1
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Liu J, Miao X, Yao J, Wan Z, Yang X, Tian W. Investigating the clinical role and prognostic value of genes related to insulin-like growth factor signaling pathway in thyroid cancer. Aging (Albany NY) 2024; 16:2934-2952. [PMID: 38329437 PMCID: PMC10911384 DOI: 10.18632/aging.205524] [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: 09/25/2023] [Accepted: 12/27/2023] [Indexed: 02/09/2024]
Abstract
BACKGROUND Thyroid cancer (THCA) is the most common endocrine malignancy having a female predominance. The insulin-like growth factor (IGF) pathway contributed to the unregulated cell proliferation in multiple malignancies. We aimed to explore the IGF-related signature for THCA prognosis. METHOD The TCGA-THCA dataset was collected from the Cancer Genome Atlas (TCGA) for screening of key prognostic genes. The limma R package was applied for differentially expressed genes (DEGs) and the clusterProfiler R package was used for the Gene Ontology (GO) and KEGG analysis of DEGs. Then, the un/multivariate and least absolute shrinkage and selection operator (Lasso) Cox regression analysis was used for the establishment of RiskScore model. Receiver Operating Characteristic (ROC) analysis was used to verify the model's predictive performance. CIBERSORT and MCP-counter algorithms were applied for immune infiltration analysis. Finally, we analyzed the mutation features and the correlation between the RiskScore and cancer hallmark pathway by using the GSEA. RESULT We obtained 5 key RiskScore model genes for patient's risk stratification from the 721 DEGs. ROC analysis indicated that our model is an ideal classifier, the high-risk patients are associated with the poor prognosis, immune infiltration, high tumor mutation burden (TMB), stronger cancer stemness and stronger correlation with the typical cancer-activation pathways. A nomogram combined with multiple clinical features was developed and exhibited excellent performance upon long-term survival quantitative prediction. CONCLUSIONS We constructed an excellent prognostic model RiskScore based on IGF-related signature and concluded that the IGF signal pathway may become a reliable prognostic phenotype in THCA intervention.
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Affiliation(s)
- Junyan Liu
- Department of General Surgery, The First Medical Center, Chinese People’s Liberation Army (PLA) General Hospital, Beijing 100853, China
| | - Xin Miao
- Department of General Surgery, The First Medical Center, Chinese People’s Liberation Army (PLA) General Hospital, Beijing 100853, China
| | - Jing Yao
- Department of General Surgery, The First Medical Center, Chinese People’s Liberation Army (PLA) General Hospital, Beijing 100853, China
| | - Zheng Wan
- Department of General Surgery, The First Medical Center, Chinese People’s Liberation Army (PLA) General Hospital, Beijing 100853, China
| | - Xiaodong Yang
- Department of General Surgery, The First Medical Center, Chinese People’s Liberation Army (PLA) General Hospital, Beijing 100853, China
| | - Wen Tian
- Department of General Surgery, The First Medical Center, Chinese People’s Liberation Army (PLA) General Hospital, Beijing 100853, China
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2
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Mannam SS, Bray DP, Nwagwu CD, Zhong J, Shu HK, Eaton B, Sudmeier L, Goyal S, Deibert C, Nduom EK, Olson J, Hoang KB. Examining the Effect of ALK and EGFR Mutations on Survival Outcomes in Surgical Lung Brain Metastasis Patients. Cancers (Basel) 2023; 15:4773. [PMID: 37835467 PMCID: PMC10572022 DOI: 10.3390/cancers15194773] [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: 08/11/2023] [Revised: 09/24/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
In the context of the post-genomic era, where targeted oncological therapies like monoclonal antibodies (mAbs) and tyrosine-kinase inhibitors (TKIs) are gaining prominence, this study investigates whether these therapies can enhance survival for lung carcinoma patients with specific genetic mutations-EGFR-amplified and ALK-rearranged mutations. Prior to this study, no research series had explored how these mutations influence patient survival in cases of surgical lung brain metastases (BMs). Through a multi-site retrospective analysis, the study examined patients who underwent surgical resection for BM arising from primary lung cancer at Emory University Hospital from January 2012 to May 2022. The mutational statuses were determined from brain tissue biopsies, and survival analyses were conducted. Results from 95 patients (average age: 65.8 ± 10.6) showed that while 6.3% had anaplastic lymphoma kinase (ALK)-rearranged mutations and 20.0% had epidermal growth factor receptor (EGFR)-amplified mutations-with 9.5% receiving second-line therapies-these mutations did not significantly correlate with overall survival. Although the sample size of patients receiving targeted therapies was limited, the study highlighted improved overall survival and progression-free survival rates compared to earlier trials, suggesting advancements in systemic lung metastasis treatment. The study suggests that as more targeted therapies emerge, the prospects for increased overall survival and progression-free survival in lung brain metastasis patients will likely improve.
