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Liao Q, Wang F, Zhou W, Liao G, Zhang H, Shu Y, Chen Y. Identification of Causal Relationships between Gut Microbiota and Influenza a Virus Infection in Chinese by Mendelian Randomization. Microorganisms 2024; 12:1170. [PMID: 38930552 PMCID: PMC11205835 DOI: 10.3390/microorganisms12061170] [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: 05/17/2024] [Revised: 06/01/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
Numerous studies have reported a correlation between gut microbiota and influenza A virus (IAV) infection and disease severity. However, the causal relationship between these factors remains inadequately explored. This investigation aimed to assess the influence of gut microbiota on susceptibility to human infection with H7N9 avian IAV and the severity of influenza A (H1N1)pdm09 infection. A two-sample Mendelian randomization analysis was conducted, integrating our in-house genome-wide association study (GWAS) on H7N9 susceptibility and H1N1pdm09 severity with a metagenomics GWAS dataset from a Chinese population. Twelve and fifteen gut microbiotas were causally associated with H7N9 susceptibility or H1N1pdm09 severity, separately. Notably, Clostridium hylemonae and Faecalibacterium prausnitzii were negative associated with H7N9 susceptibility and H1N1pdm09 severity, respectively. Moreover, Streptococcus peroris and Streptococcus sanguinis were associated with H7N9 susceptibility, while Streptococcus parasanguini and Streptococcus suis were correlated with H1N1pdm09 severity. These results provide novel insights into the interplay between gut microbiota and IAV pathogenesis as well as new clues for mechanism research regarding therapeutic interventions or IAV infections. Future studies should concentrate on clarifying the regulatory mechanisms of gut microbiota and developing efficacious approaches to reduce the incidence of IAV infections, which could improve strategy for preventing and treating IAV infection worldwide.
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Affiliation(s)
- Qijun Liao
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (Q.L.); (F.W.); (W.Z.); (G.L.)
- BGI Genomics, Shenzhen 518085, China
| | - Fuxiang Wang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (Q.L.); (F.W.); (W.Z.); (G.L.)
| | - Wudi Zhou
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (Q.L.); (F.W.); (W.Z.); (G.L.)
| | - Guancheng Liao
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (Q.L.); (F.W.); (W.Z.); (G.L.)
| | - Haoyang Zhang
- School of Data and Computer Science, Sun Yat-sen University, Guangzhou 510006, China;
| | - Yuelong Shu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (Q.L.); (F.W.); (W.Z.); (G.L.)
- Key Laboratory of Pathogen Infection Prevention and Control (MOE), State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 102629, China
| | - Yongkun Chen
- Guangdong Provincial Key Laboratory of Infection Immunity and Inflammation, Department of Pathogen Biology, School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen University, Shenzhen 518055, China
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Wiltshire E, de Moura MC, Piñeyro D, Joshi RS. Cellular and clinical impact of protein phosphatase enzyme epigenetic silencing in multiple cancer tissues. Hum Genomics 2024; 18:24. [PMID: 38475971 DOI: 10.1186/s40246-024-00592-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND Protein Phosphatase Enzymes (PPE) and protein kinases simultaneously control phosphorylation mechanisms that tightly regulate intracellular signalling pathways and stimulate cellular responses. In human malignancies, PPE and protein kinases are frequently mutated resulting in uncontrolled kinase activity and PPE suppression, leading to cell proliferation, migration and resistance to anti-cancer therapies. Cancer associated DNA hypermethylation at PPE promoters gives rise to transcriptional silencing (epimutations) and is a hallmark of cancer. Despite recent advances in sequencing technologies, data availability and computational capabilities, only a fraction of PPE have been reported as transcriptionally inactive as a consequence of epimutations. METHODS In this study, we examined promoter-associated DNA methylation profiles in Protein Phosphatase Enzymes and their Interacting Proteins (PPEIP) in a cohort of 705 cancer patients in five tissues (Large intestine, Oesophagus, Lung, Pancreas and Stomach) in three cell models (primary tumours, cancer cell lines and 3D embedded cancer cell cultures). As a subset of PPEIP are known tumour suppressor genes, we analysed the impact of PPEIP promoter hypermethylation marks on gene expression, cellular networks and in a clinical setting. RESULTS Here, we report epimutations in PPEIP are a frequent occurrence in the cancer genome and manifest independent of transcriptional activity. We observed that different tumours have varying susceptibility to epimutations and identify specific cellular signalling networks that are primarily affected by epimutations. Additionally, RNA-seq analysis showed the negative impact of epimutations on most (not all) Protein Tyrosine Phosphatase transcription. Finally, we detected novel clinical biomarkers that inform on patient mortality and anti-cancer treatment sensitivity. CONCLUSIONS We propose that DNA hypermethylation marks at PPEIP frequently contribute to the pathogenesis of malignancies and within the precision medicine space, hold promise as biomarkers to inform on clinical features such as patient survival and therapeutic response.
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Affiliation(s)
- Edward Wiltshire
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, UK
| | | | - David Piñeyro
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
| | - Ricky S Joshi
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, UK.
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Chen C, Liu H, Li Y, Xu Q, Liu J. Downregulation of PTPRT elevates the expression of survivin and promotes the proliferation, migration, and invasion of lung adenocarcinoma. BMC Cancer 2024; 24:63. [PMID: 38216925 PMCID: PMC10785488 DOI: 10.1186/s12885-024-11840-7] [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: 04/19/2023] [Accepted: 01/04/2024] [Indexed: 01/14/2024] Open
Abstract
BACKGROUND Receptor-type tyrosine-protein phosphatase T (PTPRT) is a transmembrane protein that is involved in cell adhesion. We previously found that PTPRT was downregulated in multiple cancer types and the mutation of PTPRT was associated with cancer early metastasis. However, the impacts of PTPRT downregulation on tumour proliferation, invasion, and clinical interventions such as immune checkpoint inhibitor (ICI) therapies remained largely unknown. METHODS Gene expression data of non-small cell lung cancer (NSCLC) samples from The Cancer Genome Atlas database were downloaded and used to detect the differential expressed genes between PTPRT-high and PTPRT-low subgroups. Knockdown and overexpress of PTPRT in lung cancer cell lines were performed to explore the function of PTPRT in vitro. Western blot and qRT-PCR were used to evaluate the expression of cell cycle-related genes. CCK-8 assays, wound-healing migration assay, transwell assay, and colony formation assay were performed to determine the functional impacts of PTPRT on cell proliferation, migration, and invasion. KM-plotter was used to explore the significance of selected genes on patient prognosis. RESULTS PTPRT was found to be downregulated in tumours and lung cancer cell lines compared to normal samples. Cell cycle-related genes (BIRC5, OIP5, and CDCA3, etc.) were specifically upregulated in PTPRT-low lung adenocarcinoma (LUAD). Modulation of PTPRT expression in LUAD cell lines affected the expression of BIRC5 (survivin) significantly, as well as the proliferation, migration, and invasion of tumour cells. In addition, low PTPRT expression level was correlated with worse prognosis of lung cancer and several other cancer types. Furthermore, PTPRT downregulation was associated with elevated tumour mutation burden and tumour neoantigen burden in lung cancer, indicating the potential influence on tumour immunogenicity. CONCLUSION Our findings uncovered the essential roles of PTPRT in the regulation of proliferation, migration, and invasion of LUAD, and highlighted the clinical significance of PTPRT downregulation in lung cancer.
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Affiliation(s)
- Chao Chen
- Department of Thoracic Surgery, Peking University Shenzhen Hospital, Shenzhen Peking University, The Hong Kong University of Science and Technology Medical Center, Shenzhen, 518035, China.
| | - Haozhen Liu
- Department of Thoracic Surgery, Peking University Shenzhen Hospital, Shenzhen Peking University, The Hong Kong University of Science and Technology Medical Center, Shenzhen, 518035, China
| | - Yanling Li
- Department of Thoracic Surgery, Peking University Shenzhen Hospital, Shenzhen Peking University, The Hong Kong University of Science and Technology Medical Center, Shenzhen, 518035, China
| | - Qumiao Xu
- BGI Research, Hangzhou, 310030, China
| | - Jixian Liu
- Department of Thoracic Surgery, Peking University Shenzhen Hospital, Shenzhen Peking University, The Hong Kong University of Science and Technology Medical Center, Shenzhen, 518035, China.
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Albadari N, Xie Y, Li W. Deciphering treatment resistance in metastatic colorectal cancer: roles of drug transports, EGFR mutations, and HGF/c-MET signaling. Front Pharmacol 2024; 14:1340401. [PMID: 38269272 PMCID: PMC10806212 DOI: 10.3389/fphar.2023.1340401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 12/27/2023] [Indexed: 01/26/2024] Open
Abstract
In 2023, colorectal cancer (CRC) is the third most diagnosed malignancy and the third leading cause of cancer death worldwide. At the time of the initial visit, 20% of patients diagnosed with CRC have metastatic CRC (mCRC), and another 25% who present with localized disease will later develop metastases. Despite the improvement in response rates with various modulation strategies such as chemotherapy combined with targeted therapy, radiotherapy, and immunotherapy, the prognosis of mCRC is poor, with a 5-year survival rate of 14%, and the primary reason for treatment failure is believed to be the development of resistance to therapies. Herein, we provide an overview of the main mechanisms of resistance in mCRC and specifically highlight the role of drug transports, EGFR, and HGF/c-MET signaling pathway in mediating mCRC resistance, as well as discuss recent therapeutic approaches to reverse resistance caused by drug transports and resistance to anti-EGFR blockade caused by mutations in EGFR and alteration in HGF/c-MET signaling pathway.
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Affiliation(s)
| | | | - Wei Li
- College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, United States
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Ma S, Li X, Wu W, Zhang P, Yang Y, Huang L, Wan Q. Screening and identification of hub genes of scar physique via weighted gene co-expression network analysis. Medicine (Baltimore) 2023; 102:e36077. [PMID: 37986383 PMCID: PMC10659739 DOI: 10.1097/md.0000000000036077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/23/2023] [Accepted: 10/20/2023] [Indexed: 11/22/2023] Open
Abstract
Scar physique refers to the abnormal repair of skin injury in some people, which may easily lead to keloid or hypertrophic scar. However, the mechanism of scar physique is still unclear. GSE108110 was obtained from the gene expression omnibus database. Differently expression genes (DEGs) between normal skin tissue of non-scar physique individuals and normal skin tissue of scar physique individuals were screened by R package "limma". Weighted gene co-expression network analysis was performed to find highly relevant gene modules. Functional annotation of DEGs was made. Protein-protein interaction network was constructed, and the identification and analysis of hub DEGs were performed, including identification of hub DEGs associated with scar diseases, MiRNA of hub DEGs prediction, and functional annotation of miRNA. A total of 1389 up-regulate DEGs and 1672 down-regulate DEGs were screened. weighted gene co-expression network analysis analysis showed that the dendrogram and heatmap were used to quantify module similarity by correlation. The associations between clinic traits and the modules were identified based on the correlation between module and scar physique. Eight common hub genes were obtained. The comparative toxicogenomics database shows common hub genes associated with scar tissue. Gene ontology and Kyoto encyclopedia of genes and genomes analysis were significantly enriched in "fibroblast growth factor receptor signaling pathway", "epidermal growth factor receptor signaling pathway", "G1/S transition of mitotic cell cycle", protein polyubiquitination", and others. The 8 hub genes might be involved in the development of scarring and used as early diagnosis, prevention and treatment of scar physique.
