1
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Cao H, Jia C, Li Z, Yang H, Fang R, Zhang Y, Cui Y. wMKL: multi-omics data integration enables novel cancer subtype identification via weight-boosted multi-kernel learning. Br J Cancer 2024; 130:1001-1012. [PMID: 38278975 PMCID: PMC10951206 DOI: 10.1038/s41416-024-02587-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/09/2024] [Accepted: 01/15/2024] [Indexed: 01/28/2024] Open
Abstract
BACKGROUND Cancer is a heterogeneous disease driven by complex molecular alterations. Cancer subtypes determined from multi-omics data can provide novel insight into personalised precision treatment. It is recognised that incorporating prior weight knowledge into multi-omics data integration can improve disease subtyping. METHODS We develop a weighted method, termed weight-boosted Multi-Kernel Learning (wMKL) which incorporates heterogeneous data types as well as flexible weight functions, to boost subtype identification. Given a series of weight functions, we propose an omnibus combination strategy to integrate different weight-related P-values to improve subtyping precision. RESULTS wMKL models each data type with multiple kernel choices, thus alleviating the sensitivity and robustness issue due to selecting kernel parameters. Furthermore, wMKL integrates different data types by learning weights of different kernels derived from each data type, recognising the heterogeneous contribution of different data types to the final subtyping performance. The proposed wMKL outperforms existing weighted and non-weighted methods. The utility and advantage of wMKL are illustrated through extensive simulations and applications to two TCGA datasets. Novel subtypes are identified followed by extensive downstream bioinformatics analysis to understand the molecular mechanisms differentiating different subtypes. CONCLUSIONS The proposed wMKL method provides a novel strategy for disease subtyping. The wMKL is freely available at https://github.com/biostatcao/wMKL .
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Affiliation(s)
- Hongyan Cao
- Division of Health Statistics, Shanxi Provincial Key Laboratory of Major Diseases Risk Assessment, Shanxi Medical University, 030001, Taiyuan, Shanxi, China
- MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, 030001, Taiyuan, Shanxi, China
- Division of Mathematics, School of Basic Medical Science, Shanxi Medical University, 030001, Taiyuan, Shanxi, China
| | - Congcong Jia
- Division of Health Statistics, Shanxi Provincial Key Laboratory of Major Diseases Risk Assessment, Shanxi Medical University, 030001, Taiyuan, Shanxi, China
| | - Zhi Li
- Department of Hematology, Taiyuan Central Hospital of Shanxi Medical University, 030001, Taiyuan, Shanxi, China
| | - Haitao Yang
- Division of Health Statistics, School of Public Health, Hebei Medical University, 050017, Shijiazhuang, China
| | - Ruiling Fang
- Division of Health Statistics, Shanxi Provincial Key Laboratory of Major Diseases Risk Assessment, Shanxi Medical University, 030001, Taiyuan, Shanxi, China
| | - Yanbo Zhang
- Division of Health Statistics, Shanxi Provincial Key Laboratory of Major Diseases Risk Assessment, Shanxi Medical University, 030001, Taiyuan, Shanxi, China
| | - Yuehua Cui
- Department of Statistics and Probability, Michigan State University, East Lansing, MI, 48824, USA.
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2
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Komune N, Sato K, Ono M, Imaizumi A, Masuda S, Itoyama S, Manako T, Kuga R, Hongo T, Kogo R, Onishi H, Nakagawa T. Biological and genetic characterization of a newly established human external auditory canal carcinoma cell line, SCEACono2. Sci Rep 2023; 13:19636. [PMID: 37949965 PMCID: PMC10638439 DOI: 10.1038/s41598-023-46926-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 11/07/2023] [Indexed: 11/12/2023] Open
Abstract
Squamous cell carcinoma of the external auditory canal (EACSCC) is an extraordinarily rare and aggressive malignant disease. Establishment of EACSCC cell line with robust molecular characteristics is essential for the basic and translational research of EACSCC. Here, we show the newly established EACSCC cell line SCEACono2, derived from a patient with well-to-moderately differentiated EACSCC. We analyzed histologic and genetic features of SCEACono2 hiring multiple experiments, including next-generation sequencing (NGS). Immunocytochemical staining of SCEACono2 showed positivity of p53 and SCC1/2. Furthermore, SCEACono2 exhibited a unique characteristic that cytokeratin, vimentin as well as cancer stem cell markers (CD44, CD133, ALP and Oct3/4) were positive. SCEACono2 had an ability to form tumors at the temporal lesion xenograft nude mice model. NGS revealed that SCEACono2 harbored the somatic mutations of TP53 (p.G245S) and NOTCH1 (p.A465T). RNA-seq and downstream bioinformatics analysis revealed significant enrichment of genes involved in inflammation and cell adhesion in SCEACono2 compared to SCC-9 and HSC-4. STR profiling indicated no evidence of cross-contamination. In conclusion, SCEACono2 could serves as a promising and robust research resource of EACSCC in vitro and in vivo.