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Affiliation(s)
- Sneha Sai Mannam
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - David P. Bray
- Department of Neurosurgery, Jefferson University Hospital, Philadelphia, PA 19107, USA
| | - Chibueze D. Nwagwu
- Department of Neurosurgery, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Jim Zhong
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA (H.-K.S.)
| | - Hui-Kuo Shu
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA (H.-K.S.)
| | - Bree Eaton
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA (H.-K.S.)
| | - Lisa Sudmeier
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA (H.-K.S.)
| | - Subir Goyal
- Biostatistics Shared Resource, Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Christopher Deibert
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Edjah K. Nduom
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jeffrey Olson
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Kimberly B. Hoang
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA 30322, USA
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3
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Dutta S, Ganguly A, Chatterjee K, Spada S, Mukherjee S. Targets of Immune Escape Mechanisms in Cancer: Basis for Development and Evolution of Cancer Immune Checkpoint Inhibitors. BIOLOGY 2023; 12:biology12020218. [PMID: 36829496 PMCID: PMC9952779 DOI: 10.3390/biology12020218] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/22/2023] [Accepted: 01/27/2023] [Indexed: 02/03/2023]
Abstract
Immune checkpoint blockade (ICB) has emerged as a novel therapeutic tool for cancer therapy in the last decade. Unfortunately, a small number of patients benefit from approved immune checkpoint inhibitors (ICIs). Therefore, multiple studies are being conducted to find new ICIs and combination strategies to improve the current ICIs. In this review, we discuss some approved immune checkpoints, such as PD-L1, PD-1, and CTLA-4, and also highlight newer emerging ICIs. For instance, HLA-E, overexpressed by tumor cells, represents an immune-suppressive feature by binding CD94/NKG2A, on NK and T cells. NKG2A blockade recruits CD8+ T cells and activates NK cells to decrease the tumor burden. NKG2D acts as an NK cell activating receptor that can also be a potential ICI. The adenosine A2A and A2B receptors, CD47-SIRPα, TIM-3, LAG-3, TIGIT, and VISTA are targets that also contribute to cancer immunoresistance and have been considered for clinical trials. Their antitumor immunosuppressive functions can be used to develop blocking antibodies. PARPs, mARTs, and B7-H3 are also other potential targets for immunosuppression. Additionally, miRNA, mRNA, and CRISPR-Cas9-mediated immunotherapeutic approaches are being investigated with great interest. Pre-clinical and clinical studies project these targets as potential immunotherapeutic candidates in different cancer types for their robust antitumor modulation.
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Affiliation(s)
- Shovan Dutta
- The Center for Immunotherapy & Precision Immuno-Oncology (CITI), Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Anirban Ganguly
- Department of Biochemistry, All India Institute of Medical Sciences, Deoghar 814152, India
| | | | - Sheila Spada
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY 10065, USA
- Correspondence: (S.S.); (S.M.)
| | - Sumit Mukherjee
- Department of Cardiothoracic and Vascular Surgery, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Correspondence: (S.S.); (S.M.)
