1
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Subas Satish HP, Iyer S, Shi MX, Wong AW, Fischer KC, Wardak AZ, Lio D, Brouwer JM, Uren RT, Czabotar PE, Miller MS, Kluck RM. A novel inhibitory BAK antibody enables assessment of non-activated BAK in cancer cells. Cell Death Differ 2024:10.1038/s41418-024-01289-3. [PMID: 38582955 DOI: 10.1038/s41418-024-01289-3] [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: 11/13/2023] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/08/2024] Open
Abstract
BAX and BAK are pro-apoptotic members of the BCL2 family that are required to permeabilize the mitochondrial outer membrane. The proteins can adopt a non-activated monomeric conformation, or an activated conformation in which the exposed BH3 domain facilitates binding either to a prosurvival protein or to another activated BAK or BAX protein to promote pore formation. Certain cancer cells are proposed to have high levels of activated BAK sequestered by MCL1 or BCLXL, thus priming these cells to undergo apoptosis in response to BH3 mimetic compounds that target MCL1 or BCLXL. Here we report the first antibody, 14G6, that is specific for the non-activated BAK conformer. A crystal structure of 14G6 Fab bound to BAK revealed a binding site encompassing both the α1 helix and α5-α6 hinge regions of BAK, two sites involved in the unfolding of BAK during its activation. In mitochondrial experiments, 14G6 inhibited BAK unfolding triggered by three diverse BAK activators, supporting crucial roles for both α1 dissociation and separation of the core (α2-α5) and latch (α6-α9) regions in BAK activation. 14G6 bound the majority of BAK in several leukaemia cell lines, and binding decreased following treatment with BH3 mimetics, indicating only minor levels of constitutively activated BAK in those cells. In summary, 14G6 provides a new means of assessing BAK status in response to anti-cancer treatments.
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Affiliation(s)
- Hema Preethi Subas Satish
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Sweta Iyer
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Melissa X Shi
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Agnes W Wong
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Karla C Fischer
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ahmad Z Wardak
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Daisy Lio
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Jason M Brouwer
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Rachel T Uren
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Peter E Czabotar
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Michelle S Miller
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia.
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Ruth M Kluck
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia.
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia.
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2
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Balas N, Richman JS, Landier W, Shrestha S, Bruxvoort KJ, Hageman L, Meng Q, Ross E, Bosworth A, Wong FL, Bhatia R, Forman SJ, Armenian SH, Weisdorf DJ, Bhatia S. Pre-frailty after blood or marrow transplantation and the risk of subsequent mortality. Leukemia 2024:10.1038/s41375-024-02238-2. [PMID: 38580835 DOI: 10.1038/s41375-024-02238-2] [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: 02/29/2024] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/07/2024]
Abstract
We examined the prevalence, risk factors, and association between pre-frailty and subsequent mortality after blood or marrow transplantation (BMT). Study participants were drawn from the BMT Survivor Study (BMTSS) and included 3346 individuals who underwent BMT between 1974 and 2014 at one of three transplant centers and survived ≥2 years post-BMT. Participants completed the BMTSS survey at a median of 9 years from BMT and were followed for subsequent mortality for a median of 5 years after survey completion. Closest-age and same-sex biological siblings also completed the survey. Previously published self-reported indices (exhaustion, weakness, low energy expenditure, slowness, unintentional weight loss) classified participants as non-frail (0-1 indices) or pre-frail (2 indices). National Death Index was used to determine vital status and cause of death. Overall, 626 (18.7%) BMT survivors were pre-frail. BMT survivors had a 3.2-fold higher odds of being pre-frail (95% CI = 1.9-5.3) compared to siblings. Compared to non-frail survivors, pre-frail survivors had higher hazards of all-cause mortality (adjusted hazard ratio [aHR] = 1.6, 95% CI = 1.4-2.0). Female sex, pre-BMT radiation, smoking, lack of exercise, anxiety, and severe/life-threatening chronic health conditions were associated with pre-frailty. The novel association between pre-frailty and subsequent mortality provides evidence for interventions as pre-frail individuals may transition back to their robust state.
