1
|
Austin R, Aifantis I. Hematopoietic Clonal Evolution Goes Spatial. Blood Cancer Discov 2024; 5:139-141. [PMID: 38651690 DOI: 10.1158/2643-3230.bcd-24-0057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024] Open
Abstract
SUMMARY The spatial distribution of cells carrying clonal hematopoiesis mutations in the bone marrow and the potential role of interactions with the microenvironment are largely unknown. This study takes clonal evolution to the spatial level by describing a novel technique examining the spatial location of mutated clones in the bone marrow and the first evidence that mutated hematopoietic clones are spatially constrained and have heterogenous locations within millimeters of distance. See related article by Young et al., p. 153 (10).
Collapse
Affiliation(s)
- Rebecca Austin
- Department of Pathology, NYU Grossman School of Medicine, New York, New York
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, New York
| | - Iannis Aifantis
- Department of Pathology, NYU Grossman School of Medicine, New York, New York
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, New York
| |
Collapse
|
2
|
Wang J, Lu Q, Chen X, Aifantis I. Targeting MHC-I inhibitory pathways for cancer immunotherapy. Trends Immunol 2024; 45:177-187. [PMID: 38433029 DOI: 10.1016/j.it.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/31/2024] [Accepted: 01/31/2024] [Indexed: 03/05/2024]
Abstract
The MHC-I antigen presentation (AP) pathway is key to shaping mammalian CD8+ T cell immunity, with its aberrant expression closely linked to low tumor immunogenicity and immunotherapy resistance. While significant attention has been given to genetic mutations and downregulation of positive regulators that are essential for MHC-I AP, there is a growing interest in understanding how tumors actively evade MHC-I expression and/or AP through the induction of MHC-I inhibitory pathways. This emerging field of study may offer more viable therapeutic targets for future cancer immunotherapy. Here, we explore potential mechanisms by which cancer cells evade MHC-I AP and function and propose therapeutic strategies that might target these MHC-I inhibitors to restore impaired T cell immunity within the tumor microenvironment (TME).
Collapse
Affiliation(s)
- Jun Wang
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA.
| | - Qiao Lu
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
| | - Xufeng Chen
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
| | - Iannis Aifantis
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA.
| |
Collapse
|
3
|
Chen X, Lu Q, Zhou H, Liu J, Nadorp B, Lasry A, Sun Z, Lai B, Rona G, Zhang J, Cammer M, Wang K, Al-Santli W, Ciantra Z, Guo Q, You J, Sengupta D, Boukhris A, Zhang H, Liu C, Cresswell P, Dahia PLM, Pagano M, Aifantis I, Wang J. A membrane-associated MHC-I inhibitory axis for cancer immune evasion. Cell 2023; 186:3903-3920.e21. [PMID: 37557169 PMCID: PMC10961051 DOI: 10.1016/j.cell.2023.07.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 05/30/2023] [Accepted: 07/11/2023] [Indexed: 08/11/2023]
Abstract
Immune-checkpoint blockade has revolutionized cancer treatment, but some cancers, such as acute myeloid leukemia (AML), do not respond or develop resistance. A potential mode of resistance is immune evasion of T cell immunity involving aberrant major histocompatibility complex class I (MHC-I) antigen presentation (AP). To map such mechanisms of resistance, we identified key MHC-I regulators using specific peptide-MHC-I-guided CRISPR-Cas9 screens in AML. The top-ranked negative regulators were surface protein sushi domain containing 6 (SUSD6), transmembrane protein 127 (TMEM127), and the E3 ubiquitin ligase WWP2. SUSD6 is abundantly expressed in AML and multiple solid cancers, and its ablation enhanced MHC-I AP and reduced tumor growth in a CD8+ T cell-dependent manner. Mechanistically, SUSD6 forms a trimolecular complex with TMEM127 and MHC-I, which recruits WWP2 for MHC-I ubiquitination and lysosomal degradation. Together with the SUSD6/TMEM127/WWP2 gene signature, which negatively correlates with cancer survival, our findings define a membrane-associated MHC-I inhibitory axis as a potential therapeutic target for both leukemia and solid cancers.
Collapse
Affiliation(s)
- Xufeng Chen
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
| | - Qiao Lu
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
| | - Hua Zhou
- Applied Bioinformatics Laboratories, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Jia Liu
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
| | - Bettina Nadorp
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
| | - Audrey Lasry
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
| | - Zhengxi Sun
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
| | - Baoling Lai
- Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Gergely Rona
- The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Jiangyan Zhang
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
| | - Michael Cammer
- Microscopy Core, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Kun Wang
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
| | - Wafa Al-Santli
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
| | - Zoe Ciantra
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Qianjin Guo
- Department of Medicine, Division of Hematology and Medical Oncology, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Jia You
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
| | - Debrup Sengupta
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Ahmad Boukhris
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
| | | | - Cheng Liu
- Eureka Therapeutics Inc., Emeryville, CA 94608, USA
| | - Peter Cresswell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Patricia L M Dahia
- Department of Medicine, Division of Hematology and Medical Oncology, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Michele Pagano
- The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Iannis Aifantis
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA.
| | - Jun Wang
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA.
| |
Collapse
|
4
|
Contreras Yametti GP, Evensen NA, Schloss JM, Aldebert C, Duan E, Zhang Y, Hu J, Chambers TM, Scheurer ME, Teachey DT, Rabin KR, Raetz EA, Aifantis I, Carroll WL, Witkowski MT. Flow cytometric assessment of leukemia-associated monocytes in childhood B-cell acute lymphoblastic leukemia outcome. Blood Adv 2023; 7:3928-3931. [PMID: 37196626 PMCID: PMC10405191 DOI: 10.1182/bloodadvances.2023010044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/19/2023] Open
Affiliation(s)
| | - Nikki A. Evensen
- Department of Pediatrics and Pathology, Perlmutter Cancer Center, NYU Langone Health, New York, NY
| | - Jennifer M. Schloss
- Department of Pediatrics and Pathology, Perlmutter Cancer Center, NYU Langone Health, New York, NY
| | - Clemence Aldebert
- Department of Pediatrics and Pathology, Perlmutter Cancer Center, NYU Langone Health, New York, NY
| | - Emily Duan
- Department of Pediatrics and Pathology, Perlmutter Cancer Center, NYU Langone Health, New York, NY
| | - Yan Zhang
- Division of Biostatistics, Department of Population Health, NYU Langone Health, New York, NY
| | - Jiyuan Hu
- Division of Biostatistics, Department of Population Health, NYU Langone Health, New York, NY
| | - Tiffany M. Chambers
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | - Michael E. Scheurer
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | - David T. Teachey
- Department of Pediatrics and the Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Karen R. Rabin
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | - Elizabeth A. Raetz
- Division of Pediatric Hematology Oncology, Department of Pediatrics, NYU Langone Health, New York, NY
| | | | - William L. Carroll
- Division of Pediatric Hematology Oncology, Department of Pediatrics, NYU Langone Health, New York, NY
- Department of Pediatrics and Pathology, Perlmutter Cancer Center, NYU Langone Health, New York, NY
| | - Matthew T. Witkowski
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO
| |
Collapse
|
5
|
Tan J, Shenker-Tauris N, Rodriguez-Hernaez J, Wang E, Sakellaropoulos T, Boccalatte F, Thandapani P, Skok J, Aifantis I, Fenyö D, Xia B, Tsirigos A. Cell-type-specific prediction of 3D chromatin organization enables high-throughput in silico genetic screening. Nat Biotechnol 2023; 41:1140-1150. [PMID: 36624151 PMCID: PMC10329734 DOI: 10.1038/s41587-022-01612-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 11/14/2022] [Indexed: 01/11/2023]
Abstract
Investigating how chromatin organization determines cell-type-specific gene expression remains challenging. Experimental methods for measuring three-dimensional chromatin organization, such as Hi-C, are costly and have technical limitations, restricting their broad application particularly in high-throughput genetic perturbations. We present C.Origami, a multimodal deep neural network that performs de novo prediction of cell-type-specific chromatin organization using DNA sequence and two cell-type-specific genomic features-CTCF binding and chromatin accessibility. C.Origami enables in silico experiments to examine the impact of genetic changes on chromatin interactions. We further developed an in silico genetic screening approach to assess how individual DNA elements may contribute to chromatin organization and to identify putative cell-type-specific trans-acting regulators that collectively determine chromatin architecture. Applying this approach to leukemia cells and normal T cells, we demonstrate that cell-type-specific in silico genetic screening, enabled by C.Origami, can be used to systematically discover novel chromatin regulation circuits in both normal and disease-related biological systems.
Collapse
Affiliation(s)
- Jimin Tan
- Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY, USA
| | - Nina Shenker-Tauris
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Applied Bioinformatics Laboratories, New York University Grossman School of Medicine, New York, NY, USA
| | - Javier Rodriguez-Hernaez
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Applied Bioinformatics Laboratories, New York University Grossman School of Medicine, New York, NY, USA
| | - Eric Wang
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- The Jackson Laboratory for Genomics Medicine, Farmington, CT, USA
| | | | - Francesco Boccalatte
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
- Department of Women's and Children's Health, University of Padua, Padua, Italy
| | - Palaniraja Thandapani
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Jane Skok
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Iannis Aifantis
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - David Fenyö
- Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY, USA
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Bo Xia
- Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY, USA.
- Society of Fellows, Harvard University, Cambridge, MA, USA.
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Aristotelis Tsirigos
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA.
- Applied Bioinformatics Laboratories, New York University Grossman School of Medicine, New York, NY, USA.
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA.
| |
Collapse
|
6
|
Glytsou C, Chen X, Zacharioudakis E, Al-Santli W, Zhou H, Nadorp B, Lee S, Lasry A, Sun Z, Papaioannou D, Cammer M, Wang K, Zal T, Zal MA, Carter BZ, Ishizawa J, Tibes R, Tsirigos A, Andreeff M, Gavathiotis E, Aifantis I. Mitophagy Promotes Resistance to BH3 Mimetics in Acute Myeloid Leukemia. Cancer Discov 2023; 13:1656-1677. [PMID: 37088914 PMCID: PMC10330144 DOI: 10.1158/2159-8290.cd-22-0601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 01/30/2023] [Accepted: 03/23/2023] [Indexed: 04/25/2023]
Abstract
BH3 mimetics are used as an efficient strategy to induce cell death in several blood malignancies, including acute myeloid leukemia (AML). Venetoclax, a potent BCL-2 antagonist, is used clinically in combination with hypomethylating agents for the treatment of AML. Moreover, MCL1 or dual BCL-2/BCL-xL antagonists are under investigation. Yet, resistance to single or combinatorial BH3-mimetic therapies eventually ensues. Integration of multiple genome-wide CRISPR/Cas9 screens revealed that loss of mitophagy modulators sensitizes AML cells to various BH3 mimetics targeting different BCL-2 family members. One such regulator is MFN2, whose protein levels positively correlate with drug resistance in patients with AML. MFN2 overexpression is sufficient to drive resistance to BH3 mimetics in AML. Insensitivity to BH3 mimetics is accompanied by enhanced mitochondria-endoplasmic reticulum interactions and augmented mitophagy flux, which acts as a prosurvival mechanism to eliminate mitochondrial damage. Genetic or pharmacologic MFN2 targeting synergizes with BH3 mimetics by impairing mitochondrial clearance and enhancing apoptosis in AML. SIGNIFICANCE AML remains one of the most difficult-to-treat blood cancers. BH3 mimetics represent a promising therapeutic approach to eliminate AML blasts by activating the apoptotic pathway. Enhanced mitochondrial clearance drives resistance to BH3 mimetics and predicts poor prognosis. Reverting excessive mitophagy can halt BH3-mimetic resistance in AML. This article is highlighted in the In This Issue feature, p. 1501.
Collapse
Affiliation(s)
- Christina Glytsou
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura & Isaac Perlmutter Cancer Center, NYU Langone Health and NYU Grossman School of Medicine, New York, NY 10016, USA
- Department of Chemical Biology, Ernest Mario School of Pharmacy, Rutgers-The State University of New Jersey, Piscataway, NJ 08854, USA
- Department of Pediatrics, Robert Wood Johnson Medical School, and Rutgers Cancer Institute of New Jersey, Rutgers-The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Xufeng Chen
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura & Isaac Perlmutter Cancer Center, NYU Langone Health and NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Emmanouil Zacharioudakis
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Montefiore Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Wafa Al-Santli
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura & Isaac Perlmutter Cancer Center, NYU Langone Health and NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Hua Zhou
- Applied Bioinformatics Laboratories, NYU School of Medicine, New York, NY 10016, USA
| | - Bettina Nadorp
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura & Isaac Perlmutter Cancer Center, NYU Langone Health and NYU Grossman School of Medicine, New York, NY 10016, USA
- Applied Bioinformatics Laboratories, NYU School of Medicine, New York, NY 10016, USA
| | - Soobeom Lee
- Department of Biology, New York University, New York, NY 10003, USA
| | - Audrey Lasry
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura & Isaac Perlmutter Cancer Center, NYU Langone Health and NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Zhengxi Sun
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura & Isaac Perlmutter Cancer Center, NYU Langone Health and NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Dimitrios Papaioannou
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura & Isaac Perlmutter Cancer Center, NYU Langone Health and NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Michael Cammer
- Microscopy Core, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Kun Wang
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura & Isaac Perlmutter Cancer Center, NYU Langone Health and NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Tomasz Zal
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Malgorzata Anna Zal
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bing Z. Carter
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jo Ishizawa
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Aristotelis Tsirigos
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Applied Bioinformatics Laboratories, NYU School of Medicine, New York, NY 10016, USA
| | - Michael Andreeff
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Evripidis Gavathiotis
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Montefiore Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Iannis Aifantis
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura & Isaac Perlmutter Cancer Center, NYU Langone Health and NYU Grossman School of Medicine, New York, NY 10016, USA
| |
Collapse
|
7
|
Balandrán JC, Lasry A, Aifantis I. The Role of Inflammation in the Initiation and Progression of Myeloid Neoplasms. Blood Cancer Discov 2023; 4:254-266. [PMID: 37052531 PMCID: PMC10320626 DOI: 10.1158/2643-3230.bcd-22-0176] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/10/2023] [Accepted: 03/10/2023] [Indexed: 04/14/2023] Open
Abstract
Myeloid malignancies are devastating hematologic cancers with limited therapeutic options. Inflammation is emerging as a novel driver of myeloid malignancy, with important implications for tumor composition, immune response, therapeutic options, and patient survival. Here, we discuss the role of inflammation in normal and malignant hematopoiesis, from clonal hematopoiesis to full-blown myeloid leukemia. We discuss how inflammation shapes clonal output from hematopoietic stem cells, how inflammation alters the immune microenvironment in the bone marrow, and novel therapies aimed at targeting inflammation in myeloid disease. SIGNIFICANCE Inflammation is emerging as an important factor in myeloid malignancies. Understanding the role of inflammation in myeloid transformation, and the interplay between inflammation and other drivers of leukemogenesis, may yield novel avenues for therapy.
Collapse
Affiliation(s)
- Juan Carlos Balandrán
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, New York
| | - Audrey Lasry
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, New York
| | - Iannis Aifantis
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, New York
| |
Collapse
|
8
|
Ma C, Wang H, Liu L, Tong J, Witkowski MT, Aifantis I, Ghassemi S, Chen W. A bioengineered immunocompetent human leukemia chip for preclinical screening of CAR T cell immunotherapy. Res Sq 2023:rs.3.rs-2762929. [PMID: 37131801 PMCID: PMC10153390 DOI: 10.21203/rs.3.rs-2762929/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Chimeric antigen receptor (CAR) T cell immunotherapy is promising for treatment of blood cancers; however, clinical benefits remain unpredictable, necessitating development of optimal CAR T cell products. Unfortunately, current preclinical evaluation platforms are inadequate due to their limited physiological relevance to humans. We herein engineered an organotypic immunocompetent chip that recapitulates microarchitectural and pathophysiological characteristics of human leukemia bone marrow stromal and immune niches for CAR T cell therapy modeling. This leukemia chip empowered real-time spatiotemporal monitoring of CAR T cell functionality, including T cell extravasation, recognition of leukemia, immune activation, cytotoxicity, and killing. We next on-chip modelled and mapped different responses post CAR T cell therapy, i.e., remission, resistance, and relapse as observed clinically and identify factors that potentially drive therapeutic failure. Finally, we developed a matrix-based analytical and integrative index to demarcate functional performance of CAR T cells with different CAR designs and generations produced from healthy donors and patients. Together, our chip introduces an enabling '(pre-)clinical-trial-on-chip' tool for CAR T cell development, which may translate to personalized therapies and improved clinical decision-making.
Collapse
Affiliation(s)
- Chao Ma
- Department of Mechanical and Aerospace Engineering, New York University, Brooklyn, NY 11201, USA
- Department of Biomedical Engineering, New York University, Brooklyn, NY 11201, USA
| | - Huishu Wang
- Department of Mechanical and Aerospace Engineering, New York University, Brooklyn, NY 11201, USA
| | - Lunan Liu
- Department of Mechanical and Aerospace Engineering, New York University, Brooklyn, NY 11201, USA
| | - Jie Tong
- Department of Mechanical and Aerospace Engineering, New York University, Brooklyn, NY 11201, USA
| | - Matthew T. Witkowski
- Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Iannis Aifantis
- Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Saba Ghassemi
- Center for Cellular Immunotherapies, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Weiqiang Chen
- Department of Mechanical and Aerospace Engineering, New York University, Brooklyn, NY 11201, USA
- Department of Biomedical Engineering, New York University, Brooklyn, NY 11201, USA
- Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| |
Collapse
|
9
|
Battistello E, Hixon KA, Comstock DE, Collings CK, Chen X, Rodriguez Hernaez J, Lee S, Cervantes KS, Hinkley MM, Ntatsoulis K, Cesarano A, Hockemeyer K, Haining WN, Witkowski MT, Qi J, Tsirigos A, Perna F, Aifantis I, Kadoch C. Stepwise activities of mSWI/SNF family chromatin remodeling complexes direct T cell activation and exhaustion. Mol Cell 2023; 83:1216-1236.e12. [PMID: 36944333 PMCID: PMC10121856 DOI: 10.1016/j.molcel.2023.02.026] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 01/11/2023] [Accepted: 02/23/2023] [Indexed: 03/23/2023]
Abstract
Highly coordinated changes in gene expression underlie T cell activation and exhaustion. However, the mechanisms by which such programs are regulated and how these may be targeted for therapeutic benefit remain poorly understood. Here, we comprehensively profile the genomic occupancy of mSWI/SNF chromatin remodeling complexes throughout acute and chronic T cell stimulation, finding that stepwise changes in localization over transcription factor binding sites direct site-specific chromatin accessibility and gene activation leading to distinct phenotypes. Notably, perturbation of mSWI/SNF complexes using genetic and clinically relevant chemical strategies enhances the persistence of T cells with attenuated exhaustion hallmarks and increased memory features in vitro and in vivo. Finally, pharmacologic mSWI/SNF inhibition improves CAR-T expansion and results in improved anti-tumor control in vivo. These findings reveal the central role of mSWI/SNF complexes in the coordination of T cell activation and exhaustion and nominate small-molecule-based strategies for the improvement of current immunotherapy protocols.
Collapse
Affiliation(s)
- Elena Battistello
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Kimberlee A Hixon
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Biological and Biomedical Sciences Program, Harvard Medical School, Boston, MA 02115, USA
| | - Dawn E Comstock
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Program in Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Clayton K Collings
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Xufeng Chen
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Javier Rodriguez Hernaez
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Soobeom Lee
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Kasey S Cervantes
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Madeline M Hinkley
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Konstantinos Ntatsoulis
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Annamaria Cesarano
- Department of Medicine, Division of Hematology/Oncology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Kathryn Hockemeyer
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - W Nicholas Haining
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Matthew T Witkowski
- Department of Pediatrics-HemeOnc and Bone Marrow Transplantation, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Cambridge, MA, USA
| | - Aristotelis Tsirigos
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA; Applied Bioinformatics Laboratories, Office of Science & Research, NYU Grossman School of Medicine, New York, NY, USA
| | - Fabiana Perna
- Department of Medicine, Division of Hematology/Oncology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Iannis Aifantis
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA.
| | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| |
Collapse
|
10
|
Austin RJ, Straube J, Halder R, Janardhanan Y, Bruedigam C, Witkowski M, Cooper L, Porter A, Braun M, Souza-Fonseca-Guimaraes F, Minnie SA, Cooper E, Jacquelin S, Song A, Bald T, Nakamura K, Hill GR, Aifantis I, Lane SW, Bywater MJ. Oncogenic drivers dictate immune control of acute myeloid leukemia. Nat Commun 2023; 14:2155. [PMID: 37059710 PMCID: PMC10104832 DOI: 10.1038/s41467-023-37592-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 03/22/2023] [Indexed: 04/16/2023] Open
Abstract
Acute myeloid leukemia (AML) is a genetically heterogeneous, aggressive hematological malignancy induced by distinct oncogenic driver mutations. The effect of specific AML oncogenes on immune activation or suppression is unclear. Here, we examine immune responses in genetically distinct models of AML and demonstrate that specific AML oncogenes dictate immunogenicity, the quality of immune response and immune escape through immunoediting. Specifically, expression of NrasG12D alone is sufficient to drive a potent anti-leukemia response through increased MHC Class II expression that can be overcome with increased expression of Myc. These data have important implications for the design and implementation of personalized immunotherapies for patients with AML.