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4
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Wang A. Noncoding RNAs endogenously rule the cancerous regulatory realm while proteins govern the normal. Comput Struct Biotechnol J 2022; 20:1935-1945. [PMID: 35521545 PMCID: PMC9062140 DOI: 10.1016/j.csbj.2022.04.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/07/2022] [Accepted: 04/11/2022] [Indexed: 01/21/2023] Open
Abstract
Cancers evolve from normal tissues and share an endogenous regulatory realm distinctive from that of normal human tissues. Unearthing such an endogenous realm faces challenges due to heterogeneous biology data. This study computes petabyte level data and reveals the endogenous regulatory networks of normal and cancers and then unearths the most important endogenous regulators for normal and cancerous realm. In normal, proteins dominate the entire realm and trans-regulate their targets across chromosomes and ribosomal proteins serve as the most important drivers. However, in cancerous realm, noncoding RNAs dominate the whole realm and pseudogenes work as the most important regulators that cis-regulate their neighbors, in which they primarily regulate their targets within 1 million base pairs but they rarely regulate their cognates with complementary sequences as thought. Therefore, two distinctive mechanisms rule the normal and cancerous realm separately, in which noncoding RNAs endogenously regulate cancers, instead of proteins as currently conceptualized. This establishes a fundamental avenue to understand the basis of cancerous and normal physiology.
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5
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Wang A, Hai R, Rider PJ, He Q. Noncoding RNAs and Deep Learning Neural Network Discriminate Multi-Cancer Types. Cancers (Basel) 2022; 14:352. [PMID: 35053515 PMCID: PMC8774129 DOI: 10.3390/cancers14020352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/31/2021] [Accepted: 01/07/2022] [Indexed: 12/20/2022] Open
Abstract
Detecting cancers at early stages can dramatically reduce mortality rates. Therefore, practical cancer screening at the population level is needed. To develop a comprehensive detection system to classify multiple cancer types, we integrated an artificial intelligence deep learning neural network and noncoding RNA biomarkers selected from massive data. Our system can accurately detect cancer vs. healthy objects with 96.3% of AUC of ROC (Area Under Curve of a Receiver Operating Characteristic curve), and it surprisingly reaches 78.77% of AUC when validated by real-world raw data from a completely independent data set. Even validating with raw exosome data from blood, our system can reach 72% of AUC. Moreover, our system significantly outperforms conventional machine learning models, such as random forest. Intriguingly, with no more than six biomarkers, our approach can easily discriminate any individual cancer type vs. normal with 99% to 100% AUC. Furthermore, a comprehensive marker panel can simultaneously multi-classify common cancers with a stable 82.15% accuracy rate for heterogeneous cancerous tissues and conditions. This detection system provides a promising practical framework for automatic cancer screening at population level. Key points: (1) We developed a practical cancer screening system, which is simple, accurate, affordable, and easy to operate. (2) Our system binarily classify cancers vs. normal with >96% AUC. (3) In total, 26 individual cancer types can be easily detected by our system with 99 to 100% AUC. (4) The system can detect multiple cancer types simultaneously with >82% accuracy.
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Affiliation(s)
- Anyou Wang
- The Institute for Integrative Genome Biology, University of California at Riverside, Riverside, CA 92521, USA
| | - Rong Hai
- The Institute for Integrative Genome Biology, University of California at Riverside, Riverside, CA 92521, USA
- Department of Microbiology and Plant Pathology, University of California at Riverside, Riverside, CA 92521, USA
| | - Paul J. Rider
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Skip Bertman Drive, Baton Rouge, LA 70803, USA;
| | - Qianchuan He
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA;
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6
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Wang A, Hai R. Noncoding RNAs Serve as the Deadliest Universal Regulators of all Cancers. Cancer Genomics Proteomics 2021; 18:43-52. [PMID: 33419895 DOI: 10.21873/cgp.20240] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/08/2020] [Accepted: 10/20/2020] [Indexed: 01/10/2023] Open
Abstract
Numerous cancer drivers have been identified, but they are specific to a given cancer type and condition; universal cancer drivers and universal cancer mechanisms still remain largely unclear. Here, we identified the deadliest universal drivers for all cancers via developing algorithms to analyze massive RNAseqs and clinical data from The Cancer Genome Atlas (TCGA). In general, noncoding RNAs primarily serve as the most important inducers and suppressors for all types of cancers. In particular, pseudogenes are primary inducers, and specifically the antisense RNA RP11-335K5.2 serves as the most universal cancerous driver, independently of the cancer type and condition. Therefore, noncoding RNAs, instead of proteins as conventionally thought, primarily drive cancer, which establishes a novel field for future cancer research and therapy.