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Affiliation(s)
- Nora Balas
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Wendy Landier
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | | | | | - Qingrui Meng
- University of Alabama at Birmingham, Birmingham, AL, USA
| | - Elizabeth Ross
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | | | - Ravi Bhatia
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | | | | | - Smita Bhatia
- University of Alabama at Birmingham, Birmingham, AL, USA.
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3
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Ghashghaei M, Liu Y, Ettles J, Bombaci G, Ramkumar N, Liu Z, Escano L, Miko SS, Kim Y, Waldron JA, Do K, MacPherson K, Yuen KA, Taibi T, Yue M, Arsalan A, Jin Z, Edin G, Karsan A, Morin GB, Kuchenbauer F, Perna F, Bushell M, Vu LP. Translation efficiency driven by CNOT3 subunit of the CCR4-NOT complex promotes leukemogenesis. Nat Commun 2024; 15:2340. [PMID: 38491013 PMCID: PMC10943099 DOI: 10.1038/s41467-024-46665-2] [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: 09/05/2023] [Accepted: 03/04/2024] [Indexed: 03/18/2024] Open
Abstract
Protein synthesis is frequently deregulated during tumorigenesis. However, the precise contexts of selective translational control and the regulators of such mechanisms in cancer is poorly understood. Here, we uncovered CNOT3, a subunit of the CCR4-NOT complex, as an essential modulator of translation in myeloid leukemia. Elevated CNOT3 expression correlates with unfavorable outcomes in patients with acute myeloid leukemia (AML). CNOT3 depletion induces differentiation and apoptosis and delayed leukemogenesis. Transcriptomic and proteomic profiling uncovers c-MYC as a critical downstream target which is translationally regulated by CNOT3. Global analysis of mRNA features demonstrates that CNOT3 selectively influences expression of target genes in a codon usage dependent manner. Furthermore, CNOT3 associates with the protein network largely consisting of ribosomal proteins and translation elongation factors in leukemia cells. Overall, our work elicits the direct requirement for translation efficiency in tumorigenesis and propose targeting the post-transcriptional circuitry via CNOT3 as a therapeutic vulnerability in AML.
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Affiliation(s)
- Maryam Ghashghaei
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Yilin Liu
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
- Department of Experimental Medicine, University of British Columbia, Vancouver, Canada
| | - James Ettles
- CRUK Beatson Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Giuseppe Bombaci
- Department of Medicine, Indiana University Simon Comprehensive Cancer Center, Indianapolis, IN, USA
| | - Niveditha Ramkumar
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Zongmin Liu
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Leo Escano
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Sandra Spencer Miko
- Genome Sciences Centre, British Columbia Cancer Research Centre, Vancouver, Canada
| | - Yerin Kim
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
- Bioinformatics program, University of British Columbia, Vancouver, Canada
| | - Joseph A Waldron
- CRUK Beatson Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Kim Do
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kyle MacPherson
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Katie A Yuen
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Thilelli Taibi
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Marty Yue
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Aaremish Arsalan
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Zhen Jin
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Glenn Edin
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Aly Karsan
- Genome Sciences Centre, British Columbia Cancer Research Centre, Vancouver, Canada
| | - Gregg B Morin
- Genome Sciences Centre, British Columbia Cancer Research Centre, Vancouver, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Florian Kuchenbauer
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Fabiana Perna
- Department of Medicine, Indiana University Simon Comprehensive Cancer Center, Indianapolis, IN, USA
- Department of Blood and Marrow Transplant and Cellular Immunotherapy, Moffit Cancer Center, Tampa, FL, USA
| | - Martin Bushell
- CRUK Beatson Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Ly P Vu
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada.
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada.