Collapse
Affiliation(s)
- Rebecca J Austin
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, 4006, Australia
- The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, 10016, USA
- Laura & Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Jasmin Straube
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, 4006, Australia
- The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia
| | - Rohit Halder
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, 4006, Australia
| | | | - Claudia Bruedigam
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, 4006, Australia
- The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia
| | - Matthew Witkowski
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, 10016, USA
- Laura & Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, 10016, USA
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Leanne Cooper
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, 4006, Australia
| | - Amy Porter
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, 4006, Australia
| | - Matthias Braun
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, 4006, Australia
| | | | - Simone A Minnie
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, 4006, Australia
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Centre, Seattle Cancer Care Alliance, Seattle, WA, USA
| | - Emily Cooper
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, 4006, Australia
| | - Sebastien Jacquelin
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, 4006, Australia
- Mater Research, Translational Research Institute, The University of Queensland, Woolloongabba, QLD, 4102, Australia
| | - Axia Song
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, 4006, Australia
| | - Tobias Bald
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, 4006, Australia
- Institute of Experimental Oncology, University Hospital of Bonn, 53127, Bonn, Germany
| | - Kyohei Nakamura
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, 4006, Australia
| | - Geoffrey R Hill
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, 4006, Australia
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Centre, Seattle Cancer Care Alliance, Seattle, WA, USA
| | - Iannis Aifantis
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, 10016, USA
- Laura & Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Steven W Lane
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, 4006, Australia.
- The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia.
- Cancer Care Services, Royal Brisbane and Women's Hospital, Herston, 4029, Australia.
| | - Megan J Bywater
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, 4006, Australia.
- The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia.
| |
Collapse
|
11
|
Lasry A, Nadorp B, Fornerod M, Nicolet D, Wu H, Walker CJ, Sun Z, Witkowski MT, Tikhonova AN, Guillamot-Ruano M, Cayanan G, Yeaton A, Robbins G, Obeng EA, Tsirigos A, Stone RM, Byrd JC, Pounds S, Carroll WL, Gruber TA, Eisfeld AK, Aifantis I. An inflammatory state remodels the immune microenvironment and improves risk stratification in acute myeloid leukemia. Nat Cancer 2023; 4:27-42. [PMID: 36581735 PMCID: PMC9986885 DOI: 10.1038/s43018-022-00480-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 11/04/2022] [Indexed: 12/31/2022]
Abstract
Acute myeloid leukemia (AML) is a hematopoietic malignancy with poor prognosis and limited treatment options. Here we provide a comprehensive census of the bone marrow immune microenvironment in adult and pediatric patients with AML. We characterize unique inflammation signatures in a subset of AML patients, associated with inferior outcomes. We identify atypical B cells, a dysfunctional B-cell subtype enriched in patients with high-inflammation AML, as well as an increase in CD8+GZMK+ and regulatory T cells, accompanied by a reduction in T-cell clonal expansion. We derive an inflammation-associated gene score (iScore) that associates with poor survival outcomes in patients with AML. Addition of the iScore refines current risk stratifications for patients with AML and may enable identification of patients in need of more aggressive treatment. This work provides a framework for classifying patients with AML based on their immune microenvironment and a rationale for consideration of the inflammatory state in clinical settings.
Collapse
Affiliation(s)
- Audrey Lasry
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Bettina Nadorp
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
- Applied Bioinformatics Laboratories, New York University School of Medicine, New York, NY, USA
| | - Maarten Fornerod
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Deedra Nicolet
- The Ohio State University Comprehensive Cancer Center, Clara D. Bloomfield Center for Leukemia Outcomes Research, Columbus, OH, USA
- Alliance Statistics and Data Center, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Huiyun Wu
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Christopher J Walker
- The Ohio State University Comprehensive Cancer Center, Clara D. Bloomfield Center for Leukemia Outcomes Research, Columbus, OH, USA
- Alliance Statistics and Data Center, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Zhengxi Sun
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Matthew T Witkowski
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Anastasia N Tikhonova
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Maria Guillamot-Ruano
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Geraldine Cayanan
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Anna Yeaton
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Gabriel Robbins
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Esther A Obeng
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Aristotelis Tsirigos
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
- Applied Bioinformatics Laboratories, New York University School of Medicine, New York, NY, USA
| | - Richard M Stone
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - John C Byrd
- Department of Internal Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - William L Carroll
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Tanja A Gruber
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
| | - Ann-Kathrin Eisfeld
- The Ohio State University Comprehensive Cancer Center, Clara D. Bloomfield Center for Leukemia Outcomes Research, Columbus, OH, USA.
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.
- Pelotonia Institute for Immuno-Oncology, The Ohio State University, Columbus, OH, USA.
| | - Iannis Aifantis
- Department of Pathology, New York University School of Medicine, New York, NY, USA.
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA.
| |
Collapse
|
12
|
Liu L, Ma C, Zhang Z, Witkowski MT, Aifantis I, Ghassemi S, Chen W. Computational model of CAR T-cell immunotherapy dissects and predicts leukemia patient responses at remission, resistance, and relapse. J Immunother Cancer 2022; 10:e005360. [PMID: 36600553 PMCID: PMC9730379 DOI: 10.1136/jitc-2022-005360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Adaptive CD19-targeted chimeric antigen receptor (CAR) T-cell transfer has become a promising treatment for leukemia. Although patient responses vary across different clinical trials, reliable methods to dissect and predict patient responses to novel therapies are currently lacking. Recently, the depiction of patient responses has been achieved using in silico computational models, with prediction application being limited. METHODS We established a computational model of CAR T-cell therapy to recapitulate key cellular mechanisms and dynamics during treatment with responses of continuous remission (CR), non-response (NR), and CD19-positive (CD19+) and CD19-negative (CD19-) relapse. Real-time CAR T-cell and tumor burden data of 209 patients were collected from clinical studies and standardized with unified units in bone marrow. Parameter estimation was conducted using the stochastic approximation expectation maximization algorithm for nonlinear mixed-effect modeling. RESULTS We revealed critical determinants related to patient responses at remission, resistance, and relapse. For CR, NR, and CD19+ relapse, the overall functionality of CAR T-cell led to various outcomes, whereas loss of the CD19+ antigen and the bystander killing effect of CAR T-cells may partly explain the progression of CD19- relapse. Furthermore, we predicted patient responses by combining the peak and accumulated values of CAR T-cells or by inputting early-stage CAR T-cell dynamics. A clinical trial simulation using virtual patient cohorts generated based on real clinical patient datasets was conducted to further validate the prediction. CONCLUSIONS Our model dissected the mechanism behind distinct responses of leukemia to CAR T-cell therapy. This patient-based computational immuno-oncology model can predict late responses and may be informative in clinical treatment and management.
Collapse
Affiliation(s)
- Lunan Liu
- Department of Mechanical and Aerospace Engineering, New York University, Brooklyn, New York, USA
| | - Chao Ma
- Department of Mechanical and Aerospace Engineering, New York University, Brooklyn, New York, USA
- Department of Biomedical Engineering, New York University, Brooklyn, New York, USA
| | - Zhuoyu Zhang
- Department of Mechanical and Aerospace Engineering, New York University, Brooklyn, New York, USA
| | - Matthew T Witkowski
- Perlmutter Cancer Center, NYU Langone Health, New York City, New York, USA
- Department of Pathology, NYU Langone Health, New York City, New York, USA
| | - Iannis Aifantis
- Perlmutter Cancer Center, NYU Langone Health, New York City, New York, USA
- Department of Pathology, NYU Langone Health, New York City, New York, USA
| | - Saba Ghassemi
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Weiqiang Chen
- Department of Mechanical and Aerospace Engineering, New York University, Brooklyn, New York, USA
- Department of Biomedical Engineering, New York University, Brooklyn, New York, USA
- Perlmutter Cancer Center, NYU Langone Health, New York City, New York, USA
- Department of Pathology, NYU Langone Health, New York City, New York, USA
| |
Collapse
|
13
|
Yeaton A, Cayanan G, Loghavi S, Dolgalev I, Leddin EM, Loo CE, Torabifard H, Nicolet D, Wang J, Corrigan K, Paraskevopoulou V, Starczynowski DT, Wang E, Abdel-Wahab O, Viny AD, Stone RM, Byrd JC, Guryanova OA, Kohli RM, Cisneros GA, Tsirigos A, Eisfeld AK, Aifantis I, Guillamot M. The Impact of Inflammation-Induced Tumor Plasticity during Myeloid Transformation. Cancer Discov 2022; 12:2392-2413. [PMID: 35924979 PMCID: PMC9547930 DOI: 10.1158/2159-8290.cd-21-1146] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 05/26/2022] [Accepted: 08/01/2022] [Indexed: 11/16/2022]
Abstract
Clonal hematopoiesis (CH) is an aging-associated condition characterized by the clonal outgrowth of mutated preleukemic cells. Individuals with CH are at an increased risk of developing hematopoietic malignancies. Here, we describe a novel animal model carrying a recurrent TET2 missense mutation frequently found in patients with CH and leukemia. In a fashion similar to CH, animals show signs of disease late in life when they develop a wide range of myeloid neoplasms, including acute myeloid leukemia (AML). Using single-cell transcriptomic profiling of the bone marrow, we show that disease progression in aged animals correlates with an enhanced inflammatory response and the emergence of an aberrant inflammatory monocytic cell population. The gene signature characteristic of this inflammatory population is associated with poor prognosis in patients with AML. Our study illustrates an example of collaboration between a genetic lesion found in CH and inflammation, leading to transformation and the establishment of blood neoplasms. SIGNIFICANCE Progression from a preleukemic state to transformation, in the presence of TET2 mutations, is coupled with the emergence of inflammation and a novel population of inflammatory monocytes. Genes characteristic of this inflammatory population are associated with the worst prognosis in patients with AML. These studies connect inflammation to progression to leukemia. See related commentary by Pietras and DeGregori, p. 2234 . This article is highlighted in the In This Issue feature, p. 2221.
Collapse
Affiliation(s)
- Anna Yeaton
- Department of Pathology, NYU Grossman School of Medicine, New York, New York
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, New York
| | - Geraldine Cayanan
- Department of Pathology, NYU Grossman School of Medicine, New York, New York
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, New York
| | - Sanam Loghavi
- Department of Hematopathology, The University of Texas, MD Anderson Cancer Center, Houston, Texas
| | - Igor Dolgalev
- Applied Bioinformatics Laboratories, Office of Science and Research, NYU School of Medicine, New York, New York
| | - Emmett M Leddin
- Department of Physics, University of Texas at Dallas, Richardson, Texas
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas
| | - Christian E Loo
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Hedieh Torabifard
- Department of Physics, University of Texas at Dallas, Richardson, Texas
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas
| | - Deedra Nicolet
- The Ohio State University Comprehensive Cancer Center, Clara D. Bloomfield Center for Leukemia Outcomes Research, Columbus, Ohio
- Alliance Statistics and Data Center, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Jingjing Wang
- Department of Pathology, NYU Grossman School of Medicine, New York, New York
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, New York
| | - Kate Corrigan
- Department of Pathology, NYU Grossman School of Medicine, New York, New York
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, New York
| | - Varvara Paraskevopoulou
- Department of Pathology, NYU Grossman School of Medicine, New York, New York
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, New York
| | - Daniel T Starczynowski
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
- Department of Cancer Biology, University of Cincinnati, Cincinnati, Ohio
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Eric Wang
- MSK Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Omar Abdel-Wahab
- MSK Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Aaron D Viny
- Department of Genetics and Development, Columbia University, New York, New York
- Columbia Stem Cell Initiative, Columbia University, New York
- Cancer Genomics and Epigenomics Program, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York
| | - Richard M Stone
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - John C Byrd
- Department of Internal Medicine, University of Cincinnati, Cincinnati, Ohio
| | - Olga A Guryanova
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, Florida
| | - Rahul M Kohli
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - G Andrés Cisneros
- Department of Physics, University of Texas at Dallas, Richardson, Texas
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas
| | - Aristotelis Tsirigos
- Applied Bioinformatics Laboratories, Office of Science and Research, NYU School of Medicine, New York, New York
| | - Ann-Kathrin Eisfeld
- The Ohio State University Comprehensive Cancer Center, Clara D. Bloomfield Center for Leukemia Outcomes Research, Columbus, Ohio
- Division of Hematology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Iannis Aifantis
- Department of Pathology, NYU Grossman School of Medicine, New York, New York
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, New York
| | - Maria Guillamot
- Department of Pathology, NYU Grossman School of Medicine, New York, New York
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, New York
| |
Collapse
|
14
|
Parlani M, Boccalatte F, Yeaton A, Wang F, Zhang J, Aifantis I, Dondossola E. 223Ra Induces Transient Functional Bone Marrow Toxicity. J Nucl Med 2022; 63:1544-1550. [PMID: 35177425 PMCID: PMC9536707 DOI: 10.2967/jnumed.121.263310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 02/10/2022] [Indexed: 11/16/2022] Open
Abstract
223Ra is a bone-seeking, α-particle-emitting radionuclide approved for the treatment of patients with metastatic prostate cancer and is currently being tested in a variety of clinical trials for primary and metastatic cancers to bone. Clinical evaluation of 223Ra hematologic safety showed a significantly increased rate of neutropenia and thrombocytopenia in patients, hinting at myelosuppression as a side effect. Methods: In this study, we investigated the consequences of 223Ra treatment on bone marrow biology by combining flow cytometry, single-cell RNA sequencing, three-dimensional multiphoton microscopy and bone marrow transplantation analyses. Results: 223Ra accumulated in bones and induced zonal radiation damage confined to the bone interface, followed by replacement of the impaired areas with adipocyte infiltration, as monitored by 3-dimensional multiphoton microscopy ex vivo. Flow cytometry and single-cell transcriptomic analyses on bone marrow hematopoietic populations revealed transient, nonspecific 223Ra-mediated cytotoxicity on resident populations, including stem, progenitor, and mature leukocytes. This toxicity was paralleled by a significant decrease in white blood cells and platelets in peripheral blood-an effect that was overcome within 40 d after treatment. 223Ra exposure did not impair full hematopoietic reconstitution, suggesting that bone marrow function is not permanently hampered. Conclusion: Our results provide a comprehensive explanation of 223Ra reversible effects on bone marrow cells and exclude long-term myelotoxicity, supporting safety for patients.
Collapse
Affiliation(s)
- Maria Parlani
- Genitourinary Medical Oncology Department and David H. Koch Center for Applied Research of Genitourinary Cancers, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Francesco Boccalatte
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, New York; and
| | - Anna Yeaton
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, New York; and
| | - Feng Wang
- Department of Genomic Medicine, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Jianhua Zhang
- Department of Genomic Medicine, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Iannis Aifantis
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, New York; and
| | - Eleonora Dondossola
- Genitourinary Medical Oncology Department and David H. Koch Center for Applied Research of Genitourinary Cancers, University of Texas M.D. Anderson Cancer Center, Houston, Texas;
| |
Collapse
|
15
|
Witkowski MT, Lee S, Wang E, Lee AK, Talbot A, Ma C, Tsopoulidis N, Brumbaugh J, Zhao Y, Roberts KG, Hogg SJ, Nomikou S, Ghebrechristos Y, Thandapani P, Mullighan CG, Hochedlinger K, Chen W, Abdel-Wahab O, Eyquem J, Aifantis I. NUDT21 limits CD19 levels through alternative mRNA polyadenylation in B cell acute lymphoblastic leukemia. Nat Immunol 2022; 23:1424-1432. [PMID: 36138187 PMCID: PMC9611506 DOI: 10.1038/s41590-022-01314-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 08/11/2022] [Indexed: 02/04/2023]
Abstract
B cell progenitor acute lymphoblastic leukemia (B-ALL) treatment has been revolutionized by T cell-based immunotherapies-including chimeric antigen receptor T cell therapy (CAR-T) and the bispecific T cell engager therapeutic, blinatumomab-targeting surface glycoprotein CD19. Unfortunately, many patients with B-ALL will fail immunotherapy due to 'antigen escape'-the loss or absence of leukemic CD19 targeted by anti-leukemic T cells. In the present study, we utilized a genome-wide CRISPR-Cas9 screening approach to identify modulators of CD19 abundance on human B-ALL blasts. These studies identified a critical role for the transcriptional activator ZNF143 in CD19 promoter activation. Conversely, the RNA-binding protein, NUDT21, limited expression of CD19 by regulating CD19 messenger RNA polyadenylation and stability. NUDT21 deletion in B-ALL cells increased the expression of CD19 and the sensitivity to CD19-specific CAR-T and blinatumomab. In human B-ALL patients treated with CAR-T and blinatumomab, upregulation of NUDT21 mRNA coincided with CD19 loss at disease relapse. Together, these studies identify new CD19 modulators in human B-ALL.
Collapse
Affiliation(s)
- Matthew T. Witkowski
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA,Authors contributes equally to this manuscript,Correspondence to: Matthew T. Witkowski, (M.T.W.) and Iannis Aifantis, (I.A.)
| | - Soobeom Lee
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA,Department of Biology, New York University, New York, NY 10003, USA,Authors contributes equally to this manuscript
| | - Eric Wang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA,Authors contributes equally to this manuscript
| | - Anna K. Lee
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Alexis Talbot
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA,Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA,Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Chao Ma
- Department of Mechanical and Aerospace Engineering, New York University, New York, NY 11201, USA,Department of Biomedical Engineering, New York University, New York, NY 11201, USA
| | - Nikolaos Tsopoulidis
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA,Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Justin Brumbaugh
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Yaqi Zhao
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Kathryn G. Roberts
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Simon J. Hogg
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Sofia Nomikou
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Yohana Ghebrechristos
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Palaniraja Thandapani
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Charles G. Mullighan
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Konrad Hochedlinger
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA,Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Weiqiang Chen
- Department of Mechanical and Aerospace Engineering, New York University, New York, NY 11201, USA,Department of Biomedical Engineering, New York University, New York, NY 11201, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Justin Eyquem
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA,Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA,Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA,Parker Institute of Cancer Immunotherapy, University of California San Francisco, San Francisco, CA, USA
| | - Iannis Aifantis
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA,Correspondence to: Matthew T. Witkowski, (M.T.W.) and Iannis Aifantis, (I.A.)
| |
Collapse
|
16
|
Kedmi R, Najar TA, Mesa KR, Grayson A, Kroehling L, Hao Y, Hao S, Pokrovskii M, Xu M, Talbot J, Wang J, Germino J, Lareau CA, Satpathy AT, Anderson MS, Laufer TM, Aifantis I, Bartleson JM, Allen PM, Paidassi H, Gardner JM, Stoeckius M, Littman DR. A RORγt + cell instructs gut microbiota-specific T reg cell differentiation. Nature 2022; 610:737-743. [PMID: 36071167 PMCID: PMC9908423 DOI: 10.1038/s41586-022-05089-y] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 07/08/2022] [Indexed: 01/19/2023]
Abstract
The mutualistic relationship of gut-resident microbiota and the host immune system promotes homeostasis that ensures maintenance of the microbial community and of a largely non-aggressive immune cell compartment1,2. The consequences of disturbing this balance include proximal inflammatory conditions, such as Crohn's disease, and systemic illnesses. This equilibrium is achieved in part through the induction of both effector and suppressor arms of the adaptive immune system. Helicobacter species induce T regulatory (Treg) and T follicular helper (TFH) cells under homeostatic conditions, but induce inflammatory T helper 17 (TH17) cells when induced Treg (iTreg) cells are compromised3,4. How Helicobacter and other gut bacteria direct T cells to adopt distinct functions remains poorly understood. Here we investigated the cells and molecular components required for iTreg cell differentiation. We found that antigen presentation by cells expressing RORγt, rather than by classical dendritic cells, was required and sufficient for induction of Treg cells. These RORγt+ cells-probably type 3 innate lymphoid cells and/or Janus cells5-require the antigen-presentation machinery, the chemokine receptor CCR7 and the TGFβ activator αv integrin. In the absence of any of these factors, there was expansion of pathogenic TH17 cells instead of iTreg cells, induced by CCR7-independent antigen-presenting cells. Thus, intestinal commensal microbes and their products target multiple antigen-presenting cells with pre-determined features suited to directing appropriate T cell differentiation programmes, rather than a common antigen-presenting cell that they endow with appropriate functions.
