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Turgambayeva A, Duisekova S, Tashenova G, Tulebayeva A, Kapanova G, Akhenbekova A, Farooqi AA. Role of TRP channels in carcinogenesis and metastasis: Pathophysiology and regulation by non-coding RNAs. Noncoding RNA Res 2024; 9:359-366. [PMID: 38511066 PMCID: PMC10950581 DOI: 10.1016/j.ncrna.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 03/22/2024] Open
Abstract
In 2021, David Julius and Ardem Patapoutian received Nobel Prize in Physiology or Medicine for their ground-breaking discoveries in the functional characterization of receptors for temperature and touch. Transient receptor potential (TRP) channels have captivated tremendous appreciation as promising drug targets over the past few years because of central involvement in different cancers. Based on the insights gleaned from decades of high-quality research, basic and clinical scientists have unveiled how Transient receptor potential channels regulated cancer onset and progression. Pioneering studies have sparked renewed interest and researchers have started to scratch the surface of mechanistic role of these channels in wide variety of cancers. In this review we have attempted to provide a summary of most recent updates and advancements made in the biology of these channels in context of cancers. We have partitioned this review into different subsections on the basis of emerging evidence about characteristically distinct role of TRPV (TRPV1, TRPV5), TRPM (TRPM3, TRPM7) and TRPC in cancers. Regulation of TRP channels by non-coding RNAs is also a very exciting area of research which will be helpful in developing a sharper understanding of the multi-step aspects of cancers.
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Affiliation(s)
- Assiya Turgambayeva
- Department Public Health and Management, NJSC, Astana Medical University, Astana, Kazakhstan
| | - Samal Duisekova
- Department Public Health and Management, NJSC, Astana Medical University, Astana, Kazakhstan
| | - Gulnara Tashenova
- Asfendiyarov Kazakh National Medical University, Almaty 050000, Kazakhstan
| | - Aigul Tulebayeva
- Asfendiyarov Kazakh National Medical University, Almaty 050000, Kazakhstan
| | - Gulnara Kapanova
- Al-Farabi Kazakh National University, 71 Al-Farabi Ave, Almaty 050040, Kazakhstan
- Scientific Center of Anti-Infectious Drugs, 75 Al-Farabi Ave, Almaty 050040, Kazakhstan
| | - Aida Akhenbekova
- Asfendiyarov Kazakh National Medical University, Almaty 050000, Kazakhstan
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Murciano-Goroff YR, Uppal M, Chen M, Harada G, Schram AM. Basket Trials: Past, Present, and Future. ANNUAL REVIEW OF CANCER BIOLOGY 2024; 8:59-80. [PMID: 38938274 PMCID: PMC11210107 DOI: 10.1146/annurev-cancerbio-061421-012927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Abstract
Large-scale tumor molecular profiling has revealed that diverse cancer histologies are driven by common pathways with unifying biomarkers that can be exploited therapeutically. Disease-agnostic basket trials have been increasingly utilized to test biomarker-driven therapies across cancer types. These trials have led to drug approvals and improved the lives of patients while simultaneously advancing our understanding of cancer biology. This review focuses on the practicalities of implementing basket trials, with an emphasis on molecularly targeted trials. We examine the biologic subtleties of genomic biomarker and patient selection, discuss previous successes in drug development facilitated by basket trials, describe certain novel targets and drugs, and emphasize practical considerations for participant recruitment and study design. This review also highlights strategies for aiding patient access to basket trials. As basket trials become more common, steps to ensure equitable implementation of these studies will be critical for molecularly targeted drug development.
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Affiliation(s)
| | - Manik Uppal
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Monica Chen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Guilherme Harada
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alison M Schram
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
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Wei L, Deng C, Zhang B, Wang G, Meng Y, Qin H. SP4 Facilitates Esophageal Squamous Cell Carcinoma Progression by Activating PHF14 Transcription and Wnt/Β-Catenin Signaling. Mol Cancer Res 2024; 22:55-69. [PMID: 37768180 PMCID: PMC10758695 DOI: 10.1158/1541-7786.mcr-22-0835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 06/13/2023] [Accepted: 09/25/2023] [Indexed: 09/29/2023]
Abstract
Specificity protein 4 transcription factor (SP4), a member of the Sp/Krüppel-like family (KLF), could bind to GT and GC box promoters, and plays an essential role in transcriptional activating. Despite SP4 having been detected to be highly expressed in a variety of human tumors, its biological effect and underlying molecular mechanism in esophageal squamous cell carcinoma (ESCC) remains unclear. Our research discovered that high SP4 expression is detected in primary ESCC specimens and cell lines and is strongly associated with the ESCC tumor grade and poor prognosis. In vitro, knockdown of SP4 suppressed cell proliferation and cell-cycle progression and promoted apoptosis, whereas overexpression of SP4 did the opposite. In vivo, inhibiting SP4 expression in ESCC cells suppresses tumor growth. Subsequently, we demonstrated that SP4 acts as the transcriptional upstream of PHF14, which binds to PHF14 promoter region, thus promoting PHF14 transcription. PHF14 was also significantly expressed in patient tissues and various ESCC cell lines and its expression promoted cell proliferation and inhibited apoptosis. Moreover, knockdown of SP4 inhibited the Wnt/β-catenin signaling pathway, whereas overexpression of PHF14 eliminated the effects of SP4 knockdown in ESCC cells. These results demonstrate that SP4 activates the Wnt/β-catenin signaling pathway by driving PHF14 transcription, thereby promoting ESCC progression, which indicates that SP4 might act as a prospective prognostic indicator or therapeutic target for patients with ESCC. IMPLICATIONS This study identified SP4/PH14 axis as a new mechanism to promote the progression of ESCC, which may serve as a novel therapeutic target for patients with ESCC.
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Affiliation(s)
- Li Wei
- Department of Surgery and Anesthesia, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Chaowei Deng
- Department of Cell Biology and Genetics/Institute of Genetics and Developmental Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Bo Zhang
- Department of Peripheral Vascular Disease, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Guanghui Wang
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Yan Meng
- Department of Peripheral Vascular Disease, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Hao Qin
- Department of Peripheral Vascular Disease, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
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Olivera-Salguero R, Seguí E, Cejalvo JM, Oliveira M, Tolosa P, Vidal M, Malumbres M, Gavilá J, Saura C, Pernas S, López R, Margelí M, Balmaña J, Muñoz M, Blancas I, Boni V, Ciruelos E, Galve E, Perelló A, Sánchez-Bayona R, de la Cruz S, de la Hoya M, Galván P, Sanfeliu E, Gonzalez-Farre B, Sirenko V, Blanch-Torras A, Canes J, Masanas H, Olmos R, Forns M, Prat A, Casas A, Pascual T. HOPE (SOLTI-1903) breast cancer study: real-world, patient-centric, clinical practice study to assess the impact of genomic data on next treatment decision-choice in patients with locally advanced or metastatic breast cancer. Front Oncol 2023; 13:1151496. [PMID: 37188177 PMCID: PMC10175800 DOI: 10.3389/fonc.2023.1151496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/18/2023] [Indexed: 05/17/2023] Open
Abstract
Background Metastatic breast cancer (mBC) causes nearly all BC-related deaths. Next-generation sequencing (NGS) technologies allow for the application of personalized medicine using targeted therapies that could improve patients' outcomes. However, NGS is not routinely used in the clinical practice and its cost induces access-inequity among patients. We hypothesized that promoting active patient participation in the management of their disease offering access to NGS testing and to the subsequent medical interpretation and recommendations provided by a multidisciplinary molecular advisory board (MAB) could contribute to progressively overcome this challenge. We designed HOPE (SOLTI-1903) breast cancer trial, a study where patients voluntarily lead their inclusion through a digital tool (DT). The main objectives of HOPE study are to empower mBC patients, gather real-world data on the use of molecular information in the management of mBC and to generate evidence to assess the clinical utility for healthcare systems. Trial design After self-registration through the DT, the study team validates eligibility criteria and assists patients with mBC in the subsequent steps. Patients get access to the information sheet and sign the informed consent form through an advanced digital signature. Afterwards, they provide the most recent (preferably) metastatic archival tumor sample for DNA-sequencing and a blood sample obtained at the time of disease progression for ctDNA analysis. Paired results are reviewed by the MAB, considering patient's medical history. The MAB provides a further interpretation of molecular results and potential treatment recommendations, including ongoing clinical trials and further (germline) genetic testing. Participants self-document their treatment and disease evolution for the next 2 years. Patients are encouraged to involve their physicians in the study. HOPE also includes a patient empowerment program with educational workshops and videos about mBC and precision medicine in oncology. The primary endpoint of the study was to describe the feasibility of a patient-centric precision oncology program in mBC patients when a comprehensive genomic profile is available to decide on a subsequent line of treatment. Clinical trial registration www.soltihope.com, identifier NCT04497285.
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Affiliation(s)
| | - Elia Seguí
- SOLTI Cancer Research Group, Barcelona, Spain
- Medical Oncology Department, Hospital Clinic of Barcelona, Barcelona, Spain
- Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Juan Miguel Cejalvo
- SOLTI Cancer Research Group, Barcelona, Spain
- Hospital Clínico Universitario de Valencia, INCLIVA (Instituto de Investigación Sanitaria), Universidad Valencia, Valencia, Spain
| | - Mafalda Oliveira
- SOLTI Cancer Research Group, Barcelona, Spain
- Medical Oncology Department, Vall d’Hebron University Hospital, Barcelona, Spain
- Breast Cancer Group, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Pablo Tolosa
- SOLTI Cancer Research Group, Barcelona, Spain
- Medical Oncology Department, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Maria Vidal
- SOLTI Cancer Research Group, Barcelona, Spain
- Medical Oncology Department, Hospital Clinic of Barcelona, Barcelona, Spain
- Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
- Breast Cancer Unit, Institute of Oncology Barcelona (IOB) – Quirónsalud, Barcelona, Spain
| | - Marcos Malumbres
- Cancer Cell Cycle Group, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Cell Division and Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Joaquín Gavilá
- SOLTI Cancer Research Group, Barcelona, Spain
- Instituto Valenciano de Oncología (IVO), Valencia, Spain
| | - Cristina Saura
- SOLTI Cancer Research Group, Barcelona, Spain
- Medical Oncology Department, Vall d’Hebron University Hospital, Barcelona, Spain
| | - Sonia Pernas
- SOLTI Cancer Research Group, Barcelona, Spain
- Medical Oncology Department, Catalan Institute of Oncology (ICO)/Institut d’Investigació Biomédica de Bellvitge (IDIBELL), L’Hospitalet de Llobregat, Barcelona, Spain
| | - Rafael López
- SOLTI Cancer Research Group, Barcelona, Spain
- Medical Oncology Department and Translational Medical Oncology Group, Clinical University Hospital and Health Research Institute of Santiago de Compostela (IDIS)-CIBERONC, Santiago de Compostela, Spain
| | - Mireia Margelí
- SOLTI Cancer Research Group, Barcelona, Spain
- Catalan Institute of Oncology (ICO), Hospital Germans Trias i Pujol/Badalona Applied Research Group in Oncology (B-ARGO Group), Oncology Department, Badalona, Spain
| | - Judith Balmaña
- SOLTI Cancer Research Group, Barcelona, Spain
- Medical Oncology Department, Vall d’Hebron University Hospital, Barcelona, Spain
| | - Montserrat Muñoz
- SOLTI Cancer Research Group, Barcelona, Spain
- Medical Oncology Department, Hospital Clinic of Barcelona, Barcelona, Spain
- Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Isabel Blancas
- SOLTI Cancer Research Group, Barcelona, Spain
- Hospital Universitario San Cecilio, Instituto de Investigación Biosanitaria de Granada (ibs. Granada) and Medicine Department, Granada University, Granada, Spain
| | - Valentina Boni
- SOLTI Cancer Research Group, Barcelona, Spain
- Next Madrid, Universitary Hospital Quiron Salud Madrid, Madrid, Spain
| | - Eva Ciruelos
- SOLTI Cancer Research Group, Barcelona, Spain
- Medical Oncology Department, Hospital Universitario 12 de Octubre, Madrid, Spain
- Centro Integral Oncológico Clara Campal HM (CIOCC), Madrid, Spain
| | - Elena Galve
- SOLTI Cancer Research Group, Barcelona, Spain
- Hospital Universitario Basurto (OSI Bilbao-Basurto), Bilbao, Spain
| | - Antonia Perelló
- SOLTI Cancer Research Group, Barcelona, Spain
- Hospital Universitari Son Espases, Palma de Mallorca, Spain
| | - Rodrigo Sánchez-Bayona
- SOLTI Cancer Research Group, Barcelona, Spain
- Medical Oncology Department, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Susana de la Cruz
- SOLTI Cancer Research Group, Barcelona, Spain
- Medical Oncology Department, Complejo Hospitalario de Navarra, Pamplona, Spain
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, CIBERONC, Hospital Clinico San Carlos, Instituto de Investigación Sanitaria San Carlos, Madrid, Spain
| | - Patricia Galván
- Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Esther Sanfeliu
- SOLTI Cancer Research Group, Barcelona, Spain
- Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
- Pathology Department, Hospital Clinic of Barcelona, Barcelona, Spain
| | - Blanca Gonzalez-Farre
- SOLTI Cancer Research Group, Barcelona, Spain
- Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
- Pathology Department, Hospital Clinic of Barcelona, Barcelona, Spain
| | - Valeria Sirenko
- Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | | | - Jordi Canes
- SOLTI Cancer Research Group, Barcelona, Spain
| | | | - Rosa Olmos
- Asociación Española de Cáncer de Mama Metastásico, Oviedo, Spain
| | - Margarita Forns
- Asociación Española de Cáncer de Mama Metastásico, Oviedo, Spain
| | - Aleix Prat
- SOLTI Cancer Research Group, Barcelona, Spain
- Medical Oncology Department, Hospital Clinic of Barcelona, Barcelona, Spain
- Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
- Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
| | - Ana Casas
- SOLTI Cancer Research Group, Barcelona, Spain
- Fundación Actitud Frente al Cáncer, Sevilla, Spain
- *Correspondence: Tomás Pascual, ; Ana Casas,
| | - Tomás Pascual
- SOLTI Cancer Research Group, Barcelona, Spain
- Medical Oncology Department, Hospital Clinic of Barcelona, Barcelona, Spain
- *Correspondence: Tomás Pascual, ; Ana Casas,
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Targeting oncogene and non-oncogene addiction to inflame the tumour microenvironment. Nat Rev Drug Discov 2022; 21:440-462. [PMID: 35292771 DOI: 10.1038/s41573-022-00415-5] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2022] [Indexed: 12/12/2022]
Abstract
Immune checkpoint inhibitors (ICIs) have revolutionized the clinical management of multiple tumours. However, only a few patients respond to ICIs, which has generated considerable interest in the identification of resistance mechanisms. One such mechanism reflects the ability of various oncogenic pathways, as well as stress response pathways required for the survival of transformed cells (a situation commonly referred to as 'non-oncogene addiction'), to support tumour progression not only by providing malignant cells with survival and/or proliferation advantages, but also by establishing immunologically 'cold' tumour microenvironments (TMEs). Thus, both oncogene and non-oncogene addiction stand out as promising targets to robustly inflame the TME and potentially enable superior responses to ICIs.
