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Li DM, Li GS, Li JD, Chen F, Huang H, Huang WY, Huang ZG, Dang YW, Tang YL, Tang ZQ, Tang WJ, Chen G, Lu HP. Clinical significance and prospective mechanism of increased CDKN2A expression in small cell lung cancer. Clin Transl Oncol 2024; 26:1519-1531. [PMID: 38206516 PMCID: PMC11108933 DOI: 10.1007/s12094-023-03376-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 12/14/2023] [Indexed: 01/12/2024]
Abstract
BACKGROUND Although it has been shown that cyclin dependent kinase inhibitor 2A (CDKN2A) plays a significant role in a number of malignancies, its clinicopathological value and function in small cell lung cancer (SCLC) is unclear and warrants additional research. METHODS The clinical significance of CDKN2A expression in SCLC was examined by multiple methods, including comprehensive integration of mRNA level by high throughput data, Kaplan-Meier survival analysis for prognostic value, and validation of its protein expression using in-house immunohistochemistry. RESULTS The expression of CDKN2A mRNA in 357 cases of SCLC was evidently higher than that in the control group (n = 525) combing the data from 20 research centers worldwide. The standardized mean difference (SMD) was 3.07, and the area under the curve (AUC) of summary receiver operating characteristic curve (sROC) was 0.97 for the overexpression of CDKN2A. ACC, COAD, KICH, KIRC, PCPG, PRAD, UCEC, UVM patients with higher CDKN2A expression had considerably worse overall survival rates than those with lower CDKN2A expression with the hazard ratio (HR) > 1. CONCLUSION CDKN2A upregulation extensively enhances the carcinogenesis and progression of SCLC.
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Affiliation(s)
- Dong-Ming Li
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, Nanning, People's Republic of China
| | - Guo-Sheng Li
- Cardiothoracic Surgery, The First Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, Nanning, People's Republic of China
| | - Jian-Di Li
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, Nanning, People's Republic of China
| | - Feng Chen
- Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, Nanning, People's Republic of China
| | - Hong Huang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, Nanning, People's Republic of China
| | - Wan-Ying Huang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, Nanning, People's Republic of China
| | - Zhi-Guang Huang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, Nanning, People's Republic of China
| | - Yi-Wu Dang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, Nanning, People's Republic of China
| | - Yu-Lu Tang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, Nanning, People's Republic of China
| | - Zhong-Qing Tang
- Department of Pathology, Wuzhou Gongren Hospital, The Seventh Affiliated Hospital of Guangxi Medical University, No.1, Nansanxiang Gaodi Road, Guangxi Zhuang Autonomous Region, Wuzhou, 543000, People's Republic of China
| | - Wen-Jia Tang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, Nanning, People's Republic of China
| | - Gang Chen
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, Nanning, People's Republic of China
| | - Hui-Ping Lu
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, Nanning, People's Republic of China.
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Olaoba OT, Adelusi TI, Yang M, Maidens T, Kimchi ET, Staveley-O’Carroll KF, Li G. Driver Mutations in Pancreatic Cancer and Opportunities for Targeted Therapy. Cancers (Basel) 2024; 16:1808. [PMID: 38791887 PMCID: PMC11119842 DOI: 10.3390/cancers16101808] [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: 04/12/2024] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
Pancreatic cancer is the sixth leading cause of cancer-related mortality globally. As the most common form of pancreatic cancer, pancreatic ductal adenocarcinoma (PDAC) represents up to 95% of all pancreatic cancer cases, accounting for more than 300,000 deaths annually. Due to the lack of early diagnoses and the high refractory response to the currently available treatments, PDAC has a very poor prognosis, with a 5-year overall survival rate of less than 10%. Targeted therapy and immunotherapy are highly effective and have been used for the treatment of many types of cancer; however, they offer limited benefits in pancreatic cancer patients due to tumor-intrinsic and extrinsic factors that culminate in drug resistance. The identification of key factors responsible for PDAC growth and resistance to different treatments is highly valuable in developing new effective therapeutic strategies. In this review, we discuss some molecules which promote PDAC initiation and progression, and their potential as targets for PDAC treatment. We also evaluate the challenges associated with patient outcomes in clinical trials and implications for future research.
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Affiliation(s)
- Olamide T. Olaoba
- Department of Surgery, University of Connecticut Health Center, Farmington, CT 06030, USA; (O.T.O.); (T.I.A.); (M.Y.); (E.T.K.)
- Department of Immunology, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Temitope I. Adelusi
- Department of Surgery, University of Connecticut Health Center, Farmington, CT 06030, USA; (O.T.O.); (T.I.A.); (M.Y.); (E.T.K.)
| | - Ming Yang
- Department of Surgery, University of Connecticut Health Center, Farmington, CT 06030, USA; (O.T.O.); (T.I.A.); (M.Y.); (E.T.K.)
| | - Tessa Maidens
- Department of Surgery, University of Missouri, Columbia, MO 65212, USA;
| | - Eric T. Kimchi
- Department of Surgery, University of Connecticut Health Center, Farmington, CT 06030, USA; (O.T.O.); (T.I.A.); (M.Y.); (E.T.K.)
| | - Kevin F. Staveley-O’Carroll
- Department of Surgery, University of Connecticut Health Center, Farmington, CT 06030, USA; (O.T.O.); (T.I.A.); (M.Y.); (E.T.K.)
| | - Guangfu Li
- Department of Surgery, University of Connecticut Health Center, Farmington, CT 06030, USA; (O.T.O.); (T.I.A.); (M.Y.); (E.T.K.)
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Paranal RM, Wood LD, Klein AP, Roberts NJ. Understanding familial risk of pancreatic ductal adenocarcinoma. Fam Cancer 2024:10.1007/s10689-024-00383-2. [PMID: 38609521 DOI: 10.1007/s10689-024-00383-2] [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: 01/27/2024] [Accepted: 03/24/2024] [Indexed: 04/14/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a deadly disease that is the result of an accumulation of sequential genetic alterations. These genetic alterations can either be inherited, such as pathogenic germline variants that are associated with an increased risk of cancer, or acquired, such as somatic mutations that occur during the lifetime of an individual. Understanding the genetic basis of inherited risk of PDAC is essential to advancing patient care and outcomes through improved clinical surveillance, early detection initiatives, and targeted therapies. In this review we discuss factors associated with an increased risk of PDAC, the prevalence of genetic variants associated with an increased risk in patients with PDAC, estimates of PDAC risk in carriers of pathogenic germline variants in genes associated with an increased risk of PDAC. The role of common variants in pancreatic cancer risk will also be discussed.
