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Worley J, Noh H, You D, Turunen MM, Ding H, Paull E, Griffin AT, Grunn A, Zhang M, Guillan K, Bush EC, Brosius SJ, Hibshoosh H, Mundi PS, Sims P, Dalerba P, Dela Cruz FS, Kung AL, Califano A. Identification and Pharmacological Targeting of Treatment-Resistant, Stem-like Breast Cancer Cells for Combination Therapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.08.562798. [PMID: 38798673 PMCID: PMC11118419 DOI: 10.1101/2023.11.08.562798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Tumors frequently harbor isogenic yet epigenetically distinct subpopulations of multi-potent cells with high tumor-initiating potential-often called Cancer Stem-Like Cells (CSLCs). These can display preferential resistance to standard-of-care chemotherapy. Single-cell analyses can help elucidate Master Regulator (MR) proteins responsible for governing the transcriptional state of these cells, thus revealing complementary dependencies that may be leveraged via combination therapy. Interrogation of single-cell RNA sequencing profiles from seven metastatic breast cancer patients, using perturbational profiles of clinically relevant drugs, identified drugs predicted to invert the activity of MR proteins governing the transcriptional state of chemoresistant CSLCs, which were then validated by CROP-seq assays. The top drug, the anthelmintic albendazole, depleted this subpopulation in vivo without noticeable cytotoxicity. Moreover, sequential cycles of albendazole and paclitaxel-a commonly used chemotherapeutic -displayed significant synergy in a patient-derived xenograft (PDX) from a TNBC patient, suggesting that network-based approaches can help develop mechanism-based combinatorial therapies targeting complementary subpopulations.
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Affiliation(s)
- Jeremy Worley
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
- J.P. Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY USA 10032
| | - Heeju Noh
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
| | - Daoqi You
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Mikko M Turunen
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
| | - Hongxu Ding
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
- Department of Pharmacy Practice & Science, College of Pharmacy, University of Arizona, Tucson, Arizona, USA 85721
| | - Evan Paull
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
| | - Aaron T Griffin
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
| | - Adina Grunn
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
| | - Mingxuan Zhang
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
| | - Kristina Guillan
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Erin C Bush
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
| | - Samantha J Brosius
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Hanina Hibshoosh
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, USA 10032
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, USA 10032
| | - Prabhjot S Mundi
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, USA 10032
| | - Peter Sims
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
| | - Piero Dalerba
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, USA 10032
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, USA 10032
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, USA 10032
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
| | - Filemon S Dela Cruz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Andrew L Kung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Andrea Califano
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, USA 10032
- Department of Biochemistry & Molecular Biophysics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
- Department of Biomedical Informatics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
- J.P. Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY USA 10032
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2
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Singh P, Lanman NA, Kendall HLR, Wilson L, Long R, Franco OE, Buskin A, Miles CG, Hayward SW, Heer R, Robson CN. Human prostate organoid generation and the identification of prostate development drivers using inductive rodent tissues. Development 2023; 150:dev201328. [PMID: 37376888 PMCID: PMC10357030 DOI: 10.1242/dev.201328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 06/20/2023] [Indexed: 06/29/2023]
Abstract
The reactivation of developmental genes and pathways during adulthood may contribute to pathogenesis of diseases such as prostate cancer. Analysis of the mechanistic links between development and disease could be exploited to identify signalling pathways leading to disease in the prostate. However, the mechanisms underpinning prostate development require further characterisation to interrogate fully the link between development and disease. Previously, our group developed methods to produce prostate organoids using induced pluripotent stem cells (iPSCs). Here, we show that human iPSCs can be differentiated into prostate organoids using neonatal rat seminal vesicle mesenchyme in vitro. The organoids can be used to study prostate development or modified to study prostate cancer. We also elucidated molecular drivers of prostate induction through RNA-sequencing analyses of the rat urogenital sinus and neonatal seminal vesicles. We identified candidate drivers of prostate development evident in the inductive mesenchyme and epithelium involved with prostate specification. Our top candidates included Spx, Trib3, Snai1, Snai2, Nrg2 and Lrp4. This work lays the foundations for further interrogation of the reactivation of developmental genes in adulthood, leading to prostate disease.
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Affiliation(s)
- Parmveer Singh
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne, NE2 4AD, UK
| | - Nadia A. Lanman
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907, USA
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Hannah L. R. Kendall
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne, NE2 4AD, UK
| | - Laura Wilson
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne, NE2 4AD, UK
| | - Ryan Long
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne, NE2 4AD, UK
| | - Omar E. Franco
- Department of Surgery, NorthShore University HealthSystem, Evanston, IL 60201, USA
- University of Chicago Pritzker School of Medicine, Chicago, IL 60637, USA
| | - Adriana Buskin
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne, NE2 4AD, UK
| | - Colin G. Miles
- Translational and Clinical Research Institute, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK
| | - Simon W. Hayward
- Department of Surgery, NorthShore University HealthSystem, Evanston, IL 60201, USA
- University of Chicago Pritzker School of Medicine, Chicago, IL 60637, USA
| | - Rakesh Heer
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne, NE2 4AD, UK
- Department of Urology, Freeman Hospital, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE7 7DN, UK
| | - Craig N. Robson
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne, NE2 4AD, UK
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Laise P, Bosker G, Califano A, Alvarez MJ. A Patient-to-Model-to-Patient (PMP) Cancer Drug Discovery Protocol for Identifying and Validating Therapeutic Agents Targeting Tumor Regulatory Architecture. Curr Protoc 2022; 2:e544. [PMID: 36083100 DOI: 10.1002/cpz1.544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The current Achilles heel of cancer drug discovery is the inability to forge precise and predictive connections among mechanistic drivers of the cancer cell state, therapeutically significant molecular targets, effective drugs, and responsive patient subgroups. Although advances in molecular biology have helped identify molecular markers and stratify patients into molecular subtypes, these associational strategies typically fail to provide a mechanistic rationale to identify cancer vulnerabilities. Recently, integrative systems biology methodologies have been used to reverse engineer cellular networks and identify master regulators (MRs), proteins whose activity is both necessary and sufficient to implement phenotypic states under physiological and pathological conditions, which are organized into highly interconnected regulatory modules called tumor checkpoints. Because of their functional relevance, MRs represent ideal pharmacological targets and biomarkers. Here, we present a six-step patient-to-model-to-patient protocol that employs computational and experimental methodologies to reconstruct and interrogate the regulatory logic of human cancer cells for identifying and therapeutically targeting the tumor checkpoint with novel as well as existing pharmacological agents. This protocol systematically identifies, from specific patient tumor samples, the MRs that comprise the tumor checkpoint. Then, it identifies in vitro and in vivo models that, by recapitulating the patient's tumor checkpoint, constitute the appropriate cell lines and xenografts to further elucidate the tissue context-specific drug mechanism of action (MOA) and permit precise, biomarker-based preclinical validations of drug efficacy. The combination of determination of a drug's context-specific MOA and precise identification of patients' tumor checkpoints provides a personalized, mechanism-based biomarker to enrich prospective clinical trials with patients likely to respond. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC.