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Affiliation(s)
- Shuxian Ma
- Department of Anesthesiology, The Second Hospital of Hebei Medical University, Xinhua District, Shijiazhuang City, Hebei Province, China
| | - Xuze Li
- Department of Anesthesiology, The Second Hospital of Hebei Medical University, Xinhua District, Shijiazhuang City, Hebei Province, China
| | - Wenhao Wu
- Department of Anesthesiology, The Second Hospital of Hebei Medical University, Xinhua District, Shijiazhuang City, Hebei Province, China
| | - Pei Zhang
- Intensive Care Unit of Department of Anesthesiology, The Second Hospital of Hebei Medical University, Xinhua District, Shijiazhuang City, Hebei Province, China
| | - Yanjie Yang
- Department of Anesthesiology, The Second Hospital of Hebei Medical University, Xinhua District, Shijiazhuang City, Hebei Province, China
| | - Lining Huang
- Department of Anesthesiology, The Second Hospital of Hebei Medical University, Xinhua District, Shijiazhuang City, Hebei Province, China
| | - Qian Wan
- Department of Anesthesiology, The Second Hospital of Hebei Medical University, Xinhua District, Shijiazhuang City, Hebei Province, China
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Gao Y, Guan L, Jia R, Xiao W, Han Y, Li Y, Tang P, Yu Z, Zhang H. High expression of PPFIA1 in human esophageal squamous cell carcinoma correlates with tumor metastasis and poor prognosis. BMC Cancer 2023; 23:417. [PMID: 37158817 PMCID: PMC10169376 DOI: 10.1186/s12885-023-10872-9] [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: 12/28/2022] [Accepted: 04/21/2023] [Indexed: 05/10/2023] Open
Abstract
BACKGROUND PTPRF interacting protein alpha 1 (PPFIA1) is reportedly related to the occurrence and progression of several kinds of malignancies. However, its role in esophageal squamous cell carcinoma (ESCC) is unclear. This current study investigated the prognostic significance and biological functions of PPFIA1 in ESCC. METHODS Oncomine, Gene Expression Profiling Interactive Analysis (GEPIA), and Gene Expression Omnibus (GEO) were used to investigate PPFIA1 expression in esophageal cancer. The relationship between PPFIA1 expression and clinicopathological characteristics and patient survival was evaluated in GSE53625 dataset, and verified in the cDNA array based on qRT-PCR and tissue microarray (TMA) dataset based on immunohistochemistry. The impact of PPFIA1 on the migration and invasion of cancer cells were investigated by wound-healing and transwell assays, respectively. RESULTS The expression of PPFIA1 was obviously increased in ESCC tissues versus adjacent esophageal tissues according to online database analyses (all P < 0.05). High PPFIA1 expression was closely related to several clinicopathological characteristics, including tumor location, histological grade, tumor invasion depth, lymph node metastasis, and tumor-node-metastasis (TNM) stage. High PPFIA1 expression was related to worse outcomes and was identified as an independent prognostic factor of overall survival in ESCC patients (GSE53625 dataset, P = 0.019; cDNA array dataset, P < 0.001; TMA dataset, P = 0.039). Downregulation of PPFIA1 expression can significantly reduce the migration and invasion ability of ESCC cells. CONCLUSION PPFIA1 is related to the migration and invasion of ESCC cells, and can be used as a potential biomarker to evaluate the prognosis of ESCC patients.
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Affiliation(s)
- Yongyin Gao
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin, 300060, China
| | - Lizhao Guan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Ran Jia
- National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and PeKing Union Medical College, Shenzhen, 518116, China
| | - Wanyi Xiao
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin, 300060, China
| | - Youming Han
- Binhai Hospital of Tianjin Medical University General Hospital, Tianjin, 300456, China
| | - Yue Li
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin, 300060, China
| | - Peng Tang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin, 300060, China.
| | - Zhentao Yu
- National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and PeKing Union Medical College, Shenzhen, 518116, China.
| | - Hongdian Zhang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin, 300060, China.
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Mokhtari K, Peymani M, Rashidi M, Hushmandi K, Ghaedi K, Taheriazam A, Hashemi M. Colon cancer transcriptome. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023; 180-181:49-82. [PMID: 37059270 DOI: 10.1016/j.pbiomolbio.2023.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/31/2023] [Accepted: 04/06/2023] [Indexed: 04/16/2023]
Abstract
Over the last four decades, methodological innovations have continuously changed transcriptome profiling. It is now feasible to sequence and quantify the transcriptional outputs of individual cells or thousands of samples using RNA sequencing (RNA-seq). These transcriptomes serve as a connection between cellular behaviors and their underlying molecular mechanisms, such as mutations. This relationship, in the context of cancer, provides a chance to unravel tumor complexity and heterogeneity and uncover novel biomarkers or treatment options. Since colon cancer is one of the most frequent malignancies, its prognosis and diagnosis seem to be critical. The transcriptome technology is developing for an earlier and more accurate diagnosis of cancer which can provide better protectivity and prognostic utility to medical teams and patients. A transcriptome is a whole set of expressed coding and non-coding RNAs in an individual or cell population. The cancer transcriptome includes RNA-based changes. The combined genome and transcriptome of a patient may provide a comprehensive picture of their cancer, and this information is beginning to affect treatment decision-making in real-time. A full assessment of the transcriptome of colon (colorectal) cancer has been assessed in this review paper based on risk factors such as age, obesity, gender, alcohol use, race, and also different stages of cancer, as well as non-coding RNAs like circRNAs, miRNAs, lncRNAs, and siRNAs. Similarly, they have been examined independently in the transcriptome study of colon cancer.
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Affiliation(s)
- Khatere Mokhtari
- Department of Modern Biology, ACECR Institute of Higher Education (Isfahan Branch), Isfahan, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| | - Mohsen Rashidi
- Department Pharmacology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, 4815733971, Iran; The Health of Plant and Livestock Products Research Center, Mazandaran University of Medical Sciences, Sari, 4815733971, Iran
| | - Kiavash Hushmandi
- Department of Food Hygiene and Quality Control, Division of Epidemiology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
| | - Afshin Taheriazam
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Orthopedics, Faculty of Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Mehrdad Hashemi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
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Sun W, Zhao F, Hu T, Wu Z, Xu Y, Dong Y, Zheng B, Wang C, Yan W, Zhu X, Wu J, McKay MJ, Arozarena I, Alos L, Teixido C, Chen Y. Oncogenic alterations reveal key strategies for precision oncology in melanoma treatment. ANNALS OF TRANSLATIONAL MEDICINE 2022; 10:1246. [PMID: 36544693 PMCID: PMC9761125 DOI: 10.21037/atm-22-5346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 11/18/2022] [Indexed: 11/29/2022]
Abstract
Background Molecular profiling with next-generation sequencing (NGS) has been applied in multiple solid tumors, including melanomas, to identify potential drug targets. However, the association between clinical outcomes and the molecular alterations has not yet been fully clarified. Methods A total of 108 patients with melanoma were included in this study, 95 of whom had both sequencing data and clinical outcomes were collected. We analyzed the genetic alterations of 108 malignant melanoma patients using the OncoCare panel, which covers 559 genes. Results A model was also established to predict side effects through a combination analysis of clinical data and somatic variants, yielding an area under the receiver operating characteristic curve (AUROC) score of 0.8. We also identified epidermal growth factor receptor (EGFR) mutation was excellent predictor for progression-free survival (PFS) for patient who received immunotherapy (log-rank P=0.01), while tumor mutation burden (TMB) was found to not be significantly associated with PFS (log-rank P=0.87). Combining clinical features with genetic analysis, we found that patients carrying both DNA POLD1/ALOX12B or POLD1/PTPRT mutations had a significantly lower survival rate. Conclusions Overall, these results demonstrate the benefits of applying NGS clinical panels and shed light on future directions of personalized therapeutics for the treatment of melanoma.
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Affiliation(s)
- Wei Sun
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai, China;,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Fang Zhao
- Department of Dermatology, University Hospital Essen, Essen, Germany
| | - Tu Hu
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai, China;,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhiqiang Wu
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai, China;,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yu Xu
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai, China;,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yan Dong
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai, China;,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Biqiang Zheng
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai, China;,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chunmeng Wang
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai, China;,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wangjun Yan
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai, China;,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiaoli Zhu
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China;,Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Jian Wu
- MyGenostics Inc., Beijing, China
| | - Michael J. McKay
- Department of Radiation Oncology, Northern Cancer Service, Burnie, Australia
| | - Imanol Arozarena
- Navarrabiomed-Fundación Miguel Servet-Idisna, Complejo Hospitalario de Navarra, Pamplona, Spain
| | - Llucia Alos
- Department of Pathology, Hospital Clinic of Barcelona, Barcelona, Spain
| | - Cristina Teixido
- Department of Pathology, Hospital Clinic of Barcelona, Barcelona, Spain
| | - Yong Chen
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai, China;,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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Shang X, Zhang W, Zhang X, Yu M, Liu J, Cheng Y, Cheng B. PTPRD/PTPRT mutation as a predictive biomarker of immune checkpoint inhibitors across multiple cancer types. Front Immunol 2022; 13:991091. [PMID: 36248841 PMCID: PMC9556668 DOI: 10.3389/fimmu.2022.991091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 09/13/2022] [Indexed: 11/23/2022] Open
Abstract
Background Immune checkpoint inhibitors (ICIs) are dramatically changing the treatment landscape of a variety of cancers. Nevertheless, the variability in ICI responses highlight the importance in identifying predictive biomarkers. PTPRD and PTPRT (PTPRD/PTPRT) are the phosphatases of JAK-STAT signaling, a critical pathway in anti-cancer immunity regulation. However, the pan-cancer association between PTPRD/PTPRT mutation and the efficacy of ICIs remains unclear across pan-cancer patients. Methods We analyzed the association between PTPRD/PTPRT mutations and patient outcomes using clinical data and genomic mutations from TCGA pan-cancer cohort. Furthermore, the ICI-treatment cohort was used to evaluate the relationship between PTPRD/PTPRT mutation and the efficacy of ICIs. Another ICIs-treatment cohort was used to validate the findings. The TCGA pan-cancer dataset was analyzed to explore the correlation between PTPRD/PTPRT mutations and immune signatures. Moreover, we combined four factors to construct a nomogram model that could be used to predict the survival of pan-cancer patients receiving ICI treatment. The calibration curves and area under the curve were applied to assess the performance of the model. Results PTPRD/PTPRT mutations were shown to be associated with a worse prognosis in TCGA cohort (P < 0.05). In the Samstein cohort, prolonged overall survival (OS) was observed in PTPRD/PTPRT mutant cancers, compared with wild-type cancers (mOS: 40.00 vs 16.00 months, HR = 0.570, 95%CI: 0.479-0.679, P < 0.0001). In the validation cohort, significant OS advantage was observed in PTPRD/PTPRT mutant patients (mOS: 31.32 vs 15.53 months, HR = 0.658, 95%CI: 0.464-0.934, P = 0.0292). Furthermore, PTPRD/PTPRT mutations were associated with a higher tumor mutational burden, MSI score, and TCR score (P < 0.0001). Enhanced immune signatures were found in the PTPRD/PTPRT mutant cancers (P < 0.05). Finally, we successfully established a nomogram model that could be used to predict the survival of NSCLC patients who received ICI treatment. Based on the risk score of the model, patients in the low-risk group showed a better mOS than those in the high-risk group (mOS: 2.75 vs 1.08 years, HR = 0.567, 95%CI: 0.492-0.654; P < 0.001). Conclusions PTPRD/PTPRT mutations may be a potential biomarker for predicting ICI treatment responsiveness in multiple cancer types.