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Affiliation(s)
- Anyou Wang
- The Institute for Integrative Genome Biology, University of California at Riverside, Riverside, CA, U.S.A.;
| | - Rong Hai
- The Institute for Integrative Genome Biology, University of California at Riverside, Riverside, CA, U.S.A.,Department of Microbiology and Plant Pathology, University of California at Riverside, Riverside, CA, U.S.A
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7
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Cai H, Chew SK, Li C, Tsai MK, Andrejka L, Murray CW, Hughes NW, Shuldiner EG, Ashkin EL, Tang R, Hung KL, Chen LC, Lee SYC, Yousefi M, Lin WY, Kunder CA, Cong L, McFarland CD, Petrov DA, Swanton C, Winslow MM. A Functional Taxonomy of Tumor Suppression in Oncogenic KRAS-Driven Lung Cancer. Cancer Discov 2021; 11:1754-1773. [PMID: 33608386 PMCID: PMC8292166 DOI: 10.1158/2159-8290.cd-20-1325] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 12/25/2020] [Accepted: 02/12/2021] [Indexed: 12/13/2022]
Abstract
Cancer genotyping has identified a large number of putative tumor suppressor genes. Carcinogenesis is a multistep process, but the importance and specific roles of many of these genes during tumor initiation, growth, and progression remain unknown. Here we use a multiplexed mouse model of oncogenic KRAS-driven lung cancer to quantify the impact of 48 known and putative tumor suppressor genes on diverse aspects of carcinogenesis at an unprecedented scale and resolution. We uncover many previously understudied functional tumor suppressors that constrain cancer in vivo. Inactivation of some genes substantially increased growth, whereas the inactivation of others increases tumor initiation and/or the emergence of exceptionally large tumors. These functional in vivo analyses revealed an unexpectedly complex landscape of tumor suppression that has implications for understanding cancer evolution, interpreting clinical cancer genome sequencing data, and directing approaches to limit tumor initiation and progression. SIGNIFICANCE: Our high-throughput and high-resolution analysis of tumor suppression uncovered novel genetic determinants of oncogenic KRAS-driven lung cancer initiation, overall growth, and exceptional growth. This taxonomy is consistent with changing constraints during the life history of cancer and highlights the value of quantitative in vivo genetic analyses in autochthonous cancer models.This article is highlighted in the In This Issue feature, p. 1601.
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Affiliation(s)
- Hongchen Cai
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Su Kit Chew
- Cancer Evolution and Genome Instability Laboratory, University College London Cancer Institute, London, United Kingdom
| | - Chuan Li
- Department of Biology, Stanford University, Stanford, California
| | - Min K Tsai
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Laura Andrejka
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Christopher W Murray
- Cancer Biology Program, Stanford University School of Medicine, Stanford, California
| | - Nicholas W Hughes
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | | | - Emily L Ashkin
- Cancer Biology Program, Stanford University School of Medicine, Stanford, California
| | - Rui Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - King L Hung
- Cancer Biology Program, Stanford University School of Medicine, Stanford, California
| | - Leo C Chen
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Shi Ya C Lee
- Cancer Evolution and Genome Instability Laboratory, University College London Cancer Institute, London, United Kingdom
| | - Maryam Yousefi
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Wen-Yang Lin
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Christian A Kunder
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Le Cong
- Department of Genetics, Stanford University School of Medicine, Stanford, California
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | | | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, California.
- Cancer Biology Program, Stanford University School of Medicine, Stanford, California
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, University College London Cancer Institute, London, United Kingdom.
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Monte M Winslow
- Department of Genetics, Stanford University School of Medicine, Stanford, California.
