, Germany
| | - Christoph Weise
- Institute of Chemistry and Biochemistry, Core Facility BioSupraMol, Freie Universität Berlin, Berlin, Germany
| | - Benno Kuropka
- Institute of Chemistry and Biochemistry, Core Facility BioSupraMol, Freie Universität Berlin, Berlin, Germany
| | - Achim D. Gruber
- Faculty of Veterinary Medicine, Department of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Lars Mundhenk
- Faculty of Veterinary Medicine, Department of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
- * E-mail:
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13
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Buenafe AC, Dorrell C, Reddy AP, Klimek J, Marks DL. Proteomic analysis distinguishes extracellular vesicles produced by cancerous versus healthy pancreatic organoids. Sci Rep 2022; 12:3556. [PMID: 35241737 PMCID: PMC8894448 DOI: 10.1038/s41598-022-07451-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 02/14/2022] [Indexed: 02/07/2023] Open
Abstract
Extracellular vesicles (EVs) are produced and released by both healthy and malignant cells and bear markers indicative of ongoing biological processes. In the present study we utilized high resolution flow cytometry to detect EVs in the plasma of patients with pancreatic ductal adenocarcinoma (PDAC) and in the supernatants of PDAC and healthy control (HC) pancreatic organoid cultures. Using ultrafiltration and size exclusion chromatography, PDAC and HC pancreatic organoid EVs were isolated for mass spectrometry analysis. Proteomic and functional protein network analysis showed a striking distinction in that EV proteins profiled in pancreatic cancer organoids were involved in vesicular transport and tumorigenesis while EV proteins in healthy organoids were involved in cellular homeostasis. Thus, the most abundant proteins identified in either case represented non-overlapping cellular programs. Tumor-promoting candidates LAMA5, SDCBP and TENA were consistently upregulated in PDAC EVs. Validation of specific markers for PDAC EVs versus healthy pancreatic EVs will provide the biomarkers and enhanced sensitivity necessary to monitor early disease or disease progression, with or without treatment. Moreover, disease-associated changes in EV protein profiles provide an opportunity to investigate alterations in cellular programming with disease progression.
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Affiliation(s)
- Abigail C Buenafe
- Papé Family Pediatric Research Institute, Oregon Health and Science University, Portland, OR, USA.
| | - Craig Dorrell
- Oregon Stem Cell Center, Papé Family Pediatric Research Institute, Oregon Health and Science University, Portland, OR, USA
| | - Ashok P Reddy
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR, USA
| | - John Klimek
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR, USA
| | - Daniel L Marks
- Papé Family Pediatric Research Institute, Oregon Health and Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
- Brenden-Colson Center for Pancreatic Care, Oregon Health and Science University, Portland, OR, USA
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14
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Li M, Liu Z, Song J, Wang T, Wang H, Wang Y, Guo J. Identification of Down-Regulated ADH1C is Associated With Poor Prognosis in Colorectal Cancer Using Bioinformatics Analysis. Front Mol Biosci 2022; 9:791249. [PMID: 35300114 PMCID: PMC8921497 DOI: 10.3389/fmolb.2022.791249] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 02/08/2022] [Indexed: 12/19/2022] Open
Abstract
Colorectal cancer (CRC) is the second most deadly cancer in the whole world, with the underlying mechanisms largely indistinct. Therefore, we aimed to identify significant pathways and genes involved in the initiation, formation and poor prognosis of CRC using bioinformatics methods. In this study, we compared gene expression profiles of CRC cases with those from normal colorectal tissues from three chip datasets (GSE33113, GSE23878 and GSE41328) to identify 105 differentially expressed genes (DEGs) that were common to the three datasets. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses showed that the highest proportion of up-regulated DEGs was involved in extracellular region and cytokine-cytokine receptor interaction pathways. Integral components of membrane and bile secretion pathways were identified as containing down-regulated DEGs. 13 hub DEGs were chosen and their expression were further validated by GEPIA. Only four DEGs (ADH1C, CLCA4, CXCL8 and GUCA2A) were associated with a significantly lower overall survival after the prognosis analysis. Lower ADH1C protein level and higher CXCL8 protein level were verified by immunohistochemical staining and western blot in clinical CRC and normal colorectal tissues. In conclusion, our study indicated that the extracellular tumor microenvironment and bile metabolism pathways play critical roles in the formation and progression of CRC. Furthermore, we confirmed ADH1C being down-regulated in CRC and reported ADH1C as a prognostic predictor for the first time.