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Qi L, Lindsay H, Kogiso M, Du Y, Braun FK, Zhang H, Guo L, Zhao S, Injac SG, Baxter PA, Su JM, Xiao S, Erickson SW, Earley EJ, Teicher B, Smith MA, Li XN. Evaluation of an EZH2 inhibitor in patient-derived orthotopic xenograft models of pediatric brain tumors alone and in combination with chemo- and radiation therapies. J Transl Med 2022; 102:185-193. [PMID: 34802040 PMCID: PMC10228180 DOI: 10.1038/s41374-021-00700-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/27/2021] [Accepted: 10/29/2021] [Indexed: 11/09/2022] Open
Abstract
Brain tumors are the leading cause of cancer-related death in children. Tazemetostat is an FDA-approved enhancer of zeste homolog (EZH2) inhibitor. To determine its role in difficult-to-treat pediatric brain tumors, we examined EZH2 levels in a panel of 22 PDOX models and confirmed EZH2 mRNA over-expression in 9 GBM (34.6 ± 12.7-fold) and 11 medulloblastoma models (6.2 ± 1.7 in group 3, 6.0 ± 2.4 in group 4) accompanied by elevated H3K27me3 expression. Therapeutic efficacy was evaluated in 4 models (1 GBM, 2 medulloblastomas and 1 ATRT) via systematically administered tazemetostat (250 and 400 mg/kg, gavaged, twice daily) alone and in combination with cisplatin (5 mg/kg, i.p., twice) and/or radiation (2 Gy/day × 5 days). Compared with the untreated controls, tazemetostat significantly (Pcorrected < 0.05) prolonged survival times in IC-L1115ATRT (101% at 400 mg/kg) and IC-2305GBM (32% at 250 mg/kg, 45% at 400 mg/kg) in a dose-dependent manner. The addition of tazemetostat with radiation was evaluated in 3 models, with only one [IC-1078MB (group 4)] showing a substantial, though not statistically significant, prolongation in survival compared to radiation treatment alone. Combining tazemetostat (250 mg/kg) with cisplatin was not superior to cisplatin alone in any model. Analysis of in vivo drug resistance detected predominance of EZH2-negative cells in the remnant PDOX tumors accompanied by decreased H3K27me2 and H3K27me3 expressions. These data supported the use of tazemetostat in a subset of pediatric brain tumors and suggests that EZH2-negative tumor cells may have caused therapy resistance and should be prioritized for the search of new therapeutic targets.
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Affiliation(s)
- Lin Qi
- Texas Children's Cancer Center, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
- Ann & Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Pharmacology, School of Medicine, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Holly Lindsay
- Texas Children's Cancer Center, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
| | - Mari Kogiso
- Texas Children's Cancer Center, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
| | - Yuchen Du
- Texas Children's Cancer Center, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
- Ann & Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Frank K Braun
- Texas Children's Cancer Center, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
| | - Huiyuan Zhang
- Texas Children's Cancer Center, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
| | - Lei Guo
- Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, USA
| | - Sibo Zhao
- Texas Children's Cancer Center, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
| | - Sarah G Injac
- Texas Children's Cancer Center, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
| | - Patricia A Baxter
- Texas Children's Cancer Center, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
| | - Jack Mf Su
- Texas Children's Cancer Center, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
| | - Sophie Xiao
- Ann & Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | | | | | | | | | - Xiao-Nan Li
- Texas Children's Cancer Center, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA.
- Ann & Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
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Park TY, Leiserson MD, Klau GW, Raphael BJ. SuperDendrix algorithm integrates genetic dependencies and genomic alterations across pathways and cancer types. CELL GENOMICS 2022; 2. [PMID: 35382456 PMCID: PMC8979493 DOI: 10.1016/j.xgen.2022.100099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Recent genome-wide CRISPR-Cas9 loss-of-function screens have identified genetic dependencies across many cancer cell lines. Associations between these dependencies and genomic alterations in the same cell lines reveal phenomena such as oncogene addiction and synthetic lethality. However, comprehensive identification of such associations is complicated by complex interactions between genes across genetically heterogeneous cancer types. We introduce and apply the algorithm SuperDendrix to CRISPR-Cas9 loss-of-function screens from 769 cancer cell lines, to identify differential dependencies across cell lines and to find associations between differential dependencies and combinations of genomic alterations and cell-type-specific markers. These associations respect the position and type of interactions within pathways: for example, we observe increased dependencies on downstream activators of pathways, such as NFE2L2, and decreased dependencies on upstream activators of pathways, such as CDK6. SuperDendrix also reveals dozens of dependencies on lineage-specific transcription factors, identifies cancer-type-specific correlations between dependencies, and enables annotation of individual mutated residues. Using SuperDendrix, Park et al. examine associations between genetic dependencies in 769 cancer cell lines. They report 127 genetic dependencies explained by combinations of mutually exclusive somatic mutations congregating into a few oncogenic pathways across cancer subtypes. These present a small number of prominent and highly specific genetic vulnerabilities in cancer. Graphical abstract
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Murphy P, Glynn D, Dias S, Hodgson R, Claxton L, Beresford L, Cooper K, Tappenden P, Ennis K, Grosso A, Wright K, Cantrell A, Stevenson M, Palmer S. Modelling approaches for histology-independent cancer drugs to inform NICE appraisals: a systematic review and decision-framework. Health Technol Assess 2022; 25:1-228. [PMID: 34990339 DOI: 10.3310/hta25760] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The first histology-independent marketing authorisation in Europe was granted in 2019. This was the first time that a cancer treatment was approved based on a common biomarker rather than the location in the body at which the tumour originated. This research aims to explore the implications for National Institute for Health and Care Excellence appraisals. METHODS Targeted reviews were undertaken to determine the type of evidence that is likely to be available at the point of marketing authorisation and the analyses required to support National Institute for Health and Care Excellence appraisals. Several challenges were identified concerning the design and conduct of trials for histology-independent products, the greater levels of heterogeneity within the licensed population and the use of surrogate end points. We identified approaches to address these challenges by reviewing key statistical literature that focuses on the design and analysis of histology-independent trials and by undertaking a systematic review to evaluate the use of response end points as surrogate outcomes for survival end points. We developed a decision framework to help to inform approval and research policies for histology-independent products. The framework explored the uncertainties and risks associated with different approval policies, including the role of further data collection, pricing schemes and stratified decision-making. RESULTS We found that the potential for heterogeneity in treatment effects, across tumour types or other characteristics, is likely to be a central issue for National Institute for Health and Care Excellence appraisals. Bayesian hierarchical methods may serve as a useful vehicle to assess the level of heterogeneity across tumours and to estimate the pooled treatment effects for each tumour, which can inform whether or not the assumption of homogeneity is reasonable. Our review suggests that response end points may not be reliable surrogates for survival end points. However, a surrogate-based modelling approach, which captures all relevant uncertainty, may be preferable to the use of immature survival data. Several additional sources of heterogeneity were identified as presenting potential challenges to National Institute for Health and Care Excellence appraisal, including the cost of testing, baseline risk, quality of life and routine management costs. We concluded that a range of alternative approaches will be required to address different sources of heterogeneity to support National Institute for Health and Care Excellence appraisals. An exemplar case study was developed to illustrate the nature of the assessments that may be required. CONCLUSIONS Adequately designed and analysed basket studies that assess the homogeneity of outcomes and allow borrowing of information across baskets, where appropriate, are recommended. Where there is evidence of heterogeneity in treatment effects and estimates of cost-effectiveness, consideration should be given to optimised recommendations. Routine presentation of the scale of the consequences of heterogeneity and decision uncertainty may provide an important additional approach to the assessments specified in the current National Institute for Health and Care Excellence methods guide. FURTHER RESEARCH Further exploration of Bayesian hierarchical methods could help to inform decision-makers on whether or not there is sufficient evidence of homogeneity to support pooled analyses. Further research is also required to determine the appropriate basis for apportioning genomic testing costs where there are multiple targets and to address the challenges of uncontrolled Phase II studies, including the role and use of surrogate end points. FUNDING This project was funded by the National Institute for Health Research (NIHR) Evidence Synthesis programme and will be published in full in Health Technology Assessment; Vol. 25, No. 76. See the NIHR Journals Library website for further project information.
