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Bayat L, Abbasi S, Balasuriya N, Schild-Poulter C. Critical residues in the Ku70 von Willebrand A domain mediate Ku interaction with the LigIV-XRCC4 complex in non-homologous end-joining. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119815. [PMID: 39151475 DOI: 10.1016/j.bbamcr.2024.119815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 08/02/2024] [Accepted: 08/09/2024] [Indexed: 08/19/2024]
Abstract
The Ku heterodimer (Ku70/Ku80) is central to the non-homologous end-joining (NHEJ) pathway. Ku binds to the broken DNA ends and promotes the assembly of the DNA repair complex. The N-terminal Ku70 von Willebrand A (vWA) domain is known to mediate protein-protein interactions important for the repair process. In particular, the D192 and D195 residues within helix 5 of the Ku70 vWA domain were shown to be essential for NHEJ function, although the precise role of these residues was not identified. Here, we set up a miniTurbo screening system to identify Ku70 D192/D195 residue-specific interactors in a conditional, human Ku70-knockout cell line in response to DNA damage. Using fusion protein constructs of Ku70 wild-type and mutant (D192A/D195R) with miniTurbo, we identified a number of candidate proximal interactors in response to DNA damage treatment, including DNA Ligase IV (LigIV), a known and essential NHEJ complex member. Interestingly, LigIV was enriched in our wildtype screen but not the Ku70 D192A/D195R screen, suggesting its interaction is disrupted by the mutation. Validation experiments demonstrated that the DNA damage-induced interaction between Ku70 and LigIV was disrupted by the Ku70 D192A/D195R mutations. Our findings provide greater detail about the interaction surface between the Ku70 vWA domain and LigIV and offer strong evidence that the D192 and D195 residues are important for NHEJ completion through an interaction with LigIV. Altogether, this work reveals novel potential proximal interactors of Ku in response to DNA damage and identifies Ku70 D192/D195 residues as essential for LigIV interaction with Ku during NHEJ.
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Affiliation(s)
- Laila Bayat
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON N6A 5B7, Canada
| | - Sanna Abbasi
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON N6A 5B7, Canada
| | - Nileeka Balasuriya
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON N6A 5B7, Canada
| | - Caroline Schild-Poulter
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON N6A 5B7, Canada.
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Zhang Y, Yao L, Chung CR, Huang Y, Li S, Zhang W, Pang Y, Lee TY. KinPred-RNA-kinase activity inference and cancer type classification using machine learning on RNA-seq data. iScience 2024; 27:109333. [PMID: 38523792 PMCID: PMC10959666 DOI: 10.1016/j.isci.2024.109333] [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: 08/26/2023] [Revised: 12/07/2023] [Accepted: 02/21/2024] [Indexed: 03/26/2024] Open
Abstract
Kinases as important enzymes can transfer phosphate groups from high-energy and phosphate-donating molecules to specific substrates and play essential roles in various cellular processes. Existing algorithms for kinase activity from phosphorylated proteomics data are often costly, requiring valuable samples. Moreover, methods to extract kinase activities from bulk RNA sequencing data remain undeveloped. In this study, we propose a computational framework KinPred-RNA to derive kinase activities from bulk RNA-sequencing data in cancer samples. KinPred-RNA framework, using the extreme gradient boosting (XGBoost) regression model, outperforms random forest regression, multiple linear regression, and support vector machine regression models in predicting kinase activities from cancer-related RNA sequencing data. Efficient gene signatures from the LINCS-L1000 dataset were used as inputs for KinPred-RNA. The results highlight its potential to be related to biological function. In conclusion, KinPred RNA constitutes a significant advance in cancer research by potentially facilitating the identification of cancer.
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Affiliation(s)
- Yuntian Zhang
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China
- School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Lantian Yao
- School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen 518172, China
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Chia-Ru Chung
- Department of Computer Science and Information Engineering, National Central University, Taoyuan 320953, Taiwan
| | - Yixian Huang
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China
- School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Shangfu Li
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Wenyang Zhang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Yuxuan Pang
- Division of Health Medical Intelligence, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Tzong-Yi Lee
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
- Center for Intelligent Drug Systems and Smart Bio-devices (IDSB), National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
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3
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Huang M, Wu Y, Li Y, Chen X, Feng J, Li Z, Li J, Chen J, Lu Y, Feng Y. Circadian clock-related genome-wide mendelian randomization identifies putatively genes for ulcerative colitis and its comorbidity. BMC Genomics 2024; 25:130. [PMID: 38302916 PMCID: PMC10832088 DOI: 10.1186/s12864-024-10003-z] [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: 11/22/2023] [Accepted: 01/10/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND Circadian rhythm is crucial to the function of the immune system. Disorders of the circadian rhythm can contribute to inflammatory diseases such as Ulcerative colitis (UC). This Mendelian Randomization (MR) analysis applies genetic tools to represent the aggregated statistical results of exposure to circadian rhythm disorders and UC and its comorbidities, allowing for causal inferences. METHODS Summary statistics of protein, DNA methylation and gene expression quantitative trait loci in individuals of European ancestry (pQTL, mQTL, and eQTL, respectively) were used. Genetic variants located within or near 152 circadian clock-related genes and closely related to circadian rhythm disorders were selected as instrumental variables. Causal relationships with UC and its comorbidities were then estimated through employed Summary data-based Mendelian Randomization (SMR) and Inverse-Variance-Weighted MR (IVW-MR). RESULTS Through preliminary SMR analysis, we identified a potential causal relationship between circadian clock-related genes and UC along with its comorbidities, which was further confirmed by IVW-MR analysis. Our study identified strong evidence of positive correlation involving seven overlapping genes (CSNK1E, OPRL1, PIWIL2, RORC, MAX, PPP5C, and AANAT) through MWAS and TWAS in UC, four overlapping genes (OPRL1, CHRNB2, FBXL17, and SIRT1) in UC with PSC, and three overlapping genes (ARNTL, USP7, and KRAS) in UC with arthropathy. CONCLUSIONS This SMR study demonstrates the causal effect of circadian rhythm disorders in UC and its comorbidities. Furthermore, our investigation pinpointed candidate genes that could potentially serve as drug targets.
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Affiliation(s)
- Mengfen Huang
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yuan Wu
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yiting Li
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xueru Chen
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jieni Feng
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zuming Li
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jiqiang Li
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou, China.
| | - Jiankun Chen
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou, China.
| | - Yue Lu
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou, China.
| | - Yan Feng
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou, China.