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Affiliation(s)
- Noritaka Komune
- Department of Otorhinolaryngology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-Ku, Fukuoka, 812-8582, Japan.
| | - Kuniaki Sato
- Department of Otorhinolaryngology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-Ku, Fukuoka, 812-8582, Japan
| | - Mayumi Ono
- Department of Otorhinolaryngology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-Ku, Fukuoka, 812-8582, Japan
| | - Akira Imaizumi
- Department of Cancer Therapy and Research, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-Ku, Fukuoka, 812-8582, Japan
| | - Shogo Masuda
- Department of Otorhinolaryngology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-Ku, Fukuoka, 812-8582, Japan
| | - Shinsaku Itoyama
- Department of Otorhinolaryngology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-Ku, Fukuoka, 812-8582, Japan
| | - Tomomi Manako
- Department of Otorhinolaryngology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-Ku, Fukuoka, 812-8582, Japan
| | - Ryosuke Kuga
- Department of Otorhinolaryngology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-Ku, Fukuoka, 812-8582, Japan
| | - Takahiro Hongo
- Department of Otorhinolaryngology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-Ku, Fukuoka, 812-8582, Japan
| | - Ryunosuke Kogo
- Department of Otorhinolaryngology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-Ku, Fukuoka, 812-8582, Japan
| | - Hideya Onishi
- Department of Cancer Therapy and Research, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-Ku, Fukuoka, 812-8582, Japan
| | - Takashi Nakagawa
- Department of Otorhinolaryngology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-Ku, Fukuoka, 812-8582, Japan
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3
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Simon AG, Esser LK, Ellinger J, Ritter M, Kristiansen G, Muders MH, Mayr T, Toma MI. RNA Sequencing Reveals Alterations and Similarities in Cell Metabolism, Hypoxia and Immune Evasion in Primary Cell Cultures of Clear Cell Renal Cell Carcinoma. Front Oncol 2022; 12:883195. [PMID: 35646693 PMCID: PMC9130782 DOI: 10.3389/fonc.2022.883195] [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: 02/24/2022] [Accepted: 04/08/2022] [Indexed: 11/17/2022] Open
Abstract
The treatment of advanced renal cell carcinoma remains a challenge. To develop novel therapeutic approaches, primary cell cultures as an in vitro model are considered more representative than commercial cell lines. In this study, we analyzed the gene expression of previously established primary cell cultures of clear cell renal cell carcinoma by bulk (3’m)RNA sequencing and compared it to the tissue of origin. The objectives were the identification of dysregulated pathways under cell culture conditions. Furthermore, we assessed the suitability of primary cell cultures for studying crucial biological pathways, including hypoxia, growth receptor signaling and immune evasion. RNA sequencing of primary cell cultures of renal cell carcinoma and a following Enrichr database analysis revealed multiple dysregulated pathways under cell culture conditions. 444 genes were significantly upregulated and 888 genes downregulated compared to the tissue of origin. The upregulated genes are crucial in DNA repair, cell cycle, hypoxia and metabolic shift towards aerobic glycolysis. A downregulation was observed for genes involved in pathways of immune cell differentiation and cell adhesion. We furthermore observed that 7275 genes have a similar mRNA expression in cell cultures and in tumor tissue, including genes involved in the immune checkpoint signaling or in pathways responsible for tyrosine kinase receptor resistance. Our findings confirm that primary cell cultures are a representative tool for specified experimental approaches. The results presented in this study give further valuable insights into the complex adaptation of patient-derived cells to a new microenvironment, hypoxia and other cell culture conditions, which are often neglected in daily research, and allow new translational and therapeutic approaches.