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Affiliation(s)
- Ming Li
- School of Basic Medical Sciences, Hebei University, Baoding, China
| | - Ziming Liu
- College of Clinical Medicine, Hebei University, Baoding, China
| | - Jia Song
- School of Basic Medical Sciences, Hebei University, Baoding, China
| | - Tian Wang
- College of Clinical Medicine, Hebei University, Baoding, China
| | - Hongjie Wang
- School of Basic Medical Sciences, Hebei University, Baoding, China
- Affiliated Hospital of Hebei University, Baoding, China
| | - Yanan Wang
- Department of Pathology, Affiliated Hospital of Hebei University, Baoding, China
- *Correspondence: Yanan Wang, ; Jiguang Guo,
| | - Jiguang Guo
- School of Basic Medical Sciences, Hebei University, Baoding, China
- *Correspondence: Yanan Wang, ; Jiguang Guo,
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15
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Chloride Channels and Transporters: Roles beyond Classical Cellular Homeostatic pH or Ion Balance in Cancers. Cancers (Basel) 2022; 14:cancers14040856. [PMID: 35205604 PMCID: PMC8870652 DOI: 10.3390/cancers14040856] [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: 12/31/2021] [Revised: 01/28/2022] [Accepted: 02/06/2022] [Indexed: 01/04/2023] Open
Abstract
Simple Summary Roles of chloride-associated transporters have been raised in various cancers. Although complicated ion movements, crosstalk among channels/transporters through homeostatic electric regulation, difficulties with experimental implementation such as activity measurement of intracellular location were disturbed to verify the precise modulation of channels/transporters, recently defined cancerous function and communication with tumor microenvironment of chloride channels/transporters should be highlighted beyond classical homeostatic ion balance. Chloride-associated transporters as membrane-associated components of chloride movement, regulations of transmembrane member 16A, calcium-activated chloride channel regulators, transmembrane member 206, chloride intracellular channels, voltage-gated chloride channels, cystic fibrosis transmembrane conductance regulator, voltage-dependent anion channel, volume-regulated anion channel, and chloride-bicarbonate exchangers are discussed. Abstract The canonical roles of chloride channels and chloride-associated transporters have been physiologically determined; these roles include the maintenance of membrane potential, pH balance, and volume regulation and subsequent cellular functions such as autophagy and cellular proliferative processes. However, chloride channels/transporters also play other roles, beyond these classical function, in cancerous tissues and under specific conditions. Here, we focused on the chloride channel-associated cancers and present recent advances in understanding the environments of various types of cancer caused by the participation of many chloride channel or transporters families and discuss the challenges and potential targets for cancer treatment. The modulation of chloride channels/transporters might promote new aspect of cancer treatment strategies.
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16
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Ye Y, Wang J, Liang F, Song P, Yan X, Wu S, Huang X, Han P. Identification of key genes for HNSCC from public databases using bioinformatics analysis. Cancer Cell Int 2021; 21:549. [PMID: 34663338 PMCID: PMC8524914 DOI: 10.1186/s12935-021-02254-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 10/07/2021] [Indexed: 11/16/2022] Open
Abstract
Background The cause and underlying molecular mechanisms of head and neck squamous cell carcinoma (HNSCC) are unclear. Our study aims to identify the key genes associated with HNSCC and reveal potential biomarkers. Methods In this study, the expression profile dataset GSE83519 of the Gene Expression Omnibus database and the RNA sequencing dataset of HNSCC of The Cancer Genome Atlas were included for analysis. Sixteen differentially expressed genes were screened from these two datasets using R software. Gene Expression Profiling Interactive Analysis 2 (GEPIA2) was then adopted for survival analysis, and finally, three key genes related to the overall survival of HNSCC patients were identified. Furthermore, we verified these three genes using the Oncomine database and from real-time PCR and immunohistochemistry results from HNSCC tissues. Results The expression data of 44 samples from GSE83519 and 545 samples from TCGA-HNSC were collected. Using bioinformatics, the two databases were integrated, and 16 DEGs were screened out. Gene Ontology (GO) enrichment analysis showed that the biological functions of DEGs focused primarily on the apical plasma membrane and regulation of anoikis. Kyoto Encyclopedia of Genes and Genomes (KEGG) signalling pathway analysis showed that these DEGs were mainly involved in drug metabolism-cytochrome P450 and serotonergic synapses. Survival analysis identified three key genes, CEACAM5, CEACAM6 and CLCA4, that were closely related to HNSCC prognosis. The Oncomine database, qRT–PCR and IHC verified that all 3 key genes were downregulated in most HNSCC tissues compared to adjacent normal tissues. Conclusions This study indicates that integrated bioinformatics analyses play an important role in screening for differentially expressed genes and pathways in HNSCC, helping us better understand the biomarkers and molecular mechanism of HNSCC.
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Affiliation(s)
- Yuchu Ye
- Sun Yat-Sen Memorial Hospital, Department of Otolaryngology Head and Neck Surgery, Sun Yat-Sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Jingyi Wang
- Sun Yat-Sen Memorial Hospital, Department of Otolaryngology Head and Neck Surgery, Sun Yat-Sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Faya Liang
- Sun Yat-Sen Memorial Hospital, Department of Otolaryngology Head and Neck Surgery, Sun Yat-Sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Pan Song
- Sun Yat-Sen Memorial Hospital, Department of Otolaryngology Head and Neck Surgery, Sun Yat-Sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Xiaoqing Yan
- Sun Yat-Sen Memorial Hospital, Department of Otolaryngology Head and Neck Surgery, Sun Yat-Sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Sangqing Wu
- Sun Yat-Sen Memorial Hospital, Department of Otolaryngology Head and Neck Surgery, Sun Yat-Sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Xiaoming Huang
- Sun Yat-Sen Memorial Hospital, Department of Otolaryngology Head and Neck Surgery, Sun Yat-Sen University, Guangzhou, China. .,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.
| | - Ping Han
- Sun Yat-Sen Memorial Hospital, Department of Otolaryngology Head and Neck Surgery, Sun Yat-Sen University, Guangzhou, China. .,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.