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Affiliation(s)
- Peter Murphy
- Centre for Reviews and Dissemination, University of York, York, UK
| | - David Glynn
- Centre for Health Economics, University of York, York, UK
| | - Sofia Dias
- Centre for Reviews and Dissemination, University of York, York, UK
| | - Robert Hodgson
- Centre for Reviews and Dissemination, University of York, York, UK
| | - Lindsay Claxton
- Centre for Reviews and Dissemination, University of York, York, UK
| | - Lucy Beresford
- Centre for Reviews and Dissemination, University of York, York, UK
| | - Katy Cooper
- School of Health and Related Research (ScHARR) Technology Assessment Group, University of Sheffield, Sheffield, UK
| | - Paul Tappenden
- School of Health and Related Research (ScHARR) Technology Assessment Group, University of Sheffield, Sheffield, UK
| | - Kate Ennis
- School of Health and Related Research (ScHARR) Technology Assessment Group, University of Sheffield, Sheffield, UK
| | | | - Kath Wright
- Centre for Reviews and Dissemination, University of York, York, UK
| | - Anna Cantrell
- School of Health and Related Research (ScHARR) Technology Assessment Group, University of Sheffield, Sheffield, UK
| | - Matt Stevenson
- School of Health and Related Research (ScHARR) Technology Assessment Group, University of Sheffield, Sheffield, UK
| | - Stephen Palmer
- Centre for Health Economics, University of York, York, UK
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Zhang T, Zhang SW, Li Y. Identifying Driver Genes for Individual Patients through Inductive Matrix Completion. Bioinformatics 2021; 37:4477-4484. [PMID: 34175939 DOI: 10.1093/bioinformatics/btab477] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 04/30/2021] [Accepted: 06/25/2021] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION The driver genes play a key role in the evolutionary process of cancer. Effectively identifying these driver genes is crucial to cancer diagnosis and treatment. However, due to the high heterogeneity of cancers, it remains challenging to identify the driver genes for individual patients. Although some computational methods have been proposed to tackle this problem, they seldom consider the fact that the genes functionally similar to the well-established driver genes may likely play similar roles in cancer process, which potentially promotes the driver gene identification. Thus, here we developed a novel approach of IMCDriver to promote the driver gene identification both for cohorts and individual patients. RESULTS IMCDriver first considers the well-established driver genes as prior information, and adopts the using multi-omics data (e.g., somatic mutation, gene expression and protein-protein interaction) to compute the similarity between patients/genes. Then, IMCDriver prioritizes the personalized mutated genes according to their functional similarity to the well-established driver genes via Inductive Matrix Completion. Finally, IMCDriver identifies the highly rank-ordered genes as the personalized driver genes. The results on five cancer datasets from TCGA show that our IMCDriver outperforms other existing state-of-the-art methods both in the cohort and patient-specific driver gene identification. IMCDriver also reveals some novel driver genes that potentially drive cancer development. In addition, even for the driver genes rarely mutated among a population, IMCDriver can still identify them and prioritize them with high priorities. AVAILABILITY Code available at https://github.com/NWPU-903PR/IMCDriver. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Tong Zhang
- Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, China Xi'an.,School of Electrical and Mechanical Engineering, Pingdingshan University, Pingdingshan, China
| | - Shao-Wu Zhang
- Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, China Xi'an
| | - Yan Li
- Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, China Xi'an
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10
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Wu J, Lin D, Jiu L, Liu Q, Gu Z, Luo J, Zhao Y. Exploring epigenetic biomarkers of universal specificities and commonalities among pan-cancer cohorts in The Cancer Genome Atlas. Epigenomics 2021; 13:599-612. [PMID: 33787302 DOI: 10.2217/epi-2021-0050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To explore the mechanism of cancer by employing a comprehensive analysis of DNA methylation patterns and variations among pan-cancer cohorts. Materials & methods: This research focused on the discovery of universally specific or common biomarkers by mathematical statistics and machine learning methods in The Cancer Genome Atlas. Results: We found 138 differently methylated CpGs (DMCs) with a common methylation trend and eight common differently methylated regions in different cancer cohorts. Additionally, we found 99 DMCs to distinguish 32 different cancer cohorts in random forest analysis because of the specificity mechanism, but each DMC still had high instability. Conclusion: Our results could facilitate the development of biomarkers that are universally specific and common features across pan-cancer cohorts.
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Affiliation(s)
- Jie Wu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.,Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.,Department of Nutrition and Health, Beijing Advanced Innovation Center for Food Nutrition & Human Health, China Agricultural University, Beijing, 100193, China
| | - Deng Lin
- Department of Nutrition and Health, Beijing Advanced Innovation Center for Food Nutrition & Human Health, China Agricultural University, Beijing, 100193, China
| | - Liandi Jiu
- Department of Nutrition and Health, Beijing Advanced Innovation Center for Food Nutrition & Human Health, China Agricultural University, Beijing, 100193, China
| | - Qi Liu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.,Department of Nutrition and Health, Beijing Advanced Innovation Center for Food Nutrition & Human Health, China Agricultural University, Beijing, 100193, China
| | - Zhenglong Gu
- Department of Nutrition and Health, Beijing Advanced Innovation Center for Food Nutrition & Human Health, China Agricultural University, Beijing, 100193, China.,Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Junjie Luo
- Department of Nutrition and Health, Beijing Advanced Innovation Center for Food Nutrition & Human Health, China Agricultural University, Beijing, 100193, China
| | - Yiqiang Zhao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.,Department of Nutrition and Health, Beijing Advanced Innovation Center for Food Nutrition & Human Health, China Agricultural University, Beijing, 100193, China
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11
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Collignon A, Hospital MA, Montersino C, Courtier F, Charbonnier A, Saillard C, D'Incan E, Mohty B, Guille A, Adelaïde J, Carbuccia N, Garnier S, Mozziconacci MJ, Zemmour C, Pakradouni J, Restouin A, Castellano R, Chaffanet M, Birnbaum D, Collette Y, Vey N. A chemogenomic approach to identify personalized therapy for patients with relapse or refractory acute myeloid leukemia: results of a prospective feasibility study. Blood Cancer J 2020; 10:64. [PMID: 32488055 PMCID: PMC7266815 DOI: 10.1038/s41408-020-0330-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 04/06/2020] [Accepted: 04/23/2020] [Indexed: 02/05/2023] Open
Abstract
Targeted next-generation sequencing (tNGS) and ex vivo drug sensitivity/resistance profiling (DSRP) have laid foundations defining the functional genomic landscape of acute myeloid leukemia (AML) and premises of personalized medicine to guide treatment options for patients with aggressive and/or chemorefractory hematological malignancies. Here, we have assessed the feasibility of a tailored treatment strategy (TTS) guided by systematic parallel ex vivo DSRP and tNGS for patients with relapsed/refractory AML (number NCT02619071). A TTS issued by an institutional personalized committee could be achieved for 47/55 included patients (85%), 5 based on tNGS only, 6 on DSRP only, while 36 could be proposed on the basis of both, yielding more options and a better rationale. The TSS was available in <21 days for 28 patients (58.3%). On average, 3 to 4 potentially active drugs were selected per patient with only five patient samples being resistant to the entire drug panel. Seventeen patients received a TTS-guided treatment, resulting in four complete remissions, one partial remission, and five decreased peripheral blast counts. Our results show that chemogenomic combining tNGS with DSRP to determine a TTS is a promising approach to propose patient-specific treatment options within 21 days.
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Affiliation(s)
- A Collignon
- Haematology Department, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France
| | - M A Hospital
- Haematology Department, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France
| | - C Montersino
- Inserm, CNRS, Institut Paoli-Calmettes, CRCM, TrGET Preclinical Platform, Aix-Marseille Université, Marseille, France
| | - F Courtier
- Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Predictive Oncology, Aix-Marseille Université, Marseille, France
| | - A Charbonnier
- Haematology Department, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France
| | - C Saillard
- Haematology Department, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France
| | - E D'Incan
- Haematology Department, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France
| | - B Mohty
- Haematology Department, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France
| | - A Guille
- Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Predictive Oncology, Aix-Marseille Université, Marseille, France
| | - J Adelaïde
- Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Predictive Oncology, Aix-Marseille Université, Marseille, France
| | - N Carbuccia
- Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Predictive Oncology, Aix-Marseille Université, Marseille, France
| | - S Garnier
- Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Predictive Oncology, Aix-Marseille Université, Marseille, France
| | - M J Mozziconacci
- Department of Biopathology, Institut Paoli-Calmettes, Marseille, France
| | - C Zemmour
- Department of Clinical Research & Innovation, Institut Paoli-Calmettes, Biostatistics & Methodology Unit, Aix Marseille Université, INSERM, IRD, SESSTIM, Marseille, France
| | - J Pakradouni
- Department of Clinical Research & Innovation, Sponsor Unit, Institut Paoli-Calmettes, Marseille, France
| | - A Restouin
- Inserm, CNRS, Institut Paoli-Calmettes, CRCM, TrGET Preclinical Platform, Aix-Marseille Université, Marseille, France
| | - R Castellano
- Inserm, CNRS, Institut Paoli-Calmettes, CRCM, TrGET Preclinical Platform, Aix-Marseille Université, Marseille, France
| | - M Chaffanet
- Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Predictive Oncology, Aix-Marseille Université, Marseille, France
| | - D Birnbaum
- Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Predictive Oncology, Aix-Marseille Université, Marseille, France.
| | - Y Collette
- Inserm, CNRS, Institut Paoli-Calmettes, CRCM, TrGET Preclinical Platform, Aix-Marseille Université, Marseille, France.
| | - N Vey
- Haematology Department, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France.
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12
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Ru B, Sun J, Kang Q, Tong Y, Zhang J. A framework for identifying dysregulated chromatin regulators as master regulators in human cancer. Bioinformatics 2019; 35:1805-1812. [PMID: 30358822 DOI: 10.1093/bioinformatics/bty836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/22/2018] [Accepted: 10/24/2018] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Chromatin regulators (CRs) are frequently dysregulated to reprogram the epigenetic landscape of the cancer genome. However, the underpinnings of the dysregulation of CRs and their downstream effectors remain to be elucidated. RESULTS Here, we designed an integrated framework based on multi-omics data to identify candidate master regulatory CRs affected by genomic alterations across eight cancer types in The Cancer Genome Atlas. Most of them showed consistent activated or repressed (i.e. oncogenic or tumor-suppressive) roles in cancer initiation and progression. In order to further explore the insight mechanism of the dysregulated CRs, we developed an R package ModReg based on differential connectivity to identify CRs as modulators of transcription factors (TFs) involved in tumorigenesis. Our analysis revealed that the connectivity between TFs and their target genes (TGs) tended to be disrupted in the patients who had a high expression of oncogenic CRs or low-expression of tumor-suppressive CRs. As a proof-of-principle study, 14 (82.4%) of the top-ranked 17 driver CRs in liver cancer were able to be validated by literature mining or experiments including shRNA knockdown and dCas9-based epigenetic editing. Moreover, we confirmed that CR SIRT7 physically interacted with TF NFE2L2, and positively modulated the transcriptional program of NFE2L2 by affecting ∼64% of its TGs. AVAILABILITY AND IMPLEMENTATION ModReg is freely accessible at http://cis.hku.hk/software/ModReg.tar.gz. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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13
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Lou K, Steri V, Ge AY, Hwang YC, Yogodzinski CH, Shkedi AR, Choi ALM, Mitchell DC, Swaney DL, Hann B, Gordan JD, Shokat KM, Gilbert LA. KRAS G12C inhibition produces a driver-limited state revealing collateral dependencies. Sci Signal 2019; 12:12/583/eaaw9450. [PMID: 31138768 DOI: 10.1126/scisignal.aaw9450] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Inhibitors targeting KRASG12C, a mutant form of the guanosine triphosphatase (GTPase) KRAS, are a promising new class of oncogene-specific therapeutics for the treatment of tumors driven by the mutant protein. These inhibitors react with the mutant cysteine residue by binding covalently to the switch-II pocket (S-IIP) that is present only in the inactive guanosine diphosphate (GDP)-bound form of KRASG12C, sparing the wild-type protein. We used a genome-scale CRISPR interference (CRISPRi) functional genomics platform to systematically identify genetic interactions with a KRASG12C inhibitor in cellular models of KRASG12C mutant lung and pancreatic cancer. Our data revealed genes that were selectively essential in this oncogenic driver-limited cell state, meaning that their loss enhanced cellular susceptibility to direct KRASG12C inhibition. We termed such genes "collateral dependencies" (CDs) and identified two classes of combination therapies targeting these CDs that increased KRASG12C target engagement or blocked residual survival pathways in cells and in vivo. From our findings, we propose a framework for assessing genetic dependencies induced by oncogene inhibition.