Collapse
Affiliation(s)
- Ranit Kedmi
- Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY, USA
| | - Tariq A Najar
- Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY, USA
| | - Kailin R Mesa
- Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY, USA
| | - Allyssa Grayson
- Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY, USA.,Howard Hughes Medical Institute, New York, NY, USA
| | - Lina Kroehling
- Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY, USA
| | - Yuhan Hao
- Center for Genomics and Systems Biology, New York University, New York, NY, USA.,New York Genome Center, New York, NY, USA
| | - Stephanie Hao
- Technology Innovation Lab, New York Genome Center, New York, NY, USA
| | - Maria Pokrovskii
- Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY, USA.,Calico Life Sciences, LLC, South San Francisco, CA, USA
| | - Mo Xu
- Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY, USA.,National Institute for Biological Sciences, Beijing, China
| | - Jhimmy Talbot
- Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY, USA.,Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Jiaxi Wang
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Joe Germino
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Caleb A Lareau
- Department of Pathology, Stanford University, Stanford, CA, USA.,Parker Institute for Cancer Immunotherapy, Stanford University, Stanford, CA, USA.,Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University, Stanford, CA, USA.,Parker Institute for Cancer Immunotherapy, Stanford University, Stanford, CA, USA.,Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Mark S Anderson
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Terri M Laufer
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Medicine, C. Michael Crescenz Veterans Administration Medical Center, Philadelphia, PA, USA
| | - Iannis Aifantis
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Juliet M Bartleson
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.,Federation Bio, South San Francisco, CA, USA
| | - Paul M Allen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Helena Paidassi
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, Lyon, France
| | - James M Gardner
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA.,Department of Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Marlon Stoeckius
- Technology Innovation Lab, New York Genome Center, New York, NY, USA.,10X Genomics, Stockholm, Sweden
| | - Dan R Littman
- Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY, USA. .,Howard Hughes Medical Institute, New York, NY, USA.
| |
Collapse
|
17
|
Lee AK, Aifantis I, Thandapani P. Emerging roles for tRNAs in hematopoiesis and hematological malignancies. Trends Immunol 2022; 43:466-477. [PMID: 35490133 DOI: 10.1016/j.it.2022.03.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 11/26/2022]
Abstract
tRNAs are central players in decoding the genetic code linking codons in mRNAs with cognate amino acids during protein synthesis. Recent discoveries have placed tRNAs as key regulators of gene expression during hematopoiesis, especially in hematopoietic stem cell (HSC) maintenance and immune development. These functions have been shown to be influenced by dynamic changes in tRNA expression, post-transcriptional base modifications, tRNA-interacting proteins, and tRNA fragmentation; these events underlie the complexity of tRNA-mediated regulatory events in hematopoiesis. In this review, we discuss these recent findings and highlight how deregulation of tRNA biogenesis can contribute to hematological malignancies.
Collapse
Affiliation(s)
- Anna K Lee
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Iannis Aifantis
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA.
| | - Palaniraja Thandapani
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA.
| |
Collapse
|
18
|
Carcamo S, Nguyen CB, Grossi E, Filipescu D, Alpsoy A, Dhiman A, Sun D, Narang S, Imig J, Martin TC, Parsons R, Aifantis I, Tsirigos A, Aguirre-Ghiso JA, Dykhuizen EC, Hasson D, Bernstein E. Altered BAF occupancy and transcription factor dynamics in PBAF-deficient melanoma. Cell Rep 2022; 39:110637. [PMID: 35385731 PMCID: PMC9013128 DOI: 10.1016/j.celrep.2022.110637] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 01/04/2022] [Accepted: 03/16/2022] [Indexed: 12/25/2022] Open
Abstract
ARID2 is the most recurrently mutated SWI/SNF complex member in melanoma; however, its tumor-suppressive mechanisms in the context of the chromatin landscape remain to be elucidated. Here, we model ARID2 deficiency in melanoma cells, which results in defective PBAF complex assembly with a concomitant genomic redistribution of the BAF complex. Upon ARID2 depletion, a subset of PBAF and shared BAF-PBAF-occupied regions displays diminished chromatin accessibility and associated gene expression, while BAF-occupied enhancers gain chromatin accessibility and expression of genes linked to the process of invasion. As a function of altered accessibility, the genomic occupancy of melanoma-relevant transcription factors is affected and significantly correlates with the observed transcriptional changes. We further demonstrate that ARID2-deficient cells acquire the ability to colonize distal organs in multiple animal models. Taken together, our results reveal a role for ARID2 in mediating BAF and PBAF subcomplex chromatin dynamics with consequences for melanoma metastasis.
Collapse
Affiliation(s)
- Saul Carcamo
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute Bioinformatics for Next Generation Sequencing (BiNGS) Shared Resource Facility, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Christie B Nguyen
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Elena Grossi
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dan Filipescu
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Aktan Alpsoy
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Alisha Dhiman
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Dan Sun
- Division of Hematology and Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sonali Narang
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, New York, NY 10016, USA
| | - Jochen Imig
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, New York, NY 10016, USA
| | - Tiphaine C Martin
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ramon Parsons
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Iannis Aifantis
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, New York, NY 10016, USA
| | - Aristotelis Tsirigos
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, New York, NY 10016, USA; Applied Bioinformatics Laboratories, NYU School of Medicine, New York, NY 10016, USA
| | - Julio A Aguirre-Ghiso
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Division of Hematology and Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Otolaryngology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Emily C Dykhuizen
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Dan Hasson
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute Bioinformatics for Next Generation Sequencing (BiNGS) Shared Resource Facility, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Emily Bernstein
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| |
Collapse
|
19
|
Wang E, Mi X, Thompson MC, Montoya S, Notti RQ, Afaghani J, Durham BH, Penson A, Witkowski MT, Lu SX, Bourcier J, Hogg SJ, Erickson C, Cui D, Cho H, Singer M, Totiger TM, Chaudhry S, Geyer M, Alencar A, Linley AJ, Palomba ML, Coombs CC, Park JH, Zelenetz A, Roeker L, Rosendahl M, Tsai DE, Ebata K, Brandhuber B, Hyman DM, Aifantis I, Mato A, Taylor J, Abdel-Wahab O. Mechanisms of Resistance to Noncovalent Bruton's Tyrosine Kinase Inhibitors. N Engl J Med 2022; 386:735-743. [PMID: 35196427 PMCID: PMC9074143 DOI: 10.1056/nejmoa2114110] [Citation(s) in RCA: 84] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND Covalent (irreversible) Bruton's tyrosine kinase (BTK) inhibitors have transformed the treatment of multiple B-cell cancers, especially chronic lymphocytic leukemia (CLL). However, resistance can arise through multiple mechanisms, including acquired mutations in BTK at residue C481, the binding site of covalent BTK inhibitors. Noncovalent (reversible) BTK inhibitors overcome this mechanism and other sources of resistance, but the mechanisms of resistance to these therapies are currently not well understood. METHODS We performed genomic analyses of pretreatment specimens as well as specimens obtained at the time of disease progression from patients with CLL who had been treated with the noncovalent BTK inhibitor pirtobrutinib. Structural modeling, BTK-binding assays, and cell-based assays were conducted to study mutations that confer resistance to noncovalent BTK inhibitors. RESULTS Among 55 treated patients, we identified 9 patients with relapsed or refractory CLL and acquired mechanisms of genetic resistance to pirtobrutinib. We found mutations (V416L, A428D, M437R, T474I, and L528W) that were clustered in the kinase domain of BTK and that conferred resistance to both noncovalent BTK inhibitors and certain covalent BTK inhibitors. Mutations in BTK or phospholipase C gamma 2 (PLCγ2), a signaling molecule and downstream substrate of BTK, were found in all 9 patients. Transcriptional activation reflecting B-cell-receptor signaling persisted despite continued therapy with noncovalent BTK inhibitors. CONCLUSIONS Resistance to noncovalent BTK inhibitors arose through on-target BTK mutations and downstream PLCγ2 mutations that allowed escape from BTK inhibition. A proportion of these mutations also conferred resistance across clinically approved covalent BTK inhibitors. These data suggested new mechanisms of genomic escape from established covalent and novel noncovalent BTK inhibitors. (Funded by the American Society of Hematology and others.).
Collapse
Affiliation(s)
- Eric Wang
- From the Human Oncology and Pathogenesis Program (E.W., X.M., B.H.D., A.P., S.X.L., J.B., S.J.H., C.E., D.C., H.C., M.S., O.A.-W.), the Leukemia Service (M.C.T., M.G., J.H.P., L.R., A.M., O.A.-W.), and the Lymphoma Service (M.L.P., A.Z.), Department of Medicine, and the Department of Pathology (B.H.D.), Memorial Sloan Kettering Cancer Center, the Laboratory of Molecular Electron Microscopy, Rockefeller University (R.Q.N.), and the Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine (M.T.W., I.A.) - all in New York; Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami (S.M., J.A., T.M.T., S.C., A.A., J.T.); the Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom (A.J.L.); University of North Carolina Medical Center, Chapel Hill (C.C.C.); and Loxo Oncology at Lilly, Boulder, CO (M.R., D.E.T., K.E., B.B., D.M.H.)
| | - Xiaoli Mi
- From the Human Oncology and Pathogenesis Program (E.W., X.M., B.H.D., A.P., S.X.L., J.B., S.J.H., C.E., D.C., H.C., M.S., O.A.-W.), the Leukemia Service (M.C.T., M.G., J.H.P., L.R., A.M., O.A.-W.), and the Lymphoma Service (M.L.P., A.Z.), Department of Medicine, and the Department of Pathology (B.H.D.), Memorial Sloan Kettering Cancer Center, the Laboratory of Molecular Electron Microscopy, Rockefeller University (R.Q.N.), and the Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine (M.T.W., I.A.) - all in New York; Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami (S.M., J.A., T.M.T., S.C., A.A., J.T.); the Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom (A.J.L.); University of North Carolina Medical Center, Chapel Hill (C.C.C.); and Loxo Oncology at Lilly, Boulder, CO (M.R., D.E.T., K.E., B.B., D.M.H.)
| | - Meghan C Thompson
- From the Human Oncology and Pathogenesis Program (E.W., X.M., B.H.D., A.P., S.X.L., J.B., S.J.H., C.E., D.C., H.C., M.S., O.A.-W.), the Leukemia Service (M.C.T., M.G., J.H.P., L.R., A.M., O.A.-W.), and the Lymphoma Service (M.L.P., A.Z.), Department of Medicine, and the Department of Pathology (B.H.D.), Memorial Sloan Kettering Cancer Center, the Laboratory of Molecular Electron Microscopy, Rockefeller University (R.Q.N.), and the Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine (M.T.W., I.A.) - all in New York; Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami (S.M., J.A., T.M.T., S.C., A.A., J.T.); the Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom (A.J.L.); University of North Carolina Medical Center, Chapel Hill (C.C.C.); and Loxo Oncology at Lilly, Boulder, CO (M.R., D.E.T., K.E., B.B., D.M.H.)
| | - Skye Montoya
- From the Human Oncology and Pathogenesis Program (E.W., X.M., B.H.D., A.P., S.X.L., J.B., S.J.H., C.E., D.C., H.C., M.S., O.A.-W.), the Leukemia Service (M.C.T., M.G., J.H.P., L.R., A.M., O.A.-W.), and the Lymphoma Service (M.L.P., A.Z.), Department of Medicine, and the Department of Pathology (B.H.D.), Memorial Sloan Kettering Cancer Center, the Laboratory of Molecular Electron Microscopy, Rockefeller University (R.Q.N.), and the Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine (M.T.W., I.A.) - all in New York; Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami (S.M., J.A., T.M.T., S.C., A.A., J.T.); the Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom (A.J.L.); University of North Carolina Medical Center, Chapel Hill (C.C.C.); and Loxo Oncology at Lilly, Boulder, CO (M.R., D.E.T., K.E., B.B., D.M.H.)
| | - Ryan Q Notti
- From the Human Oncology and Pathogenesis Program (E.W., X.M., B.H.D., A.P., S.X.L., J.B., S.J.H., C.E., D.C., H.C., M.S., O.A.-W.), the Leukemia Service (M.C.T., M.G., J.H.P., L.R., A.M., O.A.-W.), and the Lymphoma Service (M.L.P., A.Z.), Department of Medicine, and the Department of Pathology (B.H.D.), Memorial Sloan Kettering Cancer Center, the Laboratory of Molecular Electron Microscopy, Rockefeller University (R.Q.N.), and the Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine (M.T.W., I.A.) - all in New York; Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami (S.M., J.A., T.M.T., S.C., A.A., J.T.); the Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom (A.J.L.); University of North Carolina Medical Center, Chapel Hill (C.C.C.); and Loxo Oncology at Lilly, Boulder, CO (M.R., D.E.T., K.E., B.B., D.M.H.)
| | - Jumana Afaghani
- From the Human Oncology and Pathogenesis Program (E.W., X.M., B.H.D., A.P., S.X.L., J.B., S.J.H., C.E., D.C., H.C., M.S., O.A.-W.), the Leukemia Service (M.C.T., M.G., J.H.P., L.R., A.M., O.A.-W.), and the Lymphoma Service (M.L.P., A.Z.), Department of Medicine, and the Department of Pathology (B.H.D.), Memorial Sloan Kettering Cancer Center, the Laboratory of Molecular Electron Microscopy, Rockefeller University (R.Q.N.), and the Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine (M.T.W., I.A.) - all in New York; Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami (S.M., J.A., T.M.T., S.C., A.A., J.T.); the Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom (A.J.L.); University of North Carolina Medical Center, Chapel Hill (C.C.C.); and Loxo Oncology at Lilly, Boulder, CO (M.R., D.E.T., K.E., B.B., D.M.H.)
| | - Benjamin H Durham
- From the Human Oncology and Pathogenesis Program (E.W., X.M., B.H.D., A.P., S.X.L., J.B., S.J.H., C.E., D.C., H.C., M.S., O.A.-W.), the Leukemia Service (M.C.T., M.G., J.H.P., L.R., A.M., O.A.-W.), and the Lymphoma Service (M.L.P., A.Z.), Department of Medicine, and the Department of Pathology (B.H.D.), Memorial Sloan Kettering Cancer Center, the Laboratory of Molecular Electron Microscopy, Rockefeller University (R.Q.N.), and the Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine (M.T.W., I.A.) - all in New York; Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami (S.M., J.A., T.M.T., S.C., A.A., J.T.); the Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom (A.J.L.); University of North Carolina Medical Center, Chapel Hill (C.C.C.); and Loxo Oncology at Lilly, Boulder, CO (M.R., D.E.T., K.E., B.B., D.M.H.)
| | - Alex Penson
- From the Human Oncology and Pathogenesis Program (E.W., X.M., B.H.D., A.P., S.X.L., J.B., S.J.H., C.E., D.C., H.C., M.S., O.A.-W.), the Leukemia Service (M.C.T., M.G., J.H.P., L.R., A.M., O.A.-W.), and the Lymphoma Service (M.L.P., A.Z.), Department of Medicine, and the Department of Pathology (B.H.D.), Memorial Sloan Kettering Cancer Center, the Laboratory of Molecular Electron Microscopy, Rockefeller University (R.Q.N.), and the Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine (M.T.W., I.A.) - all in New York; Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami (S.M., J.A., T.M.T., S.C., A.A., J.T.); the Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom (A.J.L.); University of North Carolina Medical Center, Chapel Hill (C.C.C.); and Loxo Oncology at Lilly, Boulder, CO (M.R., D.E.T., K.E., B.B., D.M.H.)
| | - Matthew T Witkowski
- From the Human Oncology and Pathogenesis Program (E.W., X.M., B.H.D., A.P., S.X.L., J.B., S.J.H., C.E., D.C., H.C., M.S., O.A.-W.), the Leukemia Service (M.C.T., M.G., J.H.P., L.R., A.M., O.A.-W.), and the Lymphoma Service (M.L.P., A.Z.), Department of Medicine, and the Department of Pathology (B.H.D.), Memorial Sloan Kettering Cancer Center, the Laboratory of Molecular Electron Microscopy, Rockefeller University (R.Q.N.), and the Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine (M.T.W., I.A.) - all in New York; Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami (S.M., J.A., T.M.T., S.C., A.A., J.T.); the Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom (A.J.L.); University of North Carolina Medical Center, Chapel Hill (C.C.C.); and Loxo Oncology at Lilly, Boulder, CO (M.R., D.E.T., K.E., B.B., D.M.H.)
| | - Sydney X Lu
- From the Human Oncology and Pathogenesis Program (E.W., X.M., B.H.D., A.P., S.X.L., J.B., S.J.H., C.E., D.C., H.C., M.S., O.A.-W.), the Leukemia Service (M.C.T., M.G., J.H.P., L.R., A.M., O.A.-W.), and the Lymphoma Service (M.L.P., A.Z.), Department of Medicine, and the Department of Pathology (B.H.D.), Memorial Sloan Kettering Cancer Center, the Laboratory of Molecular Electron Microscopy, Rockefeller University (R.Q.N.), and the Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine (M.T.W., I.A.) - all in New York; Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami (S.M., J.A., T.M.T., S.C., A.A., J.T.); the Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom (A.J.L.); University of North Carolina Medical Center, Chapel Hill (C.C.C.); and Loxo Oncology at Lilly, Boulder, CO (M.R., D.E.T., K.E., B.B., D.M.H.)
| | - Jessie Bourcier
- From the Human Oncology and Pathogenesis Program (E.W., X.M., B.H.D., A.P., S.X.L., J.B., S.J.H., C.E., D.C., H.C., M.S., O.A.-W.), the Leukemia Service (M.C.T., M.G., J.H.P., L.R., A.M., O.A.-W.), and the Lymphoma Service (M.L.P., A.Z.), Department of Medicine, and the Department of Pathology (B.H.D.), Memorial Sloan Kettering Cancer Center, the Laboratory of Molecular Electron Microscopy, Rockefeller University (R.Q.N.), and the Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine (M.T.W., I.A.) - all in New York; Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami (S.M., J.A., T.M.T., S.C., A.A., J.T.); the Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom (A.J.L.); University of North Carolina Medical Center, Chapel Hill (C.C.C.); and Loxo Oncology at Lilly, Boulder, CO (M.R., D.E.T., K.E., B.B., D.M.H.)
| | - Simon J Hogg
- From the Human Oncology and Pathogenesis Program (E.W., X.M., B.H.D., A.P., S.X.L., J.B., S.J.H., C.E., D.C., H.C., M.S., O.A.-W.), the Leukemia Service (M.C.T., M.G., J.H.P., L.R., A.M., O.A.-W.), and the Lymphoma Service (M.L.P., A.Z.), Department of Medicine, and the Department of Pathology (B.H.D.), Memorial Sloan Kettering Cancer Center, the Laboratory of Molecular Electron Microscopy, Rockefeller University (R.Q.N.), and the Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine (M.T.W., I.A.) - all in New York; Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami (S.M., J.A., T.M.T., S.C., A.A., J.T.); the Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom (A.J.L.); University of North Carolina Medical Center, Chapel Hill (C.C.C.); and Loxo Oncology at Lilly, Boulder, CO (M.R., D.E.T., K.E., B.B., D.M.H.)
| | - Caroline Erickson
- From the Human Oncology and Pathogenesis Program (E.W., X.M., B.H.D., A.P., S.X.L., J.B., S.J.H., C.E., D.C., H.C., M.S., O.A.-W.), the Leukemia Service (M.C.T., M.G., J.H.P., L.R., A.M., O.A.-W.), and the Lymphoma Service (M.L.P., A.Z.), Department of Medicine, and the Department of Pathology (B.H.D.), Memorial Sloan Kettering Cancer Center, the Laboratory of Molecular Electron Microscopy, Rockefeller University (R.Q.N.), and the Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine (M.T.W., I.A.) - all in New York; Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami (S.M., J.A., T.M.T., S.C., A.A., J.T.); the Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom (A.J.L.); University of North Carolina Medical Center, Chapel Hill (C.C.C.); and Loxo Oncology at Lilly, Boulder, CO (M.R., D.E.T., K.E., B.B., D.M.H.)
| | - Dan Cui
- From the Human Oncology and Pathogenesis Program (E.W., X.M., B.H.D., A.P., S.X.L., J.B., S.J.H., C.E., D.C., H.C., M.S., O.A.-W.), the Leukemia Service (M.C.T., M.G., J.H.P., L.R., A.M., O.A.-W.), and the Lymphoma Service (M.L.P., A.Z.), Department of Medicine, and the Department of Pathology (B.H.D.), Memorial Sloan Kettering Cancer Center, the Laboratory of Molecular Electron Microscopy, Rockefeller University (R.Q.N.), and the Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine (M.T.W., I.A.) - all in New York; Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami (S.M., J.A., T.M.T., S.C., A.A., J.T.); the Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom (A.J.L.); University of North Carolina Medical Center, Chapel Hill (C.C.C.); and Loxo Oncology at Lilly, Boulder, CO (M.R., D.E.T., K.E., B.B., D.M.H.)
| | - Hana Cho
- From the Human Oncology and Pathogenesis Program (E.W., X.M., B.H.D., A.P., S.X.L., J.B., S.J.H., C.E., D.C., H.C., M.S., O.A.-W.), the Leukemia Service (M.C.T., M.G., J.H.P., L.R., A.M., O.A.-W.), and the Lymphoma Service (M.L.P., A.Z.), Department of Medicine, and the Department of Pathology (B.H.D.), Memorial Sloan Kettering Cancer Center, the Laboratory of Molecular Electron Microscopy, Rockefeller University (R.Q.N.), and the Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine (M.T.W., I.A.) - all in New York; Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami (S.M., J.A., T.M.T., S.C., A.A., J.T.); the Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom (A.J.L.); University of North Carolina Medical Center, Chapel Hill (C.C.C.); and Loxo Oncology at Lilly, Boulder, CO (M.R., D.E.T., K.E., B.B., D.M.H.)