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Affiliation(s)
- Raymond M Paranal
- The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Human Genetics Predoctoral Training Program, the McKusick-Nathans Department of Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Laura D Wood
- The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alison P Klein
- The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Epidemiology, Johns Hopkins University School of Public Health, Baltimore, MD, USA.
| | - Nicholas J Roberts
- The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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Jacobs MF, Stoffel EM. Genetic and other risk factors for pancreatic ductal adenocarcinoma (PDAC). Fam Cancer 2024:10.1007/s10689-024-00372-5. [PMID: 38573398 DOI: 10.1007/s10689-024-00372-5] [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: 01/05/2024] [Accepted: 03/07/2024] [Indexed: 04/05/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is often diagnosed at an advanced stage, resulting in poor prognosis and low 5-year survival rates. While early evidence suggests increased long-term survival in those with screen-detected resectable cancers, surveillance imaging is currently only recommended for individuals with a lifetime risk of PDAC ≥ 5%. Identification of risk factors for PDAC provides opportunities for early detection, risk reducing interventions, and targeted therapies, thus potentially improving patient outcomes. Here, we summarize modifiable and non-modifiable risk factors for PDAC. We review hereditary cancer syndromes associated with risk for PDAC and their implications for patients and their relatives. In addition, other biologically relevant pathways and environmental and lifestyle risk factors are discussed. Future work may focus on elucidating additional genetic, environmental, and lifestyle risk factors that may modify PDAC risk to continue to identify individuals at increased risk for PDAC who may benefit from surveillance and risk reducing interventions.
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Affiliation(s)
- Michelle F Jacobs
- Division of Genetic Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Elena M Stoffel
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA.
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Meng J, Zong C, Wang M, Chen Y, Zhao S. Constructing a Prognostic Model of Uterine Corpus Endometrial Carcinoma and Predicting Drug-Sensitivity Responses Using Programmed Cell Death-Related Pathways. J Cancer 2024; 15:2948-2959. [PMID: 38706893 PMCID: PMC11064274 DOI: 10.7150/jca.92201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/17/2024] [Indexed: 05/07/2024] Open
Abstract
Background: Uterine Corpus Endometrial Carcinoma (UCEC) is the most common type of cancer that develops in the uterus, specifically originating from the endometrium, the inner lining of the uterus. Programmed cell death (PCD) is a highly regulated process that eliminates damaged, aged, or unwanted cells in the body. Dysregulation of PCD pathways can contribute to the formation and progression of various cancers, including UCEC. Methods: Fourteen PCD pathways (autophagy-dependent cell death, alkaliptosis, apoptosis, cuproptosis, entotic cell death, ferroptosis, immunogenic cell death, lysosome-dependent cell death, MPT-driven necrosis, necroptosis, netotic cell death, oxeiptosis, parthanatos, and pyroptosis) were involved in building a prognostic signature. The model was trained and tested using data from the TCGA-UCEC and validated with the GSE119041 dataset. Results: A 12-gene PCD signature (DRAM1, ELAPOR1, MAPT, TRIM58, UCHL1, CDKN2A, CYFIP2, AKT2, LINC00618, TTPA, TRIM46, and NOS2) was established and validated in an independent dataset. UCEC patients with a high PCD score (PCDS) exhibited worse prognosis. Furthermore, PCDS was found to be associated with immune related cells and key tumor microenvironment components through multiple methods. It was observed that UCEC patients with a high PCD score may not benefit from immunotherapy, but some chemo drugs like Bortezomib may be useful. Conclusion: In conclusion, a novel PCD model was established by comprehensively analyzing diverse cell death patterns. This model accurately predicts the clinical prognosis and drug sensitivity of UCEC. The findings suggest that the PCD signature can serve as a valuable tool in assessing prognosis and guiding treatment decisions for UCEC patients.
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Affiliation(s)
- Jingwen Meng
- Wuxi Maternity and Child Health Care Hospital, Affiliated Women's Hospital of Jiangnan University, Wuxi, China
| | - Chen Zong
- Wuxi Maternity and Child Health Care Hospital, Affiliated Women's Hospital of Jiangnan University, Wuxi, China
| | - Meixia Wang
- Department of Gynecology and Obstetrics, Wenzhou Hospital of Integrated Traditional Chinese and Western Medicine, Wenzhou, China
| | - Yu Chen
- Wuxi Maternity and Child Health Care Hospital, Affiliated Women's Hospital of Jiangnan University, Wuxi, China
| | - Shaojie Zhao
- Wuxi Maternity and Child Health Care Hospital, Affiliated Women's Hospital of Jiangnan University, Wuxi, China
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Stefanoudakis D, Frountzas M, Schizas D, Michalopoulos NV, Drakaki A, Toutouzas KG. Significance of TP53, CDKN2A, SMAD4 and KRAS in Pancreatic Cancer. Curr Issues Mol Biol 2024; 46:2827-2844. [PMID: 38666907 PMCID: PMC11049225 DOI: 10.3390/cimb46040177] [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: 02/28/2024] [Revised: 03/16/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
The present review demonstrates the major tumor suppressor genes, including TP53, CDKN2A and SMAD4, associated with pancreatic cancer. Each gene's role, prevalence and impact on tumor development and progression are analyzed, focusing on the intricate molecular landscape of pancreatic cancer. In addition, this review underscores the prognostic significance of specific mutations, such as loss of TP53, and explores some potential targeted therapies tailored to these molecular signatures. The findings highlight the importance of genomic analyses for risk assessment, early detection and the design of personalized treatment approaches in pancreatic cancer. Overall, this review provides a comprehensive analysis of the molecular intricacies of pancreatic tumors, paving the way for more effective and tailored therapeutic interventions.
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Affiliation(s)
- Dimitrios Stefanoudakis
- First Propaedeutic Department of Surgery, Hippocration General Hospital, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece; (D.S.); (N.V.M.)
| | - Maximos Frountzas
- First Propaedeutic Department of Surgery, Hippocration General Hospital, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece; (D.S.); (N.V.M.)
| | - Dimitrios Schizas
- First Department of Surgery, Laikon General Hospital, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece;
| | - Nikolaos V. Michalopoulos
- First Propaedeutic Department of Surgery, Hippocration General Hospital, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece; (D.S.); (N.V.M.)
| | - Alexandra Drakaki
- Division of Hematology and Oncology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Konstantinos G. Toutouzas
- First Propaedeutic Department of Surgery, Hippocration General Hospital, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece; (D.S.); (N.V.M.)