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Affiliation(s)
- Kevin Lou
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Veronica Steri
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.,Preclinical Therapeutics Core, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alex Y Ge
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.,Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Y Christina Hwang
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.,Department of Medicine and Division of Hematology/Oncology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Christopher H Yogodzinski
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.,Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Arielle R Shkedi
- Institute for Neurodegenerative Diseases and Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Alex L M Choi
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.,Department of Medicine and Division of Hematology/Oncology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Dominique C Mitchell
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.,Department of Medicine and Division of Hematology/Oncology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Danielle L Swaney
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.,Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
| | - Byron Hann
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.,Preclinical Therapeutics Core, University of California, San Francisco, San Francisco, CA 94158, USA
| | - John D Gordan
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.,Department of Medicine and Division of Hematology/Oncology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kevan M Shokat
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA. .,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Luke A Gilbert
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA. .,Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA.,Innovative Genomics Institute, University of California, San Francisco, San Francisco, CA 94158, USA
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14
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Ru B, Tong Y, Zhang J. MR4Cancer: a web server prioritizing master regulators for cancer. Bioinformatics 2019; 35:636-642. [PMID: 30052770 DOI: 10.1093/bioinformatics/bty658] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 07/17/2018] [Accepted: 07/20/2018] [Indexed: 01/10/2023] Open
Abstract
MOTIVATION During cancer stage transition, a master regulator (MR) refers to the key gene controlling cancer initiation and progression by orchestrating the associated target genes (termed as its regulon). Due to their inherent importance, MRs can serve as critical biomarkers for cancer diagnosis and prognosis, and therapeutic targets. However, it is challenging to infer key MRs that might explain gene expression profile changes between two groups due to lack of context-specific regulons, whose expression level can collectively reflect the activity of likely MRs. There is also a need to design an easy-to-use tool of MR identification for research community. RESULTS First, we generated cancer-specific regulons for 26 cancer types by analyzing high-throughput omics data from TCGA, and extracted noncancer-specific regulons from public databases. We subsequently developed a web server MR4Cancer, integrating the regulons with statistical inference to identify and prioritize MRs driving a phenotypic divergence of interest. Based on the input gene list (e.g. differentially expressed genes) or expression profile with two groups, MR4Cancer outputs ranked MRs by enrichment testing against the predefined regulons. Gene Ontology and canonical pathway analyses are also conducted to elucidate the function of likely MRs. Moreover, MR4Cancer provides dynamic network visualization for MR-target relations, and users can interactively interrogate the network to produce new hypotheses and high-quality figures for publication. Finally, the presented case studies highlighted the performance of MR4Cancer. We expect this user-friendly and powerful web tool will provide researchers novel insights into tumorigenesis and therapeutic intervention. AVAILABILITY AND IMPLEMENTATION http://cis.hku.hk/MR4Cancer. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Beibei Ru
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Yin Tong
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Jiangwen Zhang
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
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15
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Collaborating genomic, transcriptomic and microbiomic alterations lead to canine extreme intestinal polyposis. Oncotarget 2018; 9:29162-29179. [PMID: 30018743 PMCID: PMC6044369 DOI: 10.18632/oncotarget.25646] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 06/01/2018] [Indexed: 12/13/2022] Open
Abstract
Extreme intestinal polyposis in pet dogs has not yet been reported in literature. We identified a dog patient who developed numerous intestinal polyps, with the severity resembling human classic familial adenomatous polyposis (FAP), except the jejunum-ileum junction being the most polyp-dense. We investigated this dog, in comparison with 22 other dogs with spontaneous intestinal tumors but no severe polyposis, and with numerous published human cancers. We found, not APC mutation, but three other alteration pathways as likely reasons of this canine extreme polyposis. First, somatic truncation mutation W411X of FBXW7, a component of an E3 ubiquitin ligase, over-activates MYC and cell cycle-promoting network, accelerating crypt cell proliferation. Second, genes of protein trafficking and localization are downregulated, likely associated with germline mutation G406D of STAMBPL1, a K63-deubiquitinase, and MYC network activation. This inhibits epithelial apical-basolateral polarity establishment, preventing crypt cell differentiation. Third, Bacteroides uniformis, a commensal gut anaerobe, thrives and expresses abundantly thioredoxin and nitroreductase. These bacterial products could reduce oxidative stress linked to host germline mutation R51X of CYB5RL, a cytochrome b5 reductase homologue, decreasing cell death. Our work emphasizes the close collaboration of alterations across the genome, transcriptome and microbiome in promoting tumorigenesis.
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16
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Champion M, Brennan K, Croonenborghs T, Gentles AJ, Pochet N, Gevaert O. Module Analysis Captures Pancancer Genetically and Epigenetically Deregulated Cancer Driver Genes for Smoking and Antiviral Response. EBioMedicine 2018; 27:156-166. [PMID: 29331675 PMCID: PMC5828545 DOI: 10.1016/j.ebiom.2017.11.028] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 11/23/2017] [Accepted: 11/29/2017] [Indexed: 12/12/2022] Open
Abstract
The availability of increasing volumes of multi-omics profiles across many cancers promises to improve our understanding of the regulatory mechanisms underlying cancer. The main challenge is to integrate these multiple levels of omics profiles and especially to analyze them across many cancers. Here we present AMARETTO, an algorithm that addresses both challenges in three steps. First, AMARETTO identifies potential cancer driver genes through integration of copy number, DNA methylation and gene expression data. Then AMARETTO connects these driver genes with co-expressed target genes that they control, defined as regulatory modules. Thirdly, we connect AMARETTO modules identified from different cancer sites into a pancancer network to identify cancer driver genes. Here we applied AMARETTO in a pancancer study comprising eleven cancer sites and confirmed that AMARETTO captures hallmarks of cancer. We also demonstrated that AMARETTO enables the identification of novel pancancer driver genes. In particular, our analysis led to the identification of pancancer driver genes of smoking-induced cancers and 'antiviral' interferon-modulated innate immune response. SOFTWARE AVAILABILITY AMARETTO is available as an R package at https://bitbucket.org/gevaertlab/pancanceramaretto.
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Affiliation(s)
- Magali Champion
- Stanford Center for Biomedical Informatics Research (BMIR), Department of Medicine & Biomedical Data Science, Stanford University, United States
| | - Kevin Brennan
- Stanford Center for Biomedical Informatics Research (BMIR), Department of Medicine & Biomedical Data Science, Stanford University, United States
| | - Tom Croonenborghs
- Program in Translational Neuropsychiatric Genomics, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Broad Institute of Harvard and Massachusetts Institute of Technology, United States; Advanced Integrated Sensing Lab, Campus Geel, Department of Computer Science, University of Leuven, Belgium
| | - Andrew J Gentles
- Department of Medicine, Center for Cancer Systems Biology, Stanford University, United States
| | - Nathalie Pochet
- Program in Translational Neuropsychiatric Genomics, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Broad Institute of Harvard and Massachusetts Institute of Technology, United States
| | - Olivier Gevaert
- Stanford Center for Biomedical Informatics Research (BMIR), Department of Medicine & Biomedical Data Science, Stanford University, United States.
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17
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The role of CIP2A in cancer: A review and update. Biomed Pharmacother 2017; 96:626-633. [DOI: 10.1016/j.biopha.2017.08.146] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 08/01/2017] [Accepted: 08/13/2017] [Indexed: 12/11/2022] Open
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18
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Breast Cancer Risk Associated with Genotype Polymorphisms of the Aurora Kinase a Gene (AURKA): a Case-Control Study in a High Altitude Ecuadorian Mestizo Population. Pathol Oncol Res 2017. [PMID: 28647900 DOI: 10.1007/s12253-017-0267-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Breast cancer (BC) is the leading cause of cancer related death among women in 2014. The AURKA gene that encodes the protein called Aurora kinase A plays an important role in the progression of the cell cycle, by controlling and promoting the entry into the phase of mitosis. The single nucleotide polymorphism AURKA T91A (rs2273535) (Phe21Ile) has been identified as functional alternator of this kinase, the Ile allele is associated with the occurrence of chromosome segregation errors and tumor progression. Therefore, it is essential to know how BC risk is associated with histopathological characteristics, immunohistochemical characteristics, and genotype polymorphism in a high altitude Ecuadorian mestizo population. In this retrospective case-control study 200 individuals were analyzed. DNA was extracted from 100 healthy and 100 affected women. Genotypes were determined by genomic sequencing. We found significant association between the AURKA T91A (rs2273535) (Phe21Ile) genotype and an increased risk of BC development: Phe/Ile (odds ratio [OR] = 2.6; 95% confidence interval [CI] = 1.4-4.9; P = 0.004), Ile/Ile (OR = 3.8; 95% CI = 1.6-9.0; P = 0.002), and Phe/Ile + Ile/Ile (OR = 2.9; 95% CI = 1.6-5.2; P = 0.001). Additionally, the rs2273535 variant was associated with the tumor grade SBR III (OR = 9.6; 95% CI = 1.0-91.9; P = 0.048) and the Ki-67 ≥ 20 (OR = 16.5; 95% CI = 2.7-101.3; P = 0.002). In brief, this study provides the first evidence where the Ile allele of the AURKA gene could act as potentially predictive biomarker of BC in the high altitude Ecuadorian mestizo population that lives at 2800 m above sea level (masl).
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19
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Konen J, Summerbell E, Dwivedi B, Galior K, Hou Y, Rusnak L, Chen A, Saltz J, Zhou W, Boise LH, Vertino P, Cooper L, Salaita K, Kowalski J, Marcus AI. Image-guided genomics of phenotypically heterogeneous populations reveals vascular signalling during symbiotic collective cancer invasion. Nat Commun 2017; 8:15078. [PMID: 28497793 PMCID: PMC5437311 DOI: 10.1038/ncomms15078] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 02/27/2017] [Indexed: 02/06/2023] Open
Abstract
Phenotypic heterogeneity is widely observed in cancer cell populations. Here, to probe this heterogeneity, we developed an image-guided genomics technique termed spatiotemporal genomic and cellular analysis (SaGA) that allows for precise selection and amplification of living and rare cells. SaGA was used on collectively invading 3D cancer cell packs to create purified leader and follower cell lines. The leader cell cultures are phenotypically stable and highly invasive in contrast to follower cultures, which show phenotypic plasticity over time and minimally invade in a sheet-like pattern. Genomic and molecular interrogation reveals an atypical VEGF-based vasculogenesis signalling that facilitates recruitment of follower cells but not for leader cell motility itself, which instead utilizes focal adhesion kinase-fibronectin signalling. While leader cells provide an escape mechanism for followers, follower cells in turn provide leaders with increased growth and survival. These data support a symbiotic model of collective invasion where phenotypically distinct cell types cooperate to promote their escape. The mechanisms linking phenotypic heterogeneity to collective cancer invasion are unclear. Here the authors develop an image-guided genomic technique to select and amplify leader and follower cells from in vitro invading cell packs and find a cooperative symbiotic relationship between these two cell populations.
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Affiliation(s)
- J Konen
- Graduate Program in Cancer Biology, Emory University, 1365C Clifton Road, Atlanta, Georgia 30322, USA
| | - E Summerbell
- Graduate Program in Cancer Biology, Emory University, 1365C Clifton Road, Atlanta, Georgia 30322, USA
| | - B Dwivedi
- Winship Cancer Institute, Emory University, 1365C Clifton Road, Atlanta, Georgia 30322, USA
| | - K Galior
- Department of Chemistry, Emory University, 506 Atwood Drive, Atlanta, Georgia 30322, USA
| | - Y Hou
- Department of Biomedical Informatics, Emory University, 36 Eagle Row, Atlanta, Georgia 30322, USA
| | - L Rusnak
- Graduate Program in Cancer Biology, Emory University, 1365C Clifton Road, Atlanta, Georgia 30322, USA
| | - A Chen
- Graduate Program in Cancer Biology, Emory University, 1365C Clifton Road, Atlanta, Georgia 30322, USA
| | - J Saltz
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York 11794, USA
| | - W Zhou
- Winship Cancer Institute, Emory University, 1365C Clifton Road, Atlanta, Georgia 30322, USA.,Department of Hematology and Medical Oncology, Emory University, 1365C Clifton Road, Atlanta, Georgia 30322, USA
| | - L H Boise
- Winship Cancer Institute, Emory University, 1365C Clifton Road, Atlanta, Georgia 30322, USA.,Department of Hematology and Medical Oncology, Emory University, 1365C Clifton Road, Atlanta, Georgia 30322, USA
| | - P Vertino
- Winship Cancer Institute, Emory University, 1365C Clifton Road, Atlanta, Georgia 30322, USA.,Department of Radiation Oncology, Emory University, 1365C Clifton Road, Atlanta, Georgia 30322, USA
| | - L Cooper
- Department of Biomedical Informatics, Emory University, 36 Eagle Row, Atlanta, Georgia 30322, USA
| | - K Salaita
- Department of Chemistry, Emory University, 506 Atwood Drive, Atlanta, Georgia 30322, USA
| | - J Kowalski
- Winship Cancer Institute, Emory University, 1365C Clifton Road, Atlanta, Georgia 30322, USA.,Department of Biostatistics and Bioinformatics, Emory University, 1365C Clifton Road, Atlanta, Georgia 30322, USA
| | - A I Marcus
- Winship Cancer Institute, Emory University, 1365C Clifton Road, Atlanta, Georgia 30322, USA.,Department of Hematology and Medical Oncology, Emory University, 1365C Clifton Road, Atlanta, Georgia 30322, USA
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20
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Abstract
How can we treat cancer more effectively? Traditionally, tumours from the same anatomical site are treated as one tumour entity. This concept has been challenged by recent breakthroughs in cancer genomics and translational research that have enabled molecular tumour profiling. The identification and validation of cancer drivers that are shared between different tumour types, spurred the new paradigm to target driver pathways across anatomical sites by off-label drug use, or within so-called basket or umbrella trials which are designed to test whether molecular alterations in one tumour entity can be extrapolated to all others. However, recent clinical and preclinical studies suggest that there are tissue- and cell type-specific differences in tumorigenesis and the organization of oncogenic signalling pathways. In this Opinion article, we focus on the molecular, cellular, systemic and environmental determinants of organ-specific tumorigenesis and the mechanisms of context-specific oncogenic signalling outputs. Investigation, recognition and in-depth biological understanding of these differences will be vital for the design of next-generation clinical trials and the implementation of molecularly guided cancer therapies in the future.