| | - Michael Singer
- From the Human Oncology and Pathogenesis Program (E.W., X.M., B.H.D., A.P., S.X.L., J.B., S.J.H., C.E., D.C., H.C., M.S., O.A.-W.), the Leukemia Service (M.C.T., M.G., J.H.P., L.R., A.M., O.A.-W.), and the Lymphoma Service (M.L.P., A.Z.), Department of Medicine, and the Department of Pathology (B.H.D.), Memorial Sloan Kettering Cancer Center, the Laboratory of Molecular Electron Microscopy, Rockefeller University (R.Q.N.), and the Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine (M.T.W., I.A.) - all in New York; Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami (S.M., J.A., T.M.T., S.C., A.A., J.T.); the Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom (A.J.L.); University of North Carolina Medical Center, Chapel Hill (C.C.C.); and Loxo Oncology at Lilly, Boulder, CO (M.R., D.E.T., K.E., B.B., D.M.H.)
| | - Tulasigeri M Totiger
- From the Human Oncology and Pathogenesis Program (E.W., X.M., B.H.D., A.P., S.X.L., J.B., S.J.H., C.E., D.C., H.C., M.S., O.A.-W.), the Leukemia Service (M.C.T., M.G., J.H.P., L.R., A.M., O.A.-W.), and the Lymphoma Service (M.L.P., A.Z.), Department of Medicine, and the Department of Pathology (B.H.D.), Memorial Sloan Kettering Cancer Center, the Laboratory of Molecular Electron Microscopy, Rockefeller University (R.Q.N.), and the Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine (M.T.W., I.A.) - all in New York; Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami (S.M., J.A., T.M.T., S.C., A.A., J.T.); the Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom (A.J.L.); University of North Carolina Medical Center, Chapel Hill (C.C.C.); and Loxo Oncology at Lilly, Boulder, CO (M.R., D.E.T., K.E., B.B., D.M.H.)
| | - Sana Chaudhry
- From the Human Oncology and Pathogenesis Program (E.W., X.M., B.H.D., A.P., S.X.L., J.B., S.J.H., C.E., D.C., H.C., M.S., O.A.-W.), the Leukemia Service (M.C.T., M.G., J.H.P., L.R., A.M., O.A.-W.), and the Lymphoma Service (M.L.P., A.Z.), Department of Medicine, and the Department of Pathology (B.H.D.), Memorial Sloan Kettering Cancer Center, the Laboratory of Molecular Electron Microscopy, Rockefeller University (R.Q.N.), and the Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine (M.T.W., I.A.) - all in New York; Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami (S.M., J.A., T.M.T., S.C., A.A., J.T.); the Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom (A.J.L.); University of North Carolina Medical Center, Chapel Hill (C.C.C.); and Loxo Oncology at Lilly, Boulder, CO (M.R., D.E.T., K.E., B.B., D.M.H.)
| | - Mark Geyer
- From the Human Oncology and Pathogenesis Program (E.W., X.M., B.H.D., A.P., S.X.L., J.B., S.J.H., C.E., D.C., H.C., M.S., O.A.-W.), the Leukemia Service (M.C.T., M.G., J.H.P., L.R., A.M., O.A.-W.), and the Lymphoma Service (M.L.P., A.Z.), Department of Medicine, and the Department of Pathology (B.H.D.), Memorial Sloan Kettering Cancer Center, the Laboratory of Molecular Electron Microscopy, Rockefeller University (R.Q.N.), and the Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine (M.T.W., I.A.) - all in New York; Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami (S.M., J.A., T.M.T., S.C., A.A., J.T.); the Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom (A.J.L.); University of North Carolina Medical Center, Chapel Hill (C.C.C.); and Loxo Oncology at Lilly, Boulder, CO (M.R., D.E.T., K.E., B.B., D.M.H.)
| | - Alvaro Alencar
- From the Human Oncology and Pathogenesis Program (E.W., X.M., B.H.D., A.P., S.X.L., J.B., S.J.H., C.E., D.C., H.C., M.S., O.A.-W.), the Leukemia Service (M.C.T., M.G., J.H.P., L.R., A.M., O.A.-W.), and the Lymphoma Service (M.L.P., A.Z.), Department of Medicine, and the Department of Pathology (B.H.D.), Memorial Sloan Kettering Cancer Center, the Laboratory of Molecular Electron Microscopy, Rockefeller University (R.Q.N.), and the Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine (M.T.W., I.A.) - all in New York; Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami (S.M., J.A., T.M.T., S.C., A.A., J.T.); the Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom (A.J.L.); University of North Carolina Medical Center, Chapel Hill (C.C.C.); and Loxo Oncology at Lilly, Boulder, CO (M.R., D.E.T., K.E., B.B., D.M.H.)
| | - Adam J Linley
- From the Human Oncology and Pathogenesis Program (E.W., X.M., B.H.D., A.P., S.X.L., J.B., S.J.H., C.E., D.C., H.C., M.S., O.A.-W.), the Leukemia Service (M.C.T., M.G., J.H.P., L.R., A.M., O.A.-W.), and the Lymphoma Service (M.L.P., A.Z.), Department of Medicine, and the Department of Pathology (B.H.D.), Memorial Sloan Kettering Cancer Center, the Laboratory of Molecular Electron Microscopy, Rockefeller University (R.Q.N.), and the Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine (M.T.W., I.A.) - all in New York; Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami (S.M., J.A., T.M.T., S.C., A.A., J.T.); the Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom (A.J.L.); University of North Carolina Medical Center, Chapel Hill (C.C.C.); and Loxo Oncology at Lilly, Boulder, CO (M.R., D.E.T., K.E., B.B., D.M.H.)
| | - M Lia Palomba
- From the Human Oncology and Pathogenesis Program (E.W., X.M., B.H.D., A.P., S.X.L., J.B., S.J.H., C.E., D.C., H.C., M.S., O.A.-W.), the Leukemia Service (M.C.T., M.G., J.H.P., L.R., A.M., O.A.-W.), and the Lymphoma Service (M.L.P., A.Z.), Department of Medicine, and the Department of Pathology (B.H.D.), Memorial Sloan Kettering Cancer Center, the Laboratory of Molecular Electron Microscopy, Rockefeller University (R.Q.N.), and the Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine (M.T.W., I.A.) - all in New York; Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami (S.M., J.A., T.M.T., S.C., A.A., J.T.); the Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom (A.J.L.); University of North Carolina Medical Center, Chapel Hill (C.C.C.); and Loxo Oncology at Lilly, Boulder, CO (M.R., D.E.T., K.E., B.B., D.M.H.)
| | - Catherine C Coombs
- From the Human Oncology and Pathogenesis Program (E.W., X.M., B.H.D., A.P., S.X.L., J.B., S.J.H., C.E., D.C., H.C., M.S., O.A.-W.), the Leukemia Service (M.C.T., M.G., J.H.P., L.R., A.M., O.A.-W.), and the Lymphoma Service (M.L.P., A.Z.), Department of Medicine, and the Department of Pathology (B.H.D.), Memorial Sloan Kettering Cancer Center, the Laboratory of Molecular Electron Microscopy, Rockefeller University (R.Q.N.), and the Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine (M.T.W., I.A.) - all in New York; Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami (S.M., J.A., T.M.T., S.C., A.A., J.T.); the Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom (A.J.L.); University of North Carolina Medical Center, Chapel Hill (C.C.C.); and Loxo Oncology at Lilly, Boulder, CO (M.R., D.E.T., K.E., B.B., D.M.H.)
| | - Jae H Park
- From the Human Oncology and Pathogenesis Program (E.W., X.M., B.H.D., A.P., S.X.L., J.B., S.J.H., C.E., D.C., H.C., M.S., O.A.-W.), the Leukemia Service (M.C.T., M.G., J.H.P., L.R., A.M., O.A.-W.), and the Lymphoma Service (M.L.P., A.Z.), Department of Medicine, and the Department of Pathology (B.H.D.), Memorial Sloan Kettering Cancer Center, the Laboratory of Molecular Electron Microscopy, Rockefeller University (R.Q.N.), and the Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine (M.T.W., I.A.) - all in New York; Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami (S.M., J.A., T.M.T., S.C., A.A., J.T.); the Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom (A.J.L.); University of North Carolina Medical Center, Chapel Hill (C.C.C.); and Loxo Oncology at Lilly, Boulder, CO (M.R., D.E.T., K.E., B.B., D.M.H.)
| | - Andrew Zelenetz
- From the Human Oncology and Pathogenesis Program (E.W., X.M., B.H.D., A.P., S.X.L., J.B., S.J.H., C.E., D.C., H.C., M.S., O.A.-W.), the Leukemia Service (M.C.T., M.G., J.H.P., L.R., A.M., O.A.-W.), and the Lymphoma Service (M.L.P., A.Z.), Department of Medicine, and the Department of Pathology (B.H.D.), Memorial Sloan Kettering Cancer Center, the Laboratory of Molecular Electron Microscopy, Rockefeller University (R.Q.N.), and the Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine (M.T.W., I.A.) - all in New York; Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami (S.M., J.A., T.M.T., S.C., A.A., J.T.); the Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom (A.J.L.); University of North Carolina Medical Center, Chapel Hill (C.C.C.); and Loxo Oncology at Lilly, Boulder, CO (M.R., D.E.T., K.E., B.B., D.M.H.)
| | - Lindsey Roeker
- From the Human Oncology and Pathogenesis Program (E.W., X.M., B.H.D., A.P., S.X.L., J.B., S.J.H., C.E., D.C., H.C., M.S., O.A.-W.), the Leukemia Service (M.C.T., M.G., J.H.P., L.R., A.M., O.A.-W.), and the Lymphoma Service (M.L.P., A.Z.), Department of Medicine, and the Department of Pathology (B.H.D.), Memorial Sloan Kettering Cancer Center, the Laboratory of Molecular Electron Microscopy, Rockefeller University (R.Q.N.), and the Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine (M.T.W., I.A.) - all in New York; Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami (S.M., J.A., T.M.T., S.C., A.A., J.T.); the Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom (A.J.L.); University of North Carolina Medical Center, Chapel Hill (C.C.C.); and Loxo Oncology at Lilly, Boulder, CO (M.R., D.E.T., K.E., B.B., D.M.H.)
| | - Mary Rosendahl
- From the Human Oncology and Pathogenesis Program (E.W., X.M., B.H.D., A.P., S.X.L., J.B., S.J.H., C.E., D.C., H.C., M.S., O.A.-W.), the Leukemia Service (M.C.T., M.G., J.H.P., L.R., A.M., O.A.-W.), and the Lymphoma Service (M.L.P., A.Z.), Department of Medicine, and the Department of Pathology (B.H.D.), Memorial Sloan Kettering Cancer Center, the Laboratory of Molecular Electron Microscopy, Rockefeller University (R.Q.N.), and the Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine (M.T.W., I.A.) - all in New York; Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami (S.M., J.A., T.M.T., S.C., A.A., J.T.); the Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom (A.J.L.); University of North Carolina Medical Center, Chapel Hill (C.C.C.); and Loxo Oncology at Lilly, Boulder, CO (M.R., D.E.T., K.E., B.B., D.M.H.)
| | - Donald E Tsai
- From the Human Oncology and Pathogenesis Program (E.W., X.M., B.H.D., A.P., S.X.L., J.B., S.J.H., C.E., D.C., H.C., M.S., O.A.-W.), the Leukemia Service (M.C.T., M.G., J.H.P., L.R., A.M., O.A.-W.), and the Lymphoma Service (M.L.P., A.Z.), Department of Medicine, and the Department of Pathology (B.H.D.), Memorial Sloan Kettering Cancer Center, the Laboratory of Molecular Electron Microscopy, Rockefeller University (R.Q.N.), and the Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine (M.T.W., I.A.) - all in New York; Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami (S.M., J.A., T.M.T., S.C., A.A., J.T.); the Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom (A.J.L.); University of North Carolina Medical Center, Chapel Hill (C.C.C.); and Loxo Oncology at Lilly, Boulder, CO (M.R., D.E.T., K.E., B.B., D.M.H.)
| | - Kevin Ebata
- From the Human Oncology and Pathogenesis Program (E.W., X.M., B.H.D., A.P., S.X.L., J.B., S.J.H., C.E., D.C., H.C., M.S., O.A.-W.), the Leukemia Service (M.C.T., M.G., J.H.P., L.R., A.M., O.A.-W.), and the Lymphoma Service (M.L.P., A.Z.), Department of Medicine, and the Department of Pathology (B.H.D.), Memorial Sloan Kettering Cancer Center, the Laboratory of Molecular Electron Microscopy, Rockefeller University (R.Q.N.), and the Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine (M.T.W., I.A.) - all in New York; Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami (S.M., J.A., T.M.T., S.C., A.A., J.T.); the Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom (A.J.L.); University of North Carolina Medical Center, Chapel Hill (C.C.C.); and Loxo Oncology at Lilly, Boulder, CO (M.R., D.E.T., K.E., B.B., D.M.H.)
| | - Barbara Brandhuber
- From the Human Oncology and Pathogenesis Program (E.W., X.M., B.H.D., A.P., S.X.L., J.B., S.J.H., C.E., D.C., H.C., M.S., O.A.-W.), the Leukemia Service (M.C.T., M.G., J.H.P., L.R., A.M., O.A.-W.), and the Lymphoma Service (M.L.P., A.Z.), Department of Medicine, and the Department of Pathology (B.H.D.), Memorial Sloan Kettering Cancer Center, the Laboratory of Molecular Electron Microscopy, Rockefeller University (R.Q.N.), and the Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine (M.T.W., I.A.) - all in New York; Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami (S.M., J.A., T.M.T., S.C., A.A., J.T.); the Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom (A.J.L.); University of North Carolina Medical Center, Chapel Hill (C.C.C.); and Loxo Oncology at Lilly, Boulder, CO (M.R., D.E.T., K.E., B.B., D.M.H.)
| | - David M Hyman
- From the Human Oncology and Pathogenesis Program (E.W., X.M., B.H.D., A.P., S.X.L., J.B., S.J.H., C.E., D.C., H.C., M.S., O.A.-W.), the Leukemia Service (M.C.T., M.G., J.H.P., L.R., A.M., O.A.-W.), and the Lymphoma Service (M.L.P., A.Z.), Department of Medicine, and the Department of Pathology (B.H.D.), Memorial Sloan Kettering Cancer Center, the Laboratory of Molecular Electron Microscopy, Rockefeller University (R.Q.N.), and the Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine (M.T.W., I.A.) - all in New York; Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami (S.M., J.A., T.M.T., S.C., A.A., J.T.); the Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom (A.J.L.); University of North Carolina Medical Center, Chapel Hill (C.C.C.); and Loxo Oncology at Lilly, Boulder, CO (M.R., D.E.T., K.E., B.B., D.M.H.)
| | - Iannis Aifantis
- From the Human Oncology and Pathogenesis Program (E.W., X.M., B.H.D., A.P., S.X.L., J.B., S.J.H., C.E., D.C., H.C., M.S., O.A.-W.), the Leukemia Service (M.C.T., M.G., J.H.P., L.R., A.M., O.A.-W.), and the Lymphoma Service (M.L.P., A.Z.), Department of Medicine, and the Department of Pathology (B.H.D.), Memorial Sloan Kettering Cancer Center, the Laboratory of Molecular Electron Microscopy, Rockefeller University (R.Q.N.), and the Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine (M.T.W., I.A.) - all in New York; Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami (S.M., J.A., T.M.T., S.C., A.A., J.T.); the Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom (A.J.L.); University of North Carolina Medical Center, Chapel Hill (C.C.C.); and Loxo Oncology at Lilly, Boulder, CO (M.R., D.E.T., K.E., B.B., D.M.H.)
| | - Anthony Mato
- From the Human Oncology and Pathogenesis Program (E.W., X.M., B.H.D., A.P., S.X.L., J.B., S.J.H., C.E., D.C., H.C., M.S., O.A.-W.), the Leukemia Service (M.C.T., M.G., J.H.P., L.R., A.M., O.A.-W.), and the Lymphoma Service (M.L.P., A.Z.), Department of Medicine, and the Department of Pathology (B.H.D.), Memorial Sloan Kettering Cancer Center, the Laboratory of Molecular Electron Microscopy, Rockefeller University (R.Q.N.), and the Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine (M.T.W., I.A.) - all in New York; Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami (S.M., J.A., T.M.T., S.C., A.A., J.T.); the Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom (A.J.L.); University of North Carolina Medical Center, Chapel Hill (C.C.C.); and Loxo Oncology at Lilly, Boulder, CO (M.R., D.E.T., K.E., B.B., D.M.H.)
| | - Justin Taylor
- From the Human Oncology and Pathogenesis Program (E.W., X.M., B.H.D., A.P., S.X.L., J.B., S.J.H., C.E., D.C., H.C., M.S., O.A.-W.), the Leukemia Service (M.C.T., M.G., J.H.P., L.R., A.M., O.A.-W.), and the Lymphoma Service (M.L.P., A.Z.), Department of Medicine, and the Department of Pathology (B.H.D.), Memorial Sloan Kettering Cancer Center, the Laboratory of Molecular Electron Microscopy, Rockefeller University (R.Q.N.), and the Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine (M.T.W., I.A.) - all in New York; Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami (S.M., J.A., T.M.T., S.C., A.A., J.T.); the Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom (A.J.L.); University of North Carolina Medical Center, Chapel Hill (C.C.C.); and Loxo Oncology at Lilly, Boulder, CO (M.R., D.E.T., K.E., B.B., D.M.H.)
| | - Omar Abdel-Wahab
- From the Human Oncology and Pathogenesis Program (E.W., X.M., B.H.D., A.P., S.X.L., J.B., S.J.H., C.E., D.C., H.C., M.S., O.A.-W.), the Leukemia Service (M.C.T., M.G., J.H.P., L.R., A.M., O.A.-W.), and the Lymphoma Service (M.L.P., A.Z.), Department of Medicine, and the Department of Pathology (B.H.D.), Memorial Sloan Kettering Cancer Center, the Laboratory of Molecular Electron Microscopy, Rockefeller University (R.Q.N.), and the Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine (M.T.W., I.A.) - all in New York; Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami (S.M., J.A., T.M.T., S.C., A.A., J.T.); the Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom (A.J.L.); University of North Carolina Medical Center, Chapel Hill (C.C.C.); and Loxo Oncology at Lilly, Boulder, CO (M.R., D.E.T., K.E., B.B., D.M.H.)
| |
Collapse
|
20
|
Muto T, Guillamot M, Yeung J, Fang J, Bennett J, Nadorp B, Lasry A, Redondo LZ, Choi K, Gong Y, Walker CS, Hueneman K, Bolanos LC, Barreyro L, Lee LH, Greis KD, Vasyliev N, Khodadadi-Jamayran A, Nudler E, Lujambio A, Lowe SW, Aifantis I, Starczynowski DT. TRAF6 functions as a tumor suppressor in myeloid malignancies by directly targeting MYC oncogenic activity. Cell Stem Cell 2022; 29:298-314.e9. [PMID: 35045331 PMCID: PMC8822959 DOI: 10.1016/j.stem.2021.12.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/05/2021] [Accepted: 12/15/2021] [Indexed: 02/05/2023]
Abstract
Clonal hematopoiesis (CH) is an aging-associated condition characterized by the clonal outgrowth of pre-leukemic cells that acquire specific mutations. Although individuals with CH are healthy, they are at an increased risk of developing myeloid malignancies, suggesting that additional alterations are needed for the transition from a pre-leukemia stage to frank leukemia. To identify signaling states that cooperate with pre-leukemic cells, we used an in vivo RNAi screening approach. One of the most prominent genes identified was the ubiquitin ligase TRAF6. Loss of TRAF6 in pre-leukemic cells results in overt myeloid leukemia and is associated with MYC-dependent stem cell signatures. TRAF6 is repressed in a subset of patients with myeloid malignancies, suggesting that subversion of TRAF6 signaling can lead to acute leukemia. Mechanistically, TRAF6 ubiquitinates MYC, an event that does not affect its protein stability but rather represses its functional activity by antagonizing an acetylation modification.
