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Ludwig M, Birkeland A, Smith J, Gensterblum-Miller E, Zhai JI, Kulkarni A, Jiang H, Brenner C. A Genome Wide CRISPR Pro filing Approach Identi fies Mechanisms of Cisplatin Resistance in Head and Neck Squamous Cell Carcinoma. RESEARCH SQUARE 2024:rs.3.rs-3922565. [PMID: 38464196 PMCID: PMC10925415 DOI: 10.21203/rs.3.rs-3922565/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Background Head and neck squamous cell carcinoma (HNSCC) is a lethal disease with poor survival rates, especially for cancers arising in the oral cavity or larynx. Cisplatin is a key chemotherapeutic for HNSCC; however poor survival rates may be partially due to cisplatin resistance observed in some HNSCCs. Here, we examined the utility of genome-wide CRISPR knockout profiling for nominating pivotal mechanisms of cisplatin resistance in HNSCC models. Methods We characterized the cisplatin sensitivity of 18 HNSCC cell lines. Next, we used a genome-wide CRISPR/Cas9 library to identify genes involved in cisplatin resistance. We next performed validation assays in the UM-SCC-49 cell line model. Results Our data prioritized 207 genes as pivotal for cisplatin resistance in HNSCC, including novel genes VGLL3, CIRHA1, NCOR1, SPANXA1, MAP2K7, ULK1, and CDK16. Gene set enrichment analysis identified several NOTCH family genes comprising the top pathway driving cisplatin resistance, which we then validated using a targeted NOTCH1 knockout model. Interestingly, we noted that HNSCC models with natural NOTCH pathway alterations including single allele mutations and/or frameshift alterations had diverse responses to cisplatin treatment suggesting that complex and multi-faceted mechanisms contribute to cisplatin resistance in HNSCC. Conclusions Collectively, our study validates a genome-wide CRISPR/Cas9 approach for the discovery of resistance mechanisms in HNSCC, adds to the growing evidence that NOTCH1 status should be evaluated as a biomarker of cisplatin response and provides a framework for future work aimed at overcoming cisplatin resistance.
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Qiu J, Wang Z, Xu Y, Zhao L, Zhang P, Gao H, Wang Q, Xia Q. Low expression of SLC34A1 is associated with poor prognosis in clear cell renal cell carcinoma. BMC Urol 2023; 23:45. [PMID: 36978048 PMCID: PMC10044763 DOI: 10.1186/s12894-023-01212-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
OBJECTIVE Clear cell renal cell carcinoma (ccRCC) is a malignant renal tumor that is highly prone to metastasis and recurrence. The exact pathogenesis of this cancer is still not well understood. This study aimed to identify novel hub genes in renal clear cell carcinoma and determine their diagnostic and prognostic value. METHODS Intersection genes were obtained from multiple databases, and protein-protein interaction analysis and functional enrichment analysis were performed to identify key pathways related to the intersection genes. Hub genes were identified using the cytoHubba plugin in Cytoscape. GEPIA and UALCAN were utilized to observe differences in mRNA and protein expression of hub genes between KIRC and adjacent normal tissues. The Wilcoxon rank sum test was used to analyze hub gene levels between paired KIRC and matched non-cancer samples. IHC results were obtained from the HPA online database, and according to the median gene expression level, they were divided into a high-expression group and a low-expression group. The correlation of these groups with the prognosis of KIRC patients was analyzed. Logistic regression and the Wilcoxon rank sum test were used to test the relationship between SLC34A1 level and clinicopathological features. The diagnostic value of SLC34A1 was evaluated by drawing the receiver operating characteristic (ROC) curve and calculating the area under the curve (AUC). Cox regression analysis was used to analyze the relationship between clinicopathological features, SLC34A1 expression, and KIRC survival rate. LinkedOmics was