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Busarello E, Biancon G, Lauria F, Ibnat Z, Ramirez C, Tomè G, Aass KR, VanOudenhove J, Standal T, Viero G, Halene S, Tebaldi T. Interpreting single-cell messages in normal and aberrant hematopoiesis with the Cell Marker Accordion. bioRxiv 2024:2024.03.08.584053. [PMID: 38559181 PMCID: PMC10979856 DOI: 10.1101/2024.03.08.584053] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Single-cell technologies offer a unique opportunity to explore cellular heterogeneity in hematopoiesis, reveal malignant hematopoietic cells with clinically significant features and measure gene signatures linked to pathological pathways. However, reliable identification of cell types is a crucial bottleneck in single-cell analysis. Available databases contain dissimilar nomenclature and non-concurrent marker sets, leading to inconsistent annotations and poor interpretability. Furthermore, current tools focus mostly on physiological cell types, lacking extensive applicability in disease. We developed the Cell Marker Accordion, a user-friendly platform for the automatic annotation and biological interpretation of single-cell populations based on consistency weighted markers. We validated our approach on peripheral blood and bone marrow single-cell datasets, using surface markers and expert-based annotation as the ground truth. In all cases, we significantly improved the accuracy in identifying cell types with respect to any single source database. Moreover, the Cell Marker Accordion can identify disease-critical cells and pathological processes, extracting potential biomarkers in a wide variety of contexts in human and murine single-cell datasets. It characterizes leukemia stem cell subtypes, including therapy-resistant cells in acute myeloid leukemia patients; it identifies malignant plasma cells in multiple myeloma samples; it dissects cell type alterations in splicing factor-mutant cells from myelodysplastic syndrome patients; it discovers activation of innate immunity pathways in bone marrow from mice treated with METTL3 inhibitors. The breadth of these applications elevates the Cell Marker Accordion as a flexible, faithful and standardized tool to annotate and interpret hematopoietic populations in single-cell datasets focused on the study of hematopoietic development and disease.
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Affiliation(s)
- Emma Busarello
- Laboratory of RNA and Disease Data Science, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Giulia Biancon
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Fabio Lauria
- Institute of Biophysics, CNR Unit at Trento, Italy
| | - Zuhairia Ibnat
- Laboratory of RNA and Disease Data Science, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Christian Ramirez
- Laboratory of RNA and Disease Data Science, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Gabriele Tomè
- Laboratory of RNA and Disease Data Science, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
- Institute of Biophysics, CNR Unit at Trento, Italy
| | - Kristin R Aass
- Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Jennifer VanOudenhove
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Therese Standal
- Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | | | - Stephanie Halene
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Toma Tebaldi
- Laboratory of RNA and Disease Data Science, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
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Kim TK, Han X, Hu Q, Vandsemb EN, Fielder CM, Hong J, Kim KW, Mason EF, Plowman RS, Wang J, Wang Q, Zhang JP, Badri T, Sanmamed MF, Zheng L, Zhang T, Alawa J, Lee SW, Zeidan AM, Halene S, Pillai MM, Chandhok NS, Lu J, Xu ML, Gore SD, Chen L. PD-1H/VISTA mediates immune evasion in acute myeloid leukemia. J Clin Invest 2024; 134:e164325. [PMID: 38060328 PMCID: PMC10836799 DOI: 10.1172/jci164325] [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: 08/15/2022] [Accepted: 12/06/2023] [Indexed: 02/02/2024] Open
Abstract
Acute myeloid leukemia (AML) presents a pressing medical need in that it is largely resistant to standard chemotherapy as well as modern therapeutics, such as targeted therapy and immunotherapy, including anti-programmed cell death protein (anti-PD) therapy. We demonstrate that programmed death-1 homolog (PD-1H), an immune coinhibitory molecule, is highly expressed in blasts from the bone marrow of AML patients, while normal myeloid cell subsets and T cells express PD-1H. In studies employing syngeneic and humanized AML mouse models, overexpression of PD-1H promoted the growth of AML cells, mainly by evading T cell-mediated immune responses. Importantly, ablation of AML cell-surface PD-1H by antibody blockade or genetic knockout significantly inhibited AML progression by promoting T cell activity. In addition, the genetic deletion of PD-1H from host normal myeloid cells inhibited AML progression, and the combination of PD-1H blockade with anti-PD therapy conferred a synergistic antileukemia effect. Our findings provide the basis for PD-1H as a potential therapeutic target for treating human AML.
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Affiliation(s)
- Tae Kon Kim
- Division of Hematology/Oncology, Department of Medicine
- Vanderbilt Center for Immunobiology, and
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center
- Vanderbilt Ingram Cancer Center, Nashville, Tennessee, USA
- Section of Medical Oncology
- Section of Hematology, Department of Medicine, and
| | - Xue Han
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
- Pelotonia Institute for Immuno-Oncology, OSUCCC–James Cancer Hospital
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
| | - Qianni Hu
- Division of Hematology/Oncology, Department of Medicine
| | - Esten N. Vandsemb
- Department of Acute Medicine, Oslo University Hospital, Oslo, Norway
| | | | - Junshik Hong
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | | | - Emily F. Mason
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center
| | - R. Skipper Plowman
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center
| | - Jun Wang
- Department of Pathology, New York University Grossman School of Medicine, New York, New York, USA
| | - Qi Wang
- Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou University Second Hospital, Lanzhou, China
| | - Jian-Ping Zhang
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Ti Badri
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Miguel F. Sanmamed
- Division of Immunology and Immunotherapy, CIMA, Universidad de Navarra, Pamplona, Spain
| | - Linghua Zheng
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
- Pelotonia Institute for Immuno-Oncology, OSUCCC–James Cancer Hospital
| | - Tianxiang Zhang
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Jude Alawa
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Sang Won Lee
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | | | | | | | - Namrata S. Chandhok
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Jun Lu
- Department of Genetics and
| | - Mina L. Xu
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Steven D. Gore
- Section of Hematology, Department of Medicine, and
- National Cancer Institute, Cancer Therapy Evaluation Program, Investigational Drug Branch, Bethesda, Maryland, USA
| | - Lieping Chen
- Section of Medical Oncology
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
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4
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Bewersdorf JP, Shallis RM, Sharon E, Park S, Ramaswamy R, Roe CE, Irish JM, Caldwell A, Wei W, Yacoub A, Madanat YF, Zeidner JF, Altman JK, Odenike O, Yerrabothala S, Kovacsovics T, Podoltsev NA, Halene S, Little RF, Piekarz R, Gore SD, Kim TK, Zeidan AM. A multicenter phase Ib trial of the histone deacetylase inhibitor entinostat in combination with pembrolizumab in patients with myelodysplastic syndromes/neoplasms or acute myeloid leukemia refractory to hypomethylating agents. Ann Hematol 2024; 103:105-116. [PMID: 38036712 DOI: 10.1007/s00277-023-05552-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/13/2023] [Indexed: 12/02/2023]
Abstract
Patients with myelodysplastic syndromes/neoplasms (MDS) or acute myeloid leukemia (AML) with hypomethylating agent failure have a poor prognosis. Myeloid-derived suppressor cells (MDSCs) can contribute to MDS progression and mediate resistance to anti-PD1 therapy. As histone deacetylase inhibitors (HDACi) decrease MDSCs in preclinical models, we conducted an investigator-initiated, NCI-Cancer Therapy Evaluation Program-sponsored, multicenter, dose escalation, and expansion phase Ib trial (NCT02936752) of the HDACi entinostat and the anti-PD1 antibody pembrolizumab. Twenty-eight patients (25 MDS and 3 AML) were enrolled. During dose escalation (n=13 patients), there was one dose-limiting toxicity (DLT) on dose level (DL) 1 (G5 pneumonia/bronchoalveolar hemorrhage) and two DLTs at DL 2 (G3 pharyngeal mucositis and G3 anorexia). Per the 3 + 3 dose escalation design, DL 1 (entinostat 8 mg PO days 1 and 15 + pembrolizumab 200 mg IV day 1 every 21 days) was expanded and another 15 patients were enrolled. Hematologic adverse events (AEs) were common. The most common non-hematologic ≥G3 AEs were infection (32%), hypoxia/respiratory failure (11%), and dyspnea (11%). There were no protocol-defined responses among the 28 patients enrolled. Two patients achieved a marrow complete remission (mCR). Using a systems immunology approach with mass cytometry and machine learning analysis, mCR patients had increased classical monocytes and macrophages but there was no significant change of MDSCs. In conclusion, combining entinostat with pembrolizumab in patients with advanced MDS and AML was associated with limited clinical efficacy and substantial toxicity. Absence of an effect on MDSCs could be a potential explanation for the limited efficacy of this combination. ClinicalTrial.gov Identifier: NCT02936752.
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Affiliation(s)
- Jan Philipp Bewersdorf
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, Yale School of Medicine, Yale University, New Haven, CT, USA.
- Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Rory M Shallis
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Elad Sharon
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD, USA
| | - Silvia Park
- Division of Hematology/Oncology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rahul Ramaswamy
- Division of Hematology/Oncology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Caroline E Roe
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Center for Immunobiology, Vanderbilt University, Nashville, TN, USA
| | - Jonathan M Irish
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Center for Immunobiology, Vanderbilt University, Nashville, TN, USA
| | - Anne Caldwell
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Wei Wei
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Abdulraheem Yacoub
- The Division of Hematologic Malignancies and Cellular Therapeutics (HMCT), The University of Kansas Cancer Center, Westwood, KS, USA
| | - Yazan F Madanat
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
| | - Joshua F Zeidner
- Lineberger Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Jessica K Altman
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
| | | | | | | | - Nikolai A Podoltsev
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Stephanie Halene
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Richard F Little
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD, USA
| | - Richard Piekarz
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD, USA
| | - Steven D Gore
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD, USA
| | - Tae Kon Kim
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, Yale School of Medicine, Yale University, New Haven, CT, USA.
- Division of Hematology/Oncology, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.
- Vanderbilt Center for Immunobiology, Vanderbilt University, Nashville, TN, USA.
| | - Amer M Zeidan
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, Yale School of Medicine, Yale University, New Haven, CT, USA.
- Hematology Section, Department of Internal Medicine, Yale School of Medicine, Yale University, 333 Cedar Street, PO Box 208028, New Haven, CT, 06520-8028, USA.