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4
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Schwede M, Jahn K, Kuipers J, Miles LA, Bowman RL, Robinson T, Furudate K, Uryu H, Tanaka T, Sasaki Y, Ediriwickrema A, Benard B, Gentles AJ, Levine R, Beerenwinkel N, Takahashi K, Majeti R. Mutation order in acute myeloid leukemia identifies uncommon patterns of evolution and illuminates phenotypic heterogeneity. Leukemia 2024:10.1038/s41375-024-02211-z. [PMID: 38467769 DOI: 10.1038/s41375-024-02211-z] [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: 10/30/2023] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 03/13/2024]
Abstract
Acute myeloid leukemia (AML) has a poor prognosis and a heterogeneous mutation landscape. Although common mutations are well-studied, little research has characterized how the sequence of mutations relates to clinical features. Using published, single-cell DNA sequencing data from three institutions, we compared clonal evolution patterns in AML to patient characteristics, disease phenotype, and outcomes. Mutation trees, which represent the order of select mutations, were created for 207 patients from targeted panel sequencing data using 1 639 162 cells, 823 mutations, and 275 samples. In 224 distinct orderings of mutated genes, mutations related to DNA methylation typically preceded those related to cell signaling, but signaling-first cases did occur, and had higher peripheral cell counts, increased signaling mutation homozygosity, and younger patient age. Serial sample analysis suggested that NPM1 and DNA methylation mutations provide an advantage to signaling mutations in AML. Interestingly, WT1 mutation evolution shared features with signaling mutations, such as WT1-early being proliferative and occurring in younger individuals, trends that remained in multivariable regression. Some mutation orderings had a worse prognosis, but this was mediated by unfavorable mutations, not mutation order. These findings add a dimension to the mutation landscape of AML, identifying uncommon patterns of leukemogenesis and shedding light on heterogeneous phenotypes.
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Affiliation(s)
- Matthew Schwede
- Department of Medicine, Division of Hematology, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, School of Medicine, Stanford, CA, USA
| | - Katharina Jahn
- Biomedical Data Science, Institute for Computer Science, Free University of Berlin, Berlin, Germany
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jack Kuipers
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Linde A Miles
- Division of Experimental Hematology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
| | - Robert L Bowman
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Troy Robinson
- Human Oncology and Pathogenesis Program, Molecular Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ken Furudate
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hidetaka Uryu
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tomoyuki Tanaka
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yuya Sasaki
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Asiri Ediriwickrema
- Department of Medicine, Division of Hematology, Stanford University, Stanford, CA, USA
- Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Brooks Benard
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Andrew J Gentles
- Department of Biomedical Data Science, Stanford University, School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Medicine, Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA, USA
| | - Ross Levine
- Human Oncology and Pathogenesis Program, Molecular Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Koichi Takahashi
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Ravindra Majeti
- Department of Medicine, Division of Hematology, Stanford University, Stanford, CA, USA.
- Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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5
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Chen CC, Silberman RE, Ma D, Perry JA, Khalid D, Pikman Y, Amon A, Hemann MT, Rowe RG. Inherent genome instability underlies trisomy 21-associated myeloid malignancies. Leukemia 2024; 38:521-529. [PMID: 38245602 DOI: 10.1038/s41375-024-02151-8] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 01/22/2024]
Abstract
Constitutional trisomy 21 (T21) is a state of aneuploidy associated with high incidence of childhood acute myeloid leukemia (AML). T21-associated AML is preceded by transient abnormal myelopoiesis (TAM), which is triggered by truncating mutations in GATA1 generating a short GATA1 isoform (GATA1s). T21-associated AML emerges due to secondary mutations in hematopoietic clones bearing GATA1s. Since aneuploidy generally impairs cellular fitness, the paradoxically elevated risk of myeloid malignancy in T21 is not fully understood. We hypothesized that individuals with T21 bear inherent genome instability in hematopoietic lineages that promotes leukemogenic mutations driving the genesis of TAM and AML. We found that individuals with T21 show increased chromosomal copy number variations (CNVs) compared to euploid individuals, suggesting that genome instability could be underlying predisposition to TAM and AML. Acquisition of GATA1s enforces myeloid skewing and maintenance of the hematopoietic progenitor state independently of T21; however, GATA1s in T21 hematopoietic progenitor cells (HPCs) further augments genome instability. Increased dosage of the chromosome 21 (chr21) gene DYRK1A impairs homology-directed DNA repair as a mechanism of elevated mutagenesis. These results posit a model wherein inherent genome instability in T21 drives myeloid malignancy in concert with GATA1s mutations.