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Affiliation(s)
- Xiaoling Shang
- Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Wengang Zhang
- Department of Medical Oncology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xun Zhang
- Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Miao Yu
- Shandong Provincial Third Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jingwen Liu
- The Internet of Things, Shandong University of Science and Technology, Qingdao, China
| | - Yufeng Cheng
- Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Bo Cheng
- Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, China
- *Correspondence: Bo Cheng,
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Liang Q, Peng J, Xu Z, Li Z, Jiang F, Ouyang L, Wu S, Fu C, Liu Y, Liu Y, Yan Y. Pan-cancer analysis of the prognosis and immunological role of AKAP12: A potential biomarker for resistance to anti-VEGF inhibitors. Front Genet 2022; 13:943006. [PMID: 36110213 PMCID: PMC9468827 DOI: 10.3389/fgene.2022.943006] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
The primary or acquired resistance to anti-VEGF inhibitors remains a common problem in cancer treatment. Therefore, identifying potential biomarkers enables a better understanding of the precise mechanism. Through the GEO database, three profiles associated with bevacizumab (BV) resistance to ovarian cancer, glioma, and non-small-cell lung carcinoma, respectively, were collected for the screening process, and two genes were found. A-kinase anchor protein 12 (AKAP12), one of these two genes, correlates with tumorigenesis of some cancers. However, the role of AKAP12 in pan-cancer remains poorly defined. The present study first systematically analyzed the association of AKAP12 with anti-VEGF inhibitors’ sensitivity, clinical prognosis, DNA methylation, protein phosphorylation, and immune cell infiltration across various cancers via bioinformatic tools. We found that AKAP12 was upregulated in anti-VEGF therapy-resistant cancers, including ovarian cancer (OV), glioblastoma (GBM), lung cancer, and colorectal cancer (CRC). A high AKAP12 expression revealed dismal prognoses in OV, GBM, and CRC patients receiving anti-VEGF inhibitors. Moreover, AKAP12 expression was negatively correlated with cancer sensitivity towards anti-VEGF therapy. Clinical prognosis analysis showed that AKAP12 expression predicted worse prognoses of various cancer types encompassing colon adenocarcinoma (COAD), OV, GBM, and lung squamous cell carcinoma (LUSC). Gene mutation status may be a critical cause for the involvement of AKAP12 in resistance. Furthermore, lower expression of AKAP12 was detected in nearly all cancer types, and hypermethylation may explain its decreased expression. A decreased phosphorylation of T1760 was observed in breast cancer, clear-cell renal cell carcinoma, and lung adenocarcinoma. For the immunologic significance, AKAP12 was positively related to the abundance of pro-tumor cancer-associated fibroblasts (CAFs) in various types of cancer. The results of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis suggested that “cell junction organization” and “MAPK pathway” participated in the effect of AKAP12. Importantly, we discovered that AKAP12 expression was greatly associated with metastasis of lung adenocarcinoma as well as differential and angiogenesis of retinoblastoma through investigating the single-cell sequencing data. Our study showed that the dual role of AKAP12 in various cancers and AKAP12 could serve as a biomarker of anti-VEGF resistance in OV, GBM, LUSC, and COAD.
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Affiliation(s)
- Qiuju Liang
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Institute for Rational and Safe Medication Practices, Xiangya Hospital, Central South University, Changsha, China
| | - Jinwu Peng
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
- Department of Pathology, Xiangya Changde Hospital, Changde, China
| | - Zhijie Xu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Zhilan Li
- Department of Pathology, Xiangya Changde Hospital, Changde, China
| | - Feng Jiang
- Department of Pathology, Xiangya Changde Hospital, Changde, China
| | - Lingzi Ouyang
- Department of Pathology, Xiangya Changde Hospital, Changde, China
| | - Shangjun Wu
- Department of Pathology, Xiangya Changde Hospital, Changde, China
| | - Chencheng Fu
- Department of Pathology, Xiangya Changde Hospital, Changde, China
| | - Ying Liu
- Department of Pathology, Xiangya Changde Hospital, Changde, China
| | - Yuanhong Liu
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Institute for Rational and Safe Medication Practices, Xiangya Hospital, Central South University, Changsha, China
| | - Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Institute for Rational and Safe Medication Practices, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Yuanliang Yan,
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11
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Tsai C, Nguyen B, Luthra A, Chou JF, Feder L, Tang LH, Strong VE, Molena D, Jones DR, Coit DG, Ilson DH, Ku GY, Cowzer D, Cadley J, Capanu M, Schultz N, Beal K, Moss NS, Janjigian YY, Maron SB. Outcomes and Molecular Features of Brain Metastasis in Gastroesophageal Adenocarcinoma. JAMA Netw Open 2022; 5:e2228083. [PMID: 36001319 PMCID: PMC9403772 DOI: 10.1001/jamanetworkopen.2022.28083] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
IMPORTANCE Brain metastasis (BrM) in gastroesophageal adenocarcinoma (GEA) is a rare and poorly understood phenomenon associated with poor prognosis. OBJECTIVES To examine the clinical and genomic features of patients with BrM from GEA and evaluate factors associated with survival. DESIGN, SETTING, AND PARTICIPANTS In this single-institution retrospective cohort study, 68 patients with BrM from GEA diagnosed between January 1, 2008, and December 31, 2020, were identified via review of billing codes and imaging reports from the electronic medical record with follow-up through November 3, 2021. Genomic data were derived from the Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets clinical sequencing platform. EXPOSURES Treatment with BrM resection and/or radiotherapy. MAIN OUTCOMES AND MEASURES Overall survival after BrM diagnosis. RESULTS Sixty-eight patients (median age at diagnosis, 57.4 years [IQR, 49.8-66.4 years]; 59 [86.8%] male; 55 [85.9%] White) participated in the study. A total of 57 (83.8%) had primary tumors in the distal esophagus or gastroesophageal junction. Median time from initial diagnosis to BrM diagnosis was 16.9 months (IQR, 8.5-27.7 months). Median survival from BrM diagnosis was 8.7 months (95% CI, 5.5-11.5 months). Overall survival was 35% (95% CI, 25%-48%) at 1 year and 24% (95% CI, 16%-37%) at 2 years. In a multivariable analysis, an Eastern Cooperative Oncology Group performance status of 2 or greater (hazard ratio [HR], 4.66; 95% CI, 1.47-14.70; P = .009) and lack of surgical or radiotherapeutic intervention (HR, 7.71; 95% CI, 2.01-29.60; P = .003) were associated with increased risk of all-cause mortality, whereas 3 or more extracranial sites of disease (HR, 1.85; 95% CI, 0.64-5.29; P = .25) and 4 or more BrMs (HR, 2.15; 95% CI, 0.93-4.98; P = .07) were not statistically significant. A total of 31 patients (45.6%) had ERBB2 (formerly HER2 or HER2/neu)-positive tumors, and alterations in ERBB2 were enriched in BrM relative to primary tumors (8 [47.1%] vs 7 [20.6%], P = .05), as were alterations in PTPRT (7 [41.2%] vs 4 [11.8%], P = .03). CONCLUSIONS AND RELEVANCE This study suggests that that a notable proportion of patients with BrM from GEA achieve survival exceeding 1 and 2 years from BrM diagnosis, a more favorable prognosis than previously reported. Good performance status and treatment with combination surgery and radiotherapy were associated with the best outcomes. ERBB2 positivity and amplification as well as PTPRT alterations were enriched in BrM tissue compared with primary tumors; therefore, further study should be pursued to identify whether these variables represent genomic risk factors for BrM development.
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Affiliation(s)
- Charlton Tsai
- Department of Medicine, New York Presbyterian/Weill Cornell Medicine, New York, New York
| | - Bastien Nguyen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Anisha Luthra
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Joanne F. Chou
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lara Feder
- Division of Solid Tumor Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Laura H. Tang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Vivian E. Strong
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Daniela Molena
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David R. Jones
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Daniel G. Coit
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David H. Ilson
- Division of Solid Tumor Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Geoffrey Y. Ku
- Division of Solid Tumor Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Darren Cowzer
- Division of Solid Tumor Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - John Cadley
- Department of Digital Informatics and Technology Solutions, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marinela Capanu
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nikolaus Schultz
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kathryn Beal
- Department of Radiation Oncology and Brain Metastasis Center, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nelson S. Moss
- Department of Neurosurgery and Brain Metastasis Center, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yelena Y. Janjigian
- Division of Solid Tumor Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Steven B. Maron
- Division of Solid Tumor Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
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12
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Association of PTPRT Mutations with Cancer Metastasis in Multiple Cancer Types. BIOMED RESEARCH INTERNATIONAL 2022; 2022:9386477. [PMID: 35789644 PMCID: PMC9250438 DOI: 10.1155/2022/9386477] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/21/2022] [Accepted: 05/30/2022] [Indexed: 11/18/2022]
Abstract
Metastasis is one of the characteristics of advanced cancer and the primary cause of cancer-related deaths from cancer, but the mechanism underlying metastasis is unclear, and there is a lack of metastasis markers. PTPRT is a protein-coding gene involved in both signal transduction and cellular adhesion. It is also known as a tumor suppressor gene that inhibits cell malignant proliferation by inhibiting the STAT3 pathway. Recent studies have reported that PTPRT is involved in the early metastatic seeding of colorectal cancer; however, the correlation between PTPRT and metastasis in other types of cancer has not been revealed. A combined analysis using a dataset from the genomics evidence neoplasia information exchange (GENIE) and cBioPortal revealed that PTPRT mutation is associated with poor prognosis in pan-cancer and non-small-cell lung cancer. The mutations of PTPRT or “gene modules” containing PTPRT are significantly enriched in patients with metastatic cancer in multiple cancers, suggesting that the PTPRT mutations serve as potential biomarkers of cancer metastasis.