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5
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Stahl M, Bewersdorf JP, Xie Z, Porta MGD, Komrokji R, Xu ML, Abdel-Wahab O, Taylor J, Steensma DP, Starczynowski DT, Sekeres MA, Sanz G, Sallman DA, Roboz GJ, Platzbecker U, Patnaik MM, Padron E, Odenike O, Nimer SD, Nazha A, Majeti R, Loghavi S, Little RF, List AF, Kim TK, Hourigan CS, Hasserjian RP, Halene S, Griffiths EA, Gore SD, Greenberg P, Figueroa ME, Fenaux P, Efficace F, DeZern AE, Daver NG, Churpek JE, Carraway HE, Buckstein R, Brunner AM, Boultwood J, Borate U, Bejar R, Bennett JM, Wei AH, Santini V, Savona MR, Zeidan AM. Classification, risk stratification and response assessment in myelodysplastic syndromes/neoplasms (MDS): A state-of-the-art report on behalf of the International Consortium for MDS (icMDS). Blood Rev 2023; 62:101128. [PMID: 37704469 DOI: 10.1016/j.blre.2023.101128] [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] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/31/2023] [Accepted: 08/16/2023] [Indexed: 09/15/2023]
Abstract
The guidelines for classification, prognostication, and response assessment of myelodysplastic syndromes/neoplasms (MDS) have all recently been updated. In this report on behalf of the International Consortium for MDS (icMDS) we summarize these developments. We first critically examine the updated World Health Organization (WHO) classification and the International Consensus Classification (ICC) of MDS. We then compare traditional and molecularly based risk MDS risk assessment tools. Lastly, we discuss limitations of criteria in measuring therapeutic benefit and highlight how the International Working Group (IWG) 2018 and 2023 response criteria addressed these deficiencies and are endorsed by the icMDS. We also address the importance of patient centered care by discussing the value of quality-of-life assessment. We hope that the reader of this review will have a better understanding of how to classify MDS, predict clinical outcomes and evaluate therapeutic outcomes.
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Affiliation(s)
- Maximilian Stahl
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Jan Philipp Bewersdorf
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zhuoer Xie
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Matteo Giovanni Della Porta
- IRCCS Humanitas Clinical and Research Center & Humanitas University, Department of Biomedical Sciences, via Manzoni 56, 20089, Rozzano, Milan, Italy
| | - Rami Komrokji
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Mina L Xu
- Departments of Pathology & Laboratory Medicine, Yale University School of Medicine and Yale Cancer Center, New Haven, CT, USA
| | - Omar Abdel-Wahab
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Justin Taylor
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | - Daniel T Starczynowski
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Mikkael A Sekeres
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Guillermo Sanz
- Health Research Institute La Fe, Valencia, Spain; Hospital Universitario y Politécnico La Fe, Valencia, Spain; CIBERONC, IS Carlos III, Madrid, Spain
| | - David A Sallman
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Gail J Roboz
- Weill Cornell Medical College and New York Presbyterian Hospital, New York, NY, USA
| | | | - Mrinal M Patnaik
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Eric Padron
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Olatoyosi Odenike
- Leukemia Program, University of Chicago Medicine and University of Chicago Comprehensive Cancer Center, Chicago, IL, USA
| | - Stephen D Nimer
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Aziz Nazha
- Department of Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Ravi Majeti
- Division of Hematology, Department of Medicine, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Sanam Loghavi
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Richard F Little
- National Cancer Institute, Cancer Therapy Evaluation Program, Rockville, MD, USA
| | - Alan F List
- Precision BioSciences, Inc., Durham, NC, USA
| | - Tae Kon Kim
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Christopher S Hourigan
- Laboratory of Myeloid Malignancies, Hematology Branch, National Heart, Lung, and Blood Institute, and Myeloid Malignancies Program, National Institutes of Health, Bethesda, MD, 20892, USA
| | | | - Stephanie Halene
- Section of Hematology, Department of Internal Medicine, Yale University School of Medicine and Yale Cancer Center, New Haven, CT, USA
| | | | - Steven D Gore
- National Cancer Institute, Cancer Therapy Evaluation Program, Rockville, MD, USA
| | - Peter Greenberg
- Division of Hematology, Department of Medicine, Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Maria E Figueroa
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Pierre Fenaux
- Hôpital Saint Louis, Assistance Publique Hôpitaux de Paris and Paris Cité University, Paris, France
| | - Fabio Efficace
- Italian Group for Adult Hematologic Diseases (GIMEMA), Health Outcomes Research Unit, Rome, Italy
| | - Amy E DeZern
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Hospital, Baltimore, MD, USA
| | - Naval G Daver
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jane E Churpek
- Department of Hematology, Oncology, and Palliative Care, Carbone Cancer Center, The University of Wisconsin-Madison, Madison, WI, USA
| | - Hetty E Carraway
- Leukemia Program, Hematology and Medical Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Rena Buckstein
- Department of Medical Oncology/ Hematology, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Andrew M Brunner
- Leukemia Program, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Jacqueline Boultwood
- Blood Cancer UK Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Uma Borate
- Ohio State University Comprehensive Cancer Center/ James Cancer Hospital, Ohio State University, Columbus, OH, USA
| | - Rafael Bejar
- Division of Hematology and Oncology, Moores Cancer Center, UC San Diego, La Jolla, CA, USA
| | - John M Bennett
- University of Rochester Medical Center, Department of Pathology and Laboratory Medical Center, Rochester, NY, USA
| | - Andrew H Wei
- Department of Haematology, Peter MacCallum Cancer Centre, Royal Melbourne Hospital, Walter and Eliza Hall Institute of Medical Research and University of Melbourne, Victoria, Australia
| | | | - Michael R Savona
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Amer M Zeidan
- Section of Hematology, Department of Internal Medicine, Yale University School of Medicine and Yale Cancer Center, New Haven, CT, USA.
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Gao Y, Zimmer JT, Vasic R, Liu C, Gbyli R, Zheng SJ, Patel A, Liu W, Qi Z, Li Y, Nelakanti R, Song Y, Biancon G, Xiao AZ, Slavoff S, Kibbey RG, Flavell RA, Simon MD, Tebaldi T, Li HB, Halene S. ALKBH5 modulates hematopoietic stem and progenitor cell energy metabolism through m 6A modification-mediated RNA stability control. Cell Rep 2023; 42:113163. [PMID: 37742191 PMCID: PMC10636609 DOI: 10.1016/j.celrep.2023.113163] [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: 08/12/2022] [Revised: 08/01/2023] [Accepted: 09/08/2023] [Indexed: 09/26/2023] Open
Abstract
N6-methyladenosine (m6A) RNA modification controls numerous cellular processes. To what extent these post-transcriptional regulatory mechanisms play a role in hematopoiesis has not been fully elucidated. We here show that the m6A demethylase alkB homolog 5 (ALKBH5) controls mitochondrial ATP production and modulates hematopoietic stem and progenitor cell (HSPC) fitness in an m6A-dependent manner. Loss of ALKBH5 results in increased RNA methylation and instability of oxoglutarate-dehydrogenase (Ogdh) messenger RNA and reduction of OGDH protein levels. Limited OGDH availability slows the tricarboxylic acid (TCA) cycle with accumulation of α-ketoglutarate (α-KG) and conversion of α-KG into L-2-hydroxyglutarate (L-2-HG). L-2-HG inhibits energy production in both murine and human hematopoietic cells in vitro. Impaired mitochondrial energy production confers competitive disadvantage to HSPCs and limits clonogenicity of Mll-AF9-induced leukemia. Our study uncovers a mechanism whereby the RNA m6A demethylase ALKBH5 regulates the stability of metabolic enzyme transcripts, thereby controlling energy metabolism in hematopoiesis and leukemia.
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Affiliation(s)
- Yimeng Gao
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, and Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA.
| | - Joshua T Zimmer
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
| | - Radovan Vasic
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, and Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Medicine, University of Toronto, Toronto, ON M5S3H2, Canada
| | - Chengyang Liu
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, and Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Rana Gbyli
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, and Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Genetics and Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Shu-Jian Zheng
- Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA; Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Amisha Patel
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, and Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Wei Liu
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, and Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Zhihong Qi
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, and Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yaping Li
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, and Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Raman Nelakanti
- Department of Genetics and Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Yuanbin Song
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, and Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Giulia Biancon
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, and Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Andrew Z Xiao
- Department of Genetics and Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Sarah Slavoff
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA; Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Richard G Kibbey
- Department of Internal Medicine, Yale University, New Haven, CT 06520, USA; Department of Cellular & Molecular Physiology, Yale University, New Haven, CT 06520, USA
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Matthew D Simon
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
| | - Toma Tebaldi
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, and Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
| | - Hua-Bing Li
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Stephanie Halene
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, and Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA.
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7
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VanOudenhove J, Liu Y, Nelakanti R, Kim D, Busarello E, Ovalle NT, Qi Z, Mamillapalli P, Siddon A, Bai Z, Axtmayer A, Corso C, Kothari S, Foss F, Isufi I, Tebaldi T, Gowda L, Fan R, Seropian S, Halene S. Impact of Memory T Cells on SARS-COV-2 Vaccine Response in Hematopoietic Stem Cell Transplant. bioRxiv 2023:2023.10.26.564259. [PMID: 37961434 PMCID: PMC10634862 DOI: 10.1101/2023.10.26.564259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
During the COVID-19 pandemic, hematopoietic stem cell transplant (HSCT) recipients faced an elevated mortality rate from SARS-CoV-2 infection, ranging between 10-40%. The SARS-CoV-2 mRNA vaccines are important tools in preventing severe disease, yet their efficacy in the post-transplant setting remains unclear, especially in patients subjected to myeloablative chemotherapy and immunosuppression. We evaluated the humoral and adaptive immune responses to the SARS-CoV-2 mRNA vaccination series in 42 HSCT recipients and 5 healthy controls. Peripheral blood mononuclear nuclear cells and serum were prospectively collected before and after each dose of the SARS-CoV-2 vaccine. Post-vaccination responses were assessed by measuring anti-spike IgG and nucleocapsid titers, and antigen specific T cell activity, before and after vaccination. In order to examine mechanisms behind a lack of response, pre-and post-vaccine samples were selected based on humoral and cellular responses for single-cell RNA sequencing with TCR and BCR sequencing. Our observations revealed that while all participants eventually mounted a humoral response, transplant recipients had defects in memory T cell populations that were associated with an absence of T cell response, some of which could be detected pre-vaccination.