Collapse
Affiliation(s)
- Tomoya Muto
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229 USA.,These authors contributed equally
| | - Maria Guillamot
- Department of Pathology and Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA.,These authors contributed equally
| | - Jennifer Yeung
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina College of Pharmacy, Columbia, SC 29208, USA
| | - Jing Fang
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina College of Pharmacy, Columbia, SC 29208, USA
| | - Joshua Bennett
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina College of Pharmacy, Columbia, SC 29208, USA
| | - Bettina Nadorp
- Department of Pathology and Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Audrey Lasry
- Department of Pathology and Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Luna Zea Redondo
- Department of Pathology and Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Kwangmin Choi
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229 USA
| | - Yixiao Gong
- Department of Pathology and Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Callum S. Walker
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229 USA
| | - Kathleen Hueneman
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229 USA
| | - Lyndsey C. Bolanos
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229 USA
| | - Laura Barreyro
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229 USA
| | - Lynn H. Lee
- Division of Oncology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229 USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229 USA
| | - Kenneth D. Greis
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, 45229 USA
| | - Nikita Vasyliev
- Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Alireza Khodadadi-Jamayran
- Applied Bioinformatics Laboratories and Genome Technology Center, NYU School of Medicine, New York, NY 10016, USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Amaia Lujambio
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Scott W. Lowe
- Department of Cancer Biology and Genetics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 201815, USA
| | - Iannis Aifantis
- Department of Pathology and Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA.
| | - Daniel T. Starczynowski
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229 USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229 USA.,Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, 45229 USA.,Lead contact,Correspondence: (I.A.), (D.T.S.)
| |
Collapse
|
21
|
Bride KL, Hu H, Tikhonova A, Fuller TJ, Vincent TL, Shraim R, Li MM, Carroll WL, Raetz EA, Aifantis I, Teachey DT. Rational drug combinations with CDK4/6 inhibitors in acute lymphoblastic Leukemia. Haematologica 2021; 107:1746-1757. [PMID: 34937317 PMCID: PMC9335101 DOI: 10.3324/haematol.2021.279410] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Indexed: 11/09/2022] Open
Abstract
Despite improvements in outcomes for children with B and T-cell acute lymphoblastic leukemia (B-ALL and T-ALL), patients with resistant or relapsed disease fare poorly. Previous studies have demonstrated the essential role of cyclin D3 in T-ALL disease initiation and progression and that targeting of the CDK4/6-cyclin D complex can suppress T-ALL proliferation, leading to efficient cell death in animal models. Studies in leukemia and other malignancies, suggest that schedule is important when combining CDK4/6 inhibitors (CDKis) with cytotoxic agents. Based on these observations, we broadened evaluation of two CDKis, palbociclib (PD-0332991, Pfizer) and ribociclib (LEE011, Novartis) in B and T-ALL as single agent and in combination with conventional cytotoxic chemotherapy, using different schedules in preclinical models. As monotherapy, CDKis caused cell cycle arrest with a significant decrease in S phase entry and were active in vivo across a broad number of patient-derived xenograft samples. Prolonged monotherapy induces resistance, for which we identified a potential novel mechanism using transcriptome profiling. Importantly, simultaneous but not sequential treatment of CDKis with conventional chemotherapy (dexamethasone, L-asparaginase and vincristine) led to improved efficacy compared to monotherapy in vivo. We provide novel evidence that combining CDKis and conventional chemotherapy can be safe and effective. These results led to the rational design of a clinical trial.
Collapse
Affiliation(s)
- Karen L Bride
- Department of Pediatrics, Division of Hematology/Oncology and Cellular Therapy, Cohen Children's Medical Center, New Hyde Park
| | - Hai Hu
- Perlmutter Cancer Center and Department of Pediatrics, NYU Langone Health, NY, NY
| | | | - Tori J Fuller
- Children's Hospital of Philadelphia; Philadelphia, PA
| | | | - Rawan Shraim
- Children's Hospital of Philadelphia; Philadelphia, PA
| | - Marilyn M Li
- Children's Hospital of Philadelphia; Philadelphia, PA
| | - William L Carroll
- Perlmutter Cancer Center and Department of Pediatrics, NYU Langone Health, NY, NY
| | - Elizabeth A Raetz
- Perlmutter Cancer Center and Department of Pediatrics, NYU Langone Health, NY, NY
| | - Iannis Aifantis
- Perlmutter Cancer Center and Department of Pediatrics, NYU Langone Health, NY, NY
| | | |
Collapse
|
22
|
Lasry A, Aifantis I. LILRB3 as a regulator of AML survival. Nat Cancer 2021; 2:1122-1123. [PMID: 35122058 DOI: 10.1038/s43018-021-00285-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Audrey Lasry
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA.
| | - Iannis Aifantis
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA.
| |
Collapse
|
23
|
Akhmetzyanova I, Aaron T, Galbo P, Tikhonova A, Dolgalev I, Tanaka M, Aifantis I, Zheng D, Zang X, Fooksman D. Tissue-resident macrophages promote early dissemination of multiple myeloma via IL-6 and TNFα. Blood Adv 2021; 5:3592-3608. [PMID: 34550328 PMCID: PMC8945576 DOI: 10.1182/bloodadvances.2021005327] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 05/26/2021] [Indexed: 01/11/2023] Open
Abstract
Multiple myeloma (MM) is a plasma cell malignancy characterized by the presence of multiple foci in the skeleton. These distinct tumor foci represent cycles of tumor growth and dissemination that seed new clusters and drive disease progression. By using an intratibial Vk*MYC murine myeloma model, we found that CD169+ radiation-resistant tissue-resident macrophages (MPs) were critical for early dissemination of myeloma and disease progression. Depletion of these MPs had no effect on tumor proliferation, but it did reduce egress of myeloma from bone marrow (BM) and its spread to other bones. Depletion of MPs as a single therapy and in combination with BM transplantation improved overall survival. Dissemination of myeloma was correlated with an increased inflammatory signature in BM MPs. It was also correlated with the production of interleukin-6 (IL-6) and tumor necrosis factor α (TNFα) by tumor-associated MPs. Exogenous intravenous IL-6 and TNFα can trigger myeloma intravasation in the BM by increasing vascular permeability in the BM and by enhancing the motility of myeloma cells by reducing the adhesion of CD138. Moreover, mice that lacked IL-6 had defects in disseminating myeloma similar to those in MP-depleted recipients. Mice that were deficient in TNFα or TNFα receptor (TNFR) had defects in disseminating MM, and engraftment was also impaired. These effects on dissemination of myeloma required production of cytokines in the radiation-resistant compartment that contained these radiation-resistant BM MPs. Taken together, we propose that egress of myeloma cells from BM is regulated by localized inflammation in foci, driven in part by CD169+ MPs.
Collapse
Affiliation(s)
| | - Tonya Aaron
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY
| | - Phillip Galbo
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY
| | - Anastasia Tikhonova
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Department of Pathology, New York University Langone School of Medicine, New York, NY
| | - Igor Dolgalev
- Department of Pathology, New York University Langone School of Medicine, New York, NY
| | - Masato Tanaka
- School of Life Science, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan; and
| | - Iannis Aifantis
- Department of Pathology, New York University Langone School of Medicine, New York, NY
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY
| | - Xingxing Zang
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY
| | - David Fooksman
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY
| |
Collapse
|
24
|
Lu Q, Liu J, Zhao S, Gomez Castro MF, Laurent-Rolle M, Dong J, Ran X, Damani-Yokota P, Tang H, Karakousi T, Son J, Kaczmarek ME, Zhang Z, Yeung ST, McCune BT, Chen RE, Tang F, Ren X, Chen X, Hsu JCC, Teplova M, Huang B, Deng H, Long Z, Mudianto T, Jin S, Lin P, Du J, Zang R, Su TT, Herrera A, Zhou M, Yan R, Cui J, Zhu J, Zhou Q, Wang T, Ma J, Koralov SB, Zhang Z, Aifantis I, Segal LN, Diamond MS, Khanna KM, Stapleford KA, Cresswell P, Liu Y, Ding S, Xie Q, Wang J. SARS-CoV-2 exacerbates proinflammatory responses in myeloid cells through C-type lectin receptors and Tweety family member 2. Immunity 2021; 54:1304-1319.e9. [PMID: 34048708 PMCID: PMC8106883 DOI: 10.1016/j.immuni.2021.05.006] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 03/12/2021] [Accepted: 05/05/2021] [Indexed: 02/07/2023]
Abstract
Despite mounting evidence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) engagement with immune cells, most express little, if any, of the canonical receptor of SARS-CoV-2, angiotensin-converting enzyme 2 (ACE2). Here, using a myeloid cell receptor-focused ectopic expression screen, we identified several C-type lectins (DC-SIGN, L-SIGN, LSECtin, ASGR1, and CLEC10A) and Tweety family member 2 (TTYH2) as glycan-dependent binding partners of the SARS-CoV-2 spike. Except for TTYH2, these molecules primarily interacted with spike via regions outside of the receptor-binding domain. Single-cell RNA sequencing analysis of pulmonary cells from individuals with coronavirus disease 2019 (COVID-19) indicated predominant expression of these molecules on myeloid cells. Although these receptors do not support active replication of SARS-CoV-2, their engagement with the virus induced robust proinflammatory responses in myeloid cells that correlated with COVID-19 severity. We also generated a bispecific anti-spike nanobody that not only blocked ACE2-mediated infection but also the myeloid receptor-mediated proinflammatory responses. Our findings suggest that SARS-CoV-2-myeloid receptor interactions promote immune hyperactivation, which represents potential targets for COVID-19 therapy.
Collapse
Affiliation(s)
- Qiao Lu
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
| | - Jia Liu
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
| | - Shuai Zhao
- Westlake Laboratory of Life Sciences and Biomedicine, Center for Infectious Diseases Research, Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China; Institute of Basics Medical Sciences, Westlake Institute for Advanced Study, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China
| | | | - Maudry Laurent-Rolle
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06519, USA
| | | | - Xiaojuan Ran
- Westlake Laboratory of Life Sciences and Biomedicine, Center for Infectious Diseases Research, Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China; Institute of Basics Medical Sciences, Westlake Institute for Advanced Study, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China
| | - Payal Damani-Yokota
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Hongzhen Tang
- Westlake Laboratory of Life Sciences and Biomedicine, Center for Infectious Diseases Research, Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China; Institute of Basics Medical Sciences, Westlake Institute for Advanced Study, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China
| | - Triantafyllia Karakousi
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
| | - Juhee Son
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Maria E Kaczmarek
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Ze Zhang
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
| | - Stephen T Yeung
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Broc T McCune
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Rita E Chen
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Fei Tang
- BIOPIC, Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xianwen Ren
- BIOPIC, Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xufeng Chen
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Jack C C Hsu
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Marianna Teplova
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
| | | | - Haijing Deng
- Westlake Laboratory of Life Sciences and Biomedicine, Center for Infectious Diseases Research, Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China; Institute of Basics Medical Sciences, Westlake Institute for Advanced Study, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China
| | - Zhilin Long
- Westlake Laboratory of Life Sciences and Biomedicine, Center for Infectious Diseases Research, Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China; Institute of Basics Medical Sciences, Westlake Institute for Advanced Study, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China
| | - Tenny Mudianto
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Shumin Jin
- Westlake Laboratory of Life Sciences and Biomedicine, Center for Infectious Diseases Research, Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China; Institute of Basics Medical Sciences, Westlake Institute for Advanced Study, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China
| | - Peng Lin
- Westlake Laboratory of Life Sciences and Biomedicine, Center for Infectious Diseases Research, Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China; Institute of Basics Medical Sciences, Westlake Institute for Advanced Study, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China
| | - Jasper Du
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Ruochen Zang
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Tina Tianjiao Su
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Alberto Herrera
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Ming Zhou
- Westlake Laboratory of Life Sciences and Biomedicine, Center for Infectious Diseases Research, Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China; Institute of Basics Medical Sciences, Westlake Institute for Advanced Study, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China
| | - Renhong Yan
- Joint Research Center of Hangzhou First Hospital Group and Westlake University, Center for Infectious Diseases Research, Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China
| | - Jia Cui
- Kactus Biosystems Co., Ltd., Shanghai 201114, China
| | - James Zhu
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Qiang Zhou
- Joint Research Center of Hangzhou First Hospital Group and Westlake University, Center for Infectious Diseases Research, Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China
| | - Tao Wang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jianzhu Ma
- Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA
| | - Sergei B Koralov
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Zemin Zhang
- BIOPIC, Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Iannis Aifantis
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Leopoldo N Segal
- Division of Pulmonary and Critical Care Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Michael S Diamond
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kamal M Khanna
- The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA; Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Kenneth A Stapleford
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Peter Cresswell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Yue Liu
- Ab Studio, Inc., Hayward, CA 94545, USA
| | - Siyuan Ding
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Qi Xie
- Westlake Laboratory of Life Sciences and Biomedicine, Center for Infectious Diseases Research, Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China; Institute of Basics Medical Sciences, Westlake Institute for Advanced Study, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China.
| | - Jun Wang
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA.
| |
Collapse
|
25
|
Abstract
Single-cell sequencing approaches offer exploration of tissue architecture at unprecedented resolution. These tools are especially powerful when deconvoluting highly specialized microenvironments, such as stem cell (SC) niches. Here, we review single-cell studies that map the cellular and transcriptional makeup of stem and progenitor niches and discuss how these high-resolution analyses fundamentally advance our understanding of how niche factors shape SC biology and activity. In-depth characterization of the blueprint of SC-niche crosstalk, as well as understanding how it becomes dysregulated, will undoubtedly inform the development of more efficient therapies for malignancies and other pathologies.
Collapse
Affiliation(s)
- Anastasia N Tikhonova
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA.
| | - Audrey Lasry
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Rebecca Austin
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Iannis Aifantis
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA.
| |
Collapse
|
26
|
Wang E, Zhou H, Nadorp B, Cayanan G, Chen X, Yeaton AH, Nomikou S, Witkowski MT, Narang S, Kloetgen A, Thandapani P, Ravn-Boess N, Tsirigos A, Aifantis I. Surface antigen-guided CRISPR screens identify regulators of myeloid leukemia differentiation. Cell Stem Cell 2021; 28:718-731.e6. [PMID: 33450187 PMCID: PMC8145876 DOI: 10.1016/j.stem.2020.12.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 10/19/2020] [Accepted: 12/09/2020] [Indexed: 12/16/2022]
Abstract
Lack of cellular differentiation is a hallmark of many human cancers, including acute myeloid leukemia (AML). Strategies to overcome such a differentiation blockade are an approach for treating AML. To identify targets for differentiation-based therapies, we applied an integrated cell surface-based CRISPR platform to assess genes involved in maintaining the undifferentiated state of leukemia cells. Here we identify the RNA-binding protein ZFP36L2 as a critical regulator of AML maintenance and differentiation. Mechanistically, ZFP36L2 interacts with the 3' untranslated region of key myeloid maturation genes, including the ZFP36 paralogs, to promote their mRNA degradation and suppress terminal myeloid cell differentiation. Genetic inhibition of ZFP36L2 restores the mRNA stability of these targeted transcripts and ultimately triggers myeloid differentiation in leukemia cells. Epigenome profiling of several individuals with primary AML revealed enhancer modules near ZFP36L2 that associated with distinct AML cell states, establishing a coordinated epigenetic and post-transcriptional mechanism that shapes leukemic differentiation.
Collapse
Affiliation(s)
- Eric Wang
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA.
| | - Hua Zhou
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA; Applied Bioinformatics Laboratories, NYU School of Medicine, New York, NY 10016, USA
| | - Bettina Nadorp
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Geraldine Cayanan
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Xufeng Chen
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Anna H Yeaton
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Sofia Nomikou
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Matthew T Witkowski
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Sonali Narang
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Andreas Kloetgen
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Palaniraja Thandapani
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Niklas Ravn-Boess
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Aristotelis Tsirigos
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA; Applied Bioinformatics Laboratories, NYU School of Medicine, New York, NY 10016, USA; Institute for Computational Medicine, NYU School of Medicine, New York, NY 10016, USA
| | - Iannis Aifantis
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA.
| |
Collapse
|
27
|
Xiong H, Mancini M, Gobert M, Shen S, Furtado GC, Lira SA, Parkhurst CN, Garambois V, Brengues M, Tadokoro CE, Trimarchi T, Gómez-López G, Singh A, Khiabanian H, Minuzzo S, Indraccolo S, Lobry C, Aifantis I, Herranz D, Lafaille JJ, Maraver A. Spleen plays a major role in DLL4-driven acute T-cell lymphoblastic leukemia. Theranostics 2021; 11:1594-1608. [PMID: 33408769 PMCID: PMC7778594 DOI: 10.7150/thno.48067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 11/12/2020] [Indexed: 01/20/2023] Open
Abstract
The Notch pathway is highly active in almost all patients with T-cell acute lymphoblastic leukemia (T-ALL), but the implication of Notch ligands in T-ALL remains underexplored. Methods: We used a genetic mouse model of Notch ligand delta like 4 (DLL4)-driven T-ALL and performed thymectomies and splenectomies in those animals. We also used several patient-derived T-ALL (PDTALL) models, including one with DLL4 expression on the membrane and we treated PDTALL cells in vitro and in vivo with demcizumab, a blocking antibody against human DLL4 currently being tested in clinical trials in patients with solid cancer. Results: We show that surgical removal of the spleen abrogated T-ALL development in our preclinical DLL4-driven T-ALL mouse model. Mechanistically, we found that the spleen, and not the thymus, promoted the accumulation of circulating CD4+CD8+ T cells before T-ALL onset, suggesting that DLL4-driven T-ALL derives from these cells. Then, we identified a small subset of T-ALL patients showing higher levels of DLL4 expression. Moreover, in mice xenografted with a DLL4-positive PDTALL model, treatment with demcizumab had the same therapeutic effect as global Notch pathway inhibition using the potent γ-secretase inhibitor dibenzazepine. This result demonstrates that, in this PDTALL model, Notch pathway activity depends on DLL4 signaling, thus validating our preclinical mouse model. Conclusion: DLL4 expression in human leukemic cells can be a source of Notch activity in T-ALL, and the spleen plays a major role in a genetic mouse model of DLL4-driven T-ALL.
Collapse
|
28
|
Koscsó B, Kurapati S, Rodrigues RR, Nedjic J, Gowda K, Shin C, Soni C, Ashraf AZ, Purushothaman I, Palisoc M, Xu S, Sun H, Chodisetti SB, Lin E, Mack M, Kawasawa YI, He P, Rahman ZSM, Aifantis I, Shulzhenko N, Morgun A, Bogunovic M. Gut-resident CX3CR1 hi macrophages induce tertiary lymphoid structures and IgA response in situ. Sci Immunol 2020; 5:5/46/eaax0062. [PMID: 32276965 DOI: 10.1126/sciimmunol.aax0062] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 12/27/2019] [Accepted: 02/28/2020] [Indexed: 12/12/2022]
Abstract
Intestinal mononuclear phagocytes (MPs) are composed of heterogeneous dendritic cell (DC) and macrophage subsets necessary for the initiation of immune response and control of inflammation. Although MPs in the normal intestine have been extensively studied, the heterogeneity and function of inflammatory MPs remain poorly defined. We performed phenotypical, transcriptional, and functional analyses of inflammatory MPs in infectious Salmonella colitis and identified CX3CR1+ MPs as the most prevalent inflammatory cell type. CX3CR1+ MPs were further divided into three distinct populations, namely, Nos2 +CX3CR1lo, Ccr7 +CX3CR1int (lymph migratory), and Cxcl13 +CX3CR1hi (mucosa resident), all of which were transcriptionally aligned with macrophages and derived from monocytes. In follow-up experiments in vivo, intestinal CX3CR1+ macrophages were superior to conventional DC1 (cDC1) and cDC2 in inducing Salmonella-specific mucosal IgA. We next examined spatial organization of the immune response induced by CX3CR1+ macrophage subsets and identified mucosa-resident Cxcl13 +CX3CR1hi macrophages as the antigen-presenting cells responsible for recruitment and activation of CD4+ T and B cells to the sites of Salmonella invasion, followed by tertiary lymphoid structure formation and the local pathogen-specific IgA response. Using mice we developed with a floxed Ccr7 allele, we showed that this local IgA response developed independently of migration of the Ccr7 +CX3CR1int population to the mesenteric lymph nodes and contributed to the total mucosal IgA response to infection. The differential activity of intestinal macrophage subsets in promoting mucosal IgA responses should be considered in the development of vaccines to prevent Salmonella infection and in the design of anti-inflammatory therapies aimed at modulating macrophage function in inflammatory bowel disease.