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Affiliation(s)
- Günter Schneider
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Ismaningerstr. 22, 81675 München, Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Marc Schmidt-Supprian
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
- Department of Medicine III, Klinikum rechts der Isar, Technische Universität München, Ismaningerstr. 22, 81675 München, Germany
| | - Roland Rad
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Ismaningerstr. 22, 81675 München, Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Dieter Saur
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Ismaningerstr. 22, 81675 München, Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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21
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Fang J, Cai C, Wang Q, Lin P, Zhao Z, Cheng F. Systems Pharmacology-Based Discovery of Natural Products for Precision Oncology Through Targeting Cancer Mutated Genes. CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY 2017; 6:177-187. [PMID: 28294568 PMCID: PMC5356618 DOI: 10.1002/psp4.12172] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 01/09/2017] [Accepted: 01/10/2017] [Indexed: 02/05/2023]
Abstract
Massive cancer genomics data have facilitated the rapid revolution of a novel oncology drug discovery paradigm through targeting clinically relevant driver genes or mutations for the development of precision oncology. Natural products with polypharmacological profiles have been demonstrated as promising agents for the development of novel cancer therapies. In this study, we developed an integrated systems pharmacology framework that facilitated identifying potential natural products that target mutated genes across 15 cancer types or subtypes in the realm of precision medicine. High performance was achieved for our systems pharmacology framework. In case studies, we computationally identified novel anticancer indications for several US Food and Drug Administration-approved or clinically investigational natural products (e.g., resveratrol, quercetin, genistein, and fisetin) through targeting significantly mutated genes in multiple cancer types. In summary, this study provides a powerful tool for the development of molecularly targeted cancer therapies through targeting the clinically actionable alterations by exploiting the systems pharmacology of natural products.
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Affiliation(s)
- J Fang
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, P.R. China
| | - C Cai
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, P.R. China
| | - Q Wang
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, P.R. China
| | - P Lin
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, P.R. China
| | - Z Zhao
- Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, Texas, USA.,Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - F Cheng
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, P.R. China.,Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA.,Center for Complex Networks Research, Northeastern University, Boston, Massachusetts, USA
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22
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Paolella BR, Gibson WJ, Urbanski LM, Alberta JA, Zack TI, Bandopadhayay P, Nichols CA, Agarwalla PK, Brown MS, Lamothe R, Yu Y, Choi PS, Obeng EA, Heckl D, Wei G, Wang B, Tsherniak A, Vazquez F, Weir BA, Root DE, Cowley GS, Buhrlage SJ, Stiles CD, Ebert BL, Hahn WC, Reed R, Beroukhim R. Copy-number and gene dependency analysis reveals partial copy loss of wild-type SF3B1 as a novel cancer vulnerability. eLife 2017; 6. [PMID: 28177281 PMCID: PMC5357138 DOI: 10.7554/elife.23268] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/06/2017] [Indexed: 12/13/2022] Open
Abstract
Genomic instability is a hallmark of human cancer, and results in widespread somatic copy number alterations. We used a genome-scale shRNA viability screen in human cancer cell lines to systematically identify genes that are essential in the context of particular copy-number alterations (copy-number associated gene dependencies). The most enriched class of copy-number associated gene dependencies was CYCLOPS (Copy-number alterations Yielding Cancer Liabilities Owing to Partial losS) genes, and spliceosome components were the most prevalent. One of these, the pre-mRNA splicing factor SF3B1, is also frequently mutated in cancer. We validated SF3B1 as a CYCLOPS gene and found that human cancer cells harboring partial SF3B1 copy-loss lack a reservoir of SF3b complex that protects cells with normal SF3B1 copy number from cell death upon partial SF3B1 suppression. These data provide a catalog of copy-number associated gene dependencies and identify partial copy-loss of wild-type SF3B1 as a novel, non-driver cancer gene dependency.
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Affiliation(s)
- Brenton R Paolella
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - William J Gibson
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Laura M Urbanski
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - John A Alberta
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Department of Neurobiology, Harvard Medical School, Boston, United States
| | - Travis I Zack
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Pratiti Bandopadhayay
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Caitlin A Nichols
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Pankaj K Agarwalla
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, United States
| | - Meredith S Brown
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Rebecca Lamothe
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Yong Yu
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Peter S Choi
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Esther A Obeng
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Dirk Heckl
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Guo Wei
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States
| | - Belinda Wang
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Aviad Tsherniak
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States
| | - Francisca Vazquez
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States
| | - Barbara A Weir
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States
| | - David E Root
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States
| | - Glenn S Cowley
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States
| | - Sara J Buhrlage
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Charles D Stiles
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Department of Neurobiology, Harvard Medical School, Boston, United States
| | - Benjamin L Ebert
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - William C Hahn
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, United States
| | - Robin Reed
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Rameen Beroukhim
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, United States
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23
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Mutant DNA methylation regulators endow hematopoietic stem cells with the preleukemic stem cell property, a requisite of leukemia initiation and relapse. Front Med 2016; 9:412-20. [PMID: 26482067 DOI: 10.1007/s11684-015-0423-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 08/20/2015] [Indexed: 12/17/2022]
Abstract
Genetic mutations are considered to drive the development of acute myeloid leukemia (AML). With therapid progress in sequencing technologies, many newly reported genes that are recurrently mutated in AML have been found to govern the initiation and relapse of AML. These findings suggest the need to distinguish the driver mutations, especially the most primitive single mutation, from the subsequent passenger mutations. Recent research on DNA methyltransferase 3A (DNMT3A) mutations provides the first proof-of-principle investigation on the identification of preleukemic stem cells (pre-LSCs) in AML patients. Although DNMT3A mutations alone may only transform hematopoietic stem cells into pre-LSCs without causing the full-blown leukemia, the function of this driver mutation appear to persist from AML initiation up to relapse. Therefore, identifying and targeting preleukemic mutations, such as DNMT3A mutations, in AML is a promising strategy for treatment and reduction of relapse risk.
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24
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Ren W, Shen S, Sun Z, Shu P, Shen X, Bu C, Ai F, Zhang X, Tang A, Tian L, Li G, Li X, Ma J. Jak-STAT3 pathway triggers DICER1 for proteasomal degradation by ubiquitin ligase complex of CUL4A(DCAF1) to promote colon cancer development. Cancer Lett 2016; 375:209-220. [PMID: 26965998 DOI: 10.1016/j.canlet.2016.02.055] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 02/06/2016] [Accepted: 02/29/2016] [Indexed: 12/13/2022]
Abstract
Chronic intestinal inflammation is closely associated with colon cancer development and STAT3 seems to take center stage in bridging chronic inflammation to colon cancer progress. Here, we discovered that DICER1 was significantly downregulated in response to IL-6 or LPS stimulation and identified a novel mechanism for DICER1 downregulation via proteasomal degradation by ubiquitin ligase complex of CUL4A(DCAF1) in colon cancer cells. Meanwhile, PI3K-AKT signaling pathway phosphorylated DICER1 and contributed to its proteasomal degradation. The regulation of DICER1 by CUL4A(DCAF1) affected cell growth and apoptosis which is controlled by IL-6 activated Jak-STAT3 pathway. Intervention of CUL4A(DCAF1) ubiquitin ligase complex led to fluctuation in expression levels of DICER1 and microRNAs, and thus affected tumor growth in a mouse xenograft model. A panel of microRNAs that were downregulated by IL-6 stimulation was rescued by siRNA-CUL4A, and their predicated functions are involved in regulation of cell proliferation, apoptosis and motility. Furthermore, clinical specimen analysis revealed that decreased DICER1 expression was negatively correlated with STAT3 activation and cancer progression in human colon cancers. DICER1 and p-STAT3 expression levels correlated with 5-year overall survival of colon cancer patients. Consequently, this study proposes that inflammation-induced Jak-STAT3 signaling leads to colon cancer development through proteasomal degradation of DICER1 by ubiquitin ligase complex of CUL4A(DCAF1), which suggests a novel therapeutic opportunity for colon cancer.
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Affiliation(s)
- Weiguo Ren
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China; Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha, Hunan, China; Cancer Research Institute, Central South University, Key Laboratory of Carcinogenesis, Ministry of Health, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Changsha, Hunan, China
| | - Shourong Shen
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China; Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha, Hunan, China
| | - Zhenqiang Sun
- Cancer Research Institute, Central South University, Key Laboratory of Carcinogenesis, Ministry of Health, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Changsha, Hunan, China
| | - Peng Shu
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Xiaohua Shen
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Chibin Bu
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Feiyan Ai
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China; Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha, Hunan, China
| | - Xuemei Zhang
- Cancer Research Institute, Central South University, Key Laboratory of Carcinogenesis, Ministry of Health, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Changsha, Hunan, China
| | - Anliu Tang
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China; Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha, Hunan, China
| | - Li Tian
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China; Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha, Hunan, China
| | - Guiyuan Li
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha, Hunan, China; Cancer Research Institute, Central South University, Key Laboratory of Carcinogenesis, Ministry of Health, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Changsha, Hunan, China
| | - Xiayu Li
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China; Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha, Hunan, China.
| | - Jian Ma
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China; Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha, Hunan, China; Cancer Research Institute, Central South University, Key Laboratory of Carcinogenesis, Ministry of Health, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Changsha, Hunan, China.
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25
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Wang D, Gu J. Integrative clustering methods of multi-omics data for molecule-based cancer classifications. QUANTITATIVE BIOLOGY 2016. [DOI: 10.1007/s40484-016-0063-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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26
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Abstract
Pancreatic cancer is the fourth leading cause of cancer death in our society, with a mortality that virtually parallels its incidence, a median survival of <12 months even with maximal therapy, and a 5-year survival rate of <5 %. The diversity of clinical outcomes and the molecular heterogeneity of histopathologically similar cancer types, incomplete knowledge of the genomic aberrations that drive carcinogenesis and the lack of therapeutics that specifically target most known genomic aberrations necessitates large-scale detailed analysis of cancer genomes to identify novel potential therapeutic strategies. As part of the International Cancer Genome Consortium (ICGC), the Australian Pancreatic Cancer Genome Initiative (APGI) used exomic sequencing and copy number analysis to define genomic aberrations that characterize a large, clinically focused, prospectively accrued cohort of patients with pancreatic cancer. The cohort consisted of early (clinical stages I and II) non-pre-treated patients with pancreatic ductal adenocarcinoma who underwent operative resection with curative intent. We devised approaches to adjust for low epithelial content in primary tumours and to define the genomic landscape of pancreatic cancer to identify novel candidate driver genes and mechanisms. We aim to develop stratified, molecular phenotype-guided therapeutic strategies using existing therapeutics that are either rescued, repurposed, in development, or are known to be effective in an undefined subgroup of PC patients. These are then tested in primary patient-derived xenografts and cell lines from the above deeply characterized cohort. In addition, we return information to treating clinicians that influences patient care and are launching a clinical trial called IMPaCT (Individualized Molecular Pancreatic Cancer Therapy). This umbrella design trial randomizes patients with metastatic disease to either standard first-line therapy with gemcitabine, or a molecular phenotype-guided approach using next-generation sequencing strategies to screen for actionable mutations defined through the ICGC effort.
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27
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Shimada K, Hayano M, Pagano NC, Stockwell BR. Cell-Line Selectivity Improves the Predictive Power of Pharmacogenomic Analyses and Helps Identify NADPH as Biomarker for Ferroptosis Sensitivity. Cell Chem Biol 2016; 23:225-235. [PMID: 26853626 DOI: 10.1016/j.chembiol.2015.11.016] [Citation(s) in RCA: 213] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 11/09/2015] [Accepted: 11/20/2015] [Indexed: 02/07/2023]
Abstract
Precision medicine in oncology requires not only identification of cancer-associated mutations but also effective drugs for each cancer genotype, which is still a largely unsolved problem. One approach for the latter challenge has been large-scale testing of small molecules in genetically characterized cell lines. We hypothesized that compounds with high cell-line-selective lethality exhibited consistent results across such pharmacogenomic studies. We analyzed the compound sensitivity data of 6,259 lethal compounds from the NCI-60 project. A total of 2,565 cell-line-selective lethal compounds were identified and grouped into 18 clusters based on their median growth inhibitory GI50 profiles across the 60 cell lines, which were shown to represent distinct mechanisms of action. Further transcriptome analysis revealed a biomarker, NADPH abundance, for predicting sensitivity to ferroptosis-inducing compounds, which we experimentally validated. In summary, incorporating cell-line-selectivity filters improves the predictive power of pharmacogenomic analyses and enables discovery of biomarkers that predict the sensitivity of cells to specific cell death inducers.
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Affiliation(s)
- Kenichi Shimada
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
| | - Miki Hayano
- Department of Pharmacology, Columbia University, New York, NY 10027, USA
| | - Nen C Pagano
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Brent R Stockwell
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; Department of Chemistry, Columbia University, New York, NY 10027, USA; Howard Hughes Medical Institute, Columbia University, 1208 Northwest Corner Building, MC 4846, 550 West 120th Street, New York, NY 10027, USA.