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13
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Ou C, Peng Q, Zeng C. An integrative prognostic and immune analysis of PTPRD in cancer. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2022; 19:5361-5379. [PMID: 35603359 DOI: 10.3934/mbe.2022251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
PTPRD plays an indispensable role in the occurrence of multiple tumors. However, pan-cancer analysis is unavailable. The purpose of this research was to preliminarily study its prognostic landscape across various tumors and investigate its relationship with immunotherapy. We exhibited the expression profile, survival analysis, and genomic alterations of PTPRD based on the TIMER, GEPIA, UALCAN, PrognoScan and cBioPortal database. The frequency of PTPRD mutation and its correlation with response to immunotherapy were evaluated using the cBioPortal database. The relationship between PTPRD and immune-cell infiltration was analyzed by the TIMER and TISIDB databases. A protein interaction network was constructed by the STRING database. GO and KEGG enrichment analysis was executed by the Metascape database. A correlation between PTPRD expression and prognosis was found in various cancers. Aberrant PTPRD expression was closely related to immune infiltration. In non-small cell lung cancer and melanoma, patients with PTPRD mutations had better overall survival with immune checkpoint inhibitors, and these patients had higher TMB scores. PTPRD mutation was involved in numerous biological processes, including immunological signaling pathways. A PTPRD protein interaction network was constructed, and genes that interacted with PTPRD were identified. Functional enrichment analysis demonstrated that a variety of GO biological processes and KEGG pathways associated with PTPRD were involved in the therapeutic mechanisms. These results revealed that PTPRD might function as a biomarker for prognosis and immune infiltration in cancers, throwing new light on cancer therapeutics.
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Affiliation(s)
- Chunpei Ou
- Department of Orthopedics and Traumatology, Shenzhen Longhua District Central Hospital, Shenzhen 518110, China
| | - Qin Peng
- Department of Health Management, Shenzhen Longhua District Central Hospital, Shenzhen 518110, China
| | - Changchun Zeng
- Department of Medical Laboratory, Shenzhen Longhua District Central Hospital, Guangdong Medical University, Shenzhen 518110, China
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14
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Zhang W, Shi F, Kong Y, Li Y, Sheng C, Wang S, Wang Q. Association of PTPRT mutations with immune checkpoint inhibitors response and outcome in melanoma and non-small cell lung cancer. Cancer Med 2021; 11:676-691. [PMID: 34862763 PMCID: PMC8817076 DOI: 10.1002/cam4.4472] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 10/13/2021] [Accepted: 11/18/2021] [Indexed: 12/18/2022] Open
Abstract
Purpose Protein tyrosine phosphatase receptor type T (PTPRT), which is a well‐known phosphatase and mutates frequently in melanoma and non‐small cell lung cancer (NSCLC). Our research aims to elucidate its mutation association with immune checkpoint inhibitors (ICI) efficacy. Methods We integrated whole‐exome sequencing (WES)‐based somatic mutation profiles and clinical characteristics of 631 melanoma samples received ICI agents from eight studies and 109 NSCLC samples from two studies. For validation, 321 melanoma and 350 NSCLC immunotherapy samples with targeted next‐generation sequencing (NGS) were employed. Besides, an independent NSCLC cohort contained 240 samples was also collected for further corroboration. Distinct immune infiltration was evaluated according to the PTPRT mutational status. Results In the WES melanoma cohort, patients with PTPRT mutations harbored a significantly elevated ICI response rate (40.5% vs. 28.6%, p = 0.036) and a prolonged survival outcome (35.3 vs. 24.9 months, p = 0.006). In the WES NSCLC cohort, the favorable response and immunotherapy survival were also observed in PTPRT‐mutated patients (p = 0.036 and 0.019, respectively). For the validation cohorts, the associations of PTRPT mutations with better prognoses were identified in melanoma, NSCLC, and pan‐cancer patients with targeted‐NGS (all p < 0.05). Moreover, immunology analyses showed the higher mutation burden, increased lymphocyte infiltration, decreased‐ activated‐stroma, and immune response pathways were detected in patients with PTPRT mutations. Conclusion Our investigation indicates that PTPRT mutations may be considered as a potential indicator for assessing ICI efficacy in melanoma and NSCLC, even across multiple cancers. Further prospective validation cohorts are warranted.
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Affiliation(s)
- Wenjing Zhang
- Department of Health Statistics, Key Laboratory of Medicine and Health of Shandong Province, School of Public Health, Weifang Medical University, Weifang, China
| | - Fuyan Shi
- Department of Health Statistics, Key Laboratory of Medicine and Health of Shandong Province, School of Public Health, Weifang Medical University, Weifang, China
| | - Yujia Kong
- Department of Health Statistics, Key Laboratory of Medicine and Health of Shandong Province, School of Public Health, Weifang Medical University, Weifang, China
| | - Yuting Li
- Tianjin Cancer Institute, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Chao Sheng
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Suzhen Wang
- Department of Health Statistics, Key Laboratory of Medicine and Health of Shandong Province, School of Public Health, Weifang Medical University, Weifang, China
| | - Qinghua Wang
- Department of Health Statistics, Key Laboratory of Medicine and Health of Shandong Province, School of Public Health, Weifang Medical University, Weifang, China
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15
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Watts K, Wills C, Madi A, Palles C, Maughan TS, Kaplan R, Al-Tassan NA, Kerr R, Kerr D, Gray V, West H, Houlston RS, Escott-Price V, Cheadle JP. Genome-wide association studies of toxicity to oxaliplatin and fluoropyrimidine chemotherapy with or without cetuximab in 1800 patients with advanced colorectal cancer. Int J Cancer 2021; 149:1713-1722. [PMID: 34270794 DOI: 10.1002/ijc.33739] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/12/2021] [Accepted: 06/08/2021] [Indexed: 01/03/2023]
Abstract
Chemotherapies administered at normal therapeutic dosages can cause significant side-effects and may result in early treatment discontinuation. Inter-individual variation in toxicity highlights the need for biomarkers to personalise treatment. We sought to identify such biomarkers by conducting 40 genome-wide association studies, together with gene and gene set analyses, for any toxicity and 10 individual toxicities in 1800 patients with advanced colorectal cancer treated with oxaliplatin and fluoropyrimidine chemotherapy ± cetuximab from the MRC COIN and COIN-B trials (385 patients received FOLFOX, 360 FOLFOX + cetuximab, 707 XELOX and 348 XELOX + cetuximab). Single nucleotide polymorphisms (SNPs), genes and gene sets that reached genome-wide or suggestive significance were validated in independent patient groups. We found that MROH5 was significantly associated with neutropenia in MAGMA gene analyses in patients treated with XELOX (P = 6.6 × 10-7 ) and was independently validated in those receiving XELOX + cetuximab; pooled P = 3.7 × 10-7 . rs13260246 at 8q21.13 was significantly associated with vomiting in patients treated with XELOX (odds ratio = 5.0, 95% confidence interval = 3.0-8.3, P = 9.8 × 10-10 ) but was not independently replicated. SNPs at 139 loci had suggestive associations for toxicities and lead SNPs at five of these were independently validated (rs6030266 with diarrhoea, rs1546161 with hand-foot syndrome, rs9601722 with neutropenia, rs13413764 with lethargy and rs4600090 with nausea; all with pooled P's < 5.0 × 10-6 ). In conclusion, the association of MROH5 with neutropenia and five other putative biomarkers warrant further investigation for their potential clinical utility. Despite our comprehensive genome-wide analyses of large, well-characterised, clinical trials, we found a lack of common variants with modest effect sizes associated with toxicities.
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Affiliation(s)
- Katie Watts
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Christopher Wills
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Ayman Madi
- The Clatterbridge Cancer Centre NHS Foundation Trust, Bebington, UK
| | - Claire Palles
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, University of Birmingham, Birmingham, UK
| | - Timothy S Maughan
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Richard Kaplan
- MRC Clinical Trials Unit, University College of London, London, UK
| | - Nada A Al-Tassan
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Rachel Kerr
- Department of Oncology, University of Oxford, Oxford, UK
| | - David Kerr
- Nuffield Department of Clinical Laboratory Sciences, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Victoria Gray
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Hannah West
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Valentina Escott-Price
- Institute of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Jeremy P Cheadle
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, UK
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16
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Sun Y, Duan J, Fang W, Wang Z, Du X, Wang X, Li C, Cai S, Zhao J, Li S, Zhang L, Bai H, Wang J. Identification and validation of tissue or ctDNA PTPRD phosphatase domain deleterious mutations as prognostic and predictive biomarkers for immune checkpoint inhibitors in non-squamous NSCLC. BMC Med 2021; 19:239. [PMID: 34615542 PMCID: PMC8496052 DOI: 10.1186/s12916-021-02075-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 07/27/2021] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND With the revolutionary progress of immune checkpoint inhibitors (ICIs) achieved in non-small cell lung cancers (NSCLC), identifying patients benefiting from ICIs becomes critical and urgent. The associations of genomic alterations in protein tyrosine phosphatase receptor-type (PTPRs) and ICIs responses are unknown. METHODS Whole-exome sequencing (WES) of 73 advanced NSCLC tumors sampled before anti-PD-(L)1 therapy was carried out with corresponding clinical data collected as a discovery cohort to find the associations of PTPR mutations and ICI responses. Three validation cohorts consolidated by 7 public cohorts of 1920 NSCLC patients with WES or target sequencing data of tumor tissue-derived DNA or circulating tumor DNA (ctDNA) and relevant clinical data were applied as validation cohorts. The lung adenocarcinoma (LUAD) cohort (n=586) in The Cancer Genome Atlas (TCGA) database was used for analyzing the potential anti-tumor immunologic mechanisms. RESULTS With the highest mutation frequency among all PTPRs, PTPRD mutations in non-squamous NSCLC (ns-NSCLC) were linked to longer progression-free survivals (PFS, 324 vs 63 days, hazard ratio (HR)=0.36, p= 0.0152) and higher objective response rate (ORR, p=0.0099). In validation cohort 1 (n=377), ns-NSCLC patients with tissue PTPRD mutations had favorable PFS (9.10 vs 4.33 months, HR=0.62, p=0.0184) and ORR (p=0.013). In validation cohort 2 (n=406), ns-NSCLC patients with tissue PTPRD mutations had favorable overall survivals (OS, over 40 vs 11.94 months, HR=0.57, p=0.011). In validation cohort 3 (n=1137), ns-NSCLC patients with ctDNA PTPRD mutations had longer PFS (6.97 vs 2.73 months, HR=0.63, p=0.028) and higher ORR (p=0.047). Moreover, it was deleterious mutations in phosphatase domains (phosphatase-mut), rather than other mutations (other-mut), that were responsible of PTPRD's prediction efficiency. In addition, in validation cohort 3, ctDNA phosphatase-mut also functioned as a predictive biomarker helping identify patients benefiting more from ICIs than chemotherapy (interaction P for PFS=0.0506, for OS=0.04). Univariate and multivariate regression analysis revealed that phosphatase-mut was independent on PD-L1 expression and tumor mutation burden (TMB) to predict. In silico analysis based on TCGA LUAD cohort discovered enhanced anti-tumor immunity in phosphatase-mut patients. CONCLUSIONS Tissue or ctDNA PTPRD phosphatase domain deleterious mutations might function as a both prognostic and predictive biomarker predicting clinical outcomes of ICIs in ns-NSCLC patients, independent on TMB or PD-L1 expression.
