1
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Aney KJ, Jeong WJ, Vallejo AF, Burdziak C, Chen E, Wang A, Koak P, Wise K, Jensen K, Pe'er D, Dougan SK, Martelotto L, Nissim S. Novel Approach for Pancreas Transcriptomics Reveals the Cellular Landscape in Homeostasis and Acute Pancreatitis. Gastroenterology 2024; 166:1100-1113. [PMID: 38325760 PMCID: PMC11102849 DOI: 10.1053/j.gastro.2024.01.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 01/27/2024] [Accepted: 01/30/2024] [Indexed: 02/09/2024]
Abstract
BACKGROUND & AIMS Acinar cells produce digestive enzymes that impede transcriptomic characterization of the exocrine pancreas. Thus, single-cell RNA-sequencing studies of the pancreas underrepresent acinar cells relative to histological expectations, and a robust approach to capture pancreatic cell responses in disease states is needed. We sought to innovate a method that overcomes these challenges to accelerate study of the pancreas in health and disease. METHODS We leverage FixNCut, a single-cell RNA-sequencing approach in which tissue is reversibly fixed with dithiobis(succinimidyl propionate) before dissociation and single-cell preparation. We apply FixNCut to an established mouse model of acute pancreatitis, validate findings using GeoMx whole transcriptome atlas profiling, and integrate our data with prior studies to compare our method in both mouse and human pancreas datasets. RESULTS FixNCut achieves unprecedented definition of challenging pancreatic cells, including acinar and immune populations in homeostasis and acute pancreatitis, and identifies changes in all major cell types during injury and recovery. We define the acinar transcriptome during homeostasis and acinar-to-ductal metaplasia and establish a unique gene set to measure deviation from normal acinar identity. We characterize pancreatic immune cells, and analysis of T-cell subsets reveals a polarization of the homeostatic pancreas toward type-2 immunity. We report immune responses during acute pancreatitis and recovery, including early neutrophil infiltration, expansion of dendritic cell subsets, and a substantial shift in the transcriptome of macrophages due to both resident macrophage activation and monocyte infiltration. CONCLUSIONS FixNCut preserves pancreatic transcriptomes to uncover novel cell states during homeostasis and following pancreatitis, establishing a broadly applicable approach and reference atlas for study of pancreas biology and disease.
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Affiliation(s)
- Katherine J Aney
- Biological and Biomedical Sciences Program, Harvard Medical School, Boston, Massachusetts; Health Sciences & Technology Program, Harvard-MIT, Boston, Massachusetts; Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts; Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Woo-Jeong Jeong
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts; Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Cassandra Burdziak
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ethan Chen
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts; Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Austin Wang
- Harvard University, Cambridge, Massachusetts
| | - Pal Koak
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts; Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kellie Wise
- Adelaide Centre for Epigenetics (ACE), University of Adelaide, South Australia, Australia; South Australian immunoGENomics Cancer Institute (SAiGENCI), University of Adelaide, South Australia, Australia
| | - Kirk Jensen
- Adelaide Centre for Epigenetics (ACE), University of Adelaide, South Australia, Australia; South Australian immunoGENomics Cancer Institute (SAiGENCI), University of Adelaide, South Australia, Australia; Australian Genome Research Facility, Melbourne, Victoria, Australia
| | - Dana Pe'er
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York; Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Stephanie K Dougan
- Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Immunology, Harvard Medical School, Boston, Massachusetts
| | - Luciano Martelotto
- Adelaide Centre for Epigenetics (ACE), University of Adelaide, South Australia, Australia; South Australian immunoGENomics Cancer Institute (SAiGENCI), University of Adelaide, South Australia, Australia.
| | - Sahar Nissim
- Biological and Biomedical Sciences Program, Harvard Medical School, Boston, Massachusetts; Health Sciences & Technology Program, Harvard-MIT, Boston, Massachusetts; Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts; Dana-Farber Cancer Institute, Boston, Massachusetts; Gastroenterology Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.
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2
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Park JH, Mortaja M, Son HG, Zhao X, Sloat LM, Azin M, Wang J, Collier MR, Tummala KS, Mandinova A, Bardeesy N, Semenov YR, Mino-Kenudson M, Demehri S. Statin prevents cancer development in chronic inflammation by blocking interleukin 33 expression. Nat Commun 2024; 15:4099. [PMID: 38816352 PMCID: PMC11139893 DOI: 10.1038/s41467-024-48441-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 04/24/2024] [Indexed: 06/01/2024] Open
Abstract
Chronic inflammation is a major cause of cancer worldwide. Interleukin 33 (IL-33) is a critical initiator of cancer-prone chronic inflammation; however, its induction mechanism by environmental causes of chronic inflammation is unknown. Herein, we demonstrate that Toll-like receptor (TLR)3/4-TBK1-IRF3 pathway activation links environmental insults to IL-33 induction in the skin and pancreas inflammation. An FDA-approved drug library screen identifies pitavastatin to effectively suppress IL-33 expression by blocking TBK1 membrane recruitment/activation through the mevalonate pathway inhibition. Accordingly, pitavastatin prevents chronic pancreatitis and its cancer sequela in an IL-33-dependent manner. The IRF3-IL-33 axis is highly active in chronic pancreatitis and its associated pancreatic cancer in humans. Interestingly, pitavastatin use correlates with a significantly reduced risk of chronic pancreatitis and pancreatic cancer in patients. Our findings demonstrate that blocking the TBK1-IRF3-IL-33 signaling axis suppresses cancer-prone chronic inflammation. Statins present a safe and effective prophylactic strategy to prevent chronic inflammation and its cancer sequela.
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Affiliation(s)
- Jong Ho Park
- Center for Cancer Immunology, Krantz Family Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Anatomy, School of Medicine, Keimyung University, Daegu, South Korea
| | - Mahsa Mortaja
- Center for Cancer Immunology, Krantz Family Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Heehwa G Son
- Center for Cancer Immunology, Krantz Family Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Xutu Zhao
- Center for Cancer Immunology, Krantz Family Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Lauren M Sloat
- Center for Cancer Immunology, Krantz Family Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Marjan Azin
- Center for Cancer Immunology, Krantz Family Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jun Wang
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Michael R Collier
- Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Krishna S Tummala
- Krantz Family Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Quantitative Biosciences, Merck Research Laboratories, Boston, MA, USA
| | - Anna Mandinova
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Nabeel Bardeesy
- Krantz Family Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Yevgeniy R Semenov
- Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, USA
| | - Mari Mino-Kenudson
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Shadmehr Demehri
- Center for Cancer Immunology, Krantz Family Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
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3
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Moye AL, Dost AF, Ietswaart R, Sengupta S, Ya V, Aluya C, Fahey CG, Louie SM, Paschini M, Kim CF. Early-stage lung cancer is driven by a transitional cell state dependent on a KRAS-ITGA3-SRC axis. EMBO J 2024:10.1038/s44318-024-00113-5. [PMID: 38755258 DOI: 10.1038/s44318-024-00113-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/04/2024] [Accepted: 04/17/2024] [Indexed: 05/18/2024] Open
Abstract
Glycine-12 mutations in the GTPase KRAS (KRASG12) are an initiating event for development of lung adenocarcinoma (LUAD). KRASG12 mutations promote cell-intrinsic rewiring of alveolar type-II progenitor (AT2) cells, but to what extent such changes interplay with lung homeostasis and cell fate pathways is unclear. Here, we generated single-cell RNA-seq (scRNA-seq) profiles from AT2-mesenchyme organoid co-cultures, mice, and stage-IA LUAD patients, identifying conserved regulators of AT2 transcriptional dynamics and defining the impact of KRASG12D mutation with temporal resolution. In AT2WT organoids, we found a transient injury/plasticity state preceding AT2 self-renewal and AT1 differentiation. Early-stage AT2KRAS cells exhibited perturbed gene expression dynamics, most notably retention of the injury/plasticity state. The injury state in AT2KRAS cells of patients, mice, and organoids was distinguishable from AT2WT states via altered receptor expression, including co-expression of ITGA3 and SRC. The combination of clinically relevant KRASG12D and SRC inhibitors impaired AT2KRAS organoid growth. Together, our data show that an injury/plasticity state essential for lung repair is co-opted during AT2 self-renewal and LUAD initiation, suggesting that early-stage LUAD may be susceptible to interventions that target specifically the oncogenic nature of this cell state.
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Affiliation(s)
- Aaron L Moye
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary Medicine, Boston Children's Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Antonella Fm Dost
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary Medicine, Boston Children's Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Hubrecht Institute, Oncode Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht, The Netherlands
| | | | - Shreoshi Sengupta
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary Medicine, Boston Children's Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - VanNashlee Ya
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary Medicine, Boston Children's Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Chrystal Aluya
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary Medicine, Boston Children's Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Caroline G Fahey
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary Medicine, Boston Children's Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Harvard University and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sharon M Louie
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary Medicine, Boston Children's Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Margherita Paschini
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary Medicine, Boston Children's Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Carla F Kim
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary Medicine, Boston Children's Hospital, Boston, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
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4
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Blériot C, Dunsmore G, Alonso-Curbelo D, Ginhoux F. A temporal perspective for tumor-associated macrophage identities and functions. Cancer Cell 2024; 42:747-758. [PMID: 38670090 DOI: 10.1016/j.ccell.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 02/13/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024]
Abstract
Cancer is a progressive disease that can develop and evolve over decades, with inflammation playing a central role at each of its stages, from tumor initiation to metastasis. In this context, macrophages represent well-established bridges reciprocally linking inflammation and cancer via an array of diverse functions that have spurred efforts to classify them into subtypes. Here, we discuss the intertwines between macrophages, inflammation, and cancer with an emphasis on temporal dynamics of macrophage diversity and functions in pre-malignancy and cancer. By instilling temporal dynamism into the more static classic view of tumor-associated macrophage biology, we propose a new framework to better contextualize their significance in the inflammatory processes that precede and result from the onset of cancer and shape its evolution.
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Affiliation(s)
- Camille Blériot
- Gustave Roussy, INSERM, Villejuif, France; Institut Necker des Enfants Malades (INEM), INSERM, CNRS, Université Paris Cité, Paris, France
| | | | - Direna Alonso-Curbelo
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
| | - Florent Ginhoux
- Gustave Roussy, INSERM, Villejuif, France; Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore; Shanghai Institute of Immunology, Shanghai JiaoTong University School of Medicine, Shanghai, China; Translational Immunology Institute, SingHealth Duke-NUS, Singapore, Singapore.
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5
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Kimmelman AC, Sherman MH. The Role of Stroma in Cancer Metabolism. Cold Spring Harb Perspect Med 2024; 14:a041540. [PMID: 37696660 PMCID: PMC10925555 DOI: 10.1101/cshperspect.a041540] [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] [Indexed: 09/13/2023]
Abstract
The altered metabolism of tumor cells is a well-known hallmark of cancer and is driven by multiple factors such as mutations in oncogenes and tumor suppressor genes, the origin of the tissue where the tumor arises, and the microenvironment of the tumor. These metabolic changes support the growth of cancer cells by providing energy and the necessary building blocks to sustain proliferation. Targeting these metabolic alterations therapeutically is a potential strategy to treat cancer, but it is challenging due to the metabolic plasticity of tumors. Cancer cells have developed ways to scavenge nutrients through autophagy and macropinocytosis and can also form metabolic networks with stromal cells in the tumor microenvironment. Understanding the role of the tumor microenvironment in tumor metabolism is crucial for effective therapeutic targeting. This review will discuss tumor metabolism and the contribution of the stroma in supporting tumor growth through metabolic interactions.
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Affiliation(s)
- Alec C Kimmelman
- Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, New York 10016, USA
- Department of Radiation Oncology, New York University Grossman School of Medicine, New York, New York 10016, USA
| | - Mara H Sherman
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
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6
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Parreno V, Loubiere V, Schuettengruber B, Fritsch L, Rawal CC, Erokhin M, Győrffy B, Normanno D, Di Stefano M, Moreaux J, Butova NL, Chiolo I, Chetverina D, Martinez AM, Cavalli G. Transient loss of Polycomb components induces an epigenetic cancer fate. Nature 2024; 629:688-696. [PMID: 38658752 PMCID: PMC11096130 DOI: 10.1038/s41586-024-07328-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/15/2024] [Indexed: 04/26/2024]
Abstract
Although cancer initiation and progression are generally associated with the accumulation of somatic mutations1,2, substantial epigenomic alterations underlie many aspects of tumorigenesis and cancer susceptibility3-6, suggesting that genetic mechanisms might not be the only drivers of malignant transformation7. However, whether purely non-genetic mechanisms are sufficient to initiate tumorigenesis irrespective of mutations has been unknown. Here, we show that a transient perturbation of transcriptional silencing mediated by Polycomb group proteins is sufficient to induce an irreversible switch to a cancer cell fate in Drosophila. This is linked to the irreversible derepression of genes that can drive tumorigenesis, including members of the JAK-STAT signalling pathway and zfh1, the fly homologue of the ZEB1 oncogene, whose aberrant activation is required for Polycomb perturbation-induced tumorigenesis. These data show that a reversible depletion of Polycomb proteins can induce cancer in the absence of driver mutations, suggesting that tumours can emerge through epigenetic dysregulation leading to inheritance of altered cell fates.
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Affiliation(s)
- V Parreno
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
| | - V Loubiere
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - B Schuettengruber
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
| | - L Fritsch
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
| | - C C Rawal
- University of Southern California, Los Angeles, CA, USA
| | - M Erokhin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - B Győrffy
- Semmelweis University Department of Bioinformatics, Budapest, Hungary
- Department of Biophysics, Medical School, University of Pécs, Pécs, Hungary
| | - D Normanno
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
| | - M Di Stefano
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
| | - J Moreaux
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
- Department of Biological Hematology, CHU Montpellier, Montpellier, France
- UFR Medicine, University of Montpellier, Montpellier, France
| | - N L Butova
- University of Southern California, Los Angeles, CA, USA
| | - I Chiolo
- University of Southern California, Los Angeles, CA, USA
| | - D Chetverina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - A-M Martinez
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France.
| | - G Cavalli
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France.
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7
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Daccache JA, Naik S. Inflammatory Memory in Chronic Skin Disease. JID INNOVATIONS 2024; 4:100277. [PMID: 38708420 PMCID: PMC11068922 DOI: 10.1016/j.xjidi.2024.100277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/01/2024] [Accepted: 03/11/2024] [Indexed: 05/07/2024] Open
Abstract
Inflammation is a hallmark of remitting-relapsing dermatological diseases. Although a large emphasis has been placed on adaptive immune cells as mediators of relapse, evidence in epithelial and innate immune biology suggests that disease memory is widespread. In this study, we bring to the fore the concept of inflammatory memory or nonspecific training of long-lived cells in the skin, highlighting the epigenetic and other mechanisms that propagate memory at the cellular level. We place these findings in the context of psoriasis, a prototypic flaring disease known to have localized memory, and underscore the importance of targeting memory to limit disease flares.