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Pflüger MJ, Brosens LAA, Hruban RH. Precursor lesions in familial and hereditary pancreatic cancer. Fam Cancer 2024:10.1007/s10689-024-00359-2. [PMID: 38319536 DOI: 10.1007/s10689-024-00359-2] [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: 11/20/2023] [Accepted: 01/24/2024] [Indexed: 02/07/2024]
Abstract
Infiltrating ductal adenocarcinoma of the pancreas, referred to here as "pancreatic cancer," is one of the deadliest of all of the solid malignancies. The five-year survival rate in the United States for individuals diagnosed today with pancreatic cancer is a dismal 12%. Many invasive cancers, including pancreatic cancer, however, arise from histologically and genetically well-characterized precursor lesions, and these precancers are curable. Precursor lesions therefore are an attractive target for early detection and treatment. This is particularly true for individuals with an increased risk of developing invasive cancer, such as individuals with a strong family history of pancreatic cancer, and individuals with a germline variant known to increase the risk of developing pancreatic cancer. There is therefore a need to understand the precursor lesions that can give rise to invasive pancreatic cancer in these individuals.
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Affiliation(s)
- Michael J Pflüger
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lodewijk A A Brosens
- Department of Pathology, University Medical Center, Utrecht, The Netherlands
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ralph H Hruban
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Carnegie Room 415, 600 North Wolfe Street, Baltimore, MD, 21287, USA.
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8
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You Z, He J, Gao Z. Comprehensive analysis of the role of cuproptosis-related genes in the prognosis and immune infiltration of adrenocortical Carcinoma. Heliyon 2024; 10:e23661. [PMID: 38187219 PMCID: PMC10767392 DOI: 10.1016/j.heliyon.2023.e23661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 11/23/2023] [Accepted: 12/09/2023] [Indexed: 01/09/2024] Open
Abstract
Background Cuproptosis is a recently discovered form of nonapoptotic programmed cell death. However, no research on cuproptosis in the context of adrenocortical carcinoma has been conducted, and the prognostic value of assessing cuproptosis remains unclear. Methods In this study, we established comprehensive models to assess gene expression changes, mutation status, and prognosis prediction and developed a prognostic nomogram for cuproptosis-related genes. Using data from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), and Genotype-Tissue Expression (GTEx) databases, an analysis of 11 cuproptosis-related genes was performed. Additionally, a risk scoring method and nomogram were used to assess the relationships among cuproptosis-associated genes, transcript expression, clinical characteristics, and prognosis. The connections among tumors, immune checkpoints, and immune infiltration were also analyzed. Results The patterns observed in patients with adrenocortical carcinoma who were assessed using cuproptosis-associated risk scores provide useful information for understanding gene mutations, clinical outcomes, immune cell infiltration, and immune checkpoint analysis results. FDX1, LIPT1, MTF1, COX11, CYP2D6, DLAT, ATP7Band CDKN2A were differentially expressed in patients with adrenocortical carcinoma and normal controls. In addition, higher risk scores were significantly associated with poor overall survival and progression-free interval. The nomogram model subsequently developed to facilitate the clinical application of the analysis showed good predictive and calibration capabilities. GSE10927 and GSE33371 were used for independent cohort validation. Moreover, CDKN2A, FDX1, and other cuproptosis-related genes were significantly associated with immune infiltration and checkpoints. Conclusion We confirmed that our model had excellent predictive ability in patients with adrenocortical carcinoma. Therefore, an in-depth evaluation of patients using cuproptosis-related risk scores is clinically essential and can assist in therapy in the future.
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Affiliation(s)
- Zhiyuan You
- School of Clinical Medicine, Hangzhou Normal University, Hangzhou, 310005, China
| | - Jiqing He
- Department of Obstetrics, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, 310005, China
| | - Zhongming Gao
- Department of Neurology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, 310005, China
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Kimura H, Lahouel K, Tomasetti C, Roberts NJ. Functional characterization of all CDKN2A missense variants and comparison to in silico models of pathogenicity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.28.573507. [PMID: 38234851 PMCID: PMC10793438 DOI: 10.1101/2023.12.28.573507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Interpretation of variants identified during genetic testing is a significant clinical challenge. In this study, we developed a high-throughput CDKN2A functional assay and characterized all possible CDKN2A missense variants. We found that 40% of all missense variants were functionally deleterious. We also used our functional classification to assess the performance of in silico models that predict the effect of variants, including recently reported models based on machine learning. Notably, we found that all in silico models similarly when compared to our functional classifications with accuracies of 54.6 - 70.9%. Furthermore, while we found that functionally deleterious variants were enriched within ankyrin repeats, rarely were all missense variants at a single residue functionally deleterious. Our functional classifications are a resource to aid the interpretation of CDKN2A variants and have important implications for the application of variant interpretation guidelines, particularly the use of in silico models for clinical variant interpretation.
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Danishevich A, Bilyalov A, Nikolaev S, Khalikov N, Isaeva D, Levina Y, Makarova M, Nemtsova M, Chernevskiy D, Sagaydak O, Baranova E, Vorontsova M, Byakhova M, Semenova A, Galkin V, Khatkov I, Gadzhieva S, Bodunova N. CDKN2A Gene Mutations: Implications for Hereditary Cancer Syndromes. Biomedicines 2023; 11:3343. [PMID: 38137564 PMCID: PMC10741544 DOI: 10.3390/biomedicines11123343] [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: 11/12/2023] [Revised: 12/10/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Malignant neoplasms, including pancreatic cancer and melanoma, are major global health challenges. This study investigates melanoma pancreatic syndrome, a rare hereditary tumor syndrome associated with CDKN2A gene mutations. CDKN2A mutations contribute to a lifetime risk of melanoma ranging from 28% to 67%. This study reports the clinical features of six individuals with CDKN2A mutations and identifies recurrent alterations such as c.307_308del, c.159G>C and c.71G>C. It highlights the need for CDKN2A mutation testing in suspected cases of familial atypical multiple mole melanoma. Clinically significant variants show associations with melanoma and pancreatic cancer. The challenges of treating individuals with CDKN2A mutations are discussed, and the lack of specific targeted therapies is highlighted. Preclinical studies suggest a potential benefit of CDK4/6 inhibitors, although clinical trials show mixed results. This study underscores the importance of continued research into improved diagnostic and therapeutic strategies to address the complexities of hereditary cancer syndromes.
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Affiliation(s)
- Anastasiia Danishevich
- SBHI Moscow Clinical Scientific Center Named after Loginov MHD, 111123 Moscow, Russia (N.K.); (D.I.)
| | - Airat Bilyalov
- SBHI Moscow Clinical Scientific Center Named after Loginov MHD, 111123 Moscow, Russia (N.K.); (D.I.)