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28
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Louandre C, Donnadieu J, Lachaier E, Page C, Chauffert B, Galmiche A. Personalization of the medical treatment of solid tumours using patient-derived tumour explants (Review). Int J Oncol 2016; 48:895-9. [PMID: 26783093 DOI: 10.3892/ijo.2016.3345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 12/27/2015] [Indexed: 11/06/2022] Open
Abstract
Improving the pre-clinical characterization of therapeutic approaches and developing new biological assays that will enable treatment personalization for individual patients are promising developments in oncology. Here we describe a new approach consisting of culturing human tumour explants. This approach involves the preparation of slices from freshly-obtained, surgically-resected material that can be maintained ex vivo for several days. Recent studies have provided proof of principle that this approach can be easily implemented in order to explore the mode of action of various anticancer drugs and the responses of 'real' tumours at the individual patient level. We present the practical aspects and highlight the versatility of this approach, which allows for the analysis of the susceptibility of any individual tumour to multiple anticancer drugs in parallel. We discuss its potential as a companion assay in the design of optimal clinical trials and as a guide for the prescription of medical treatment. We discuss which future clinical and biological studies are needed to validate the information gathered from cultured tumour explants, and to integrate this information with that gathered from other assays in order to optimize the medical treatment of cancer.
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Affiliation(s)
| | - Jérome Donnadieu
- Department of Head and Neck Surgery, CHU Amiens Sud, Amiens, France
| | - Emma Lachaier
- Department of Medical Oncology, CHU Amiens Sud, Amiens, France
| | - Cyril Page
- Department of Head and Neck Surgery, CHU Amiens Sud, Amiens, France
| | - Bruno Chauffert
- Department of Medical Oncology, CHU Amiens Sud, Amiens, France
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29
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Zeron-Medina J, Ochoa de Olza M, Braña I, Rodon J. The Personalization of Therapy: Molecular Profiling Technologies and Their Application. Semin Oncol 2015; 42:775-87. [DOI: 10.1053/j.seminoncol.2015.09.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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30
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Tamaki S, Fukuta M, Sekiguchi K, Jin Y, Nagata S, Hayakawa K, Hineno S, Okamoto T, Watanabe M, Woltjen K, Ikeya M, Kato T, Toguchida J. SS18-SSX, the Oncogenic Fusion Protein in Synovial Sarcoma, Is a Cellular Context-Dependent Epigenetic Modifier. PLoS One 2015; 10:e0142991. [PMID: 26571495 PMCID: PMC4646489 DOI: 10.1371/journal.pone.0142991] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 10/29/2015] [Indexed: 12/18/2022] Open
Abstract
The prevalence and specificity of unique fusion oncogenes are high in a number of soft tissue sarcomas (STSs). The close relationship between fusion genes and clinicopathological features suggests that a correlation may exist between the function of fusion proteins and cellular context of the cell-of-origin of each tumor. However, most STSs are origin-unknown tumors and this issue has not yet been investigated in detail. In the present study, we examined the effects of the cellular context on the function of the synovial sarcoma (SS)-specific fusion protein, SS18-SSX, using human pluripotent stem cells (hPSCs) containing the drug-inducible SS18-SSX gene. We selected the neural crest cell (NCC) lineage for the first trial of this system, induced SS18-SSX at various differentiation stages from PSCs to NCC-derived mesenchymal stromal cells (MSCs), and compared its biological effects on each cell type. We found that the expression of FZD10, identified as an SS-specific gene, was induced by SS18-SSX at the PSC and NCC stages, but not at the MSC stage. This stage-specific induction of FZD10 correlated with stage-specific changes in histone marks associated with the FZD10 locus and also with the loss of the BAF47 protein, a member of the SWI/SNF chromatin-remodeling complex. Furthermore, the global gene expression profile of hPSC-derived NCCs was the closest to that of SS cell lines after the induction of SS18-SSX. These results clearly demonstrated that the cellular context is an important factor in the function of SS18-SSX as an epigenetic modifier.
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Affiliation(s)
- Sakura Tamaki
- Department of Tissue Regeneration, Institute for Frontier Medical Sciences, Kyoto University, Kyoto, Japan
| | - Makoto Fukuta
- Department of Tissue Regeneration, Institute for Frontier Medical Sciences, Kyoto University, Kyoto, Japan
- Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
- Department of Orthopaedic Surgery, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Japan
| | - Kazuya Sekiguchi
- Department of Tissue Regeneration, Institute for Frontier Medical Sciences, Kyoto University, Kyoto, Japan
- Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
- Department of Orthopaedic Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yonghui Jin
- Department of Tissue Regeneration, Institute for Frontier Medical Sciences, Kyoto University, Kyoto, Japan
| | - Sanae Nagata
- Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Kazuo Hayakawa
- Department of Tissue Regeneration, Institute for Frontier Medical Sciences, Kyoto University, Kyoto, Japan
- Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
- Department of Orthopaedic Surgery, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Japan
| | - Sho Hineno
- Department of Tissue Regeneration, Institute for Frontier Medical Sciences, Kyoto University, Kyoto, Japan
| | - Takeshi Okamoto
- Department of Orthopaedic Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Makoto Watanabe
- Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
- Life Science Research Center, Technology Research Laboratory, Shimadzu Corporation, Kyoto, Japan
| | - Knut Woltjen
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Makoto Ikeya
- Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Tomohisa Kato
- Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Junya Toguchida
- Department of Tissue Regeneration, Institute for Frontier Medical Sciences, Kyoto University, Kyoto, Japan
- Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
- Department of Orthopaedic Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- * E-mail:
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31
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Cheng F, Zhao J, Zhao Z. Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes. Brief Bioinform 2015; 17:642-56. [PMID: 26307061 DOI: 10.1093/bib/bbv068] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Indexed: 12/27/2022] Open
Abstract
Cancer is often driven by the accumulation of genetic alterations, including single nucleotide variants, small insertions or deletions, gene fusions, copy-number variations, and large chromosomal rearrangements. Recent advances in next-generation sequencing technologies have helped investigators generate massive amounts of cancer genomic data and catalog somatic mutations in both common and rare cancer types. So far, the somatic mutation landscapes and signatures of >10 major cancer types have been reported; however, pinpointing driver mutations and cancer genes from millions of available cancer somatic mutations remains a monumental challenge. To tackle this important task, many methods and computational tools have been developed during the past several years and, thus, a review of its advances is urgently needed. Here, we first summarize the main features of these methods and tools for whole-exome, whole-genome and whole-transcriptome sequencing data. Then, we discuss major challenges like tumor intra-heterogeneity, tumor sample saturation and functionality of synonymous mutations in cancer, all of which may result in false-positive discoveries. Finally, we highlight new directions in studying regulatory roles of noncoding somatic mutations and quantitatively measuring circulating tumor DNA in cancer. This review may help investigators find an appropriate tool for detecting potential driver or actionable mutations in rapidly emerging precision cancer medicine.
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Rovigatti U. Cancer modelling in the NGS era - Part I: Emerging technology and initial modelling. Crit Rev Oncol Hematol 2015; 96:274-307. [PMID: 26427785 DOI: 10.1016/j.critrevonc.2015.05.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 04/14/2015] [Accepted: 05/19/2015] [Indexed: 02/07/2023] Open
Abstract
It is today indisputable that great progresses have been made in our molecular understanding of cancer cells, but an effective implementation of such knowledge into dramatic cancer-cures is still belated and yet desperately needed. This review gives a snapshot at where we stand today in this search for cancer understanding and definitive treatments, how far we have progressed and what are the major obstacles we will have to overcome both technologically and for disease modelling. In the first part, promising 3rd/4th Generation Sequencing Technologies will be summarized (particularly IonTorrent and OxfordNanopore technologies). Cancer modelling will be then reviewed from its origin in XIX Century Germany to today's NGS applications for cancer understanding and therapeutic interventions. Developments after Molecular Biology revolution (1953) are discussed as successions of three phases. The first, PH1, labelled "Clonal Outgrowth" (from 1960s to mid 1980s) was characterized by discoveries in cytogenetics (Nowell, Rowley) and viral oncology (Dulbecco, Bishop, Varmus), which demonstrated clonality. Treatments were consequently dominated by a "cytotoxic eradication" strategy with chemotherapeutic agents. In PH2, (from the mid 1980s to our days) the description of cancer as "Gene Networks" led to targeted-gene-therapies (TGTs). TGTs are the focus of Section 3: in view of their apparent failing (Ephemeral Therapies), alternative strategies will be discussed in review part II (particularly cancer immunotherapy, CIT). Additional Pitfalls impinge on the concepts of tumour heterogeneity (inter/intra; ITH). The described pitfalls set the basis for a new phase, PH3, which is called "NGS Era" and will be also discussed with ten emerging cancer models in the Review 2nd part.
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Affiliation(s)
- Ugo Rovigatti
- University of Pisa Medical School, Oncology Department, via Roma 55, 56127 Pisa, Italy.
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Ping Y, Zhang H, Deng Y, Wang L, Zhao H, Pang L, Fan H, Xu C, Li F, Zhang Y, Gong Y, Xiao Y, Li X. IndividualizedPath: identifying genetic alterations contributing to the dysfunctional pathways in glioblastoma individuals. MOLECULAR BIOSYSTEMS 2015; 10:2031-42. [PMID: 24911613 DOI: 10.1039/c4mb00289j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Due to the extensive complexity and high genetic heterogeneity of genetic alterations in cancer, comprehensively depicting the molecular mechanisms of cancer remains difficult. Characterizing personalized pathogenesis in cancer individuals can help to reveal new details of the complex mechanisms. In this study, we proposed an integrative method called IndividualizedPath to identify genetic alterations and their downstream risk pathways from the perspective of individuals through combining the DNA copy number, gene expression data and topological structures of biological pathways. By applying the method to TCGA glioblastoma multiforme (GBM) samples, we identified 394 gene-pathway pairs in 252 GBM individuals. We found that genes with copy number alterations showed high heterogeneity across GBM individuals, whereas they affected relatively consistent biological pathways. A global landscape of gene-pathway pairs showed that EGFR linked with multiple cancer-related biological pathways confers the highest risk of GBM. GBM individuals with MET-pathway pairs showed significantly shorter survival times than those with only MET amplification. Importantly, we found that the same risk pathways were affected by different genes in distinct groups of GBM individuals with a significant pattern of mutual exclusivity. Similarly, GBM subtype analysis revealed some subtype-specific gene-pathway pairs. In addition, we found that some rare copy number alterations had a large effect on contribution to numerous cancer-related pathways. In summary, our method offers the possibility to identify personalized cancer mechanisms, which can be applied to other types of cancer through the web server (http://bioinfo.hrbmu.edu.cn/IndividualizedPath/).
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Affiliation(s)
- Yanyan Ping
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
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Ciccone M, Calin GA, Perrotti D. From the Biology of PP2A to the PADs for Therapy of Hematologic Malignancies. Front Oncol 2015; 5:21. [PMID: 25763353 PMCID: PMC4329809 DOI: 10.3389/fonc.2015.00021] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 01/16/2015] [Indexed: 11/13/2022] Open
Abstract
Over the past decades, an emerging role of phosphatases in the pathogenesis of hematologic malignancies and solid tumors has been established. The tumor-suppressor protein phosphatase 2A (PP2A) belongs to the serine-threonine phosphatases family and accounts for the majority of serine-threonine phosphatase activity in eukaryotic cells. Numerous studies have shown that inhibition of PP2A expression and/or function may contribute to leukemogenesis in several hematological malignancies. Likewise, overexpression or aberrant expression of physiologic PP2A inhibitory molecules (e.g., SET and its associated SETBP1 and CIP2A) may turn off PP2A function and participate to leukemic progression. The discovery of PP2A as tumor suppressor has prompted the evaluation of the safety and the efficacy of new compounds, which can restore PP2A activity in leukemic cells. Although further studies are needed to better understand how PP2A acts in the intricate phosphatases/kinases cancer network, the results reviewed herein strongly support the development on new PP2A-activating drugs and the immediate introduction of those available into clinical protocols for leukemia patients refractory or resistant to current available therapies.