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Affiliation(s)
| | - Shruti Naik
- Department of Pathology, NYU Langone Health, New York, New York, USA
- Ronald O. Perelman Department of Dermatology, NYU Langone Health, New York, New York, USA
- Department of Medicine, NYU Langone Health, New York, New York, USA
- Perlmutter Cancer Center, NYU Langone Health, New York, New York, USA
- Colton Center for Autoimmunity, NYU Langone Health, New York, New York, USA
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8
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Jin X, Zhang R, Fu Y, Zhu Q, Hong L, Wu A, Wang H. Unveiling aging dynamics in the hematopoietic system insights from single-cell technologies. Brief Funct Genomics 2024:elae019. [PMID: 38688725 DOI: 10.1093/bfgp/elae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 04/10/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024] Open
Abstract
As the demographic structure shifts towards an aging society, strategies aimed at slowing down or reversing the aging process become increasingly essential. Aging is a major predisposing factor for many chronic diseases in humans. The hematopoietic system, comprising blood cells and their associated bone marrow microenvironment, intricately participates in hematopoiesis, coagulation, immune regulation and other physiological phenomena. The aging process triggers various alterations within the hematopoietic system, serving as a spectrum of risk factors for hematopoietic disorders, including clonal hematopoiesis, immune senescence, myeloproliferative neoplasms and leukemia. The emerging single-cell technologies provide novel insights into age-related changes in the hematopoietic system. In this review, we summarize recent studies dissecting hematopoietic system aging using single-cell technologies. We discuss cellular changes occurring during aging in the hematopoietic system at the levels of the genomics, transcriptomics, epigenomics, proteomics, metabolomics and spatial multi-omics. Finally, we contemplate the future prospects of single-cell technologies, emphasizing the impact they may bring to the field of hematopoietic system aging research.
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Affiliation(s)
- Xinrong Jin
- Zhejiang Key Laboratory of Medical Epigenetics, School of Basic Medical Sciences, The Third People's Hospital of Deqing, Deqing Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Ruohan Zhang
- Zhejiang Key Laboratory of Medical Epigenetics, School of Basic Medical Sciences, The Third People's Hospital of Deqing, Deqing Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Yunqi Fu
- Zhejiang Key Laboratory of Medical Epigenetics, School of Basic Medical Sciences, The Third People's Hospital of Deqing, Deqing Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Qiunan Zhu
- Zhejiang Key Laboratory of Medical Epigenetics, School of Basic Medical Sciences, The Third People's Hospital of Deqing, Deqing Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Liquan Hong
- Zhejiang Key Laboratory of Medical Epigenetics, School of Basic Medical Sciences, The Third People's Hospital of Deqing, Deqing Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Aiwei Wu
- Zhejiang Key Laboratory of Medical Epigenetics, School of Basic Medical Sciences, The Third People's Hospital of Deqing, Deqing Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Hu Wang
- Zhejiang Key Laboratory of Medical Epigenetics, School of Basic Medical Sciences, The Third People's Hospital of Deqing, Deqing Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
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9
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Youssef KK, Nieto MA. Epithelial-mesenchymal transition in tissue repair and degeneration. Nat Rev Mol Cell Biol 2024:10.1038/s41580-024-00733-z. [PMID: 38684869 DOI: 10.1038/s41580-024-00733-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/26/2024] [Indexed: 05/02/2024]
Abstract
Epithelial-mesenchymal transitions (EMTs) are the epitome of cell plasticity in embryonic development and cancer; during EMT, epithelial cells undergo dramatic phenotypic changes and become able to migrate to form different tissues or give rise to metastases, respectively. The importance of EMTs in other contexts, such as tissue repair and fibrosis in the adult, has become increasingly recognized and studied. In this Review, we discuss the function of EMT in the adult after tissue damage and compare features of embryonic and adult EMT. Whereas sustained EMT leads to adult tissue degeneration, fibrosis and organ failure, its transient activation, which confers phenotypic and functional plasticity on somatic cells, promotes tissue repair after damage. Understanding the mechanisms and temporal regulation of different EMTs provides insight into how some tissues heal and has the potential to open new therapeutic avenues to promote repair or regeneration of tissue damage that is currently irreversible. We also discuss therapeutic strategies that modulate EMT that hold clinical promise in ameliorating fibrosis, and how precise EMT activation could be harnessed to enhance tissue repair.
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Affiliation(s)
| | - M Angela Nieto
- Instituto de Neurociencias (CSIC-UMH), Sant Joan d'Alacant, Spain.
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.
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10
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Antonucci L, Karin M. The Past and Future of Inflammation as a Target to Cancer Prevention. Cancer Prev Res (Phila) 2024; 17:141-155. [PMID: 38271694 PMCID: PMC10987280 DOI: 10.1158/1940-6207.capr-23-0423] [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: 10/27/2023] [Revised: 12/21/2023] [Accepted: 01/23/2024] [Indexed: 01/27/2024]
Abstract
Inflammation is an essential defense mechanism in which innate immune cells are coordinately activated on encounter of harmful stimuli, including pathogens, tissue injury, and toxic compounds and metabolites to neutralize and eliminate the instigator and initiate healing and regeneration. Properly terminated inflammation is vital to health, but uncontrolled runaway inflammation that becomes chronic begets a variety of inflammatory and metabolic diseases and increases cancer risk. Making damaged tissues behave as "wounds that do not heal" and sustaining the production of growth factors whose physiologic function is tissue healing, chronic inflammation accelerates cancer emergence from premalignant lesions. In 1863, Rudolf Virchow, a leading German pathologist, suggested a possible association between inflammation and tumor formation, but it took another 140 years to fully elucidate and appreciate the tumorigenic role of inflammation. Key findings outlined molecular events in the inflammatory cascade that promote cancer onset and progression and enabled a better appreciation of when and where inflammation should be inhibited. These efforts triggered ongoing research work to discover and develop inflammation-reducing chemopreventive strategies for decreasing cancer risk and incidence.
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Affiliation(s)
- Laura Antonucci
- Laboratory of Gene Regulation and Signal Transduction, Departments of Pharmacology and Pathology, University of California San Diego School of Medicine; La Jolla, CA 92093, USA
| | - Michael Karin
- Laboratory of Gene Regulation and Signal Transduction, Departments of Pharmacology and Pathology, University of California San Diego School of Medicine; La Jolla, CA 92093, USA
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11
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Yuan S, Almagro J, Fuchs E. Beyond genetics: driving cancer with the tumour microenvironment behind the wheel. Nat Rev Cancer 2024; 24:274-286. [PMID: 38347101 PMCID: PMC11077468 DOI: 10.1038/s41568-023-00660-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/18/2023] [Indexed: 02/17/2024]
Abstract
Cancer has long been viewed as a genetic disease of cumulative mutations. This notion is fuelled by studies showing that ageing tissues are often riddled with clones of complex oncogenic backgrounds coexisting in seeming harmony with their normal tissue counterparts. Equally puzzling, however, is how cancer cells harbouring high mutational burden contribute to normal, tumour-free mice when allowed to develop within the confines of healthy embryos. Conversely, recent evidence suggests that adult tissue cells expressing only one or a few oncogenes can, in some contexts, generate tumours exhibiting many of the features of a malignant, invasive cancer. These disparate observations are difficult to reconcile without invoking environmental cues triggering epigenetic changes that can either dampen or drive malignant transformation. In this Review, we focus on how certain oncogenes can launch a two-way dialogue of miscommunication between a stem cell and its environment that can rewire downstream events non-genetically and skew the morphogenetic course of the tissue. We review the cells and molecules of and the physical forces acting in the resulting tumour microenvironments that can profoundly affect the behaviours of transformed cells. Finally, we discuss possible explanations for the remarkable diversity in the relative importance of mutational burden versus tumour microenvironment and its clinical relevance.
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Affiliation(s)
- Shaopeng Yuan
- Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
| | - Jorge Almagro
- Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
| | - Elaine Fuchs
- Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, New York, NY, USA.
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12
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Li NN, Lun DX, Gong N, Meng G, Du XY, Wang H, Bao X, Li XY, Song JW, Hu K, Li L, Li SY, Liu W, Zhu W, Zhang Y, Li J, Yao T, Mou L, Han X, Hao F, Hu Y, Liu L, Zhu H, Wu Y, Liu B. Targeting the chromatin structural changes of antitumor immunity. J Pharm Anal 2024; 14:100905. [PMID: 38665224 PMCID: PMC11043877 DOI: 10.1016/j.jpha.2023.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/28/2023] [Accepted: 11/21/2023] [Indexed: 04/28/2024] Open
Abstract
Epigenomic imbalance drives abnormal transcriptional processes, promoting the onset and progression of cancer. Although defective gene regulation generally affects carcinogenesis and tumor suppression networks, tumor immunogenicity and immune cells involved in antitumor responses may also be affected by epigenomic changes, which may have significant implications for the development and application of epigenetic therapy, cancer immunotherapy, and their combinations. Herein, we focus on the impact of epigenetic regulation on tumor immune cell function and the role of key abnormal epigenetic processes, DNA methylation, histone post-translational modification, and chromatin structure in tumor immunogenicity, and introduce these epigenetic research methods. We emphasize the value of small-molecule inhibitors of epigenetic modulators in enhancing antitumor immune responses and discuss the challenges of developing treatment plans that combine epigenetic therapy and immunotherapy through the complex interaction between cancer epigenetics and cancer immunology.
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Affiliation(s)
- Nian-nian Li
- Weifang People's Hospital, Weifang, Shandong, 261000, China
- School of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Deng-xing Lun
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Ningning Gong
- Weifang Traditional Chinese Medicine Hospital, Weifang, Shandong, 261000, China
| | - Gang Meng
- Shaanxi Key Laboratory of Sericulture, Ankang University, Ankang, Shaanxi, 725000, China
| | - Xin-ying Du
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - He Wang
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Xiangxiang Bao
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Xin-yang Li
- Guizhou Education University, Guiyang, 550018, China
| | - Ji-wu Song
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Kewei Hu
- Weifang Traditional Chinese Medicine Hospital, Weifang, Shandong, 261000, China
| | - Lala Li
- Guizhou Normal University, Guiyang, 550025, China
| | - Si-ying Li
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Wenbo Liu
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Wanping Zhu
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Yunlong Zhang
- School of Medical Imaging, Weifang Medical University, Weifang, Shandong, 261053, China
| | - Jikai Li
- Department of Bone and Soft Tissue Oncology, Tianjin Hospital, Tianjin, 300299, China
| | - Ting Yao
- School of Life Sciences, Nankai University, Tianjin, 300071, China
- Teda Institute of Biological Sciences & Biotechnology, Nankai University, Tianjin, 300457, China
| | - Leming Mou
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Xiaoqing Han
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Furong Hao
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Yongcheng Hu
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Lin Liu
- School of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Hongguang Zhu
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Yuyun Wu
- Xinqiao Hospital of Army Military Medical University, Chongqing, 400038, China
| | - Bin Liu
- Weifang People's Hospital, Weifang, Shandong, 261000, China
- School of Life Sciences, Nankai University, Tianjin, 300071, China
- Teda Institute of Biological Sciences & Biotechnology, Nankai University, Tianjin, 300457, China
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13
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Swanton C, Bernard E, Abbosh C, André F, Auwerx J, Balmain A, Bar-Sagi D, Bernards R, Bullman S, DeGregori J, Elliott C, Erez A, Evan G, Febbraio MA, Hidalgo A, Jamal-Hanjani M, Joyce JA, Kaiser M, Lamia K, Locasale JW, Loi S, Malanchi I, Merad M, Musgrave K, Patel KJ, Quezada S, Wargo JA, Weeraratna A, White E, Winkler F, Wood JN, Vousden KH, Hanahan D. Embracing cancer complexity: Hallmarks of systemic disease. Cell 2024; 187:1589-1616. [PMID: 38552609 DOI: 10.1016/j.cell.2024.02.009] [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: 09/25/2023] [Revised: 01/25/2024] [Accepted: 02/08/2024] [Indexed: 04/02/2024]
Abstract
The last 50 years have witnessed extraordinary developments in understanding mechanisms of carcinogenesis, synthesized as the hallmarks of cancer. Despite this logical framework, our understanding of the molecular basis of systemic manifestations and the underlying causes of cancer-related death remains incomplete. Looking forward, elucidating how tumors interact with distant organs and how multifaceted environmental and physiological parameters impinge on tumors and their hosts will be crucial for advances in preventing and more effectively treating human cancers. In this perspective, we discuss complexities of cancer as a systemic disease, including tumor initiation and promotion, tumor micro- and immune macro-environments, aging, metabolism and obesity, cancer cachexia, circadian rhythms, nervous system interactions, tumor-related thrombosis, and the microbiome. Model systems incorporating human genetic variation will be essential to decipher the mechanistic basis of these phenomena and unravel gene-environment interactions, providing a modern synthesis of molecular oncology that is primed to prevent cancers and improve patient quality of life and cancer outcomes.
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Affiliation(s)
- Charles Swanton
- The Francis Crick Institute, London, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
| | - Elsa Bernard
- The Francis Crick Institute, London, UK; INSERM U981, Gustave Roussy, Villejuif, France
| | | | - Fabrice André
- INSERM U981, Gustave Roussy, Villejuif, France; Department of Medical Oncology, Gustave Roussy, Villejuif, France; Paris Saclay University, Kremlin-Bicetre, France
| | - Johan Auwerx
- Laboratory of Integrative Systems Physiology, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Allan Balmain
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | | | - René Bernards
- Division of Molecular Carcinogenesis, Oncode Institute, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Susan Bullman
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - James DeGregori
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - Ayelet Erez
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Gerard Evan
- The Francis Crick Institute, London, UK; Kings College London, London, UK
| | - Mark A Febbraio
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Andrés Hidalgo
- Department of Immunobiology, Yale University, New Haven, CT 06519, USA; Area of Cardiovascular Regeneration, Centro Nacional de Investigaciones Cardiovasculares, 28029 Madrid, Spain
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Johanna A Joyce
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | | | - Katja Lamia
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA, USA
| | - Jason W Locasale
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA; Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, USA
| | - Sherene Loi
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; The Sir Department of Medical Oncology, The University of Melbourne, Parkville, VIC, Australia
| | | | - Miriam Merad
- Department of immunology and immunotherapy, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kathryn Musgrave
- Translational and Clinical Research Institute, Newcastle University, Newcastle, UK; Department of Haematology, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Ketan J Patel
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Sergio Quezada
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Jennifer A Wargo
- Department of Surgical Oncology, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ashani Weeraratna
- Sidney Kimmel Cancer Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Eileen White
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA; Ludwig Princeton Branch, Ludwig Institute for Cancer Research, Princeton, NJ, USA
| | - Frank Winkler
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany; Clinical Cooperation Unit Neuro-oncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - John N Wood
- Molecular Nociception Group, WIBR, University College London, London, UK
| | | | - Douglas Hanahan
- Lausanne Branch, Ludwig Institute for Cancer Research, Lausanne, Switzerland; Swiss institute for Experimental Cancer Research (ISREC), EPFL, Lausanne, Switzerland; Agora Translational Cancer Research Center, Lausanne, Switzerland.