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17
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Peng Y, Li Z, Chen S, Zhou J. DHFR silence alleviated the development of liver fibrosis by affecting the crosstalk between hepatic stellate cells and macrophages. J Cell Mol Med 2021; 25:10049-10060. [PMID: 34626074 PMCID: PMC8572769 DOI: 10.1111/jcmm.16935] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 08/26/2021] [Accepted: 09/01/2021] [Indexed: 01/20/2023] Open
Abstract
Liver fibrogenesis is a dynamic cellular and tissue process which has the potential to progress into cirrhosis of even liver cancer and liver failure. The activation of hepatic stellate cells (HSCs) is the central event underlying liver fibrosis. Besides, hepatic macrophages have been proposed as potential targets in combatting fibrosis. As for the relationship between HSCs and hepatic macrophages in liver fibrosis, it is generally considered that macrophages promoted liver fibrosis via activating HSCs. However, whether activated HSCs could in turn affect macrophage polarization has rarely been studied. In this study, mRNAs with significant differences were explored using exosomal RNA‐sequencing of activated Lx‐2 cells and normal RNA‐sequencing of DHFR loss‐of‐function Lx‐2 cell models. Cell functional experiments in both Lx‐2 cells and macrophages animal model experiments were performed. The results basically confirmed exosomes secreted from activated HSCs could promote M1 polarization of macrophages further. Exosome harbouring DHFR played an important role in this process. DHFR silence in HSCs could decrease Lx‐2 activation and M1 polarization of M0 macrophages and then alleviate the development of liver fibrosis both in vitro and vivo. Our work brought a new insight that exosomal DHFR derived from HSCs had a crucial role in crosstalk between HSCs activation and macrophage polarization, which may be a potential therapeutic target in liver fibrosis.
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Affiliation(s)
- Yu Peng
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Zedong Li
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Sheng Chen
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Jun Zhou
- Department of Emergency Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
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18
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Wu L, Lian W, Zhao L. Calcium signaling in cancer progression and therapy. FEBS J 2021; 288:6187-6205. [PMID: 34288422 DOI: 10.1111/febs.16133] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 06/19/2021] [Accepted: 07/20/2021] [Indexed: 02/06/2023]
Abstract
The old Greek aphorism 'Panta Rhei' ('everything flows') is true for all living things in general. As a dynamic process, calcium signaling plays fundamental roles in cellular activities under both normal and pathological conditions, with recent researches uncovering its involvement in cell proliferation, migration, survival, gene expression, and more. The major question we address here is how calcium signaling affects cancer progression and whether it could be targeted to combine with classic chemotherapeutics or emerging immunotherapies to improve their efficacy.
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Affiliation(s)
- Ling Wu
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Guangdong Province Key Laboratory of Molecular Tumor Pathology, Southern Medical University, Guangzhou, China
| | - Weidong Lian
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Guangdong Province Key Laboratory of Molecular Tumor Pathology, Southern Medical University, Guangzhou, China
| | - Liang Zhao
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Guangdong Province Key Laboratory of Molecular Tumor Pathology, Southern Medical University, Guangzhou, China
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19
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Expression of the CLCA4 Gene in Esophageal Carcinoma and Its Impact on the Biologic Function of Esophageal Carcinoma Cells. JOURNAL OF ONCOLOGY 2021; 2021:1649344. [PMID: 34194494 PMCID: PMC8203369 DOI: 10.1155/2021/1649344] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/25/2021] [Accepted: 05/26/2021] [Indexed: 11/17/2022]
Abstract
Background Esophageal carcinoma (ESCA) is one of the malignant tumors with a high mortality rate worldwide, which seriously affects people's health. Calcium-activated chloride channel 4 (CLCA4) was reported to be a tumor inhibitor in hepatocellular carcinoma. Nevertheless, the role of CLCA4 in ESCA is still unclear. Methods RT-qPCR and western blot assay were used to test the expression pattern of CLCA4 in ESCA tissues and cells. CCK-8 assay was performed to detect the effect of CLCA4 overexpression on cell proliferation in ESCA cells. Transwell assay was used to measure the effect of CLCA4 upregulation on migration and invasion abilities of ESCA cells. Animal experiments were conducted to investigate the role of CLCA4 upregulation in tumor growth in vivo. Results CLCA4 was significantly reduced in ESCA tissues and correlated with T stage, differentiation, and lymph node metastasis. CLCA4 overexpression was found to inhibit cell proliferation, migration, invasion, and EMT progression in ESCA cells. Moreover, CLCA4 overexpression suppressed tumor growth in vivo. Conclusion CLCA4 was suggested to act as a tumor inhibitor in ESCA and might be a therapeutic target gene for the treatment of patients with ESCA.