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Affiliation(s)
- Pasquale Laise
- DarwinHealth, New York, New York
- Department of Systems Biology, Columbia University Irving Medical Center, New York, New York
| | | | - Andrea Califano
- Department of Systems Biology, Columbia University Irving Medical Center, New York, New York
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, New York
- Department of Medicine, Columbia University Irving Medical Center, New York, New York
- Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, New York
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, New York
| | - Mariano J Alvarez
- DarwinHealth, New York, New York
- Department of Systems Biology, Columbia University Irving Medical Center, New York, New York
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4
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Pletcher A, Shibata M. Prostate organogenesis. Development 2022; 149:275758. [DOI: 10.1242/dev.200394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
ABSTRACT
Prostate organogenesis begins during embryonic development and continues through puberty when the prostate becomes an important exocrine gland of the male reproductive system. The specification and growth of the prostate is regulated by androgens and is largely a result of cell-cell communication between the epithelium and mesenchyme. The fields of developmental and cancer biology have long been interested in prostate organogenesis because of its relevance for understanding prostate diseases, and research has expanded in recent years with the advent of novel technologies, including genetic-lineage tracing, single-cell RNA sequencing and organoid culture methods, that have provided important insights into androgen regulation, epithelial cell origins and cellular heterogeneity. We discuss these findings, putting them into context with what is currently known about prostate organogenesis.
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Affiliation(s)
- Andrew Pletcher
- The George Washington University School of Medicine and Health Sciences 1 Department of Anatomy and Cell Biology , , Washington, DC 20052, USA
- The George Washington University Cancer Center, The George Washington University School of Medicine and Health Sciences 2 , Washington, DC 20052, USA
| | - Maho Shibata
- The George Washington University School of Medicine and Health Sciences 1 Department of Anatomy and Cell Biology , , Washington, DC 20052, USA
- The George Washington University Cancer Center, The George Washington University School of Medicine and Health Sciences 2 , Washington, DC 20052, USA
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5
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Obradovic A, Graves D, Korrer M, Wang Y, Roy S, Naveed A, Xu Y, Luginbuhl A, Curry J, Gibson M, Idrees K, Hurley P, Jiang P, Liu XS, Uppaluri R, Drake CG, Califano A, Kim YJ. Immunostimulatory cancer-associated fibroblast subpopulations can predict immunotherapy response in head and neck cancer. Clin Cancer Res 2022; 28:2094-2109. [PMID: 35262677 DOI: 10.1158/1078-0432.ccr-21-3570] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/15/2021] [Accepted: 03/07/2022] [Indexed: 11/16/2022]
Abstract
PURPOSE Cancer-associated fibroblasts (CAF) have been implicated as potential mediators of checkpoint immunotherapy response. However, the extensive heterogeneity of these cells has precluded rigorous understanding of their immunoregulatory role in the tumor microenvironment. EXPERIMENTAL DESIGN We performed high dimensional single-cell RNA sequencing (scRNA-Seq) on four patient tumors pre- and post-treatment from a neoadjuvant trial of advanced-stage head and neck squamous cell carcinoma (HNSCC) patients that were treated with the aPD-1 therapy, nivolumab. The head and neck CAF (HNCAF) protein activity profiles, derived from this cohort of paired scRNA-Seq, were used to perform protein activity enrichment analysis on the 28-patient parental cohort of clinically annotated bulk transcriptomic profiles. Ex vivo coculture assays were used to test functional relevance of HNCAF subtypes. RESULTS Fourteen distinct cell types were identified with the fibroblast population showing significant changes in abundance following nivolumab treatment. Among the fibroblast subtypes, HNCAF-0/3 emerged as predictive of nivolumab response, while HNCAF-1 was associated with immunosuppression. Functionally, HNCAF-0/3 were found to reduce TGFβ-dependent PD-1+TIM-3+ exhaustion of CD8 T cells, increase CD103+NKG2A+ resident memory phenotypes, and enhance the overall cytolytic profile of T cells. CONCLUSIONS Our findings demonstrate the functional importance of distinct HNCAF subsets in modulating the immunoregulatory milieu of human HNSCC. Additionally, we have identified clinically actionable HNCAF subtypes that can be used as a biomarker of response and resistance in future clinical trials.
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Affiliation(s)
- Aleksandar Obradovic
- Columbia Center for Translational Immunology (CCTI), Columbia University Irving Medical Center (CUMC), New York, New York
- Department of Systems Biology, HICC, New York, New York
| | - Diana Graves
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, Tennessee
| | - Michael Korrer
- Department of Otolaryngology-Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Yu Wang
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Sohini Roy
- Department of Otolaryngology-Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Abdullah Naveed
- Department of Otolaryngology-Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Yaomin Xu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Adam Luginbuhl
- Department of Otolaryngology-Head and Neck Surgery, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Joseph Curry
- Department of Otolaryngology-Head and Neck Surgery, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Michael Gibson
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Kamran Idrees
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Paula Hurley
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Peng Jiang
- Center for Cancer Research, NCI, Bethesda, Maryland
| | - X Shirley Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ravindra Uppaluri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Surgery, Brigham and Women's Hospital, Boston, Massachusetts
| | - Charles G Drake
- Columbia Center for Translational Immunology (CCTI), Columbia University Irving Medical Center (CUMC), New York, New York
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York
- Department of Medicine, Columbia University College of Physicians and Surgeons, New York, New York
| | - Andrea Califano
- Department of Systems Biology, HICC, New York, New York
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York
- Department of Medicine, Columbia University College of Physicians and Surgeons, New York, New York
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York
- Department of Biomedical Informatics, Columbia University, New York, New York
- J.P. Sulzberger Columbia Genome Center, New York, New York
| | - Young J Kim
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, Tennessee
- Department of Otolaryngology-Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, Tennessee
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Regeneron Pharmaceutical, Tarrytown, New York
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6
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Lorenzoni M, De Felice D, Beccaceci G, Di Donato G, Foletto V, Genovesi S, Bertossi A, Cambuli F, Lorenzin F, Savino A, Avalle L, Cimadamore A, Montironi R, Weber V, Carbone FG, Barbareschi M, Demichelis F, Romanel A, Poli V, Del Sal G, Julio MKD, Gaspari M, Alaimo A, Lunardi A. ETS-related gene (ERG) undermines genome stability in mouse prostate progenitors via Gsk3β dependent Nkx3.1 degradation. Cancer Lett 2022; 534:215612. [PMID: 35259458 PMCID: PMC8968219 DOI: 10.1016/j.canlet.2022.215612] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 02/23/2022] [Accepted: 02/25/2022] [Indexed: 12/13/2022]
Abstract
21q22.2–3 deletion is the most common copy number alteration in prostate cancer (PCa). The genomic rearrangement results in the androgen-dependent de novo expression of ETS-related gene (ERG) in prostate cancer cells, a condition promoting tumor progression to advanced stages of the disease. Interestingly, ERG expression characterizes 5–30% of tumor precursor lesions – High Grade Prostatic Intraepithelial Neoplasia (HGPIN) - where its role remains unclear. Here, by combining organoids technology with Click-chemistry coupled Mass Spectrometry, we demonstrate a prominent role of ERG in remodeling the protein secretome of prostate progenitors. Functionally, by lowering autocrine Wnt-4 signaling, ERG represses canonical Wnt pathway in prostate progenitors, and, in turn, promotes the accumulation of DNA double strand breaks via Gsk3β-dependent degradation of the tumor suppressor Nkx3.1. On the other hand, by shaping extracellular paracrine signals, ERG strengthens the pro-oxidative transcriptional signature of inflammatory macrophages, which we demonstrate to infiltrate pre-malignant ERG positive prostate lesions. These findings highlight previously unrecognized functions of ERG in undermining adult prostate progenitor niche through cell autonomous and non-autonomous mechanisms. Overall, by supporting the survival and proliferation of prostate progenitors in the absence of growth stimuli and promoting the accumulation of DNA damage through destabilization of Nkx3.1, ERG could orchestrate the prelude to neoplastic transformation. Expression of ERGM40 in mouse prostate organoids promotes their survival and growth in the absence of Egf. ERGM40 alters the extracellular signaling network of mouse prostate organoids. Canonical Wnt pathway is substantially reduced in ERG + prostate organoids due to decreased autocrine signaling of Wnt4. Gsk3b promotes Nkx3.1 proteolysis and, in turn, accumulation of double strand breaks in ERG + prostate organoids. Paracrine signaling of ERG + prostate organoids modulates Arginase 1 expression in M1-polarized macrophages.