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Affiliation(s)
- Adrian Georg Simon
- Department of Pathology, University Hospital Bonn, Bonn, Germany.,Department of Pathology, University Hospital Cologne, Cologne, Germany
| | | | - Jörg Ellinger
- Department of Urology, University Hospital Bonn, Bonn, Germany
| | - Manuel Ritter
- Department of Urology, University Hospital Bonn, Bonn, Germany
| | - Glen Kristiansen
- Department of Pathology, University Hospital Bonn, Bonn, Germany
| | - Michael H Muders
- Department of Pathology, University Hospital Bonn, Bonn, Germany
| | - Thomas Mayr
- Department of Pathology, University Hospital Bonn, Bonn, Germany
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4
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Klümper N, Ralser DJ, Bawden EG, Landsberg J, Zarbl R, Kristiansen G, Toma M, Ritter M, Hölzel M, Ellinger J, Dietrich D. LAG3 ( LAG-3, CD223) DNA methylation correlates with LAG3 expression by tumor and immune cells, immune cell infiltration, and overall survival in clear cell renal cell carcinoma. J Immunother Cancer 2021; 8:jitc-2020-000552. [PMID: 32234847 PMCID: PMC7174079 DOI: 10.1136/jitc-2020-000552] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2020] [Indexed: 12/17/2022] Open
Abstract
Background Lymphocyte activating 3 (LAG3, LAG-3, CD223) is a promising target for immune checkpoint inhibition in clear cell renal cell carcinoma (KIRC). The aim of this study was to investigate the epigenetic regulation of LAG3 in KIRC by methylation. Methods We correlated quantitative LAG3 methylation levels with transcriptional activity, immune cell infiltration, and overall survival in a cohort of n=533 patients with KIRC and n=160 normal adjacent tissue (NAT) samples obtained from The Cancer Genome Atlas (TCGA). Furthermore, we analyzed LAG3 methylation in peripheral blood mononuclear cells (PBMCs) and KIRC cell lines. We validated correlations between LAG3 expression, immune cell infiltrates, survival, and methylation in an independent KIRC cohort (University Hospital Bonn (UHB) cohort, n=118) by means of immunohistochemistry and quantitative methylation-specific PCR. Results We found differential methylation profiles among PBMCs, NAT, KIRC cell lines, and KIRC tumor tissue. Methylation strongly correlated with LAG3 mRNA expression in KIRCs (TCGA cohort) and KIRC cell lines. In the UHB cohort, methylation correlated with LAG3-positive immune cells and tumor-intrinsic LAG3 protein expression. Furthermore, LAG3 methylation strongly correlated with signatures of distinct immune cell infiltrates, an interferon-y signature (TCGA cohort), and immunohistochemically quantified CD45+, CD8+, and CD4+ immune cell infiltrates (UHB cohort). LAG3 mRNA expression (TCGA cohort), methylation (both cohorts), and tumor cell-intrinsic protein expression (UHB cohort) was significantly associated with overall survival. Conclusion Our data suggest an epigenetic regulation of LAG3 expression in tumor and immune cells via DNA methylation. LAG3 expression and methylation is associated with a subset of KIRCs showing a distinct clinical course and immunogenicity. Our study provides rationale for further testing LAG3 DNA methylation as a predictive biomarker for response to LAG3 immune checkpoint inhibitors.