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20
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Wen L, Han Z, Du Y. Identification of gene biomarkers and immune cell infiltration characteristics in rectal cancer. J Gastrointest Oncol 2021; 12:964-980. [PMID: 34295549 DOI: 10.21037/jgo-21-255] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 06/04/2021] [Indexed: 12/12/2022] Open
Abstract
Background Compared with colon cancer, the increase of morbidity is more significant for rectal cancer. The current study set out to identify novel and critical biomarkers or features that may be used as promising targets for early diagnosis and treatment monitoring of rectal cancer. Methods Microarray datasets of rectal cancer with a minimum sample size of 30 and RNA-sequencing datasets of rectal adenocarcinoma (READ) were downloaded from the Gene Expression Omnibus (GEO) database and The Cancer Genome Atlas (TCGA) database. The method of robust rank aggregation was utilized to integrate differentially expressed genes (DEGs). The protein-protein interaction (PPI) network of the DEGs was structured using the STRING platform, and hub genes were identified using the Cytoscape plugin cytoHubba and an UpSet diagram. R software was employed to perform functional enrichment analysis. Receiver operating characteristic (ROC) curves based on the GEO data and Kaplan-Meier curves based on the TCGA data were drawn to assess the diagnostic and prognostic values of the hub genes. Immune cell infiltration analysis was conducted with CIBERSORT, and the diagnostic value and correlations between prognostic genes and infiltrated immune cells were analyzed by principal component analysis (PCA), ROC curves, and correlation scatter plots. Results A total of 137 robust DEGs were obtained by integrating datasets in GEO. Twenty-four hub genes, including CHGA, TTR, SAA1, SPP1, MMP1, TGFBI, COL1A1, and PCK1, were identified as a diagnostic gene biomarker group for rectal cancer, and SAA1, SPP1, and SI were identified as potential novel prognostic biomarkers. Functionally, the hub genes were mainly involved in the rectal cancer related interleukin (IL)-17 and proximal tubule bicarbonate reclamation pathways. Twelve sensitive infiltrated immune cells were identified, and were correlated with prognostic genes. Conclusions The integrated gene biomarker group combined with immune cell infiltration can effectively indicate rectal cancer.
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Affiliation(s)
- Lina Wen
- Department of Clinical Nutrition, Beijing Shijitan Hospital, Capital Medical University, Beijing, China.,Department of Oncology, Capital Medical University; Beijing Institute of Integrated Chinese and Western Medicine Oncology, Beijing, China
| | - Zongqiang Han
- Department of Laboratory Medicine, Beijing Xiaotangshan Hospital, Beijing, China
| | - Yanlin Du
- Department of Oncology, Wangjing Hospital, China Academy of Chinese Medical Sciences, Beijing, China
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21
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Patil AR, Leung MY, Roy S. Identification of Hub Genes in Different Stages of Colorectal Cancer through an Integrated Bioinformatics Approach. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:5564. [PMID: 34070979 PMCID: PMC8197092 DOI: 10.3390/ijerph18115564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 11/16/2022]
Abstract
Colorectal cancer (CRC) is the third most common cancer that contributes to cancer-related morbidity. However, the differential expression of genes in different phases of CRC is largely unknown. Moreover, very little is known about the role of stress-survival pathways in CRC. We sought to discover the hub genes and identify their roles in several key pathways, including oxidative stress and apoptosis in the different stages of CRC. To identify the hub genes that may be involved in the different stages of CRC, gene expression datasets were obtained from the gene expression omnibus (GEO) database. The differentially expressed genes (DEGs) common among the different datasets for each group were obtained using the robust rank aggregation method. Then, gene enrichment analysis was carried out with Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases. Finally, the protein-protein interaction networks were constructed using the Cytoscape software. We identified 40 hub genes and performed enrichment analysis for each group. We also used the Oncomine database to identify the DEGs related to stress-survival and apoptosis pathways involved in different stages of CRC. In conclusion, the hub genes were found to be enriched in several key pathways, including the cell cycle and p53 signaling pathway. Some of the hub genes were also reported in the stress-survival and apoptosis pathways. The hub DEGs revealed from our study may be used as biomarkers and may explain CRC development and progression mechanisms.
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Affiliation(s)
- Abhijeet R. Patil
- Computational Science Program, The University of Texas at El Paso, El Paso, TX 79968, USA; (A.R.P.); (M.-Y.L.)
| | - Ming-Ying Leung
- Computational Science Program, The University of Texas at El Paso, El Paso, TX 79968, USA; (A.R.P.); (M.-Y.L.)
- Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX 79968, USA
- Department of Mathematical Sciences, The University of Texas at El Paso, El Paso, TX 79968, USA
| | - Sourav Roy
- Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX 79968, USA
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX 79968, USA
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22
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Basnet U, Patil AR, Kulkarni A, Roy S. Role of Stress-Survival Pathways and Transcriptomic Alterations in Progression of Colorectal Cancer: A Health Disparities Perspective. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:5525. [PMID: 34063993 PMCID: PMC8196775 DOI: 10.3390/ijerph18115525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/07/2021] [Accepted: 05/19/2021] [Indexed: 12/09/2022]
Abstract
Every year, more than a million individuals are diagnosed with colorectal cancer (CRC) across the world. Certain lifestyle and genetic factors are known to drive the high incidence and mortality rates in some groups of individuals. The presence of enormous amounts of reactive oxygen species is implicated for the on-set and carcinogenesis, and oxidant scavengers are thought to be important in CRC therapy. In this review, we focus on the ethnicity-based CRC disparities in the U.S., the negative effects of oxidative stress and apoptosis, and gene regulation in CRC carcinogenesis. We also highlight the use of antioxidants for CRC treatment, along with screening for certain regulatory genetic elements and oxidative stress indicators as potential biomarkers to determine the CRC risk and progression.
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Affiliation(s)
- Urbashi Basnet
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79968, USA; (U.B.); (A.K.)
| | - Abhijeet R. Patil
- Computational Science Program, University of Texas at El Paso, El Paso, TX 79968, USA;
| | - Aditi Kulkarni
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79968, USA; (U.B.); (A.K.)
| | - Sourav Roy
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79968, USA; (U.B.); (A.K.)
- The Border Biomedical Research Center, University of Texas at El Paso, El Paso, TX 79968, USA
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Zhuang Z, Wang X, Huang M, Luo Y, Yu H. Serum calcium improved systemic inflammation marker for predicting survival outcome in rectal cancer. J Gastrointest Oncol 2021; 12:568-579. [PMID: 34012650 DOI: 10.21037/jgo-20-479] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background Systemic inflammation markers have shown prognostic values with variability in rectal cancer. Considering the association of serum calcium with inflammation, we aimed to examine whether it could improve systemic inflammation markers for survival prediction. Methods We enrolled 508 patients with stage I to III rectal cancer who underwent curative resection. The cohort was grouped by corrected serum calcium (cCa), platelet-to-lymphocyte ratio (PLR), and CaPLR (a score model combining cCa with PLR) for survival analysis. The LR (likelihood ratio) test and AIC (Akaike information criterion) were applied to compare models in survival prediction. The primary endpoint was disease-free survival (DFS). Results A total of 26.7% (136/508) patients reached recurrence after curative surgery. Both high cCa (HR 1.486; 95% CI, 1.018-2.171; P=0.040) and high PLR (HR 1.452; 95% CI, 1.059-1.991; P=0.021) were significantly associated with worse DFS. In model comparison, the AIC and LR were improved after cCa was added to PLR model in DFS prediction (AIC: 1,704.83 vs. 1,707.14 vs. 1,707.15; LR: 8.68 vs. 4.37 vs. 4.36; P=0.037). The CaPLR was developed for DFS prediction with adjusted HRs of 2.216 (95% CI, 1.256-3.909; P=0.006) and 1.679 (95% CI, 1.004-2.836; P=0.047) for high and intermediate score group respectively compared to low score group. A nomogram for predicting DFS was generated by using CaPLR and other clinical predictors, with a concordance index of 0.705 (95% CI, 0.620-0.789; P<0.001). Conclusions Serum calcium could improve systemic inflammation markers in survival prediction for patients with rectal cancer.
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Affiliation(s)
- Zhuokai Zhuang
- Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiaolin Wang
- Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Meijin Huang
- Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yanxin Luo
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Huichuan Yu
- Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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CLCA4 and MS4A12 as the significant gene biomarkers of primary colorectal cancer. Biosci Rep 2021; 40:226087. [PMID: 32797167 PMCID: PMC7441370 DOI: 10.1042/bsr20200963] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 08/13/2020] [Accepted: 08/14/2020] [Indexed: 02/07/2023] Open
Abstract
Background: Primary colorectal cancer (PCRC) is a common digestive tract cancer in the elderly. However, the treatment effect of PCRC is still limited, and the long-term survival rate is low. Therefore, further exploring the pathogenesis of PCRC, and searching for specific molecular targets for diagnosis are the development trends of precise medical treatment, which have important clinical significance. Methods: The public data were downloaded from Gene Expression Omnibus (GEO) database. Verification for repeatability of intra-group data was performed by Pearson’s correlation test and principal component analysis. Differentially expressed genes (DEGs) between normal and PCRC were identified, and the protein–protein interaction (PPI) network was constructed. Significant module and hub genes were found in the PPI network. A total of 192 PCRC patients were recruited between 2010 and 2019 from the Fourth Hospital of Hebei Medical University. RT-PCR was used to measure the relative expression of CLCA4 and MS4A12. Furthermore, the study explored the effect of expression of CLCA4 and MS4A12 for overall survival. Results: A total of 53 DEGs were identified between PCRC and normal colorectal tissues. Ten hub genes concerned to PCRC were screened, namely CLCA4, GUCA2A, GCG, SST, MS4A12, PLP1, CHGA, PYY, VIP, and GUCA2B. The PCRC patients with low expression of CLCA4 and MS4A12 has a worse overall survival than high expression of CLCA4 and MS4A12 (P<0.05). Conclusion: The research of DEGs in PCRC (53 DEGs, 10 hub genes, especially CLCA4 and MS4A12) and related signaling pathways is conducive to the differential analysis of the molecular mechanism of PCRC.