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14
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Tsanov KM, Barriga FM, Ho YJ, Alonso-Curbelo D, Livshits G, Koche RP, Baslan T, Simon J, Tian S, Wuest AN, Luan W, Wilkinson JE, Masilionis I, Dimitrova N, Iacobuzio-Donahue CA, Chaligné R, Pe’er D, Massagué J, Lowe SW. Metastatic site influences driver gene function in pancreatic cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.17.585402. [PMID: 38562717 PMCID: PMC10983983 DOI: 10.1101/2024.03.17.585402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Driver gene mutations can increase the metastatic potential of the primary tumor1-3, but their role in sustaining tumor growth at metastatic sites is poorly understood. A paradigm of such mutations is inactivation of SMAD4 - a transcriptional effector of TGFβ signaling - which is a hallmark of multiple gastrointestinal malignancies4,5. SMAD4 inactivation mediates TGFβ's remarkable anti- to pro-tumorigenic switch during cancer progression and can thus influence both tumor initiation and metastasis6-14. To determine whether metastatic tumors remain dependent on SMAD4 inactivation, we developed a mouse model of pancreatic ductal adenocarcinoma (PDAC) that enables Smad4 depletion in the pre-malignant pancreas and subsequent Smad4 reactivation in established metastases. As expected, Smad4 inactivation facilitated the formation of primary tumors that eventually colonized the liver and lungs. By contrast, Smad4 reactivation in metastatic disease had strikingly opposite effects depending on the tumor's organ of residence: suppression of liver metastases and promotion of lung metastases. Integrative multiomic analysis revealed organ-specific differences in the tumor cells' epigenomic state, whereby the liver and lungs harbored chromatin programs respectively dominated by the KLF and RUNX developmental transcription factors, with Klf4 depletion being sufficient to reverse Smad4's tumor-suppressive activity in liver metastases. Our results show how epigenetic states favored by the organ of residence can influence the function of driver genes in metastatic tumors. This organ-specific gene-chromatin interplay invites consideration of anatomical site in the interpretation of tumor genetics, with implications for the therapeutic targeting of metastatic disease.
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Affiliation(s)
- Kaloyan M. Tsanov
- Cancer Biology & Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Francisco M. Barriga
- Cancer Biology & Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Yu-Jui Ho
- Cancer Biology & Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Direna Alonso-Curbelo
- Cancer Biology & Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Geulah Livshits
- Cancer Biology & Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Richard P. Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Timour Baslan
- Cancer Biology & Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Biomedical Sciences, School of Veterinary Medicine, The University of Pennsylvania, Philadelphia, PA, USA
| | - Janelle Simon
- Cancer Biology & Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sha Tian
- Cancer Biology & Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexandra N. Wuest
- Cancer Biology & Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wei Luan
- Cancer Biology & Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - John E. Wilkinson
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Ignas Masilionis
- Computational & Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nevenka Dimitrova
- Cancer Biology & Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christine A. Iacobuzio-Donahue
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ronan Chaligné
- Computational & Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dana Pe’er
- Computational & Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Joan Massagué
- Cancer Biology & Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Scott W. Lowe
- Cancer Biology & Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
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15
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Felice DD, Alaimo A, Bressan D, Genovesi S, Marmocchi E, Annesi N, Beccaceci G, Dalfovo D, Cutrupi F, Foletto V, Lorenzoni M, Gandolfi F, Kannan S, Verma CS, Vasciaveo A, Shen MM, Romanel A, Chiacchiera F, Cambuli F, Lunardi A. Rarγ -Foxa1 signaling promotes luminal identity in prostate progenitors and is disrupted in prostate cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.06.583256. [PMID: 38496627 PMCID: PMC10942448 DOI: 10.1101/2024.03.06.583256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Retinoic acid (RA) signaling is a master regulator of vertebrate development with crucial roles in directing body axis orientation and tissue differentiation, including in the reproductive system. However, a mechanistic understanding of how RA signaling promotes cell lineage identity in different tissues is often missing. Here, leveraging prostate organoid technology, we demonstrated that RA signaling orchestrates the commitment of adult mouse prostate progenitors to glandular identity, epithelial barrier integrity, and ultimately, proper specification of the prostatic lumen. Mechanistically, RA-dependent RARγ activation promotes the expression of the pioneer factor Foxa1, which synergizes with the androgen pathway for proper luminal expansion, cytoarchitecture and function. FOXA1 nucleotide variants are common in human prostate and breast cancers and considered driver mutations, though their pathogenic mechanism is incompletely understood. Combining functional genetics experiments with structural modeling of FOXA1 folding and chromatin binding analyses, we discovered that FOXA1 F254E255 is a loss-of-function mutation leading to compromised transcriptional function and lack of luminal fate commitment of prostate progenitors. Overall, we define RA as a crucial instructive signal for glandular identity in adult prostate progenitors. We propose deregulation of vitamin A metabolism as a risk factor for benign and malignant prostate disease, and identified cancer associated FOXA1 indels affecting residue F254 as loss-of-function mutations promoting dedifferentiation of adult prostate progenitors. Summary: Retinoic acid signaling orchestrates luminal differentiation of adult prostate progenitors.
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16
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Atanasova KR, Perkins CM, Ratnayake R, Jiang J, Chen QY, Schmittgen TD, Luesch H. Epigenetic small-molecule screen for inhibition and reversal of acinar ductal metaplasia in mouse pancreatic organoids. Front Pharmacol 2024; 15:1335246. [PMID: 38510657 PMCID: PMC10953826 DOI: 10.3389/fphar.2024.1335246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 01/29/2024] [Indexed: 03/22/2024] Open
Abstract
Background: Acinar ductal metaplasia (ADM) is among the earliest initiating events in pancreatic ductal adenocarcinoma (PDAC) development. Methods: We developed a novel morphology-based screen using organoids from wildtype and p48Cre/+ (Cre) mice to discover epigenetic modulators that inhibit or reverse pancreatic ADM more effectively than the broad-spectrum HDAC inhibitor trichostatin A (TSA). Results: Of the 144 compounds screened, nine hits and two additional natural product HDAC inhibitors were validated by dose-response analysis. The class I HDAC inhibitors apicidin and FK228, and the histone methyltransferase inhibitor chaetocin demonstrated pronounced ADM inhibition and reversal without inducing significant cytotoxicity at 1 µM. Thioester prodrug class I HDAC inhibitor largazole attenuated ADM while its disulfide homodimer was effective in both ADM inhibition and reversal. Prioritized compounds were validated for ADM reversal in p48Cre/+; LSL-KrasG12D/+ (KC) mouse organoids using both morphological and molecular endpoints. Molecular index analysis of ADM reversal in KC mouse organoids demonstrated improved activity compared to TSA. Improved prodrug stability translated into a stronger phenotypic and molecular response. RNA-sequencing indicated that angiotensinogen was the top inhibited pathway during ADM reversal. Conclusion: Our findings demonstrate a unique epigenetic mechanism and suggest that the phenotypic screen developed here may be applied to discover potential treatments for PDAC.
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Affiliation(s)
- Kalina R. Atanasova
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, United States
- Center for Natural Products, Drug Discovery and Development, College of Pharmacy, University of Florida, Gainesville, FL, United States
| | - Corey M. Perkins
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, FL, United States
| | - Ranjala Ratnayake
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, United States
- Center for Natural Products, Drug Discovery and Development, College of Pharmacy, University of Florida, Gainesville, FL, United States
| | - Jinmai Jiang
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, FL, United States
| | - Qi-Yin Chen
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, United States
- Center for Natural Products, Drug Discovery and Development, College of Pharmacy, University of Florida, Gainesville, FL, United States
| | - Thomas D. Schmittgen
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, FL, United States
| | - Hendrik Luesch
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, United States
- Center for Natural Products, Drug Discovery and Development, College of Pharmacy, University of Florida, Gainesville, FL, United States
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17
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Yue J, Guo H, Xu P, Ma J, Shi W, Wu Y. Combination of IL-33 with PD-1 blockade augment mILC2s-mediated anti-tumor immunity. Cancer Immunol Immunother 2024; 73:65. [PMID: 38430390 PMCID: PMC10908611 DOI: 10.1007/s00262-023-03580-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 11/02/2023] [Indexed: 03/03/2024]
Abstract
BACKGROUND Group 2 innate lymphoid cells (ILC2s) represent one of the main tissue-specific innate lymphoid cell populations, which are key drivers of cytokine secretion in their occupational niche. However, the precise involvement of ILC2s in cancer immunity and their potential impact on immunotherapeutic approaches remain poorly understood. METHODS The proportion of ILC2s originating from various tissue sources were quantified through flow cytometry, along with the determination of CD4+ T cell and CD8+ T cell percentages. Flow cytometry was also employed to assess IFN-γ production and programmed cell death protein-1 (PD-1) expression in T cells. Immunohistochemistry was utilized to detect IL-33 expression in tumor tissues, while immunofluorescence was employed to confirm the infiltration of ILC2s in both murine and human tumor tissues. RESULTS In this study, we provide evidence that intra-tumoral ILC2s in lung adenocarcinoma (LUAD) exist in a quiescent state. However, the activation of intra-tumoral ILC2s is induced by IL-33 specifically in a natural ILC2s (nILC2, ST2+KLRG1-) phenotype. Considering the pivotal role of PD-1 in cancer immunotherapy and its immunoregulatory functions, we investigated the synergistic effects of IL-33 and anti-PD-1 and found that their combination enhances anti-tumor immunity and improves the efficacy of immunotherapy. Moreover, this combination leads to the upregulation of activated mature ILC2s (mILC2, ST2+KLRG1+) phenotype, thereby highlighting the activated ILC2s as a novel enhancer of the immunoregulatory properties of anti-PD-1. CONCLUSIONS Collectively, these findings underscore the significance of ILC2s and their contribution to the anti-tumor response in the context of cancer immunotherapy. Consequently, the simultaneous targeting of ILC2s and T cells represents a potentially promising and widely applicable strategy for immunotherapeutic interventions.
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Affiliation(s)
- Jiawei Yue
- Department of Orthopaedics, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, Jiangsu, China
| | - Hui Guo
- Department of Laboratory Medicine, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, Jiangsu, China
| | - Peng Xu
- Department of Orthopaedics, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, Jiangsu, China
| | - Jinhong Ma
- Department of Laboratory Medicine, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, Jiangsu, China
| | - Weifeng Shi
- Department of Laboratory Medicine, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, Jiangsu, China.
| | - Yumin Wu
- Department of Laboratory Medicine, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, Jiangsu, China.
- Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Institute of Nano and Soft Materials (FUNSOM) College of Nano Science &Technology (CNST) Suzhou, Jiangsu, 215123, China.
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18
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Uddin MH, Zhang D, Muqbil I, El-Rayes BF, Chen H, Philip PA, Azmi AS. Deciphering cellular plasticity in pancreatic cancer for effective treatments. Cancer Metastasis Rev 2024; 43:393-408. [PMID: 38194153 DOI: 10.1007/s10555-023-10164-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 12/19/2023] [Indexed: 01/10/2024]
Abstract
Cellular plasticity and therapy resistance are critical features of pancreatic cancer, a highly aggressive and fatal disease. The pancreas, a vital organ that produces digestive enzymes and hormones, is often affected by two main types of cancer: the pre-dominant ductal adenocarcinoma and the less common neuroendocrine tumors. These cancers are difficult to treat due to their complex biology characterized by cellular plasticity leading to therapy resistance. Cellular plasticity refers to the capability of cancer cells to change and adapt to different microenvironments within the body which includes acinar-ductal metaplasia, epithelial to mesenchymal/epigenetic/metabolic plasticity, as well as stemness. This plasticity allows heterogeneity of cancer cells, metastasis, and evasion of host's immune system and develops resistance to radiation, chemotherapy, and targeted therapy. To overcome this resistance, extensive research is ongoing exploring the intrinsic and extrinsic factors through cellular reprogramming, chemosensitization, targeting metabolic, key survival pathways, etc. In this review, we discussed the mechanisms of cellular plasticity involving cellular adaptation and tumor microenvironment and provided a comprehensive understanding of its role in therapy resistance and ways to overcome it.
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Affiliation(s)
- Md Hafiz Uddin
- Department of Oncology, Karmanos Cancer Institute, Wayne State University School of Medicine, 4100 John R, HWCRC 740, Detroit, MI, 48201, USA.
| | - Dingqiang Zhang
- Department of Natural Sciences, Lawrence Technological University, 21000 W 10 Mile Rd, Southfield, MI, 48075, USA
| | - Irfana Muqbil
- Department of Natural Sciences, Lawrence Technological University, 21000 W 10 Mile Rd, Southfield, MI, 48075, USA
| | - Bassel F El-Rayes
- Division of Hematology and Oncology, Department of Medicine, O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, 35233, USA
| | - Herbert Chen
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Philip A Philip
- Department of Oncology, Karmanos Cancer Institute, Wayne State University School of Medicine, 4100 John R, HWCRC 740, Detroit, MI, 48201, USA
- Henry Ford Health Systems, Detroit, MI, 48202, USA
| | - Asfar S Azmi
- Department of Oncology, Karmanos Cancer Institute, Wayne State University School of Medicine, 4100 John R, HWCRC 740, Detroit, MI, 48201, USA.
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19
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Han W, Shi D, Yang Q, Li X, Zhang J, Peng C, Yan F. Alteration of chromosome structure impacts gene expressions implicated in pancreatic ductal adenocarcinoma cells. BMC Genomics 2024; 25:206. [PMID: 38395755 PMCID: PMC10885383 DOI: 10.1186/s12864-024-10109-4] [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: 12/13/2023] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy with a five-year survival rate of approximately 10%. Genetic mutations are pivotal drivers in PDAC pathogenesis, but recent investigations also revealed the involvement of non-genetic alterations in the disease development. In this study, we undertook a multi-omics approach, encompassing ATAC-seq, RNA-seq, ChIP-seq, and Hi-C methodologies, to dissect gene expression alterations arising from changes in chromosome accessibility and chromatin three-dimensional interactions in PDAC. RESULTS Our findings indicate that chromosomal structural alterations can lead to abnormal expressions on key genes during PDAC development. Notably, overexpression of oncogenes FGFR2, FOXA2, CYP2R1, and CPOX can be attributed to the augmentation of promoter accessibility, coupled with long-range interactions with distal elements. Additionally, our findings indicate that chromosomal structural alterations caused by genomic instability can lead to abnormal expressions in PDACs. As an example, by analyzing chromosomal changes, we identified a putative oncogenic gene, LPAR1, which shows upregulated expression in both PDAC cell lines and clinical samples. The overexpression is correlated with alterations in LPAR1-associated 3D genome structure and chromatin state. We further demonstrated that high LPAR1 activity is required for enhanced PDAC cell migration in vitro. CONCLUSIONS Collectively, our findings reveal that the chromosomal conformational alterations, in addition to the well-known genetic mutations, are critical for PDAC tumorigenesis.