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Affiliation(s)
- Niklas Klümper
- Department of Urology, University Hospital Bonn, Bonn, Germany.,Center for Integrated Oncology Aachen/Bonn/Cologne/Dusseldorf, University Hospital Bonn, Bonn, Germany.,Institute for Experimental Oncology, University Hospital Bonn, Bonn, Germany
| | - Damian J Ralser
- Center for Integrated Oncology Aachen/Bonn/Cologne/Dusseldorf, University Hospital Bonn, Bonn, Germany.,Department of Obstetrics and Gynecology, University Hospital of Bonn, Bonn, Germany
| | - Emma Grace Bawden
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Jenny Landsberg
- Center for Integrated Oncology Aachen/Bonn/Cologne/Dusseldorf, University Hospital Bonn, Bonn, Germany.,Department of Dermatology, University Hospital Bonn, Bonn, Germany
| | - Romina Zarbl
- Center for Integrated Oncology Aachen/Bonn/Cologne/Dusseldorf, University Hospital Bonn, Bonn, Germany.,Department of Otolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
| | - Glen Kristiansen
- Center for Integrated Oncology Aachen/Bonn/Cologne/Dusseldorf, University Hospital Bonn, Bonn, Germany.,Institute of Pathology, University Hospital Bonn, Bonn, Germany
| | - Marieta Toma
- Center for Integrated Oncology Aachen/Bonn/Cologne/Dusseldorf, University Hospital Bonn, Bonn, Germany.,Institute of Pathology, University Hospital Bonn, Bonn, Germany
| | - Manuel Ritter
- Department of Urology, University Hospital Bonn, Bonn, Germany.,Center for Integrated Oncology Aachen/Bonn/Cologne/Dusseldorf, University Hospital Bonn, Bonn, Germany
| | - Michael Hölzel
- Center for Integrated Oncology Aachen/Bonn/Cologne/Dusseldorf, University Hospital Bonn, Bonn, Germany.,Institute for Experimental Oncology, University Hospital Bonn, Bonn, Germany
| | - Jörg Ellinger
- Department of Urology, University Hospital Bonn, Bonn, Germany.,Center for Integrated Oncology Aachen/Bonn/Cologne/Dusseldorf, University Hospital Bonn, Bonn, Germany
| | - Dimo Dietrich
- Center for Integrated Oncology Aachen/Bonn/Cologne/Dusseldorf, University Hospital Bonn, Bonn, Germany .,Department of Otolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
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5
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Bian X, Cao F, Wang X, Hou Y, Zhao H, Liu Y. Establishment and characterization of a new human colon cancer cell line, PUMC-CRC1. Sci Rep 2021; 11:13122. [PMID: 34162944 PMCID: PMC8222262 DOI: 10.1038/s41598-021-92491-7] [Citation(s) in RCA: 3] [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: 01/21/2021] [Accepted: 04/22/2021] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most common and fatal gastrointestinal cancers worldwide. Considering their diversity, the establishment of new continuous CRC cell lines with clear genetic backgrounds will provide useful tools for exploring molecular mechanisms, screening and evaluating antitumor drugs in CRC studies. Our de novo CRC cell line, PUMC-CRC1 (Peking Union Medical College Colorectal Cancer 1) was derived from a 47-year-old Chinese female patient diagnosed with moderately to poorly differentiated colon adenocarcinoma. Multiple experiments were used for full characterization. The new cell line was epithelial-like and was passaged for more than 40 times, with a population doubling time of 44 h in vitro, detected by cell counts. The cells exhibited complicated chromosomal abnormalities. The tumor formation rate in SCID mice was 100%. The xenograft tumor was adenocarcinoma with poor to moderate differentiation by Haematoxylin and Eosin staining (H&E) sections. Immunohistochemistry (IHC) analysis and next-generation sequencing (NGS) revealed microsatellite stable (MSS), APC (p.T1493fs) inactivation, KRAS (p.G12V) activation, and SMAD4 (p.V506A) mutation. Quality control of the cell line proved mycoplasma negative and identical STR profile with that of the original tissue, and no interspecific or intraspecific cross contamination was detected. In conclusion, PUMC-CRC1 was a newly established and well characterized human colon cancer cell line, which might be a good model for both in vitro and in vivo studies of the mechanism of colon cancer progression and the treatment strategies for MSS CRC.
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Affiliation(s)
- Xiaocui Bian
- Department of Pathology, Cell Resource Center, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing, 100005, People's Republic of China
| | - Fang Cao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, 100142, People's Republic of China
| | - Xiaowan Wang
- Department of Pathology, Cell Resource Center, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing, 100005, People's Republic of China
| | - Yuhong Hou
- Department of Pathology, Cell Resource Center, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing, 100005, People's Republic of China
| | - Haitao Zhao
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, 100730, People's Republic of China.
| | - Yuqin Liu
- Department of Pathology, Cell Resource Center, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing, 100005, People's Republic of China.