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Affiliation(s)
- Chun-Chin Chen
- Stem Cell Transplantation Program, Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Rebecca E Silberman
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- RA Capital, Boston, MA, USA
| | - Duanduan Ma
- The Barbara K. Ostrom (1978) Bioinformatics and Computing Facility, Swanson Biotechnology Center, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jennifer A Perry
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Delan Khalid
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Yana Pikman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Angelika Amon
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Michael T Hemann
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - R Grant Rowe
- Stem Cell Transplantation Program, Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
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6
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Maura F, Boyle EM, Coffey D, Maclachlan K, Gagler D, Diamond B, Ghamlouch H, Blaney P, Ziccheddu B, Cirrincione A, Chojnacka M, Wang Y, Siegel A, Hoffman JE, Kazandjian D, Hassoun H, Guzman E, Mailankody S, Shah UA, Tan C, Hultcrantz M, Scordo M, Shah GL, Landau H, Chung DJ, Giralt S, Zhang Y, Arbini A, Gao Q, Roshal M, Dogan A, Lesokhin AM, Davies FE, Usmani SZ, Korde N, Morgan GJ, Landgren O. Genomic and immune signatures predict clinical outcome in newly diagnosed multiple myeloma treated with immunotherapy regimens. Nat Cancer 2023; 4:1660-1674. [PMID: 37945755 DOI: 10.1038/s43018-023-00657-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 09/20/2023] [Indexed: 11/12/2023]
Abstract
Despite improving outcomes, 40% of patients with newly diagnosed multiple myeloma treated with regimens containing daratumumab, a CD38-targeted monoclonal antibody, progress prematurely. By integrating tumor whole-genome and microenvironment single-cell RNA sequencing from upfront phase 2 trials using carfilzomib, lenalidomide and dexamethasone with daratumumab ( NCT03290950 ), we show how distinct genomic drivers including high APOBEC mutational activity, IKZF3 and RPL5 deletions and 8q gain affect clinical outcomes. Furthermore, evaluation of paired bone marrow profiles, taken before and after eight cycles of carfilzomib, lenalidomide and dexamethasone with daratumumab, shows that numbers of natural killer cells before treatment, high T cell receptor diversity before treatment, the disappearance of sustained immune activation (that is, B cells and T cells) and monocyte expansion over time are all predictive of sustained minimal residual disease negativity. Overall, this study provides strong evidence of a complex interplay between tumor cells and the immune microenvironment that is predictive of clinical outcome and depth of treatment response in patients with newly diagnosed multiple myeloma treated with highly effective combinations containing anti-CD38 antibodies.
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Affiliation(s)
- Francesco Maura
- Myeloma Division, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA.