Collapse
Affiliation(s)
- Balázs Koscsó
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Sravya Kurapati
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA.,Biomedical Sciences PhD Program, Penn State University College of Medicine, Hershey, PA, USA
| | | | - Jelena Nedjic
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA
| | - Kavitha Gowda
- Department of Microbiology and Immunology, Penn State University College of Medicine, Hershey, PA, USA
| | - Changsik Shin
- Department of Microbiology and Immunology, Penn State University College of Medicine, Hershey, PA, USA
| | - Chetna Soni
- Department of Microbiology and Immunology, Penn State University College of Medicine, Hershey, PA, USA
| | - Azree Zaffran Ashraf
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Indira Purushothaman
- PhD Program in Anatomy at Penn State College of Medicine, Penn State University College of Medicine, Hershey, PA, USA
| | - Maryknoll Palisoc
- MD/PhD Medical Scientist Training Program, Penn State University College of Medicine, Hershey, PA, USA
| | - Sulei Xu
- Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, PA, USA
| | - Haoyu Sun
- Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, PA, USA
| | - Sathi Babu Chodisetti
- Department of Microbiology and Immunology, Penn State University College of Medicine, Hershey, PA, USA
| | - Eugene Lin
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Matthias Mack
- Department of Internal Medicine/Nephrology, University Hospital Regensburg, Regensburg, Germany
| | - Yuka Imamura Kawasawa
- Department of Pharmacology and Biochemistry and Molecular Biology, Institute of Personalized Medicine, Penn State University College of Medicine, Hershey, PA, USA
| | - Pingnian He
- Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, PA, USA
| | - Ziaur S M Rahman
- Department of Microbiology and Immunology, Penn State University College of Medicine, Hershey, PA, USA
| | - Iannis Aifantis
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA
| | - Natalia Shulzhenko
- College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | - Andrey Morgun
- College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Milena Bogunovic
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA. .,Department of Microbiology and Immunology, Penn State University College of Medicine, Hershey, PA, USA.,Inflammatory Bowel Disease Center, Milton S. Hershey Medical Center, Hershey, PA, USA
| |
Collapse
|
29
|
|
30
|
Hanniford D, Ulloa-Morales A, Sánchez-Sendra B, Karz A, Moubarak R, Tabaglio T, Berzoti-Coelho MG, Davalos V, Wu P, Vasudevaraja V, Kloetgen A, Lilja K, Imig J, Monteagudo C, Guccione E, Tsirigos A, Osman I, Aifantis I, Hernando E. Abstract PR04: Epigenetic silencing of CDR1as drives IGF2BP3-mediated melanoma invasion and metastasis. Cancer Res 2020. [DOI: 10.1158/1538-7445.mel2019-pr04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Metastasis is the primary cause of death of cancer patients. Dissecting mechanisms governing metastatic spread may uncover new biology and/or yield promising therapeutic insights. Here we investigated the role of circular RNAs (circRNAs), a class of noncoding RNAs lacking characterized functions, in metastasis, using melanoma as a model aggressive tumor. We analyzed RNA-seq of melanocytes and melanoma short-term cultures to characterize the landscape of circRNA in melanocytic cells. We observed silencing of Cerebellar Degeneration Related 1 (CDR1as), a neuronal-enriched circRNA and known regulator of the microRNA miR-7, in melanoma cell lines and short-term cultures compared to cultured melanocytes, and progressive loss from primary to metastatic disease in melanoma patient samples. Moreover, low CDR1as expression in primary tumors associates with poor prognostic histopathologic indicators and patient outcomes. We find that CDR1as loss results from H3K27me3-mediated silencing of its originating lincRNA LINC00632. We observed abundant H3K27me3, the repressive chromatin mark deposited by the PRC2 complex, in regulatory regions of LINC00632 in cell lines lacking CDR1as expression, and pharmacologic inhibition of EZH2 restored expression of both transcripts. Phenotypically, CDR1as depletion in vitro and in vivo enhances melanoma invasion and metastasis, with limited effect on cell proliferation or tumor growth. Surprisingly, we did not observe miR-7 regulation to be a catalyst of the proinvasive effects of CDR1as depletion in our models. Instead, we identified IGF2BP3 as a novel interactor of CDR1as and critical mediator downstream of CDR1as silencing. Finally, we find that CDR1as abundance associates with previously defined cellular states that engender distinct therapeutic responses to MAPK and GPX4 inhibitors. Collectively, our study reveals CDR1as silencing as a hallmark of melanoma progression; documents novel functional, prognostic and predictive roles for CDR1as; and exposes circRNAs as key players in metastasis.
This abstract is also being presented as Poster A29.
Citation Format: Douglas Hanniford, Alejandro Ulloa-Morales, Beatriz Sánchez-Sendra, Alcida Karz, Rana Moubarak, Tommaso Tabaglio, Maria Gabriela Berzoti-Coelho, Veronica Davalos, Pamela Wu, Varshini Vasudevaraja, Andreas Kloetgen, Karin Lilja, Jochen Imig, Carlos Monteagudo, Ernesto Guccione, Aristotelis Tsirigos, Iman Osman, Iannis Aifantis, Eva Hernando. Epigenetic silencing of CDR1as drives IGF2BP3-mediated melanoma invasion and metastasis [abstract]. In: Proceedings of the AACR Special Conference on Melanoma: From Biology to Target; 2019 Jan 15-18; Houston, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(19 Suppl):Abstract nr PR04.
Collapse
|
31
|
Ma C, Witkowski MT, Harris J, Dolgalev I, Sreeram S, Qian W, Tong J, Chen X, Aifantis I, Chen W. Leukemia-on-a-chip: Dissecting the chemoresistance mechanisms in B cell acute lymphoblastic leukemia bone marrow niche. Sci Adv 2020; 6:eaba5536. [PMID: 33127669 PMCID: PMC7608809 DOI: 10.1126/sciadv.aba5536] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 09/10/2020] [Indexed: 05/16/2023]
Abstract
B cell acute lymphoblastic leukemia (B-ALL) blasts hijack the bone marrow (BM) microenvironment to form chemoprotective leukemic BM "niches," facilitating chemoresistance and, ultimately, disease relapse. However, the ability to dissect these evolving, heterogeneous interactions among distinct B-ALL subtypes and their varying BM niches is limited with current in vivo methods. Here, we demonstrated an in vitro organotypic "leukemia-on-a-chip" model to emulate the in vivo B-ALL BM pathology and comparatively studied the spatial and genetic heterogeneity of the BM niche in regulating B-ALL chemotherapy resistance. We revealed the heterogeneous chemoresistance mechanisms across various B-ALL cell lines and patient-derived samples. We showed that the leukemic perivascular, endosteal, and hematopoietic niche-derived factors maintain B-ALL survival and quiescence (e.g., CXCL12 cytokine signal, VCAM-1/OPN adhesive signals, and enhanced downstream leukemia-intrinsic NF-κB pathway). Furthermore, we demonstrated the preclinical use of our model to test niche-cotargeting regimens, which may translate to patient-specific therapy screening and response prediction.
Collapse
Affiliation(s)
- Chao Ma
- Department of Mechanical and Aerospace Engineering, New York University, Brooklyn, NY 11201, USA
- Department of Biomedical Engineering, New York University, Brooklyn, NY 11201, USA
| | - Matthew T Witkowski
- Department of Pathology, NYU Langone Health, New York, NY 10016, USA
- Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA
| | - Jacob Harris
- Department of Biomedical Engineering, New York University, Brooklyn, NY 11201, USA
| | - Igor Dolgalev
- Department of Pathology, NYU Langone Health, New York, NY 10016, USA
- Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA
| | - Sheetal Sreeram
- Department of Pathology, NYU Langone Health, New York, NY 10016, USA
| | - Weiyi Qian
- Department of Mechanical and Aerospace Engineering, New York University, Brooklyn, NY 11201, USA
| | - Jie Tong
- Department of Mechanical and Aerospace Engineering, New York University, Brooklyn, NY 11201, USA
| | - Xin Chen
- Department of Mechanical and Aerospace Engineering, New York University, Brooklyn, NY 11201, USA
| | - Iannis Aifantis
- Department of Pathology, NYU Langone Health, New York, NY 10016, USA
- Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA
| | - Weiqiang Chen
- Department of Mechanical and Aerospace Engineering, New York University, Brooklyn, NY 11201, USA.
- Department of Biomedical Engineering, New York University, Brooklyn, NY 11201, USA
- Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA
| |
Collapse
|
32
|
Hsu J, Huang HT, Lee CT, Choudhuri A, Wilson NK, Abraham BJ, Moignard V, Kucinski I, Yu S, Hyde RK, Tober J, Cai X, Li Y, Guo Y, Yang S, Superdock M, Trompouki E, Calero-Nieto FJ, Ghamari A, Jiang J, Gao P, Gao L, Nguyen V, Robertson AL, Durand EM, Kathrein KL, Aifantis I, Gerber SA, Tong W, Tan K, Cantor AB, Zhou Y, Liu PP, Young RA, Göttgens B, Speck NA, Zon LI. CHD7 and Runx1 interaction provides a braking mechanism for hematopoietic differentiation. Proc Natl Acad Sci U S A 2020; 117:23626-23635. [PMID: 32883883 PMCID: PMC7519295 DOI: 10.1073/pnas.2003228117] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Hematopoietic stem and progenitor cell (HSPC) formation and lineage differentiation involve gene expression programs orchestrated by transcription factors and epigenetic regulators. Genetic disruption of the chromatin remodeler chromodomain-helicase-DNA-binding protein 7 (CHD7) expanded phenotypic HSPCs, erythroid, and myeloid lineages in zebrafish and mouse embryos. CHD7 acts to suppress hematopoietic differentiation. Binding motifs for RUNX and other hematopoietic transcription factors are enriched at sites occupied by CHD7, and decreased RUNX1 occupancy correlated with loss of CHD7 localization. CHD7 physically interacts with RUNX1 and suppresses RUNX1-induced expansion of HSPCs during development through modulation of RUNX1 activity. Consequently, the RUNX1:CHD7 axis provides proper timing and function of HSPCs as they emerge during hematopoietic development or mature in adults, representing a distinct and evolutionarily conserved control mechanism to ensure accurate hematopoietic lineage differentiation.
Collapse
Affiliation(s)
- Jingmei Hsu
- Division of Hematology/Oncology, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA 19104
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Hsuan-Ting Huang
- Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
| | - Chung-Tsai Lee
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Avik Choudhuri
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138
| | - Nicola K Wilson
- Cambridge Institute for Medical Research, Department of Haematology, Wellcome Trust/Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom CB2 OXY
| | - Brian J Abraham
- Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142
| | - Victoria Moignard
- Cambridge Institute for Medical Research, Department of Haematology, Wellcome Trust/Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom CB2 OXY
| | - Iwo Kucinski
- Cambridge Institute for Medical Research, Department of Haematology, Wellcome Trust/Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom CB2 OXY
| | - Shuqian Yu
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104
| | - R Katherine Hyde
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892
| | - Joanna Tober
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Xiongwei Cai
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Yan Li
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Yalin Guo
- Department of Microbiology and Immunology, Geisel School of Medicine, Lebanon, NH 03756
| | - Song Yang
- Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
| | - Michael Superdock
- Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
| | - Eirini Trompouki
- Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
| | - Fernando J Calero-Nieto
- Cambridge Institute for Medical Research, Department of Haematology, Wellcome Trust/Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom CB2 OXY
| | - Alireza Ghamari
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
| | - Jing Jiang
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Peng Gao
- Division of Oncology and Center for Childhood Cancer Research, Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Long Gao
- Division of Oncology and Center for Childhood Cancer Research, Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Vy Nguyen
- Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
| | - Anne L Robertson
- Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
| | - Ellen M Durand
- Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
| | - Katie L Kathrein
- Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
| | - Iannis Aifantis
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016
| | - Scott A Gerber
- Department of Genetics, Geisel School of Medicine, Lebanon, NH 03756
| | - Wei Tong
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Kai Tan
- Division of Oncology and Center for Childhood Cancer Research, Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Alan B Cantor
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
| | - Yi Zhou
- Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
| | - P Paul Liu
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142
| | - Berthold Göttgens
- Cambridge Institute for Medical Research, Department of Haematology, Wellcome Trust/Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom CB2 OXY
| | - Nancy A Speck
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104;
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Leonard I Zon
- Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115;
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138
| |
Collapse
|
33
|
Affiliation(s)
- Iannis Aifantis
- Department of Pathology and Department of Medicine, Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA.
| | - Benjamin G Neel
- Department of Pathology and Department of Medicine, Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA.
| |
Collapse
|
34
|
Bohin N, Keeley TM, Carulli AJ, Walker EM, Carlson EA, Gao J, Aifantis I, Siebel CW, Rajala MW, Myers MG, Jones JC, Brindley CD, Dempsey PJ, Samuelson LC. Rapid Crypt Cell Remodeling Regenerates the Intestinal Stem Cell Niche after Notch Inhibition. Stem Cell Reports 2020; 15:156-170. [PMID: 32531190 PMCID: PMC7363878 DOI: 10.1016/j.stemcr.2020.05.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 05/12/2020] [Accepted: 05/13/2020] [Indexed: 12/16/2022] Open
Abstract
Intestinal crypts have great capacity for repair and regeneration after intestinal stem cell (ISC) injury. Here, we define the cellular remodeling process resulting from ISC niche interruption by transient Notch pathway inhibition in adult mice. Although ISCs were retained, lineage tracing demonstrated a marked reduction in ISC function after Notch disruption. Surprisingly, Notch ligand-expressing Paneth cells were rapidly lost by apoptotic cell death. The ISC-Paneth cell changes were followed by a regenerative response, characterized by expansion of cells expressing Notch ligands Dll1 and Dll4, enhanced Notch signaling, and a proliferative surge. Lineage tracing and organoid studies showed that Dll1-expressing cells were activated to function as multipotential progenitors, generating both absorptive and secretory cells and replenishing the vacant Paneth cell pool. Our analysis uncovered a dynamic, multicellular remodeling response to acute Notch inhibition to repair the niche and restore homeostasis. Notably, this crypt regenerative response did not require ISC loss.
Collapse
Affiliation(s)
- Natacha Bohin
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA; Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Theresa M Keeley
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alexis J Carulli
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Emily M Walker
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Elizabeth A Carlson
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jie Gao
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Iannis Aifantis
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Christian W Siebel
- Department of Discovery Oncology, Genentech, Inc, South San Francisco, CA 94080, USA
| | - Michael W Rajala
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Martin G Myers
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA; Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jennifer C Jones
- Department of Pediatrics, University of Colorado Medical School, Aurora, CO 80045, USA
| | - Constance D Brindley
- Department of Pediatrics, University of Colorado Medical School, Aurora, CO 80045, USA
| | - Peter J Dempsey
- Department of Pediatrics, University of Colorado Medical School, Aurora, CO 80045, USA
| | - Linda C Samuelson
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA; Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA.
| |
Collapse
|
35
|
Witkowski MT, Dolgalev I, Evensen NA, Ma C, Chambers T, Roberts KG, Sreeram S, Dai Y, Tikhonova AN, Lasry A, Qu C, Pei D, Cheng C, Robbins GA, Pierro J, Selvaraj S, Mezzano V, Daves M, Lupo PJ, Scheurer ME, Loomis CA, Mullighan CG, Chen W, Rabin KR, Tsirigos A, Carroll WL, Aifantis I. Extensive Remodeling of the Immune Microenvironment in B Cell Acute Lymphoblastic Leukemia. Cancer Cell 2020; 37:867-882.e12. [PMID: 32470390 PMCID: PMC7341535 DOI: 10.1016/j.ccell.2020.04.015] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 03/05/2020] [Accepted: 04/22/2020] [Indexed: 12/23/2022]
Abstract
A subset of B cell acute lymphoblastic leukemia (B-ALL) patients will relapse and succumb to therapy-resistant disease. The bone marrow microenvironment may support B-ALL progression and treatment evasion. Utilizing single-cell approaches, we demonstrate B-ALL bone marrow immune microenvironment remodeling upon disease initiation and subsequent re-emergence during conventional chemotherapy. We uncover a role for non-classical monocytes in B-ALL survival, and demonstrate monocyte abundance at B-ALL diagnosis is predictive of pediatric and adult B-ALL patient survival. We show that human B-ALL blasts alter a vascularized microenvironment promoting monocytic differentiation, while depleting leukemia-associated monocytes in B-ALL animal models prolongs disease remission in vivo. Our profiling of the B-ALL immune microenvironment identifies extrinsic regulators of B-ALL survival supporting new immune-based therapeutic approaches for high-risk B-ALL treatment.
Collapse
Affiliation(s)
- Matthew T Witkowski
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA.
| | - Igor Dolgalev
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA; Applied Bioinformatics Laboratories, New York University School of Medicine, New York, NY 10016, USA
| | - Nikki A Evensen
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Chao Ma
- Department of Mechanical and Aerospace Engineering, New York University, New York, NY 11202, USA; Department of Biomedical Engineering, New York University, New York, NY 11202, USA
| | - Tiffany Chambers
- Division of Pediatric Hematology/Oncology, College of Medicine, Baylor University, Houston, TX 77030, USA
| | - Kathryn G Roberts
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Sheetal Sreeram
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Yuling Dai
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Anastasia N Tikhonova
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Audrey Lasry
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Chunxu Qu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Deqing Pei
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Cheng Cheng
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Gabriel A Robbins
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Joanna Pierro
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Shanmugapriya Selvaraj
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Experimental Pathology Research Laboratory, New York University School of Medicine, New York, NY 10016, USA
| | - Valeria Mezzano
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Experimental Pathology Research Laboratory, New York University School of Medicine, New York, NY 10016, USA
| | - Marla Daves
- Division of Pediatric Hematology/Oncology, College of Medicine, Baylor University, Houston, TX 77030, USA
| | - Philip J Lupo
- Division of Pediatric Hematology/Oncology, College of Medicine, Baylor University, Houston, TX 77030, USA
| | - Michael E Scheurer
- Division of Pediatric Hematology/Oncology, College of Medicine, Baylor University, Houston, TX 77030, USA
| | - Cynthia A Loomis
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Experimental Pathology Research Laboratory, New York University School of Medicine, New York, NY 10016, USA
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Weiqiang Chen
- Department of Mechanical and Aerospace Engineering, New York University, New York, NY 11202, USA; Department of Biomedical Engineering, New York University, New York, NY 11202, USA
| | - Karen R Rabin
- Division of Pediatric Hematology/Oncology, College of Medicine, Baylor University, Houston, TX 77030, USA
| | - Aristotelis Tsirigos
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA; Applied Bioinformatics Laboratories, New York University School of Medicine, New York, NY 10016, USA
| | - William L Carroll
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA.
| | - Iannis Aifantis
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA.
| |
Collapse
|
36
|
Zhou Y, Han C, Wang E, Lorch AH, Serafin V, Cho BK, Gutierrez Diaz BT, Calvo J, Fang C, Khodadadi-Jamayran A, Tabaglio T, Marier C, Kuchmiy A, Sun L, Yacu G, Filip SK, Jin Q, Takahashi YH, Amici DR, Rendleman EJ, Rawat R, Bresolin S, Paganin M, Zhang C, Li H, Kandela I, Politanska Y, Abdala-Valencia H, Mendillo ML, Zhu P, Palhais B, Van Vlierberghe P, Taghon T, Aifantis I, Goo YA, Guccione E, Heguy A, Tsirigos A, Wee KB, Mishra RK, Pflumio F, Accordi B, Basso G, Ntziachristos P. Posttranslational Regulation of the Exon Skipping Machinery Controls Aberrant Splicing in Leukemia. Cancer Discov 2020; 10:1388-1409. [PMID: 32444465 DOI: 10.1158/2159-8290.cd-19-1436] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 04/21/2020] [Accepted: 05/19/2020] [Indexed: 12/16/2022]
Abstract
Splicing alterations are common in diseases such as cancer, where mutations in splicing factor genes are frequently responsible for aberrant splicing. Here we present an alternative mechanism for splicing regulation in T-cell acute lymphoblastic leukemia (T-ALL) that involves posttranslational stabilization of the splicing machinery via deubiquitination. We demonstrate there are extensive exon skipping changes in disease, affecting proteasomal subunits, cell-cycle regulators, and the RNA machinery. We present that the serine/arginine-rich splicing factors (SRSF), controlling exon skipping, are critical for leukemia cell survival. The ubiquitin-specific peptidase 7 (USP7) regulates SRSF6 protein levels via active deubiquitination, and USP7 inhibition alters the exon skipping pattern and blocks T-ALL growth. The splicing inhibitor H3B-8800 affects splicing of proteasomal transcripts and proteasome activity and acts synergistically with proteasome inhibitors in inhibiting T-ALL growth. Our study provides the proof-of-principle for regulation of splicing factors via deubiquitination and suggests new therapeutic modalities in T-ALL. SIGNIFICANCE: Our study provides a new proof-of-principle for posttranslational regulation of splicing factors independently of mutations in aggressive T-cell leukemia. It further suggests a new drug combination of splicing and proteasomal inhibitors, a concept that might apply to other diseases with or without mutations affecting the splicing machinery.This article is highlighted in the In This Issue feature, p. 1241.