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6
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Xia H, Hu F, Pan L, Xu C, Huang H, Chen S, Ma H. FAM196B promotes proliferation and migration via regulating epithelial-mesenchymal transition in esophageal cancer. Cancer Biomark 2021; 31:39-46. [PMID: 33749638 DOI: 10.3233/cbm-203023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND EC (esophageal cancer) is a common cancer among people in the world. The molecular mechanism of FAM196B (family with sequence similarity 196 member B) in EC is still unclear. This article aimed to clarify the role of FAM196B in EC. METHODS The expression of FAM196B in EC tissues was detected using qRT-PCR. The prognosis of FAM196B in EC patients was determined by log-rank kaplan-Meier survival analysis and Cox regression analysis. Furthermore, shRNA was used to knockdown the expression of FAM196B in EC cell lines. MTT, wound healing assays and western blot were used to determine the role of FAM196B in EC cells. RESULTS In our research, we found that the expression of FAM196B was up-regulated in EC tissues. The increased expression of FAM196B was significantly correlated with differentiation, lymph node metastasis, stage, and poor survival. The proliferation and migration of EC cells were inhibited after FAM196B-shRNA transfection in vitro and vivo. The western blot result showed that FAM196B could regulate EMT. CONCLUSION These results suggested that FAM196B severs as an oncogene and promotes cell proliferation and migration in EC. In addition, FAM196B may be a potential therapeutic target for EC patients.
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Affiliation(s)
- Haifeng Xia
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China.,Department of Cardiothoracic Surgery, Suzhou Dushuhu Public Hospital, Suzhou, Jiangsu, China.,Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Fang Hu
- Suzhou Kintor Pharmaceutical Limited, Suzhou, Jiangsu, China.,Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Liangbin Pan
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China.,Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Chengcheng Xu
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Haitao Huang
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Shaomu Chen
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Haitao Ma
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
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7
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Li SL, Jiang TQ, Cao QW, Liu SM. Transmembrane protein ADAM29 facilitates cell proliferation, invasion and migration in clear cell renal cell carcinoma. J Chemother 2020; 33:40-50. [PMID: 33164721 DOI: 10.1080/1120009x.2020.1842035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Abnormal expression of ADAM29 has been frequently reported in several cancers, however, its role in clear cell renal cell carcinoma (ccRCC) has not evaluated in detail. Herein, we attempt to determine the biological role and the action mechanism of ADAM29 in ccRCC. Bioinformatics analysis based on the ccRCC RNA-Seq dataset from TCGA database revealed that ADAM29 was up-expressed in ccRCC tissues by comparison with normal tissues. And a significant increase of ADAM29 expression was also observed in 3 ccRCC cell lines (UT33A, Caki-1, and786-O) in comparison with normal cell line. Besides, high level of ADAM29 was found to be connected with the poor prognosis and could be considered as an independent prognosticator for patients with ccRCC. Furthermore, functional experiments in vitro demonstrated that ADAM29 promoted the growth, invasion and migration of ccRCC cells. Moreover, Western blot assays indicated that ADAM29 was positively correlated with the level of proliferation-related proteins Cyclin D1 and PCNA and motion-related proteins MMP9 and Snail. Our data indicate that ADAM29 acts as an oncogene that increases tumour cells proliferation, invasion and migration partly by regulating the expression of Cyclin D1/PCNA/MMP9/Snail, suggesting that ADAM29 may become a prognosticator and therapeutic candidate for ccRCC.