- Cancer Biology Program, Stanford University School of Medicine, Stanford, California
- Department of Pathology, Stanford University School of Medicine, Stanford, California
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8
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Kaligotla VSA, Jasti T, Kandra P. CRISPR/Cas9 in cancer: An attempt to the present trends and future prospects. Biotechnol Appl Biochem 2021; 69:1238-1251. [PMID: 34033692 DOI: 10.1002/bab.2200] [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: 10/02/2020] [Accepted: 05/12/2021] [Indexed: 11/08/2022]
Abstract
Cancer is the second leading cause of death globally. Series of sequential, repeated genetic changes and epigenetic modifications are leading to the formation of tumors. These tumors subsequently causing the infected cells to invade and transform their surrounding cells by metastasis are some hallmarks in cancer. Although tremendous efforts have been extended for structurally characterizing the numerous genomic mutations undergoing in cancer cells, there is a lack of information regarding the functions of many mutated genes. Clustered Regularly Interspaced Short Palindromic repeats/CRISPR-associated nuclease 9 (CRISPR/Cas9) has become a robust method for building changes in genome of many organisms. Recent reports have suggested that modification of CRISPR/Cas9 can provide plot form to probe the mechanisms in tumorigenesis and in cancer therapies. This review focuses on the historical perspectives of CRISPR/Cas9. The study highlights the applications and also role in cancer cell genome editing, which is helpful to understand the dynamics. Intense research in progress on mechanism of action of CRISPR/Cas9 has been reviewed and critically discussed. Further, relevant literature on animal models focusing on various approaches has been highlighted to emphasize the therapeutics of CRISPR/Cas9 with current trends and future challenges.
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Affiliation(s)
| | - Tejaswi Jasti
- Department of Biotechnology, GITAM Institute of Technology, GITAM Deemed to be University, Visakhapatnam, Andhra Pradesh, India
| | - Prameela Kandra
- Department of Biotechnology, GITAM Institute of Technology, GITAM Deemed to be University, Visakhapatnam, Andhra Pradesh, India
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9
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Reggiani F, Sauta E, Torricelli F, Zanetti E, Tagliavini E, Santandrea G, Gobbi G, Damia G, Bellazzi R, Ambrosetti D, Ciarrocchi A, Sancisi V. An integrative functional genomics approach reveals EGLN1 as a novel therapeutic target in KRAS mutated lung adenocarcinoma. Mol Cancer 2021; 20:63. [PMID: 33823854 PMCID: PMC8022436 DOI: 10.1186/s12943-021-01357-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 03/30/2021] [Indexed: 12/18/2022] Open
Affiliation(s)
- Francesca Reggiani
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, via Risorgimento 80, 42123, Reggio Emilia, Italy
| | - Elisabetta Sauta
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, via Risorgimento 80, 42123, Reggio Emilia, Italy.,Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy
| | - Federica Torricelli
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, via Risorgimento 80, 42123, Reggio Emilia, Italy
| | - Eleonora Zanetti
- Pathology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Elena Tagliavini
- Pathology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Giacomo Santandrea
- Pathology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy.,Clinical and Experimental Medicine PhD Program, University of Modena and Reggio Emilia, Modena, Italy
| | - Giulia Gobbi
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, via Risorgimento 80, 42123, Reggio Emilia, Italy
| | - Giovanna Damia
- Laboratory of Molecular Pharmacology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Riccardo Bellazzi
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy
| | - Davide Ambrosetti
- Department of Pharmacy and Biotechnology (FaBit), University of Bologna, Bologna, Italy
| | - Alessia Ciarrocchi
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, via Risorgimento 80, 42123, Reggio Emilia, Italy
| | - Valentina Sancisi
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, via Risorgimento 80, 42123, Reggio Emilia, Italy.