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Affiliation(s)
- Wenrui Han
- Yunnan Key Laboratory of Cell Metabolism and Diseases, Center for Life Sciences, School of Life Sciences, State Key Laboratory of Conservation and Utilization of Bio- resources in Yunnan, Yunnan University, 650500, Kunming, China
| | - Detong Shi
- Yunnan Key Laboratory of Cell Metabolism and Diseases, Center for Life Sciences, School of Life Sciences, State Key Laboratory of Conservation and Utilization of Bio- resources in Yunnan, Yunnan University, 650500, Kunming, China
| | - Qiu Yang
- Yunnan Key Laboratory of Cell Metabolism and Diseases, Center for Life Sciences, School of Life Sciences, State Key Laboratory of Conservation and Utilization of Bio- resources in Yunnan, Yunnan University, 650500, Kunming, China
| | - Xinxin Li
- Yunnan Key Laboratory of Cell Metabolism and Diseases, Center for Life Sciences, School of Life Sciences, State Key Laboratory of Conservation and Utilization of Bio- resources in Yunnan, Yunnan University, 650500, Kunming, China
| | - Jian Zhang
- Yunnan Key Laboratory of Cell Metabolism and Diseases, Center for Life Sciences, School of Life Sciences, State Key Laboratory of Conservation and Utilization of Bio- resources in Yunnan, Yunnan University, 650500, Kunming, China
- Southeast United Graduate School, 650500, Kunming, China
| | - Cheng Peng
- Yunnan Key Laboratory of Cell Metabolism and Diseases, Center for Life Sciences, School of Life Sciences, State Key Laboratory of Conservation and Utilization of Bio- resources in Yunnan, Yunnan University, 650500, Kunming, China.
| | - Fang Yan
- Yunnan Key Laboratory of Cell Metabolism and Diseases, Center for Life Sciences, School of Life Sciences, State Key Laboratory of Conservation and Utilization of Bio- resources in Yunnan, Yunnan University, 650500, Kunming, China.
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20
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Chatterjee J, Koleske JP, Chao A, Sauerbeck AD, Chen JK, Qi X, Ouyang M, Boggs LG, Idate R, Marco Y Marquez LI, Kummer TT, Gutmann DH. Brain injury drives optic glioma formation through neuron-glia signaling. Acta Neuropathol Commun 2024; 12:21. [PMID: 38308315 PMCID: PMC10837936 DOI: 10.1186/s40478-024-01735-w] [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: 01/10/2024] [Accepted: 01/15/2024] [Indexed: 02/04/2024] Open
Abstract
Tissue injury and tumorigenesis share many cellular and molecular features, including immune cell (T cells, monocytes) infiltration and inflammatory factor (cytokines, chemokines) elaboration. Their common pathobiology raises the intriguing possibility that brain injury could create a tissue microenvironment permissive for tumor formation. Leveraging several murine models of the Neurofibromatosis type 1 (NF1) cancer predisposition syndrome and two experimental methods of brain injury, we demonstrate that both optic nerve crush and diffuse traumatic brain injury induce optic glioma (OPG) formation in mice harboring Nf1-deficient preneoplastic progenitors. We further elucidate the underlying molecular and cellular mechanisms, whereby glutamate released from damaged neurons stimulates IL-1β release by oligodendrocytes to induce microglia expression of Ccl5, a growth factor critical for Nf1-OPG formation. Interruption of this cellular circuit using glutamate receptor, IL-1β or Ccl5 inhibitors abrogates injury-induced glioma progression, thus establishing a causative relationship between injury and tumorigenesis.
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Affiliation(s)
- Jit Chatterjee
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8111, St. Louis, MO, 63110, USA
| | - Joshua P Koleske
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8111, St. Louis, MO, 63110, USA
| | - Astoria Chao
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8111, St. Louis, MO, 63110, USA
| | - Andrew D Sauerbeck
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8111, St. Louis, MO, 63110, USA
| | - Ji-Kang Chen
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8111, St. Louis, MO, 63110, USA
| | - Xuanhe Qi
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8111, St. Louis, MO, 63110, USA
| | - Megan Ouyang
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8111, St. Louis, MO, 63110, USA
| | - Lucy G Boggs
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8111, St. Louis, MO, 63110, USA
| | - Rujuta Idate
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8111, St. Louis, MO, 63110, USA
| | - Lara Isabel Marco Y Marquez
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8111, St. Louis, MO, 63110, USA
| | - Terrence T Kummer
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8111, St. Louis, MO, 63110, USA
| | - David H Gutmann
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8111, St. Louis, MO, 63110, USA.
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21
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Xu Y, Nipper MH, Dominguez AA, Ye Z, Akanuma N, Lopez K, Deng JJ, Arenas D, Sanchez A, Sharkey FE, Court CM, Singhi AD, Wang H, Fernandez-Zapico ME, Sun LZ, Zheng S, Chen Y, Liu J, Wang P. Reconstitution of human PDAC using primary cells reveals oncogenic transcriptomic features at tumor onset. Nat Commun 2024; 15:818. [PMID: 38280869 PMCID: PMC10821902 DOI: 10.1038/s41467-024-45097-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 01/15/2024] [Indexed: 01/29/2024] Open
Abstract
Animal studies have demonstrated the ability of pancreatic acinar cells to transform into pancreatic ductal adenocarcinoma (PDAC). However, the tumorigenic potential of human pancreatic acinar cells remains under debate. To address this gap in knowledge, we expand sorted human acinar cells as 3D organoids and genetically modify them through introduction of common PDAC mutations. The acinar organoids undergo dramatic transcriptional alterations but maintain a recognizable DNA methylation signature. The transcriptomes of acinar organoids are similar to those of disease-specific cell populations. Oncogenic KRAS alone do not transform acinar organoids. However, acinar organoids can form PDAC in vivo after acquiring the four most common driver mutations of this disease. Similarly, sorted ductal cells carrying these genetic mutations can also form PDAC, thus experimentally proving that PDACs can originate from both human acinar and ductal cells. RNA-seq analysis reveal the transcriptional shift from normal acinar cells towards PDACs with enhanced proliferation, metabolic rewiring, down-regulation of MHC molecules, and alterations in the coagulation and complement cascade. By comparing PDAC-like cells with normal pancreas and PDAC samples, we identify a group of genes with elevated expression during early transformation which represent potential early diagnostic biomarkers.
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Affiliation(s)
- Yi Xu
- Department of Cell Systems & Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Michael H Nipper
- Department of Cell Systems & Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Angel A Dominguez
- Department of Cell Systems & Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Zhenqing Ye
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- Department of Population Health Sciences, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Naoki Akanuma
- Department of Cell Systems & Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Kevin Lopez
- Department of Cell Systems & Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Janice J Deng
- Department of Cell Systems & Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Destiny Arenas
- Department of Cell Systems & Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Ava Sanchez
- Department of Cell Systems & Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Francis E Sharkey
- Department of Pathology and Laboratory Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Colin M Court
- Division of Surgical Oncology and Endocrine Surgery, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Aatur D Singhi
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, 15213, USA
| | - Huamin Wang
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Martin E Fernandez-Zapico
- Schulze Center for Novel Therapeutics, Division of Oncology Research, Mayo Clinic, Rochester, MN, 55905, USA
| | - Lu-Zhe Sun
- Department of Cell Systems & Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Siyuan Zheng
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- Department of Population Health Sciences, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Yidong Chen
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- Department of Population Health Sciences, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Jun Liu
- Department of Cell Systems & Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
| | - Pei Wang
- Department of Cell Systems & Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
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22
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Lu C, Wei Y, Abbas M, Agula H, Wang E, Meng Z, Zhang R. Application of Single-Cell Assay for Transposase-Accessible Chromatin with High Throughput Sequencing in Plant Science: Advances, Technical Challenges, and Prospects. Int J Mol Sci 2024; 25:1479. [PMID: 38338756 PMCID: PMC10855595 DOI: 10.3390/ijms25031479] [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: 11/28/2023] [Revised: 01/16/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
The Single-cell Assay for Transposase-Accessible Chromatin with high throughput sequencing (scATAC-seq) has gained increasing popularity in recent years, allowing for chromatin accessibility to be deciphered and gene regulatory networks (GRNs) to be inferred at single-cell resolution. This cutting-edge technology now enables the genome-wide profiling of chromatin accessibility at the cellular level and the capturing of cell-type-specific cis-regulatory elements (CREs) that are masked by cellular heterogeneity in bulk assays. Additionally, it can also facilitate the identification of rare and new cell types based on differences in chromatin accessibility and the charting of cellular developmental trajectories within lineage-related cell clusters. Due to technical challenges and limitations, the data generated from scATAC-seq exhibit unique features, often characterized by high sparsity and noise, even within the same cell type. To address these challenges, various bioinformatic tools have been developed. Furthermore, the application of scATAC-seq in plant science is still in its infancy, with most research focusing on root tissues and model plant species. In this review, we provide an overview of recent progress in scATAC-seq and its application across various fields. We first conduct scATAC-seq in plant science. Next, we highlight the current challenges of scATAC-seq in plant science and major strategies for cell type annotation. Finally, we outline several future directions to exploit scATAC-seq technologies to address critical challenges in plant science, ranging from plant ENCODE(The Encyclopedia of DNA Elements) project construction to GRN inference, to deepen our understanding of the roles of CREs in plant biology.
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Affiliation(s)
- Chao Lu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (C.L.); (Y.W.)
- Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Yunxiao Wei
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (C.L.); (Y.W.)
| | - Mubashir Abbas
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (C.L.); (Y.W.)
| | - Hasi Agula
- Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Edwin Wang
- Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Zhigang Meng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (C.L.); (Y.W.)
| | - Rui Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (C.L.); (Y.W.)
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23
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Levra Levron C, Elettrico L, Duval C, Piacenti G, Proserpio V, Donati G. Bridging tissue repair and epithelial carcinogenesis: epigenetic memory and field cancerization. Cell Death Differ 2024:10.1038/s41418-023-01254-6. [PMID: 38228801 DOI: 10.1038/s41418-023-01254-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/18/2023] [Accepted: 12/21/2023] [Indexed: 01/18/2024] Open
Abstract
The epigenome coordinates spatial-temporal specific gene expression during development and in adulthood, for the maintenance of homeostasis and upon tissue repair. The upheaval of the epigenetic landscape is a key event in the onset of many pathologies including tumours, where epigenetic changes cooperate with genetic aberrations to establish the neoplastic phenotype and to drive cell plasticity during its evolution. DNA methylation, histone modifiers and readers or other chromatin components are indeed often altered in cancers, such as carcinomas that develop in epithelia. Lining the surfaces and the cavities of our body and acting as a barrier from the environment, epithelia are frequently subjected to acute or chronic tissue damages, such as mechanical injuries or inflammatory episodes. These events can activate plasticity mechanisms, with a deep impact on cells' epigenome. Despite being very effective, tissue repair mechanisms are closely associated with tumour onset. Here we review the similarities between tissue repair and carcinogenesis, with a special focus on the epigenetic mechanisms activated by cells during repair and opted by carcinoma cells in multiple epithelia. Moreover, we discuss the recent findings on inflammatory and wound memory in epithelia and describe the epigenetic modifications that characterise them. Finally, as wound memory in epithelial cells promotes carcinogenesis, we highlight how it represents an early step for the establishment of field cancerization.
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Affiliation(s)
- Chiara Levra Levron
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Luca Elettrico
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Carlotta Duval
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Gabriele Piacenti
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Valentina Proserpio
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
- Italian Institute for Genomic Medicine, Candiolo (TO), Italy
| | - Giacomo Donati
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy.
- Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy.
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24
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Mehta A, Stanger BZ. Lineage Plasticity: The New Cancer Hallmark on the Block. Cancer Res 2024; 84:184-191. [PMID: 37963209 PMCID: PMC10841583 DOI: 10.1158/0008-5472.can-23-1067] [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: 04/19/2023] [Revised: 09/12/2023] [Accepted: 11/07/2023] [Indexed: 11/16/2023]
Abstract
Plasticity refers to the ability of cells to adopt a spectrum of states or phenotypes. In cancer, it is a critical contributor to tumor initiation, progression, invasiveness, and therapy resistance, and it has recently been recognized as an emerging cancer hallmark. Plasticity can occur as a result of cell-intrinsic factors (e.g., genetic, transcriptional, or epigenetic fluctuations), or through cell-extrinsic cues (e.g., signaling from components of the tumor microenvironment or selective pressure from therapy). Over the past decade, technological advances, analysis of patient samples, and studies in mouse model systems have led to a deeper understanding of how such plastic states come about. In this review, we discuss: (i) the definition of plasticity; (ii) methods to measure and quantify plasticity; (iii) the clinical relevance of plasticity; and (iv) therapeutic hypotheses to modulate plasticity in the clinic.
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Affiliation(s)
- Arnav Mehta
- Department of Medicine, Massachusetts General Hospital, Boston, MA
- Massachusetts General Hospital Cancer Center, Massachusetts General Hospital, Boston, MA
- Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Ben Z. Stanger
- Abramson Family Cancer Research Institute, Perelman School of Medicine at University of Pennsylvania, Philadelphia, PA
- Department of Medicine, Perelman School of Medicine at University of Pennsylvania, Philadelphia, PA
- Department of Cell and Developmental Biology, Perelman School of Medicine at University of Pennsylvania, Philadelphia, PA
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25
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Wang Y, Ge WL, Wang SJ, Liu YY, Zhang ZH, Hua Y, Zhang XF, Zhang JJ. MiR-548t-5p regulates pancreatic ductal adenocarcinoma metastasis through an IL-33-dependent crosstalk between cancer cells and M2 macrophages. Cell Cycle 2024; 23:169-187. [PMID: 38267823 PMCID: PMC11037285 DOI: 10.1080/15384101.2024.2309026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 01/03/2024] [Indexed: 01/26/2024] Open
Abstract
IL-33 has been associated with pro- and anticancer functions in cancer. However, its role in pancreatic cancer metastasis remains unknown. This study aimed to explore the role of miR-548t-5p/IL-33 axis in the metastasis of pancreatic cancer. Luciferase activity assay, qRT-PCR, Western blot and ELISA were performed to prove whether IL-33 is the target of miR-548t-5p. In vivo metastasis assay and cellular transwell assay were performed to explore the role of miR-548t-5p/IL-33 axis in the invasion and metastasis of pancreatic cancer. Co-culture experiments and immunohistochemistry were performed to observe whether IL-33 affects cell invasion and metastasis dependent on the involvement of M2 macrophages. THP-1 cell induction experiment and flow cytometry were performed to explore the effect of IL-33 on macrophage polarization. CCK-8, colony formation, cell apoptosis, cell cycle, cell wound healing and transwell assay were performed to investigate the effect of IL-33 induced M2 macrophages on cell malignant biological behavior by coculturing pancreatic cancer cells with the conditioned medium (CM) from macrophages. We found that miR-548t-5p regulated the expression and secretion of IL-33 in pancreatic cancer cells by directly targeting IL-33 mRNA. IL-33 secreted by cancer cells promoted the recruitment and activation of macrophages to a M2-like phenotype. In turn, IL-33 induced M2 macrophages promoted the migration and invasion of cancer cells. Moreover, IL-33 affected pancreatic cancer cell invasion dependent on the involvement of M2 macrophages in the co-culture system. Thus, our study suggested that manipulation of this IL-33-dependent crosstalk has a therapeutic potential for the treatment of pancreatic cancer metastasis.