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8
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Kim D, Biancon G, Bai Z, VanOudenhove J, Liu Y, Kothari S, Gowda L, Kwan JM, Buitrago-Pocasangre NC, Lele N, Asashima H, Racke MK, Wilson JE, Givens TS, Tomayko MM, Schulz WL, Longbrake EE, Hafler DA, Halene S, Fan R. Microfluidic Immuno-Serolomic Assay Reveals Systems Level Association with COVID-19 Pathology and Vaccine Protection. Small Methods 2023; 7:e2300594. [PMID: 37312418 PMCID: PMC10592458 DOI: 10.1002/smtd.202300594] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 05/23/2023] [Indexed: 06/15/2023]
Abstract
How to develop highly informative serology assays to evaluate the quality of immune protection against coronavirus disease-19 (COVID-19) has been a global pursuit over the past years. Here, a microfluidic high-plex immuno-serolomic assay is developed to simultaneously measure50 plasma or serum samples for50 soluble markers including 35proteins, 11 anti-spike/receptor binding domian (RBD) IgG antibodies spanningmajor variants, and controls. This assay demonstrates the quintuplicate test in a single run with high throughput, low sample volume, high reproducibilityand accuracy. It is applied to the measurement of 1012 blood samples including in-depth analysis of sera from 127 patients and 21 healthy donors over multiple time points, either with acute COVID infection or vaccination. The protein analysis reveals distinct immune mediator modules that exhibit a reduced degree of diversity in protein-protein cooperation in patients with hematologic malignancies or receiving B cell depletion therapy. Serological analysis identifies that COVID-infected patients with hematologic malignancies display impaired anti-RBD antibody response despite high level of anti-spike IgG, which can be associated with limited clonotype diversity and functional deficiency in B cells. These findings underscore the importance to individualize immunization strategies for these high-risk patients and provide an informative tool to monitor their responses at the systems level.
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Affiliation(s)
- Dongjoo Kim
- Department of Biomedical Engineering, Yale University, New Haven, CT, 06520, USA
| | - Giulia Biancon
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Zhiliang Bai
- Department of Biomedical Engineering, Yale University, New Haven, CT, 06520, USA
| | - Jennifer VanOudenhove
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Yuxin Liu
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Shalin Kothari
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Lohith Gowda
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Jennifer M Kwan
- Cardiovascular Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
| | | | - Nikhil Lele
- Department of Neurology, Yale University, New Haven, CT, 06520, USA
| | | | | | | | | | - Mary M Tomayko
- Departments of Dermatology, Yale University, New Haven, CT, 06520, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Wade L Schulz
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Erin E Longbrake
- Department of Neurology, Yale University, New Haven, CT, 06520, USA
| | - David A Hafler
- Department of Neurology, Yale University, New Haven, CT, 06520, USA
- Department of Immunobiology, Yale University, New Haven, CT, 06520, USA
| | - Stephanie Halene
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520, USA
- Yale Center for RNA Science and Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
- Yale Cancer Center and Stem Cell Center, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT, 06520, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520, USA
- Yale Cancer Center and Stem Cell Center, Yale School of Medicine, New Haven, CT, 06520, USA
- Human and Translational Immunology, Yale School of Medicine, New Haven, CT, 06520, USA
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9
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Liu Y, DiStasio M, Su G, Asashima H, Enninful A, Qin X, Deng Y, Nam J, Gao F, Bordignon P, Cassano M, Tomayko M, Xu M, Halene S, Craft JE, Hafler D, Fan R. High-plex protein and whole transcriptome co-mapping at cellular resolution with spatial CITE-seq. Nat Biotechnol 2023; 41:1405-1409. [PMID: 36823353 PMCID: PMC10567548 DOI: 10.1038/s41587-023-01676-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [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: 03/28/2022] [Accepted: 01/12/2023] [Indexed: 02/25/2023]
Abstract
In this study, we extended co-indexing of transcriptomes and epitopes (CITE) to the spatial dimension and demonstrated high-plex protein and whole transcriptome co-mapping. We profiled 189 proteins and whole transcriptome in multiple mouse tissue types with spatial CITE sequencing and then further applied the method to measure 273 proteins and transcriptome in human tissues, revealing spatially distinct germinal center reactions in tonsil and early immune activation in skin at the Coronavirus Disease 2019 mRNA vaccine injection site.
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Affiliation(s)
- Yang Liu
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Department of Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Marcello DiStasio
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Department of Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Graham Su
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Hiromitsu Asashima
- Department of Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Archibald Enninful
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Xiaoyu Qin
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Yanxiang Deng
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Jungmin Nam
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Fu Gao
- Department of Medicine, Yale School of Medicine, New Haven, CT, USA
| | | | | | - Mary Tomayko
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Department of Dermatology, Yale School of Medicine, New Haven, CT, USA
| | - Mina Xu
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Stephanie Halene
- Department of Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Joseph E Craft
- Department of Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT, USA
| | - David Hafler
- Department of Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT, USA
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA.
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA.
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA.
- Department of Medicine, Yale School of Medicine, New Haven, CT, USA.
- Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT, USA.
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10
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Bewersdorf JP, Xie Z, Bejar R, Borate U, Boultwood J, Brunner AM, Buckstein R, Carraway HE, Churpek JE, Daver NG, Porta MGD, DeZern AE, Fenaux P, Figueroa ME, Gore SD, Griffiths EA, Halene S, Hasserjian RP, Hourigan CS, Kim TK, Komrokji R, Kuchroo VK, List AF, Loghavi S, Majeti R, Odenike O, Patnaik MM, Platzbecker U, Roboz GJ, Sallman DA, Santini V, Sanz G, Sekeres MA, Stahl M, Starczynowski DT, Steensma DP, Taylor J, Abdel-Wahab O, Xu ML, Savona MR, Wei AH, Zeidan AM. Current landscape of translational and clinical research in myelodysplastic syndromes/neoplasms (MDS): Proceedings from the 1 st International Workshop on MDS (iwMDS) Of the International Consortium for MDS (icMDS). Blood Rev 2023; 60:101072. [PMID: 36934059 DOI: 10.1016/j.blre.2023.101072] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 01/10/2023] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 03/18/2023]
Abstract
Biological events that contribute to the pathogenesis of myelodysplastic syndromes/neoplasms (MDS) are becoming increasingly characterized and are being translated into rationally designed therapeutic strategies. Herein, we provide updates from the first International Workshop on MDS (iwMDS) of the International Consortium for MDS (icMDS) detailing recent advances in understanding the genetic landscape of MDS, including germline predisposition, epigenetic and immune dysregulation, the complexities of clonal hematopoiesis progression to MDS, as well as novel animal models of the disease. Connected to this progress is the development of novel therapies targeting specific molecular alterations, the innate immune system, and immune checkpoint inhibitors. While some of these agents have entered clinical trials (e.g., splicing modulators, IRAK1/4 inhibitors, anti-CD47 and anti-TIM3 antibodies, and cellular therapies), none have been approved for MDS. Additional preclinical and clinical work is needed to develop a truly individualized approach to the care of MDS patients.
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Affiliation(s)
- Jan Philipp Bewersdorf
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zhuoer Xie
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Rafael Bejar
- Division of Hematology and Oncology, Moores Cancer Center, UC San Diego, La Jolla, CA, USA
| | - Uma Borate
- Ohio State University Comprehensive Cancer/ James Cancer Hospital, Ohio State University, Columbus, OH, USA
| | - Jacqueline Boultwood
- Blood Cancer UK Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew M Brunner
- Leukemia Program, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Rena Buckstein
- Department of Medical Oncology/Hematology, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Hetty E Carraway
- Leukemia Program, Hematology and Medical Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Jane E Churpek
- Department of Hematology, Oncology, and Palliative Care, Carbone Cancer Center, The University of Wisconsin-Madison, Madison, WI, USA
| | - Naval G Daver
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Matteo Giovanni Della Porta
- IRCCS Humanitas Clinical and Research Center & Humanitas University, Department of Biomedical Sciences, via Manzoni 56, 20089 Rozzano - Milan, Italy
| | - Amy E DeZern
- Division of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Hospital, Baltimore, MD, USA
| | - Pierre Fenaux
- Hôpital Saint Louis, Assistance Publique Hôpitaux de Paris and Paris Cité University, Paris, France
| | - Maria E Figueroa
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Steven D Gore
- National Cancer Institute, Cancer Therapy Evaluation Program, Bethesda, MD, USA
| | | | - Stephanie Halene
- Section of Hematology, Department of Internal Medicine, Yale University School of Medicine and Yale Cancer Center, New Haven, CT, USA
| | | | - Christopher S Hourigan
- Laboratory of Myeloid Malignancies, Hematology Branch, National Heart, Lung, and Blood Institute, and Myeloid Malignancies Program, National Institutes of Health, Bethesda, MD, USA
| | - Tae Kon Kim
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rami Komrokji
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Vijay K Kuchroo
- Evergrande Center for Immunologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Alan F List
- Precision BioSciences, Inc., Durham, NC, USA
| | - Sanam Loghavi
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ravindra Majeti
- Division of Hematology, Department of Medicine, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Olatoyosi Odenike
- Leukemia Program, University of Chicago Medicine and University of Chicago Comprehensive Cancer Center, Chicago, IL, USA
| | - Mrinal M Patnaik
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Gail J Roboz
- Weill Cornell Medical College, New York, NY, USA
| | - David A Sallman
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | | | - Guillermo Sanz
- Health Research Institute La Fe, Valencia, Spain; Hospital Universitario y Politécnico La Fe, Valencia, Spain; CIBERONC, IS Carlos III, Madrid, Spain
| | - Mikkael A Sekeres
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Maximilian Stahl
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Daniel T Starczynowski
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | | | - Justin Taylor
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Omar Abdel-Wahab
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mina L Xu
- Departments of Pathology & Laboratory Medicine, Yale University School of Medicine and Yale Cancer Center, New Haven, CT, USA
| | - Michael R Savona
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Andrew H Wei
- Department of Haematology, Peter MacCallum Cancer Centre, Royal Melbourne Hospital, Walter and Eliza Hall Institute of Medical Research and University of Melbourne, Victoria, Australia
| | - Amer M Zeidan
- Section of Hematology, Department of Internal Medicine, Yale University School of Medicine and Yale Cancer Center, New Haven, CT, USA.