| | - Eileen M Boyle
- Myeloma Research Program, NYU Langone, Perlmutter Cancer Center, New York, NY, USA
| | - David Coffey
- Myeloma Division, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Kylee Maclachlan
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Dylan Gagler
- Myeloma Research Program, NYU Langone, Perlmutter Cancer Center, New York, NY, USA
| | - Benjamin Diamond
- Myeloma Division, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Hussein Ghamlouch
- Myeloma Research Program, NYU Langone, Perlmutter Cancer Center, New York, NY, USA
| | - Patrick Blaney
- Myeloma Research Program, NYU Langone, Perlmutter Cancer Center, New York, NY, USA
| | - Bachisio Ziccheddu
- Myeloma Division, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Anthony Cirrincione
- Myeloma Division, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Monika Chojnacka
- Myeloma Division, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Yubao Wang
- Myeloma Research Program, NYU Langone, Perlmutter Cancer Center, New York, NY, USA
| | - Ariel Siegel
- Myeloma Research Program, NYU Langone, Perlmutter Cancer Center, New York, NY, USA
| | - James E Hoffman
- Myeloma Division, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Dickran Kazandjian
- Myeloma Division, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Hani Hassoun
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Emily Guzman
- Genome Technology Center, NYU Langone, Perlmutter Cancer Center, New York, NY, USA
| | - Sham Mailankody
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Urvi A Shah
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Carlyn Tan
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Malin Hultcrantz
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Michael Scordo
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Hematopathology Service, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gunjan L Shah
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Heather Landau
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David J Chung
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sergio Giralt
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yanming Zhang
- Cytogenetics Laboratory, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arnaldo Arbini
- Myeloma Research Program, NYU Langone, Perlmutter Cancer Center, New York, NY, USA
| | - Qi Gao
- Hematopathology Service, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mikhail Roshal
- Hematopathology Service, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ahmet Dogan
- Hematopathology Service, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexander M Lesokhin
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Faith E Davies
- Myeloma Research Program, NYU Langone, Perlmutter Cancer Center, New York, NY, USA
| | - Saad Z Usmani
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Neha Korde
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Gareth J Morgan
- Myeloma Research Program, NYU Langone, Perlmutter Cancer Center, New York, NY, USA.
| | - Ola Landgren
- Myeloma Division, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA.
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7
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Hong T, Li J, Guo L, Cavalier M, Wang T, Dou Y, DeLaFuente A, Fang S, Guzman A, Wohlan K, Kapadia C, Rosas C, Yang Y, Yin CC, Li S, You MJ, Cheng X, Goodell MA, Zhou Y, Huang Y. TET2 modulates spatial relocalization of heterochromatin in aged hematopoietic stem and progenitor cells. Nat Aging 2023; 3:1387-1400. [PMID: 37884767 DOI: 10.1038/s43587-023-00505-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 09/21/2023] [Indexed: 10/28/2023]
Abstract
DNA methylation deregulation at partially methylated domains (PMDs) represents an epigenetic signature of aging and cancer, yet the underlying molecular basis and resulting biological consequences remain unresolved. We report herein a mechanistic link between disrupted DNA methylation at PMDs and the spatial relocalization of H3K9me3-marked heterochromatin in aged hematopoietic stem and progenitor cells (HSPCs) or those with impaired DNA methylation. We uncover that TET2 modulates the spatial redistribution of H3K9me3-marked heterochromatin to mediate the upregulation of endogenous retroviruses (ERVs) and interferon-stimulated genes (ISGs), hence contributing to functional decline of aged HSPCs. TET2-deficient HSPCs retain perinuclear distribution of heterochromatin and exhibit age-related clonal expansion. Reverse transcriptase inhibitors suppress ERVs and ISGs expression, thereby restoring age-related defects in aged HSPCs. Collectively, our findings deepen the understanding of the functional interplay between DNA methylation and histone modifications, which is vital for maintaining heterochromatin function and safeguarding genome stability in stem cells.
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Affiliation(s)
- Tingting Hong
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Jia Li
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA.
- State Key Laboratory of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China.
| | - Lei Guo
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Maryn Cavalier
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Tianlu Wang
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Yaling Dou
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Aaron DeLaFuente
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Shaohai Fang
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Anna Guzman
- Department of Molecular Cell Biology, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | - Katherina Wohlan
- Department of Molecular Cell Biology, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | - Chiraag Kapadia
- Department of Molecular Cell Biology, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | - Carina Rosas
- Department of Molecular Cell Biology, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | - Yaling Yang
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - C Cameron Yin
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shaoying Li
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - M James You
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Margaret A Goodell
- Department of Molecular Cell Biology, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | - Yubin Zhou
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA.