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Affiliation(s)
- Marco Lorenzoni
- Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, Trento, Italy
| | - Dario De Felice
- Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, Trento, Italy
| | - Giulia Beccaceci
- Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, Trento, Italy
| | - Giorgia Di Donato
- Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, Trento, Italy
| | - Veronica Foletto
- Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, Trento, Italy
| | - Sacha Genovesi
- Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, Trento, Italy
| | - Arianna Bertossi
- Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, Trento, Italy
| | - Francesco Cambuli
- Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, Trento, Italy
| | - Francesca Lorenzin
- Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, Trento, Italy
| | - Aurora Savino
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Lidia Avalle
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Alessia Cimadamore
- Pathological Anatomy, School of Medicine, United Hospitals, Polytechnic University of the Marche Region, Ancona, Italy
| | - Rodolfo Montironi
- Molecular Medicine and Cell Therapy Foundation, Polytechnic University of the Marche Region, Via Tronto, 10, Ancona, Italy
| | - Veronica Weber
- Unit of Surgical Pathology, Santa Chiara Hospital, Trento, Italy
| | | | | | - Francesca Demichelis
- Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, Trento, Italy
| | - Alessandro Romanel
- Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, Trento, Italy
| | - Valeria Poli
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Giannino Del Sal
- University of Trieste Department Life Sciences, ICGEB-Area Science Park Trieste, IFOM, Milan, Italy
| | - Marianna Kruithof-de Julio
- Urology Research Laboratory, Department for BioMedical Research DBMR, University of Bern, Bern, Switzerland; Translational Organoid Resource CORE, Department for BioMedical Research, University of Bern, Bern, Switzerland; Bern Center for Precision Medicine, Inselspital, University Hospital of Bern, Bern, Switzerland; Department of Urology, Inselspital, University Hospital of Bern, Bern, Switzerland
| | - Marco Gaspari
- Research Centre for Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Catanzaro, Italy.
| | - Alessandro Alaimo
- Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, Trento, Italy.
| | - Andrea Lunardi
- Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, Trento, Italy.
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7
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Han L, Wang M, Yang Y, Xu H, Wei L, Huang X. Detection of Prognostic Biomarkers for Hepatocellular Carcinoma through CircRNA-associated CeRNA Analysis. J Clin Transl Hepatol 2022; 10:80-89. [PMID: 35233376 PMCID: PMC8845162 DOI: 10.14218/jcth.2020.00144] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/10/2021] [Accepted: 04/27/2021] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND AND AIMS The prognosis of hepatocellular carcinoma (HCC) is extremely poor; therefore, there is an urgent need for novel prognostic molecular biomarkers of HCC. The current investigation utilized circular (circ)RNA-associated competing endogenous (ce)RNAs analysis in order to identify significant prognostic biomarkers of HCC. METHODS CircRNAs and mRNAs that were differentially expressed between normal and HCC tissues were identified. Their respective functions were predicted with Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes enrichment analyses. A nomogram was used for model verification. RESULTS A ceRNA network composed of differentially expressed circRNAs and mRNAs was constructed. Significant hub nodes in the ceRNA network were hsa_circ_0004662, hsa_circ_0005735, hsa_circ_0006990, hsa_circ_0018403 and hsa_circ_0100609. By using this information, a prognostic risk assessment tool was developed based on the expressions of seven genes (PLOD2, TARS, RNF19B, CCT2, RAN, C5orf30 and MCM10). Furthermore, multivariate Cox regression analysis revealed risk and T-stage parameters as independent prognostic factors. The nomograms that were constructed from risk and T-stage groups were used to further assess the prediction of HCC patient survival rates. The nomogram, which consisted of risk and T-stage scores assessment models, was found to be an independent factor for predicting prognosis of HCC. CONCLUSIONS Five circRNAs, including hsa_circ_0004662, hsa_circ_0005735, hsa_circ_0006990, hsa_circ_0018403 and hsa_circ_0100609, that may play key roles in the progression of HCC were identified. Seven gene signatures were identified, which were associated with the aforementioned circRNAs, including PLOD2, TARS, RNF19B, CCT2, RAN, C5orf30 and MCM10, all of which were significant genes involved in the pathophysiology of HCC. These genes may be used as a prognosticating tool in HCC patients.
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Affiliation(s)
- Li Han
- Department of Nursing, Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Maolong Wang
- Department of Thoracic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Yuling Yang
- Department of Infectious diseases, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Hanlin Xu
- Department of Thoracic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Lili Wei
- Department of Nursing, Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Xia Huang
- Department of Nursing, Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
- Correspondence to: Xia Huang, Department of Nursing, Affiliated Hospital of Qingdao University, 16Jiangsu Road, Qingdao, Shandong 266000, China. Tel: +86-18661807107, Fax: +86-532-82911875, E-mail:
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8
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Yu CY, Mitrofanova A. Mechanism-Centric Approaches for Biomarker Detection and Precision Therapeutics in Cancer. Front Genet 2021; 12:687813. [PMID: 34408770 PMCID: PMC8365516 DOI: 10.3389/fgene.2021.687813] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/28/2021] [Indexed: 12/18/2022] Open
Abstract
Biomarker discovery is at the heart of personalized treatment planning and cancer precision therapeutics, encompassing disease classification and prognosis, prediction of treatment response, and therapeutic targeting. However, many biomarkers represent passenger rather than driver alterations, limiting their utilization as functional units for therapeutic targeting. We suggest that identification of driver biomarkers through mechanism-centric approaches, which take into account upstream and downstream regulatory mechanisms, is fundamental to the discovery of functionally meaningful markers. Here, we examine computational approaches that identify mechanism-centric biomarkers elucidated from gene co-expression networks, regulatory networks (e.g., transcriptional regulation), protein-protein interaction (PPI) networks, and molecular pathways. We discuss their objectives, advantages over gene-centric approaches, and known limitations. Future directions highlight the importance of input and model interpretability, method and data integration, and the role of recently introduced technological advantages, such as single-cell sequencing, which are central for effective biomarker discovery and time-cautious precision therapeutics.
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Affiliation(s)
- Christina Y. Yu
- Department of Biomedical and Health Informatics, School of Health Professions, Rutgers, The State University of New Jersey, Newark, NJ, United States
| | - Antonina Mitrofanova
- Department of Biomedical and Health Informatics, School of Health Professions, Rutgers, The State University of New Jersey, Newark, NJ, United States
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States
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9
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Kukkonen K, Taavitsainen S, Huhtala L, Uusi-Makela J, Granberg KJ, Nykter M, Urbanucci A. Chromatin and Epigenetic Dysregulation of Prostate Cancer Development, Progression, and Therapeutic Response. Cancers (Basel) 2021; 13:3325. [PMID: 34283056 PMCID: PMC8268970 DOI: 10.3390/cancers13133325] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 02/07/2023] Open
Abstract
The dysregulation of chromatin and epigenetics has been defined as the overarching cancer hallmark. By disrupting transcriptional regulation in normal cells and mediating tumor progression by promoting cancer cell plasticity, this process has the ability to mediate all defined hallmarks of cancer. In this review, we collect and assess evidence on the contribution of chromatin and epigenetic dysregulation in prostate cancer. We highlight important mechanisms leading to prostate carcinogenesis, the emergence of castration-resistance upon treatment with androgen deprivation therapy, and resistance to antiandrogens. We examine in particular the contribution of chromatin structure and epigenetics to cell lineage commitment, which is dysregulated during tumorigenesis, and cell plasticity, which is altered during tumor progression.