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Affiliation(s)
- Yan Wang
- Endoscopy Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- The Friendship Hospital of Ili Kazakh Autonomous Prefecture, Ili & Jiangsu Joint Institute of Health, Yining, China
| | - Wan-Li Ge
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Shao-Jun Wang
- Department of Biochemistry, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yu-Yong Liu
- Department of Biochemistry, Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhi-Han Zhang
- Department of Biochemistry, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yang Hua
- Department of Biochemistry, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xiong-Fei Zhang
- Department of Biochemistry, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jing-Jing Zhang
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Pancreas Institute, Nanjing Medical University, Nanjing, China
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26
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Falvo DJ, Grimont A, Zumbo P, Fall WB, Yang JL, Osterhoudt A, Pan G, Rendeiro AF, Meng Y, Wilkinson JE, Dündar F, Elemento O, Yantiss RK, Hissong E, Koche R, Betel D, Chandwani R. A reversible epigenetic memory of inflammatory injury controls lineage plasticity and tumor initiation in the mouse pancreas. Dev Cell 2023; 58:2959-2973.e7. [PMID: 38056453 PMCID: PMC10843773 DOI: 10.1016/j.devcel.2023.11.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 07/14/2023] [Accepted: 11/10/2023] [Indexed: 12/08/2023]
Abstract
Inflammation is essential to the disruption of tissue homeostasis and can destabilize the identity of lineage-committed epithelial cells. Here, we employ lineage-traced mouse models, single-cell transcriptomic and chromatin analyses, and CUT&TAG to identify an epigenetic memory of inflammatory injury in the pancreatic acinar cell compartment. Despite resolution of pancreatitis, our data show that acinar cells fail to return to their molecular baseline, with retention of elevated chromatin accessibility and H3K4me1 at metaplasia genes, such that memory represents an incomplete cell fate decision. In vivo, we find this epigenetic memory controls lineage plasticity, with diminished metaplasia in response to a second insult but increased tumorigenesis with an oncogenic Kras mutation. The lowered threshold for oncogenic transformation, in turn, can be restored by blockade of MAPK signaling. Together, we define the chromatin dynamics, molecular encoding, and recall of a prolonged epigenetic memory of inflammatory injury that impacts future responses but remains reversible.
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Affiliation(s)
- David J Falvo
- Department of Surgery, Weill Cornell Medicine, New York, NY 10065, USA; Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Adrien Grimont
- Department of Surgery, Weill Cornell Medicine, New York, NY 10065, USA; Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Paul Zumbo
- Institute for Computational Biomedicine, Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY 10065, USA; Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY 10065, USA
| | - William B Fall
- Department of Surgery, Weill Cornell Medicine, New York, NY 10065, USA; Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Julie L Yang
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Alexa Osterhoudt
- Department of Surgery, Weill Cornell Medicine, New York, NY 10065, USA; Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Grace Pan
- Department of Surgery, Weill Cornell Medicine, New York, NY 10065, USA; Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Andre F Rendeiro
- Institute for Computational Biomedicine, Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY 10065, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Yinuo Meng
- Department of Surgery, Weill Cornell Medicine, New York, NY 10065, USA; Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - John E Wilkinson
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Friederike Dündar
- Institute for Computational Biomedicine, Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY 10065, USA; Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY 10065, USA
| | - Olivier Elemento
- Institute for Computational Biomedicine, Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY 10065, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Rhonda K Yantiss
- Department of Pathology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Erika Hissong
- Department of Pathology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Richard Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Doron Betel
- Institute for Computational Biomedicine, Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY 10065, USA; Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY 10065, USA; Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Rohit Chandwani
- Department of Surgery, Weill Cornell Medicine, New York, NY 10065, USA; Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA; Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY 10065, USA.
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27
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Mzoughi S, Schwarz M, Wang X, Demircioglu D, Ulukaya G, Mohammed K, Tullio FD, Company C, Dramaretska Y, Leushacke M, Giotti B, Lannagan T, Lozano-Ojalvo D, Hasson D, Tsankov AM, Sansom OJ, Marine JC, Barker N, Gargiulo G, Guccione E. A Mutation-driven oncofetal regression fuels phenotypic plasticity in colorectal cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.10.570854. [PMID: 38106050 PMCID: PMC10723414 DOI: 10.1101/2023.12.10.570854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Targeting cancer stem cells (CSCs) is crucial for effective cancer treatment 1 . However, the molecular mechanisms underlying resistance to LGR5 + CSCs depletion in colorectal cancer (CRC) 2,3 remain largely elusive. Here, we unveil the existence of a primitive cell state dubbed the oncofetal (OnF) state, which works in tandem with the LGR5 + stem cells (SCs) to fuel tumor evolution in CRC. OnF cells emerge early during intestinal tumorigenesis and exhibit features of lineage plasticity. Normally suppressed by the Retinoid X Receptor (RXR) in mature SCs, the OnF program is triggered by genetic deletion of the gatekeeper APC. We demonstrate that diminished RXR activity unlocks an epigenetic circuity governed by the cooperative action of YAP and AP1, leading to OnF reprogramming. This high-plasticity state is inherently resistant to conventional chemotherapies and its adoption by LGR5 + CSCs enables them to enter a drug-tolerant state. Furthermore, through phenotypic tracing and ablation experiments, we uncover a functional redundancy between the OnF and stem cell (SC) states and show that targeting both cellular states is essential for sustained tumor regression in vivo . Collectively, these findings establish a mechanistic foundation for developing effective combination therapies with enduring impact on CRC treatment.
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Daniel AR, Su C, Williams NT, Li Z, Huang J, Lopez O, Luo L, Ma Y, Campos LDS, Selitsky SR, Modliszewski JL, Liu S, Hernansaiz-Ballesteros R, Mowery YM, Cardona DM, Lee CL, Kirsch DG. Temporary Knockdown of p53 During Focal Limb Irradiation Increases the Development of Sarcomas. CANCER RESEARCH COMMUNICATIONS 2023; 3:2455-2467. [PMID: 37982576 PMCID: PMC10697056 DOI: 10.1158/2767-9764.crc-23-0104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 09/21/2023] [Accepted: 11/14/2023] [Indexed: 11/21/2023]
Abstract
Approximately half of patients with cancer receive radiotherapy and, as cancer survivorship increases, the low rate of radiation-associated sarcomas is rising. Pharmacologic inhibition of p53 has been proposed as an approach to ameliorate acute injury of normal tissues from genotoxic therapies, but how this might impact the risk of therapy-induced cancer and normal tissue injuries remains unclear. We utilized mice that express a doxycycline (dox)-inducible p53 short hairpin RNA to reduce Trp53 expression temporarily during irradiation. Mice were placed on a dox diet 10 days prior to receiving 30 or 40 Gy hind limb irradiation in a single fraction and then returned to normal chow. Mice were examined weekly for sarcoma development and scored for radiation-induced normal tissue injuries. Radiation-induced sarcomas were subjected to RNA sequencing. Following single high-dose irradiation, 21% of animals with temporary p53 knockdown during irradiation developed a sarcoma in the radiation field compared with 2% of control animals. Following high-dose irradiation, p53 knockdown preserves muscle stem cells, and increases sarcoma development. Mice with severe acute radiation-induced injuries exhibit an increased risk of developing late persistent wounds, which were associated with sarcomagenesis. RNA sequencing revealed radiation-induced sarcomas upregulate genes related to translation, epithelial-mesenchymal transition (EMT), inflammation, and the cell cycle. Comparison of the transcriptomes of human and mouse sarcomas that arose in irradiated tissues revealed regulation of common gene programs, including elevated EMT pathway gene expression. These results suggest that blocking p53 during radiotherapy could minimize acute toxicity while exacerbating late effects including second cancers. SIGNIFICANCE Strategies to prevent or mitigate acute radiation toxicities include pharmacologic inhibition of p53 and other cell death pathways. Our data show that temporarily reducing p53 during irradiation increases late effects including sarcomagenesis.
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Affiliation(s)
- Andrea R. Daniel
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| | - Chang Su
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| | - Nerissa T. Williams
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| | - Zhiguo Li
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina
| | - Jianguo Huang
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| | - Omar Lopez
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| | - Lixia Luo
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| | - Yan Ma
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| | | | - Sara R. Selitsky
- QuantBio LLC, Durham, North Carolina
- Tempus Labs, Inc., Chicago, Illinois
| | | | - Siyao Liu
- QuantBio LLC, Durham, North Carolina
- Tempus Labs, Inc., Chicago, Illinois
| | | | - Yvonne M. Mowery
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
- Department of Head and Neck Surgery & Communication Sciences, Duke University Medical Center, Durham, North Carolina
| | - Diana M. Cardona
- Department of Pathology, Duke University Medical Center, Durham, North Carolina
| | - Chang-Lung Lee
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
- Department of Pathology, Duke University Medical Center, Durham, North Carolina
| | - David G. Kirsch
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina
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Llorente A, Blasco MT, Espuny I, Guiu M, Ballaré C, Blanco E, Caballé A, Bellmunt A, Salvador F, Morales A, Nuñez M, Loren G, Imbastari F, Fidalgo M, Figueras-Puig C, Gibler P, Graupera M, Monteiro F, Riera A, Holen I, Avgustinova A, Di Croce L, Gomis RR. MAF amplification licenses ERα through epigenetic remodelling to drive breast cancer metastasis. Nat Cell Biol 2023; 25:1833-1847. [PMID: 37945904 PMCID: PMC10709142 DOI: 10.1038/s41556-023-01281-y] [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: 09/16/2022] [Accepted: 10/09/2023] [Indexed: 11/12/2023]
Abstract
MAF amplification increases the risk of breast cancer (BCa) metastasis through mechanisms that are still poorly understood yet have important clinical implications. Oestrogen-receptor-positive (ER+) BCa requires oestrogen for both growth and metastasis, albeit by ill-known mechanisms. Here we integrate proteomics, transcriptomics, epigenomics, chromatin accessibility and functional assays from human and syngeneic mouse BCa models to show that MAF directly interacts with oestrogen receptor alpha (ERα), thereby promoting a unique chromatin landscape that favours metastatic spread. We identify metastasis-promoting genes that are de novo licensed following oestrogen exposure in a MAF-dependent manner. The histone demethylase KDM1A is key to the epigenomic remodelling that facilitates the expression of the pro-metastatic MAF/oestrogen-driven gene expression program, and loss of KDM1A activity prevents this metastasis. We have thus determined that the molecular basis underlying MAF/oestrogen-mediated metastasis requires genetic, epigenetic and hormone signals from the systemic environment, which influence the ability of BCa cells to metastasize.
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Affiliation(s)
- Alicia Llorente
- Cancer Science Program, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - María Teresa Blasco
- Cancer Science Program, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
| | - Irene Espuny
- Cancer Science Program, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Marc Guiu
- Cancer Science Program, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Cecilia Ballaré
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Enrique Blanco
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Adrià Caballé
- Biostatistics and Bioinformatics Unit, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Anna Bellmunt
- Cancer Science Program, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Fernando Salvador
- Cancer Science Program, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Andrea Morales
- Cancer Science Program, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Marc Nuñez
- Cancer Science Program, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Guillem Loren
- Cancer Science Program, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Francesca Imbastari
- Cancer Science Program, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Marta Fidalgo
- Cancer Science Program, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Endothelial Pathobiology and Microenvironment Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
| | - Cristina Figueras-Puig
- Cancer Science Program, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Patrizia Gibler
- Cancer Science Program, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Mariona Graupera
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Endothelial Pathobiology and Microenvironment Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Freddy Monteiro
- Functional Genomics Core Facility, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Antoni Riera
- Cancer Science Program, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat de Barcelona, Barcelona, Spain
| | - Ingunn Holen
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | | | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Roger R Gomis
- Cancer Science Program, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
- Universitat de Barcelona, Barcelona, Spain.
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30
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Hu C, Huang C, Hsu M, Chien H, Wu P, Chen Y, Jeng Y, Tang S, Chung M, Shen C, Chang M, Chang Y, Tien Y, Lee W. Oncogenic KRAS, Mucin 4, and Activin A-Mediated Fibroblast Activation Cooperate for PanIN Initiation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301240. [PMID: 37964407 PMCID: PMC10754145 DOI: 10.1002/advs.202301240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 08/22/2023] [Indexed: 11/16/2023]
Abstract
Over 90% of patients with pancreatic ductal adenocarcinoma (PDAC) have oncogenic KRAS mutations. Nevertheless, mutated KRAS alone is insufficient to initiate pancreatic intraepithelial neoplasia (PanIN), the precursor of PDAC. The identities of the other factors/events required to drive PanIN formation remain elusive. Here, optic-clear 3D histology is used to analyze entire pancreases of 2-week-old Pdx1-Cre; LSL-KrasG12D/+ (KC) mice to detect the earliest emergence of PanIN and observed that the occurrence is independent of physical location. Instead, it is found that the earliest PanINs overexpress Muc4 and associate with αSMA+ fibroblasts in both transgenic mice and human specimens. Mechanistically, KrasG12D/+ pancreatic cells upregulate Muc4 through genetic alterations to increase proliferation and fibroblast recruitments via Activin A secretion and consequently enhance cell transformation for PanIN formation. Inhibition of Activin A signaling using Follistatin (FST) diminishes early PanIN-associated fibroblast recruitment, effectively curtailing PanIN initiation and growth in KC mice. These findings emphasize the vital role of interactions between oncogenic KrasG12D/+ -driven genetic alterations and induced microenvironmental changes in PanIN initiation, suggesting potential avenues for early PDAC diagnostic and management approaches.