used to obtain the genes most related to SLC34A1 and their functional enrichment. Genetic mutations and methylation levels of SLC34A1 in KIRC were obtained from the cBioPortal website and the MethSurv website, respectively. RESULTS Fifty-eight ccRCC differential genes were identified from six datasets, and they were mainly enriched in 10 functional items and 4 pathways. A total of 5 hub genes were identified. According to the GEPIA database analysis, low expression of SLC34A1, CASR, and ALDOB in tumors led to poor prognosis. Low expression of SLC34A1 mRNA was found to be related to clinicopathological features of patients. SLC34A1 expression in normal tissues could accurately identify tumors (AUC 0.776). SLC34A1 was also found to be an independent predictor of ccRCC in univariate and multivariate Cox analyses. The mutation rate of the SLC34A1 gene was 13%. Eight of the 10 DNA methylated CpG sites were associated with the prognosis of ccRCC. SLC34A1 expression in ccRCC was positively correlated with B cells, eosinophils, neutrophils, T cells, TFH, and Th17 cells, and negatively correlated with Tem, Tgd, and Th2 cells. CONCLUSION The expression level of SLC34A1 in KIRC samples was found to be decreased, which predicted a decreased survival rate of KIRC. SLC34A1 may serve as a molecular prognostic marker and therapeutic target for KIRC patients.
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Affiliation(s)
- Jiechuan Qiu
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 9677 Jingshidong Road, Jinan City, 250001, Shandong Province, China
| | - Zicheng Wang
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 9677 Jingshidong Road, Jinan City, 250001, Shandong Province, China
| | - Yingkun Xu
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400042, China
| | - Leizuo Zhao
- Department of Urology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, China
- Department of Urology, Dongying People's Hospital, Dongying, 257000, China
| | - Peizhi Zhang
- Department of Urology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, China
| | - Han Gao
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 9677 Jingshidong Road, Jinan City, 250001, Shandong Province, China
| | - Qingliang Wang
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 9677 Jingshidong Road, Jinan City, 250001, Shandong Province, China
| | - Qinghua Xia
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 9677 Jingshidong Road, Jinan City, 250001, Shandong Province, China.
- Department of Urology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, China.
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The c-MYC-WDR43 signalling axis promotes chemoresistance and tumour growth in colorectal cancer by inhibiting p53 activity. Drug Resist Updat 2023; 66:100909. [PMID: 36525936 DOI: 10.1016/j.drup.2022.100909] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/27/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022]
Abstract
Oxaliplatin chemoresistance is a major challenge in the clinical treatment of colorectal cancer (CRC), which is one of the most common malignancies worldwide. In this study, we identified the tryptophan-aspartate repeat domain 43 (WDR43) as a potentially critical oncogenic factor in CRC pathogenesis through bioinformatics analysis. It was found that WDR43 is highly expressed in CRC tissues, and WDR43 overexpression is associated with poor prognosis of CRC patients. WDR43 knockdown significantly inhibits cell growth by arresting cell cycle and enhancing the effect of oxaliplatin chemotherapy both in vitro and in vivo. Mechanistically, upon oxaliplatin stimulation, c-MYC promotes the transcriptional regulation and expression of WDR43. WDR43 enhances the ubiquitination of p53 by MDM2 through binding to RPL11, thereby reducing the stability of the p53 protein, which induces proliferation and chemoresistance of CRC cells. Thus, the overexpression of WDR43 promotes CRC progression, and could be a potential therapeutic target of chemoresistance in CRC.