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Xiao P, Liu YK, Han W, Hu Y, Zhang BY, Liu WL. Exosomal Delivery of FTO Confers Gefitinib Resistance to Recipient Cells through ABCC10 Regulation in an m6A-dependent Manner. Mol Cancer Res 2021; 19:726-738. [PMID: 33563765 DOI: 10.1158/1541-7786.mcr-20-0541] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 10/23/2020] [Accepted: 01/12/2021] [Indexed: 11/16/2022]
Abstract
Gefitinib is suitable for the treatment of locally advanced or metastatic non-small cell lung cancer. However, the development of acquired resistance limits its long-term efficacy in regardless of significant clinical benefit to patients. Therefore, to elucidate the mechanism of gefitinib resistance in addition to target gene mutation may greatly increase its clinical efficacy. It was found first that N 6-methyladenosine RNA demethylase FTO was significantly enriched in serum exosomes of gefitinib-resistant (GR) patients compared with that of gefitinib-sensitive (GS) patients through exosomal RNA sequencing. Meanwhile, the average m6A proportion in GR patients was significantly lower when compared with that in GS patients. Besides, GR cell-derived exosome internalization attenuated the total m6A abundance and gefitinib sensitivity of PC9 cells. Not only FTO knockdown enhanced the gefitinib sensitivity of GR cells but also FTO reduction in donor exosomes alleviated the acquired resistance of recipient PC9 cells. GR cell-derived exosomal-FTO promoted ABCC10 of recipient cells in a m6A-dependent manner. FTO/YTHDF2/ABCC10 axis played a role in intercellular transmission of GR cell-derived exosome-mediated gefitinib resistance both in vitro and in vivo. In general, this research showed that m6A modification was involved in the decrease of gefitinib sensitivity. GR cell-derived exosomes could decrease gefitinib sensitivity of recipient cells in exosomal delivery of FTO-dependent manner. FTO/YTHDF2/ABCC10 axis played a role in intercellular transmission of GR cell-derived exosome-mediated gefitinib resistance. IMPLICATIONS: Our results elucidated another potential molecular mechanism of gefitinib resistance in non-small cell lung cancer besides secondary EGFR mutations.
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Affiliation(s)
- Peng Xiao
- Department of Thoracic Surgery, The Third Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Yu-Kang Liu
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Wei Han
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Yan Hu
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Bo-You Zhang
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Wen-Liang Liu
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, P.R. China.
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26
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Kudryavtseva AV, Kalinin DV, Pavlov VS, Savvateeva MV, Fedorova MS, Pudova EA, Kobelyatskaya AA, Golovyuk AL, Guvatova ZG, Razmakhaev GS, Demidova TB, Simanovsky SA, Slavnova EN, Poloznikov AА, Polyakov AP, Melnikova NV, Dmitriev AA, Krasnov GS, Snezhkina AV. Mutation profiling in eight cases of vagal paragangliomas. BMC Med Genomics 2020; 13:115. [PMID: 32948195 PMCID: PMC7500026 DOI: 10.1186/s12920-020-00763-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 08/05/2020] [Indexed: 12/25/2022] Open
Abstract
Background Vagal paragangliomas (VPGLs) belong to a group of rare head and neck neuroendocrine tumors. VPGLs arise from the vagus nerve and are less common than carotid paragangliomas. Both diagnostics and therapy of the tumors raise significant challenges. Besides, the genetic and molecular mechanisms behind VPGL pathogenesis are poorly understood. Methods The collection of VPGLs obtained from 8 patients of Russian population was used in the study. Exome library preparation and high-throughput sequencing of VPGLs were performed using an Illumina technology. Results Based on exome analysis, we identified pathogenic/likely pathogenic variants of the SDHx genes, frequently mutated in paragangliomas/pheochromocytomas. SDHB variants were found in three patients, whereas SDHD was mutated in two cases. Moreover, likely pathogenic missense variants were also detected in SDHAF3 and SDHAF4 genes encoding for assembly factors for the succinate dehydrogenase (SDH) complex. In a patient, we found a novel variant of the IDH2 gene that was predicted as pathogenic by a series of algorithms used (such as SIFT, PolyPhen2, FATHMM, MutationTaster, and LRT). Additionally, pathogenic/likely pathogenic variants were determined for several genes, including novel genes and some genes previously reported as associated with different types of tumors. Conclusions Results indicate a high heterogeneity among VPGLs, however, it seems that driver events in most cases are associated with mutations in the SDHx genes and SDH assembly factor-coding genes that lead to disruptions in the SDH complex.