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Affiliation(s)
- Chun‐Mei Hu
- Genomics Research CenterAcademia SinicaTaipei11529Taiwan
| | - Chien‐Chang Huang
- Genomics Research CenterAcademia SinicaTaipei11529Taiwan
- Biomedical Translation Research CenterAcademia SinicaTaipei11529Taiwan
| | - Min‐Fen Hsu
- Genomics Research CenterAcademia SinicaTaipei11529Taiwan
| | - Hung‐Jen Chien
- Genomics Research CenterAcademia SinicaTaipei11529Taiwan
| | - Pei‐Jung Wu
- Genomics Research CenterAcademia SinicaTaipei11529Taiwan
| | - Yi‐Ing Chen
- Genomics Research CenterAcademia SinicaTaipei11529Taiwan
| | - Yung‐Ming Jeng
- Department of PathologyNational Taiwan University HospitalTaipei10041Taiwan
- Graduate Institute of Pathology, College of MedicineNational Taiwan UniversityTaipei10041Taiwan
| | - Shiue‐Cheng Tang
- Department of Medical ScienceNational Tsing Hua UniversityHsinchu30013Taiwan
| | - Mei‐Hsin Chung
- Department of PathologyNational Taiwan University Hospital−Hsinchu BranchHsinchu30331Taiwan
| | - Chia‐Ning Shen
- Genomics Research CenterAcademia SinicaTaipei11529Taiwan
- Biomedical Translation Research CenterAcademia SinicaTaipei11529Taiwan
| | - Ming‐Chu Chang
- Department of Internal MedicineNational Taiwan University HospitalTaipei10041Taiwan
| | - Yu‐Ting Chang
- Department of Internal MedicineNational Taiwan University HospitalTaipei10041Taiwan
| | - Yu‐Wen Tien
- Department of SurgeryNational Taiwan University HospitalTaipei10041Taiwan
| | - Wen‐Hwa Lee
- Genomics Research CenterAcademia SinicaTaipei11529Taiwan
- Drug Development CenterChina Medical UniversityTaichung40402Taiwan
- Department of Biological ChemistryUniversity of CaliforniaIrvineCA92697USA
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31
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Jiang Z, Zheng X, Li M, Liu M. Improving the prognosis of pancreatic cancer: insights from epidemiology, genomic alterations, and therapeutic challenges. Front Med 2023; 17:1135-1169. [PMID: 38151666 DOI: 10.1007/s11684-023-1050-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 11/15/2023] [Indexed: 12/29/2023]
Abstract
Pancreatic cancer, notorious for its late diagnosis and aggressive progression, poses a substantial challenge owing to scarce treatment alternatives. This review endeavors to furnish a holistic insight into pancreatic cancer, encompassing its epidemiology, genomic characterization, risk factors, diagnosis, therapeutic strategies, and treatment resistance mechanisms. We delve into identifying risk factors, including genetic predisposition and environmental exposures, and explore recent research advancements in precursor lesions and molecular subtypes of pancreatic cancer. Additionally, we highlight the development and application of multi-omics approaches in pancreatic cancer research and discuss the latest combinations of pancreatic cancer biomarkers and their efficacy. We also dissect the primary mechanisms underlying treatment resistance in this malignancy, illustrating the latest therapeutic options and advancements in the field. Conclusively, we accentuate the urgent demand for more extensive research to enhance the prognosis for pancreatic cancer patients.
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Affiliation(s)
- Zhichen Jiang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
- Department of General Surgery, Division of Gastroenterology and Pancreas, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, 310014, China
| | - Xiaohao Zheng
- Department of Pancreatic and Gastric Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Min Li
- Department of Medicine, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA.
| | - Mingyang Liu
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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32
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Huang X, Li L, Ou C, Shen M, Li X, Zhang M, Wu R, Kou X, Gao L, Liu F, Luo R, Wu Q, Gong C. Tumor Environment Regression Therapy Implemented by Switchable Prune-to-Essence Nanoplatform Unleashed Systemic Immune Responses. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303715. [PMID: 37875395 PMCID: PMC10724435 DOI: 10.1002/advs.202303715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 10/01/2023] [Indexed: 10/26/2023]
Abstract
Coevolution of tumor cells and surrounding stroma results in protective protumoral environment, in which abundant vessel, stiff structure and immunosuppression promote each other, cooperatively incurring deterioration and treatment compromise. Reversing suchenvironment may transform tumors from treatment-resistant to treatment-vulnerable. However, effective reversion requires synergistic comprehensive regression of such environment under precise control. Here, the first attempt to collaboratively retrograde coevolutionary tumor environment to pre-oncogenesis status, defined as tumor environment regression therapy, is made for vigorous immune response eruption by a switchable prune-to-essence nanoplatform (Pres) with simplified composition and fabrication process. Through magnetic targeting and multimodal imaging of Pres, tumor environment regression therapy is guided, optimized and accomplished in a trinity way: Antiangiogenesis is executed to rarefy vessels to impede tumor progression. By seizing the time, cancer associated fibroblasts are eliminated to diminish collagen and loosen the stiff structure for deep penetration of Pres, which alternately functioned in deeper tumors, forming a positive feedback loop. Through this loop, immune cell infiltration, immunosuppression mitigation and immunogenic cells death induction are all fulfilled and further escalated in the regressed environment. These transformations consequently unleashed systemic immune responses and generated immune memory against carcinoma. This study provides new insights intotreatment of solid tumors.
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Affiliation(s)
- Xianzhou Huang
- Department of BiotherapyCancer center and State Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041China
| | - Lu Li
- Department of BiotherapyCancer center and State Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041China
| | - Chunqing Ou
- Department of BiotherapyCancer center and State Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041China
| | - Meiling Shen
- Department of BiotherapyCancer center and State Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041China
| | - Xinchao Li
- Department of BiotherapyCancer center and State Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041China
| | - Miaomiao Zhang
- Department of BiotherapyCancer center and State Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041China
| | - Rui Wu
- Department of BiotherapyCancer center and State Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041China
| | - Xiaorong Kou
- Department of BiotherapyCancer center and State Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041China
| | - Ling Gao
- Department of Medical OncologyCancer CenterWest China HospitalSichuan UniversityChengdu610041China
| | - Furong Liu
- Department of BiotherapyCancer center and State Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041China
| | - Rui Luo
- Department of BiotherapyCancer center and State Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041China
| | - Qinjie Wu
- Department of BiotherapyCancer center and State Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041China
| | - Changyang Gong
- Department of BiotherapyCancer center and State Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041China
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Abidov M, Sokolova K, Danilova I, Baykenova M, Gette I, Mychlynina E, Aydin Ozgur B, Gurol AO, Yilmaz MT. Hepatic insulin synthesis increases in rat models of diabetes mellitus type 1 and 2 differently. PLoS One 2023; 18:e0294432. [PMID: 38019818 PMCID: PMC10686419 DOI: 10.1371/journal.pone.0294432] [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: 07/14/2023] [Accepted: 11/01/2023] [Indexed: 12/01/2023] Open
Abstract
Insulin-positive (+) cells (IPCs), detected in multiple organs, are of great interest as a probable alternative to ameliorate pancreatic beta-cells dysfunction and insulin deficiency in diabetes. Liver is a potential source of IPCs due to it common embryological origin with pancreas. We previously demonstrated the presence of IPCs in the liver of healthy and diabetic rats, but detailed description and analysis of the factors, which potentially can induced ectopic hepatic expression of insulin in type 1 (T1D) and type 2 diabetes (T2D), were not performed. In present study we evaluate mass of hepatic IPCs in the rat models of T1D and T2D and discuss factors, which may stimulate it generation: glycaemia, organ injury, involving of hepatic stem/progenitor cell compartment, expression of transcription factors and inflammation. Quantity of IPCs in the liver was up by 1.7-fold in rats with T1D and 10-fold in T2D compared to non-diabetic (ND) rats. We concluded that ectopic hepatic expression of insulin gene is activated by combined action of a number of factors, with inflammation playing a decision role.
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Affiliation(s)
- Musa Abidov
- Institute of Immunopathology and Preventive Medicine, Ljubljana, Slovenia
| | - Ksenia Sokolova
- Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russian Federation
| | - Irina Danilova
- Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russian Federation
| | - Madina Baykenova
- Kostanay Oblast Tuberculosis Dispensary, Kostanay, Republic of Kazakhstan
| | - Irina Gette
- Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russian Federation
| | - Elena Mychlynina
- Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russian Federation
| | - Burcin Aydin Ozgur
- Department of Medical Biology and Genetics, Faculty of Medicine, Demiroglu Bilim University, Istanbul, Turkey
- Diabetes Application and Research Center, Demiroglu Bilim University, Istanbul, Turkey
| | - Ali Osman Gurol
- Department of Immunology, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
- Diabetes Application and Research Center, Istanbul University, Istanbul, Turkey
| | - M. Temel Yilmaz
- International Diabetes Center, Acibadem University, Istanbul, Turkey
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Jing T, Xu X, Wu C, Wei D, Yuan L, Huang Y, Liu Y, Wang B. POH1 facilitates pancreatic carcinogenesis through MYC-driven acinar-to-ductal metaplasia and is a potential therapeutic target. Cancer Lett 2023; 577:216444. [PMID: 37844756 DOI: 10.1016/j.canlet.2023.216444] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/26/2023] [Accepted: 10/11/2023] [Indexed: 10/18/2023]
Abstract
Pancreatic acinar cells undergo acinar-to-ductal metaplasia (ADM), a necessary process for pancreatic ductal adenocarcinoma (PDAC) initiation. However, the regulatory role of POH1, a deubiquitinase linked to several types of cancer, in ADM and PDAC is unclear. In this study, we investigated the role of POH1 in ADM and PDAC using murine models. Our findings suggest that pancreatic-specific deletion of Poh1 alleles attenuates ADM and impairs pancreatic carcinogenesis, improving murine survival. Mechanistically, POH1 deubiquitinates and stabilizes the MYC protein, which potentiates ADM and PDAC. Furthermore, POH1 is highly expressed in PDAC samples, and clinical evidence establishes a positive correlation between aberrantly expressed POH1 and poor prognosis in PDAC patients. Targeting POH1 with a specific small-molecule inhibitor significantly reduces pancreatic tumor formation, highlighting POH1 as a promising therapeutic target for PDAC treatment. Overall, POH1-mediated MYC deubiquitination is crucial for ADM and PDAC onset, and targeting POH1 could be an effective strategy for PDAC treatment, offering new avenues for PDAC targeted therapy.
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Affiliation(s)
- Tiantian Jing
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200032, China
| | - Xiaoli Xu
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200032, China
| | - Chengsi Wu
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200032, China
| | - Dianhui Wei
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200032, China
| | - Lili Yuan
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200032, China
| | - Yiwen Huang
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200032, China
| | - Yizhen Liu
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Boshi Wang
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200032, China.
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Atanasova KR, Perkins CM, Ratnayake R, Jiang J, Chen QY, Schmittgen TD, Luesch H. Epigenetic Small-Molecule Screen for Inhibition and Reversal of Acinar Ductal Metaplasia in Mouse Pancreatic Organoids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.27.567685. [PMID: 38077007 PMCID: PMC10705242 DOI: 10.1101/2023.11.27.567685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Background Acinar ductal metaplasia (ADM) is among the earliest initiating events in pancreatic ductal adenocarcinoma (PDAC) development. Methods We developed a novel morphology-based screen using organoids from wildtype and p48 Cre/+ (Cre) mice to discover epigenetic modulators that inhibit or reverse pancreatic ADM more effectively than the broad-spectrum HDAC inhibitor trichostatin A (TSA). Results Of the 144 compounds screened, nine hits and two additional natural product HDAC inhibitors were validated by dose-response analysis. The class I HDAC inhibitors apicidin and FK228, and the histone methyltransferase inhibitor chaetocin demonstrated pronounced ADM inhibition and reversal without inducing significant cytotoxicity at 1 µM. Thioester prodrug class I HDAC inhibitor largazole attenuated ADM while its disulfide homodimer was effective in both ADM inhibition and reversal. Prioritized compounds were validated for ADM reversal in p48 Cre/+ ;LSL-Kras G12D/+ (KC) mouse organoids using both morphological and molecular endpoints. Molecular index analysis of ADM reversal in KC mouse organoids demonstrated improved activity compared to TSA. Improved prodrug stability translated into a stronger phenotypic and molecular response. RNA-sequencing indicated that angiotensinogen was the top inhibited pathway during ADM reversal. Conclusion Our findings demonstrate a unique epigenetic mechanism and suggest that the phenotypic screen developed here may be applied to discover potential treatments for PDAC.
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Nazaret A, Fan JL, Lavallée VP, Cornish AE, Kiseliovas V, Masilionis I, Chun J, Bowman RL, Eisman SE, Wang J, Shi L, Levine RL, Mazutis L, Blei D, Pe'er D, Azizi E. Deep generative model deciphers derailed trajectories in acute myeloid leukemia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.11.566719. [PMID: 38014231 PMCID: PMC10680623 DOI: 10.1101/2023.11.11.566719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Single-cell genomics has the potential to map cell states and their dynamics in an unbiased way in response to perturbations like disease. However, elucidating the cell-state transitions from healthy to disease requires analyzing data from perturbed samples jointly with unperturbed reference samples. Existing methods for integrating and jointly visualizing single-cell datasets from distinct contexts tend to remove key biological differences or do not correctly harmonize shared mechanisms. We present Decipher, a model that combines variational autoencoders with deep exponential families to reconstruct derailed trajectories ( https://github.com/azizilab/decipher ). Decipher jointly represents normal and perturbed single-cell RNA-seq datasets, revealing shared and disrupted dynamics. It further introduces a novel approach to visualize data, without the need for methods such as UMAP or TSNE. We demonstrate Decipher on data from acute myeloid leukemia patient bone marrow specimens, showing that it successfully characterizes the divergence from normal hematopoiesis and identifies transcriptional programs that become disrupted in each patient when they acquire NPM1 driver mutations.
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Terekhanova NV, Karpova A, Liang WW, Strzalkowski A, Chen S, Li Y, Southard-Smith AN, Iglesia MD, Wendl MC, Jayasinghe RG, Liu J, Song Y, Cao S, Houston A, Liu X, Wyczalkowski MA, Lu RJH, Caravan W, Shinkle A, Naser Al Deen N, Herndon JM, Mudd J, Ma C, Sarkar H, Sato K, Ibrahim OM, Mo CK, Chasnoff SE, Porta-Pardo E, Held JM, Pachynski R, Schwarz JK, Gillanders WE, Kim AH, Vij R, DiPersio JF, Puram SV, Chheda MG, Fuh KC, DeNardo DG, Fields RC, Chen F, Raphael BJ, Ding L. Epigenetic regulation during cancer transitions across 11 tumour types. Nature 2023; 623:432-441. [PMID: 37914932 PMCID: PMC10632147 DOI: 10.1038/s41586-023-06682-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 09/27/2023] [Indexed: 11/03/2023]
Abstract
Chromatin accessibility is essential in regulating gene expression and cellular identity, and alterations in accessibility have been implicated in driving cancer initiation, progression and metastasis1-4. Although the genetic contributions to oncogenic transitions have been investigated, epigenetic drivers remain less understood. Here we constructed a pan-cancer epigenetic and transcriptomic atlas using single-nucleus chromatin accessibility data (using single-nucleus assay for transposase-accessible chromatin) from 225 samples and matched single-cell or single-nucleus RNA-sequencing expression data from 206 samples. With over 1 million cells from each platform analysed through the enrichment of accessible chromatin regions, transcription factor motifs and regulons, we identified epigenetic drivers associated with cancer transitions. Some epigenetic drivers appeared in multiple cancers (for example, regulatory regions of ABCC1 and VEGFA; GATA6 and FOX-family motifs), whereas others were cancer specific (for example, regulatory regions of FGF19, ASAP2 and EN1, and the PBX3 motif). Among epigenetically altered pathways, TP53, hypoxia and TNF signalling were linked to cancer initiation, whereas oestrogen response, epithelial-mesenchymal transition and apical junction were tied to metastatic transition. Furthermore, we revealed a marked correlation between enhancer accessibility and gene expression and uncovered cooperation between epigenetic and genetic drivers. This atlas provides a foundation for further investigation of epigenetic dynamics in cancer transitions.