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4
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Burger KL, Fernandez MR, Meads MB, Sudalagunta P, Oliveira PS, Renatino Canevarolo R, Alugubelli RR, Tungsevik A, De Avila G, Silva M, Graeter AI, Dai HA, Vincelette ND, Prabhu A, Magaletti D, Yang C, Li W, Kulkarni A, Hampton O, Koomen JM, Roush WR, Monastyrskyi A, Berglund AE, Silva AS, Cleveland JL, Shain KH. CK1δ and CK1ε Signaling Sustains Mitochondrial Metabolism and Cell Survival in Multiple Myeloma. Cancer Res 2023; 83:3901-3919. [PMID: 37702657 PMCID: PMC10690099 DOI: 10.1158/0008-5472.can-22-2350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 06/09/2023] [Accepted: 09/08/2023] [Indexed: 09/14/2023]
Abstract
Multiple myeloma remains an incurable malignancy due to acquisition of intrinsic programs that drive therapy resistance. Here we report that casein kinase-1δ (CK1δ) and CK1ε are therapeutic targets in multiple myeloma that are necessary to sustain mitochondrial metabolism. Specifically, the dual CK1δ/CK1ε inhibitor SR-3029 had potent in vivo and ex vivo anti-multiple myeloma activity, including against primary multiple myeloma patient specimens. RNA sequencing (RNA-seq) and metabolic analyses revealed inhibiting CK1δ/CK1ε disables multiple myeloma metabolism by suppressing genes involved in oxidative phosphorylation (OxPhos), reducing citric acid cycle intermediates, and suppressing complexes I and IV of the electron transport chain. Finally, sensitivity of multiple myeloma patient specimens to SR-3029 correlated with elevated expression of mitochondrial genes, and RNA-seq from 687 multiple myeloma patient samples revealed that increased CSNK1D, CSNK1E, and OxPhos genes correlate with disease progression and inferior outcomes. Thus, increases in mitochondrial metabolism are a hallmark of multiple myeloma progression that can be disabled by targeting CK1δ/CK1ε. SIGNIFICANCE CK1δ and CK1ε are attractive therapeutic targets in multiple myeloma whose expression increases with disease progression and connote poor outcomes, and that are necessary to sustain expression of genes directing OxPhos.
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Affiliation(s)
- Karen L. Burger
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Mario R. Fernandez
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Mark B. Meads
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Praneeth Sudalagunta
- Department of Metabolism & Physiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Paula S. Oliveira
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Rafael Renatino Canevarolo
- Department of Metabolism & Physiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | | | - Alexandre Tungsevik
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Gabe De Avila
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Maria Silva
- Department of Metabolism & Physiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Allison I. Graeter
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | | | - Nicole D. Vincelette
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Antony Prabhu
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Dario Magaletti
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Chunying Yang
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Weimin Li
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | | | | | - John M. Koomen
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | | | - Andrii Monastyrskyi
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Anders E. Berglund
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Ariosto S. Silva
- Department of Metabolism & Physiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - John L. Cleveland
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Kenneth H. Shain
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
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Zhu H, Chen J, Wen Z, Li J, Yu Q, Liao W, Luo X. The role of circadian clock genes in colorectal carcinoma: Novel insights into regulatory mechanism and implications in clinical therapy. Life Sci 2023; 333:122145. [PMID: 37797685 DOI: 10.1016/j.lfs.2023.122145] [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: 08/03/2023] [Revised: 09/23/2023] [Accepted: 10/02/2023] [Indexed: 10/07/2023]
Abstract
Colorectal cancer (CRC) is a lethal malignancy with limited treatment strategies. Accumulating evidence indicates that CRC tumorigenesis, progression and metastasis are intimately associated with circadian clock, an inherent 24-h cycle oscillation of biochemical, physiological functions in almost every eukaryote. In the present review, we summarize the altered expression level of circadian genes in CRC and the prognosis associated with gene abundance switch. We illustrate the function and potential mechanisms of circadian genes in CRC pathogenesis and progression. Moreover, circadian based-therapeutic strategies including chronotherapy, therapeutics targeting potential circadian components, and melatonin treatment in CRC are also highlighted.
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Affiliation(s)
- Haodong Zhu
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Radiology, Xiangya Hospital, Central South University, Changsha, Hunan 410078, PR China; Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan 410078, PR China
| | - Jiawei Chen
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Radiology, Xiangya Hospital, Central South University, Changsha, Hunan 410078, PR China; Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan 410078, PR China
| | - Zeqin Wen
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha, Hunan 410078, PR China
| | - Jinfei Li
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Radiology, Xiangya Hospital, Central South University, Changsha, Hunan 410078, PR China; Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan 410078, PR China
| | - Qinyang Yu
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Radiology, Xiangya Hospital, Central South University, Changsha, Hunan 410078, PR China; Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan 410078, PR China
| | - Weihua Liao
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Radiology, Xiangya Hospital, Central South University, Changsha, Hunan 410078, PR China
| | - Xiangjian Luo
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Radiology, Xiangya Hospital, Central South University, Changsha, Hunan 410078, PR China; Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan 410078, PR China; Key Laboratory of Biological Nanotechnology of National Health Commission, Central South University, Changsha, Hunan 410078, PR China; Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410078, PR China; Molecular Imaging Research Center of Central South University, Changsha, Hunan 410078, PR China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410078, PR China.
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6
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Shechter S, Ya'ar Bar S, Khattib H, Gage MJ, Avni D. Riok1, A Novel Potential Target in MSI-High p53 Mutant Colorectal Cancer Cells. Molecules 2023; 28:molecules28114452. [PMID: 37298928 DOI: 10.3390/molecules28114452] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/23/2023] [Accepted: 05/27/2023] [Indexed: 06/12/2023] Open
Abstract
The vulnerabilities of cancer cells constitute a promising strategy for drug therapeutics. This paper integrates proteomics, bioinformatics, and cell genotype together with in vitro cell proliferation assays to identify key biological processes and potential novel kinases that could account, at least in part, for the clinical differences observed in colorectal cancer (CRC) patients. This study started by focusing on CRC cell lines stratified by their microsatellite (MS) state and p53 genotype. It shows that cell-cycle checkpoint, metabolism of proteins and RNA, signal transduction, and WNT signaling processes are significantly more active in MSI-High p53-WT cell lines. Conversely, MSI-High cell lines with a mutant (Mut) p53 gene showed hyperactivation of cell signaling, DNA repair, and immune-system processes. Several kinases were linked to these phenotypes, from which RIOK1 was selected for additional exploration. We also included the KRAS genotype in our analysis. Our results showed that RIOK1's inhibition in CRC MSI-High cell lines was dependent on both the p53 and KRAS genotypes. Explicitly, Nintedanib showed relatively low cytotoxicity in MSI-High with both mutant p53 and KRAS (HCT-15) but no inhibition in p53 and KRAS WT (SW48) MSI-High cells. This trend was flipped in CRC MSI-High bearing opposite p53-KRAS genotypes (e.g., p53-Mut KRAS-WT or p53-WT KRAS-Mut), where observed cytotoxicity was more extensive compared to the p53-KRAS WT-WT or Mut-Mut cells, with HCT 116 (KRAS-Mut and p53-WT) being the most sensitive to RIOK1 inhibition. These results highlight the potential of our in silico computational approach to identify novel kinases in CRC sub-MSI-High populations as well as the importance of clinical genomics in determining drug potency.