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11
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Stahl M, Abdel-Wahab O, Wei AH, Savona MR, Xu ML, Xie Z, Taylor J, Starczynowski D, Sanz GF, Sallman DA, Santini V, Roboz GJ, Patnaik MM, Padron E, Odenike O, Nazha A, Nimer SD, Majeti R, Little RF, Gore S, List AF, Kutchroo V, Komrokji RS, Kim TK, Kim N, Hourigan CS, Hasserjian RP, Halene S, Griffiths EA, Greenberg PL, Figueroa M, Fenaux P, Efficace F, DeZern AE, Della Porta MG, Daver NG, Churpek JE, Carraway HE, Brunner AM, Borate U, Bennett JM, Bejar R, Boultwood J, Loghavi S, Bewersdorf JP, Platzbecker U, Steensma DP, Sekeres MA, Buckstein RJ, Zeidan AM. An agenda to advance research in myelodysplastic syndromes: a TOP 10 priority list from the first international workshop in MDS. Blood Adv 2023; 7:2709-2714. [PMID: 36260702 PMCID: PMC10333740 DOI: 10.1182/bloodadvances.2022008747] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 08/17/2022] [Revised: 09/06/2022] [Accepted: 09/14/2022] [Indexed: 11/20/2022] Open
Affiliation(s)
- Maximilian Stahl
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA
| | - Omar Abdel-Wahab
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Andrew H. Wei
- Peter MacCallum Cancer Centre, Royal Melbourne Hospital, University of Melbourne and Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Michael R. Savona
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Mina L. Xu
- Departments of Pathology & Laboratory Medicine, Yale University School of Medicine and Yale Cancer Center, New Haven, CT
| | - Zhuoer Xie
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center, Tampa, FL
| | - Justin Taylor
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL
| | - Daniel Starczynowski
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Guillermo F. Sanz
- Hematology Department, Hospital Universitario y Politécnico La Fe, Valencia, Spain
- Health Research Institute La Fe, Valencia, Spain
- CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - David A. Sallman
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center, Tampa, FL
| | | | - Gail J. Roboz
- Weill Cornell Medicine and The New York Presbyterian Hospital, New York, NY
| | - Mrinal M. Patnaik
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN
| | - Eric Padron
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center, Tampa, FL
| | | | - Aziz Nazha
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
| | - Stephen D. Nimer
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL
| | - Ravindra Majeti
- Division of Hematology, Department of Medicine, Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | - Richard F. Little
- National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Steven Gore
- National Cancer Institute, National Institutes of Health, Bethesda, MD
| | | | - Vijay Kutchroo
- Evergrande Center for Immunologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA
| | - Rami S. Komrokji
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center, Tampa, FL
| | - Tae Kon Kim
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Nina Kim
- National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Christopher S. Hourigan
- Laboratory of Myeloid Malignancies, Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | | | - Stephanie Halene
- Section of Hematology, Department of Internal Medicine, Yale University School of Medicine and Yale Cancer Center, New Haven, CT
| | | | - Peter L. Greenberg
- Division of Hematology, Department of Medicine, Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | - Maria Figueroa
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL
| | | | - Fabio Efficace
- Italian Group for Adult Hematologic Diseases (GIMEMA), Data Center and Health Outcomes Research Unit, Rome, Italy
| | - Amy E. DeZern
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, MD
| | - Matteo G. Della Porta
- Humanitas Clinical and Research Center & Humanitas University, Department of Biomedical Sciences, Milan, Italy
| | - Naval G. Daver
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jane E. Churpek
- Department of Hematology, Oncology, and Palliative Care, Carbone Cancer Center, The University of Wisconsin-Madison, Madison, WI
| | - Hetty E. Carraway
- Leukemia Program, Hematology and Medical Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | | | - Uma Borate
- Division of Hematology, Department of Internal Medicine, James Cancer Center, Ohio State University, Columbus, OH
| | - John M. Bennett
- Hematopathology Division, Departments of Pathology and Medicine, University of Rochester Medical Center, Rochester, NY
| | - Rafael Bejar
- Division of Hematology and Oncology, Moores Cancer Center, UC San Diego, La Jolla, CA
| | - Jacqueline Boultwood
- Blood Cancer UK Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Sanam Loghavi
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jan Philipp Bewersdorf
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Uwe Platzbecker
- Department of Hematology and Cellular Therapy, Medical Clinic and Policlinic I, Leipzig University Hospital, Leipzig, Germany
| | | | - Mikkael A. Sekeres
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL
| | - Rena J. Buckstein
- Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, Canada
| | - Amer M. Zeidan
- Section of Hematology, Department of Internal Medicine, Yale University School of Medicine and Yale Cancer Center, New Haven, CT
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12
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Kazemain E, Figueiredo J, Skarbinski J, McBride R, Simon V, Karger AB, Lee FEH, Hirsch FR, Cox A, Klein S, Fan R, Halene S, Zidar DA, Crawford JM, Thyagarajan B, Gleason C, Mathson A, Srivastava K, Moshele P, Amoss T, Runnstrom M, Linderman S, Rodilla AM, Mack PC, Shyr Y, Yin A, Shea P, VanOudenhove J, Siddiqui H, Wilson BM, Elkin EP, Hsiao CA, Ziemba Y, Schleicher CB, Fox S, Kushi LH, Reckamp K, Merchant A, Merin N. Abstract 798: SeroNet Pooling Project of immunocompromised populations. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-798] [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: 04/07/2023]
Abstract
Abstract
Introduction: COVID-19 vaccination substantially reduces morbidity and mortality associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and severe illness. However, despite effective COVID-19 vaccines many questions remain about the efficacy of vaccines and the durability and robustness of immune responses, especially in immunocompromised persons. The NCI-funded Serological Sciences Network (SeroNet) is a coordinated effort including 11 sites to advance research on the immune response to SARS-CoV-2 infection and COVID-19 vaccination among diverse and vulnerable populations. The goals of the Pooling Project are: (1) to conduct real-world data (RWD) analyses using electronic medical records (EMR) data from four health care systems (Kaiser Permanente Northern California, Northwell Health, Veterans Affairs-Case Western, and Cedars-Sinai) to determine vaccine effectiveness in (a) cancer patients; (b) autoimmune diseases and (c) solid organ transplant recipients (SOTR); (2) to conduct meta-analyses of prospective cohort studies from eight SeroNet institutions (Cedars-Sinai, Johns Hopkins, Northwell Health, Emory University, University of Minnesota, Mount Sinai, Yale University) to determine post-vaccine immune responses in (a) lung cancer patients; (b) hematologic cancers/hematopoietic stem cell transplant (HSCT) recipients; (c) SOTR; (d) lupus.
Methods: For our RWD analyses, data is extracted from EMR using standardized algorithms using ICD-10 codes to identify immunocompromised persons (hematologic and solid organ malignancy; SOTR; autoimmune disease, including inflammatory bowel disease, rheumatoid arthritis, and SLE). We use common case definitions to extract data on demographic, laboratory values, clinical co-morbidity, COVID-19 vaccination, SARS-CoV-2 infection and severe COVID-19, and disease-specific variables. In addition, we pool individual-level data from prospective cohorts enrolling patients with cancer and other immunosuppressed conditions from across network. Surveys and biospecimens from serology and immune profiling are collected at pre-specified timepoints across longitudinal cohorts.
Results: Currently, we have EMR data extracted from 4 health systems including >715,000 cancer patients, >9,500 SOTR and >180,000 with autoimmune conditions. Prospective cohorts across the network have longitudinal data on >450 patients with lung cancer, >1,200 patients with hematologic malignancies, >400 SOTR and >400 patients with lupus. We will report results examining vaccine effectiveness for prevention of SARS-CoV-2 infection, severe COVID-19 and post-acute sequelae of COVID-19 (PAS-C or long COVID) in cancer patients compared to other immunocompromised conditions.
Conclusion: Our goal is to inform public health guidelines on COVID-19 vaccine and boosters to reduce SARS-CoV-2 infection and severe illness in immunocompromised populations.
Citation Format: Elham Kazemain, Jane Figueiredo, Jacek Skarbinski, Russell McBride, Viviana Simon, Amy B. Karger, F. Eun-Hyung Lee, Fred R. Hirsch, Andrea Cox, Sabra Klein, Rong Fan, Stephanie Halene, David A. Zidar, James M. Crawford, Bharat Thyagarajan, Charles Gleason, Alex Mathson, Komal Srivastava, Puleng Moshele, Toby Amoss, Martin Runnstrom, Susanne Linderman, Ananda M. Rodilla, Philip C. Mack, Yu Shyr, Anna Yin, Patrick Shea, Jennifer VanOudenhove, Hinnah Siddiqui, Brigid M. Wilson, Eric P. Elkin, Crystal A. Hsiao, Yonah Ziemba, Cheryl B. Schleicher, Sharon Fox, Lawrence H. Kushi, Karen Reckamp, Akil Merchant, Noah Merin. SeroNet Pooling Project of immunocompromised populations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 798.
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Affiliation(s)
| | | | | | | | - Viviana Simon
- 3Icahn School of Medicine at Mount Sinai, New York, NY
| | | | | | | | - Andrea Cox
- 6John Hopkins University School of Medicine, Baltimore, MD
| | - Sabra Klein
- 7Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD
| | - Rong Fan
- 8Yale School of Medicine, New Haven, CT
| | | | - David A. Zidar
- 9Case Western Reserve University School of Medicine, Cleveland, OH
| | - James M. Crawford
- 10Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, Hempstead, NY
| | | | | | | | | | | | | | | | | | | | | | - Yu Shyr
- 14Vanderbilt University, Nashville, TN
| | - Anna Yin
- 6John Hopkins University School of Medicine, Baltimore, MD
| | - Patrick Shea
- 6John Hopkins University School of Medicine, Baltimore, MD
| | | | - Hinnah Siddiqui
- 16Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH
| | - Brigid M. Wilson
- 16Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH
| | | | | | - Yonah Ziemba
- 10Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, Hempstead, NY
| | - Cheryl B. Schleicher
- 10Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, Hempstead, NY
| | - Sharon Fox
- 10Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, Hempstead, NY
| | | | | | | | - Noah Merin
- 1Cedars-Sinai Medical Center, Los Angeles, CA
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13
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VanOudenhove J, Halene S, Mendez L. Is it the time to integrate novel sequencing technologies into clinical practice? Curr Opin Hematol 2023; 30:70-77. [PMID: 36602939 DOI: 10.1097/moh.0000000000000754] [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] [Indexed: 01/06/2023]
Abstract
PURPOSE OF REVIEW The aim of this study was to provide insight into how novel next-generation sequencing (NGS) techniques are set to revolutionize clinical practice. RECENT FINDINGS Advances in sequencing technologies have focused on improved capture of mutations and reads and cellular resolution. Both short and long read DNA sequencing technology are being refined and combined in novel ways with other multiomic approaches to gain unprecedented biological insight into disease. Single-cell (sc)DNA-seq and integrated scDNA-seq with immunophenotyping provide granular information on disease composition such as clonal hierarchy, co-mutation status, zygosity, clonal diversity and genotype phenotype correlations. These and other techniques can identify rare cell populations providing the opportunity for increased sensitivity in measurable residual disease monitoring and precise characterization of residual clones permitting distinction of leukemic from pre/nonmalignant clones. SUMMARY Increasing genetics-based mechanistic insights and classification of myeloid diseases along with a decrease in the cost of high-throughput NGS mean novel sequencing technologies are closer to being a reality in standard clinical practice. These technologies are poised to improve diagnostics, our ability to monitor treatment response and minimal residual disease and allow the study of premalignant conditions such as clonal haematopoiesis.