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Sergey Nikolaev
- SBHI Moscow Clinical Scientific Center Named after Loginov MHD, 111123 Moscow, Russia (N.K.); (D.I.)
| | - Nodirbec Khalikov
- SBHI Moscow Clinical Scientific Center Named after Loginov MHD, 111123 Moscow, Russia (N.K.); (D.I.)
| | - Daria Isaeva
- SBHI Moscow Clinical Scientific Center Named after Loginov MHD, 111123 Moscow, Russia (N.K.); (D.I.)
| | - Yuliya Levina
- SBHI Moscow Clinical Scientific Center Named after Loginov MHD, 111123 Moscow, Russia (N.K.); (D.I.)
| | - Maria Makarova
- LLC Evogen, 115191 Moscow, Russia
- Federal State Budgetary Institution Russian Scientific Center of Roentgenoradiology, Ministry of Healthcare of the Russian Federation, 117997 Moscow, Russia
| | - Marina Nemtsova
- LLC Evogen, 115191 Moscow, Russia
- Research Centre for Medical Genetics of N.P. Bochkov, 115522 Moscow, Russia
- Federal State Autonomous Educational Institution of Higher Education I.M. Sechenov, Ministry of Health of Russian Federation, 119991 Moscow, Russia
| | - Denis Chernevskiy
- LLC Evogen, 115191 Moscow, Russia
- FSBEI HE “Privolzhsky Research Medical University”, Ministry of Health of Russian Federation, 603950 Nizhny Novgorod, Russia
| | - Olesya Sagaydak
- LLC Evogen, 115191 Moscow, Russia
- Federal State Budgetary Institution National Medical Research Center of Cardiology Named after Academician E.I. Chazov, Ministry of Health of the Russian Federation, 121552 Moscow, Russia
| | - Elena Baranova
- LLC Evogen, 115191 Moscow, Russia
- Russian Medical Academy of Continuous Professional Education, Russia, 125993 Moscow, Russia
| | - Maria Vorontsova
- Faculty of Medicine, Lomonosov Moscow State University, 119991 Moscow, Russia
- The National Medical Research Center for Endocrinology, 117292 Moscow, Russia
| | - Mariya Byakhova
- Moscow Healthcare Department, Moscow State Budgetary Healthcare Institution Moscow City Oncological Hospital No. 1, 117152 Moscow, Russia
| | - Anna Semenova
- Moscow Healthcare Department, Moscow State Budgetary Healthcare Institution Moscow City Oncological Hospital No. 1, 117152 Moscow, Russia
| | - Vsevolod Galkin
- Moscow Healthcare Department, Moscow State Budgetary Healthcare Institution Moscow City Oncological Hospital No. 1, 117152 Moscow, Russia
| | - Igor Khatkov
- SBHI Moscow Clinical Scientific Center Named after Loginov MHD, 111123 Moscow, Russia (N.K.); (D.I.)
| | | | - Natalia Bodunova
- SBHI Moscow Clinical Scientific Center Named after Loginov MHD, 111123 Moscow, Russia (N.K.); (D.I.)
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Srilatha M, Malla R, Adem MP, Foote JB, Nagaraju GP. Obesity associated pancreatic ductal adenocarcinoma: Therapeutic challenges. Semin Cancer Biol 2023; 97:12-20. [PMID: 37926347 DOI: 10.1016/j.semcancer.2023.11.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 10/27/2023] [Accepted: 11/01/2023] [Indexed: 11/07/2023]
Abstract
Obesity is a prominent health issue worldwide and directly impacts pancreatic health, with obese individuals exhibiting a significant risk for increasing pancreatic ductal adenocarcinoma (PDAC). Several factors potentially explain the increased risk for the development of PDAC, including obesity-induced chronic inflammation within and outside of the pancreas, development of insulin resistance and metabolic dysfunction, promotion of immune suppression within the pancreas during inflammation, pre- and malignant stages, variations in hormones levels (adiponectin, ghrelin, and leptin) produced from the adipose tissue, and acquisition of somatic mutations in tumor once- and suppressor proteins critical for pancreatic tumorigenesis. In this manuscript, we will explore the broad impact of these obesity-induced risk factors on the development and progression of PDAC, focusing on changes within the tumor microenvironment (TME) as they pertain to prevention, current therapeutic strategies, and future directions for targeting obesity management as they relate to the prevention of pancreatic tumorigenesis.
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Affiliation(s)
- Mundla Srilatha
- Department of Biotechnology, Sri Venkateswara University, Tirupati, Andhra Pradesh 517502, India
| | - Ramarao Malla
- Cancer Biology Laboratory, Department of Biochemistry and Bioinformatics, School of Science, GITAM (Deemed to be University), Visakhapatnam, Andhra Pradesh 530045, India
| | - Megha Priya Adem
- Department of Biotechnology, Sri Padmavati Mahila Visvavidyalayam (Women's University), Tirupati, Andhra Pradesh 517502, India
| | - Jeremy B Foote
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35233, USA
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Wang H, Zhang G, Dong L, Chen L, Liang L, Ge L, Gai D, Shen X. Identification and study of cuproptosis-related genes in prognostic model of multiple myeloma. Hematology 2023; 28:2249217. [PMID: 37610069 DOI: 10.1080/16078454.2023.2249217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 08/11/2023] [Indexed: 08/24/2023] Open
Abstract
BACKGROUND Multiple myeloma (MM) is a highly heterogeneous disease. Cuproptosis is a novel mode of death that is closely associated with several diseases, such as hepatocellular carcinoma. However, its role in MM is unknown. METHODS MM transcriptomic and clinical data were obtained from UCSC Xena and gene expression omnibus (GEO) databases. Following MM samples were divided into different subtypes based on the cuproptosis genes, the differentially expressed genes (DEGs) among different subtypes, namely, candidate cuproptosis related genes were analyzed by univariate Cox and least absolute shrinkage and selection operator (LASSO) regression to construct a cuproptosis-related risk model. After the independent prognostic analysis was performed, a nomogram was constructed. Finally, Functional enrichment analysis and immune infiltration analysis were performed in the high- and low-risk groups, potential therapeutic agents were then predicted. RESULTS The 784 MM samples in UCSC Xena cohorts were divided into three different subtypes, and 4 out of 346 candidate cuproptosis related genes, namely CDKN2A, BCL3, KCNA3 and TTC14 were used to construct a risk model. Risk score was considered a reliable independent prognostic factor for MM patients. It was investigated that the pathway of cell cycle was significantly enriched in the high-risk group. In addition, immune score, ESTIMATE score and cytolytic activity were significantly different between different risk groups, as well as 13 immune cells such as memory B cells. Nine drugs were predicted in our study. CONCLUSION A cuproptosis-related prognostic model was constructed, which may have a potential guiding role in the treatment of MM.