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Affiliation(s)
- Konsta Kukkonen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, 33520 Tampere, Finland; (K.K.); (S.T.); (L.H.); (J.U.-M.); (K.J.G.); (M.N.)
| | - Sinja Taavitsainen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, 33520 Tampere, Finland; (K.K.); (S.T.); (L.H.); (J.U.-M.); (K.J.G.); (M.N.)
| | - Laura Huhtala
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, 33520 Tampere, Finland; (K.K.); (S.T.); (L.H.); (J.U.-M.); (K.J.G.); (M.N.)
| | - Joonas Uusi-Makela
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, 33520 Tampere, Finland; (K.K.); (S.T.); (L.H.); (J.U.-M.); (K.J.G.); (M.N.)
| | - Kirsi J. Granberg
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, 33520 Tampere, Finland; (K.K.); (S.T.); (L.H.); (J.U.-M.); (K.J.G.); (M.N.)
| | - Matti Nykter
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, 33520 Tampere, Finland; (K.K.); (S.T.); (L.H.); (J.U.-M.); (K.J.G.); (M.N.)
| | - Alfonso Urbanucci
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway
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10
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Obradovic A, Chowdhury N, Haake SM, Ager C, Wang V, Vlahos L, Guo XV, Aggen DH, Rathmell WK, Jonasch E, Johnson JE, Roth M, Beckermann KE, Rini BI, McKiernan J, Califano A, Drake CG. Single-cell protein activity analysis identifies recurrence-associated renal tumor macrophages. Cell 2021; 184:2988-3005.e16. [PMID: 34019793 PMCID: PMC8479759 DOI: 10.1016/j.cell.2021.04.038] [Citation(s) in RCA: 163] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 02/10/2021] [Accepted: 04/23/2021] [Indexed: 12/11/2022]
Abstract
Clear cell renal carcinoma (ccRCC) is a heterogeneous disease with a variable post-surgical course. To assemble a comprehensive ccRCC tumor microenvironment (TME) atlas, we performed single-cell RNA sequencing (scRNA-seq) of hematopoietic and non-hematopoietic subpopulations from tumor and tumor-adjacent tissue of treatment-naive ccRCC resections. We leveraged the VIPER algorithm to quantitate single-cell protein activity and validated this approach by comparison to flow cytometry. The analysis identified key TME subpopulations, as well as their master regulators and candidate cell-cell interactions, revealing clinically relevant populations, undetectable by gene-expression analysis. Specifically, we uncovered a tumor-specific macrophage subpopulation characterized by upregulation of TREM2/APOE/C1Q, validated by spatially resolved, quantitative multispectral immunofluorescence. In a large clinical validation cohort, these markers were significantly enriched in tumors from patients who recurred following surgery. The study thus identifies TREM2/APOE/C1Q-positive macrophage infiltration as a potential prognostic biomarker for ccRCC recurrence, as well as a candidate therapeutic target.
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MESH Headings
- Adult
- Apolipoproteins E/genetics
- Apolipoproteins E/metabolism
- Biomarkers, Tumor/genetics
- Carcinoma, Renal Cell/genetics
- Carcinoma, Renal Cell/metabolism
- Carcinoma, Renal Cell/pathology
- Cohort Studies
- Female
- Gene Expression/genetics
- Gene Expression Regulation, Neoplastic/genetics
- Humans
- Kidney/metabolism
- Kidney Neoplasms/pathology
- Lymphocytes, Tumor-Infiltrating/pathology
- Macrophages/metabolism
- Male
- Membrane Glycoproteins/genetics
- Membrane Glycoproteins/metabolism
- Middle Aged
- Neoplasm Recurrence, Local/genetics
- Neoplasm Recurrence, Local/metabolism
- Prognosis
- Receptors, Complement/genetics
- Receptors, Complement/metabolism
- Receptors, Immunologic/genetics
- Receptors, Immunologic/metabolism
- Sequence Analysis, RNA/methods
- Single-Cell Analysis/methods
- Tumor Microenvironment
- Tumor-Associated Macrophages/metabolism
- Tumor-Associated Macrophages/physiology
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Affiliation(s)
- Aleksandar Obradovic
- Columbia Center for Translational Immunology (CCTI), Columbia University Irving Medical Center (CUMC), New York, NY 10032, USA; Department of Systems Biology, HICC, New York, NY 10032, USA
| | - Nivedita Chowdhury
- Columbia Center for Translational Immunology (CCTI), Columbia University Irving Medical Center (CUMC), New York, NY 10032, USA; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | | | - Casey Ager
- Columbia Center for Translational Immunology (CCTI), Columbia University Irving Medical Center (CUMC), New York, NY 10032, USA
| | - Vinson Wang
- Department of Urology, Herbert Irving Comprehensive Cancer Center (HICC), New York, NY 10032, USA
| | - Lukas Vlahos
- Department of Systems Biology, HICC, New York, NY 10032, USA
| | - Xinzheng V Guo
- Columbia Center for Translational Immunology (CCTI), Columbia University Irving Medical Center (CUMC), New York, NY 10032, USA
| | - David H Aggen
- Columbia Center for Translational Immunology (CCTI), Columbia University Irving Medical Center (CUMC), New York, NY 10032, USA
| | | | - Eric Jonasch
- Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Marc Roth
- Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Brian I Rini
- Vanderbilt University Medical Center, Nashville, TN, USA
| | - James McKiernan
- Department of Urology, Herbert Irving Comprehensive Cancer Center (HICC), New York, NY 10032, USA; HICC, Columbia University, New York, NY, USA
| | - Andrea Califano
- Department of Systems Biology, HICC, New York, NY 10032, USA; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; HICC, Columbia University, New York, NY, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY; Department of Biomedical Informatics, Columbia University, New York, NY, USA; Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY, USA; J.P. Sulzberger Columbia Genome Center, New York, NY, USA.
| | - Charles G Drake
- Columbia Center for Translational Immunology (CCTI), Columbia University Irving Medical Center (CUMC), New York, NY 10032, USA; Department of Urology, Herbert Irving Comprehensive Cancer Center (HICC), New York, NY 10032, USA; HICC, Columbia University, New York, NY, USA.
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11
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Hahn WC, Bader JS, Braun TP, Califano A, Clemons PA, Druker BJ, Ewald AJ, Fu H, Jagu S, Kemp CJ, Kim W, Kuo CJ, McManus M, B Mills G, Mo X, Sahni N, Schreiber SL, Talamas JA, Tamayo P, Tyner JW, Wagner BK, Weiss WA, Gerhard DS. An expanded universe of cancer targets. Cell 2021; 184:1142-1155. [PMID: 33667368 PMCID: PMC8066437 DOI: 10.1016/j.cell.2021.02.020] [Citation(s) in RCA: 117] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 01/05/2021] [Accepted: 02/05/2021] [Indexed: 12/15/2022]
Abstract
The characterization of cancer genomes has provided insight into somatically altered genes across tumors, transformed our understanding of cancer biology, and enabled tailoring of therapeutic strategies. However, the function of most cancer alleles remains mysterious, and many cancer features transcend their genomes. Consequently, tumor genomic characterization does not influence therapy for most patients. Approaches to understand the function and circuitry of cancer genes provide complementary approaches to elucidate both oncogene and non-oncogene dependencies. Emerging work indicates that the diversity of therapeutic targets engendered by non-oncogene dependencies is much larger than the list of recurrently mutated genes. Here we describe a framework for this expanded list of cancer targets, providing novel opportunities for clinical translation.