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Affiliation(s)
- Jennifer VanOudenhove
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center and Smilow Cancer Hospital, Yale University School of Medicine, New Haven, Connecticut, USA
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14
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Fischer MA, Song Y, Arrate MP, Gbyli R, Villaume MT, Smith BN, Childress MA, Stricker TP, Halene S, Savona MR. Selective inhibition of MCL1 overcomes venetoclax resistance in a murine model of myelodysplastic syndromes. Haematologica 2023; 108:522-531. [PMID: 35979721 PMCID: PMC9890032 DOI: 10.3324/haematol.2022.280631] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 08/11/2022] [Indexed: 02/03/2023] Open
Abstract
Treatment for myelodysplastic syndromes (MDS) remains insufficient due to clonal heterogeneity and lack of effective clinical therapies. Dysregulation of apoptosis is observed across MDS subtypes regardless of mutations and represents an attractive therapeutic opportunity. Venetoclax (VEN), a selective inhibitor of anti-apoptotic protein B-cell lymphoma- 2 (BCL2), has yielded impressive responses in older patients with acute myeloid leukemia (AML) and high risk MDS. BCL2 family anti-apoptotic proteins BCL-XL and induced myeloid cell leukemia 1 (MCL1) are implicated in leukemia survival, and upregulation of MCL1 is seen in VEN-resistant AML and MDS. We determined in vitro sensitivity of MDS patient samples to selective inhibitors of BCL2, BCL-XL and MCL1. While VEN response positively correlated with MDS with excess blasts, all MDS subtypes responded to MCL1 inhibition. Treatment with combined VEN + MCL1 inhibtion was synergistic in all MDS subtypes without significant injury to normal hematopoiesis and reduced MDS engraftment in MISTRG6 mice, supporting the pursuit of clinical trials with combined BCL2 + MCL1 inhibition in MDS.
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Affiliation(s)
- Melissa A Fischer
- Department of Medicine; Cancer Biology Program, Vanderbilt University School of Medicine
| | - Yuanbin Song
- Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China; Smilow Cancer Center, Yale University School of Medicine, New Haven
| | | | - Rana Gbyli
- Smilow Cancer Center, Yale University School of Medicine, New Haven
| | - Matthew T Villaume
- Department of Medicine; Cancer Biology Program, Vanderbilt University School of Medicine
| | - Brianna N Smith
- Department of Medicine; Cancer Biology Program, Vanderbilt University School of Medicine; Department of Pediatrics
| | - Merrida A Childress
- Department of Medicine; Cancer Biology Program, Vanderbilt University School of Medicine
| | - Thomas P Stricker
- Vanderbilt-Ingram Cancer Center; Department of Pathology, Microbiology, and Immunology
| | - Stephanie Halene
- Smilow Cancer Center, Yale University School of Medicine, New Haven
| | - Michael R Savona
- Department of Medicine; Cancer Biology Program, Vanderbilt University School of Medicine; Vanderbilt-Ingram Cancer Center; Center for Immunobiology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232.
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15
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Biancon G, Busarello E, Joshi P, Lesch BJ, Halene S, Tebaldi T. Deconvolution of in vivo protein-RNA contacts using fractionated eCLIP-seq. STAR Protoc 2022; 3:101823. [PMID: 36595959 PMCID: PMC9676202 DOI: 10.1016/j.xpro.2022.101823] [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] [Received: 08/10/2022] [Revised: 09/15/2022] [Accepted: 10/06/2022] [Indexed: 11/18/2022] Open
Abstract
Thousands of RNA-binding proteins orchestrate RNA processing and altered protein-RNA interactions frequently lead to disease. Here, we present experimental and computational analysis pipelines of fractionated eCLIP-seq (freCLIP-seq), a modification of enhanced UV-crosslinking and RNA immunoprecipitation followed by sequencing. FreCLIP-seq allows transcriptome-wide analysis of protein-RNA interactions at single-nucleotide level and provides an additional level of resolution by isolating binding signals of individual RNA-binding proteins within a multicomponent complex. Binding occupancy can be inferred from read counts and crosslinking events. For complete details on the use and execution of this protocol, please refer to Biancon et al. (2022).
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Affiliation(s)
- Giulia Biancon
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA.
| | - Emma Busarello
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Poorval Joshi
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Bluma J Lesch
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Stephanie Halene
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA; Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT, USA; Department of Pathology, Yale University School of Medicine, New Haven, CT, USA.
| | - Toma Tebaldi
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA; Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy.
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16
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Öz HH, Cheng EC, Di Pietro C, Tebaldi T, Biancon G, Zeiss C, Zhang PX, Huang PH, Esquibies SS, Britto CJ, Schupp JC, Murray TS, Halene S, Krause DS, Egan ME, Bruscia EM. Recruited monocytes/macrophages drive pulmonary neutrophilic inflammation and irreversible lung tissue remodeling in cystic fibrosis. Cell Rep 2022; 41:111797. [PMID: 36516754 PMCID: PMC9833830 DOI: 10.1016/j.celrep.2022.111797] [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] [Received: 01/25/2022] [Revised: 09/30/2022] [Accepted: 11/16/2022] [Indexed: 12/15/2022] Open
Abstract
Persistent neutrophil-dominated lung inflammation contributes to lung damage in cystic fibrosis (CF). However, the mechanisms that drive persistent lung neutrophilia and tissue deterioration in CF are not well characterized. Starting from the observation that, in patients with CF, c-c motif chemokine receptor 2 (CCR2)+ monocytes/macrophages are abundant in the lungs, we investigate the interplay between monocytes/macrophages and neutrophils in perpetuating lung tissue damage in CF. Here we show that CCR2+ monocytes in murine CF lungs drive pathogenic transforming growth factor β (TGF-β) signaling and sustain a pro-inflammatory environment by facilitating neutrophil recruitment. Targeting CCR2 to lower the numbers of monocytes in CF lungs ameliorates neutrophil inflammation and pathogenic TGF-β signaling and prevents lung tissue damage. This study identifies CCR2+ monocytes as a neglected contributor to the pathogenesis of CF lung disease and as a therapeutic target for patients with CF, for whom lung hyperinflammation and tissue damage remain an issue despite recent advances in CF transmembrane conductance regulator (CFTR)-specific therapeutic agents.
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Affiliation(s)
- Hasan H Öz
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
| | - Ee-Chun Cheng
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
| | | | - Toma Tebaldi
- Department of Hematology, Yale School of Medicine, New Haven, CT, USA; Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA; Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
| | - Giulia Biancon
- Department of Hematology, Yale School of Medicine, New Haven, CT, USA; Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA
| | - Caroline Zeiss
- Department of Comparative Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Ping-Xia Zhang
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA; Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA; Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Pamela H Huang
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
| | - Sofia S Esquibies
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
| | - Clemente J Britto
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Jonas C Schupp
- Department of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA; Department of Respiratory Medicine, Hannover Medical School and Biomedical Research in End-stage and Obstructive Lung Disease Hannover, German Lung Research Center (DZL), Hannover, Germany
| | - Thomas S Murray
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
| | - Stephanie Halene
- Department of Hematology, Yale School of Medicine, New Haven, CT, USA; Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA
| | - Diane S Krause
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA; Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA; Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Marie E Egan
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA; Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, CT, USA
| | - Emanuela M Bruscia
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA; Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA.
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17
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Zeidan AM, Bewersdorf JP, Buckstein R, Sekeres MA, Steensma DP, Platzbecker U, Loghavi S, Boultwood J, Bejar R, Bennett JM, Borate U, Brunner AM, Carraway H, Churpek JE, Daver NG, Della Porta M, DeZern AE, Efficace F, Fenaux P, Figueroa ME, Greenberg P, Griffiths EA, Halene S, Hasserjian RP, Hourigan CS, Kim N, Kim TK, Komrokji RS, Kutchroo V, List AF, Little RF, Majeti R, Nazha A, Nimer SD, Odenike O, Padron E, Patnaik MM, Roboz GJ, Sallman DA, Sanz G, Stahl M, Starczynowski DT, Taylor J, Xie Z, Xu M, Savona MR, Wei AH, Abdel-Wahab O, Santini V. Finding consistency in classifications of myeloid neoplasms: a perspective on behalf of the International Workshop for Myelodysplastic Syndromes. Leukemia 2022; 36:2939-2946. [PMID: 36266326 DOI: 10.1038/s41375-022-01724-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/28/2022] [Accepted: 10/04/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Amer M Zeidan
- Section of Hematology, Department of Internal Medicine, Yale University School of Medicine and Yale Cancer Center, New Haven, CT, USA.