- Department of Translational Medical Sciences, School of Medicine, Texas A&M University, Houston, TX, USA.
| | - Yun Huang
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA.
- Department of Translational Medical Sciences, School of Medicine, Texas A&M University, Houston, TX, USA.
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8
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Yoshimura S, Panetta JC, Hu J, Li L, Gocho Y, Du G, Umezawa A, Karol SE, Pui CH, Mullighan CG, Konopleva M, Stock W, Teachey DT, Jain N, Yang JJ. Preclinical pharmacokinetic and pharmacodynamic evaluation of dasatinib and ponatinib for the treatment of T-cell acute lymphoblastic leukemia. Leukemia 2023:10.1038/s41375-023-01900-5. [PMID: 37076694 DOI: 10.1038/s41375-023-01900-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 04/21/2023]
Abstract
LCK is a novel therapeutic target in ~40% of T-cell acute lymphoblastic leukemia (T-ALL), and dasatinib and ponatinib can act as LCK inhibitors with therapeutic effects. We herein report a comprehensive preclinical pharmacokinetic and pharmacodynamic evaluation of dasatinib and ponatinib in LCK-activated T-ALL. In 51 human T-ALL cases, these two drugs showed similar patterns of cytotoxic activity, with ponatinib being slightly more potent. Given orally in mice, ponatinib was associated with slower clearance with a longer Tmax and higher AUC0-24 h, although maximum pLCK inhibition was comparable between the two drugs. After establishing the exposure-to-response models, we simulated the steady-state pLCK inhibitory effects of each drug at currently approved dosages in humans: dasatinib at 140 mg and ponatinib at 45 mg once daily are both sufficient to achieve >50% pLCK inhibition for 13.0 and 13.9 h/day, respectively, comparable to pharmacodynamic profiles of these agents in BCR::ABL1 leukemias. Moreover, we developed a dasatinib-resistant T-ALL cell line model with LCK T316I mutation, in which ponatinib retained partial activity against LCK. In conclusion, we described the pharmacokinetic and pharmacodynamic profiles of dasatinib and ponatinib as LCK inhibitors in T-ALL, providing critical data for the development of human trials of these agents.
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Affiliation(s)
- Satoshi Yoshimura
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Advanced Pediatric Medicine, Tohoku University School of Medicine, Tokyo, Japan
| | - John C Panetta
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jianzhong Hu
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
- Amgen, 1 Amgen Center Drive, Thousand Oaks, CA, USA
| | - Lie Li
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yoshihiro Gocho
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Guoqing Du
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Akihiro Umezawa
- Department of Advanced Pediatric Medicine, Tohoku University School of Medicine, Tokyo, Japan
| | - Seth E Karol
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Marina Konopleva
- Department of Oncology and Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Wendy Stock
- Department of Medicine Section of Hematology-Oncology, University of Chicago, Chicago, IL, USA
| | - David T Teachey
- Department of Pediatrics, University of Pennsylvania, Philadelphia, PA, USA
| | - Nitin Jain
- Department of Leukemia, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jun J Yang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA.