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Affiliation(s)
- Haili Wang
- Shanxi Medical University, Taiyuan, People's Republic of China
- Department of Hematology, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, People's Republic of China
| | - Guoxiang Zhang
- Department of Hematology, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, People's Republic of China
| | - Lu Dong
- Department of Hematology, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, People's Republic of China
| | - Lu Chen
- Department of Hematology, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, People's Republic of China
| | - Li Liang
- Department of Hematology, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, People's Republic of China
| | - Li Ge
- Department of Hematology, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, People's Republic of China
| | - Dongzheng Gai
- Department of Hematology, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, People's Republic of China
| | - Xuliang Shen
- Shanxi Medical University, Taiyuan, People's Republic of China
- Department of Hematology, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, People's Republic of China
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Kwak JJ, Lee KS, Lee J, Kim YJ, Choi EY, Byeon SH, Chang WS, Kim YR, Kim JS, Shin S, Lee ST, Kim SS, Lee CS. Next-Generation Sequencing of Vitreoretinal Lymphoma by Vitreous Liquid Biopsy: Diagnostic Potential and Genotype/Phenotype Correlation. Invest Ophthalmol Vis Sci 2023; 64:27. [PMID: 37975847 PMCID: PMC10664732 DOI: 10.1167/iovs.64.14.27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/31/2023] [Indexed: 11/19/2023] Open
Abstract
Purpose To determine the diagnostic potential of next-generation sequencing (NGS) in vitreous samples, analyze genotype-phenotype characteristics, and compare NGS of matched vitreous and brain samples in patients with associated central nervous system lymphoma (CNSL). Methods A total of 32 patients suspected of vitreoretinal lymphoma (VRL) who underwent diagnostic vitrectomy and NGS were included in this retrospective observational case-series. Fresh vitreous specimens from diagnostic vitrectomy of VRL-suspected patients underwent NGS using a custom panel targeting 747 candidate genes for lymphoma. They also underwent malignancy cytology, interleukin (IL)-10/IL-6, immunoglobulin heavy chain (IGH)/immunoglobulin kappa light chain (IGK) monoclonality testing. MYD88 L265P mutation was examined from anterior chamber tap samples. The diagnosis of VRL was made based on typical clinical characteristics for VRL, as well as malignant cytology, IGH/IGK clonality, or IL-10/IL-6 > 1. Sensitivity and specificity of NGS were compared with conventional diagnostic tests. Brain tissues suspected of lymphoma were collected by stereotactic biopsy and underwent NGS. Genetic variations detected in NGS of vitreous and brain tissue specimens were compared. Results The sensitivity values for cytology, IL-10/IL-6 > 1, clonality assays for IGH and IGK, MYD88 L265P detection in anterior chamber tap samples, and vitreous NGS were 0.23, 0.83, 0.68, 0.79, 0.67, and 0.85, with specificity values of 1.00, 0.83, 0.50, 0.25, 0.83, and 0.83, respectively. The sensitivity (0.85) of vitreous NGS was the highest compared to other conventional diagnostic tests for VRL. The most common mutations were MYD88 (91%), CDKN2A (36%), PIM1 (32%), IGLL5 (27%), and ETV6 (23%). Although several gene alterations demonstrated heterogeneity between the brain and eyes, some common mutational profiles were observed in matched vitreous and brain samples. Conclusions Overall, NGS of the vitreous demonstrated high sensitivity among conventional diagnostic tests. VRL and CNSL appeared to have both shared and distinct genetic variations, which may suggest site-specific variations from a common origin.
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Affiliation(s)
- Jay Jiyong Kwak
- Department of Ophthalmology, The Institute of Vision Research, Yonsei University College of Medicine, Seoul, Korea
| | - Kwang Seob Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Junwon Lee
- Department of Ophthalmology, The Institute of Vision Research, Yonsei University College of Medicine, Seoul, Korea
| | - Yong Joon Kim
- Department of Ophthalmology, The Institute of Vision Research, Yonsei University College of Medicine, Seoul, Korea
| | - Eun Young Choi
- Department of Ophthalmology, The Institute of Vision Research, Yonsei University College of Medicine, Seoul, Korea
| | - Suk Ho Byeon
- Department of Ophthalmology, The Institute of Vision Research, Yonsei University College of Medicine, Seoul, Korea
| | - Won Seok Chang
- Department of Neurosurgery, Yonsei University College of Medicine, Seoul, Korea
| | - Yu Ri Kim
- Division of Hematology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Jin Seok Kim
- Division of Hematology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Saeam Shin
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Sung Soo Kim
- Department of Ophthalmology, The Institute of Vision Research, Yonsei University College of Medicine, Seoul, Korea
| | - Christopher Seungkyu Lee
- Department of Ophthalmology, The Institute of Vision Research, Yonsei University College of Medicine, Seoul, Korea
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Elebo N, Abdel-Shafy EA, Cacciatore S, Nweke EE. Exploiting the molecular subtypes and genetic landscape in pancreatic cancer: the quest to find effective drugs. Front Genet 2023; 14:1170571. [PMID: 37790705 PMCID: PMC10544984 DOI: 10.3389/fgene.2023.1170571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 08/29/2023] [Indexed: 10/05/2023] Open
Abstract
Pancreatic Ductal Adenocarcinoma (PDAC) is a very lethal disease that typically presents at an advanced stage and is non-compliant with most treatments. Recent technologies have helped delineate associated molecular subtypes and genetic variations yielding important insights into the pathophysiology of this disease and having implications for the identification of new therapeutic targets. Drug repurposing has been evaluated as a new paradigm in oncology to accelerate the application of approved or failed target-specific molecules for the treatment of cancer patients. This review focuses on the impact of molecular subtypes on key genomic alterations in PDAC, and the progress made thus far. Importantly, these alterations are discussed in light of the potential role of drug repurposing in PDAC.
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Affiliation(s)
- Nnenna Elebo
- Department of Surgery, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, Gauteng, South Africa
- Bioinformatics Unit, International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa
| | - Ebtesam A. Abdel-Shafy
- Bioinformatics Unit, International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa
- National Research Centre, Cairo, Egypt
| | - Stefano Cacciatore
- Bioinformatics Unit, International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa
| | - Ekene Emmanuel Nweke
- Department of Surgery, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, Gauteng, South Africa
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15
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Liu X, Wang X, Zhang H, Yan Z, Gaňová M, Lednický T, Řezníček T, Xu Y, Zeng W, Korabečná M, Neužil P. Smartphone integrated handheld (SPEED) digital polymerase chain reaction device. Biosens Bioelectron 2023; 232:115319. [PMID: 37087984 DOI: 10.1016/j.bios.2023.115319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/06/2023] [Accepted: 04/12/2023] [Indexed: 04/25/2023]
Abstract
We demonstrate a smartphone integrated handheld (SPEED) digital polymerase chain reaction (dPCR) device for point-of-care application. The device has dimensions of ≈100 × 200 × 35 mm3 and a weight of ≈400 g. It can perform 45 PCR cycles in ≈49 min. The device also features integrated, miniaturized modules for thermal cycling, image taking, and wireless data communication. These functions are controlled by self-developed Android-based applications. The only consumable is the developed silicon-based dPCR chip, which has the potential to be recycled. The device's precision and accuracy are comparable with commercial dPCR machines. We have verified the SPEED dPCR prototype's utility in the testing of severe acute respiratory syndrome coronavirus 2, the detection of cancer-associated gene sequences, and the confirmations of Down syndrome diagnoses. Due to its low upfront capital investment, as well as its nominal running cost, we envision that the SPEED dPCR device will help to perform cancer screenings and non-invasive prenatal tests for the general population. It will also aid in the timely identification and monitoring of infectious disease testing, thereby expediting alerts with respect to potential emerging pandemics.