Collapse
Affiliation(s)
- Yalu Zhou
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Cuijuan Han
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Eric Wang
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, New York
| | - Adam H Lorch
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Valentina Serafin
- Oncohematology Laboratory, Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Byoung-Kyu Cho
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois
| | - Blanca T Gutierrez Diaz
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Julien Calvo
- Team Niche and Cancer in hematopoiesis, CEA, Fontenay-aux-Roses, France.,Laboratory of Hematopoietic Stem Cells and Leukemia/Service Stem Cells and Radiation/iRCM/JACOB/DRF, CEA, Fontenay-aux-Roses, France
| | - Celestia Fang
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Alireza Khodadadi-Jamayran
- Applied Bioinformatics Laboratories, Office of Science and Research, New York University School of Medicine, New York, New York
| | - Tommaso Tabaglio
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Christian Marier
- Genome Technology Center, New York University School of Medicine, New York, New York
| | - Anna Kuchmiy
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Limin Sun
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - George Yacu
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Szymon K Filip
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois
| | - Qi Jin
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Yoh-Hei Takahashi
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - David R Amici
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Emily J Rendleman
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Radhika Rawat
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Silvia Bresolin
- Oncohematology Laboratory, Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Maddalena Paganin
- Oncohematology Laboratory, Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Cheng Zhang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - Irawati Kandela
- Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois
| | - Yuliya Politanska
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Hiam Abdala-Valencia
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Marc L Mendillo
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Ping Zhu
- H3 Biomedicine, Inc., Cambridge, Massachusetts
| | - Bruno Palhais
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Pieter Van Vlierberghe
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Tom Taghon
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Department of Diagnostic Sciences, Ghent University, Ghent, Belgium.,Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Iannis Aifantis
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, New York
| | - Young Ah Goo
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Proteomics Center of Excellence, Northwestern University, Evanston, Illinois
| | - Ernesto Guccione
- Department of Oncological Sciences and Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York.,Department of Pharmacological Sciences and Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Adriana Heguy
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, New York.,Genome Technology Center, New York University School of Medicine, New York, New York
| | - Aristotelis Tsirigos
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, New York.,Applied Bioinformatics Laboratories, Office of Science and Research, New York University School of Medicine, New York, New York
| | - Keng Boon Wee
- Applied Bioinformatics Laboratories, Office of Science and Research, New York University School of Medicine, New York, New York.,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
| | - Rama K Mishra
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Center for Molecular Innovation and Drug Discovery, Northwestern University, Chicago, Illinois
| | - Francoise Pflumio
- Team Niche and Cancer in hematopoiesis, CEA, Fontenay-aux-Roses, France.,Laboratory of Hematopoietic Stem Cells and Leukemia/Service Stem Cells and Radiation/iRCM/JACOB/DRF, CEA, Fontenay-aux-Roses, France
| | - Benedetta Accordi
- Oncohematology Laboratory, Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Giuseppe Basso
- Oncohematology Laboratory, Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Panagiotis Ntziachristos
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois. .,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois
| |
Collapse
|
37
|
Abstract
RNA splicing is an essential process that governs many aspects of cellular proliferation, survival, and differentiation. Considering the importance of RNA splicing in gene regulation, alterations in this pathway have been implicated in many human cancers. Large-scale genomic studies have uncovered a spectrum of splicing machinery mutations that contribute to tumorigenesis. Moreover, cancer cells are capable of hijacking the expression of RNA-binding proteins (RBPs), leading to dysfunctional gene splicing and tumor-specific dependencies. Advances in next-generation RNA sequencing have revealed tumor-specific isoforms associated with these alterations, including the presence of neoantigens, which serve as potential immunotherapeutic targets. In this review, we discuss the various mechanisms by which cancer cells exploit RNA splicing to promote tumor growth and the current therapeutic landscape for splicing-based therapies.
Collapse
Affiliation(s)
- Eric Wang
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA.
| | - Iannis Aifantis
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| |
Collapse
|
38
|
Kloetgen A, Thandapani P, Ntziachristos P, Ghebrechristos Y, Nomikou S, Lazaris C, Chen X, Hu H, Bakogianni S, Wang J, Fu Y, Boccalatte F, Zhong H, Paietta E, Trimarchi T, Zhu Y, Van Vlierberghe P, Inghirami GG, Lionnet T, Aifantis I, Tsirigos A. Three-dimensional chromatin landscapes in T cell acute lymphoblastic leukemia. Nat Genet 2020; 52:388-400. [PMID: 32203470 PMCID: PMC7138649 DOI: 10.1038/s41588-020-0602-9] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 02/25/2020] [Indexed: 01/04/2023]
Abstract
Differences in three-dimensional (3D) chromatin architecture can influence the integrity of topologically associating domains (TADs) and rewire specific enhancer-promoter interactions, impacting gene expression and leading to human disease. Here we investigate the 3D chromatin architecture in T cell acute lymphoblastic leukemia (T-ALL) by using primary human leukemia specimens and examine the dynamic responses of this architecture to pharmacological agents. Systematic integration of matched in situ Hi-C, RNA-seq and CTCF ChIP-seq datasets revealed widespread differences in intra-TAD chromatin interactions and TAD boundary insulation in T-ALL. Our studies identify and focus on a TAD 'fusion' event associated with absence of CTCF-mediated insulation, enabling direct interactions between the MYC promoter and a distal super-enhancer. Moreover, our data also demonstrate that small-molecule inhibitors targeting either oncogenic signal transduction or epigenetic regulation can alter specific 3D interactions found in leukemia. Overall, our study highlights the impact, complexity and dynamic nature of 3D chromatin architecture in human acute leukemia.
Collapse
Affiliation(s)
- Andreas Kloetgen
- Department of Pathology, New York University School of Medicine, New York, NY, USA.,Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Palaniraja Thandapani
- Department of Pathology, New York University School of Medicine, New York, NY, USA.,Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Panagiotis Ntziachristos
- Department of Pathology, New York University School of Medicine, New York, NY, USA.,Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA.,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
| | - Yohana Ghebrechristos
- Department of Pathology, New York University School of Medicine, New York, NY, USA.,Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Sofia Nomikou
- Department of Pathology, New York University School of Medicine, New York, NY, USA.,Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Charalampos Lazaris
- Department of Pathology, New York University School of Medicine, New York, NY, USA.,Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Xufeng Chen
- Department of Pathology, New York University School of Medicine, New York, NY, USA.,Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Hai Hu
- Department of Pathology, New York University School of Medicine, New York, NY, USA.,Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Sofia Bakogianni
- Department of Pathology, New York University School of Medicine, New York, NY, USA.,Department of Microbiology, New York University School of Medicine, Alexandria Center for Life Sciences, New York, NY, USA
| | - Jingjing Wang
- Department of Pathology, New York University School of Medicine, New York, NY, USA.,Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Yi Fu
- Department of Cell Biology, Institute for Systems Genetics, New York University, New York, NY, USA
| | - Francesco Boccalatte
- Department of Pathology, New York University School of Medicine, New York, NY, USA.,Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Hua Zhong
- Division of Biostatistics, Department of Population Health, New York University School of Medicine, New York, NY, USA
| | | | - Thomas Trimarchi
- Department of Pathology, New York University School of Medicine, New York, NY, USA.,Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA.,BridgeBio Pharma, Palo Alto, CA, USA
| | - Yixing Zhu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | | | - Giorgio G Inghirami
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Timothee Lionnet
- Department of Cell Biology, Institute for Systems Genetics, New York University, New York, NY, USA
| | - Iannis Aifantis
- Department of Pathology, New York University School of Medicine, New York, NY, USA. .,Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA.
| | - Aristotelis Tsirigos
- Department of Pathology, New York University School of Medicine, New York, NY, USA. .,Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA. .,Applied Bioinformatics Laboratories, Office of Science and Research, New York University School of Medicine, New York, NY, USA.
| |
Collapse
|
39
|
Abstract
Mounting evidence links genetic lesions with genome topology alterations and aberrant gene activation. However, the role of epigenetic plasticity remains elusive. Emerging studies implicate DNA methylation, transcriptional elongation, long noncoding RNAs (lncRNAs), and CCCTC-binding factor (CTCF)-RNA interactions, but systematic approaches are needed to fully decipher the role of epigenetic plasticity in genome integrity and function.
Collapse
Affiliation(s)
- Charalampos Lazaris
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA.
| | - Iannis Aifantis
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Aristotelis Tsirigos
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA; Applied Bioinformatics Laboratories, Office of Science & Research, New York University School of Medicine, New York, NY 10016, USA
| |
Collapse
|
40
|
Witkowski MT, Kousteni S, Aifantis I. Mapping and targeting of the leukemic microenvironment. J Exp Med 2020; 217:e20190589. [PMID: 31873722 PMCID: PMC7041707 DOI: 10.1084/jem.20190589] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/04/2019] [Accepted: 11/13/2019] [Indexed: 12/13/2022] Open
Abstract
Numerous studies support a role of the microenvironment in maintenance of the leukemic clone, as well as in treatment resistance. It is clear that disruption of the normal bone marrow microenvironment is sufficient to promote leukemic transformation and survival in both a cell autonomous and non-cell autonomous manner. In this review, we provide a snapshot of the various cell types shown to contribute to the leukemic microenvironment as well as treatment resistance. Several of these studies suggest that leukemic blasts occupy specific cellular and biochemical "niches." Effective dissection of critical leukemic niche components using single-cell approaches has allowed a more precise and extensive characterization of complexity that underpins both the healthy and malignant bone marrow microenvironment. Knowledge gained from these observations can have an important impact in the development of microenvironment-directed targeted approaches aimed at mitigating disease relapse.
Collapse
Affiliation(s)
- Matthew T. Witkowski
- Department of Pathology, New York University School of Medicine, New York, NY
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY
| | - Stavroula Kousteni
- Department of Physiology & Cellular Biophysics, Columbia University Irving Medical Center, New York, NY
| | - Iannis Aifantis
- Department of Pathology, New York University School of Medicine, New York, NY
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY
| |
Collapse
|
41
|
Hanniford D, Ulloa-Morales A, Karz A, Berzoti-Coelho MG, Moubarak RS, Sánchez-Sendra B, Kloetgen A, Davalos V, Imig J, Wu P, Vasudevaraja V, Argibay D, Lilja K, Tabaglio T, Monteagudo C, Guccione E, Tsirigos A, Osman I, Aifantis I, Hernando E. Epigenetic Silencing of CDR1as Drives IGF2BP3-Mediated Melanoma Invasion and Metastasis. Cancer Cell 2020; 37:55-70.e15. [PMID: 31935372 PMCID: PMC7184928 DOI: 10.1016/j.ccell.2019.12.007] [Citation(s) in RCA: 187] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 08/17/2019] [Accepted: 12/11/2019] [Indexed: 12/13/2022]
Abstract
Metastasis is the primary cause of death of cancer patients. Dissecting mechanisms governing metastatic spread may uncover important tumor biology and/or yield promising therapeutic insights. Here, we investigated the role of circular RNAs (circRNA) in metastasis, using melanoma as a model aggressive tumor. We identified silencing of cerebellar degeneration-related 1 antisense (CDR1as), a regulator of miR-7, as a hallmark of melanoma progression. CDR1as depletion results from epigenetic silencing of LINC00632, its originating long non-coding RNA (lncRNA) and promotes invasion in vitro and metastasis in vivo through a miR-7-independent, IGF2BP3-mediated mechanism. Moreover, CDR1as levels reflect cellular states associated with distinct therapeutic responses. Our study reveals functional, prognostic, and predictive roles for CDR1as and expose circRNAs as key players in metastasis.
Collapse
Affiliation(s)
- Douglas Hanniford
- Department of Pathology, New York University Langone Medical Center, New York, NY, USA; Interdisciplinary Melanoma Cooperative Group, New York University Langone Medical Center, New York, NY, USA.
| | - Alejandro Ulloa-Morales
- Department of Pathology, New York University Langone Medical Center, New York, NY, USA; Interdisciplinary Melanoma Cooperative Group, New York University Langone Medical Center, New York, NY, USA
| | - Alcida Karz
- Department of Pathology, New York University Langone Medical Center, New York, NY, USA; Interdisciplinary Melanoma Cooperative Group, New York University Langone Medical Center, New York, NY, USA
| | - Maria Gabriela Berzoti-Coelho
- Department of Pathology, New York University Langone Medical Center, New York, NY, USA; Department of Clinical Analysis, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Rana S Moubarak
- Department of Pathology, New York University Langone Medical Center, New York, NY, USA; Interdisciplinary Melanoma Cooperative Group, New York University Langone Medical Center, New York, NY, USA
| | | | - Andreas Kloetgen
- Department of Pathology, New York University Langone Medical Center, New York, NY, USA; Interdisciplinary Melanoma Cooperative Group, New York University Langone Medical Center, New York, NY, USA
| | - Veronica Davalos
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Jochen Imig
- Department of Pathology, New York University Langone Medical Center, New York, NY, USA; Interdisciplinary Melanoma Cooperative Group, New York University Langone Medical Center, New York, NY, USA
| | - Pamela Wu
- Institute for Systems Genetics, New York University Langone Medical Center, New York, NY, USA
| | - Varshini Vasudevaraja
- Applied Bioinformatics Laboratories, New York University Langone Medical Center, New York, NY, USA
| | - Diana Argibay
- Department of Pathology, New York University Langone Medical Center, New York, NY, USA; Interdisciplinary Melanoma Cooperative Group, New York University Langone Medical Center, New York, NY, USA
| | - Karin Lilja
- Department of Pathology, New York University Langone Medical Center, New York, NY, USA
| | - Tommaso Tabaglio
- Institute of Molecular and Cell Biology, A(∗)STAR, Singapore, Singapore
| | | | - Ernesto Guccione
- Institute of Molecular and Cell Biology, A(∗)STAR, Singapore, Singapore; Department of Oncological Sciences, Icahn School of Medicine, Mount Sinai, New York, NY, USA
| | - Aristotelis Tsirigos
- Department of Pathology, New York University Langone Medical Center, New York, NY, USA; Applied Bioinformatics Laboratories, New York University Langone Medical Center, New York, NY, USA
| | - Iman Osman
- Departments of Urology and Medicine, New York University Langone Medical Center, New York, NY, USA; Interdisciplinary Melanoma Cooperative Group, New York University Langone Medical Center, New York, NY, USA
| | - Iannis Aifantis
- Department of Pathology, New York University Langone Medical Center, New York, NY, USA; Interdisciplinary Melanoma Cooperative Group, New York University Langone Medical Center, New York, NY, USA
| | - Eva Hernando
- Department of Pathology, New York University Langone Medical Center, New York, NY, USA; Interdisciplinary Melanoma Cooperative Group, New York University Langone Medical Center, New York, NY, USA.
| |
Collapse
|
42
|
Papaioannou D, Petri A, Dovey OM, Terreri S, Wang E, Collins FA, Woodward LA, Walker AE, Nicolet D, Pepe F, Kumchala P, Bill M, Walker CJ, Karunasiri M, Mrózek K, Gardner ML, Camilotto V, Zitzer N, Cooper JL, Cai X, Rong-Mullins X, Kohlschmidt J, Archer KJ, Freitas MA, Zheng Y, Lee RJ, Aifantis I, Vassiliou G, Singh G, Kauppinen S, Bloomfield CD, Dorrance AM, Garzon R. Publisher Correction: The long non-coding RNA HOXB-AS3 regulates ribosomal RNA transcription in NPM1-mutated acute myeloid leukemia. Nat Commun 2020; 11:204. [PMID: 31911614 PMCID: PMC6946642 DOI: 10.1038/s41467-019-13969-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
| | - Andreas Petri
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
| | - Oliver M Dovey
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Sara Terreri
- Institute of Genetics and Biophysics (IGB-ABT), National Council of Research (CNR), Naples, Italy
| | - Eric Wang
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Frances A Collins
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, USA
| | - Lauren A Woodward
- Department of Molecular Genetics, Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Allison E Walker
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, USA
| | - Deedra Nicolet
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, USA.,Alliance for Clinical Trials in Oncology Statistics and Data Center, The Ohio State University, Columbus, OH, USA
| | - Felice Pepe
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, USA
| | - Prasanthi Kumchala
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, USA
| | - Marius Bill
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, USA
| | | | - Malith Karunasiri
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, USA
| | - Krzysztof Mrózek
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, USA
| | - Miranda L Gardner
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, USA.,Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
| | - Virginia Camilotto
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK.,Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Nina Zitzer
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, USA
| | - Jonathan L Cooper
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Xiongwei Cai
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Xiaoqing Rong-Mullins
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, USA.,Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, OH, USA
| | - Jessica Kohlschmidt
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, USA.,Alliance for Clinical Trials in Oncology Statistics and Data Center, The Ohio State University, Columbus, OH, USA
| | - Kellie J Archer
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, USA.,Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, OH, USA
| | - Michael A Freitas
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, USA.,Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
| | - Yi Zheng
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Robert J Lee
- Division of Pharmaceutics, College of Pharmacy, The Ohio State University, Columbus, OH, USA
| | - Iannis Aifantis
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - George Vassiliou
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK.,Department of Haematology, Cambridge University Hospitals NHS Trust, Cambridge, UK
| | - Guramrit Singh
- Department of Molecular Genetics, Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Sakari Kauppinen
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
| | - Clara D Bloomfield
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, USA
| | | | - Ramiro Garzon
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, USA.
| |
Collapse
|
43
|
Sakellaropoulos T, Vougas K, Narang S, Koinis F, Kotsinas A, Polyzos A, Moss TJ, Piha-Paul S, Zhou H, Kardala E, Damianidou E, Alexopoulos LG, Aifantis I, Townsend PA, Panayiotidis MI, Sfikakis P, Bartek J, Fitzgerald RC, Thanos D, Mills Shaw KR, Petty R, Tsirigos A, Gorgoulis VG. A Deep Learning Framework for Predicting Response to Therapy in Cancer. Cell Rep 2019; 29:3367-3373.e4. [PMID: 31825821 DOI: 10.1016/j.celrep.2019.11.017] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 07/16/2019] [Accepted: 11/05/2019] [Indexed: 02/07/2023] Open
Abstract
A major challenge in cancer treatment is predicting clinical response to anti-cancer drugs on a personalized basis. Using a pharmacogenomics database of 1,001 cancer cell lines, we trained deep neural networks for prediction of drug response and assessed their performance on multiple clinical cohorts. We demonstrate that deep neural networks outperform the current state in machine learning frameworks. We provide a proof of concept for the use of deep neural network-based frameworks to aid precision oncology strategies.
Collapse
Affiliation(s)
- Theodore Sakellaropoulos
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Konstantinos Vougas
- Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou Str., Athens 11527, Greece; Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National and Kapodistrian University of Athens, 75 Mikras Asias Str., Athens 11527, Greece.
| | - Sonali Narang
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Filippos Koinis
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National and Kapodistrian University of Athens, 75 Mikras Asias Str., Athens 11527, Greece
| | - Athanassios Kotsinas
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National and Kapodistrian University of Athens, 75 Mikras Asias Str., Athens 11527, Greece
| | - Alexander Polyzos
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Tyler J Moss
- Sheikh Khalifa Bin Zayed al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
| | - Sarina Piha-Paul
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
| | - Hua Zhou
- Applied Bioinformatics Laboratories, NYU School of Medicine, New York, NY 10016, USA
| | - Eleni Kardala
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National and Kapodistrian University of Athens, 75 Mikras Asias Str., Athens 11527, Greece
| | - Eleni Damianidou
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National and Kapodistrian University of Athens, 75 Mikras Asias Str., Athens 11527, Greece
| | - Leonidas G Alexopoulos
- School of Mechanical Engineering, National Technical University of Athens, Zografou 15780, Greece
| | - Iannis Aifantis
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Paul A Townsend
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, Manchester Cancer Research Centre, NIHR Manchester Biomedical Research Centre, University of Manchester, Manchester M20 4GJ, UK
| | - Mihalis I Panayiotidis
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK; Department of Electron Microscopy & Molecular Pathology, Cyprus Institute of Neurology & Genetics, Nicosia, 2371, Cyprus
| | - Petros Sfikakis
- 1st Department of Propaedeutic Internal Medicine, Medical School, Laikon Hospital, National and Kapodistrian University of Athens, 75 Mikras Asias Str., Athens 11527, Greece; Center for New Biotechnologies and Precision Medicine, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Str., Athens 11527, Greece
| | - Jiri Bartek
- Genome Integrity Unit, Danish Cancer Society Research Centre, Strandboulevarden 49, Copenhagen 2100, Denmark; Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Hněvotínská, Olomouc 1333/5 779 00, Czech Republic; Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm SE-171 77, Sweden
| | - Rebecca C Fitzgerald
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Dimitris Thanos
- Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou Str., Athens 11527, Greece
| | - Kenna R Mills Shaw
- Sheikh Khalifa Bin Zayed al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
| | - Russell Petty
- Division of Molecular and Clinical Medicine, Ninewells Hospital and School of Medicine, University of Dundee, Dundee DD1 9SY, UK
| | - Aristotelis Tsirigos
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA; Applied Bioinformatics Laboratories, NYU School of Medicine, New York, NY 10016, USA.
| | - Vassilis G Gorgoulis
- Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou Str., Athens 11527, Greece; Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National and Kapodistrian University of Athens, 75 Mikras Asias Str., Athens 11527, Greece; Division of Cancer Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, Manchester Cancer Research Centre, NIHR Manchester Biomedical Research Centre, University of Manchester, Manchester M20 4GJ, UK; 1st Department of Propaedeutic Internal Medicine, Medical School, Laikon Hospital, National and Kapodistrian University of Athens, 75 Mikras Asias Str., Athens 11527, Greece.
| |
Collapse
|
44
|
Saint Fleur-Lominy S, Maus M, Vaeth M, Lange I, Zee I, Suh D, Liu C, Wu X, Tikhonova A, Aifantis I, Feske S. STIM1 and STIM2 Mediate Cancer-Induced Inflammation in T Cell Acute Lymphoblastic Leukemia. Cell Rep 2019; 24:3045-3060.e5. [PMID: 30208327 PMCID: PMC6170166 DOI: 10.1016/j.celrep.2018.08.030] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 06/04/2018] [Accepted: 08/10/2018] [Indexed: 12/12/2022] Open
Abstract
T cell acute lymphoblastic leukemia (T-ALL) is commonly associated with activating mutations in the NOTCH1 pathway. Recent reports have shown a link between NOTCH1 signaling and intracellular Ca2+ homeostasis in T-ALL. Here, we investigate the role of store-operated Ca2+ entry (SOCE) mediated by the Ca2+ channel ORAI1 and its activators STIM1 and STIM2 in T-ALL. Deletion of STIM1 and STIM2 in leukemic cells abolishes SOCE and significantly prolongs the survival of mice in a NOTCH1-dependent model of T-ALL. The survival advantage is unrelated to the leukemic cell burden but is associated with the SOCE-dependent ability of malignant T lymphoblasts to cause inflammation in leukemia-infiltrated organs. Mice with STIM1/STIM2-deficient T-ALL show a markedly reduced necroinflammatory response in leukemia-infiltrated organs and downregulation of signaling pathways previously linked to cancer-induced inflammation. Our study shows that leukemic T lymphoblasts cause inflammation of leukemia-infiltrated organs that is dependent on SOCE. T cell acute lymphoblastic leukemia (T-ALL) is an aggressive cancer of T cell progenitors affecting children and adults. Saint Fleur-Lominy et al. show that calcium influx mediated by STIM1 and STIM2 promotes the proinflammatory function of leukemic cells and premature death from leukemia.