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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9
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Dong W, Wang J, Tian L, Zhang J, Settles EW, Qin C, Steinken-Kollath DR, Itogawa AN, Celona KR, Yi J, Bryant M, Mead H, Jaramillo SA, Lu H, Li A, Zumwalt RE, Dadwal S, Feng P, Yuan W, Whelan SPJ, Keim PS, Barker BM, Caligiuri MA, Yu J. Factor Xa cleaves SARS-CoV-2 spike protein to block viral entry and infection. Nat Commun 2023; 14:1936. [PMID: 37024459 PMCID: PMC10079155 DOI: 10.1038/s41467-023-37336-9] [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: 08/27/2022] [Accepted: 03/13/2023] [Indexed: 04/08/2023] Open
Abstract
Serine proteases (SP), including furin, trypsin, and TMPRSS2 cleave the SARS-CoV-2 spike (S) protein, enabling the virus to enter cells. Here, we show that factor (F) Xa, an SP involved in blood coagulation, is upregulated in COVID-19 patients. In contrast to other SPs, FXa exerts antiviral activity. Mechanistically, FXa cleaves S protein, preventing its binding to ACE2, and thus blocking viral entry and infection. However, FXa is less effective against variants carrying the D614G mutation common in all pandemic variants. The anticoagulant rivaroxaban, a direct FXa inhibitor, inhibits FXa-mediated S protein cleavage and facilitates viral entry, whereas the indirect FXa inhibitor fondaparinux does not. In the lethal SARS-CoV-2 K18-hACE2 model, FXa prolongs survival yet its combination with rivaroxaban but not fondaparinux abrogates that protection. These results identify both a previously unknown function for FXa and an associated antiviral host defense mechanism against SARS-CoV-2 and suggest caution in considering direct FXa inhibitors for preventing or treating thrombotic complications in COVID-19 patients.
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Affiliation(s)
- Wenjuan Dong
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, CA, 91010, USA
- Hematologic Malignancies Research Institute, City of Hope National Medical Center, Los Angeles, CA, 91010, USA
| | - Jing Wang
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, CA, 91010, USA
- Hematologic Malignancies Research Institute, City of Hope National Medical Center, Los Angeles, CA, 91010, USA
| | - Lei Tian
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, CA, 91010, USA
- Hematologic Malignancies Research Institute, City of Hope National Medical Center, Los Angeles, CA, 91010, USA
| | - Jianying Zhang
- Department of Computational and Quantitative Medicine, City of Hope National Medical Center, Los Angeles, CA, 91010, USA
| | - Erik W Settles
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Chao Qin
- Section of Infection and Immunity, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA
| | | | - Ashley N Itogawa
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Kimberly R Celona
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Jinhee Yi
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Mitchell Bryant
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Heather Mead
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Sierra A Jaramillo
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Hongjia Lu
- Department of Molecular Microbiology and Immunology, Keck School of Medicine of University of Southern California, Los Angeles, CA, 90033, USA
| | - Aimin Li
- Pathology Core of Shared Resources Core, Beckman Research Institute, City of Hope National Medical Center, Los Angeles, CA, 91010, USA
| | - Ross E Zumwalt
- Department of Pathology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Sanjeet Dadwal
- Division of Infectious Diseases, Department of Medicine, City of Hope National Medical Center, Los Angeles, CA, 91010, USA
| | - Pinghui Feng
- Section of Infection and Immunity, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA
| | - Weiming Yuan
- Department of Molecular Microbiology and Immunology, Keck School of Medicine of University of Southern California, Los Angeles, CA, 90033, USA
| | - Sean P J Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Paul S Keim
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Bridget Marie Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Michael A Caligiuri
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, CA, 91010, USA.
- Hematologic Malignancies Research Institute, City of Hope National Medical Center, Los Angeles, CA, 91010, USA.
- City of Hope Comprehensive Cancer Center, Los Angeles, CA, 91010, USA.
| | - Jianhua Yu
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, CA, 91010, USA.
- Hematologic Malignancies Research Institute, City of Hope National Medical Center, Los Angeles, CA, 91010, USA.
- City of Hope Comprehensive Cancer Center, Los Angeles, CA, 91010, USA.
- Department of Immuno-Oncology, City of Hope, Los Angeles, CA, 91010, USA.