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Affiliation(s)
- William C Hahn
- Dana-Farber Cancer Institute, Department of Medical Oncology, 450 Brookline Avenue, Boston, MA, USA.
| | - Joel S Bader
- Department of Biomedical Engineering and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Theodore P Braun
- Knight Cancer Institute and Division of Hematology and Medical Oncology, Oregon Health & Science University, Portland, OR, USA
| | - Andrea Califano
- Department of Systems Biology, Biomedical Informatics, Biochemistry and Molecular Biophysics, and Medicine, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | | | - Brian J Druker
- Knight Cancer Institute and Division of Hematology and Medical Oncology, Oregon Health & Science University, Portland, OR, USA
| | - Andrew J Ewald
- Department of Cell Biology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Haian Fu
- Department of Pharmacology and Chemical Biology, Emory Chemical Biology Discovery Center, and Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Subhashini Jagu
- Office of Cancer Genomics, Center for Cancer Genomics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Christopher J Kemp
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - William Kim
- Moores Cancer Center, Center for Novel Therapeutics and Department of Medicine, UC San Diego, La Jolla, CA, USA
| | - Calvin J Kuo
- Hematology Division, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael McManus
- Department of Microbiology and Immunology, UCSF Diabetes Center, and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Gordon B Mills
- Department of Cell, Development and Cancer Biology, Knight Cancer Institute, Oregon Health and Sciences University, Portland, OR, USA
| | - Xiulei Mo
- Department of Pharmacology and Chemical Biology, Emory Chemical Biology Discovery Center, and Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Nidhi Sahni
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, USA
| | | | - Jessica A Talamas
- Dana-Farber Cancer Institute, Department of Medical Oncology, 450 Brookline Avenue, Boston, MA, USA
| | - Pablo Tamayo
- Moores Cancer Center, Center for Novel Therapeutics and Department of Medicine, UC San Diego, La Jolla, CA, USA
| | - Jeffrey W Tyner
- Knight Cancer Institute, Oregon Health & Science University and Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | | | - William A Weiss
- Departments of Neurology, Neurological Surgery, Pediatrics, and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Daniela S Gerhard
- Office of Cancer Genomics, Center for Cancer Genomics, National Cancer Institute, NIH, Bethesda, MD, USA
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12
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Arumugam K, Shin W, Schiavone V, Vlahos L, Tu X, Carnevali D, Kesner J, Paull EO, Romo N, Subramaniam P, Worley J, Tan X, Califano A, Cosma MP. The Master Regulator Protein BAZ2B Can Reprogram Human Hematopoietic Lineage-Committed Progenitors into a Multipotent State. Cell Rep 2020; 33:108474. [PMID: 33296649 DOI: 10.1016/j.celrep.2020.108474] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 09/25/2020] [Accepted: 11/12/2020] [Indexed: 01/03/2023] Open
Abstract
Bi-species, fusion-mediated, somatic cell reprogramming allows precise, organism-specific tracking of unknown lineage drivers. The fusion of Tcf7l1-/- murine embryonic stem cells with EBV-transformed human B cell lymphocytes, leads to the generation of bi-species heterokaryons. Human mRNA transcript profiling at multiple time points permits the tracking of the reprogramming of B cell nuclei to a multipotent state. Interrogation of a human B cell regulatory network with gene expression signatures identifies 8 candidate master regulator proteins. Of these 8 candidates, ectopic expression of BAZ2B, from the bromodomain family, efficiently reprograms hematopoietic committed progenitors into a multipotent state and significantly enhances their long-term clonogenicity, stemness, and engraftment in immunocompromised mice. Unbiased systems biology approaches let us identify the early driving events of human B cell reprogramming.
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Affiliation(s)
- Karthik Arumugam
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - William Shin
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Valentina Schiavone
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Lukas Vlahos
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Xiaochuan Tu
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Davide Carnevali
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Jordan Kesner
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Evan O Paull
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Neus Romo
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Prem Subramaniam
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Jeremy Worley
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Xiangtian Tan
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Andrea Califano
- Department of Systems Biology, Columbia University, New York, NY, USA; Herbert Irving Comprehensive Cancer Center, J.P. Sulzberger Columbia Genome Center, Department of Biomedical Informatics, Department of Biochemistry and Molecular Biophysics, Department of Medicine, Columbia University, New York, NY, USA.
| | - Maria Pia Cosma
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain; ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain; Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China; CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
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13
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Jung Y, Kim JK, Lee E, Cackowski FC, Decker AM, Krebsbach PH, Taichman RS. CXCL12γ induces human prostate and mammary gland development. Prostate 2020; 80:1145-1156. [PMID: 32659025 PMCID: PMC7491592 DOI: 10.1002/pros.24043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/11/2020] [Indexed: 01/01/2023]
Abstract
BACKGROUND Epithelial stem cells (ESCs) demonstrate a capacity to maintain normal tissues homeostasis and ESCs with a deregulated behavior can contribute to cancer development. The ability to reprogram normal tissue epithelial cells into prostate or mammary stem-like cells holds great promise to help understand cell of origin and lineage plasticity in prostate and breast cancers in addition to understanding normal gland development. We previously showed that an intracellular chemokine, CXCL12γ induced cancer stem cells and neuroendocrine characteristics in both prostate and breast adenocarcinoma cell lines. However, its role in normal prostate or mammary epithelial cell fate and development remains unknown. Therefore, we sought to elucidate the functional role of CXCL12γ in the regulation of ESCs and tissue development. METHODS Prostate epithelial cells (PNT2) or mammary epithelial cells (MCF10A) with overexpressed CXCL12γ was characterized by quantitative real-time polymerase chain reaction, Western blots, and immunofluorescence for lineage marker expression, and fluorescence activated cell sorting analyses and sphere formation assays to examine stem cell surface phenotype and function. Xenotransplantation animal models were used to evaluate gland or acini formation in vivo. RESULTS Overexpression of CXCL12γ promotes the reprogramming of cells with a differentiated luminal phenotype to a nonluminal phenotype in both prostate (PNT2) and mammary (MCF10A) epithelial cells. The CXCL12γ-mediated nonluminal type cells results in an increase of epithelial stem-like phenotype including the subpopulation of EPCAMLo /CD49fHi /CD24Lo /CD44Hi cells capable of sphere formation. Critically, overexpression of CXCL12γ promotes the generation of robust gland-like structures from both prostate and mammary epithelial cells in in vivo xenograft animal models. CONCLUSIONS CXCL12γ supports the reprogramming of epithelial cells into nonluminal cell-derived stem cells, which facilitates gland development.
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Affiliation(s)
- Younghun Jung
- Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, MI 48109, USA
- Department of Biologic and Materials Sciences, University of Michigan School of Dentistry, Ann Arbor, MI 48109, USA
- Co-senior authors
| | - Jin Koo Kim
- Section of Periodontics, University of California Los Angeles School of Dentistry, Los Angeles, CA 90095, USA
| | - Eunsohl Lee
- Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, MI 48109, USA
| | - Frank C. Cackowski
- Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
- Department of Oncology, Wayne State University and Karmanos Cancer Institute, Detroit, MI 48201, USA
| | - Ann M. Decker
- Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, MI 48109, USA
| | - Paul H. Krebsbach
- Section of Periodontics, University of California Los Angeles School of Dentistry, Los Angeles, CA 90095, USA
| | - Russell S. Taichman
- Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, MI 48109, USA
- Department of Periodontics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Co-senior authors
- Corresponding Author Russell S. Taichman D.M.D., D.M.Sc., School of Dentistry, The University of Alabama at Birmingham, 1720 2nd Avenue South, Birmingham, AL 35294-0007, Phone: 205-934-4720,
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14
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Yu Y, Jiang W. Pluripotent stem cell differentiation as an emerging model to study human prostate development. Stem Cell Res Ther 2020; 11:285. [PMID: 32678004 PMCID: PMC7364497 DOI: 10.1186/s13287-020-01801-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 06/18/2020] [Accepted: 07/01/2020] [Indexed: 12/11/2022] Open
Abstract
Prostate development is a complex process, and knowledge about this process is increasingly required for both basic developmental biology studies and clinical prostate cancer research, as prostate tumorigenesis can be regarded as the restoration of development in the adult prostate. Using rodent animal models, scientists have revealed that the development of the prostate is mainly mediated by androgen receptor (AR) signaling and that some other signaling pathways also play indispensable roles. However, there are still many unknowns in human prostate biology, mainly due to the limited availability of proper fetal materials. Here, we first briefly review prostate development with a focus on the AR, WNT, and BMP signaling pathways is necessary for prostate budding/BMP signaling pathways. Based on the current progress in in vitro prostatic differentiation and organoid techniques, we propose human pluripotent stem cells as an emerging model to study human prostate development.