| | - Jan Philipp Bewersdorf
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rena Buckstein
- Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, Canada
| | - Mikkael A Sekeres
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | | | - Sanam Loghavi
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jacqueline Boultwood
- Blood Cancer UK Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Rafael Bejar
- Division of Hematology and Oncology, Moores Cancer Center, UC San Diego, La Jolla, CA, USA
| | - John M Bennett
- Hematopathology Division, Departments of Pathology and Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Uma Borate
- Division of Hematology, Department of Internal Medicine, James Cancer Center, Ohio State University, Columbus, OH, USA
| | - Andrew M Brunner
- Leukemia Program, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Hetty Carraway
- Leukemia Program, Hematology and Medical Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Jane E Churpek
- Department of Hematology, Oncology, and Palliative Care, Carbone Cancer Center, The University of Wisconsin-Madison, Madison, WI, USA
| | - Naval G Daver
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Matteo Della Porta
- Department of Biomedical Sciences, Humanitas Clinical and Research Center & Humanitas University, Milan, Italy
| | - Amy E DeZern
- Johns Hopkins Sidney Kimmel Comprehensive Cancer Centre, Baltimore, MD, USA
| | - Fabio Efficace
- Italian Group for Adult Hematologic Diseases (GIMEMA), Data Center and Health Outcomes Research Unit, Rome, Italy
| | | | - Maria E Figueroa
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Peter Greenberg
- Division of Hematology, Department of Medicine, Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Stephanie Halene
- Section of Hematology, Department of Internal Medicine, Yale University School of Medicine and Yale Cancer Center, New Haven, CT, USA
| | | | - Christopher S Hourigan
- Laboratory of Myeloid Malignancies, Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nina Kim
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Tae Kon Kim
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rami S Komrokji
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Vijay Kutchroo
- Evergrande Center for Immunologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Alan F List
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Richard F Little
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ravi Majeti
- Division of Hematology, Department of Medicine, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Aziz Nazha
- Department of Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Stephen D Nimer
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Olatoyosi Odenike
- The University of Chicago Medicine and University of Chicago Comprehensive Cancer Center, Chicago, IL, USA
| | - Eric Padron
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Mrinal M Patnaik
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Gail J Roboz
- Weill Cornell Medical College, New York, NY, USA
| | - David A Sallman
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Guillermo Sanz
- Hematology Department, Hospital Universitario y Politécnico La Fe, Valencia, Spain; Health Research Institute La Fe, Valencia, Spain; and CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - Maximilian Stahl
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Daniel T Starczynowski
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Justin Taylor
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Zhuoer Xie
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Mina Xu
- Departments of Pathology & Laboratory Medicine, Yale University School of Medicine and Yale Cancer Center, New Haven, CT, USA
| | - Michael R Savona
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Andrew H Wei
- Peter MacCallum Cancer Centre, Royal Melbourne Hospital, University of Melbourne and Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Omar Abdel-Wahab
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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18
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Adema V, Ma F, Kanagal-Shamanna R, Thongon N, Montalban-Bravo G, Yang H, Peslak SA, Wang F, Acha P, Sole F, Lockyer P, Cassari M, Maciejewski JP, Visconte V, Gañán-Gómez I, Song Y, Bueso-Ramos C, Pellegrini M, Tan TM, Bejar R, Carew JS, Halene S, Santini V, Al-Atrash G, Clise-Dwyer K, Garcia-Manero G, Blobel GA, Colla S. Targeting the EIF2AK1 Signaling Pathway Rescues Red Blood Cell Production in SF3B1-Mutant Myelodysplastic Syndromes With Ringed Sideroblasts. Blood Cancer Discov 2022; 3:554-567. [PMID: 35926182 PMCID: PMC9894566 DOI: 10.1158/2643-3230.bcd-21-0220] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 04/26/2022] [Accepted: 07/29/2022] [Indexed: 02/01/2023] Open
Abstract
SF3B1 mutations, which occur in 20% of patients with myelodysplastic syndromes (MDS), are the hallmarks of a specific MDS subtype, MDS with ringed sideroblasts (MDS-RS), which is characterized by the accumulation of erythroid precursors in the bone marrow and primarily affects the elderly population. Here, using single-cell technologies and functional validation studies of primary SF3B1-mutant MDS-RS samples, we show that SF3B1 mutations lead to the activation of the EIF2AK1 pathway in response to heme deficiency and that targeting this pathway rescues aberrant erythroid differentiation and enables the red blood cell maturation of MDS-RS erythroblasts. These data support the development of EIF2AK1 inhibitors to overcome transfusion dependency in patients with SF3B1-mutant MDS-RS with impaired red blood cell production. SIGNIFICANCE MDS-RS are characterized by significant anemia. Patients with MDS-RS die from a shortage of red blood cells and the side effects of iron overload due to their constant need for transfusions. Our study has implications for the development of therapies to achieve long-lasting hematologic responses. This article is highlighted in the In This Issue feature, p. 476.
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Affiliation(s)
- Vera Adema
- Department of Leukemia, The University of Texas MD Anderson Cancer Center,
Houston, Texas
| | - Feiyang Ma
- Division of Rheumatology, Department of Internal Medicine, Michigan
Medicine, University of Michigan, Ann Arbor, Michigan
| | - Rashmi Kanagal-Shamanna
- Department of Hematopathology, The University of Texas MD Anderson Cancer
Center, Houston, Texas
| | - Natthakan Thongon
- Department of Leukemia, The University of Texas MD Anderson Cancer Center,
Houston, Texas
| | | | - Hui Yang
- Department of Leukemia, The University of Texas MD Anderson Cancer Center,
Houston, Texas
| | - Scott A. Peslak
- Division of Hematology/Oncology, Department of Medicine, Hospital of the
University of Pennsylvania, Philadelphia, Pennsylvania
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia,
Pennsylvania
| | - Feng Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer
Center, Houston, Texas
| | - Pamela Acha
- MDS Research Group, Josep Carreras Leukaemia Research Institute, Universitat
Autonoma de Barcelona, Badalona, Spain
| | - Francesc Sole
- MDS Research Group, Josep Carreras Leukaemia Research Institute, Universitat
Autonoma de Barcelona, Badalona, Spain
| | - Pamela Lockyer
- Department of Leukemia, The University of Texas MD Anderson Cancer Center,
Houston, Texas
| | - Margherita Cassari
- MDS Unit, Azienda Ospedaliero Universitaria Careggi, University of Florence,
Florence, Italy
| | - Jaroslaw P. Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer
Institute, Cleveland Clinic Foundation, Cleveland, Ohio
| | - Valeria Visconte
- Department of Translational Hematology and Oncology Research, Taussig Cancer
Institute, Cleveland Clinic Foundation, Cleveland, Ohio
| | - Irene Gañán-Gómez
- Department of Leukemia, The University of Texas MD Anderson Cancer Center,
Houston, Texas
| | - Yuanbin Song
- Department of Hematologic Oncology, State Key Laboratory of Oncology in
South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University
Cancer Center, Guangzhou, P.R. China
| | - Carlos Bueso-Ramos
- Department of Hematopathology, The University of Texas MD Anderson Cancer
Center, Houston, Texas
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of
California, Los Angeles, California
| | - Tuyet M. Tan
- Moores Cancer Center, Univerity of California San Diego, San Diego,
California
| | - Rafael Bejar
- Moores Cancer Center, Univerity of California San Diego, San Diego,
California
| | | | - Stephanie Halene
- Section of Hematology, Department of Internal Medicine and Yale
Comprehensive Cancer Center, Yale University School of Medicine, New Haven,
Connecticut
| | - Valeria Santini
- MDS Unit, Azienda Ospedaliero Universitaria Careggi, University of Florence,
Florence, Italy
| | - Gheath Al-Atrash
- Department of Stem Cell Transplantation and Hematopoietic Biology and
Malignancy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Karen Clise-Dwyer
- Department of Stem Cell Transplantation and Hematopoietic Biology and
Malignancy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Gerd A. Blobel
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia,
Pennsylvania
| | - Simona Colla
- Department of Leukemia, The University of Texas MD Anderson Cancer Center,
Houston, Texas
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19
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Zheng Y, Sefik E, Astle J, Karatepe K, Öz HH, Solis AG, Jackson R, Luo HR, Bruscia EM, Halene S, Shan L, Flavell RA. Human neutrophil development and functionality are enabled in a humanized mouse model. Proc Natl Acad Sci U S A 2022; 119:e2121077119. [PMID: 36269862 PMCID: PMC9618085 DOI: 10.1073/pnas.2121077119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 11/23/2021] [Accepted: 08/09/2022] [Indexed: 02/03/2023] Open
Abstract
Mice with a functional human immune system serve as an invaluable tool to study the development and function of the human immune system in vivo. A major technological limitation of all current humanized mouse models is the lack of mature and functional human neutrophils in circulation and tissues. To overcome this, we generated a humanized mouse model named MISTRGGR, in which the mouse granulocyte colony-stimulating factor (G-CSF) was replaced with human G-CSF and the mouse G-CSF receptor gene was deleted in existing MISTRG mice. By targeting the G-CSF cytokine-receptor axis, we dramatically improved the reconstitution of mature circulating and tissue-infiltrating human neutrophils in MISTRGGR mice. Moreover, these functional human neutrophils in MISTRGGR are recruited upon inflammatory and infectious challenges and help reduce bacterial burden. MISTRGGR mice represent a unique mouse model that finally permits the study of human neutrophils in health and disease.
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Affiliation(s)
- Yunjiang Zheng
- Department of Immunobiology, Yale University, New Haven, CT 06520
| | - Esen Sefik
- Department of Immunobiology, Yale University, New Haven, CT 06520
| | - John Astle
- Department of Immunobiology, Yale University, New Haven, CT 06520
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226
| | - Kutay Karatepe
- Department of Cell Biology, Yale University, New Haven, CT 06520
- Yale Stem Cell Center, Yale University, New Haven, CT 06520
| | - Hasan H. Öz
- Section of Pediatric Pulmonology, Allergy, Immunology & Sleep Medicine, Department of Pediatrics, Yale University School of Medicine, New Haven, CT 06520
| | - Angel G. Solis
- Department of Immunobiology, Yale University, New Haven, CT 06520
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Ruaidhrí Jackson
- Department of Immunobiology, Yale University, New Haven, CT 06520
- Department of Immunology, Harvard Medical School, Boston, MA 02115
| | - Hongbo R. Luo
- Department of Laboratory Medicine, The Stem Cell Program, Boston Children’s Hospital, Boston, MA 02115
- Department of Pathology, Harvard Medical School, Boston, MA 02115
| | - Emanuela M. Bruscia
- Section of Pediatric Pulmonology, Allergy, Immunology & Sleep Medicine, Department of Pediatrics, Yale University School of Medicine, New Haven, CT 06520
| | - Stephanie Halene
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT 06520
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520
| | - Liang Shan
- Department of Immunobiology, Yale University, New Haven, CT 06520
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Richard A. Flavell
- Department of Immunobiology, Yale University, New Haven, CT 06520
- Howard Hughes Medical Institute (HHMI), New Haven, CT 06520
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20
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Griffin KN, Walters BW, Li H, Wang H, Biancon G, Tebaldi T, Kaya CB, Kanyo J, Lam TT, Cox AL, Halene S, Chung JJ, Lesch BJ. Widespread association of the Argonaute protein AGO2 with meiotic chromatin suggests a distinct nuclear function in mammalian male reproduction. Genome Res 2022; 32:gr.276578.122. [PMID: 36109149 PMCID: PMC9528986 DOI: 10.1101/gr.276578.122] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 07/21/2022] [Indexed: 11/25/2022]
Abstract
Argonaute 2 (AGO2) is a ubiquitously expressed protein critical for regulation of mRNA translation and vital to animal development. AGO2 protein is found in both cytoplasmic and nuclear compartments, and although its cytoplasmic role is well studied, the biological relevance of nuclear AGO2 is unclear. Here, we address this problem in vivo using spermatogenic cells as a model. We find that AGO2 transiently binds both chromatin and nucleus-specific mRNA transcripts of hundreds of genes required for sperm production during male meiosis in mice, and that germline conditional knockout (cKO) of Ago2 causes depletion of the encoded proteins. Correspondingly, Ago2 cKO males show abnormal sperm head morphology and reduced sperm count, along with reduced postnatal viability of offspring. Together, our data reveal an unexpected nuclear role for AGO2 in enhancing expression of developmentally important genes during mammalian male reproduction.