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Affiliation(s)
- Shun-Lai Li
- Department of Urology, The Fifth People's Hospital of Jinan, Jinan, P.R. China
| | - Ting-Qi Jiang
- Department of Urology, The Fifth People's Hospital of Jinan, Jinan, P.R. China
| | - Qing-Wei Cao
- Department of Urology, Shandong Provincial Hospital, Jinan, Shandong, P.R. China
| | - Shan-Mei Liu
- Department of Urology, The Fifth People's Hospital of Jinan, Jinan, P.R. China
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8
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Mini E, Lapucci A, Perrone G, D'Aurizio R, Napoli C, Brugia M, Landini I, Tassi R, Picariello L, Simi L, Mancini I, Messerini L, Magi A, Pinzani P, Mazzei T, Tonelli F, Nobili S. RNA sequencing reveals PNN and KCNQ1OT1 as predictive biomarkers of clinical outcome in stage III colorectal cancer patients treated with adjuvant chemotherapy. Int J Cancer 2019; 145:2580-2593. [PMID: 30973654 DOI: 10.1002/ijc.32326] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 03/13/2019] [Accepted: 04/01/2019] [Indexed: 12/16/2022]
Abstract
Five-year overall survival of stage III colorectal cancer (CRC) patients treated with standard adjuvant chemotherapy (ACHT) is highly variable. Genomic biomarkers and/or transcriptomic profiles identified lack of adequate validation. Aim of our study was to identify and validate molecular biomarkers predictive of ACHT response in stage III CRC patients by a transcriptomic approach. From a series of CRC patients who received ACHT, two stage III extreme cohorts (unfavorable vs. favorable prognosis) were selected. RNA-sequencing was performed from fresh frozen explants. Tumors were characterized for somatic mutations. Validation was performed in stage III CRC patients extracted from two GEO datasets. According to disease-free survival (DFS), 108 differentially expressed genes (104/4 up/downregulated in the unfavorable prognosis group) were identified. Among 104 upregulated genes, 42 belonged to olfactory signaling pathways, 62 were classified as pseudogenes (n = 17), uncharacterized noncoding RNA (n = 10), immune response genes (n = 4), microRNA (n = 1), cancer-related genes (n = 14) and cancer-unrelated genes (n = 16). Three out of four down-regulated genes were cancer-related. Mutational status (i.e., RAS, BRAF, PIK3CA) did not differ among the cohorts. In the validation cohort, multivariate analysis showed high PNN and KCNQ1OT1 expression predictive of shorter DFS in ACHT treated patients (p = 0.018 and p = 0.014, respectively); no difference was observed in untreated patients. This is the first study that identifies by a transcriptomic approach and validates PNN and KCNQ1OT1 as molecular biomarkers predictive of chemotherapy response in stage III CRC patients. After a further validation in an independent cohort, PNN and KCNQ1OT1 evaluation could be proposed to prospectively identify stage III CRC patients benefiting from ACHT.
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Affiliation(s)
- Enrico Mini
- Department of Health Sciences, University of Florence, Florence, Italy.,DENOTHE Excellence Center, University of Florence, Florence, Italy
| | - Andrea Lapucci
- Department of Health Sciences, University of Florence, Florence, Italy.,DENOTHE Excellence Center, University of Florence, Florence, Italy
| | - Gabriele Perrone
- Department of Health Sciences, University of Florence, Florence, Italy.,DENOTHE Excellence Center, University of Florence, Florence, Italy
| | - Romina D'Aurizio
- Institute of Informatics and Telematics (IIT), National Research Council (CNR), Pisa, Italy
| | - Cristina Napoli
- Department of Health Sciences, University of Florence, Florence, Italy.,DENOTHE Excellence Center, University of Florence, Florence, Italy
| | - Marco Brugia
- Department of Health Sciences, University of Florence, Florence, Italy
| | - Ida Landini
- Department of Health Sciences, University of Florence, Florence, Italy.,DENOTHE Excellence Center, University of Florence, Florence, Italy
| | - Renato Tassi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Lucia Picariello
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Lisa Simi
- Molecular and Clinical Biochemistry Laboratory, Careggi University Hospital, Florence, Italy
| | - Irene Mancini
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Luca Messerini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Alberto Magi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Pamela Pinzani
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy.,Molecular and Clinical Biochemistry Laboratory, Careggi University Hospital, Florence, Italy
| | - Teresita Mazzei
- Department of Health Sciences, University of Florence, Florence, Italy
| | - Francesco Tonelli
- Department of Surgery and Translational Medicine, University of Florence, Florence, Italy
| | - Stefania Nobili
- Department of Health Sciences, University of Florence, Florence, Italy.,DENOTHE Excellence Center, University of Florence, Florence, Italy
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9
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Feng Y, Tong X, Zhang B, Mao G, Huang H, Ma H. Effect of FAM196B in human lung adenocarcinoma. J Cancer 2018; 9:2451-2459. [PMID: 30026842 PMCID: PMC6036892 DOI: 10.7150/jca.24907] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 04/11/2018] [Indexed: 12/13/2022] Open