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Affiliation(s)
- Yiting Sun
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 17 Pan-jia-yuan South Lane, Chaoyang District, Beijing, 100021, China
| | - Jianchun Duan
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 17 Pan-jia-yuan South Lane, Chaoyang District, Beijing, 100021, China
| | - Wenfeng Fang
- Medical Oncology, Sun Yat-sen University Cancer Center, 651# East Dong Feng Road, Guangzhou, 510060, Guangdong, China
| | - Zhijie Wang
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 17 Pan-jia-yuan South Lane, Chaoyang District, Beijing, 100021, China
| | - Xinyang Du
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 17 Pan-jia-yuan South Lane, Chaoyang District, Beijing, 100021, China
| | - Xin Wang
- Thoracic Surgery Department, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chengcheng Li
- The Medical Department, Burning Rock Biotech, Guangzhou, China
| | - Shangli Cai
- The Medical Department, Burning Rock Biotech, Guangzhou, China
| | - Jie Zhao
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 17 Pan-jia-yuan South Lane, Chaoyang District, Beijing, 100021, China
| | - Sini Li
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 17 Pan-jia-yuan South Lane, Chaoyang District, Beijing, 100021, China
| | - Li Zhang
- Medical Oncology, Sun Yat-sen University Cancer Center, 651# East Dong Feng Road, Guangzhou, 510060, Guangdong, China.
| | - Hua Bai
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 17 Pan-jia-yuan South Lane, Chaoyang District, Beijing, 100021, China.
| | - Jie Wang
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 17 Pan-jia-yuan South Lane, Chaoyang District, Beijing, 100021, China.
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17
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Gao J, Li F, Liu Z, Huang M, Chen H, Liao G, Meng J, Wang Q, Zhao H, Li C, Ji J, Cai S, Du N. Multiple genetic variants predict the progression-free survival of bevacizumab plus chemotherapy in advanced ovarian cancer: A retrospective study. Medicine (Baltimore) 2021; 100:e27130. [PMID: 34477158 PMCID: PMC8415939 DOI: 10.1097/md.0000000000027130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 06/17/2021] [Indexed: 12/25/2022] Open
Abstract
Bevacizumab (BV) plus chemotherapy is broadly used in advanced ovarian cancer (OC). However, the efficacy of BV-based regimens for advanced OC patients is not satisfactory. Therefore, it is urgent to explore the predictive genetic biomarkers for BV.Tumor tissues from advanced OC patients receiving BV-based regimens were analyzed with a 150-gene targeted panel for next generation sequencing. The associations between gene alterations or clinicopathology features and progression-free survival (PFS) were analyzed by Kaplan-Meier curves or Cox regression. The association of the genetic alteration in potential predictive genes and expressions of 11 vascular endothelial growth factor-related genes were analyzed in The Cancer Genome Atlas cohort using 292 OC cases.Sixty two Chinese advanced OC patients treated with BV-based therapy were included. The median PFS of was 6.9 months, and objective response rate was 14.5%. In multivariate Cox regression analysis, the status of endothelial growth factor receptor (EGFR) (hazard ratio = 6.39, 95% confidence interval [CI] 2.25-18.13, P < .001) and human epidermal growth factor receptor 2 (HER2) (hazard ratio = 3.58, 95% CI 1.27-10.08, P = .016) were significantly correlated with PFS. MYC Proto-Oncogene amplification seemed to have a positive trend (hazard ratio = 0.21, 95% CI 0.05-1.02, P = .052). Moreover, EGFR and HER2 alterations were not prognostic factors of overall survival for OC in The Cancer Genome Atlas OC cohort. The vascular endothelial growth factor-related signature analysis indicated vascular endothelial factor A expression was upregulated with EGFR alterations (P = .034) which may be involved in BV resistance, and HER2 alterations were associated with hypoxia inducible factor 1 subunit alpha overexpression significantly (P = .029).EGFR or HER2 alterations are negative predictors of PFS for OC patient treated with BV plus chemotherapy. Therefore, the clinicians may consider to use alternative regimens such as anti-EGFR or anti-HER2 targeted therapy instead of BV-based regimens on these patients when standard care fail.
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Affiliation(s)
- Jie Gao
- Department of Oncology, First Affiliated Hospital of PLA General Hospital, China
| | - Fang Li
- Department of Medical Oncology, Chinese PLA General Hospital, China
| | - Zihao Liu
- Department of Oncology, First Affiliated Hospital of PLA General Hospital, China
| | - Mengli Huang
- The Medical Department, 3D Medicines Inc., Shanghai, China
| | - Huoming Chen
- Department of Oncology, Chinese PLA Rocket General Hospital, China
| | - Guoqing Liao
- Department of Oncology, The 8th Medical Center of Chinese PLA General Hospital, China
| | - Jichang Meng
- Department of Oncology, Bethune International Peace Hospital, Shijiazhuang, Hebei, China
| | - Qing Wang
- The Medical Department, 3D Medicines Inc., Shanghai, China
| | - Hui Zhao
- Department of Oncology, First Affiliated Hospital of PLA General Hospital, China
| | - Chenxi Li
- Department of Oncology, First Affiliated Hospital of PLA General Hospital, China
| | - Jing Ji
- The Medical Department, 3D Medicines Inc., Shanghai, China
| | - Shangli Cai
- The Medical Department, 3D Medicines Inc., Shanghai, China
| | - Nan Du
- Department of Oncology, First Affiliated Hospital of PLA General Hospital, China
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18
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Wang X, Wu B, Yan Z, Wang G, Chen S, Zeng J, Tao F, Xu B, Ke H, Li M. Association of PTPRD/PTPRT Mutation With Better Clinical Outcomes in NSCLC Patients Treated With Immune Checkpoint Blockades. Front Oncol 2021; 11:650122. [PMID: 34123798 PMCID: PMC8192300 DOI: 10.3389/fonc.2021.650122] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 04/27/2021] [Indexed: 12/25/2022] Open
Abstract
The common gamma receptor–dependent cytokines and their JAK-STAT pathways play important roles in T cell immunity and have been demonstrated to be related with response to immune checkpoint blockades (ICBs). PTPRD and PTPRT are phosphatases involved in JAK-STAT pathway. However, their clinical significance for non-small cell lung cancer (NSCLC) treated with ICBs is still unclear. Genomic and survival data of NSCLC patients administrated with anti–PD-1/PD-L1 or anti–CTLA-4 antibodies (Rizvi2015; Hellmann2018; Rizvi2018 Samstein2019) were retrieved from publicly accessible data. Genomic, survival and mRNA data of 1007 patients with NSCLC were obtained from The Cancer Genome Atlas (TCGA). PTPRD/PTPRT mutation was significantly associated with better progression-free survival (PFS) in three independent Rizvi2015, Hellmann2018 and Rizvi2018 cohorts. The median PFS for PTPRD/PTPRT mutant-type vs. wild-type NSCLC patients were not reached vs. 6.3 months (Rizvi2015, HR = 0.16; 95% CI, 0.02-1.17; P=0.03), 24.0 vs. 5.4 months (Hellmann2018, HR, 0.49; 95% CI, 0.26-0.94; P=0.03), 5.6 vs. 3.0 months (Rizvi2018, HR = 0.64; 95% CI, 0.44-0.92; P=0.01) and 6.8 vs. 3.5 months (Pooled cohort, HR, 0.54; 95% CI, 0.39-0.73; P<0.0001) respectively. PTPRD/PTPRT mutation was an independent predictive factor for PFS in pooled cohort (P = 0.01). Additionally, PTPRD/PTPRT mutation associated with better overall survival (OS) in Samstein2019 cohort (19 vs. 10 months, P=0.03). While similar clinical benefits were not observed in patients without ICBs treatment (TCGA cohort, P=0.78). In the further exploratory analysis, PTPRD/PTPRT mutation was significantly associated with increased tumor mutation burden and higher mRNA expression of JAK1 and STAT1. Gene Set Enrichment Analysis revealed prominent enrichment of signatures related to antigen processing and presentation in patients with PTPRD/PTPRT mutation. This work suggested that PTPRD/PTPRT mutation might be a potential positive predictor for ICBs in NSCLC. These results need to be further confirmed in future.
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Affiliation(s)
- Xiaoyan Wang
- Department of Respiratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Bingchen Wu
- Department of Oncology, Hospital of Chinese Medicine of Changxing County, Huzhou, China
| | - Zhengqing Yan
- The Medical Department, 3D Medicines Inc., Shanghai, China
| | - Guoqiang Wang
- The Medical Department, 3D Medicines Inc., Shanghai, China
| | - Shiqing Chen
- The Medical Department, 3D Medicines Inc., Shanghai, China
| | - Jian Zeng
- Department of Thoracic Surgery, Zhejiang Cancer Hospital, University of Chinese Academy of Sciences, Hangzhou, China
| | - Feng Tao
- Department of Respiratory Medicine, The Affiliated Hospital of Jiaxing University, Jiaxing, China
| | - Bichun Xu
- Department of Radiotherapy, Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Honggang Ke
- Department of Cardiothoracic Surgery, Affiliated Hospital of Nantong University, Nantong, China
| | - Mei Li
- Department of Medical Oncology, Affiliated Hospital of Nantong University, Nantong, China
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19
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Jimenez-Luna C, González-Flores E, Ortiz R, Martínez-González LJ, Antúnez-Rodríguez A, Expósito-Ruiz M, Melguizo C, Caba O, Prados J. Circulating PTGS2, JAG1, GUCY2C and PGF mRNA in Peripheral Blood and Serum as Potential Biomarkers for Patients with Metastatic Colon Cancer. J Clin Med 2021; 10:2248. [PMID: 34067294 PMCID: PMC8196898 DOI: 10.3390/jcm10112248] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/18/2021] [Accepted: 05/20/2021] [Indexed: 12/24/2022] Open
Abstract
Genes involved in the angiogenic process have been proposed for the diagnosis and therapeutic response of metastatic colorectal cancer (CRC). This study aimed to investigate the value of PTGS2, JAG1, GUCY2C and PGF-circulating RNA as biomarkers in metastatic CRC. Blood cells and serum mRNA from 59 patients with metastatic CRC and 47 healthy controls were analyzed by digital PCR. The area under the receiver operating characteristic curve (AUC) was used to estimate the diagnostic value of each mRNA alone or mRNA combinations. A significant upregulation of the JAG1, PTGS2 and GUCY2C genes in blood cells and serum samples from metastatic CRC patients was detected. Circulating mRNA levels in the serum of all genes were significantly more abundant than in blood. The highest discrimination ability between metastatic CRC patients and healthy donors was obtained with PTGS2 (AUC of 0.984) and GUCY2C (AUC of 0.896) in serum samples. Biomarker combinations did not improve the discriminatory capacity of biomarkers separately. Analyzed biomarkers showed no correlation with overall survival or progression-free survival, but GUCY2C and GUCY2C/PTGS2 expression in serum correlated significantly with the response to antiangiogenic agents. These findings demonstrate that assessment of genes involved in the angiogenic process may be a potential non-invasive diagnostic tool for metastatic CRC and its response to antiangiogenic therapy.