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Affiliation(s)
- Sharon Shechter
- Department of Chemistry, University of Massachusetts Lowell, Lowell, MA 01854-2874, USA
| | - Sapir Ya'ar Bar
- Department of Natural Compound, Nutrition, and Health, MIGAL Galilee Research Institute, Kiryat Shmona 1101600, Israel
| | - Hamdan Khattib
- Department of Natural Compound, Nutrition, and Health, MIGAL Galilee Research Institute, Kiryat Shmona 1101600, Israel
| | - Matthew J Gage
- Department of Chemistry, University of Massachusetts Lowell, Lowell, MA 01854-2874, USA
| | - Dorit Avni
- Department of Natural Compound, Nutrition, and Health, MIGAL Galilee Research Institute, Kiryat Shmona 1101600, Israel
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Association of β-Catenin, APC, SMAD3/4, Tp53, and Cyclin D1 Genes in Colorectal Cancer: A Systematic Review and Meta-Analysis. Genet Res (Camb) 2022; 2022:5338956. [PMID: 36072013 PMCID: PMC9402361 DOI: 10.1155/2022/5338956] [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: 03/21/2022] [Accepted: 06/27/2022] [Indexed: 11/25/2022] Open
Abstract
Objectives Accumulating evidence indicates that the expression and/or variants of several genes play an essential role in the progress of colorectal cancer (CRC). The current study is a meta-analysis undertaken to estimate the prognosis and survival associated with CTNNB1/β-catenin, APC, Wnt, SMAD3/4, TP53, and Cyclin D1 genes among CRC patients. Methods The authors searched PubMed, EMBASE, and Science Direct for relevant reports published between 2000 and 2020 and analyzed them to determine any relationship between the (immunohistochemically/sequencing-detected) gene expression and variants of the selected genes and the survival of CRC patients. Results The analysis included 34,074 patients from 64 studies. To evaluate association, hazard ratios (HRs) were estimated for overall survival (OS) or disease-free survival (DFS), with a 95% confidence interval (CIs). Pooled results showed that β-catenin overexpression, APC mutation, SMAD-3 or 4 loss of expression, TP53 mutations, and Cyclin D1 expression were associated with shorter OS. β-Catenin overexpression (HR: 0.137 (95% CI: 0.131–0.406)), loss of expression of SMAD3 or 4 (HR: 0.449 (95% CI: 0.146–0.753)), the mutations of TP53 (HR: 0.179 (95% CI: 0.126–0.485)), and Cyclin D1 expression (HR: 0.485 (95% CI: 0.772–0.198)) also presented risk for shorter DFS. Conclusions The present meta-analysis indicates that overexpression or underexpression and variants of CTNNB1/β-catenin, APC, SMAD3/4, TP53, and Cyclin D1 genes potentially acted as unfavorable biomarkers for the prognosis of CRC. The Wnt gene was not associated with prognosis.
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Xu T, Jin T, Lu X, Pan Z, Tan Z, Zheng C, Liu Y, Hu X, Ba L, Ren H, Chen J, Zhu C, Ge M, Huang P. A signature of circadian rhythm genes in driving anaplastic thyroid carcinoma malignant progression. Cell Signal 2022; 95:110332. [DOI: 10.1016/j.cellsig.2022.110332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 04/07/2022] [Accepted: 04/11/2022] [Indexed: 01/02/2023]
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Characterization of Aging-Related Genes to Predict Prognosis and Evaluate the Tumor Immune Microenvironment in Malignant Melanoma. JOURNAL OF ONCOLOGY 2022; 2022:1271378. [PMID: 35368886 PMCID: PMC8970875 DOI: 10.1155/2022/1271378] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 01/25/2022] [Indexed: 12/18/2022]
Abstract
Objective. Malignant melanoma (MM) is one of the most malignant types of skin cancer and its incidence and mortality rates are increasing worldwide. Aging is well recognized as a significant risk factor for cancer. However, few studies have analyzed in depth the association between aging-related genes (AGs) and malignant melanoma prognosis with tumor immune microenvironment. Methods. Here, we downloaded 471 MM patients from The Cancer Genome Atlas (TCGA) with RNA sequence and clinicopathological data. 58 AGs from the TCGA dataset were examined using Cox regression and the LASSO assay. As a result, a gene signature for aging-related genes was created. The time-dependent ROC curve and Kaplan–Meier analysis were calculated to determine its predictive capability. Moreover, we created a nomogram for the clinicopathologic variables and the AGs gene signature to determine overall survival (OS). We also explored the association between three immune checkpoints, immune cell infiltration, and the aging-related gene signature. Results. We established an aging risk model to identify and predict the immune microenvironment in malignant melanoma. Then we developed and validated a prognosis risk model using three AGs (CSNK1E, C1QA, and SOD-2) in the GSE65904 dataset. The aging signature was positively associated with clinical and molecular characteristics and can be used as a prognostic factor for malignant melanoma. The low aging risk score was associated with a poor prognosis and indicated an immunosuppressive microenvironment. Conclusions. To summarize, we established and validated a model of aging risk based on three aging-related genes that acted as an independent prognostic predictor of overall survival. Besides, it also characterized the immune response in the malignant melanoma microenvironment and could provide a potential indicator of individualized immunotherapy in malignant melanoma.
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Parsa FG, Nobili S, Karimpour M, Aghdaei HA, Nazemalhosseini-Mojarad E, Mini E. Fanconi Anemia Pathway in Colorectal Cancer: A Novel Opportunity for Diagnosis, Prognosis and Therapy. J Pers Med 2022; 12:396. [PMID: 35330396 PMCID: PMC8950345 DOI: 10.3390/jpm12030396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/01/2022] [Accepted: 03/02/2022] [Indexed: 02/07/2023] Open
Abstract
Colorectal cancer (CRC) is the third most commonly diagnosed malignancy and has the second highest mortality rate globally. Thanks to the advent of next-generation sequencing technologies, several novel candidate genes have been proposed for CRC susceptibility. Germline biallelic mutations in one or more of the 22 currently recognized Fanconi anemia (FA) genes have been associated with Fanconi anemia disease, while germline monoallelic mutations, somatic mutations, or the promoter hypermethylation of some FANC genes increases the risk of cancer development, including CRC. The FA pathway is a substantial part of the DNA damage response system that participates in the repair of DNA inter-strand crosslinks through homologous recombination (HR) and protects genome stability via replication fork stabilization, respectively. Recent studies revealed associations between FA gene/protein tumor expression levels (i.e., FANC genes) and CRC progression and drug resistance. Moreover, the FA pathway represents a potential target in the CRC treatment. In fact, FANC gene characteristics may contribute to chemosensitize tumor cells to DNA crosslinking agents such as oxaliplatin and cisplatin besides exploiting the synthetic lethal approach for selective targeting of tumor cells. Hence, this review summarizes the current knowledge on the function of the FA pathway in DNA repair and genomic integrity with a focus on the FANC genes as potential predisposition factors to CRC. We then introduce recent literature that highlights the importance of FANC genes in CRC as promising prognostic and predictive biomarkers for disease management and treatment. Finally, we represent a brief overview of the current knowledge around the FANC genes as synthetic lethal therapeutic targets for precision cancer medicine.