Collapse
Affiliation(s)
- Shella Saint Fleur-Lominy
- Department of Medicine, New York University School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Mate Maus
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Martin Vaeth
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Ingo Lange
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Isabelle Zee
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - David Suh
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Cynthia Liu
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Xiaojun Wu
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Anastasia Tikhonova
- Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA; Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Iannis Aifantis
- Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA; Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Stefan Feske
- Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA; Department of Pathology, New York University School of Medicine, New York, NY 10016, USA.
| |
Collapse
|
45
|
Rodriguez S, Abundis C, Boccalatte F, Mehrotra P, Chiang MY, Yui MA, Wang L, Zhang H, Zollman A, Bonfim-Silva R, Kloetgen A, Palmer J, Sandusky G, Wunderlich M, Kaplan MH, Mulloy JC, Marcucci G, Aifantis I, Cardoso AA, Carlesso N. Therapeutic targeting of the E3 ubiquitin ligase SKP2 in T-ALL. Leukemia 2019; 34:1241-1252. [PMID: 31772299 PMCID: PMC7192844 DOI: 10.1038/s41375-019-0653-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 10/18/2019] [Accepted: 11/13/2019] [Indexed: 12/15/2022]
Abstract
Timed degradation of the cyclin-dependent kinase inhibitor p27Kip1 by the E3 ubiquitin ligase F-box protein SKP2 is critical for T-cell progression into cell cycle, coordinating proliferation and differentiation processes. SKP2 expression is regulated by mitogenic stimuli and by Notch signaling, a key pathway in T-cell development and in T-cell acute lymphoblastic leukemia (T-ALL); however, it is not known whether SKP2 plays a role in the development of T-ALL. Here, we determined that SKP2 function is relevant for T-ALL leukemogenesis, whereas is dispensable for T-cell development. Targeted inhibition of SKP2 by genetic deletion or pharmacological blockade markedly inhibited proliferation of human T-ALL cells in vitro and antagonized disease in vivo in murine and xenograft leukemia models, with little effect on normal tissues. We also demonstrate a novel feed forward feedback loop by which Notch and IL-7 signaling cooperatively converge on SKP2 induction and cell cycle activation. These studies show that the Notch/SKP2/p27Kip1 pathway plays a unique role in T-ALL development and provide a proof-of-concept for the use of SKP2 as a new therapeutic target in T-cell acute lymphoblastic leukemia (T-ALL).
Collapse
Affiliation(s)
- Sonia Rodriguez
- Beckman Research Institute, Gehr Leukemia Center, City of Hope, Duarte, CA, 91010, USA.,Herman B Wells Center, Indiana University Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Christina Abundis
- Beckman Research Institute, Gehr Leukemia Center, City of Hope, Duarte, CA, 91010, USA
| | - Francesco Boccalatte
- Department of Pathology and Perlmutter Cancer Center, NYU Langone Medical Center, New York, NY, 10016, USA
| | - Purvi Mehrotra
- Herman B Wells Center, Indiana University Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Mark Y Chiang
- Department of Internal Medicine, University of Michigan School of Medicine, Ann Arbor, MI, 48109, USA
| | - Mary A Yui
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Lin Wang
- Herman B Wells Center, Indiana University Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.,Department of Pathology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Huajia Zhang
- Herman B Wells Center, Indiana University Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Amy Zollman
- Herman B Wells Center, Indiana University Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Ricardo Bonfim-Silva
- Herman B Wells Center, Indiana University Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.,Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Riberão Preto, São Paulo, 14049-900, Brazil
| | - Andreas Kloetgen
- Department of Pathology and Perlmutter Cancer Center, NYU Langone Medical Center, New York, NY, 10016, USA
| | - Joycelynne Palmer
- Beckman Research Institute, Gehr Leukemia Center, City of Hope, Duarte, CA, 91010, USA
| | - George Sandusky
- Department of Pathology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Mark Wunderlich
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Mark H Kaplan
- Herman B Wells Center, Indiana University Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - James C Mulloy
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Guido Marcucci
- Beckman Research Institute, Gehr Leukemia Center, City of Hope, Duarte, CA, 91010, USA
| | - Iannis Aifantis
- Department of Pathology and Perlmutter Cancer Center, NYU Langone Medical Center, New York, NY, 10016, USA
| | - Angelo A Cardoso
- Beckman Research Institute, Gehr Leukemia Center, City of Hope, Duarte, CA, 91010, USA
| | - Nadia Carlesso
- Beckman Research Institute, Gehr Leukemia Center, City of Hope, Duarte, CA, 91010, USA. .,Herman B Wells Center, Indiana University Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
| |
Collapse
|
46
|
Papaioannou D, Petri A, Dovey OM, Terreri S, Wang E, Collins FA, Woodward LA, Walker AE, Nicolet D, Pepe F, Kumchala P, Bill M, Walker CJ, Karunasiri M, Mrózek K, Gardner ML, Camilotto V, Zitzer N, Cooper JL, Cai X, Rong-Mullins X, Kohlschmidt J, Archer KJ, Freitas MA, Zheng Y, Lee RJ, Aifantis I, Vassiliou G, Singh G, Kauppinen S, Bloomfield CD, Dorrance AM, Garzon R. The long non-coding RNA HOXB-AS3 regulates ribosomal RNA transcription in NPM1-mutated acute myeloid leukemia. Nat Commun 2019; 10:5351. [PMID: 31767858 PMCID: PMC6877618 DOI: 10.1038/s41467-019-13259-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 10/28/2019] [Indexed: 12/21/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are important regulatory molecules that are implicated in cellular physiology and pathology. In this work, we dissect the functional role of the HOXB-AS3 lncRNA in patients with NPM1-mutated (NPM1mut) acute myeloid leukemia (AML). We show that HOXB-AS3 regulates the proliferative capacity of NPM1mut AML blasts in vitro and in vivo. HOXB-AS3 is shown to interact with the ErbB3-binding protein 1 (EBP1) and guide EBP1 to the ribosomal DNA locus. Via this mechanism, HOXB-AS3 regulates ribosomal RNA transcription and de novo protein synthesis. We propose that in the context of NPM1 mutations, HOXB-AS3 overexpression acts as a compensatory mechanism, which allows adequate protein production in leukemic blasts.
Collapse
MESH Headings
- Acute Disease
- Animals
- Cell Line, Tumor
- Cell Proliferation
- HEK293 Cells
- Humans
- K562 Cells
- Leukemia, Myeloid/genetics
- Leukemia, Myeloid/pathology
- Mice, Inbred NOD
- Mice, Knockout
- Mice, SCID
- Mutation
- Nuclear Proteins/genetics
- Nucleophosmin
- Protein Biosynthesis/genetics
- RNA, Long Noncoding/genetics
- RNA, Ribosomal/genetics
- THP-1 Cells
- Transcription, Genetic
- Transplantation, Heterologous
Collapse
Affiliation(s)
| | - Andreas Petri
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
| | - Oliver M Dovey
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Sara Terreri
- Institute of Genetics and Biophysics (IGB-ABT), National Council of Research (CNR), Naples, Italy
| | - Eric Wang
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Frances A Collins
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, USA
| | - Lauren A Woodward
- Department of Molecular Genetics, Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Allison E Walker
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, USA
| | - Deedra Nicolet
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, USA
- Alliance for Clinical Trials in Oncology Statistics and Data Center, The Ohio State University, Columbus, OH, USA
| | - Felice Pepe
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, USA
| | - Prasanthi Kumchala
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, USA
| | - Marius Bill
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, USA
| | | | - Malith Karunasiri
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, USA
| | - Krzysztof Mrózek
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, USA
| | - Miranda L Gardner
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, USA
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
| | - Virginia Camilotto
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Nina Zitzer
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, USA
| | - Jonathan L Cooper
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Xiongwei Cai
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Xiaoqing Rong-Mullins
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, USA
- Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, OH, USA
| | - Jessica Kohlschmidt
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, USA
- Alliance for Clinical Trials in Oncology Statistics and Data Center, The Ohio State University, Columbus, OH, USA
| | - Kellie J Archer
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, USA
- Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, OH, USA
| | - Michael A Freitas
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, USA
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
| | - Yi Zheng
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Robert J Lee
- Division of Pharmaceutics, College of Pharmacy, The Ohio State University, Columbus, OH, USA
| | - Iannis Aifantis
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - George Vassiliou
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
- Department of Haematology, Cambridge University Hospitals NHS Trust, Cambridge, UK
| | - Guramrit Singh
- Department of Molecular Genetics, Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Sakari Kauppinen
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
| | - Clara D Bloomfield
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, USA
| | | | - Ramiro Garzon
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, USA.
| |
Collapse
|
47
|
Mandal M, Okoreeh MK, Kennedy DE, Maienschein-Cline M, Ai J, McLean KC, Kaverina N, Veselits M, Aifantis I, Gounari F, Clark MR. CXCR4 signaling directs Igk recombination and the molecular mechanisms of late B lymphopoiesis. Nat Immunol 2019; 20:1393-1403. [PMID: 31477919 PMCID: PMC6754289 DOI: 10.1038/s41590-019-0468-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 07/16/2019] [Indexed: 12/17/2022]
Abstract
In B lymphopoiesis, activation of the pre-B cell antigen receptor (pre-BCR) is associated with both cell cycle exit and Igk recombination. Yet how the pre-BCR mediates these functions remains unclear. Here, we demonstrate that the pre-BCR initiates a feed-forward amplification loop mediated by the transcription factor interferon regulatory factor 4 and the chemokine receptor C-X-C motif chemokine receptor 4 (CXCR4). CXCR4 ligation by C-X-C motif chemokine ligand 12 activates the mitogen-activated protein kinase extracellular-signal-regulated kinase, which then directs the development of small pre- and immature B cells, including orchestrating cell cycle exit, pre-BCR repression, Igk recombination and BCR expression. In contrast, pre-BCR expression and escape from interleukin-7 have only modest effects on B cell developmental transcriptional and epigenetic programs. These data show a direct and central role for CXCR4 in orchestrating late B cell lymphopoiesis. Furthermore, in the context of previous findings, our data provide a three-receptor system sufficient to recapitulate the essential features of B lymphopoiesis in vitro.
Collapse
Affiliation(s)
- Malay Mandal
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA.
- Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL, USA.
| | - Michael K Okoreeh
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA
- Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL, USA
| | - Domenick E Kennedy
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA
- Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL, USA
| | | | - Junting Ai
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA
- Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL, USA
| | - Kaitlin C McLean
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA
- Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL, USA
| | - Natalya Kaverina
- Division of Nephrology, University of Washington, Seattle, WA, USA
| | - Margaret Veselits
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA
- Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL, USA
| | - Iannis Aifantis
- Department of Pathology, NYU School of Medicine, New York, NY, USA
- Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA
| | - Fotini Gounari
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA
- Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL, USA
| | - Marcus R Clark
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA.
- Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL, USA.
| |
Collapse
|
48
|
Guillamot M, Ouazia D, Dolgalev I, Yeung ST, Kourtis N, Dai Y, Corrigan K, Zea-Redondo L, Saraf A, Florens L, Washburn MP, Tikhonova AN, Malumbres M, Gong Y, Tsirigos A, Park C, Barbieri C, Khanna KM, Busino L, Aifantis I. The E3 ubiquitin ligase SPOP controls resolution of systemic inflammation by triggering MYD88 degradation. Nat Immunol 2019; 20:1196-1207. [PMID: 31406379 PMCID: PMC7376385 DOI: 10.1038/s41590-019-0454-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 06/26/2019] [Indexed: 01/25/2023]
Abstract
The response to systemic infection and injury requires the rapid adaptation of hematopoietic stem cells (HSCs), which proliferate and divert their differentiation toward the myeloid lineage. Significant interest has emerged in understanding the signals that trigger the emergency hematopoietic program. However, the mechanisms that halt this response of HSCs, which is critical to restore homeostasis, remain unknown. Here we reveal that the E3 ubiquitin ligase Speckle-type BTB-POZ protein (SPOP) restrains the inflammatory activation of HSCs. In the absence of Spop, systemic inflammation proceeded in an unresolved manner, and the sustained response in the HSCs resulted in a lethal phenotype reminiscent of hyper-inflammatory syndrome or sepsis. Our proteomic studies decipher that SPOP restricted inflammation by ubiquitinating the innate signal transducer myeloid differentiation primary response protein 88 (MYD88). These findings unearth an HSC-intrinsic post-translational mechanism that is essential for reestablishing homeostasis after emergency hematopoiesis.
Collapse
Affiliation(s)
- Maria Guillamot
- Department of Pathology, NYU School of Medicine, New York, NY, USA.,Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA.,These authors contributed equally: Maria Guillamot, Dahmane Ouazia.,Correspondence and requests for materials should be addressed to M.G., L.B. or I.A., ; ;
| | - Dahmane Ouazia
- Department of Cancer Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,These authors contributed equally: Maria Guillamot, Dahmane Ouazia
| | - Igor Dolgalev
- Department of Pathology, NYU School of Medicine, New York, NY, USA.,Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA.,Applied Bioinformatics Laboratories, Office of Science & Research, NYU School of Medicine, New York, NY, USA
| | - Stephen T. Yeung
- Department of Microbiology, NYU School of Medicine, New York, NY, USA
| | - Nikos Kourtis
- Department of Pathology, NYU School of Medicine, New York, NY, USA.,Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA
| | - Yuling Dai
- Department of Pathology, NYU School of Medicine, New York, NY, USA.,Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA
| | - Kate Corrigan
- Department of Pathology, NYU School of Medicine, New York, NY, USA.,Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA
| | - Luna Zea-Redondo
- Department of Pathology, NYU School of Medicine, New York, NY, USA.,Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA
| | - Anita Saraf
- The Stowers Institute of Medical Research, Kansas City, MO, USA
| | | | - Michael P. Washburn
- The Stowers Institute of Medical Research, Kansas City, MO, USA.,Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, Kansas City, KS, USA
| | - Anastasia N. Tikhonova
- Department of Pathology, NYU School of Medicine, New York, NY, USA.,Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA
| | - Marina Malumbres
- Department of Pathology, NYU School of Medicine, New York, NY, USA.,Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA
| | - Yixiao Gong
- Department of Pathology, NYU School of Medicine, New York, NY, USA.,Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA
| | - Aristotelis Tsirigos
- Department of Pathology, NYU School of Medicine, New York, NY, USA.,Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA.,Applied Bioinformatics Laboratories, Office of Science & Research, NYU School of Medicine, New York, NY, USA
| | - Christopher Park
- Department of Pathology, NYU School of Medicine, New York, NY, USA.,Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA
| | - Christopher Barbieri
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.,Department of Urology, Weill Cornell Medicine, New York, NY, USA
| | - Kamal M. Khanna
- Department of Microbiology, NYU School of Medicine, New York, NY, USA
| | - Luca Busino
- Department of Cancer Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,These authors contributed equally: Maria Guillamot, Dahmane Ouazia.,These authors jointly supervised this work: Luca Busino and Iannis Aifantis.,Correspondence and requests for materials should be addressed to M.G., L.B. or I.A., ; ;
| | - Iannis Aifantis
- Department of Pathology, NYU School of Medicine, New York, NY, USA.,Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA.,These authors contributed equally: Maria Guillamot, Dahmane Ouazia.,These authors jointly supervised this work: Luca Busino and Iannis Aifantis.,Correspondence and requests for materials should be addressed to M.G., L.B. or I.A., ; ;
| |
Collapse
|
49
|
Pol CJ, Pollak NM, Jurczak MJ, Zacharia E, Karagiannides I, Kyriazis ID, Ntziachristos P, Scerbo DA, Brown BR, Aifantis I, Shulman GI, Goldberg IJ, Drosatos K. Cardiac myocyte KLF5 regulates body weight via alteration of cardiac FGF21. Biochim Biophys Acta Mol Basis Dis 2019; 1865:2125-2137. [PMID: 31029826 PMCID: PMC6614009 DOI: 10.1016/j.bbadis.2019.04.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 12/20/2018] [Accepted: 01/06/2019] [Indexed: 01/22/2023]
Abstract
Cardiac metabolism affects systemic energetic balance. Previously, we showed that Krüppel-like factor (KLF)-5 regulates cardiomyocyte PPARα and fatty acid oxidation-related gene expression in diabetes. We surprisingly found that cardiomyocyte-specific KLF5 knockout mice (αMHC-KLF5-/-) have accelerated diet-induced obesity, associated with increased white adipose tissue (WAT). Alterations in cardiac expression of the mediator complex subunit 13 (Med13) modulates obesity. αMHC-KLF5-/- mice had reduced cardiac Med13 expression likely because KLF5 upregulates Med13 expression in cardiomyocytes. We then investigated potential mechanisms that mediate cross-talk between cardiomyocytes and WAT. High fat diet-fed αMHC-KLF5-/- mice had increased levels of cardiac and plasma FGF21, while food intake, activity, plasma leptin, and natriuretic peptides expression were unchanged. Consistent with studies reporting that FGF21 signaling in WAT decreases sumoylation-driven PPARγ inactivation, αMHC-KLF5-/- mice had less SUMO-PPARγ in WAT. Increased diet-induced obesity found in αMHC-KLF5-/- mice was absent in αMHC-[KLF5-/-;FGF21-/-] double knockout mice, as well as in αMHC-FGF21-/- mice that we generated. Thus, cardiomyocyte-derived FGF21 is a component of pro-adipogenic crosstalk between heart and WAT.
Collapse
Affiliation(s)
- Christine J Pol
- Metabolic Biology Laboratory, Lewis Katz School of Medicine at Temple University, Center for Translational Medicine, Department of Pharmacology, Philadelphia, USA
| | - Nina M Pollak
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Michael J Jurczak
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT, USA
| | - Effimia Zacharia
- Metabolic Biology Laboratory, Lewis Katz School of Medicine at Temple University, Center for Translational Medicine, Department of Pharmacology, Philadelphia, USA
| | - Iordanes Karagiannides
- Inflammatory Bowel Disease Center and Neuroendocrine Assay Core, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Ioannis D Kyriazis
- Metabolic Biology Laboratory, Lewis Katz School of Medicine at Temple University, Center for Translational Medicine, Department of Pharmacology, Philadelphia, USA
| | - Panagiotis Ntziachristos
- Howard Hughes Medical Institute, Department of Pathology, NYU School of Medicine, New York, NY, USA
| | - Diego A Scerbo
- Division of Preventive Medicine and Nutrition, Columbia University, New York, NY 10032, USA
| | - Brett R Brown
- Metabolic Biology Laboratory, Lewis Katz School of Medicine at Temple University, Center for Translational Medicine, Department of Pharmacology, Philadelphia, USA
| | - Iannis Aifantis
- Howard Hughes Medical Institute, Department of Pathology, NYU School of Medicine, New York, NY, USA
| | - Gerald I Shulman
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT, USA
| | - Ira J Goldberg
- Division of Preventive Medicine and Nutrition, Columbia University, New York, NY 10032, USA
| | - Konstantinos Drosatos
- Metabolic Biology Laboratory, Lewis Katz School of Medicine at Temple University, Center for Translational Medicine, Department of Pharmacology, Philadelphia, USA.
| |
Collapse
|
50
|
Witkowski MT, Lasry A, Carroll WL, Aifantis I. Immune-Based Therapies in Acute Leukemia. Trends Cancer 2019; 5:604-618. [PMID: 31706508 DOI: 10.1016/j.trecan.2019.07.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/24/2019] [Accepted: 07/26/2019] [Indexed: 12/31/2022]
Abstract
Treatment resistance remains a leading cause of acute leukemia-related deaths. Thus, there is an unmet need to develop novel approaches to improve outcome. New immune-based therapies with chimeric antigen receptor (CAR) T cells, bi-specific T cell engagers (BiTEs), and immune checkpoint blockers (ICBs) have emerged as effective treatment options for chemoresistant B cell acute lymphoblastic leukemia (B-ALL) and acute myeloid leukemia (AML). However, many patients show resistance to these immune-based approaches. This review describes crucial lessons learned from immune-based approaches targeting high-risk B-ALL and AML, such as the leukemia-intrinsic (e.g., target antigen loss, tumor heterogeneity) and -extrinsic (e.g., immunosuppressive microenvironment) mechanisms that drive treatment resistance, and discusses alternative approaches to enhance the effectiveness of these immune-based treatment regimens.
Collapse
Affiliation(s)
- Matthew T Witkowski
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA.
| | - Audrey Lasry
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - William L Carroll
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA; Department of Pediatrics, New York University School of Medicine, New York, NY 10016, USA
| | - Iannis Aifantis
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| |
Collapse
|