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Affiliation(s)
- Xiaocheng Liu
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China
| | - Xinlu Wang
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China
| | - Haoqing Zhang
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China; Ministry of Education Key Laboratory of Biomedical Information Engineering, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, PR China
| | - Zhiqiang Yan
- School of Marine Science and Technology, Northwestern Polytechnical University, Xi'an, Shaanxi, 710072, PR China
| | - Martina Gaňová
- Central European Institute of Technology, Brno University of Technology, Purkyňova 123, 61300, Brno, Czech Republic; Faculty of Electrical Engineering, Brno University of Technology, Technická 3058/10, 61600, Brno, Czech Republic
| | - Tomáš Lednický
- Central European Institute of Technology, Brno University of Technology, Purkyňova 123, 61300, Brno, Czech Republic
| | - Tomáš Řezníček
- ITD Tech s.r.o, Osvoboditelu 1005, 735 81, Bohumín, Czech Republic
| | - Ying Xu
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China
| | - Wen Zeng
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China
| | - Marie Korabečná
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital of Prague, Albertov 4, 12800, Prague, Czech Republic
| | - Pavel Neužil
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China; Faculty of Electrical Engineering, Brno University of Technology, Technická 3058/10, 61600, Brno, Czech Republic.
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16
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Fan K, Dong Y, Li T, Li Y. Cuproptosis-associated CDKN2A is targeted by plicamycin to regulate the microenvironment in patients with head and neck squamous cell carcinoma. Front Genet 2023; 13:1036408. [PMID: 36699463 PMCID: PMC9868476 DOI: 10.3389/fgene.2022.1036408] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 12/12/2022] [Indexed: 01/11/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC), the most common malignancy of the head and neck, has an overall 5-year survival rate of <50%. Genes associated with cuproptosis, a newly identified copper-dependent form of cell death, are aberrantly expressed in various tumours. However, their role in HNSCC remains unknown. In this study, bioinformatic analysis revealed that the cuproptosis-related gene CDKN2A was correlated with the malignant behaviour of HNSCC. Kaplan-Meier (KM) curves showed that patients with high CDKN2A expression had a better prognosis. Multiomic analysis revealed that CDKN2A may be associated with cell cycle and immune cell infiltration in the tumour microenvironment and is important for maintaining systemic homeostasis in the body. Furthermore, molecular docking and molecular dynamics simulations suggested strong binding between plicamycin and CDKN2A. And plicamycin inhibits the progression of HNSCC in cellular assays. In conclusion, this study elucidated a potential mechanism of action of the cuproptosis-associated gene CDKN2A in HNSCC and revealed that plicamycin targets CDKN2A to improve the prognosis of patients.
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Mazer BL, Lee JW, Roberts NJ, Chu LC, Lennon AM, Klein AP, Eshleman JR, Fishman EK, Canto MI, Goggins MG, Hruban RH. Screening for pancreatic cancer has the potential to save lives, but is it practical? Expert Rev Gastroenterol Hepatol 2023; 17:555-574. [PMID: 37212770 PMCID: PMC10424088 DOI: 10.1080/17474124.2023.2217354] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/21/2023] [Accepted: 05/19/2023] [Indexed: 05/23/2023]
Abstract
INTRODUCTION Most patients with pancreatic cancer present with advanced stage, incurable disease. However, patients with high-grade precancerous lesions and many patients with low-stage disease can be cured with surgery, suggesting that early detection has the potential to improve survival. While serum CA19.9 has been a long-standing biomarker used for pancreatic cancer disease monitoring, its low sensitivity and poor specificity have driven investigators to hunt for better diagnostic markers. AREAS COVERED This review will cover recent advances in genetics, proteomics, imaging, and artificial intelligence, which offer opportunities for the early detection of curable pancreatic neoplasms. EXPERT OPINION From exosomes, to circulating tumor DNA, to subtle changes on imaging, we know much more now about the biology and clinical manifestations of early pancreatic neoplasia than we did just five years ago. The overriding challenge, however, remains the development of a practical approach to screen for a relatively rare, but deadly, disease that is often treated with complex surgery. It is our hope that future advances will bring us closer to an effective and financially sound approach for the early detection of pancreatic cancer and its precursors.