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Affiliation(s)
- Fatemeh Ghorbani Parsa
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran 19857-17413, Iran; (F.G.P.); (H.A.A.)
| | - Stefania Nobili
- Department of Neurosciences, Imaging and Clinical Sciences, University “G. D’Annunzio” Chieti-Pescara, 66100 Chieti, Italy;
- Center for Advanced Studies and Technology (CAST), University “G. D’Annunzio” Chieti-Pescara, 66100 Chieti, Italy
| | - Mina Karimpour
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran;
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran 19857-17413, Iran; (F.G.P.); (H.A.A.)
| | - Ehsan Nazemalhosseini-Mojarad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran 19857-17413, Iran
| | - Enrico Mini
- Department of Health Sciences, University of Florence, 50139 Florence, Italy
- DENOTHE Excellence Center, University of Florence, 50139 Florence, Italy
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11
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Harnessing Synthetic Lethal Interactions for Personalized Medicine. J Pers Med 2022; 12:jpm12010098. [PMID: 35055413 PMCID: PMC8779047 DOI: 10.3390/jpm12010098] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/07/2022] [Accepted: 01/09/2022] [Indexed: 02/01/2023] Open
Abstract
Two genes are said to have synthetic lethal (SL) interactions if the simultaneous mutations in a cell lead to lethality, but each individual mutation does not. Targeting SL partners of mutated cancer genes can kill cancer cells but leave normal cells intact. The applicability of translating this concept into clinics has been demonstrated by three drugs that have been approved by the FDA to target PARP for tumors bearing mutations in BRCA1/2. This article reviews applications of the SL concept to translational cancer medicine over the past five years. Topics are (1) exploiting the SL concept for drug combinations to circumvent tumor resistance, (2) using synthetic lethality to identify prognostic and predictive biomarkers, (3) applying SL interactions to stratify patients for targeted and immunotherapy, and (4) discussions on challenges and future directions.
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Development and Validation of Tumor Immunogenicity Based Gene Signature for Skin Cancer Risk Stratification. Int J Mol Sci 2021; 22:ijms222112025. [PMID: 34769455 PMCID: PMC8584987 DOI: 10.3390/ijms222112025] [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: 10/08/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 12/13/2022] Open
Abstract
Melanoma is one of the most aggressive types of skin cancer, with significant heterogeneity in overall survival. Currently, tumor-node-metastasis (TNM) staging is insufficient to provide accurate survival prediction and appropriate treatment decision making for several types of tumors, such as those in melanoma patients. Therefore, the identification of more reliable prognosis biomarkers is urgently essential. Recent studies have shown that low immune cells infiltration is significantly associated with unfavorable clinical outcome in melanoma patients. Here we constructed a prognostic-related gene signature for melanoma risk stratification by quantifying the levels of several cancer hallmarks and identify the Wnt/β-catenin activation pathway as a primary risk factor for low tumor immunity. A series of bioinformatics and statistical methods were combined and applied to construct a Wnt-immune-related prognosis gene signature. With this gene signature, we computed risk scores for individual patients that can predict overall survival. To evaluate the robustness of the result, we validated the signature in multiple independent GEO datasets. Finally, an overall survival-related nomogram was established based on the gene signature and clinicopathological features. The Wnt-immune-related prognostic risk score could better predict overall survival compared with standard clinicopathological features. Our results provide a comprehensive map of the oncogene-immune-related gene signature that can serve as valuable biomarkers for better clinical decision making.
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13
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Wang HC, Chan LP, Wu CC, Hsiao HH, Liu YC, Cho SF, Du JS, Liu TC, Yang CH, Pan MR, Moi SH. Progression Risk Score Estimation Based on Immunostaining Data in Oral Cancer Using Unsupervised Hierarchical Clustering Analysis: A Retrospective Study in Taiwan. J Pers Med 2021; 11:jpm11090908. [PMID: 34575686 PMCID: PMC8466609 DOI: 10.3390/jpm11090908] [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: 07/30/2021] [Revised: 09/09/2021] [Accepted: 09/10/2021] [Indexed: 11/16/2022] Open
Abstract
This study aimed to investigate whether the progression risk score (PRS) developed from cytoplasmic immunohistochemistry (IHC) biomarkers is available and applicable for assessing risk and prognosis in oral cancer patients. Participants in this retrospective case-control study were diagnosed between 2012 and 2014 and subsequently underwent surgical intervention. The specimens from surgery were stained by IHC for 16 cytoplasmic target markers. We evaluated the results of IHC staining, clinical and pathological features, progression-free survival (PFS), and overall survival (OS) of 102 oral cancer patients using a novel estimation approach with unsupervised hierarchical clustering analysis. Patients were stratified into high-risk (52) and low-risk (50) groups, according to their PRS; a metric consisting of cytoplasmic PLK1, PhosphoMet, SGK2, and SHC1 expression. Moreover, PRS could be extended for use in the Cox proportional hazard regression model to estimate survival outcomes with associated clinical parameters. Our study findings revealed that the high-risk patients had a significantly increased risk in cancer progression compared with low-risk patients (hazard ratio (HR) = 2.20, 95% confidence interval (CI) = 1.10-2.42, p = 0.026). After considering the influences of demographics, risk behaviors, and tumor characteristics, risk estimation with PRS provided distinct PFS groups for patients with oral cancer (p = 0.017, p = 0.019, and p = 0.020). Our findings support that PRS could serve as an ideal biomarker for clinical use in risk stratification and progression assessment in oral cancer.
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Affiliation(s)
- Hui-Ching Wang
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (H.-C.W.); (J.-S.D.); (M.-R.P.)
- Department of Internal Medicine, Division of Hematology and Oncology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (H.-H.H.); (Y.-C.L.); (S.-F.C.)
- Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
| | - Leong-Perng Chan
- Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
- Department of Otolaryngology-Head and Neck Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Otorhinolaryngology-Head and Neck Surgery, Kaohsiung Municipal Ta-Tung Hospital and Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
| | - Chun-Chieh Wu
- Department of Pathology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
| | - Hui-Hua Hsiao
- Department of Internal Medicine, Division of Hematology and Oncology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (H.-H.H.); (Y.-C.L.); (S.-F.C.)
- Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
| | - Yi-Chang Liu
- Department of Internal Medicine, Division of Hematology and Oncology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (H.-H.H.); (Y.-C.L.); (S.-F.C.)
- Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
| | - Shih-Feng Cho
- Department of Internal Medicine, Division of Hematology and Oncology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (H.-H.H.); (Y.-C.L.); (S.-F.C.)
- Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
| | - Jeng-Shiun Du
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (H.-C.W.); (J.-S.D.); (M.-R.P.)
- Department of Internal Medicine, Division of Hematology and Oncology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (H.-H.H.); (Y.-C.L.); (S.-F.C.)
- Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
| | - Ta-Chih Liu
- Department of Hematology-Oncology, Chang Bing Show Chwan Memorial Hospital, Changhua 505, Taiwan;
| | - Cheng-Hong Yang
- Department of Electronic Engineering, National Kaohsiung University of Science and Technology, Kaohsiung 807, Taiwan;
- Ph.D. Program in Biomedical Engineering, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Mei-Ren Pan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (H.-C.W.); (J.-S.D.); (M.-R.P.)