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10
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Proteomic Advances in Glial Tumors through Mass Spectrometry Approaches. ACTA ACUST UNITED AC 2019; 55:medicina55080412. [PMID: 31357616 PMCID: PMC6722920 DOI: 10.3390/medicina55080412] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 01/25/2023]
Abstract
Being the fourth leading cause of cancer-related death, glial tumors are highly diverse tumor entities characterized by important heterogeneity regarding tumor malignancy and prognosis. However, despite the identification of important alterations in the genome of the glial tumors, there remains a gap in understanding the mechanisms involved in glioma malignancy. Previous research focused on decoding the genomic alterations in these tumors, but due to intricate cellular mechanisms, the genomic findings do not correlate with the functional proteins expressed at the cellular level. The development of mass spectrometry (MS) based proteomics allowed researchers to study proteins expressed at the cellular level or in serum that may provide new insights on the proteins involved in the proliferation, invasiveness, metastasis and resistance to therapy in glial tumors. The integration of data provided by genomic and proteomic approaches into clinical practice could allow for the identification of new predictive, diagnostic and prognostic biomarkers that will improve the clinical management of patients with glial tumors. This paper aims to provide an updated review of the recent proteomic findings, possible clinical applications, and future research perspectives in diffuse astrocytic and oligodendroglial tumors, pilocytic astrocytomas, and ependymomas.
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11
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Price C, Gill S, Ho ZV, Davidson SM, Merkel E, McFarland JM, Leung L, Tang A, Kost-Alimova M, Tsherniak A, Jonas O, Vazquez F, Hahn WC. Genome-Wide Interrogation of Human Cancers Identifies EGLN1 Dependency in Clear Cell Ovarian Cancers. Cancer Res 2019; 79:2564-2579. [PMID: 30898838 DOI: 10.1158/0008-5472.can-18-2674] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 01/18/2019] [Accepted: 03/14/2019] [Indexed: 12/17/2022]
Abstract
We hypothesized that candidate dependencies for which there are small molecules that are either approved or in advanced development for a nononcology indication may represent potential therapeutic targets. To test this hypothesis, we performed genome-scale loss-of-function screens in hundreds of cancer cell lines. We found that knockout of EGLN1, which encodes prolyl hydroxylase domain-containing protein 2 (PHD2), reduced the proliferation of a subset of clear cell ovarian cancer cell lines in vitro. EGLN1-dependent cells exhibited sensitivity to the pan-EGLN inhibitor FG-4592. The response to FG-4592 was reversed by deletion of HIF1A, demonstrating that EGLN1 dependency was related to negative regulation of HIF1A. We also found that ovarian clear cell tumors susceptible to both genetic and pharmacologic inhibition of EGLN1 required intact HIF1A. Collectively, these observations identify EGLN1 as a cancer target with therapeutic potential. SIGNIFICANCE: These findings reveal a differential dependency of clear cell ovarian cancers on EGLN1, thus identifying EGLN1 as a potential therapeutic target in clear cell ovarian cancer patients.
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Affiliation(s)
- Colles Price
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Stanley Gill
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Zandra V Ho
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Shawn M Davidson
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Erin Merkel
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | | | - Lisa Leung
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Andrew Tang
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | | | - Aviad Tsherniak
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Oliver Jonas
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Francisca Vazquez
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - William C Hahn
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts. .,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
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12
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Sharifnia T, Hong AL, Painter CA, Boehm JS. Emerging Opportunities for Target Discovery in Rare Cancers. Cell Chem Biol 2017; 24:1075-1091. [PMID: 28938087 PMCID: PMC5857178 DOI: 10.1016/j.chembiol.2017.08.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 07/26/2017] [Accepted: 08/01/2017] [Indexed: 12/18/2022]
Abstract
Rare cancers pose unique challenges to research due to their low incidence. Barriers include a scarcity of tissue and experimental models to enable basic research and insufficient patient accrual for clinical studies. Consequently, an understanding of the genetic and cellular features of many rare cancer types and their associated vulnerabilities has been lacking. However, new opportunities are emerging to facilitate discovery of therapeutic targets in rare cancers. Online platforms are allowing patients with rare cancers to organize on an unprecedented scale, tumor genome sequencing is now routinely performed in research and clinical settings, and the efficiency of patient-derived model generation has improved. New CRISPR/Cas9 and small-molecule libraries permit cancer dependency discovery in a rapid and systematic fashion. In parallel, large-scale studies of common cancers now provide reference datasets to help interpret rare cancer profiling data. Together, these advances motivate consideration of new research frameworks to accelerate rare cancer target discovery.