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Affiliation(s)
- Yangyang Yu
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, 116 East-Lake Road, District of Wuchang, Wuhan, 430071, Hubei Province, China
| | - Wei Jiang
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, 116 East-Lake Road, District of Wuchang, Wuhan, 430071, Hubei Province, China. .,Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, China. .,Human Genetics Resource Preservation Center of Wuhan University, Wuhan, 430071, China.
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15
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Li H, Wang L, Li Z, Geng X, Li M, Tang Q, Wu C, Lu Z. SOX2 has dual functions as a regulator in the progression of neuroendocrine prostate cancer. J Transl Med 2020; 100:570-582. [PMID: 31772313 DOI: 10.1038/s41374-019-0343-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 10/18/2019] [Accepted: 10/21/2019] [Indexed: 12/14/2022] Open
Abstract
The mechanisms underlying the lineage switching from prostate adenocarcinoma (AdPC) to lethal neuroendocrine prostate cancer (NEPC) have yet to be completely elucidated. In this study, RNA sequencing data from a unique patient-derived xenograft NEPC model and a clinical NEPC cohort were used to identify the potential genes driving NEPC progression. Enrichr analysis resulted in the identification of SRY-related HMG-box gene 2 (SOX2) as a potential repressor that causes decrease in the expression of AdPC specific genes in NEPC. Assays involving the stable overexpression of SOX2 in LNCaP and CWR22RV1 cells validated this role of SOX2 in vitro. Mechanistic studies showed that the repressor role of SOX2 was attributed to the marked global hypomethylation of histone H3, which was driven by the activation of lysine-specific demethylase 1 (LSD1). Furthermore, Enrichr also predicted SOX2 as a driver gene involved in the upregulation of NEPC specific genes. However, SOX2 alone could only marginally induce the expression of some neuroendocrine markers in vitro, which was consistent with previous reports. Moreover, we also elucidated the molecular features of LNCaP-SOX2 cells that may confer resistance to androgen-deprivation therapy (ADT) and the inclination toward neuroendocrine transdifferentiation. The results of this study reveal a novel mechanism for SOX2 in the progression of NEPC via LSD1-mediated global epigenetic modulation. This discovery suggests that LSD1 may be a selective target for the prevention of NEPC progression.
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Affiliation(s)
- Haiying Li
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, PR China
| | - Lili Wang
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, PR China
| | - Zhang Li
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, PR China
| | - Xu Geng
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, PR China
| | - Ming Li
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, PR China
| | - Qi Tang
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, PR China
| | - Chunxiao Wu
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, PR China.
| | - Zhiming Lu
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, PR China.
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16
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Hepburn AC, Curry EL, Moad M, Steele RE, Franco OE, Wilson L, Singh P, Buskin A, Crawford SE, Gaughan L, Mills IG, Hayward SW, Robson CN, Heer R. Propagation of human prostate tissue from induced pluripotent stem cells. Stem Cells Transl Med 2020; 9:734-745. [PMID: 32170918 PMCID: PMC7308643 DOI: 10.1002/sctm.19-0286] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 01/10/2020] [Accepted: 01/29/2020] [Indexed: 02/06/2023] Open
Abstract
Primary culture of human prostate organoids and patient‐derived xenografts is inefficient and has limited access to clinical tissues. This hampers their use for translational study to identify new treatments. To overcome this, we established a complementary approach where rapidly proliferating and easily handled induced pluripotent stem cells enabled the generation of human prostate tissue in vivo and in vitro. By using a coculture technique with inductive urogenital sinus mesenchyme, we comprehensively recapitulated in situ 3D prostate histology, and overcame limitations in the primary culture of human prostate stem, luminal and neuroendocrine cells, as well as the stromal microenvironment. This model now unlocks new opportunities to undertake translational studies of benign and malignant prostate disease.
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Affiliation(s)
- Anastasia C Hepburn
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne, UK
| | - Emma L Curry
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne, UK
| | - Mohammad Moad
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne, UK.,Acute Internal Medicine, University Hospital of North Tees, Stockton on Tees, UK
| | - Rebecca E Steele
- Prostate Cancer UK/Movember Centre of Excellence for Prostate Cancer, Centre for Cancer Research and Cell Biology, Queen's University of Belfast, Belfast, UK
| | - Omar E Franco
- Department of Surgery, NorthShore University HealthSystem, Evanston, Illinois, USA
| | - Laura Wilson
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne, UK
| | - Parmveer Singh
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne, UK
| | - Adriana Buskin
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne, UK
| | - Susan E Crawford
- Department of Surgery, NorthShore University HealthSystem, Evanston, Illinois, USA
| | - Luke Gaughan
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne, UK
| | - Ian G Mills
- Prostate Cancer UK/Movember Centre of Excellence for Prostate Cancer, Centre for Cancer Research and Cell Biology, Queen's University of Belfast, Belfast, UK.,Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Simon W Hayward
- Department of Surgery, NorthShore University HealthSystem, Evanston, Illinois, USA
| | - Craig N Robson
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne, UK
| | - Rakesh Heer
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne, UK.,Department of Urology, Freeman Hospital, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
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17
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Wang Y, Lu T, Wo Y, Sun X, Li S, Miao S, Dong Y, Leng X, Jiao W. Identification of a putative competitive endogenous RNA network for lung adenocarcinoma using TCGA datasets. PeerJ 2019; 7:e6809. [PMID: 31065463 PMCID: PMC6485208 DOI: 10.7717/peerj.6809] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 03/18/2019] [Indexed: 12/11/2022] Open
Abstract
The mechanisms underlying the oncogenesis and progression of lung adenocarcinoma (LUAD) are currently unclear. The discovery of competitive endogenous RNA (ceRNA) regulatory networks has provided a new direction for the treatment and prognosis of patients with LUAD. However, the mechanism of action of ceRNA in LUAD remains elusive. In the present study, differentially expressed mRNAs, microRNAs (miRs) and long non-coding RNAs from the cancer genome atlas database were screened. CeRNAs for LUAD were then identified using online prediction software. Among the ceRNAs identified, family with sequence similarity 83 member A (FAM83A), miR-34c-5p, KCNQ1OT1 and FLJ26245 were observed to be significantly associated with the overall survival of patients with LUAD. Of note, FAM83A has potential significance in drug resistance, and may present a candidate biomarker for the prognosis and treatment of patients with LUAD.