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Sin-Hua Moi
- Center of Cancer Program Development, E-Da Cancer Hospital, I-Shou University, Kaohsiung 807, Taiwan
- Correspondence: ; Tel.: +886-7-6150022 (ext. 6135); Fax: +886-7-6150940
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Wang HC, Chou MC, Wu CC, Chan LP, Moi SH, Pan MR, Liu TC, Yang CH. Application of the Interaction between Tissue Immunohistochemistry Staining and Clinicopathological Factors for Evaluating the Risk of Oral Cancer Progression by Hierarchical Clustering Analysis: A Case-Control Study in a Taiwanese Population. Diagnostics (Basel) 2021; 11:diagnostics11060925. [PMID: 34063938 PMCID: PMC8224004 DOI: 10.3390/diagnostics11060925] [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: 04/27/2021] [Revised: 05/12/2021] [Accepted: 05/17/2021] [Indexed: 01/31/2023] Open
Abstract
The aim of this single-center case-control study is to investigate the feasibility and accuracy of oral cancer protein risk stratification (OCPRS) to analyze the risk of cancer progression. All patients diagnosed with oral cancer in Taiwan, between 2012 and 2014, and who underwent surgical intervention were selected for the study. The tissue was further processed for immunohistochemistry (IHC) for 21 target proteins. Analyses were performed using the results of IHC staining, clinicopathological characteristics, and survival outcomes. Novel stratifications with a hierarchical clustering approach and combinations were applied using the Cox proportional hazard regression model. Of the 163 participants recruited, 102 patients were analyzed, and OCPRS successfully identified patients with different progression-free survival (PFS) profiles in high-risk (53 subjects) versus low-risk (49 subjects) groups (p = 0.012). OCPRS was composed of cytoplasmic PLK1, phosphoMet, and SGK2 IHC staining. After controlling for the influence of clinicopathological features, high-risk patients were 2.33 times more likely to experience cancer progression than low-risk patients (p = 0.020). In the multivariate model, patients with extranodal extension (HR = 2.66, p = 0.045) demonstrated a significantly increased risk for disease progression. Risk stratification with OCPRS provided distinct PFS groups for patients with oral cancer after surgical intervention. OCPRS appears suitable for routine clinical use for progression and prognosis estimation.
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Affiliation(s)
- Hui-Ching Wang
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
- Division of Hematology and Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
| | - Meng-Chun Chou
- Department of Nursing, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
| | - Chun-Chieh Wu
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
- Department of Pathology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Leong-Perng Chan
- Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
- Department of Otolaryngology-Head and Neck Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Otorhinolaryngology-Head and Neck Surgery, Kaohsiung Municipal Ta-Tung Hospital and Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
| | - Sin-Hua Moi
- Center of Cancer Program Development, E-Da Cancer Hospital, I-Shou University, Kaohsiung 824, Taiwan;
| | - Mei-Ren Pan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
- Correspondence: (M.-R.P.); (T.-C.L.); (C.-H.Y.); Tel.: +886-7-3121101-5092-34 (M.-R.P.); +886-4-781-3888 (T.-C.L.); +886-7-381-4526 (C.-H.Y.); Fax: +886-7-3218309 (M.-R.P.)
| | - Ta-Chih Liu
- Department of Hematology-Oncology, Chang Bing Show Chwan Memorial Hospital, Changhua 505, Taiwan
- Correspondence: (M.-R.P.); (T.-C.L.); (C.-H.Y.); Tel.: +886-7-3121101-5092-34 (M.-R.P.); +886-4-781-3888 (T.-C.L.); +886-7-381-4526 (C.-H.Y.); Fax: +886-7-3218309 (M.-R.P.)
| | - Cheng-Hong Yang
- Department of Electronic Engineering, National Kaohsiung University of Science and Technology, Kaohsiung 807, Taiwan
- Ph. D. Program in Biomedical Engineering, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Correspondence: (M.-R.P.); (T.-C.L.); (C.-H.Y.); Tel.: +886-7-3121101-5092-34 (M.-R.P.); +886-4-781-3888 (T.-C.L.); +886-7-381-4526 (C.-H.Y.); Fax: +886-7-3218309 (M.-R.P.)
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15
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Wang HC, Chiang CJ, Liu TC, Wu CC, Chen YT, Chang JG, Shieh GS. Immunohistochemical Expression of Five Protein Combinations Revealed as Prognostic Markers in Asian Oral Cancer. Front Genet 2021; 12:643461. [PMID: 33936170 PMCID: PMC8083901 DOI: 10.3389/fgene.2021.643461] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/01/2021] [Indexed: 12/24/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) has a high mortality rate (∼50%), and the 5-year overall survival rate is not optimal. Cyto- and histopathological examination of cancer tissues is the main strategy for diagnosis and treatment. In the present study, we aimed to uncover immunohistochemical (IHC) markers for prognosis in Asian OSCC. From the collected 742 synthetic lethal gene pairs (of various cancer types), we first filtered genes relevant to OSCC, performed 29 IHC stains at different cellular portions and combined these IHC stains into 398 distinct pairs. Next, we identified novel IHC prognostic markers in OSCC among Taiwanese population, from the single and paired IHC staining by univariate Cox regression analysis. Increased nuclear expression of RB1 [RB1(N)↑], CDH3(C)↑-STK17A(N)↑ and FLNA(C)↑-KRAS(C)↑were associated with survival, but not independent of tumor stage, where C and N denote cytoplasm and nucleus, respectively. Furthermore, multivariate Cox regression analyses revealed that CSNK1E(C)↓-SHC1(N)↓ (P = 5.9 × 10–5; recommended for clinical use), BRCA1(N)↓-SHC1(N)↓ (P = 0.030), CSNK1E(C)↓-RB1(N)↑ (P = 0.045), [CSNK1E(C)-SHC1(N), FLNA(C)-KRAS(C)] (P = 0.000, rounded to three decimal places) and [BRCA1(N)-SHC1(N), FLNA(C)-KRAS(C)] (P = 0.020) were significant factors of poor prognosis, independent of lymph node metastasis, stage and alcohol consumption. An external dataset from The Cancer Genome Atlas HNSCC cohort confirmed that CDH3↑-STK17A↑ was a significant predictor of poor survival. Our approach identified prognostic markers with components involved in different pathways and revealed IHC marker pairs while neither single IHC was a marker, thus it improved the current state-of-the-art for identification of IHC markers.