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Affiliation(s)
- Maria Ciccone
- Department of Experimental Therapeutics, MD Anderson Cancer Center, The University of Texas , Houston, TX , USA
| | - George A Calin
- Department of Experimental Therapeutics, MD Anderson Cancer Center, The University of Texas , Houston, TX , USA
| | - Danilo Perrotti
- Department of Medicine, The Greenebaum Cancer Center, University of Maryland School of Medicine , Baltimore, MD , USA
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Sakoparnig T, Fried P, Beerenwinkel N. Identification of constrained cancer driver genes based on mutation timing. PLoS Comput Biol 2015; 11:e1004027. [PMID: 25569148 PMCID: PMC4287396 DOI: 10.1371/journal.pcbi.1004027] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 11/05/2014] [Indexed: 12/18/2022] Open
Abstract
Cancer drivers are genomic alterations that provide cells containing them with a selective advantage over their local competitors, whereas neutral passengers do not change the somatic fitness of cells. Cancer-driving mutations are usually discriminated from passenger mutations by their higher degree of recurrence in tumor samples. However, there is increasing evidence that many additional driver mutations may exist that occur at very low frequencies among tumors. This observation has prompted alternative methods for driver detection, including finding groups of mutually exclusive mutations and incorporating prior biological knowledge about gene function or network structure. Dependencies among drivers due to epistatic interactions can also result in low mutation frequencies, but this effect has been ignored in driver detection so far. Here, we present a new computational approach for identifying genomic alterations that occur at low frequencies because they depend on other events. Unlike passengers, these constrained mutations display punctuated patterns of occurrence in time. We test this driver-passenger discrimination approach based on mutation timing in extensive simulation studies, and we apply it to cross-sectional copy number alteration (CNA) data from ovarian cancer, CNA and single-nucleotide variant (SNV) data from breast tumors and SNV data from colorectal cancer. Among the top ranked predicted drivers, we find low-frequency genes that have already been shown to be involved in carcinogenesis, as well as many new candidate drivers. The mutation timing approach is orthogonal and complementary to existing driver prediction methods. It will help identifying from cancer genome data the alterations that drive tumor progression.
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Affiliation(s)
- Thomas Sakoparnig
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Patrick Fried
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
- * E-mail:
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Shah MA, Denton EL, Arrowsmith CH, Lupien M, Schapira M. A global assessment of cancer genomic alterations in epigenetic mechanisms. Epigenetics Chromatin 2014; 7:29. [PMID: 25484917 PMCID: PMC4258301 DOI: 10.1186/1756-8935-7-29] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 10/14/2014] [Indexed: 12/22/2022] Open
Abstract
Background The notion that epigenetic mechanisms may be central to cancer initiation and progression is supported by recent next-generation sequencing efforts revealing that genes involved in chromatin-mediated signaling are recurrently mutated in cancer patients. Results Here, we analyze mutational and transcriptional profiles from TCGA and the ICGC across a collection 441 chromatin factors and histones. Chromatin factors essential for rapid replication are frequently overexpressed, and those that maintain genome stability frequently mutated. We identify novel mutation hotspots such as K36M in histone H3.1, and uncover a general trend in which transcriptional profiles and somatic mutations in tumor samples favor increased transcriptionally repressive histone methylation, and defective chromatin remodeling. Conclusions This unbiased approach confirms previously published data, uncovers novel cancer-associated aberrations targeting epigenetic mechanisms, and justifies continued monitoring of chromatin-related alterations as a class, as more cancer types and distinct cancer stages are represented in cancer genomics data repositories. Electronic supplementary material The online version of this article (doi:10.1186/1756-8935-7-29) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Muhammad A Shah
- Structural Genomics Consortium, University of Toronto, MaRS Centre, South Tower, 101 College Street, Toronto, M5G 1L7 ON Canada
| | - Emily L Denton
- Structural Genomics Consortium, University of Toronto, MaRS Centre, South Tower, 101 College Street, Toronto, M5G 1L7 ON Canada ; Courant Institute, New York University, 12th floor, 715 Broadway, New York, 10003 USA
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, MaRS Centre, South Tower, 101 College Street, Toronto, M5G 1L7 ON Canada ; Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, M5G 2M9 ON Canada
| | - Mathieu Lupien
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, M5G 2M9 ON Canada
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, MaRS Centre, South Tower, 101 College Street, Toronto, M5G 1L7 ON Canada ; Department of Pharmacology and Toxicology, University of Toronto, 1 King's College Circle, Toronto, M5S 1A8 ON Canada
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Schadt EE, Buchanan S, Brennand KJ, Merchant KM. Evolving toward a human-cell based and multiscale approach to drug discovery for CNS disorders. Front Pharmacol 2014; 5:252. [PMID: 25520658 PMCID: PMC4251289 DOI: 10.3389/fphar.2014.00252] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 10/30/2014] [Indexed: 12/14/2022] Open
Abstract
A disruptive approach to therapeutic discovery and development is required in order to significantly improve the success rate of drug discovery for central nervous system (CNS) disorders. In this review, we first assess the key factors contributing to the frequent clinical failures for novel drugs. Second, we discuss cancer translational research paradigms that addressed key issues in drug discovery and development and have resulted in delivering drugs with significantly improved outcomes for patients. Finally, we discuss two emerging technologies that could improve the success rate of CNS therapies: human induced pluripotent stem cell (hiPSC)-based studies and multiscale biology models. Coincident with advances in cellular technologies that enable the generation of hiPSCs directly from patient blood or skin cells, together with methods to differentiate these hiPSC lines into specific neural cell types relevant to neurological disease, it is also now possible to combine data from large-scale forward genetics and post-mortem global epigenetic and expression studies in order to generate novel predictive models. The application of systems biology approaches to account for the multiscale nature of different data types, from genetic to molecular and cellular to clinical, can lead to new insights into human diseases that are emergent properties of biological networks, not the result of changes to single genes. Such studies have demonstrated the heterogeneity in etiological pathways and the need for studies on model systems that are patient-derived and thereby recapitulate neurological disease pathways with higher fidelity. In the context of two common and presumably representative neurological diseases, the neurodegenerative disease Alzheimer's Disease, and the psychiatric disorder schizophrenia, we propose the need for, and exemplify the impact of, a multiscale biology approach that can integrate panomic, clinical, imaging, and literature data in order to construct predictive disease network models that can (i) elucidate subtypes of syndromic diseases, (ii) provide insights into disease networks and targets and (iii) facilitate a novel drug screening strategy using patient-derived hiPSCs to discover novel therapeutics for CNS disorders.
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Affiliation(s)
- Eric E Schadt
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai New York, NY, USA ; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai New York, NY, USA
| | - Sean Buchanan
- Lilly Research Laboratories, Eli Lilly and Company Indianapolis, IN, USA
| | - Kristen J Brennand
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai New York, NY, USA
| | - Kalpana M Merchant
- Lilly Research Laboratories, Eli Lilly and Company Indianapolis, IN, USA
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Andre F, Mardis E, Salm M, Soria JC, Siu LL, Swanton C. Prioritizing targets for precision cancer medicine. Ann Oncol 2014; 25:2295-2303. [PMID: 25344359 DOI: 10.1093/annonc/mdu478] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The implementation of cancer genomic testing into the clinical setting has brought major opportunities. However, as our understanding of cancer initiation, maintenance and progression improves through detailed cancer genomic studies, the challenges associated with driver identification and target classification in the clinical setting become clearer. Here, we review recent insights into cancer genomic testing in the clinical setting, and suggest a target classification approach that considers the levels of evidence supporting the prioritization of tumour drivers for therapeutic targeting in light of complex cancer clonal and sub-clonal structures and clinical successes and failures in the field. We argue that such classification approaches, together with transparent reporting of both positive and negative clinical data and continued research to identify the sub-clonal dynamics of driver events during the disease course, will facilitate inter-trial comparisons, optimize patient informed consent and provide a critically balanced evaluation of genomic testing in clinical practice.
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Affiliation(s)
- F Andre
- Department of Medical Oncology, INSERM U981, Gustave Roussy Cancer Campus, Villejuif, France
| | - E Mardis
- The Genome Institute, Washington University School of Medicine, St Louis, USA
| | - M Salm
- Cancer Research UK London Research Institute, London, UK
| | - J-C Soria
- DITEP, Gustave Roussy Cancer Campus, Villejuif, France
| | - L L Siu
- Princess Margaret Cancer Centre, Toronto, Canada
| | - C Swanton
- Cancer Research UK London Research Institute, London, UK; UCL Hospitals and Cancer Institute, Huntley Street, London, UK.
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39
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Li T, Wang G. Computer-aided targeting of the PI3K/Akt/mTOR pathway: toxicity reduction and therapeutic opportunities. Int J Mol Sci 2014; 15:18856-91. [PMID: 25334061 PMCID: PMC4227251 DOI: 10.3390/ijms151018856] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 09/21/2014] [Accepted: 10/08/2014] [Indexed: 12/14/2022] Open
Abstract
The PI3K/Akt/mTOR pathway plays an essential role in a wide range of biological functions, including metabolism, macromolecular synthesis, cell growth, proliferation and survival. Its versatility, however, makes it a conspicuous target of many pathogens; and the consequential deregulations of this pathway often lead to complications, such as tumorigenesis, type 2 diabetes and cardiovascular diseases. Molecular targeted therapy, aimed at modulating the deregulated pathway, holds great promise for controlling these diseases, though side effects may be inevitable, given the ubiquity of the pathway in cell functions. Here, we review a variety of factors found to modulate the PI3K/Akt/mTOR pathway, including gene mutations, certain metabolites, inflammatory factors, chemical toxicants, drugs found to rectify the pathway, as well as viruses that hijack the pathway for their own synthetic purposes. Furthermore, this evidence of PI3K/Akt/mTOR pathway alteration and related pathogenesis has inspired the exploration of computer-aided targeting of this pathway to optimize therapeutic strategies. Herein, we discuss several possible options, using computer-aided targeting, to reduce the toxicity of molecularly-targeted therapy, including mathematical modeling, to reveal system-level control mechanisms and to confer a low-dosage combination therapy, the potential of PP2A as a therapeutic target, the formulation of parameters to identify patients who would most benefit from specific targeted therapies and molecular dynamics simulations and docking studies to discover drugs that are isoform specific or mutation selective so as to avoid undesired broad inhibitions. We hope this review will stimulate novel ideas for pharmaceutical discovery and deepen our understanding of curability and toxicity by targeting the PI3K/Akt/mTOR pathway.
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Affiliation(s)
- Tan Li
- Department of Biology, South University of Science and Technology of China, 1088 Xueyuan Rd., Shenzhen 518055, China.
| | - Guanyu Wang
- Department of Biology, South University of Science and Technology of China, 1088 Xueyuan Rd., Shenzhen 518055, China.
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40
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Hansen AR, Bedard PL. Clinical application of high-throughput genomic technologies for treatment selection in breast cancer. Breast Cancer Res 2014; 15:R97. [PMID: 24135425 PMCID: PMC3979162 DOI: 10.1186/bcr3558] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Large-scale collaborative initiatives using next-generation DNA sequencing and other high-throughput technologies have begun to characterize the genomic landscape of breast cancer. These landmark studies have identified infrequent driver mutations that are potential targets for therapeutic intervention with approved or investigational drug treatments, among other important discoveries. Recently, many institutions have launched molecular screening programs that apply high-throughput genomic technologies to patients with advanced solid malignancies, including breast cancer, to inform clinical decision-making. This article provides an overview of the recent molecular insights in breast cancer, including potentially actionable somatic alterations, the technological platforms currently available in a clinical diagnostics setting to detect these alterations, and ongoing institutional or regional molecular screening programs in advanced breast cancer.
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41
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Cohen RL, Settleman J. From cancer genomics to precision oncology--tissue's still an issue. Cell 2014; 157:1509-14. [PMID: 24949964 DOI: 10.1016/j.cell.2014.05.027] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 05/21/2014] [Indexed: 10/25/2022]
Abstract
Rapidly evolving genome technology has enabled extensive molecular analysis of limited tumor biopsy material, thereby facilitating the broader implementation of personalized cancer medicine. However, genomics-based patient stratification across diverse tumor types is unlikely to supplant tissue-of-origin considerations in addressing clinical needs, including the development and application of novel "rationally targeted" cancer therapies.