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Affiliation(s)
- Benjamin L. Mazer
- The Sol Goldman Pancreatic Cancer Research Center, the Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Pathology, the Johns Hopkins University School of Medicine, Baltimore, MD
| | - Jae W. Lee
- The Sol Goldman Pancreatic Cancer Research Center, the Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Pathology, the Johns Hopkins University School of Medicine, Baltimore, MD
| | - Nicholas J. Roberts
- The Sol Goldman Pancreatic Cancer Research Center, the Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Pathology, the Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Oncology, the Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Linda C. Chu
- Department of Radiology, the Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Anne Marie Lennon
- Department of Medicine, Division of Gastroenterology and Hepatology, the Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alison P. Klein
- The Sol Goldman Pancreatic Cancer Research Center, the Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Pathology, the Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Oncology, the Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - James R. Eshleman
- The Sol Goldman Pancreatic Cancer Research Center, the Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Pathology, the Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Oncology, the Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elliot K. Fishman
- Department of Radiology, the Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Marcia Irene Canto
- Department of Medicine, Division of Gastroenterology and Hepatology, the Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michael G. Goggins
- The Sol Goldman Pancreatic Cancer Research Center, the Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Pathology, the Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Oncology, the Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ralph H. Hruban
- The Sol Goldman Pancreatic Cancer Research Center, the Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Pathology, the Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Oncology, the Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Zhang Q, Ma L, Zhou H, Zhou Y, Liu S, Li Q. A prognostic signature of cuproptosis and TCA-related genes for hepatocellular carcinoma. Front Oncol 2022; 12:1040736. [PMID: 36324575 PMCID: PMC9619237 DOI: 10.3389/fonc.2022.1040736] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 10/03/2022] [Indexed: 11/26/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is the most common malignant tumor of the liver. Cuproptosis is a newly defined form of cell death. Copper ion induces cell death by binding to the tricarboxylic acid cycle (TCA). The effect of cuproptosis-related and TCA-related genes on the clinical prognosis of HCC is still unclear. In this study, we explores the genetic changes of cuproptosis-related genes that affect the TCA process and their potential therapeutic value in HCC patients. Methods The cuproptosis and TCA-related genes were obtained from cuproptosis-related articles and the molecular signatures database. The prognosis signatures of eight related genes were constructed using the last absolute shrinkage and selection operator (LASSO), and Receiver Operating Characteristic (ROC) curves were used to evaluate the signature. In addition, we analyzed downstream functional enrichment and immune infiltration to explore cuproptosis-inducing drugs and immunotherapeutic responses. All these analyses were validated using multiple datasets of the International Cancer Genome Consortium (ICGC). Results TCA and copper malnutrition-related genes (CDKN2A, IDH1, OGDHL, IDH3G, IDH3B, GLS, DLAT, LIPT1) were finally included. According to the risk score, they were divided into high-risk and low-risk groups. Survival analysis showed that the overall survival (OS) of the high-risk group was significantly lower than that of the low-risk group. We established a risk prognostic feature to predict the OS of patients with HCC. Based on this feature and the clinical stage, we constructed a nomogram. Functional enrichment analysis revealed pathways related to organelle division and the cell cycle. Different risk scores had different immune abundances in immune cells (including macrophages and regulatory T-cells) and immune pathways (including antigen-presenting cells co-stimulation). Moreover, the drug sensitivity of eleschomol and PD-L1 in the high-risk group was better than that in the low-risk group. The status of TP53 somatic mutation was also closely related to the risk score. Conclusion In this study, we established a new prediction signature of eight genes related to cuproptosis and the TCA process, which can effectively predict the prognosis of HCC patients.
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Germline Testing for Individuals with Pancreatic Adenocarcinoma and Novel Genetic Risk Factors. Hematol Oncol Clin North Am 2022; 36:943-960. [DOI: 10.1016/j.hoc.2022.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Jin L, Mei W, Liu X, Sun X, Xin S, Zhou Z, Zhang J, Zhang B, Chen P, Cai M, Ye L. Identification of cuproptosis -related subtypes, the development of a prognosis model, and characterization of tumor microenvironment infiltration in prostate cancer. Front Immunol 2022; 13:974034. [PMID: 36203594 PMCID: PMC9530990 DOI: 10.3389/fimmu.2022.974034] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/30/2022] [Indexed: 12/03/2022] Open
Abstract
Cuproptosis, Copper Induced Cell Death, is a newly defined type of programmed cell death, involving in the regulation of tricarboxylic acid (TCA) cycle. Dysfunction of cuproptosis induces cytotoxicity and influences the proliferation of multiple tumors. However, the direct prognostic effect of cuproptosis related genes and corresponding regulating mechanisms amid prostate cancer remains unknown. A multi-omics analysis strategy was adopted to explore the role of ten cuproptosis related genes in The Cancer Genome Atlas- Prostate Adenocarcinoma (TCGA-PRAD). Firstly, mRNA expression, Copy Number Variance (CNV), mutation, DNA methylation and prognostic power of the ten genes were illustrated. Based on transcriptomic data, we developed a novel prognostic model named the Cuproptosis-related gene score (CRGScore), Their biological functions were then detected by enrichment analysis and unsupervised cluster analysis. Following that, their correlation with Tumor Immune Microenvironment (TIME), immunotherapy, Biochemical Recurrence (BCR) and chemotherapeutic resistance were elaborated by relevant bioinformatics algorithms. Ten cuproptosis related genes exhibited extensive alteration of CNV and DNA methylation and showed significant influence on the prognosis of prostate cancer patients. These genes mainly enriched in E2F and G2M targets and mitosis pathways, Samples with high CRGScore showed enhancement resulting in the increased infiltration of T cell, B cell, NK cells. They also demonstrated close correlations with the BCR status, expression of eight immune checkpoints and chemotherapeutic resistances in prostate cancer. Our comprehensive analysis of CRGScore revealed an extensive regulatory mechanism by which they affect the tumor-immune-stromal microenvironment, clinicopathological features, and prognosis. We also determined the therapeutic liability of CRGScore in targeted therapy and immunotherapy. These findings highlight the crucial clinical implications of CRGScore and provide new ideas for guiding personalized immunotherapy strategies for patients with Pca.
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Affiliation(s)
- Liang Jin
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China,Department of Urology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China,Department of Orthopaedics, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Wangli Mei
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China,Department of Urology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xiang Liu
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China,Department of Urology, Shanghai Putuo District People’s Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xianchao Sun
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Shiyong Xin
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China,Department of Urology, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
| | - Zhen Zhou
- Department of Urology, Shanghai Putuo District People’s Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jiaxin Zhang
- Department of Urology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Bihui Zhang
- Department of Urology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Ping Chen
- School of Life Sciences and Technology, Tongji University, Shanghai, China,*Correspondence: Lin Ye, ; Ming Cai, ; Ping Chen,
| | - Ming Cai
- Department of Orthopaedics, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China,*Correspondence: Lin Ye, ; Ming Cai, ; Ping Chen,
| | - Lin Ye
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China,Department of Urology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China,*Correspondence: Lin Ye, ; Ming Cai, ; Ping Chen,
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Clinical Significance of Germline Pathogenic Variants among 51 Cancer Predisposition Genes in an Unselected Cohort of Italian Pancreatic Cancer Patients. Cancers (Basel) 2022; 14:cancers14184447. [PMID: 36139606 PMCID: PMC9496779 DOI: 10.3390/cancers14184447] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/29/2022] [Accepted: 09/02/2022] [Indexed: 12/24/2022] Open
Abstract
Multigene germline panel testing is recommended for Pancreatic Cancer (PC) patients; however, for non-BRCA1/2 genes, the clinical utility is unclear. A comprehensive multi-gene assessment in unselected Italian PC patients is missing. We evaluated the prevalence and impact of Pathogenic Variants (PV) in 51 PC susceptibility genes in a real-world series of 422 Italian PC patients unselected for Family History (FH), compared the clinical characteristics and conducted survival analyses. 17% of patients had PVs (70/422), mainly in BRCA1/2 (4.5%, all <70 y), CDKN2A (4.5%, all >50 y), ATM (2.1%). PV carriers were younger (64 vs. 67; p = 0.02) and had more frequent personal/FH of PC, melanoma and breast/ovarian cancer (all p < 0.05). The Overall Survival (OS) was longer in patients carrying PVs (HR 0.78; p = 0.090), comprising ATM carriers (HR 0.33; p = 0.054). In the oxaliplatin-treated subset, PV carriers showed better control of the disease, although this was not statistically significant (67% vs. 56%). CDKN2A, BRCA2 and ATM were the most frequently altered genes. ATM PVs were positively associated with OS in 41% of PV carriers, 60% of whom carried CDKN2A,BRCA2 or ATM PVs, had negative FH and would have been missed by traditional referral. Thus, CDKN2A and ATM should be added to BRCA1/2 testing regardless of FH.