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Affiliation(s)
- Cristina Jimenez-Luna
- Institute of Biopathology and Regenerative Medicine (IBIMER), Center of Biomedical Research (CIBM), University of Granada, 18100 Granada, Spain; (C.J.-L.); (R.O.); (O.C.); (J.P.)
- Department of Anatomy and Embryology, Faculty of Medicine, University of Granada, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria ibs. Granada, 18012 Granada, Spain;
| | - Encarnación González-Flores
- Instituto de Investigación Biosanitaria ibs. Granada, 18012 Granada, Spain;
- Medical Oncology Service, Hospital Virgen de las Nieves, 18014 Granada, Spain
| | - Raul Ortiz
- Institute of Biopathology and Regenerative Medicine (IBIMER), Center of Biomedical Research (CIBM), University of Granada, 18100 Granada, Spain; (C.J.-L.); (R.O.); (O.C.); (J.P.)
- Department of Anatomy and Embryology, Faculty of Medicine, University of Granada, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria ibs. Granada, 18012 Granada, Spain;
| | - Luis J. Martínez-González
- GENyO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, 18016 Granada, Spain; (L.J.M.-G.); (A.A.-R.)
| | - Alba Antúnez-Rodríguez
- GENyO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, 18016 Granada, Spain; (L.J.M.-G.); (A.A.-R.)
| | - Manuela Expósito-Ruiz
- Unit of Biostatistics, Department of Statistics and Operations Research, School of Medicine, University of Granada, 18071 Granada, Spain;
| | - Consolación Melguizo
- Institute of Biopathology and Regenerative Medicine (IBIMER), Center of Biomedical Research (CIBM), University of Granada, 18100 Granada, Spain; (C.J.-L.); (R.O.); (O.C.); (J.P.)
- Department of Anatomy and Embryology, Faculty of Medicine, University of Granada, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria ibs. Granada, 18012 Granada, Spain;
| | - Octavio Caba
- Institute of Biopathology and Regenerative Medicine (IBIMER), Center of Biomedical Research (CIBM), University of Granada, 18100 Granada, Spain; (C.J.-L.); (R.O.); (O.C.); (J.P.)
- Department of Anatomy and Embryology, Faculty of Medicine, University of Granada, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria ibs. Granada, 18012 Granada, Spain;
| | - Jose Prados
- Institute of Biopathology and Regenerative Medicine (IBIMER), Center of Biomedical Research (CIBM), University of Granada, 18100 Granada, Spain; (C.J.-L.); (R.O.); (O.C.); (J.P.)
- Department of Anatomy and Embryology, Faculty of Medicine, University of Granada, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria ibs. Granada, 18012 Granada, Spain;
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20
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Lapke N, Chen CH, Chang TC, Chao A, Lu YJ, Lai CH, Tan KT, Chen HC, Lu HY, Chen SJ. Genetic alterations and their therapeutic implications in epithelial ovarian cancer. BMC Cancer 2021; 21:499. [PMID: 33947352 PMCID: PMC8097933 DOI: 10.1186/s12885-021-08233-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 04/21/2021] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Genetic alterations for epithelial ovarian cancer are insufficiently characterized. Previous studies are limited regarding included histologies, gene numbers, copy number variant (CNV) detection, and interpretation of pathway alteration patterns of individual patients. METHODS We sequenced 410 genes to analyze mutations and CNV of 82 ovarian carcinomas, including high-grade serous (n = 37), endometrioid (n = 22) and clear cell (n = 23) histologies. Eligibility for targeted therapy was determined for each patient by a pathway-based approach. The analysis covered DNA repair, receptor tyrosine kinase, PI3K/AKT/MTOR, RAS/MAPK, cell cycle, and hedgehog pathways, and included 14 drug targets. RESULTS Postulated PARP, MTOR, and CDK4/6 inhibition sensitivity were most common. BRCA1/2 alterations, PTEN loss, and gain of PIK3CA and CCND1 were characteristic for high-grade serous carcinomas. Mutations of ARID1A, PIK3CA, and KRAS, and ERBB2 gain were enriched in the other histologies. PTEN mutations and high tumor mutational burden were characteristic for endometrioid carcinomas. Drug target downstream alterations impaired actionability in all histologies, and many alterations would not have been discovered by key gene mutational analysis. Individual patients often had more than one actionable drug target. CONCLUSIONS Genetic alterations in ovarian carcinomas are complex and differ among histologies. Our results aid the personalization of therapy and biomarker analysis for clinical studies, and indicate a high potential for combinations of targeted therapies.
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MESH Headings
- Adenocarcinoma, Clear Cell/genetics
- Adenocarcinoma, Clear Cell/pathology
- Adenocarcinoma, Clear Cell/therapy
- Carcinoma/genetics
- Carcinoma/pathology
- Carcinoma/therapy
- Carcinoma, Endometrioid/genetics
- Carcinoma, Endometrioid/pathology
- Carcinoma, Endometrioid/therapy
- Carcinoma, Ovarian Epithelial/genetics
- Carcinoma, Ovarian Epithelial/pathology
- Carcinoma, Ovarian Epithelial/therapy
- Cell Cycle/genetics
- DNA Copy Number Variations
- DNA Mutational Analysis/methods
- DNA Repair/genetics
- Female
- Gene Expression Regulation, Neoplastic
- Hedgehog Proteins/genetics
- High-Throughput Nucleotide Sequencing/methods
- Humans
- Mutation
- Ovarian Neoplasms/genetics
- Ovarian Neoplasms/pathology
- Ovarian Neoplasms/therapy
- Precision Medicine
- Retrospective Studies
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Affiliation(s)
- Nina Lapke
- ACT Genomics, Co. Ltd., 3F., No.345, Xinhu 2nd Rd., Neihu Dist, Taipei City, 114, Taiwan
- ACT Genomics, Co. Ltd., Units 803 - 807, 8F, Building 15W, No.15 Science Park West Avenue, Hong Kong Science Park, Pak Shek Kok. NT, Hong Kong, Hong Kong
| | - Chien-Hung Chen
- ACT Genomics, Co. Ltd., 3F., No.345, Xinhu 2nd Rd., Neihu Dist, Taipei City, 114, Taiwan
| | - Ting-Chang Chang
- Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital and Chang Gung University, Linkou Medical Center, 5 Fushin St., Guishan District, Taoyuan, 333, Taiwan
- Gynecologic Cancer Research Center, Chang Gung Memorial Hospital, 5 Fushin St., Guishan District, Taoyuan, 333, Taiwan
| | - Angel Chao
- Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital and Chang Gung University, Linkou Medical Center, 5 Fushin St., Guishan District, Taoyuan, 333, Taiwan
- Gynecologic Cancer Research Center, Chang Gung Memorial Hospital, 5 Fushin St., Guishan District, Taoyuan, 333, Taiwan
| | - Yen-Jung Lu
- ACT Genomics, Co. Ltd., 3F., No.345, Xinhu 2nd Rd., Neihu Dist, Taipei City, 114, Taiwan.
| | - Chyong-Huey Lai
- Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital and Chang Gung University, Linkou Medical Center, 5 Fushin St., Guishan District, Taoyuan, 333, Taiwan
- Gynecologic Cancer Research Center, Chang Gung Memorial Hospital, 5 Fushin St., Guishan District, Taoyuan, 333, Taiwan
| | - Kien Thiam Tan
- ACT Genomics, Co. Ltd., 3F., No.345, Xinhu 2nd Rd., Neihu Dist, Taipei City, 114, Taiwan
| | - Hua-Chien Chen
- ACT Genomics, Co. Ltd., 3F., No.345, Xinhu 2nd Rd., Neihu Dist, Taipei City, 114, Taiwan
| | - Hsiao-Yun Lu
- ACT Genomics, Co. Ltd., 3F., No.345, Xinhu 2nd Rd., Neihu Dist, Taipei City, 114, Taiwan
| | - Shu-Jen Chen
- ACT Genomics, Co. Ltd., 3F., No.345, Xinhu 2nd Rd., Neihu Dist, Taipei City, 114, Taiwan
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21
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MicroRNA-Based Therapeutics for Drug-Resistant Colorectal Cancer. Pharmaceuticals (Basel) 2021; 14:ph14020136. [PMID: 33567635 PMCID: PMC7915952 DOI: 10.3390/ph14020136] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/29/2021] [Accepted: 02/04/2021] [Indexed: 12/13/2022] Open
Abstract
Although therapeutic approaches for patients with colorectal cancer (CRC) have improved in the past decades, the problem of drug resistance still persists and acts as a major obstacle for effective therapy. Many studies have shown that drug resistance is related to reduced drug uptake, modification of drug targets, and/or transformation of cell cycle checkpoints. A growing body of evidence indicates that several microRNAs (miRNAs) may contribute to the drug resistance to chemotherapy, targeted therapy, and immunotherapy by regulating the drug resistance-related target genes in CRC. These drug resistance-related miRNAs may be used as promising biomarkers for predicting drug response or as potential therapeutic targets for treating patients with CRC. In this review, we summarized the recent discoveries regarding anti-cancer drug-related miRNAs and their molecular mechanisms in CRC. Furthermore, we discussed the challenges associated with the clinical application of miRNAs as biomarkers for the diagnosis of drug-resistant patients and as therapeutic targets for CRC treatment.