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Affiliation(s)
- Robert L Cohen
- Calico Life Sciences, Suite 1200, 601 Gateway Boulevard, South San Francisco, CA 94080, USA
| | - Jeff Settleman
- Discovery Oncology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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42
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Affiliation(s)
- Rizwan Haq
- Department of Dermatology, Massachusetts General Hospital
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43
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Nicolaides NC, O'Shannessy DJ, Albone E, Grasso L. Co-development of diagnostic vectors to support targeted therapies and theranostics: essential tools in personalized cancer therapy. Front Oncol 2014; 4:141. [PMID: 24982846 PMCID: PMC4056284 DOI: 10.3389/fonc.2014.00141] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 05/24/2014] [Indexed: 12/14/2022] Open
Abstract
Novel technologies are being developed to improve patient therapy through the identification of targets and surrogate molecular signatures that can help direct appropriate treatment regimens for efficacy and drug safety. This is particularly the case in oncology whereby patient tumor and biofluids are routinely isolated and analyzed for genetic, immunohistochemical, and/or soluble markers to determine if a predictive biomarker signature (i.e., mutated gene product, differentially expressed protein, altered cell surface antigen, etc.) exists as a means for selecting optimal treatment. These biomarkers may be drug-specific targets and/or differentially expressed nucleic acids, proteins, or cell lineage profiles that can directly affect the patient’s disease tissue or immune response to a therapeutic regimen. Improvements in diagnostics that can prescreen predictive response biomarker profiles will continue to optimize the ability to enhance patient therapy via molecularly defined disease-specific treatment. Conversely, patients lacking predictive response biomarkers will no longer needlessly be exposed to drugs that are unlikely to provide clinical benefit, thereby enabling patients to pursue other therapeutic options and lowering overall healthcare costs by avoiding futile treatment. While patient molecular profiling offers a powerful tool to direct treatment options, the difficulty in identifying disease-specific targets or predictive biomarker signatures that stratify a significant fraction within a disease indication remains challenging. A goal for drug developers is to identify and implement new strategies that can rapidly enable the development of beneficial disease-specific therapies for broad patient-specific targeting without the need of tedious predictive biomarker discovery and validation efforts, currently a bottleneck for development timelines. Successful strategies may gain an advantage by employing repurposed, less-expensive existing agents while potentially improving the therapeutic activity of novel, target-specific therapies that may otherwise have off-target toxicities or less efficacy in cells exhibiting certain pathways. Here, we discuss the use of co-developing diagnostic-targeting vectors to identify patients whose malignant tissue can specifically uptake a targeted anti-cancer drug vector prior to treatment. Using this system, a patient can be predetermined in real-time as to whether or not their tumor(s) can specifically uptake a drug-linked diagnostic vector, thus inferring the uptake of a similar vector linked to an anti-cancer agent. If tumor-specific uptake is observed, then the patient may be suitable for drug-linked vector therapy and have a higher likelihood of clinical benefit while patients with no tumor uptake should consider other therapeutic options. This approach offers complementary opportunities to rapidly develop broad tumor-specific agents for use in personalized medicine.
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Affiliation(s)
- Nicholas C Nicolaides
- Department of Translational Medicine and Diagnostics, Morphotek Inc. , Exton, PA , USA
| | - Daniel J O'Shannessy
- Department of Translational Medicine and Diagnostics, Morphotek Inc. , Exton, PA , USA
| | - Earl Albone
- Department of Translational Medicine and Diagnostics, Morphotek Inc. , Exton, PA , USA
| | - Luigi Grasso
- Department of Translational Medicine and Diagnostics, Morphotek Inc. , Exton, PA , USA
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de Souza JES, Fonseca AF, Valieris R, Carraro DM, Wang JYJ, Kolodner RD, de Souza SJ. S-score: a scoring system for the identification and prioritization of predicted cancer genes. PLoS One 2014; 9:e94147. [PMID: 24710071 PMCID: PMC3978018 DOI: 10.1371/journal.pone.0094147] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 03/13/2014] [Indexed: 12/31/2022] Open
Abstract
A new method, which allows for the identification and prioritization of predicted cancer genes for future analysis, is presented. This method generates a gene-specific score called the “S-Score” by incorporating data from different types of analysis including mutation screening, methylation status, copy-number variation and expression profiling. The method was applied to the data from The Cancer Genome Atlas and allowed the identification of known and potentially new oncogenes and tumor suppressors associated with different clinical features including shortest term of survival in ovarian cancer patients and hormonal subtypes in breast cancer patients. Furthermore, for the first time a genome-wide search for genes that behave as oncogenes and tumor suppressors in different tumor types was performed. We envisage that the S-score can be used as a standard method for the identification and prioritization of cancer genes for follow-up studies.
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Affiliation(s)
- Jorge E. S. de Souza
- Institute of Bioinformatics and Biotechnology, São Paulo, Brazil
- Center for Cell Therapy and Regional Blood Center, Department of Clinical Medicine, Faculty of Medicine, University of São Paulo, Ribeirão Preto, Brazil
- International Research Center, CIPE/AC Camargo Cancer Center, São Paulo, Brazil
| | - André F. Fonseca
- Institute of Bioinformatics and Biotechnology, São Paulo, Brazil
- Brain Institute, UFRN, Natal, Brazil
| | - Renan Valieris
- Institute of Bioinformatics and Biotechnology, São Paulo, Brazil
- International Research Center, CIPE/AC Camargo Cancer Center, São Paulo, Brazil
| | - Dirce M. Carraro
- International Research Center, CIPE/AC Camargo Cancer Center, São Paulo, Brazil
| | - Jean Y. J. Wang
- Moores-UCSD Cancer Center and Department of Medicine, University of California San Diego School of Medicine, San Diego, California, United States of America
| | - Richard D. Kolodner
- Moores-UCSD Cancer Center and Department of Medicine, University of California San Diego School of Medicine, San Diego, California, United States of America
- Ludwig Institute for Cancer Research, San Diego Branch, Department of Medicine and Cellular and Molecular Medicine, Moores-UCSD Cancer Center and Institute of Genomic Medicine, University of California San Diego School of Medicine, San Diego, California, United States of America
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Dotto GP. Multifocal epithelial tumors and field cancerization: stroma as a primary determinant. J Clin Invest 2014; 124:1446-53. [PMID: 24691479 DOI: 10.1172/jci72589] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
It is increasingly evident that cancer results from altered organ homeostasis rather than from deregulated control of single cells or groups of cells. This applies especially to epithelial cancer, the most common form of human solid tumors and a major cause of cancer lethality. In the vast majority of cases, in situ epithelial cancer lesions do not progress into malignancy, even if they harbor many of the genetic changes found in invasive and metastatic tumors. While changes in tumor stroma are frequently viewed as secondary to changes in the epithelium, recent evidence indicates that they can play a primary role in both cancer progression and initiation. These processes may explain the phenomenon of field cancerization, i.e., the occurrence of multifocal and recurrent epithelial tumors that are preceded by and associated with widespread changes of surrounding tissue or organ "fields."
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Chang DK, Grimmond SM, Biankin AV. Pancreatic cancer genomics. Curr Opin Genet Dev 2014; 24:74-81. [PMID: 24480245 DOI: 10.1016/j.gde.2013.12.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 12/03/2013] [Indexed: 02/07/2023]
Abstract
Pancreatic cancer is one of the most lethal malignancies. The overall median survival even with treatment is only 6-9 months, with almost 90% succumbing to the disease within a year of diagnosis. It is characterised by an intense desmoplastic stroma that may contribute to therapeutic resistance, and poses significant challenges for genomic sequencing studies. It is recalcitrant to almost all therapies and consequently remains the fourth leading cause of cancer death in Western societies. Genomic studies are unveiling a vast heterogeneity of mutated genes, and this diversity may explain why conventional clinical trial designs have mostly failed to demonstrate efficacy in unselected patients. Those that are available offer only marginal benefits overall, but are associated with clinically significant responses in as yet undefined subgroups. This chapter describes our current understanding of the genomics of pancreatic cancer and the potential impact of these findings on our approaches to treatment.
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Affiliation(s)
- David K Chang
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, Scotland G61 1BD, United Kingdom; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, Scotland G4 0SF, United Kingdom; The Kinghorn Cancer Centre, Cancer Division, Garvan Institute of Medical Research, 370 Victoria Street, Darlinghurst, Sydney, NSW 2010, Australia; St Vincent's Clinical School, Faculty of Medicine, University of NSW, Australia; Department of Surgery, Bankstown Hospital, Eldridge Road, Bankstown, Sydney, NSW 2200, Australia; South Western Sydney Clinical School, Faculty of Medicine, University of NSW, Liverpool, NSW 2170, Australia
| | - Sean M Grimmond
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, Scotland G61 1BD, United Kingdom; Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD, Australia.
| | - Andrew V Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, Scotland G61 1BD, United Kingdom; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, Scotland G4 0SF, United Kingdom; The Kinghorn Cancer Centre, Cancer Division, Garvan Institute of Medical Research, 370 Victoria Street, Darlinghurst, Sydney, NSW 2010, Australia; St Vincent's Clinical School, Faculty of Medicine, University of NSW, Australia; Department of Surgery, Bankstown Hospital, Eldridge Road, Bankstown, Sydney, NSW 2200, Australia; South Western Sydney Clinical School, Faculty of Medicine, University of NSW, Liverpool, NSW 2170, Australia.
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Sedgewick AJ, Benz SC, Rabizadeh S, Soon-Shiong P, Vaske CJ. Learning subgroup-specific regulatory interactions and regulator independence with PARADIGM. Bioinformatics 2013; 29:i62-70. [PMID: 23813010 PMCID: PMC3694636 DOI: 10.1093/bioinformatics/btt229] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
UNLABELLED High-dimensional '-omics' profiling provides a detailed molecular view of individual cancers; however, understanding the mechanisms by which tumors evade cellular defenses requires deep knowledge of the underlying cellular pathways within each cancer sample. We extended the PARADIGM algorithm (Vaske et al., 2010, Bioinformatics, 26, i237-i245), a pathway analysis method for combining multiple '-omics' data types, to learn the strength and direction of 9139 gene and protein interactions curated from the literature. Using genomic and mRNA expression data from 1936 samples in The Cancer Genome Atlas (TCGA) cohort, we learned interactions that provided support for and relative strength of 7138 (78%) of the curated links. Gene set enrichment found that genes involved in the strongest interactions were significantly enriched for transcriptional regulation, apoptosis, cell cycle regulation and response to tumor cells. Within the TCGA breast cancer cohort, we assessed different interaction strengths between breast cancer subtypes, and found interactions associated with the MYC pathway and the ER alpha network to be among the most differential between basal and luminal A subtypes. PARADIGM with the Naive Bayesian assumption produced gene activity predictions that, when clustered, found groups of patients with better separation in survival than both the original version of PARADIGM and a version without the assumption. We found that this Naive Bayes assumption was valid for the vast majority of co-regulators, indicating that most co-regulators act independently on their shared target. AVAILABILITY http://paradigm.five3genomics.com. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Andrew J Sedgewick
- Joint Carnegie Mellon - University of Pittsburgh Ph.D Program in Computational Biology, Pittsburgh, PA 15260, USA
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Abstract
SUMMARY Cancer genomics data produced by next-generation sequencing support the notion that epigenetic mechanisms play a central role in cancer. We have previously developed Chromohub, an open access online interface where users can map chemical, structural and biological data from public repositories on phylogenetic trees of protein families involved in chromatin mediated-signaling. Here, we describe a cancer genomics interface that was recently added to Chromohub; the frequency of mutation, amplification and change in expression of chromatin factors across large cohorts of cancer patients is regularly extracted from The Cancer Genome Atlas and the International Cancer Genome Consortium and can now be mapped on phylogenetic trees of epigenetic protein families. Explorators of chromatin signaling can now easily navigate the cancer genomics landscape of writers, readers and erasers of histone marks, chromatin remodeling complexes, histones and their chaperones. AVAILABILITY AND IMPLEMENTATION http://www.thesgc.org/chromohub/.
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Affiliation(s)
- Muhammad A Shah
- Structural Genomics Consortium, and Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5G 1L7, Canada
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Li KC, Marcovici P, Phelps A, Potter C, Tillack A, Tomich J, Tridandapani S. Digitization of medicine: how radiology can take advantage of the digital revolution. Acad Radiol 2013; 20:1479-94. [PMID: 24200474 DOI: 10.1016/j.acra.2013.09.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Revised: 09/07/2013] [Accepted: 09/08/2013] [Indexed: 01/10/2023]
Abstract
In the era of medical cost containment, radiologists must continually maintain their actual and perceived value to patients, payers, and referring providers. Exploitation of current and future digital technologies may be the key to defining and promoting radiology's "brand" and assure our continued relevance in providing predictive, preventive, personalized, and participatory medicine. The Association of University of Radiologists Radiology Research Alliance Digitization of Medicine Task Force was formed to explore the opportunities and challenges of the digitization of medicine that are relevant to radiologists, which include the reporting paradigm, computational biology, and imaging informatics. In addition to discussing these opportunities and challenges, we consider how change occurs in medicine, and how change may be effected in medical imaging community. This review article is a summary of the research of the task force and hopefully can be used as a stimulus for further discussions and development of action plans by radiology leaders.
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Affiliation(s)
- King C Li
- Department of Radiology, Wake Forest School of Medicine, One Medical Center Boulevard, Winston-Salem, NC 27157.
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Dotto P. Field cancerization and dormant epithelial cancer: Stromal mesenchyme takes the stage. Ann Dermatol Venereol 2013. [DOI: 10.1016/j.annder.2013.09.652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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