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Munro MJ, Wickremesekera SK, Tan ST, Peng L. Proteomic analysis of low- and high-grade human colon adenocarcinoma tissues and tissue-derived primary cell lines reveals unique biological functions of tumours and new protein biomarker candidates. Clin Proteomics 2022; 19:27. [PMID: 35842572 PMCID: PMC9287856 DOI: 10.1186/s12014-022-09364-y] [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: 03/04/2022] [Accepted: 06/22/2022] [Indexed: 11/10/2022] Open
Abstract
Background Colon cancer is the third most common cancer and second highest cause of cancer deaths worldwide. The aim of the study was to find new biomarkers for diagnosis, prognosis and therapeutic drug targets for this disease. Methods Four low-grade and four high-grade human colon adenocarcinoma tumours with patient-matched normal colon tissues were analysed. Additionally, tissue-derived primary cell lines were established from each tumour tissue. The cell lines were validated using DNA sequencing to confirm that they are a suitable in vitro model for colon adenocarcinoma based on conserved gene mutations. Label-free quantitation proteomics was performed to compare the proteomes of colon adenocarcinoma samples to normal colon samples, and of colon adenocarcinoma tissues to tissue-derived cell lines to find significantly differentially abundant proteins. The functions enriched within the differentially expressed proteins were assessed using STRING. Proteomics data was validated by Western blotting. Results A total of 4767 proteins were identified across all tissues, and 4711 across primary tissue-derived cell lines. Of these, 3302 proteins were detected in both the tissues and the cell lines. On average, primary cell lines shared about 70% of proteins with their parent tissue, and they retained mutations to key colon adenocarcinoma-related genes and did not diverge far genetically from their parent tissues. Colon adenocarcinoma tissues displayed upregulation of RNA processing, steroid biosynthesis and detoxification, and downregulation of cytoskeletal organisation and loss of normal muscle function. Tissue-derived cell lines exhibited increased interferon-gamma signalling and aberrant ferroptosis. Overall, 318 proteins were significantly up-regulated and 362 proteins significantly down-regulated by comparisons of high-grade with low-grade tumours and low-grade tumour with normal colon tissues from both sample types. Conclusions The differences exhibited between tissues and cell lines highlight the additional information that can be obtained from patient-derived primary cell lines. DNA sequencing and proteomics confirmed that these cell lines can be considered suitable in vitro models of the parent tumours. Various potential biomarkers for colon adenocarcinoma initiation and progression and drug targets were identified and discussed, including seven novel markers: ACSL4, ANK2, AMER3, EXOSC1, EXOSC6, GCLM, and TFRC. Supplementary Information The online version contains supplementary material available at 10.1186/s12014-022-09364-y.
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Affiliation(s)
- Matthew J Munro
- School of Biological Sciences and Centre for Biodiscovery, Victoria University of Wellington, Wellington, 6140, New Zealand.,Gillies McIndoe Research Institute, Newtown, PO Box 7184, Wellington, 6242, New Zealand
| | - Susrutha K Wickremesekera
- Gillies McIndoe Research Institute, Newtown, PO Box 7184, Wellington, 6242, New Zealand.,Upper Gastrointestinal, Hepatobiliary & Pancreatic Section, Department of General Surgery, Wellington Regional Hospital, Wellington, 6021, New Zealand
| | - Swee T Tan
- Gillies McIndoe Research Institute, Newtown, PO Box 7184, Wellington, 6242, New Zealand. .,Wellington Regional Plastic, Maxillofacial & Burns Unit, Hutt Hospital, Lower Hutt, 5040, New Zealand. .,Department of Surgery, The Royal Melbourne Hospital, The University of Melbourne, Melbourne, VIC, 3050, Australia.
| | - Lifeng Peng
- School of Biological Sciences and Centre for Biodiscovery, Victoria University of Wellington, Wellington, 6140, New Zealand.