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Affiliation(s)
- Nadezhda V Terekhanova
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Alla Karpova
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Wen-Wei Liang
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | | | - Siqi Chen
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Yize Li
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Austin N Southard-Smith
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Michael D Iglesia
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Michael C Wendl
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Reyka G Jayasinghe
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Jingxian Liu
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Yizhe Song
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Song Cao
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Andrew Houston
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Xiuting Liu
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Matthew A Wyczalkowski
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Rita Jui-Hsien Lu
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Wagma Caravan
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Andrew Shinkle
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Nataly Naser Al Deen
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - John M Herndon
- Department of Surgery, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
| | - Jacqueline Mudd
- Department of Surgery, Washington University in St Louis, St Louis, MO, USA
| | - Cong Ma
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Hirak Sarkar
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Kazuhito Sato
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Omar M Ibrahim
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Chia-Kuei Mo
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Sara E Chasnoff
- Department of Surgery, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
| | - Eduard Porta-Pardo
- Josep Carreras Leukaemia Research Institute, Barcelona, Spain
- Barcelona Supercomputing Center, Barcelona, Spain
| | - Jason M Held
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
| | - Russell Pachynski
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
| | - Julie K Schwarz
- Department of Radiation Oncology, Washington University in St Louis, St Louis, MO, USA
| | - William E Gillanders
- Department of Surgery, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
| | - Albert H Kim
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
- Department of Neurological Surgery, Washington University in St Louis, St Louis, MO, USA
| | - Ravi Vij
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
| | - John F DiPersio
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
| | - Sidharth V Puram
- Department of Otolaryngology-Head & Neck Surgery, Washington University in St Louis, St Louis, MO, USA
| | - Milan G Chheda
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
| | - Katherine C Fuh
- Department of Obstetrics and Gynecology, University of California, San Francisco, San Francisco, CA, USA
- Department of Obstetrics and Gynecology, Washington University in St Louis, St Louis, MO, USA
| | - David G DeNardo
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
| | - Ryan C Fields
- Department of Surgery, Washington University in St Louis, St Louis, MO, USA.
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA.
| | - Feng Chen
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA.
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA.
| | - Benjamin J Raphael
- Department of Computer Science, Princeton University, Princeton, NJ, USA.
| | - Li Ding
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA.
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA.
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA.
- Department of Genetics, Washington University in St Louis, St Louis, MO, USA.
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Caronni N, La Terza F, Vittoria FM, Barbiera G, Mezzanzanica L, Cuzzola V, Barresi S, Pellegatta M, Canevazzi P, Dunsmore G, Leonardi C, Montaldo E, Lusito E, Dugnani E, Citro A, Ng MSF, Schiavo Lena M, Drago D, Andolfo A, Brugiapaglia S, Scagliotti A, Mortellaro A, Corbo V, Liu Z, Mondino A, Dellabona P, Piemonti L, Taveggia C, Doglioni C, Cappello P, Novelli F, Iannacone M, Ng LG, Ginhoux F, Crippa S, Falconi M, Bonini C, Naldini L, Genua M, Ostuni R. IL-1β + macrophages fuel pathogenic inflammation in pancreatic cancer. Nature 2023; 623:415-422. [PMID: 37914939 DOI: 10.1038/s41586-023-06685-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 09/27/2023] [Indexed: 11/03/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease with high resistance to therapies1. Inflammatory and immunomodulatory signals co-exist in the pancreatic tumour microenvironment, leading to dysregulated repair and cytotoxic responses. Tumour-associated macrophages (TAMs) have key roles in PDAC2, but their diversity has prevented therapeutic exploitation. Here we combined single-cell and spatial genomics with functional experiments to unravel macrophage functions in pancreatic cancer. We uncovered an inflammatory loop between tumour cells and interleukin-1β (IL-1β)-expressing TAMs, a subset of macrophages elicited by a local synergy between prostaglandin E2 (PGE2) and tumour necrosis factor (TNF). Physical proximity with IL-1β+ TAMs was associated with inflammatory reprogramming and acquisition of pathogenic properties by a subset of PDAC cells. This occurrence was an early event in pancreatic tumorigenesis and led to persistent transcriptional changes associated with disease progression and poor outcomes for patients. Blocking PGE2 or IL-1β activity elicited TAM reprogramming and antagonized tumour cell-intrinsic and -extrinsic inflammation, leading to PDAC control in vivo. Targeting the PGE2-IL-1β axis may enable preventive or therapeutic strategies for reprogramming of immune dynamics in pancreatic cancer.
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Affiliation(s)
- Nicoletta Caronni
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy.
| | - Federica La Terza
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Francesco M Vittoria
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Giulia Barbiera
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Luca Mezzanzanica
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Vincenzo Cuzzola
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Simona Barresi
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | | | - Garett Dunsmore
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Carlo Leonardi
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Elisa Montaldo
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Eleonora Lusito
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Erica Dugnani
- Diabetes Research Institute (DRI), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Antonio Citro
- Diabetes Research Institute (DRI), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Melissa S F Ng
- Singapore Immunology Network (SIgN), A*STAR, Singapore, Singapore
| | | | - Denise Drago
- Center for Omics Sciences (COSR), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Annapaola Andolfo
- Center for Omics Sciences (COSR), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Silvia Brugiapaglia
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Alessandro Scagliotti
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Alessandra Mortellaro
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Zhaoyuan Liu
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Anna Mondino
- IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Lorenzo Piemonti
- Vita-Salute San Raffaele University, Milan, Italy
- Diabetes Research Institute (DRI), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Claudio Doglioni
- Vita-Salute San Raffaele University, Milan, Italy
- IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Paola Cappello
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Francesco Novelli
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Matteo Iannacone
- Vita-Salute San Raffaele University, Milan, Italy
- IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Lai Guan Ng
- Shanghai Immune Therapy Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Florent Ginhoux
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Singapore Immunology Network (SIgN), A*STAR, Singapore, Singapore
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Translational Immunology Institute, SingHealth/Duke-NUS Academic Medical Centre, Singapore, Singapore
| | - Stefano Crippa
- Vita-Salute San Raffaele University, Milan, Italy
- Pancreas Translational and Clinical Research Center, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Massimo Falconi
- Vita-Salute San Raffaele University, Milan, Italy
- Pancreas Translational and Clinical Research Center, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Chiara Bonini
- Vita-Salute San Raffaele University, Milan, Italy
- IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Luigi Naldini
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Marco Genua
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Renato Ostuni
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy.
- Vita-Salute San Raffaele University, Milan, Italy.
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Ruiz CF, Garcia C, Jacox JB, Lawres L, Muzumdar MD. Decoding the obesity-cancer connection: lessons from preclinical models of pancreatic adenocarcinoma. Life Sci Alliance 2023; 6:e202302228. [PMID: 37648285 PMCID: PMC10474221 DOI: 10.26508/lsa.202302228] [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: 06/20/2023] [Revised: 08/15/2023] [Accepted: 08/21/2023] [Indexed: 09/01/2023] Open
Abstract
Obesity is a metabolic state of energy excess and a risk factor for over a dozen cancer types. Because of the rising worldwide prevalence of obesity, decoding the mechanisms by which obesity promotes tumor initiation and early progression is a societal imperative and could broadly impact human health. Here, we review results from preclinical models that link obesity to cancer, using pancreatic adenocarcinoma as a paradigmatic example. We discuss how obesity drives cancer development by reprogramming the pretumor or tumor cell and its micro- and macro-environments. Specifically, we describe evidence for (1) altered cellular metabolism, (2) hormone dysregulation, (3) inflammation, and (4) microbial dysbiosis in obesity-driven pancreatic tumorigenesis, denoting variables that confound interpretation of these studies, and highlight remaining gaps in knowledge. Recent advances in preclinical modeling and emerging unbiased analytic approaches will aid in further unraveling the complex link between obesity and cancer, informing novel strategies for prevention, interception, and therapy in pancreatic adenocarcinoma and other obesity-associated cancers.
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Affiliation(s)
- Christian F Ruiz
- https://ror.org/03v76x132 Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- https://ror.org/03v76x132 Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - Cathy Garcia
- https://ror.org/03v76x132 Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- https://ror.org/03v76x132 Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - Jeremy B Jacox
- https://ror.org/03v76x132 Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- https://ror.org/03v76x132 Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
- https://ror.org/03v76x132 Department of Medicine (Section of Medical Oncology), Yale University School of Medicine, New Haven, CT, USA
| | - Lauren Lawres
- https://ror.org/03v76x132 Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Mandar D Muzumdar
- https://ror.org/03v76x132 Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- https://ror.org/03v76x132 Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
- https://ror.org/03v76x132 Department of Medicine (Section of Medical Oncology), Yale University School of Medicine, New Haven, CT, USA
- https://ror.org/03v76x132 Yale Cancer Center, Yale University, New Haven, CT, USA
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Nishimon R, Yoshida K, Sanuki F, Nakashima Y, Miyake T, Sato T, Tomiyama Y, Nishina S, Moriya T, Shiotani A, Hino K. Pancreatic ductal adenocarcinoma with acinar-to-ductal metaplasia-like cancer cells shows increased cellular proliferation. Pancreatology 2023; 23:811-817. [PMID: 37659916 DOI: 10.1016/j.pan.2023.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 08/09/2023] [Accepted: 08/25/2023] [Indexed: 09/04/2023]
Abstract
BACKGROUND/OBJECTIVES Acinar-to-ductal metaplasia (ADM) has been shown to contribute to the development of pancreatic ductal adenocarcinoma (PDAC) in genetically engineered mouse models, but little is known about whether acinar cell plasticity contributes to carcinogenesis in human PDAC. We aimed to assess whether cancer cells that stain positive for amylase and CK19 (ADM-like cancer cells) are present in human resected PDAC and to investigate their role in tumor progression. METHODS We immunohistochemically investigated the presence of ADM-like cancer cells, and compared the clinical and histological parameters of PDAC patients with and without ADM-like cancer cells. RESULTS ADM-like cancer cells were detected in 16 of 60 (26.7%) PDAC specimens. Positive staining for anterior gradient protein 2 (AGR2) was observed in 14 of 16 (87.5%) PDAC specimens with ADM-like cancer cells. On the other hand, the intensity of AGR2 expression (negative, low/moderate or high) was lower in PDAC with ADM-like cancer cells (9/7) than in PDAC without these cells (11/33) (P = 0.032). The presence of ADM-like cancer cells was significantly correlated with increased cell proliferation (P = 0.012) and tended to be associated with MUC1 expression (P = 0.067). CONCLUSIONS These results indicated that acinar cells may act as the origin of human PDAC, and that their presence may be useful for the stratification of human PDAC to predict prognosis.
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Affiliation(s)
- Reiji Nishimon
- Department of Gastroenterology and Hepatology, Kawasaki Medical School, Kurashiki, Japan
| | - Koji Yoshida
- Department of Gastroenterology and Hepatology, Kawasaki Medical School, Kurashiki, Japan
| | - Fumiaki Sanuki
- Department of Pathology, Kawasaki Medical School, Kurashiki, Japan
| | - Yoshihiro Nakashima
- Department of Gastroenterology and Hepatology, Kawasaki Medical School, Kurashiki, Japan
| | - Tomoo Miyake
- Department of Gastroenterology and Hepatology, Kawasaki Medical School, Kurashiki, Japan
| | - Tatsuki Sato
- Department of Gastroenterology and Hepatology, Kawasaki Medical School, Kurashiki, Japan
| | - Yasuyuki Tomiyama
- Department of Gastroenterology and Hepatology, Kawasaki Medical School, Kurashiki, Japan
| | - Sohji Nishina
- Department of Gastroenterology and Hepatology, Kawasaki Medical School, Kurashiki, Japan
| | - Takuya Moriya
- Department of Pathology, Kawasaki Medical School, Kurashiki, Japan
| | - Akiko Shiotani
- Department of Gastroenterology and Hepatology, Kawasaki Medical School, Kurashiki, Japan
| | - Keisuke Hino
- Department of Gastroenterology and Hepatology, Kawasaki Medical School, Kurashiki, Japan.
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41
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Grillo G, Keshavarzian T, Linder S, Arlidge C, Mout L, Nand A, Teng M, Qamra A, Zhou S, Kron KJ, Murison A, Hawley JR, Fraser M, van der Kwast TH, Raj GV, He HH, Zwart W, Lupien M. Transposable Elements Are Co-opted as Oncogenic Regulatory Elements by Lineage-Specific Transcription Factors in Prostate Cancer. Cancer Discov 2023; 13:2470-2487. [PMID: 37694973 PMCID: PMC10618745 DOI: 10.1158/2159-8290.cd-23-0331] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 07/30/2023] [Accepted: 09/08/2023] [Indexed: 09/12/2023]
Abstract
Transposable elements hold regulatory functions that impact cell fate determination by controlling gene expression. However, little is known about the transcriptional machinery engaged at transposable elements in pluripotent and mature versus oncogenic cell states. Through positional analysis over repetitive DNA sequences of H3K27ac chromatin immunoprecipitation sequencing data from 32 normal cell states, we report pluripotent/stem and mature cell state-specific "regulatory transposable elements." Pluripotent/stem elements are binding sites for pluripotency factors (e.g., NANOG, SOX2, OCT4). Mature cell elements are docking sites for lineage-specific transcription factors, including AR and FOXA1 in prostate epithelium. Expanding the analysis to prostate tumors, we identify a subset of regulatory transposable elements shared with pluripotent/stem cells, including Tigger3a. Using chromatin editing technology, we show how such elements promote prostate cancer growth by regulating AR transcriptional activity. Collectively, our results suggest that oncogenesis arises from lineage-specific transcription factors hijacking pluripotent/stem cell regulatory transposable elements. SIGNIFICANCE We show that oncogenesis relies on co-opting transposable elements from pluripotent stem cells as regulatory elements altering the recruitment of lineage-specific transcription factors. We further discover how co-option is dependent on active chromatin states with important implications for developing treatment options against drivers of oncogenesis across the repetitive DNA. This article is featured in Selected Articles from This Issue, p. 2293.
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Affiliation(s)
- Giacomo Grillo
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Tina Keshavarzian
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Simon Linder
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Christopher Arlidge
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Lisanne Mout
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ankita Nand
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Mona Teng
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Aditi Qamra
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Stanley Zhou
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Ken J. Kron
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Alex Murison
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - James R. Hawley
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Michael Fraser
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Theodorus H. van der Kwast
- Laboratory Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ganesh V. Raj
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Housheng Hansen He
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
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42
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Zhou RW, Harpaz N, Itzkowitz SH, Parsons RE. Molecular mechanisms in colitis-associated colorectal cancer. Oncogenesis 2023; 12:48. [PMID: 37884500 PMCID: PMC10603140 DOI: 10.1038/s41389-023-00492-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/30/2023] [Accepted: 09/11/2023] [Indexed: 10/28/2023] Open
Abstract
Sustained chronic inflammation of the large intestine leads to tissue damage and repair, which is associated with an increased incidence of colitis-associated colorectal cancer (CAC). The genetic makeup of CAC is somewhat similar to sporadic colorectal carcinoma (sCRC), but there are differences in the sequence and timing of alterations in the carcinogenesis process. Several models have been developed to explain the development of CAC, particularly the "field cancerization" model, which proposes that chronic inflammation accelerates mutagenesis and selects for the clonal expansion of phenotypically normal, pro-tumorigenic cells. In contrast, the "Big Bang" model posits that tumorigenic clones with multiple driver gene mutations emerge spontaneously. The details of CAC tumorigenesis-and how they differ from sCRC-are not yet fully understood. In this Review, we discuss recent genetic, epigenetic, and environmental findings related to CAC pathogenesis in the past five years, with a focus on unbiased, high-resolution genetic profiling of non-dysplastic field cancerization in the context of inflammatory bowel disease (IBD).