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Affiliation(s)
- Kimberly N Griffin
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | | | - Haixin Li
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Huafeng Wang
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Giulia Biancon
- Section of Hematology, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Toma Tebaldi
- Section of Hematology, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
| | - Carolyn B Kaya
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Jean Kanyo
- Keck MS & Proteomics Resource, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - TuKiet T Lam
- Keck MS & Proteomics Resource, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Andy L Cox
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Stephanie Halene
- Section of Hematology, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Department of Pathology, Gynecology & Reproductive Sciences, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Jean-Ju Chung
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Department of Obstetrics, Gynecology & Reproductive Sciences, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Bluma J Lesch
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Department of Obstetrics, Gynecology & Reproductive Sciences, Yale University School of Medicine, New Haven, Connecticut 06510, USA
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21
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Kim D, Biancon G, Bai Z, VanOudenhove J, Liu Y, Kothari S, Gowda L, Kwan JM, Buitrago-Pocasangre NC, Lele N, Asashima H, Racke MK, Wilson JE, Givens TS, Tomayko MM, Schulz WL, Longbrake EE, Hafler DA, Halene S, Fan R. Microfluidic immuno-serology assay revealed a limited diversity of protection against COVID-19 in patients with altered immunity. bioRxiv 2022:2022.08.31.506117. [PMID: 36093346 PMCID: PMC9460970 DOI: 10.1101/2022.08.31.506117] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The immune response to SARS-CoV-2 for patients with altered immunity such as hematologic malignancies and autoimmune disease may differ substantially from that in general population. These patients remain at high risk despite wide-spread adoption of vaccination. It is critical to examine the differences at the systems level between the general population and the patients with altered immunity in terms of immunologic and serological responses to COVID-19 infection and vaccination. Here, we developed a novel microfluidic chip for high-plex immuno-serological assay to simultaneously measure up to 50 plasma or serum samples for up to 50 soluble markers including 35 plasma proteins, 11 anti-spike/RBD IgG antibodies spanning all major variants, and controls. Our assay demonstrated the quintuplicate test in a single run with high throughput, low sample volume input, high reproducibility and high accuracy. It was applied to the measurement of 1,012 blood samples including in-depth analysis of sera from 127 patients and 21 healthy donors over multiple time points, either with acute COVID infection or vaccination. The protein association matrix analysis revealed distinct immune mediator protein modules that exhibited a reduced degree of diversity in protein-protein cooperation in patients with hematologic malignancies and patients with autoimmune disorders receiving B cell depletion therapy. Serological analysis identified that COVID infected patients with hematologic malignancies display impaired anti-RBD antibody response despite high level of anti-spike IgG, which could be associated with limited clonotype diversity and functional deficiency in B cells and was further confirmed by single-cell BCR and transcriptome sequencing. These findings underscore the importance to individualize immunization strategy for these high-risk patients and provide an informative tool to monitor their responses at the systems level.
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Affiliation(s)
- Dongjoo Kim
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Giulia Biancon
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA
| | - Zhiliang Bai
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Jennifer VanOudenhove
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA
| | - Yuxin Liu
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA
| | - Shalin Kothari
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA
| | - Lohith Gowda
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA
| | - Jennifer M Kwan
- Cardiovascular Medicine, Yale School of Medicine, New Haven, CT 06520, USA
| | | | - Nikhil Lele
- Department of Neurology, Yale University, New Haven, CT 06520, USA
| | | | | | | | | | - Mary M Tomayko
- Departments of Dermatology, Yale University, New Haven, CT 06520, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Wade L Schulz
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA
| | - Erin E Longbrake
- Department of Neurology, Yale University, New Haven, CT 06520, USA
| | - David A Hafler
- Department of Neurology, Yale University, New Haven, CT 06520, USA
- Department of Immunobiology, Yale University, New Haven, CT 06520, USA
| | - Stephanie Halene
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
- Yale Center for RNA Science and Medicine, Yale School of Medicine, New Haven, CT 06520, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
- Human and Translational Immunology, Yale School of Medicine, New Haven, CT 06520, USA
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22
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Deng Y, Bartosovic M, Ma S, Zhang D, Kukanja P, Xiao Y, Su G, Liu Y, Qin X, Rosoklija GB, Dwork AJ, Mann JJ, Xu ML, Halene S, Craft JE, Leong KW, Boldrini M, Castelo-Branco G, Fan R. Spatial profiling of chromatin accessibility in mouse and human tissues. Nature 2022; 609:375-383. [PMID: 35978191 PMCID: PMC9452302 DOI: 10.1038/s41586-022-05094-1] [Citation(s) in RCA: 91] [Impact Index Per Article: 45.5] [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: 08/05/2021] [Accepted: 07/08/2022] [Indexed: 12/12/2022]
Abstract
Cellular function in tissue is dependent on the local environment, requiring new methods for spatial mapping of biomolecules and cells in the tissue context1. The emergence of spatial transcriptomics has enabled genome-scale gene expression mapping2-5, but the ability to capture spatial epigenetic information of tissue at the cellular level and genome scale is lacking. Here we describe a method for spatially resolved chromatin accessibility profiling of tissue sections using next-generation sequencing (spatial-ATAC-seq) by combining in situ Tn5 transposition chemistry6 and microfluidic deterministic barcoding5. Profiling mouse embryos using spatial-ATAC-seq delineated tissue-region-specific epigenetic landscapes and identified gene regulators involved in the development of the central nervous system. Mapping the accessible genome in the mouse and human brain revealed the intricate arealization of brain regions. Applying spatial-ATAC-seq to tonsil tissue resolved the spatially distinct organization of immune cell types and states in lymphoid follicles and extrafollicular zones. This technology progresses spatial biology by enabling spatially resolved chromatin accessibility profiling to improve our understanding of cell identity, cell state and cell fate decision in relation to epigenetic underpinnings in development and disease.
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Affiliation(s)
- Yanxiang Deng
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Marek Bartosovic
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Sai Ma
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Di Zhang
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Petra Kukanja
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Yang Xiao
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Graham Su
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Yang Liu
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Xiaoyu Qin
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Gorazd B Rosoklija
- Department of Psychiatry, Columbia University, New York, NY, USA
- Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY, USA
- Macedonian Academy of Sciences & Arts, Skopje, Republic of Macedonia
| | - Andrew J Dwork
- Department of Psychiatry, Columbia University, New York, NY, USA
- Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY, USA
- Macedonian Academy of Sciences & Arts, Skopje, Republic of Macedonia
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - J John Mann
- Department of Psychiatry, Columbia University, New York, NY, USA
- Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY, USA
- Department of Radiology, Columbia University, New York, NY, USA
| | - Mina L Xu
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Stephanie Halene
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
- Section of Hematology, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
- Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Joseph E Craft
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Kam W Leong
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Maura Boldrini
- Department of Psychiatry, Columbia University, New York, NY, USA
- Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY, USA
| | - Gonçalo Castelo-Branco
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden.
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA.
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA.
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA.
- Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT, USA.
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23
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Sefik E, Qu R, Junqueira C, Kaffe E, Mirza H, Zhao J, Brewer JR, Han A, Steach HR, Israelow B, Blackburn HN, Velazquez SE, Chen YG, Halene S, Iwasaki A, Meffre E, Nussenzweig M, Lieberman J, Wilen CB, Kluger Y, Flavell RA. Inflammasome activation in infected macrophages drives COVID-19 pathology. Nature 2022; 606:585-593. [PMID: 35483404 PMCID: PMC9288243 DOI: 10.1038/s41586-022-04802-1] [Citation(s) in RCA: 225] [Impact Index Per Article: 112.5] [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: 07/30/2021] [Accepted: 04/25/2022] [Indexed: 01/18/2023]
Abstract
Severe COVID-19 is characterized by persistent lung inflammation, inflammatory cytokine production, viral RNA and a sustained interferon (IFN) response, all of which are recapitulated and required for pathology in the SARS-CoV-2-infected MISTRG6-hACE2 humanized mouse model of COVID-19, which has a human immune system1-20. Blocking either viral replication with remdesivir21-23 or the downstream IFN-stimulated cascade with anti-IFNAR2 antibodies in vivo in the chronic stages of disease attenuates the overactive immune inflammatory response, especially inflammatory macrophages. Here we show that SARS-CoV-2 infection and replication in lung-resident human macrophages is a critical driver of disease. In response to infection mediated by CD16 and ACE2 receptors, human macrophages activate inflammasomes, release interleukin 1 (IL-1) and IL-18, and undergo pyroptosis, thereby contributing to the hyperinflammatory state of the lungs. Inflammasome activation and the accompanying inflammatory response are necessary for lung inflammation, as inhibition of the NLRP3 inflammasome pathway reverses chronic lung pathology. Notably, this blockade of inflammasome activation leads to the release of infectious virus by the infected macrophages. Thus, inflammasomes oppose host infection by SARS-CoV-2 through the production of inflammatory cytokines and suicide by pyroptosis to prevent a productive viral cycle.
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Affiliation(s)
- Esen Sefik
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Rihao Qu
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
| | - Caroline Junqueira
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
| | - Eleanna Kaffe
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Haris Mirza
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Jun Zhao
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - J Richard Brewer
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Ailin Han
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Holly R Steach
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Benjamin Israelow
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Holly N Blackburn
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Surgery, Yale University School of Medicine, New Haven, CT, USA
| | - Sofia E Velazquez
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Y Grace Chen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Stephanie Halene
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Eric Meffre
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Michel Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Judy Lieberman
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Craig B Wilen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Yuval Kluger
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
- Program of Applied Mathematics, Yale University, New Haven, CT, USA
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA.