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22
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He Z, Li A, Lin D, Gu Y, Chen Y, Ou Q, Li L, Yao H, Yu Y. Association of immune checkpoint inhibitor with survival in patients with cancers with protein tyrosine phosphatase receptor T mutation. Clin Transl Med 2020; 10:e214. [PMID: 33135355 PMCID: PMC7591738 DOI: 10.1002/ctm2.214] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/07/2020] [Accepted: 10/12/2020] [Indexed: 12/24/2022] Open
Affiliation(s)
- Zifan He
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Medical Oncology, Phase I Clinical Trial Centre, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Anlin Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Medical Oncology, Phase I Clinical Trial Centre, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,The First Clinical Medical College, Guangdong Medical University, Zhanjiang, China
| | - Dagui Lin
- Department of Colorectal Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yang Gu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Medical Oncology, Phase I Clinical Trial Centre, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yongjian Chen
- Department of Medical Oncology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Qiyun Ou
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Medical Oncology, Phase I Clinical Trial Centre, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Liren Li
- Department of Colorectal Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Herui Yao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Medical Oncology, Phase I Clinical Trial Centre, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yunfang Yu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Medical Oncology, Phase I Clinical Trial Centre, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
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23
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Zhang F, Wang B, Qin T, Wang L, Zhang Q, Lu Y, Song B, Yu X, Li L. IL-6 induces tumor suppressor protein tyrosine phosphatase receptor type D by inhibiting miR-34a to prevent IL-6 signaling overactivation. Mol Cell Biochem 2020; 473:1-13. [PMID: 32602014 DOI: 10.1007/s11010-020-03803-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 06/18/2020] [Indexed: 12/14/2022]
Abstract
Protein tyrosine phosphatase receptor type D (PTPRD) is a tumor suppressor gene that is epigenetically silenced and mutated in several cancers, including breast cancer. Since IL-6/STAT3 signaling is often hyperactivated in breast cancer and STAT3 is a direct PTPRD substrate, we investigated the role of PTPRD in breast cancer and the association between PTPRD and IL-6/STAT3 signaling. We found that PTPRD acts as a tumor suppressor in breast cancer tissues and that high PTPRD expression is positively associated with tumor size, lymph node metastasis, PCNA expression, and patient survival. Moreover, breast cancers with high PTPRD expression tend to exhibit high IL-6 and low phosphorylated-STAT3 expression. IL-6 was found to inhibit miR-34a transcription and induce PTPRD expression in breast cancer and breast epithelial cells, whereas PTPRD was shown to mediate activated STAT3 dephosphorylation and to be a conserved, direct target of miR-34a. IL-6-induced PTPRD upregulation was blocked by miR-34a mimics, whereas experimental PTPRD overexpression suppressed MDA-MB-231 cell migration, invasion, and epithelial to mesenchymal transition, decreased STAT3 phosphorylation, and increased miR-34a transcription. Our findings suggest that PTPRD mediates activated STAT3 dephosphorylation and is induced by the IL-6/STAT3-mediated transcriptional inhibition of miR-34a, thereby establishing a negative feedback loop that inhibits IL-6/STAT3 signaling overactivation.
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Affiliation(s)
- Fan Zhang
- Department of General Surgery, The Second Affiliated Hospital of Dalian Medical University, Dalian, 116032, China
| | - Bo Wang
- Department of Pathology and Forensic Medicine, College of Basic Medical Science, Dalian Medical University, Lvshun South Road, Dalian, 116044, China
| | - Tao Qin
- Department of Pathology and Forensic Medicine, College of Basic Medical Science, Dalian Medical University, Lvshun South Road, Dalian, 116044, China
| | - Lu Wang
- Department of Pathology and Forensic Medicine, College of Basic Medical Science, Dalian Medical University, Lvshun South Road, Dalian, 116044, China
| | - Qingqing Zhang
- Department of Pathology and Forensic Medicine, College of Basic Medical Science, Dalian Medical University, Lvshun South Road, Dalian, 116044, China
| | - Ying Lu
- Department of Pathology and Forensic Medicine, College of Basic Medical Science, Dalian Medical University, Lvshun South Road, Dalian, 116044, China
| | - Bo Song
- Department of Pathology and Forensic Medicine, College of Basic Medical Science, Dalian Medical University, Lvshun South Road, Dalian, 116044, China
| | - Xiaotang Yu
- Department of Pathology and Forensic Medicine, College of Basic Medical Science, Dalian Medical University, Lvshun South Road, Dalian, 116044, China.
| | - Lianhong Li
- Department of Pathology and Forensic Medicine, College of Basic Medical Science, Dalian Medical University, Lvshun South Road, Dalian, 116044, China.
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24
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Qian L, Soderquist C, Schrank‐Hacker A, Strauser H, Dupoux V, Tang CN, Smith JR, Sun A, Majumdar S, Nguyen T, Widura S, Landsburg DJ, Schuster SJ, Baxter RHG, Bogusz AM. Deletion 20q12 is associated with histological transformation of nodal marginal zone lymphoma to diffuse large B-cell lymphoma. Am J Hematol 2020; 95:238-244. [PMID: 31804739 DOI: 10.1002/ajh.25694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 11/26/2019] [Accepted: 11/29/2019] [Indexed: 11/06/2022]
Abstract
The genetic and molecular abnormalities underlying histological transformation (HT) of nodal marginal zone lymphoma (NMZL) to diffuse large B-cell lymphoma (DLBCL) are not well known. While del(20q12) is commonly deleted in myelodysplastic syndrome it has not previously been associated with DLBCL. We recently described a case of DLBCL harboring del(20q12) in a patient with a history of MZL involving lymph nodes and skin. Here we report eight matched cases of transformed MZL(tMZL): six from nodal MZL (tNMZL) and two from splenic MZL (tSMZL). We found >20% del(20q12) in 4/6 tNMZL, but not in tSMZL, nor in unmatched DLBCL, MZL with increased large cells (MZL-ILC), or MZL cases. To examine whether transformation is associated with a specific gene signature, the matched cases were analyzed for multiplexed gene expression using the Nanostring PanCancer Pathways panel. The differential gene expression signature revealed enrichment of inflammatory markers, as previously observed in MZL. Also, tMZL and de novo DLBCL were enriched for extracellular matrix proteins such as collagen and fibronectin, vascular development protein PDGFRβ, DNA repair protein RAD51, and oncogenic secrete protein Wnt11. A subset of genes is expressed differentially in del(20q12) tMZL cases vs non-del(20q12) tMZL cases. These results suggest a specific pathway is involved in the histological transformation of NMZL, which could serve as an indicator of aggressive clinical course in this otherwise indolent neoplasm.
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Affiliation(s)
- Lei Qian
- Department of Medical Genetics & Molecular Biochemistry, Lewis Katz School of MedicineTemple University Philadelphia Pennsylvania
| | - Craig Soderquist
- Department of Pathology and Cell BiologyColumbia University Medical Center New York Pennsylvania
| | - April Schrank‐Hacker
- Department of Pathology and Laboratory MedicineHospital of the University of Pennsylvania Philadelphia Pennsylvania
| | - Honore Strauser
- Department of Pathology and Laboratory MedicineHospital of the University of Pennsylvania Philadelphia Pennsylvania
| | - Vanessa Dupoux
- Department of Pathology and Laboratory MedicineHospital of the University of Pennsylvania Philadelphia Pennsylvania
| | - Chi Ngong Tang
- Department of Pathology and Laboratory MedicineHospital of the University of Pennsylvania Philadelphia Pennsylvania
| | - Jennifer R. Smith
- Department of Pathology and Laboratory MedicineHospital of the University of Pennsylvania Philadelphia Pennsylvania
| | - Ang Sun
- Department of BiologyTemple University Philadelphia Pennsylvania
| | - Sonali Majumdar
- Wistar Genomics Shared ResourceThe Wistar Institute Philadelphia Pennsylvania
| | - Tran Nguyen
- Wistar Genomics Shared ResourceThe Wistar Institute Philadelphia Pennsylvania
| | - Sandy Widura
- Wistar Genomics Shared ResourceThe Wistar Institute Philadelphia Pennsylvania
| | - Daniel J. Landsburg
- Department of Medicine, Perelman School of MedicineUniversity of Pennsylvania Philadelphia Pennsylvania
- Lymphoma Program, Abramson Cancer CenterUniversity of Pennsylvania Philadelphia Pennsylvania
| | - Stephen J. Schuster
- Department of Medicine, Perelman School of MedicineUniversity of Pennsylvania Philadelphia Pennsylvania
- Lymphoma Program, Abramson Cancer CenterUniversity of Pennsylvania Philadelphia Pennsylvania
| | - Richard H. G. Baxter
- Department of Medical Genetics & Molecular Biochemistry, Lewis Katz School of MedicineTemple University Philadelphia Pennsylvania
| | - Agata M. Bogusz
- Department of Pathology and Laboratory MedicineHospital of the University of Pennsylvania Philadelphia Pennsylvania
- Lymphoma Program, Abramson Cancer CenterUniversity of Pennsylvania Philadelphia Pennsylvania
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25
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Tao CW, Chen MY, Tseng CM, Lapke N, Chen SJ, Tan KT. Advanced Lung Adenocarcinoma Patient with ERBB2 Amplification Identified by Comprehensive Genomic Profiling Benefits from Trastuzumab. Case Rep Oncol Med 2020; 2020:9072173. [PMID: 32190395 PMCID: PMC7071810 DOI: 10.1155/2020/9072173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 02/12/2020] [Indexed: 02/06/2023] Open
Abstract
For non-small-cell lung cancer (NSCLC) patients without established actionable alterations in genes such as EGFR or ALK, options for targeted therapy remain limited in clinical practice. About 5% of lung adenocarcinoma patients have tumors with ERBB2 genetic alterations, with even fewer patients harboring ERBB2 amplification. Currently, clinical trials mainly use IHC, FISH, or mutation testing to identify potential responders to ERBB2-targeting agents. The use of next-generation sequencing (NGS) to detect ERBB2 alterations, including copy number variants, is rare. In this study, we present an EGFR- and ALK-negative advanced NSCLC case for which we conducted comprehensive tumor genomic profiling to identify potentially actionable alterations. The tumor harbored an ERBB2 amplification, and trastuzumab-based therapy resulted in an excellent response, with a necrotic regression of the patient's lung lesion. Although he developed brain metastasis four months after trastuzumab initiation, he survived for an additional period of eight months without local recurrence or other systemic metastasis. This case report shows that the use of comprehensive genetic testing enables the identification of rare actionable alterations in NSCLC patients without other options for targeted treatment.