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Affiliation(s)
- Royce W Zhou
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Molecular Medicine Program, Internal Medicine Residency Program, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Noam Harpaz
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Steven H Itzkowitz
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Ramon E Parsons
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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43
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Cammareri P, Myant KB. Be like water, my cells: cell plasticity and the art of transformation. Front Cell Dev Biol 2023; 11:1272730. [PMID: 37886398 PMCID: PMC10598658 DOI: 10.3389/fcell.2023.1272730] [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: 08/04/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023] Open
Abstract
Cellular plasticity defines the capacity of cells to adopt distinct identities during development, tissue homeostasis and regeneration. Dynamic fluctuations between different states, within or across lineages, are regulated by changes in chromatin accessibility and in gene expression. When deregulated, cellular plasticity can contribute to cancer initiation and progression. Cancer cells are remarkably plastic which contributes to phenotypic and functional heterogeneity within tumours as well as resistance to targeted therapies. It is for these reasons that the scientific community has become increasingly interested in understanding the molecular mechanisms governing cancer cell plasticity. The purpose of this mini-review is to discuss different examples of cellular plasticity associated with metaplasia and epithelial-mesenchymal transition with a focus on therapy resistance.
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Affiliation(s)
| | - Kevin B. Myant
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, United Kingdom
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44
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Jassim A, Rahrmann EP, Simons BD, Gilbertson RJ. Cancers make their own luck: theories of cancer origins. Nat Rev Cancer 2023; 23:710-724. [PMID: 37488363 DOI: 10.1038/s41568-023-00602-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/20/2023] [Indexed: 07/26/2023]
Abstract
Cancer has been a leading cause of death for decades. This dismal statistic has increased efforts to prevent the disease or to detect it early, when treatment is less invasive, relatively inexpensive and more likely to cure. But precisely how tissues are transformed continues to provoke controversy and debate, hindering cancer prevention and early intervention strategies. Various theories of cancer origins have emerged, including the suggestion that it is 'bad luck': the inevitable consequence of random mutations in proliferating stem cells. In this Review, we discuss the principal theories of cancer origins and the relative importance of the factors that underpin them. The body of available evidence suggests that developing and ageing tissues 'walk a tightrope', retaining adequate levels of cell plasticity to generate and maintain tissues while avoiding overstepping into transformation. Rather than viewing cancer as 'bad luck', understanding the complex choreography of cell intrinsic and extrinsic factors that characterize transformation holds promise to discover effective new ways to prevent, detect and stop cancer before it becomes incurable.
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Affiliation(s)
- Amir Jassim
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Eric P Rahrmann
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Ben D Simons
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge, UK
| | - Richard J Gilbertson
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK.
- Department of Oncology, University of Cambridge, Cambridge, UK.
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45
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Shields MA, Metropulos AE, Spaulding C, Hirose T, Ohno S, Pham TN, Munshi HG. BET inhibition rescues ciliogenesis and ameliorates pancreatitis-driven phenotypic changes in mice with Par3 loss. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.14.557654. [PMID: 37745543 PMCID: PMC10515915 DOI: 10.1101/2023.09.14.557654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The apical-basal polarity of pancreatic acinar cells is essential for maintaining tissue architecture. However, the mechanisms by which polarity proteins regulate acinar pancreas tissue homeostasis are poorly understood. Here, we evaluate the role of Par3 in acinar pancreas injury and homeostasis. While Par3 loss in the mouse pancreas disrupts tight junctions, Par3 loss is dispensable for pancreatogenesis. However, with aging, Par3 loss results in low-grade inflammation, acinar degeneration, and pancreatic lipomatosis. Par3 loss also exacerbates pancreatitis-induced acinar cell loss, resulting in pronounced pancreatic lipomatosis and failure to regenerate. Moreover, Par3 loss in mice harboring mutant Kras causes extensive pancreatic intraepithelial neoplastic (PanIN) lesions and large pancreatic cysts. We also show that Par3 loss restricts injury-induced primary ciliogenesis. Significantly, targeting BET proteins enhances primary ciliogenesis during pancreatitis-induced injury and, in mice with Par3 loss, limits pancreatitis-induced acinar loss and facilitates acinar cell regeneration. Combined, this study demonstrates how Par3 restrains pancreatitis- and Kras-induced changes in the pancreas and identifies a potential role for BET inhibitors to attenuate pancreas injury and facilitate pancreas tissue regeneration.
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Affiliation(s)
- Mario A. Shields
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- The Robert H. Lurie Comprehensive Cancer Center, Chicago, IL, USA
| | - Anastasia E. Metropulos
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Jesse Brown VA Medical Center, Chicago, IL, USA
| | - Christina Spaulding
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Jesse Brown VA Medical Center, Chicago, IL, USA
| | - Tomonori Hirose
- Department of Molecular Biology, Yokohama City University School of Medicine, Yokohama, Japan
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Shigeo Ohno
- Department of Molecular Biology, Yokohama City University School of Medicine, Yokohama, Japan
| | - Thao N.D. Pham
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- The Robert H. Lurie Comprehensive Cancer Center, Chicago, IL, USA
| | - Hidayatullah G. Munshi
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- The Robert H. Lurie Comprehensive Cancer Center, Chicago, IL, USA
- Jesse Brown VA Medical Center, Chicago, IL, USA
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46
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Panzeri I, Fagnocchi L, Apostle S, Tompkins M, Wolfrum E, Madaj Z, Hostetter G, Liu Y, Schaefer K, Chih-Hsiang Y, Bergsma A, Drougard A, Dror E, Chandler D, Schramek D, Triche TJ, Pospisilik JA. Developmental priming of cancer susceptibility. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.12.557446. [PMID: 37745326 PMCID: PMC10515831 DOI: 10.1101/2023.09.12.557446] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
DNA mutations are necessary drivers of cancer, yet only a small subset of mutated cells go on to cause the disease. To date, the mechanisms that determine which rare subset of cells transform and initiate tumorigenesis remain unclear. Here, we take advantage of a unique model of intrinsic developmental heterogeneity (Trim28+/D9) and demonstrate that stochastic early life epigenetic variation can trigger distinct cancer-susceptibility 'states' in adulthood. We show that these developmentally primed states are characterized by differential methylation patterns at typically silenced heterochromatin, and that these epigenetic signatures are detectable as early as 10 days of age. The differentially methylated loci are enriched for genes with known oncogenic potential. These same genes are frequently mutated in human cancers, and their dysregulation correlates with poor prognosis. These results provide proof-of-concept that intrinsic developmental heterogeneity can prime individual, life-long cancer risk.
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Affiliation(s)
- Ilaria Panzeri
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Luca Fagnocchi
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Stefanos Apostle
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Megan Tompkins
- Vivarium and Transgenics Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Emily Wolfrum
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Zachary Madaj
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Galen Hostetter
- Pathology and Biorepository Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Yanqing Liu
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Kristen Schaefer
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
- Department of Genetics and Genome Science, Case Western Reserve University, Cleveland, Ohio, USA
| | - Yang Chih-Hsiang
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA USA
| | - Alexis Bergsma
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
- Parkinson’s Disease Center, Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
| | - Anne Drougard
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Erez Dror
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Darrell Chandler
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Daniel Schramek
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Timothy J. Triche
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - J. Andrew Pospisilik
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
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47
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Bednar F, Pasca di Magliano M. Calligraphy tool offers clues to the origin of pancreatic cancer. Nature 2023; 621:265-266. [PMID: 37587278 DOI: 10.1038/d41586-023-02518-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
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48
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Liu X, Liu X, Du Y, Zou D, Tian C, Li Y, Lan X, David CJ, Sun Q, Chen M. Aberrant accumulation of Kras-dependent pervasive transcripts during tumor progression renders cancer cells dependent on PAF1 expression. Cell Rep 2023; 42:112979. [PMID: 37572321 DOI: 10.1016/j.celrep.2023.112979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 06/05/2023] [Accepted: 07/31/2023] [Indexed: 08/14/2023] Open
Abstract
KRAS is the most commonly mutated oncogene in human cancer, and mutant KRAS is responsible for over 90% of pancreatic ductal adenocarcinoma (PDAC), the most lethal cancer. Here, we show that RNA polymerase II-associated factor 1 complex (PAF1C) is specifically required for survival of PDAC but not normal adult pancreatic cells. We show that PAF1C maintains cancer cell genomic stability by restraining overaccumulation of enhancer RNAs (eRNAs) and promoter upstream transcripts (PROMPTs) driven by mutant Kras. Loss of PAF1C leads to cancer-specific lengthening and accumulation of pervasive transcripts on chromatin and concomitant aberrant R-loop formation and DNA damage, which, in turn, trigger cell death. We go on to demonstrate that the global transcriptional hyperactivation driven by Kras signaling during tumorigenesis underlies the specific demand for PAF1C by cancer cells. Our work provides insights into how enhancer transcription hyperactivation causes general transcription factor addiction during tumorigenesis.
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Affiliation(s)
- Xinhong Liu
- State Key Laboratory of Molecular Oncology, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xiangzheng Liu
- State Key Laboratory of Molecular Oncology, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yingxue Du
- Tsinghua University School of Life Sciences, Beijing 100084, China
| | - Di Zou
- State Key Laboratory of Molecular Oncology, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Chen Tian
- State Key Laboratory of Molecular Oncology, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yong Li
- State Key Laboratory of Molecular Oncology, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xun Lan
- State Key Laboratory of Molecular Oncology, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Charles J David
- State Key Laboratory of Molecular Oncology, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Qianwen Sun
- Tsinghua University School of Life Sciences, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Mo Chen
- State Key Laboratory of Molecular Oncology, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing 100084, China.
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49
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Pérez-González A, Bévant K, Blanpain C. Cancer cell plasticity during tumor progression, metastasis and response to therapy. NATURE CANCER 2023; 4:1063-1082. [PMID: 37537300 PMCID: PMC7615147 DOI: 10.1038/s43018-023-00595-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 06/01/2023] [Indexed: 08/05/2023]
Abstract
Cell plasticity represents the ability of cells to be reprogrammed and to change their fate and identity, enabling homeostasis restoration and tissue regeneration following damage. Cell plasticity also contributes to pathological conditions, such as cancer, enabling cells to acquire new phenotypic and functional features by transiting across distinct cell states that contribute to tumor initiation, progression, metastasis and resistance to therapy. Here, we review the intrinsic and extrinsic mechanisms driving cell plasticity that promote tumor growth and proliferation as well as metastasis and drug tolerance. Finally, we discuss how cell plasticity could be exploited for anti-cancer therapy.
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Affiliation(s)
- Andrea Pérez-González
- Laboratory of Stem Cells and Cancer, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Kevin Bévant
- Laboratory of Stem Cells and Cancer, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Cédric Blanpain
- Laboratory of Stem Cells and Cancer, Université Libre de Bruxelles (ULB), Brussels, Belgium.
- WELBIO, ULB, Bruxelles, Belgium.
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50
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Botten GA, Zhang Y, Dudnyk K, Kim YJ, Liu X, Sanders JT, Imanci A, Droin N, Cao H, Kaphle P, Dickerson KE, Kumar KR, Chen M, Chen W, Solary E, Ly P, Zhou J, Xu J. Structural variation cooperates with permissive chromatin to control enhancer hijacking-mediated oncogenic transcription. Blood 2023; 142:336-351. [PMID: 36947815 PMCID: PMC10447518 DOI: 10.1182/blood.2022017555] [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: 06/28/2022] [Revised: 02/24/2023] [Accepted: 03/10/2023] [Indexed: 03/24/2023] Open
Abstract
Structural variants (SVs) involving enhancer hijacking can rewire chromatin topologies to cause oncogene activation in human cancers, including hematologic malignancies; however, because of the lack of tools to assess their effects on gene regulation and chromatin organization, the molecular determinants for the functional output of enhancer hijacking remain poorly understood. Here, we developed a multimodal approach to integrate genome sequencing, chromosome conformation, chromatin state, and transcriptomic alteration for quantitative analysis of transcriptional effects and structural reorganization imposed by SVs in leukemic genomes. We identified known and new pathogenic SVs, including recurrent t(5;14) translocations that cause the hijacking of BCL11B enhancers for the allele-specific activation of TLX3 in a subtype of pediatric leukemia. Epigenetic perturbation of SV-hijacked BCL11B enhancers impairs TLX3 transcription, which are required for the growth of t(5;14) leukemia cells. By CRISPR engineering of patient-derived t(5;14) in isogenic leukemia cells, we uncovered a new mechanism whereby the transcriptional output of SV-induced BCL11B enhancer hijacking is dependent on the loss of DNA hypermethylation at the TLX3 promoter. Our results highlight the importance of the cooperation between genetic alteration and permissive chromatin as a critical determinant of SV-mediated oncogene activation, with implications for understanding aberrant gene transcription after epigenetic therapies in patients with leukemia. Hence, leveraging the interdependency of genetic alteration on chromatin variation may provide new opportunities to reprogram gene regulation as targeted interventions in human disease.
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Affiliation(s)
- Giovanni A. Botten
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX
| | - Yuannyu Zhang
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX
- Department of Pathology, Center of Excellence for Leukemia Studies, St. Jude Children’s Research Hospital, Memphis, TN
| | - Kseniia Dudnyk
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Yoon Jung Kim
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX
| | - Xin Liu
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX
| | - Jacob T. Sanders
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Aygun Imanci
- Université Paris-Saclay, INSERM U1287, Gustave Roussy Cancer Center, Villejuif, France
| | - Nathalie Droin
- Université Paris-Saclay, INSERM U1287, Gustave Roussy Cancer Center, Villejuif, France
| | - Hui Cao
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX
- Department of Pathology, Center of Excellence for Leukemia Studies, St. Jude Children’s Research Hospital, Memphis, TN
| | - Pranita Kaphle
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX
| | - Kathryn E. Dickerson
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX
| | - Kirthi R. Kumar
- Medical City Dallas, Medical City Children’s Hospital, Dallas, TX
| | - Mingyi Chen
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Weina Chen
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Eric Solary
- Université Paris-Saclay, INSERM U1287, Gustave Roussy Cancer Center, Villejuif, France
| | - Peter Ly
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Jian Zhou
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Jian Xu
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX
- Department of Pathology, Center of Excellence for Leukemia Studies, St. Jude Children’s Research Hospital, Memphis, TN
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