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Affiliation(s)
- Yuanyong Wang
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Tong Lu
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Yang Wo
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Xiao Sun
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Shicheng Li
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Shuncheng Miao
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Yanting Dong
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Xiaoliang Leng
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Wenjie Jiao
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
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18
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Bansal M, He J, Peyton M, Kustagi M, Iyer A, Comb M, White M, Minna JD, Califano A. Elucidating synergistic dependencies in lung adenocarcinoma by proteome-wide signaling-network analysis. PLoS One 2019; 14:e0208646. [PMID: 30615629 PMCID: PMC6322741 DOI: 10.1371/journal.pone.0208646] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 11/20/2018] [Indexed: 12/26/2022] Open
Abstract
To understand drug combination effect, it is necessary to decipher the interactions between drug targets-many of which are signaling molecules. Previously, such signaling pathway models are largely based on the compilation of literature data from heterogeneous cellular contexts. Indeed, de novo reconstruction of signaling interactions from large-scale molecular profiling is still lagging, compared to similar efforts in transcriptional and protein-protein interaction networks. To address this challenge, we introduce a novel algorithm for the systematic inference of protein kinase pathways, and applied it to published mass spectrometry-based phosphotyrosine profile data from 250 lung adenocarcinoma (LUAD) samples. The resulting network includes 43 TKs and 415 inferred, LUAD-specific substrates, which were validated at >60% accuracy by SILAC assays, including "novel' substrates of the EGFR and c-MET TKs, which play a critical oncogenic role in lung cancer. This systematic, data-driven model supported drug response prediction on an individual sample basis, including accurate prediction and validation of synergistic EGFR and c-MET inhibitor activity in cells lacking mutations in either gene, thus contributing to current precision oncology efforts.
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Affiliation(s)
- Mukesh Bansal
- Psychogenics Inc., Paramus, New Jersey, United States of America
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Jing He
- Department of Systems Biology, Columbia University, New York, NY, United States of America
- Center for Computational Biology and Bioinformatics (C2B2), Columbia University, New York, NY, United States of America
- Department of Biomedical Informatics (DBMI), Columbia University, New York, NY, United States of America
| | - Michael Peyton
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
| | - Manjunath Kustagi
- Department of Systems Biology, Columbia University, New York, NY, United States of America
| | - Archana Iyer
- Department of Systems Biology, Columbia University, New York, NY, United States of America
| | - Michael Comb
- Cell Signaling Technology, 3 Trask Lane, Danvers, MA, United States of America
| | - Michael White
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
| | - John D. Minna
- Hamon Center for Therapeutic Oncology Research, Simmons Comprehensive Cancer Center, Departments of Pharmacology, and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Andrea Califano
- Department of Systems Biology, Columbia University, New York, NY, United States of America
- Center for Computational Biology and Bioinformatics (C2B2), Columbia University, New York, NY, United States of America
- Department of Biomedical Informatics (DBMI), Columbia University, New York, NY, United States of America
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, United States of America
- Institute for Cancer Genetics, Columbia University, New York, NY, United States of America
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, United States of America
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19
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Le Magnen C, Virk RK, Dutta A, Kim JY, Panja S, Lopez-Bujanda ZA, Califano A, Drake CG, Mitrofanova A, Abate-Shen C. Cooperation of loss of NKX3.1 and inflammation in prostate cancer initiation. Dis Model Mech 2018; 11:dmm035139. [PMID: 30266798 PMCID: PMC6262819 DOI: 10.1242/dmm.035139] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 09/07/2018] [Indexed: 02/06/2023] Open
Abstract
Although it is known that inflammation plays a critical role in prostate tumorigenesis, the underlying processes are not well understood. Based on analysis of genetically engineered mouse models combined with correlative analysis of expression profiling data from human prostate tumors, we demonstrate a reciprocal relationship between inflammation and the status of the NKX3.1 homeobox gene associated with prostate cancer initiation. We find that cancer initiation in aged Nkx3.1 mutant mice correlates with enrichment of specific immune populations and increased expression of immunoregulatory genes. Furthermore, expression of these immunoregulatory genes is similarly increased in human prostate tumors having low levels of NKX3.1 expression. We further show that induction of prostatitis in Nkx3.1 mutant mice accelerates prostate cancer initiation, which is coincident with aberrant cellular plasticity and differentiation. Correspondingly, human prostate tumors having low levels of NKX3.1 have de-regulated expression of genes associated with these cellular processes. We propose that loss of function of NKX3.1 accelerates inflammation-driven prostate cancer initiation potentially via aberrant cellular plasticity and impairment of cellular differentiation.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Clémentine Le Magnen
- Departments of Medicine and Urology, Institute of Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Renu K Virk
- Department of Pathology and Cell Biology, Columbia University Medical Center, NY 10032, USA
| | - Aditya Dutta
- Departments of Medicine and Urology, Institute of Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Jaime Yeji Kim
- Department of Medicine, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Sukanya Panja
- Department of Health Informatics, Rutgers School of Health Professions, Rutgers, The State University of New Jersey, Newark, NJ 07101, USA
| | - Zoila A Lopez-Bujanda
- Graduate Program in Pathobiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Medicine, Columbia Center for Translational Immunology, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Andrea Califano
- Departments of Systems Biology and Biochemistry and Molecular Biophysics, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Charles G Drake
- Department of Medicine, Columbia Center for Translational Immunology, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Antonina Mitrofanova
- Department of Health Informatics, Rutgers School of Health Professions, Rutgers, The State University of New Jersey, Newark, NJ 07101, USA
- Department of Systems Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Cory Abate-Shen
- Departments of Urology, Medicine, Pathology & Cell Biology, and Systems Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
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20
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Nagel S, Meyer C, Kaufmann M, Zaborski M, MacLeod RAF, Drexler HG. Aberrant activity of NKL homeobox gene NKX3-2 in a T-ALL subset. PLoS One 2018; 13:e0197194. [PMID: 29746601 PMCID: PMC5944955 DOI: 10.1371/journal.pone.0197194] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 04/27/2018] [Indexed: 01/26/2023] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is a hematopoietic malignancy originating from T-cell progenitors in which differentiation is blocked at early stages. Physiological expression of specific NKL homeobox genes obeys a hematopoietic NKL-code implicated in the process of lymphopoiesis while in differentiated T-cells these genes are silenced. We propose that this developmental expression pattern underlies the observation that NKL homeobox genes are the most ubiquitous group of transcription factors deregulated in T-ALL, including TLX1, TLX3, NKX2-5 and NKX3-1. Here, we describe a novel member of the NKL homeobox gene subclass, NKX3-2 (BAPX1), which is aberrantly activated in 18% of pediatric T-ALL patients analyzed while being normally expressed in developing spleen. Identification of NKX3-2 expression in T-ALL cell line CCRF-CEM qualified these cells to model its deregulation and function in a leukemic context. Genomic and chromosomal analyses demonstrated normal configuration of the NKX3-2 locus at chromosome 4p15, thus excluding cytogenetic dysregulation. Comparative expression profiling analysis of NKX3-2 patient data revealed deregulated activity of BMP- and MAPK-signalling. These candidate pathways were experimentally confirmed to mediate aberrant NKX3-2 expression. We also show that homeobox gene SIX6, plus MIR17HG and GATA3 are downstream targets of NKX3-2 and plausibly contribute to the pathogenesis of this malignancy by suppressing T-cell differentiation. Finally, NKL homeobox gene NKX2-5 was activated by NKX3-2 in CCRF-CEM and by FOXG1 in PEER, representing mutually inhibitory activators of this translocated oncogene. Together, our findings reveal a novel oncogenic NKL homeobox gene subclass member which is aberrantly expressed in a large subset of T-ALL patients and participates in a deregulated gene network likely to arise in developing spleen.