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Affiliation(s)
- Hui-Ching Wang
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Division of Hematology and Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | | | - Ta-Chih Liu
- Department of Hematology-Oncology, Chang Bing Show Chwan Memorial Hospital, Changhua, Taiwan
| | - Chun-Chieh Wu
- Department of Pathology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yi-Ting Chen
- Department of Pathology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Jan-Gowth Chang
- Epigenome Research Center, China Medical University Hospital, Taichung, Taiwan.,Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan.,Center for Precision Medicine, China Medical University Hospital, Taichung, Taiwan.,School of Medicine, China Medical University, Taichung, Taiwan.,Department of Bioinformatics and Medical Engineering, Asia University, Taichung, Taiwan
| | - Grace S Shieh
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan.,Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan.,Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, Taiwan.,Data Science Degree Program, Academia Sinica and National Taiwan University, Taipei, Taiwan
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16
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Liu G, Xie W, Jin M, Li P, Liu L, Liu L, Huang G. Transcriptomic analysis reveals a WNT signaling pathway-based gene signature prognostic for non-small cell carcinoma. Aging (Albany NY) 2020; 12:19159-19172. [PMID: 33027769 PMCID: PMC7732286 DOI: 10.18632/aging.103724] [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: 05/25/2020] [Accepted: 07/03/2020] [Indexed: 01/24/2023]
Abstract
The value of combining multiple candidate genes into a panel to improve biomarker performance is increasingly emphasized. Genes associated with WNT signaling are widely-reported to provide prognostic signatures in non-small cell carcinoma (NSCLC). Screening of genes involved in this signaling pathway facilitated selection of an optimal candidate biomarker gene combination and development of an NSCLC prognostic model based on expression of these genes. Risk scores derived from the model performed well in predicting survival; in the training dataset, samples achieving a high risk score exhibit a shorter survival interval (median survival time 34.8 months, 95% CI 31.1-41.0) than did samples achieving a low risk score (median survival time 72.0 months, 95% CI 59.3-87.5, p=2e-11), and exhibited higher oncogene and lower tumor suppressor gene expression. Receiver-operator characteristic curves based on three-year survival demonstrate that the model outperformed clinical prognostic indicators. In addition, the model was validated in four independent cohorts, demonstrating robust NSCLC prognostic value. Correlation analyses reveal that the model offers efficacy independent of other clinical indicators. Gene Set Enrichment Analysis (GSEA) reveals that the model reflects variable tissue functional states relevant to NSCLC biology. In summary, the signature model shows potential as a valuable and robust NSCLC prognostic indicator.
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Affiliation(s)
- Gang Liu
- Institute of Biological Sciences, Fudan University, Shanghai, P.R. China,Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai, P.R. China
| | - Wenhui Xie
- Department of Nuclear Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, P.R. China
| | - Mingming Jin
- Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai, P.R. China
| | - Ping Li
- Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai, P.R. China
| | - Liu Liu
- Department of Nuclear Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, P.R. China
| | - Lei Liu
- Institute of Biological Sciences, Fudan University, Shanghai, P.R. China
| | - Gang Huang
- Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai, P.R. China
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17
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Tian XP, Xie D, Huang WJ, Ma SY, Wang L, Liu YH, Zhang X, Huang HQ, Lin TY, Rao HL, Li M, Liu F, Zhang F, Zhong LY, Liang L, Lan XL, Li J, Liao B, Li ZH, Tang QL, Liang Q, Shao CK, Zhai QL, Cheng RF, Sun Q, Ru K, Gu X, Lin XN, Yi K, Shuang YR, Chen XD, Dong W, Sang W, Sun C, Liu H, Zhu ZG, Rao J, Guo QN, Zhou Y, Meng XL, Zhu Y, Hu CL, Jiang YR, Zhang Y, Gao HY, He WJ, Xia ZJ, Pan XY, Lan H, Li GW, Liu L, Bao HZ, Song LY, Kang TB, Cai QQ. A gene-expression-based signature predicts survival in adults with T-cell lymphoblastic lymphoma: a multicenter study. Leukemia 2020; 34:2392-2404. [PMID: 32080345 DOI: 10.1038/s41375-020-0757-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 01/10/2020] [Accepted: 02/10/2020] [Indexed: 12/21/2022]
Abstract
We aimed to establish a discriminative gene-expression-based classifier to predict survival outcomes of T-cell lymphoblastic lymphoma (T-LBL) patients. After exploring global gene-expression profiles of progressive (n = 22) vs. progression-free (n = 28) T-LBL patients, 43 differentially expressed mRNAs were identified. Then an eleven-gene-based classifier was established using LASSO Cox regression based on NanoString quantification. In the training cohort (n = 169), high-risk patients stratified using the classifier had significantly lower progression-free survival (PFS: hazards ratio 4.123, 95% CI 2.565-6.628; p < 0.001), disease-free survival (DFS: HR 3.148, 95% CI 1.857-5.339; p < 0.001), and overall survival (OS: HR 3.790, 95% CI 2.237-6.423; p < 0.001) compared with low-risk patients. The prognostic accuracy of the classifier was validated in the internal testing (n = 84) and independent validation cohorts (n = 360). A prognostic nomogram consisting of five independent variables including the classifier, lactate dehydrogenase levels, ECOG-PS, central nervous system involvement, and NOTCH1/FBXW7 status showed significantly greater prognostic accuracy than each single variable alone. The addition of a five-miRNA-based signature further enhanced the accuracy of this nomogram. Furthermore, patients with a nomogram score ≥154.2 significantly benefited from the BFM protocol. In conclusion, our nomogram comprising the 11-gene-based classifier may make contributions to individual prognosis prediction and treatment decision-making.