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Affiliation(s)
- Chi-Wei Tao
- Division of Respiratory Therapy, Department of Internal Medicine, Cheng-Hsin General Hospital, Taipei, Taiwan
| | - Mei-Yin Chen
- Division of Respiratory Therapy, Department of Internal Medicine, Cheng-Hsin General Hospital, Taipei, Taiwan
| | - Ching-Min Tseng
- Division of Respiratory Therapy, Department of Internal Medicine, Cheng-Hsin General Hospital, Taipei, Taiwan
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26
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Bae WJ, Ahn JM, Byeon HE, Kim S, Lee D. PTPRD-inactivation-induced CXCL8 promotes angiogenesis and metastasis in gastric cancer and is inhibited by metformin. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2019; 38:484. [PMID: 31805999 PMCID: PMC6896474 DOI: 10.1186/s13046-019-1469-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 10/28/2019] [Indexed: 01/21/2023]
Abstract
Background Protein tyrosine phosphatase receptor delta (PTPRD) is frequently inactivated in various types of cancers. Here, we explored the underlying mechanism of PTPRD-loss-induced cancer metastasis and investigated an efficient treatment option for PTPRD-inactivated gastric cancers (GCs). Methods PTPRD expression was evaluated by immunohistochemistry. Microarray analysis was used to identify differentially expressed genes in PTPRD-inactivated cancer cells. Quantitative reverse transcription (qRT-PCR), western blotting, and/or enzyme-linked immunosorbent assays were used to investigate the PTPRD-CXCL8 axis and the expression of other related genes. An in vitro tube formation assay was performed using HUVECs. The efficacy of metformin was assessed by MTS assay. Results PTPRD was frequently downregulated in GCs and the loss of PTPRD expression was associated with advanced stage, worse overall survival, and a higher risk of distant metastasis. Microarray analysis revealed a significant increase in CXCL8 expression upon loss of PTPRD. This was validated in various GC cell lines using transient and stable PTPRD knockdown. PTPRD-loss-induced angiogenesis was mediated by CXCL8, and the increase in CXCL8 expression was mediated by both ERK and STAT3 signaling. Thus, specific inhibitors targeting ERK or STAT3 abrogated the corresponding signaling nodes and inhibited PTPRD-loss-induced angiogenesis. Additionally, metformin was found to efficiently inhibit PTPRD-loss-induced angiogenesis, decrease cell viability in PTPRD-inactivated cancers, and reverse the decrease in PTPRD expression. Conclusions Thus, the PTPRD-CXCL8 axis may serve as a potential therapeutic target, particularly for the suppression of metastasis in PTPRD-inactivated GCs. Hence, we propose that the therapeutic efficacy of metformin in PTPRD-inactivated cancers should be further investigated.
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Affiliation(s)
- Won Jung Bae
- Department of Pathology, Ajou University School of Medicine, 164, Worldcup-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do, 16499, Republic of Korea
| | - Ji Mi Ahn
- Department of Pathology, Ajou University School of Medicine, 164, Worldcup-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do, 16499, Republic of Korea
| | - Hye Eun Byeon
- Institute of Medical Science, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Seokwhi Kim
- Department of Pathology, Ajou University School of Medicine, 164, Worldcup-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do, 16499, Republic of Korea
| | - Dakeun Lee
- Department of Pathology, Ajou University School of Medicine, 164, Worldcup-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do, 16499, Republic of Korea.
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Wu A, Yang X, Zhang B, Wang S, Li G. miR-516a-3p promotes proliferation, migration, and invasion and inhibits apoptosis in lung adenocarcinoma by targeting PTPRD. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2019; 12:4222-4231. [PMID: 31933822 PMCID: PMC6949792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 09/24/2019] [Indexed: 06/10/2023]
Abstract
Background: Multiple previous studies have indicated miR-516a-3p was associated with carcinogenesis in lung cancer. However, its biologic functions in lung adenocarcinoma remain unknown. The aim of this study was to investigate the expression of miR-516a-3p in lung adenocarcinoma, its molecular mechanisms of miR-516a-3p, and its effects on cell proliferation, migration, invasion, and apoptosis. Methods: The expression of miR-516a-3p and PTPRD was tested by reverse transcription-quantitative polymerase chain reaction. Cell migration and invasion assays were used to evaluate the migration and invasion ability of cells. Flow cytometry was performed to observe the effects of miR-516a-3p on the cell apoptosis. Western blot analysis was used to assess the protein levels of PTPRD. Luciferase reporter assay was utilized to identify whether PTPRD was a direct target of miR-516a-3p. Results: There was upregulated expression of miR-516a-3p in lung adenocarcinoma tissues as well as cell lines. In addition, miR-516a-3p expression knock-down could inhibit cell proliferation, invasion, and migration, but promote apoptosis in lung adenocarcinoma. By contrast, overexpression of miR-516a-3p resulted in the opposite effect. Dual luciferase assay, RT-PCR and western blot analysis results confirmed that PTPRD was a direct target for miR-516a-3p. Further studies also found PTPRD was down-regulated in lung adenocarcinoma and there was a negative correlation between miR-516a-3p and PTPRD expression in lung adenocarcinoma. Moreover, miR-516a-3p and PTPRD were significantly correlated with the clinical stage of lung adenocarcinoma. Conclusions: Our current findings showed that miR-516a-3p was up-regulated in lung adenocarcinoma, functioning as a tumor-promoting gene by targeting PTPRD.
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Affiliation(s)
- Anhao Wu
- Department of Thoracic Surgery Ward II, Third Affiliated Hospital, Kunming Medical University, Tumor Hospital of Yunnan Kunming ProvinceKunming, Yunnan, P. R. China
| | - Xin Yang
- Department of Blood Transfusion, The First People’s Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and TechnologyKunming, Yunnan, P. R. China
| | - Bing Zhang
- Department of Thoracic Surgery Ward II, Third Affiliated Hospital, Kunming Medical University, Tumor Hospital of Yunnan Kunming ProvinceKunming, Yunnan, P. R. China
| | - Shuting Wang
- Department of Thoracic Surgery Ward II, Third Affiliated Hospital, Kunming Medical University, Tumor Hospital of Yunnan Kunming ProvinceKunming, Yunnan, P. R. China
| | - Gaofeng Li
- Department of Thoracic Surgery Ward II, Third Affiliated Hospital, Kunming Medical University, Tumor Hospital of Yunnan Kunming ProvinceKunming, Yunnan, P. R. China
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TP53 DNA Binding Domain Mutations Predict Progression-Free Survival of Bevacizumab Therapy in Metastatic Colorectal Cancer. Cancers (Basel) 2019; 11:cancers11081079. [PMID: 31366114 PMCID: PMC6721375 DOI: 10.3390/cancers11081079] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 07/22/2019] [Accepted: 07/26/2019] [Indexed: 12/21/2022] Open
Abstract
(1) Background: Bevacizumab-based regimens are a standard treatment for metastatic colorectal cancer (mCRC) patients, however meaningful clinical biomarkers for treatment benefit remain scarce. (2) Methods: Tumor samples from 36 mCRC patients treated with bevacizumab-based chemotherapy underwent comprehensive genomic profiling. Alterations in frequently altered genes and important signaling pathways were correlated with progression-free survival (PFS). (3) Results: Overall genetic alteration analysis of investigated genes and pathways did not identify promising new predictors of PFS. However, when considering mutation subtypes, TP53 DNA binding domain (DBD) missense mutations were associated with prolonged PFS (HR, 0.41; 95% CI, 0.13−0.65; p = 0.005). In contrast, TP53 truncating mutations were associated with short PFS (HR, 2.95; 95% CI, 1.45−27.50; p = 0.017). Importantly, neither TP53 mutation subtype was associated with overall response rate. In multivariate analysis, TP53 DBD missense mutations remained an independent PFS predictor (HR, 0.31; 95% CI, 0.13–0.77; p = 0.011). The other genetic factor independently associated with PFS were PTPRT/PTPRD deleterious alterations, which we previously identified in a screen for biomarkers of bevacizumab response. (4) Conclusions: TP53 DBD missense mutations may predict prolonged PFS in mCRC patients treated with bevacizumab-based therapy. Analyses of TP53 mutations as clinical biomarkers should take the biological impact of different mutation subtypes into consideration to improve patient stratification.
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Ruckert MT, de Andrade PV, Santos VS, Silveira VS. Protein tyrosine phosphatases: promising targets in pancreatic ductal adenocarcinoma. Cell Mol Life Sci 2019; 76:2571-2592. [PMID: 30982078 PMCID: PMC11105579 DOI: 10.1007/s00018-019-03095-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 03/25/2019] [Accepted: 04/08/2019] [Indexed: 12/21/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the most common type of pancreatic cancer. It is the fourth leading cause of cancer-related death and is associated with a very poor prognosis. KRAS driver mutations occur in approximately 95% of PDAC cases and cause the activation of several signaling pathways such as mitogen-activated protein kinase (MAPK) pathways. Regulation of these signaling pathways is orchestrated by feedback loops mediated by the balance between protein tyrosine kinases (PTKs) and protein tyrosine phosphatases (PTPs), leading to activation or inhibition of its downstream targets. The human PTPome comprises 125 members, and these proteins are classified into three distinct families according to their structure. Since PTP activity description, it has become clear that they have both inhibitory and stimulatory effects on cancer-associated signaling processes and that deregulation of PTP function is closely associated with tumorigenesis. Several PTPs have displayed either tumor suppressor or oncogenic characteristics during the development and progression of PDAC. In this sense, PTPs have been presented as promising candidates for the treatment of human pancreatic cancer, and many PTP inhibitors have been developed since these proteins were first associated with cancer. Nevertheless, some challenges persist regarding the development of effective and safe methods to target these molecules and deliver these drugs. In this review, we discuss the role of PTPs in tumorigenesis as tumor suppressor and oncogenic proteins. We have focused on the differential expression of these proteins in PDAC, as well as their clinical implications and possible targeting for pharmacological inhibition in cancer therapy.
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Affiliation(s)
- Mariana Tannús Ruckert
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, São Paulo, Brazil
| | - Pamela Viani de Andrade
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, São Paulo, Brazil
| | - Verena Silva Santos
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, São Paulo, Brazil
| | - Vanessa Silva Silveira
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, São Paulo, Brazil.
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Uhl GR, Martinez MJ. PTPRD: neurobiology, genetics, and initial pharmacology of a pleiotropic contributor to brain phenotypes. Ann N Y Acad Sci 2019; 1451:112-129. [PMID: 30648269 PMCID: PMC6629525 DOI: 10.1111/nyas.14002] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 11/12/2018] [Accepted: 12/19/2018] [Indexed: 12/12/2022]
Abstract
Receptor-type protein tyrosine phosphatase, receptor type D (PTPRD) has likely roles as a neuronal cell adhesion molecule and synaptic specifier. Interest in its neurobiology and genomics has been stimulated by results from human genetics and mouse models for phenotypes related to addiction, restless leg syndrome, neurofibrillary pathology in Alzheimer's disease, cognitive impairment/intellectual disability, mood lability, and obsessive-compulsive disorder. We review PTPRD's discovery, gene family, candidate homomeric and heteromeric binding partners, phosphatase activities, brain distribution, human genetic associations with nervous system phenotypes, and mouse model data relevant to these phenotypes. We discuss the recently reported discovery of the first small molecule inhibitor of PTPRD phosphatase, the identification of its addiction-related effects, and the implications of these findings for the PTPRD-associated brain phenotypes. In assembling PTPRD neurobiology, human genetics, and mouse genetic and pharmacological datasets, we provide a compelling picture of the roles played by PTPRD, its variation, and its potential as a target for novel therapeutics.
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Affiliation(s)
- George R Uhl
- Neurology and Research Services, New Mexico VA Healthcare System, Albuquerque, New Mexico.,Departments of Neurology, Neuroscience, Molecular Genetics and Microbiology, University of New Mexico, Albuquerque, New Mexico.,Biomedical Research Institute of New Mexico, Albuquerque, New Mexico.,Departments of Neurology, Neuroscience and Mental Health, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Maria J Martinez
- Neurology and Research Services, New Mexico VA Healthcare System, Albuquerque, New Mexico.,Biomedical Research Institute of New Mexico, Albuquerque, New Mexico
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