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Affiliation(s)
- Anna V Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
| | - Dmitry V Kalinin
- Vishnevsky Institute of Surgery, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Vladislav S Pavlov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Maria V Savvateeva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Maria S Fedorova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Elena A Pudova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Alexander L Golovyuk
- Vishnevsky Institute of Surgery, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Zulfiya G Guvatova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - George S Razmakhaev
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Tatiana B Demidova
- A. N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Sergey A Simanovsky
- A. N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Elena N Slavnova
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Andrey А Poloznikov
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Andrey P Polyakov
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Nataliya V Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexey A Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - George S Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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How Dysregulated Ion Channels and Transporters Take a Hand in Esophageal, Liver, and Colorectal Cancer. Rev Physiol Biochem Pharmacol 2020; 181:129-222. [PMID: 32875386 DOI: 10.1007/112_2020_41] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Over the last two decades, the understanding of how dysregulated ion channels and transporters are involved in carcinogenesis and tumor growth and progression, including invasiveness and metastasis, has been increasing exponentially. The present review specifies virtually all ion channels and transporters whose faulty expression or regulation contributes to esophageal, hepatocellular, and colorectal cancer. The variety reaches from Ca2+, K+, Na+, and Cl- channels over divalent metal transporters, Na+ or Cl- coupled Ca2+, HCO3- and H+ exchangers to monocarboxylate carriers and organic anion and cation transporters. In several cases, the underlying mechanisms by which these ion channels/transporters are interwoven with malignancies have been fully or at least partially unveiled. Ca2+, Akt/NF-κB, and Ca2+- or pH-dependent Wnt/β-catenin signaling emerge as cross points through which ion channels/transporters interfere with gene expression, modulate cell proliferation, trigger epithelial-to-mesenchymal transition, and promote cell motility and metastasis. Also miRs, lncRNAs, and DNA methylation represent potential links between the misexpression of genes encoding for ion channels/transporters, their malfunctioning, and cancer. The knowledge of all these molecular interactions has provided the basis for therapeutic strategies and approaches, some of which will be broached in this review.
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Zhang X, Mao F, Wong NK, Bao Y, Lin Y, Liu K, Li J, Xiang Z, Ma H, Xiao S, Zhang Y, Yu Z. CLIC2α Chloride Channel Orchestrates Immunomodulation of Hemocyte Phagocytosis and Bactericidal Activity in Crassostrea gigas. iScience 2020; 23:101328. [PMID: 32674055 PMCID: PMC7363696 DOI: 10.1016/j.isci.2020.101328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 06/02/2020] [Accepted: 06/26/2020] [Indexed: 02/07/2023] Open
Abstract
Chloride ion plays critical roles in modulating immunological interactions. Herein, we demonstrated that the anion channel CLIC2α mediates Cl− flux to regulate hemocytes functions in the Pacific oyster (Crassostrea gigas). Specifically, during infection by Vibrio parahemolyticus, chloride influx was activated following onset of phagocytosis. Phosphorylation of Akt was stimulated by Cl− ions entering host cells, further contributing to signal transduction regulating internalization of bacteria through the PI3K/Akt signaling pathway. Concomitantly, Cl− entered phagosomes, promoted the acidification and maturation of phagosomes, and contributed to production of HOCl to eradicate engulfed bacteria. Finally, genomic screening reveals CLIC2α as a major Cl− channel gene responsible for regulating Cl− influx in oysters. Knockdown of CLIC2α predictably impeded phagosome acidification and restricted bacterial killing in oysters. In conclusion, our work has established CLIC2α as a prominent regulator of Cl− influx and thus Cl− function in C. gigas in bacterial infection contexts. Influx of chloride ions is switched on during phagocytosis in oyster hemocytes PI3K/Akt signaling pathway mediates chloride-dependent activation of phagocytosis Cl− promotes phagosomal acidification and HOCl production CLIC2α is the principal chloride channel encoding gene within oyster genome
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Affiliation(s)
- Xiangyu Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, Innovation Academy of South China Sea Ecology and Environmental Engineering (ISEE), South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou 510301, P. R. China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510301, P. R. China; University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Fan Mao
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, Innovation Academy of South China Sea Ecology and Environmental Engineering (ISEE), South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou 510301, P. R. China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510301, P. R. China
| | - Nai-Kei Wong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, Innovation Academy of South China Sea Ecology and Environmental Engineering (ISEE), South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou 510301, P. R. China; National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, The Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen 518112, P. R. China
| | - Yongbo Bao
- Zhejiang Key Laboratory of Aquatic Germplasm Resources, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, P. R. China
| | - Yue Lin
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, Innovation Academy of South China Sea Ecology and Environmental Engineering (ISEE), South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou 510301, P. R. China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510301, P. R. China; University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Kunna Liu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, Innovation Academy of South China Sea Ecology and Environmental Engineering (ISEE), South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou 510301, P. R. China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510301, P. R. China; University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jun Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, Innovation Academy of South China Sea Ecology and Environmental Engineering (ISEE), South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou 510301, P. R. China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510301, P. R. China
| | - Zhiming Xiang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, Innovation Academy of South China Sea Ecology and Environmental Engineering (ISEE), South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou 510301, P. R. China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510301, P. R. China
| | - Haitao Ma
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, Innovation Academy of South China Sea Ecology and Environmental Engineering (ISEE), South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou 510301, P. R. China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510301, P. R. China
| | - Shu Xiao
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, Innovation Academy of South China Sea Ecology and Environmental Engineering (ISEE), South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou 510301, P. R. China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510301, P. R. China
| | - Yang Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, Innovation Academy of South China Sea Ecology and Environmental Engineering (ISEE), South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou 510301, P. R. China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510301, P. R. China.