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10
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Wedge E, Ahmadov U, Hansen TB, Gao Z, Tulstrup M, Côme C, Nonavinkere Srivatsan S, Ahmed T, Jespersen JS, Schlotmann BC, Schöllkopf C, Raaschou-Jensen K, Ødum N, Kjems J, Bak RO, Walter MJ, Grønbæk K, Kristensen LS. Impact of U2AF1 mutations on circular RNA expression in myelodysplastic neoplasms. Leukemia 2023; 37:1113-1125. [PMID: 36922625 DOI: 10.1038/s41375-023-01866-4] [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: 10/03/2022] [Revised: 02/16/2023] [Accepted: 02/28/2023] [Indexed: 03/18/2023]
Abstract
Mutations in U2AF1 are relatively common in myelodysplastic neoplasms (MDS) and are associated with an inferior prognosis, but the molecular mechanisms underlying this are not fully elucidated. Circular RNAs (circRNAs) have been implicated in cancer, but it is unknown how mutations in splicing factors may impact on circRNA biogenesis. Here, we used RNA-sequencing to investigate the effects of U2AF1 mutations on circRNA expression in K562 cells with a doxycycline-inducible U2AF1S34 mutation, in a mouse model with a doxycycline-inducible U2AF1S34 mutation, and in FACS-sorted CD34+ bone marrow cells from MDS patients with either U2AF1S34 or U2AF1Q157 mutations. In all contexts, we found an increase in global circRNA levels in the U2AF1-mutated setting, which was independent of expression changes in the cognate linear host genes. In patients, the U2AF1S34 and U2AF1Q157 mutations were both associated with an overall increased expression of circRNAs. circRNAs generated by a non-Alu-mediated mechanism generally showed the largest increase in expression levels. Several well-described cancer-associated circRNAs, including circZNF609 and circCSNK1G3, were upregulated in MDS patients with U2AF1 mutations compared to U2AF1-wildtype MDS controls. In conclusion, high circRNA expression is observed in association with U2AF1 mutations in three biological systems, presenting an interesting possibility for biomarker and therapeutic investigation.
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Affiliation(s)
- Eileen Wedge
- Department of Hematology, Copenhagen University Hospital, Copenhagen, Denmark
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, Copenhagen, Denmark
- The Danish Stem Cell Center (Danstem), University of Copenhagen, Copenhagen, Denmark
| | - Ulvi Ahmadov
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Thomas B Hansen
- Department of Molecular Biology and Genetics, Aarhus, Denmark
| | - Zongliang Gao
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Morten Tulstrup
- Department of Hematology, Copenhagen University Hospital, Copenhagen, Denmark
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, Copenhagen, Denmark
- The Danish Stem Cell Center (Danstem), University of Copenhagen, Copenhagen, Denmark
| | - Christophe Côme
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, Copenhagen, Denmark
- The Danish Stem Cell Center (Danstem), University of Copenhagen, Copenhagen, Denmark
| | | | - Tanzir Ahmed
- Division of Oncology, Washington University School of Medicine, St Louis, MO, USA
| | - Jakob S Jespersen
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, Copenhagen, Denmark
- The Danish Stem Cell Center (Danstem), University of Copenhagen, Copenhagen, Denmark
- The Finsen Laboratory, Copenhagen University Hospital, Copenhagen, Denmark
| | - Balthasar C Schlotmann
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, Copenhagen, Denmark
- The Danish Stem Cell Center (Danstem), University of Copenhagen, Copenhagen, Denmark
- The Finsen Laboratory, Copenhagen University Hospital, Copenhagen, Denmark
| | - Claudia Schöllkopf
- Department of Hematology, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Niels Ødum
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Jørgen Kjems
- Department of Molecular Biology and Genetics, Aarhus, Denmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
| | - Rasmus O Bak
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Matthew J Walter
- Division of Oncology, Washington University School of Medicine, St Louis, MO, USA
| | - Kirsten Grønbæk
- Department of Hematology, Copenhagen University Hospital, Copenhagen, Denmark.
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, Copenhagen, Denmark.
- The Danish Stem Cell Center (Danstem), University of Copenhagen, Copenhagen, Denmark.
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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