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22
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Rashid S, Gupta S, McCormick SR, Tsao H. New Insights into Melanoma Tumor Syndromes. JID INNOVATIONS 2022; 2:100152. [DOI: 10.1016/j.xjidi.2022.100152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 06/08/2022] [Accepted: 06/13/2022] [Indexed: 10/14/2022] Open
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Bian Z, Fan R, Xie L. A Novel Cuproptosis-Related Prognostic Gene Signature and Validation of Differential Expression in Clear Cell Renal Cell Carcinoma. Genes (Basel) 2022; 13:genes13050851. [PMID: 35627236 PMCID: PMC9141858 DOI: 10.3390/genes13050851] [Citation(s) in RCA: 158] [Impact Index Per Article: 79.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/02/2022] [Accepted: 05/05/2022] [Indexed: 12/12/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most prevalent subtype of renal cell carcinoma, which is characterized by metabolic reprogramming. Cuproptosis, a novel form of cell death, is highly linked to mitochondrial metabolism and mediated by protein lipoylation. However, the clinical impacts of cuproptosis-related genes (CRGs) in ccRCC largely remain unclear. In the current study, we systematically evaluated the genetic alterations of cuproptosis-related genes in ccRCC. Our results revealed that CDKN2A, DLAT, DLD, FDX1, GLS, PDHA1 and PDHB exhibited differential expression between ccRCC and normal tissues (|log2(fold change)| > 2/3 and p < 0.05). Utilizing an iterative sure independence screening (SIS) method, we separately constructed the prognostic signature of CRGs for predicting the overall survival (OS) and progression-free survival (PFS) in ccRCC patients. The prognostic score of CRGs yielded an area under the curve (AUC) of 0.658 and 0.682 for the prediction of 5-year OS and PFS, respectively. In the Kaplan−Meier survival analysis of OS, a higher risk score of cuproptosis-related gene signature was significantly correlated with worse overall survival (HR = 2.72 (2.01−3.68), log-rank p = 1.76 × 10−7). Patients with a higher risk had a significantly shorter PFS (HR = 2.83 (2.08−3.85), log-rank p = 3.66 × 10−7). Two independent validation datasets (GSE40435 (N = 101), GSE53757 (N = 72)) were collected for meta-analysis, suggesting that CDKN2A (log2(fold change) = 1.46, 95%CI: 1.75−2.35) showed significantly higher expression in ccRCC tissues while DLAT (log2(fold change) = −0.54, 95%CI: −0.93−−0.15) and FDX1 (log2(fold change) = −1.01, 95%CI: −1.61−−0.42) were lowly expressed. The expression of CDKN2A and FDX1 in ccRCC was also significantly associated with immune infiltration levels and programmed cell death protein 1 (PD-1) expression (CDKN2A: r = 0.24, p = 2.14 × 10−8; FDX1: r = −0.17, p = 1.37 × 10−4). In conclusion, the cuproptosis-related gene signature could serve as a potential prognostic predictor for ccRCC patients and may offer novel insights into the cancer treatment.
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Affiliation(s)
- Zilong Bian
- Department of Big Data in Health Science, School of Public Health, Zhejiang University School of Medicine, Hangzhou 310058, China;
- Correspondence: (Z.B.); (L.X.)
| | - Rong Fan
- Department of Big Data in Health Science, School of Public Health, Zhejiang University School of Medicine, Hangzhou 310058, China;
| | - Lingmin Xie
- Department of Surgical Oncology, Affiliated Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
- Correspondence: (Z.B.); (L.X.)
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24
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Kimura H, Paranal RM, Nanda N, Wood LD, Eshleman JR, Hruban RH, Goggins MG, Klein AP, Roberts NJ. Functional CDKN2A assay identifies frequent deleterious alleles misclassified as variants of uncertain significance. eLife 2022; 11:71137. [PMID: 35001868 PMCID: PMC8824478 DOI: 10.7554/elife.71137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 01/06/2022] [Indexed: 12/25/2022] Open
Abstract
Pathogenic germline CDKN2A variants are associated with an increased risk of pancreatic ductal adenocarcinoma (PDAC). CDKN2A variants of uncertain significance (VUSs) are reported in up to 4.3% of patients with PDAC and result in significant uncertainty for patients and their family members as an unknown fraction are functionally deleterious, and therefore, likely pathogenic. Functional characterization of CDKN2A VUSs is needed to reclassify variants and inform clinical management. Twenty-nine germline CDKN2A VUSs previously reported in patients with PDAC or in ClinVar were evaluated using a validated in vitro cell proliferation assay. Twelve of the 29 CDKN2A VUSs were functionally deleterious (11 VUSs) or potentially functionally deleterious (1 VUS) and were reclassified as likely pathogenic variants. Thus, over 40% of CDKN2A VUSs identified in patients with PDAC are functionally deleterious and likely pathogenic. When incorporating VUSs found to be functionally deleterious, and reclassified as likely pathogenic, the prevalence of pathogenic/likely pathogenic CDKN2A in patients with PDAC reported in the published literature is increased to up to 4.1% of patients, depending on family history. Therefore, CDKN2A VUSs may play a significant, unappreciated role in risk of pancreatic cancer. These findings have significant implications for the counselling and care of patients and their relatives.
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Affiliation(s)
- Hirokazu Kimura
- The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University, Baltimore, United States
| | - Raymond M Paranal
- The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University, Baltimore, United States.,Human Genetics Predoctoral Training Program, the McKusick-Nathans Institute of Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, United States
| | - Neha Nanda
- The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University, Baltimore, United States
| | - Laura D Wood
- The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University, Baltimore, United States.,Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, United States
| | - James R Eshleman
- The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University, Baltimore, United States.,Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, United States.,Department of Epidemiology, The Johns Hopkins University Bloomberg School of Public Health, Baltimore, United States
| | - Ralph H Hruban
- The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University, Baltimore, United States.,Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, United States
| | - Michael G Goggins
- The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University, Baltimore, United States.,Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, United States
| | - Alison P Klein
- The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University, Baltimore, United States.,Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, United States.,Department of Epidemiology, The Johns Hopkins University Bloomberg School of Public Health, Baltimore, United States
| | | | - Nicholas J Roberts
- The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University, Baltimore, United States.,Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, United States
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