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Affiliation(s)
- Xiao-Peng Tian
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, PR China
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Dan Xie
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Wei-Juan Huang
- Department of Pharmacology, College of Pharmacy, Jinan University, Guangzhou, PR China
| | - Shu-Yun Ma
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, PR China
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Liang Wang
- Department of Hematology, Zhujiang Hospital of Southern Medical University, Guangzhou, PR China
- Department of Hematology, Beijing Tongren Hospital, Capital Medical University, Beijing, PR China
| | - Yan-Hui Liu
- Department of Pathology, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, PR China
| | - Xi Zhang
- Department of Hematology, Xinqiao Hospital, Third Military Medical University, Chongqing, PR China
| | - Hui-Qiang Huang
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Tong-Yu Lin
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Hui-Lan Rao
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Mei Li
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Fang Liu
- Department of Pathology, The First People's Hospital of Foshan, Foshan, PR China
| | - Fen Zhang
- Department of Pathology, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, PR China
| | - Li-Ye Zhong
- Department of Hematology, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, PR China
| | - Li Liang
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, PR China
| | - Xiao-Liang Lan
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, PR China
| | - Juan Li
- Department of Hematology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China
| | - Bing Liao
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China
| | - Zhi-Hua Li
- Department of Oncology, Sun-Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, PR China
| | - Qiong-Lan Tang
- Department of Oncology, Sun-Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, PR China
| | - Qiong Liang
- Department of Pathology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China
| | - Chun-Kui Shao
- Department of Pathology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China
| | - Qiong-Li Zhai
- Department of Pathology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, PR China
| | - Run-Fen Cheng
- Department of Pathology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, PR China
| | - Qi Sun
- Department of Pathology, Hematological Hospital of Chinese Academy of Medical Sciences, Tianjin, PR China
| | - Kun Ru
- Department of Pathology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, PR China
| | - Xia Gu
- Department of Pathology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, PR China
| | - Xi-Na Lin
- Department of Pathology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, PR China
| | - Kun Yi
- Department of Oncology, Jiangxi Provincial Cancer Hospital, Nanchang, PR China
| | - Yue-Rong Shuang
- Department of Hematology, Jiangxi Provincial Cancer Hospital, Nanchang, PR China
| | - Xiao-Dong Chen
- Department of Pathology, General Hospital of Guangzhou Military Command of PLA, Guangzhou, PR China
| | - Wei Dong
- Department of Hematology, Shunde Hospital of Southern Medical University, Shunde, PR China
| | - Wei Sang
- Department of Hematology, The First Affiliated Hospital of Xuzhou Medical University, Xuzhou, PR China
| | - Cai Sun
- Department of Pathology, The First Affiliated Hospital of Xuzhou Medical University, Xuzhou, PR China
| | - Hui Liu
- Department of Pathology, The First Affiliated Hospital of Xuzhou Medical University, Xuzhou, PR China
| | - Zhi-Gang Zhu
- Department of Hematology and Oncology, Guangzhou First People's Hospital, Guangzhou, PR China
| | - Jun Rao
- Department of Hematology, Xinqiao Hospital, Third Military Medical University, Chongqing, PR China
| | - Qiao-Nan Guo
- Department of Pathology, Xinqiao Hospital, Third Military Medical University, Chongqing, PR China
| | - Ying Zhou
- Department of Medical Oncology, Jiangmen Central Hospital, Jiangmen, PR China
| | - Xiang-Ling Meng
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, PR China
| | - Yong Zhu
- Department of Gastrointestinal Surgery, The Fourth Affiliated Hospital of Anhui Medical University, Hefei, PR China
| | - Chang-Lu Hu
- Department of Medical Oncology, Anhui Provincial Cancer Hospital, Hefei, PR China
| | - Yi-Rong Jiang
- Department of Hematology, The First People's Hospital of Dongguan, Dongguan, PR China
| | - Ying Zhang
- Department of Oncology, Affiliated Hospital of Guangdong Medical University, Guangzhou, PR China
| | - Hong-Yi Gao
- Department of Pathology, Guangdong Province Hospital for Women and Children Health Care, Guangzhou, PR China
| | - Wen-Jun He
- Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, PR China
| | - Zhong-Jun Xia
- Department of Hematology, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Xue-Yi Pan
- Department of Hematology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, PR China
| | - Hai Lan
- Department of Hematology, Shunde Affiliated Hospital of Guangzhou University of Chinese Medicine, Shunde, PR China
| | - Guo-Wei Li
- Department of Hematology, Huizhou Municipal Central Hospital, Huizhou, PR China
| | - Lu Liu
- Department of Lymphoma And Hematology, Jilin Cancer Hospital, Changchun, PR China
| | - Hui-Zheng Bao
- Department of Lymphoma And Hematology, Jilin Cancer Hospital, Changchun, PR China
| | - Li-Yan Song
- Department of Pharmacology, College of Pharmacy, Jinan University, Guangzhou, PR China
| | - Tie-Bang Kang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Qing-Qing Cai
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, PR China.
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou, PR China.
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Tang L, Chen R, Xu X. Synthetic lethality: A promising therapeutic strategy for hepatocellular carcinoma. Cancer Lett 2020; 476:120-128. [PMID: 32070778 DOI: 10.1016/j.canlet.2020.02.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/11/2020] [Accepted: 02/12/2020] [Indexed: 12/24/2022]
Abstract
Hepatocellular carcinoma (HCC), the main cause of liver cancer-related death, is one of the main cancers in terms of incidence and mortality. However, HCC is difficult to target and develops strong drug resistance. Therefore, a new treatment strategy is urgently needed. The clinical application of the concept of synthetic lethality in recent years provides a new therapeutic direction for the accurate treatment of HCC. Here, we introduce the concept of synthetic lethality, the screening used to study synthetic lethality, and the identified and potential genetic interactions that induce synthetic lethality in HCC. In addition, we propose opportunities and challenges for translating synthetic lethal interactions to the clinical treatment of HCC.
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Affiliation(s)
- Linsong Tang
- Department of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China; NHFPC Key Lab of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, 310003, China.
| | - Ronggao Chen
- Department of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China; NHFPC Key Lab of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, 310003, China.
| | - Xiao Xu
- Department of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China; NHFPC Key Lab of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, 310003, China.
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19
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Abstract
Genomic sequencing analyses of a variety of human cancers have revealed that massive mutations of cancer-relevant genes are the major alterations in cancerous cells, and their mutation frequencies or rates are highly associated with the development, progression, metastasis, and drug resistance of cancers as well as their clinical outcomes and prognosis. One predominant genetic alternation in human epithelial ovarian cancer (EOC) is the mutation of TP53 that encodes the tumor suppressor p53 protein. This essay will review the most recent progress in understanding the role of TP53 mutations in development, progression, and metastasis of EOC, and discuss the potential of TP53 mutations as diagnostic and prognostic biomarkers as well as therapeutic targets for EOC.
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Affiliation(s)
- Yu Zhang
- Department of Gynecology and Obstetrics, Xiang-Ya Hospital, Central South University, Changsha 410008, China
| | - Lan Cao
- Department of Gynecology and Obstetrics, Xiang-Ya Hospital, Central South University, Changsha 410008, China
| | - Daniel Nguyen
- Department of Biochemistry and Molecular Biology, Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, USA
| | - Hua Lu
- Department of Biochemistry and Molecular Biology, Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, USA
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20
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Chang JG, Chen CC, Wu YY, Che TF, Huang YS, Yeh KT, Shieh GS, Yang PC. Uncovering synthetic lethal interactions for therapeutic targets and predictive markers in lung adenocarcinoma. Oncotarget 2016; 7:73664-73680. [PMID: 27655641 PMCID: PMC5342006 DOI: 10.18632/oncotarget.12046] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 08/24/2016] [Indexed: 12/28/2022] Open
Abstract
Two genes are called synthetic lethal (SL) if their simultaneous mutation leads to cell death, but mutation of either individual does not. Targeting SL partners of mutated cancer genes can selectively kill cancer cells, but leave normal cells intact. We present an integrated approach to uncover SL gene pairs as novel therapeutic targets of lung adenocarcinoma (LADC). Of 24 predicted SL pairs, PARP1-TP53 was validated by RNAi knockdown to have synergistic toxicity in H1975 and invasive CL1-5 LADC cells; additionally FEN1-RAD54B, BRCA1-TP53, BRCA2-TP53 and RB1-TP53 were consistent with the literature. While metastasis remains a bottleneck in cancer treatment and inhibitors of PARP1 have been developed, this result may have therapeutic potential for LADC, in which TP53 is commonly mutated. We also demonstrated that silencing PARP1 enhanced the cell death induced by the platinum-based chemotherapy drug carboplatin in lung cancer cells (CL1-5 and H1975). IHC of RAD54B↑, BRCA1↓-RAD54B↑, FEN1(N)↑-RAD54B↑ and PARP1↑-RAD54B↑ were shown to be prognostic markers for 131 Asian LADC patients, and all markers except BRCA1↓-RAD54B↑ were further confirmed by three independent gene expression data sets (a total of 426 patients) including The Cancer Genome Atlas (TCGA) cohort of LADC. Importantly, we identified POLB-TP53 and POLB as predictive markers for the TCGA cohort (230 subjects), independent of age and stage. Thus, POLB and POLB-TP53 may be used to stratify future non-Asian LADC patients for therapeutic strategies.