| | - Ziniu Yu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, Innovation Academy of South China Sea Ecology and Environmental Engineering (ISEE), South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou 510301, P. R. China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510301, P. R. China.
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Identification and Verification of Core Genes in Colorectal Cancer. BIOMED RESEARCH INTERNATIONAL 2020; 2020:8082697. [PMID: 32462020 PMCID: PMC7232680 DOI: 10.1155/2020/8082697] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 03/25/2020] [Accepted: 04/18/2020] [Indexed: 02/06/2023]
Abstract
Colorectal cancer, a malignant neoplasm that occurs in the colorectal mucosa, is one of the most common types of gastrointestinal cancer. Colorectal cancer has been studied extensively, but the molecular mechanisms of this malignancy have not been characterized. This study identified and verified core genes associated with colorectal cancer using integrated bioinformatics analysis. Three gene expression profiles (GSE15781, GSE110223, and GSE110224) were downloaded from the Gene Expression Omnibus (GEO) databases. A total of 87 common differentially expressed genes (DEGs) among GSE15781, GSE110223, and GSE110224 were identified, including 19 upregulated genes and 68 downregulated genes. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis was performed for common DEGs using clusterProfiler. These common DEGs were significantly involved in cancer-associated functions and signaling pathways. Then, we constructed protein-protein interaction networks of these common DEGs using Cytoscape software, which resulted in the identification of the following 10 core genes: SST, PYY, CXCL1, CXCL8, CXCL3, ZG16, AQP8, CLCA4, MS4A12, and GUCA2A. Analysis using qRT-PCR has shown that SST, CXCL8, and MS4A12 were significant differentially expressed between colorectal cancer tissues and normal colorectal tissues (P < 0.05). Gene Expression Profiling Interactive Analysis (GEPIA) overall survival (OS) has shown that low expressions of AQP8, ZG16, CXCL3, and CXCL8 may predict poor survival outcome in colorectal cancer. In conclusion, the core genes identified in this study contributed to the understanding of the molecular mechanisms involved in colorectal cancer development and may be targets for early diagnosis, prevention, and treatment of colorectal cancer.
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Gao X, Yang J. Identification of Genes Related to Clinicopathological Characteristics and Prognosis of Patients with Colorectal Cancer. DNA Cell Biol 2020; 39:690-699. [PMID: 32027181 DOI: 10.1089/dna.2019.5088] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The aim of this study was to identify genes with clinical significance in colorectal cancer (CRC). Gene expression profiles of 585 CRC tissues and 61 normal colorectal tissues from Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases were used to identify differentially expressed genes (DEGs) between CRC and normal colorectal tissues. DAVID and KOBAS tools were used to explore Gene Ontology (GO) and KEGG pathways enriched by DEGs, respectively. In addition, TCGA data sets were also used to identify prognostic factors and develop a prognostic prediction model for CRC. A total of 353 DEGs including 117 upregulated and 236 downregulated genes in CRC were identified based on GSE32323 data set. These DEGs were significantly enriched in the biological process related to the regulation of cell proliferation and 50 signaling pathways, such as "TGF-beta signaling pathway," "Wnt signaling pathway," and "Jak-STAT signaling pathway." GCG, ADH1B, SLC4A4, ZG16, and CLCA4 were the top five downregulated in CRC. FOXQ1, LGR5, CLDN1, KRT23, and DPEP1 were the top five upregulated in CRC. KRT23 expression could affect tumor stage and regional lymph node metastasis in CRC patients. FOXQ1 expression could affect tumor distant metastasis in CRC patients. Survival analysis indicated that SLC4A4 expression was associated with the prognosis of CRC patients. Prognostic prediction model developed based on age, tumor stage, and SLC4A4 expression exhibited an efficient performance in predicting 1-, 3-, and 5-year overall survival of CRC patients. In conclusion, the current study identified several genes and pathways related to CRC, which provided new insight in understanding molecular mechanism of tumorigenesis and development of CRC.
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Affiliation(s)
- Xueren Gao
- School of Pharmacy, Yancheng Teachers' University, Yancheng, China
| | - Jiaojiao Yang
- Department of Microbiology and Immunology, Shanxi Medical University, Tai yuan, China
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