Abstract
Lung cancer is the leading cause of cancer-related mortality worldwide. The present study focused on the function of family with sequence similarity 196 member B (FAM196B) in lung adenocarcinoma (LUAD). We analyzed lung carcinoma patients' data from the Cancer Genome Atlas (TCGA), and verify the change of FAM196B expression in 30 LUAD tissues and matched adjacent non-tumor tissues (> 5 cm) by tissue microarray. To investigate the role of FAM196B in LUAD, we used lentivirus-mediated short hairpin RNA (shRNA) to knockdown FAM196B expression in human LUAD cell line A549 and H1299 and assessed it by RT-qPCR and western blot. Celigo Imaging Cytometry System, MTT assays and colony formation were conducted to evaluate cell proliferation. Cell apoptosis were assayed by Annexin V staining. We found that FAM196B was significantly upregulated (P=5.06E-06) in LUAD compared with adjacent non-tumor tissues. Cell proliferation was inhibited in FAM196B-silenced A549 and H1299 cells using Celigo Imaging Cytometry System, MTT assays and colony formation assays. Apoptosis rate was significantly increased in FAM196B-shRNA group than the control group. In conclusion, Knockdown of FAM196B can inhibit cell proliferation, cell colony formation capacity, and promote cell apoptosis in A549 and H1299 cell lines. FAM196B may be one novel potential targets for treating patients with LUAD.
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Affiliation(s)
- Yu Feng
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215000, China
| | - Xing Tong
- Department of Pathology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215000, China
| | - Biao Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215000, China
| | - Guocai Mao
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215000, China
| | - Haitao Huang
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215000, China
| | - Haitao Ma
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215000, China
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10
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Solute carrier family 34 member 2 overexpression contributes to tumor growth and poor patient survival in colorectal cancer. Biomed Pharmacother 2018; 99:645-654. [PMID: 29653487 DOI: 10.1016/j.biopha.2018.01.124] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 01/14/2018] [Accepted: 01/24/2018] [Indexed: 02/07/2023] Open
Abstract
Solute carrier family 34 member 2 (SLC34A2) is a well-known sodium-dependent phosphate transporter that has recently been linked to cancer development. However, its specific oncogenic role remains controversial in numerous human malignancies, and is currently unknown in colorectal cancer (CRC). Therefore, in this study we firstly used Oncomine database to determine its expression in cancer tissues and found it is overexpressed in thyroid, ovarian and renal cancer, while it is opposite in lung, breast and pancreas cancer. Using qRT-PCR and western blot, we then demonstrated its overexpression in CRC tissues as compared with adjacent normal tissues (n = 20). In a retrospective cohort enrolling 190 CRC patients, we proved its expression was significantly correlated with N stage. Furthermore, high SLC34A2 expression is associated with higher postoperative metastasis rate and serves as an independent adverse factor affecting patient prognosis. In subgroup analysis, SLC34A2 expression could stratify the patient prognosis in stage II and III CRC, but failed in stage IV CRC. In cellular assays in vitro, knockdown of SLC34A2 dramatically inhibited the proliferation and colony formation, induced the apoptosis and arrests the cell cycle progression of HCT-116 CRC cells. In cellular assays in vivo, knockdown of SLC34A2 significantly inhibited the growth of xenografts, decreasing Ki-67 and proliferating cell nuclear antigen (PCNA) expression and increasing apoptosis rate. Taken together, our study indicates SLC34A2 plays a crucial promoting role in CRC development and therefore has great potential to be further developed as a reliable biomarker for CRC diagnosis and treatment.
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11
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Torres-Ruiz R, Rodriguez-Perales S, Bueno C, Menendez P. Modeling mixed-lineage-rearranged leukemia initiation in CD34 + cells: a "CRISPR" solution. Haematologica 2017; 102:1467-1468. [PMID: 28860233 DOI: 10.3324/haematol.2017.173740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Raúl Torres-Ruiz
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain .,Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain
| | - Sandra Rodriguez-Perales
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
| | - Clara Bueno
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBER-ONC), ISCIII, Barcelona, Spain
| | - Pablo Menendez
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain .,Centro de Investigación Biomédica en Red de Cáncer (CIBER-ONC), ISCIII, Barcelona, Spain.,Instituciò Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluis Companys, Barcelona, Spain
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