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Affiliation(s)
- Stefan Nagel
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- * E-mail:
| | - Corinna Meyer
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Maren Kaufmann
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Margarete Zaborski
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Roderick A. F. MacLeod
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans G. Drexler
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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21
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Ding H, Douglass EF, Sonabend AM, Mela A, Bose S, Gonzalez C, Canoll PD, Sims PA, Alvarez MJ, Califano A. Quantitative assessment of protein activity in orphan tissues and single cells using the metaVIPER algorithm. Nat Commun 2018; 9:1471. [PMID: 29662057 PMCID: PMC5902599 DOI: 10.1038/s41467-018-03843-3] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 03/13/2018] [Indexed: 12/30/2022] Open
Abstract
We and others have shown that transition and maintenance of biological states is controlled by master regulator proteins, which can be inferred by interrogating tissue-specific regulatory models (interactomes) with transcriptional signatures, using the VIPER algorithm. Yet, some tissues may lack molecular profiles necessary for interactome inference (orphan tissues), or, as for single cells isolated from heterogeneous samples, their tissue context may be undetermined. To address this problem, we introduce metaVIPER, an algorithm designed to assess protein activity in tissue-independent fashion by integrative analysis of multiple, non-tissue-matched interactomes. This assumes that transcriptional targets of each protein will be recapitulated by one or more available interactomes. We confirm the algorithm's value in assessing protein dysregulation induced by somatic mutations, as well as in assessing protein activity in orphan tissues and, most critically, in single cells, thus allowing transformation of noisy and potentially biased RNA-Seq signatures into reproducible protein-activity signatures.
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Affiliation(s)
- Hongxu Ding
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Eugene F Douglass
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
| | - Adam M Sonabend
- Department of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA
| | - Angeliki Mela
- Department of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA
| | - Sayantan Bose
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- GlaxoSmithKline, King of Prussia, PA, 19406, USA
| | - Christian Gonzalez
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Amsterdam Neuroscience, Amsterdam, 1081, The Netherlands
| | - Peter D Canoll
- Department of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA
| | - Peter A Sims
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
| | - Mariano J Alvarez
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA.
- DarwinHealth Inc, New York, NY, 10032, USA.
| | - Andrea Califano
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA.
- DarwinHealth Inc, New York, NY, 10032, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, 10032, USA.
- J.P. Sulzberger Columbia Genome Center, Columbia University, New York, NY, 10032, USA.
- Department of Biomedical Informatics, Columbia University, New York, NY, 10032, USA.
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA.
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22
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Le Magnen C, Shen MM, Abate-Shen C. Lineage Plasticity in Cancer Progression and Treatment. ANNUAL REVIEW OF CANCER BIOLOGY 2018; 2:271-289. [PMID: 29756093 PMCID: PMC5942183 DOI: 10.1146/annurev-cancerbio-030617-050224] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Historically, it has been widely presumed that differentiated cells are determined during development and become irreversibly committed to their designated fates. In certain circumstances, however, differentiated cells can display plasticity by changing their identity, either by dedifferentiation to a progenitor-like state or by transdifferentiation to an alternative differentiated cell type. Such cellular plasticity can be triggered by physiological or oncogenic stress, or it can be experimentally induced through cellular reprogramming. Notably, physiological stresses that promote plasticity, such as severe tissue damage, inflammation, or senescence, also represent hallmarks of cancer. Furthermore, key drivers of cellular plasticity include major oncogenic and tumor suppressor pathways and can be exacerbated by drug treatment. Thus, plasticity may help cancer cells evade detection and treatment. We propose that cancer can be considered as a disease of excess plasticity, a notion that has important implications for intervention and treatment.
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Affiliation(s)
- Clémentine Le Magnen
- Department of Urology and Medicine, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Michael M Shen
- Department of Urology and Medicine, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
- Department of Systems Biology, Columbia University Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Cory Abate-Shen
- Department of Urology and Medicine, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
- Department of Systems Biology, Columbia University Medical Center, New York, NY 10032, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
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23
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Chua CW, Epsi NJ, Leung EY, Xuan S, Lei M, Li BI, Bergren SK, Hibshoosh H, Mitrofanova A, Shen MM. Differential requirements of androgen receptor in luminal progenitors during prostate regeneration and tumor initiation. eLife 2018; 7:28768. [PMID: 29334357 PMCID: PMC5807048 DOI: 10.7554/elife.28768] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 01/12/2018] [Indexed: 12/16/2022] Open
Abstract
Master regulatory genes of tissue specification play key roles in stem/progenitor cells and are often important in cancer. In the prostate, androgen receptor (AR) is a master regulator essential for development and tumorigenesis, but its specific functions in prostate stem/progenitor cells have not been elucidated. We have investigated AR function in CARNs (CAstration-Resistant Nkx3.1-expressing cells), a luminal stem/progenitor cell that functions in prostate regeneration. Using genetically--engineered mouse models and novel prostate epithelial cell lines, we find that progenitor properties of CARNs are largely unaffected by AR deletion, apart from decreased proliferation in vivo. Furthermore, AR loss suppresses tumor formation after deletion of the Pten tumor suppressor in CARNs; however, combined Pten deletion and activation of oncogenic Kras in AR-deleted CARNs result in tumors with focal neuroendocrine differentiation. Our findings show that AR modulates specific progenitor properties of CARNs, including their ability to serve as a cell of origin for prostate cancer.
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Affiliation(s)
- Chee Wai Chua
- Department of Medicine, Columbia University Medical Center, New York, United States.,Department of Genetics and Development, Columbia University Medical Center, New York, United States.,Department of Urology, Columbia University Medical Center, New York, United States.,Department of Systems Biology, Columbia University Medical Center, New York, United States.,Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, United States
| | - Nusrat J Epsi
- Department of Health Informatics, Rutgers School of Health Professions, Rutgers, The State University of New Jersey, Newark, United States.,Rutgers Biomedical and Health Sciences, Rutgers, The State University of New Jersey, Newark, United States
| | - Eva Y Leung
- Department of Medicine, Columbia University Medical Center, New York, United States.,Department of Genetics and Development, Columbia University Medical Center, New York, United States.,Department of Urology, Columbia University Medical Center, New York, United States.,Department of Systems Biology, Columbia University Medical Center, New York, United States.,Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, United States
| | - Shouhong Xuan
- Department of Medicine, Columbia University Medical Center, New York, United States.,Department of Genetics and Development, Columbia University Medical Center, New York, United States.,Department of Urology, Columbia University Medical Center, New York, United States.,Department of Systems Biology, Columbia University Medical Center, New York, United States.,Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, United States
| | - Ming Lei
- Department of Medicine, Columbia University Medical Center, New York, United States.,Department of Genetics and Development, Columbia University Medical Center, New York, United States.,Department of Urology, Columbia University Medical Center, New York, United States.,Department of Systems Biology, Columbia University Medical Center, New York, United States.,Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, United States
| | - Bo I Li
- Department of Medicine, Columbia University Medical Center, New York, United States.,Department of Genetics and Development, Columbia University Medical Center, New York, United States.,Department of Urology, Columbia University Medical Center, New York, United States.,Department of Systems Biology, Columbia University Medical Center, New York, United States.,Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, United States
| | - Sarah K Bergren
- Department of Medicine, Columbia University Medical Center, New York, United States.,Department of Genetics and Development, Columbia University Medical Center, New York, United States.,Department of Urology, Columbia University Medical Center, New York, United States.,Department of Systems Biology, Columbia University Medical Center, New York, United States.,Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, United States
| | - Hanina Hibshoosh
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, United States.,Department of Pathology and Cell Biology, Columbia University Medical Center, New York, United States
| | - Antonina Mitrofanova
- Department of Health Informatics, Rutgers School of Health Professions, Rutgers, The State University of New Jersey, Newark, United States.,Rutgers Biomedical and Health Sciences, Rutgers, The State University of New Jersey, Newark, United States
| | - Michael M Shen
- Department of Medicine, Columbia University Medical Center, New York, United States.,Department of Genetics and Development, Columbia University Medical Center, New York, United States.,Department of Urology, Columbia University Medical Center, New York, United States.,Department of Systems Biology, Columbia University Medical Center, New York, United States.,Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, United States
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