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Gahoi N, Syed P, Choudhary S, Epari S, Moiyadi A, Varma SG, Gandhi MN, Srivastava S. A Protein Microarray-Based Investigation of Cerebrospinal Fluid Reveals Distinct Autoantibody Signature in Low and High-Grade Gliomas. Front Oncol 2020; 10:543947. [PMID: 33415070 PMCID: PMC7784397 DOI: 10.3389/fonc.2020.543947] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 10/23/2020] [Indexed: 11/13/2022] Open
Abstract
Gliomas are one of the most aggressive primary brain tumors arising from neural progenitor cells. Delayed diagnosis, invasive biopsy, and diagnostic challenges stems the need for specific, minimally-invasive, and early diagnostic biomarkers. Tumor-associated (TA) autoantibodies are measurable in the biofluids long before the onset of the symptoms, suggesting their role in early diagnosis and clinical management of the patients. In the current study, cerebrospinal fluid (CSF) samples from patients with low-grade glioma (LGG) and the Glioblastoma multiforme (GBM) that characterizes advanced disease were compared with healthy control samples to identify putative TA autoantibodies, using protein microarrays. The CSF samples from LGGs (n = 10), GBM (n = 7) were compared with the control CSF samples (n = 6). Proteins showing significant antigenic response were cross-verified. Proteins NOL4 (a cancer-testis antigen) and KALRN showed an antigenic response in the CSF of GBM patients, whereas, UTP4 and CCDC28A showed an antigenic response in low grade gliomas when compared with the control samples. TA autoantibodies identified in this study from the CSF of the patients could supplement current screening modalities. Further validation of these TA autoantibodies on a larger clinical cohort could provide cues towards relevance of these proteins in early diagnosis of the disease.
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Affiliation(s)
- Nikita Gahoi
- Wadhwani Research Center for Biosciences and Bioengineering, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India.,Centre for Research in Nanotechnology and Sciences, Indian Institute of Technology Bombay, Mumbai, India
| | - Parvez Syed
- Wadhwani Research Center for Biosciences and Bioengineering, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India.,Inme Oy, Turku, Finland
| | - Saket Choudhary
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India.,Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Sridhar Epari
- Department of Pathology, Tata Memorial Centre, Mumbai, India
| | - Aliasgar Moiyadi
- Neurosurgical Services, Department of Surgical Oncology, Tata Memorial Centre and Homi Bhabha National Institute, Mumbai, India
| | - Santosh G Varma
- Deptartment of Biochemistry, Grant Govt. Medical College and Sir JJ Group of Hospitals, Mumbai, India.,Department of Biochemistry, BJ Medical College and Sassoon Hospital, Pune, India
| | - Mayuri N Gandhi
- Centre for Research in Nanotechnology and Sciences, Indian Institute of Technology Bombay, Mumbai, India
| | - Sanjeeva Srivastava
- Wadhwani Research Center for Biosciences and Bioengineering, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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Qi Y, Qi H, Liu Z, He P, Li B. Bioinformatics Analysis of Key Genes and Pathways in Colorectal Cancer. J Comput Biol 2019; 26:364-375. [PMID: 30810359 DOI: 10.1089/cmb.2018.0237] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) is the third most prevalent cancer in the world. Although great progress has been made, the specific molecular mechanism remains unclear. This study aimed to explore the differentially expressed genes (DEGs) and underlying mechanisms of CRC using bioinformatics analysis. In this study, we identified a total of 1353 DEGs in the database of GSE113513, including 715 up- and 638 downregulated genes. Gene ontology analysis results showed that upregulated DEGs were significantly enriched in cell division, cell proliferation, and DNA replication. The downregulated DEGs were enriched in immune response, relation of cell growth and inflammatory response. The Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that upregulated DEGs were enriched in cell cycle and p53 signaling pathway, whereas the downregulated DEGs were enriched in drug metabolism, metabolism of xenobiotics by cytochrome P450, and nitrogen metabolism. A total of 124 up-key genes and 35 down-key genes were identified from the protein-protein interaction networks. Furthermore, we identified five up-modules (up-A, up-B, up-C, up-D, and up-E) and three down-modules (d-A, d-B, and d-C) by module analysis. The module up-A was enriched in sister chromatid cohesion, cell division, and mitotic nuclear division. Pathways associated with cell cycle, progesterone-mediated oocyte maturation, oocyte meiosis, and p53 signaling pathway. Whereas the d-A was mainly enriched in G-protein coupled receptor signaling pathway, cell chemotaxis, and chemokine-mediated signaling pathway. The pathways enriched in chemokine signaling pathway, cytokine-cytokine receptor interaction, and alcoholism. These key genes and pathways might be used as molecular targets and diagnostic biomarkers for the treatment of CRC.