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Affiliation(s)
- Tanaz Sharifnia
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Andrew L Hong
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | - Jesse S Boehm
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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13
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Manguso RT, Pope HW, Zimmer MD, Brown FD, Yates KB, Miller BC, Collins NB, Bi K, LaFleur MW, Juneja VR, Weiss SA, Lo J, Fisher DE, Miao D, Van Allen E, Root DE, Sharpe AH, Doench JG, Haining WN. In vivo CRISPR screening identifies Ptpn2 as a cancer immunotherapy target. Nature 2017; 547:413-418. [PMID: 28723893 PMCID: PMC5924693 DOI: 10.1038/nature23270] [Citation(s) in RCA: 713] [Impact Index Per Article: 101.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 06/06/2017] [Indexed: 12/27/2022]
Abstract
Immunotherapy with PD-1 checkpoint blockade is effective in only a minority of patients with cancer, suggesting that additional treatment strategies are needed. Here we use a pooled in vivo genetic screening approach using CRISPR-Cas9 genome editing in transplantable tumours in mice treated with immunotherapy to discover previously undescribed immunotherapy targets. We tested 2,368 genes expressed by melanoma cells to identify those that synergize with or cause resistance to checkpoint blockade. We recovered the known immune evasion molecules PD-L1 and CD47, and confirmed that defects in interferon-γ signalling caused resistance to immunotherapy. Tumours were sensitized to immunotherapy by deletion of genes involved in several diverse pathways, including NF-κB signalling, antigen presentation and the unfolded protein response. In addition, deletion of the protein tyrosine phosphatase PTPN2 in tumour cells increased the efficacy of immunotherapy by enhancing interferon-γ-mediated effects on antigen presentation and growth suppression. In vivo genetic screens in tumour models can identify new immunotherapy targets in unanticipated pathways.
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Affiliation(s)
- Robert T Manguso
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
- Division of Medical Sciences, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Hans W Pope
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Margaret D Zimmer
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Flavian D Brown
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
- Division of Medical Sciences, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Kathleen B Yates
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Brian C Miller
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Natalie B Collins
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
- Division of Pediatric Hematology and Oncology, Children's Hospital, Boston, Massachusetts 02115, USA
| | - Kevin Bi
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Martin W LaFleur
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
- Division of Medical Sciences, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Vikram R Juneja
- Department of Microbiology and Immunology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Sarah A Weiss
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Jennifer Lo
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Building 149, 13th Street, Charlestown, Massachusetts 02129, USA
| | - David E Fisher
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Building 149, 13th Street, Charlestown, Massachusetts 02129, USA
| | - Diana Miao
- Division of Medical Sciences, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Eliezer Van Allen
- Division of Medical Sciences, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - David E Root
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Arlene H Sharpe
- Division of Pediatric Hematology and Oncology, Children's Hospital, Boston, Massachusetts 02115, USA
- Evergrande Center for Immunologic Diseases, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - John G Doench
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - W Nicholas Haining
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
- Division of Pediatric Hematology and Oncology, Children's Hospital, Boston, Massachusetts 02115, USA
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14
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Simanshu DK, Nissley DV, McCormick F. RAS Proteins and Their Regulators in Human Disease. Cell 2017; 170:17-33. [PMID: 28666118 PMCID: PMC5555610 DOI: 10.1016/j.cell.2017.06.009] [Citation(s) in RCA: 1118] [Impact Index Per Article: 159.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 05/22/2017] [Accepted: 06/07/2017] [Indexed: 02/07/2023]
Abstract
RAS proteins are binary switches, cycling between ON and OFF states during signal transduction. These switches are normally tightly controlled, but in RAS-related diseases, such as cancer, RASopathies, and many psychiatric disorders, mutations in the RAS genes or their regulators render RAS proteins persistently active. The structural basis of the switch and many of the pathways that RAS controls are well known, but the precise mechanisms by which RAS proteins function are less clear. All RAS biology occurs in membranes: a precise understanding of RAS' interaction with membranes is essential to understand RAS action and to intervene in RAS-driven diseases.
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Affiliation(s)
- Dhirendra K Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD 21701, USA
| | - Dwight V Nissley
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD 21701, USA
| | - Frank McCormick
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD 21701, USA; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, 1450 3(rd) Street, San Francisco, CA 94158, USA.
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