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Affiliation(s)
- Jan-Gowth Chang
- Department of Laboratory Medicine and Epigenome Research Center, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Chia-Cheng Chen
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Yi-Ying Wu
- Graduate Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ting-Fang Che
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Yi-Syuan Huang
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Kun-Tu Yeh
- Department of Pathology, Changhua Christian Hospital, Changhua, Taiwan
- Department of Pathology, School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Grace S. Shieh
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
- Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, Taiwan
| | - Pan-Chyr Yang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- Center of Genomic Medicine, National Taiwan University, Taipei, Taiwan
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
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21
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Pierzynski JA, Hildebrandt MA, Kamat AM, Lin J, Ye Y, Dinney CPN, Wu X. Genetic Variants in the Wnt/β-Catenin Signaling Pathway as Indicators of Bladder Cancer Risk. J Urol 2015; 194:1771-6. [PMID: 26173102 PMCID: PMC5087323 DOI: 10.1016/j.juro.2015.07.032] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2015] [Indexed: 12/21/2022]
Abstract
PURPOSE Genetic factors that influence bladder cancer risk remain largely unknown. Previous research has suggested that there is a strong genetic component underlying the risk of bladder cancer. The Wnt/β-catenin signaling pathway is a key modulator of cellular proliferation through its regulation of stem cell homeostasis. Furthermore, variants in the Wnt/β-catenin signaling pathway have been implicated in the development of other cancers, leading us to believe that this pathway may have a vital role in bladder cancer development. MATERIALS AND METHODS A total of 230 single nucleotide polymorphisms in 40 genes in the Wnt/β-catenin signaling pathway were genotyped in 803 bladder cancer cases and 803 healthy controls. RESULTS A total of 20 single nucleotide polymorphisms were nominally significant for risk. Individuals with 2 variants of LRP6: rs10743980 were associated with a decreased risk of bladder cancer in the recessive model in the initial analysis (OR 0.76, 95% CI 0.58-0.99, p=0.039). This was validated using the bladder genome-wide association study chip (OR 0.51, 95% CI 0.27-1.00, p=0.049 and for combined analysis p=0.007). CONCLUSIONS Together these findings implicate variants in the Wnt/β-catenin stem cell pathway as having a role in bladder cancer etiology.
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Affiliation(s)
- Jeanne A Pierzynski
- Department of Epidemiology and Division of Surgery, Department of Urology (AMK, CPND), University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Michelle A Hildebrandt
- Department of Epidemiology and Division of Surgery, Department of Urology (AMK, CPND), University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Ashish M Kamat
- Department of Epidemiology and Division of Surgery, Department of Urology (AMK, CPND), University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Jie Lin
- Department of Epidemiology and Division of Surgery, Department of Urology (AMK, CPND), University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Yuanqing Ye
- Department of Epidemiology and Division of Surgery, Department of Urology (AMK, CPND), University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Colin P N Dinney
- Department of Epidemiology and Division of Surgery, Department of Urology (AMK, CPND), University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Xifeng Wu
- Department of Epidemiology and Division of Surgery, Department of Urology (AMK, CPND), University of Texas M.D. Anderson Cancer Center, Houston, Texas.
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22
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The Overexpression of FEN1 and RAD54B May Act as Independent Prognostic Factors of Lung Adenocarcinoma. PLoS One 2015; 10:e0139435. [PMID: 26431531 PMCID: PMC4592204 DOI: 10.1371/journal.pone.0139435] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 09/14/2015] [Indexed: 11/22/2022] Open
Abstract
Synthetic lethality arises when a combination of mutations in two or more genes leads to cell death. However, the prognostic role of concordant overexpression of synthetic lethality genes in protein level rather than a combination of mutations is not clear. In this study, we explore the prognostic role of combined overexpression of paired genes in lung adenocarcinoma. We used immunohistochemical staining to investigate 24 paired genes in 93 lung adenocarcinoma patients and Kaplan-Meier analysis and Cox proportional hazards models to evaluate their prognostic roles. Among 24 paired genes, only FEN1 (Flap endonuclease 1) and RAD54B (RAD54 homolog B) were overexpressed in lung adenocarcinoma patients with poor prognosis. Patients with expression of both FEN1 and RAD54B were prone to have advanced nodal involvement and significantly poor prognosis (HR = 2.35, P = 0.0230). These results suggest that intensive follow up and targeted therapy might improve clinical outcome for patients who show expression of both FEN1 and RAD54B.
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23
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Mishra S. CSNK1A1 and Gli2 as Novel Targets Identified Through an Integrative Analysis of Gene Expression Data, Protein-Protein Interaction and Pathways Networks in Glioblastoma Tumors: Can These Two Be Antagonistic Proteins? Cancer Inform 2014; 13:93-108. [PMID: 25374452 PMCID: PMC4213195 DOI: 10.4137/cin.s18377] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 08/20/2014] [Accepted: 08/23/2014] [Indexed: 12/11/2022] Open
Abstract
Glioblastoma (GBM) is the malignant form of glioma, and the interplay of different pathways working in concert in GBM development and progression needs to be fully understood. Wnt signaling and sonic hedgehog (SHH) signaling pathways, having basic similarities, are among the major pathways aberrantly activated in GBM, and hence, need to be targeted. It becomes imperative, therefore, to explore the functioning of these pathways in context of each other in GBM. An integrative approach may help provide new biological insights, as well as solve the problem of identifying common drug targets for simultaneous targeting of these pathways. The beauty of this approach is that it can recapitulate several known facts, as well as decipher new emerging patterns, identifying those targets that could be missed when relying on one type of data at a time. This approach can be easily extended to other systems to discover key patterns in the functioning of signaling molecules. Studies were designed to assess the relationship between significant differential expression of genes of the Wnt (Wnt/β-catenin canonical and Wnt non-canonical) and SHH signaling pathways and their connectivity patterns in interaction and signaling networks. Further, the aim was to decipher underlying mechanistic patterns that may be involved in a more specific way and to generate a ranked list of genes that can be used as markers or drug targets. These studies predict that Wnt pathway plays a relatively more pro-active role than the SHH pathway in GBM. Further, CTNNB1, CSNK1A1, and Gli2 proteins may act as key drug targets common to these pathways. While CTNNB1 is a widely studied molecule in the context of GBM, the likely roles of CSNK1A1 and Gli2 are found to be relatively novel. It is surmised that Gli2 may be antagonistic to CSNK1A1, preventing the phosphorylation of CTNNB1 and SMO proteins in Wnt and SHH signaling pathway, respectively, by CSNK1A1, and thereby, aberrant activation. New insights into the possible behavior of these pathway molecules relative to each other in GBM reveal some key interesting patterns.
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Affiliation(s)
- Seema Mishra
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana State, India
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