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Affiliation(s)
- Yuewen Qi
- 1 Department of Gastroenterology, Affiliated Hospital of Chengde Medical College, Chengde, P.R. China
| | - Haowen Qi
- 2 Department of Acupuncture and Massage, Chengde Hospital of Traditional Chinese Medicine, Chengde, P.R. China
| | - Zeyuan Liu
- 3 Department of Special Medicine, Qingdao University Medical College, Qingdao, P.R. China
| | - Peiyuan He
- 1 Department of Gastroenterology, Affiliated Hospital of Chengde Medical College, Chengde, P.R. China
| | - Bingqing Li
- 1 Department of Gastroenterology, Affiliated Hospital of Chengde Medical College, Chengde, P.R. China
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Yuan Y, Qi G, Shen H, Guo A, Cao F, Zhu Y, Xiao C, Chang W, Zheng S. Clinical significance and biological function of WD repeat domain 54 as an oncogene in colorectal cancer. Int J Cancer 2018; 144:1584-1595. [PMID: 29987896 DOI: 10.1002/ijc.31736] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 05/29/2018] [Accepted: 06/20/2018] [Indexed: 01/23/2023]
Abstract
In recent years, protein-protein interactions have become an attractive candidate for identifying biomarkers and drug targets for various diseases. However, WD40 repeat (WDR) domain proteins, some of the most abundant mediators of protein interactions, are largely unexplored. In our study, 57 of 361 known WDR proteins were identified as hub nodes, and a hub (WDR54) with elevated mRNA in colorectal cancer (CRC) was selected for further study. Immunohistochemistry of specimens from 945 patients confirmed the elevated expression of WDR54 in CRC, and we found that patients with WDR54-high tumors typically had a shorter disease-specific survival (DSS) than those with WDR54-low tumors, especially for the subgroup without well-differentiated tumors. Multivariate analysis showed that WDR54-high tumors were an independent risk factor for DSS, with a hazard ratio of 2.981 (95% confidence interval, 1.425-6.234; p = 0.004). Knockdown of WDR54 significantly inhibited the growth and aggressiveness of CRC cells and reduced tumor growth in a xenograft model. Each WDR54 isoform (a, b, and c) was found to reverse the inhibitory effect of WDR54 knockdown; however, only isoform c, which exhibited the highest expression, was increased in CRC cells. Sensitization of WDR54 knockdown to an SHP2 inhibitor was consistently found in CRC cells, and the underlying mechanism involved their common function in regulating AKT and ERK signaling. In conclusion, the present study is the first to investigate the significance of WDR54 in cancer and to conclude that WDR54 serves as an oncogene in CRC and may be a potential prognostic marker and therapeutic target.
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Affiliation(s)
- Yuncang Yuan
- School of Medicine, Yunnan University, Kunming, China
- Department of Environmental Hygiene, Second Military Medical University, Shanghai, China
| | - Guoxiang Qi
- School of Medicine, Yunnan University, Kunming, China
- Department of Environmental Hygiene, Second Military Medical University, Shanghai, China
| | - Hao Shen
- Department of Environmental Hygiene, Second Military Medical University, Shanghai, China
| | - Aizhen Guo
- Department of General Practice, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China
| | - Fuao Cao
- Department of Colorectal Surgery, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Yan Zhu
- Department of Pathology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Chunjie Xiao
- School of Medicine, Yunnan University, Kunming, China
| | - Wenjun Chang
- Department of Environmental Hygiene, Second Military Medical University, Shanghai, China
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