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24
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Sefik E, Israelow B, Mirza H, Zhao J, Qu R, Kaffe E, Song E, Halene S, Meffre E, Kluger Y, Nussenzweig M, Wilen CB, Iwasaki A, Flavell RA. A humanized mouse model of chronic COVID-19. Nat Biotechnol 2022; 40:906-920. [PMID: 34921308 PMCID: PMC9203605 DOI: 10.1038/s41587-021-01155-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [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: 02/26/2021] [Accepted: 11/05/2021] [Indexed: 12/15/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is an infectious disease that can present as an uncontrolled, hyperactive immune response, causing severe immunological injury. Existing rodent models do not recapitulate the sustained immunopathology of patients with severe disease. Here we describe a humanized mouse model of COVID-19 that uses adeno-associated virus to deliver human ACE2 to the lungs of humanized MISTRG6 mice. This model recapitulates innate and adaptive human immune responses to severe acute respiratory syndrome coronavirus 2 infection up to 28 days after infection, with key features of chronic COVID-19, including weight loss, persistent viral RNA, lung pathology with fibrosis, a human inflammatory macrophage response, a persistent interferon-stimulated gene signature and T cell lymphopenia. We used this model to study two therapeutics on immunopathology, patient-derived antibodies and steroids and found that the same inflammatory macrophages crucial to containing early infection later drove immunopathology. This model will enable evaluation of COVID-19 disease mechanisms and treatments.
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Affiliation(s)
- Esen Sefik
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Benjamin Israelow
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
| | - Haris Mirza
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Jun Zhao
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Rihao Qu
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Eleanna Kaffe
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Eric Song
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Stephanie Halene
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Eric Meffre
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Yuval Kluger
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Michel Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Craig B Wilen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA.
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25
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Glasser E, Maji D, Biancon G, Puthenpeedikakkal A, Cavender C, Tebaldi T, Jenkins J, Mathews D, Halene S, Kielkopf C. Pre-mRNA splicing factor U2AF2 recognizes distinct conformations of nucleotide variants at the center of the pre-mRNA splice site signal. Nucleic Acids Res 2022; 50:5299-5312. [PMID: 35524551 PMCID: PMC9128377 DOI: 10.1093/nar/gkac287] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/03/2022] [Accepted: 04/12/2022] [Indexed: 11/24/2022] Open
Abstract
The essential pre-mRNA splicing factor U2AF2 (also called U2AF65) identifies polypyrimidine (Py) tract signals of nascent transcripts, despite length and sequence variations. Previous studies have shown that the U2AF2 RNA recognition motifs (RRM1 and RRM2) preferentially bind uridine-rich RNAs. Nonetheless, the specificity of the RRM1/RRM2 interface for the central Py tract nucleotide has yet to be investigated. We addressed this question by determining crystal structures of U2AF2 bound to a cytidine, guanosine, or adenosine at the central position of the Py tract, and compared U2AF2-bound uridine structures. Local movements of the RNA site accommodated the different nucleotides, whereas the polypeptide backbone remained similar among the structures. Accordingly, molecular dynamics simulations revealed flexible conformations of the central, U2AF2-bound nucleotide. The RNA binding affinities and splicing efficiencies of structure-guided mutants demonstrated that U2AF2 tolerates nucleotide substitutions at the central position of the Py tract. Moreover, enhanced UV-crosslinking and immunoprecipitation of endogenous U2AF2 in human erythroleukemia cells showed uridine-sensitive binding sites, with lower sequence conservation at the central nucleotide positions of otherwise uridine-rich, U2AF2-bound splice sites. Altogether, these results highlight the importance of RNA flexibility for protein recognition and take a step towards relating splice site motifs to pre-mRNA splicing efficiencies.
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Affiliation(s)
- Eliezra Glasser
- Department of Biochemistry and Biophysics, and the Center for
RNA Biology, University of Rochester School of Medicine and
Dentistry, Rochester,
NY 14642, USA
| | - Debanjana Maji
- Department of Biochemistry and Biophysics, and the Center for
RNA Biology, University of Rochester School of Medicine and
Dentistry, Rochester,
NY 14642, USA
| | - Giulia Biancon
- Section of Hematology, Department of Internal Medicine and
Yale Cancer Center, Yale University School of Medicine,
New Haven,
CT 06520, USA
| | | | - Chapin E Cavender
- Department of Biochemistry and Biophysics, and the Center for
RNA Biology, University of Rochester School of Medicine and
Dentistry, Rochester,
NY 14642, USA
| | - Toma Tebaldi
- Section of Hematology, Department of Internal Medicine and
Yale Cancer Center, Yale University School of Medicine,
New Haven,
CT 06520, USA
- Department of Cellular, Computational and Integrative Biology
(CIBIO), University of
Trento, Trento, Italy
| | - Jermaine L Jenkins
- Department of Biochemistry and Biophysics, and the Center for
RNA Biology, University of Rochester School of Medicine and
Dentistry, Rochester,
NY 14642, USA
| | - David H Mathews
- Department of Biochemistry and Biophysics, and the Center for
RNA Biology, University of Rochester School of Medicine and
Dentistry, Rochester,
NY 14642, USA
| | - Stephanie Halene
- Section of Hematology, Department of Internal Medicine and
Yale Cancer Center, Yale University School of Medicine,
New Haven,
CT 06520, USA
- Yale Center for RNA Science and Medicine, Yale University
School of Medicine, New Haven,
CT 06520, USA
- Department of Pathology, Yale University School of
Medicine, New Haven,
CT 06520, USA
| | - Clara L Kielkopf
- Department of Biochemistry and Biophysics, and the Center for
RNA Biology, University of Rochester School of Medicine and
Dentistry, Rochester,
NY 14642, USA
- Wilmot Cancer Institute, University of Rochester School of
Medicine and Dentistry, Rochester,
NY 14642, USA
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26
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Shallis RM, Bewersdorf JP, Stahl MF, Halene S, Zeidan AM. Are We Moving the Needle for Patients with TP53-Mutated Acute Myeloid Leukemia? Cancers (Basel) 2022; 14:2434. [PMID: 35626039 PMCID: PMC9140008 DOI: 10.3390/cancers14102434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/06/2022] [Accepted: 05/11/2022] [Indexed: 12/12/2022] Open
Abstract
The currently available therapeutic options for patients with TP53-mutated acute myeloid leukemia (AML) are insufficient, as they translate to a median overall of only 6-9 months, and less than 10% of patients undergoing the most aggressive treatments, such as intensive induction therapy and allogeneic hematopoietic stem cell transplantation, will be cured. The lack of clear differences in outcomes with different treatments precludes the designation of a standard of care. Recently, there has been growing attention on this critical area of need by way of better understanding the biology of TP53 alterations and the disparities in outcomes among patients in this molecular subgroup, reflected in the development and testing of agents with novel mechanisms of action. Promising preclinical and efficacy data exist for therapies that are directed at the p53 protein rendered dysfunctional via mutation or that inhibit the CD47/SIRPα axis or other immune checkpoints such as TIM-3. In this review, we discuss recently attractive and emerging therapeutic agents, their preclinical rationale and the available clinical data as a monotherapy or in combination with the currently accepted backbones in frontline and relapsed/refractory settings for patients with TP53-mutated AML.
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Affiliation(s)
- Rory M. Shallis
- Section of Hematology, Department of Internal Medicine, Yale University School of Medicine and Yale Cancer Center, New Haven, CT 06520, USA; (R.M.S.); (S.H.)
| | - Jan P. Bewersdorf
- Division of Hematologic Malignancies, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA;
| | - Maximilian F. Stahl
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA;
| | - Stephanie Halene
- Section of Hematology, Department of Internal Medicine, Yale University School of Medicine and Yale Cancer Center, New Haven, CT 06520, USA; (R.M.S.); (S.H.)
| | - Amer M. Zeidan
- Section of Hematology, Department of Internal Medicine, Yale University School of Medicine and Yale Cancer Center, New Haven, CT 06520, USA; (R.M.S.); (S.H.)
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27
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Figueiredo JC, Hirsch FR, Kushi LH, Nembhard WN, Crawford JM, Mantis N, Finster L, Merin NM, Merchant A, Reckamp KL, Melmed GY, Braun J, McGovern D, Parekh S, Corley DA, Zohoori N, Amick BC, Du R, Gregersen PK, Diamond B, Taioli E, Sariol C, Espino A, Weiskopf D, Gifoni A, Brien J, Hanege W, Lipsitch M, Zidar DA, McAlearney AS, Wajnberg A, LaBaer J, Lewis EY, Binder RA, Moormann AM, Forconi C, Forrester S, Batista J, Schieffelin J, Kim D, Biancon G, VanOudenhove J, Halene S, Fan R, Barouch DH, Alter G, Pinninti S, Boppana SB, Pati SK, Latting M, Karaba AH, Roback J, Sekaly R, Neish A, Brincks AM, Granger DA, Karger AB, Thyagarajan B, Thomas SN, Klein SL, Cox AL, Lucas T, Furr-Holden D, Key K, Jones N, Wrammerr J, Suthar M, Yu Wong S, Bowman NM, Simon V, Richardson LD, McBride R, Krammer F, Rana M, Kennedy J, Boehme K, Forrest C, Granger SW, Heaney CD, Knight Lapinski M, Wallet S, Baric RS, Schifanella L, Lopez M, Fernández S, Kenah E, Panchal AR, Britt WJ, Sanz I, Dhodapkar M, Ahmed R, Bartelt LA, Markmann AJ, Lin JT, Hagan RS, Wolfgang MC, Skarbinski J. Mission, Organization and Future Direction of the Serological Sciences Network for COVID-19 (SeroNet) Epidemiologic Cohort Studies. Open Forum Infect Dis 2022; 9:ofac171. [PMID: 35765315 PMCID: PMC9129196 DOI: 10.1093/ofid/ofac171] [Citation(s) in RCA: 2] [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: 01/11/2022] [Accepted: 04/22/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
Global efforts are needed to elucidate the epidemiology of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the underlying cause of coronavirus disease 2019 (COVID-19) including seroprevalence, risk factors and long-term sequelae, as well as immune responses following vaccination across populations and the social dimensions of prevention and treatment strategies. In the U.S., the National Cancer Institute in partnership with the National Institute of Allergy and Infectious Diseases, established the SARS-CoV-2 Serological Sciences Network (SeroNet) as the nation’s largest coordinated effort to study COVID-19. The network is comprised of multidisciplinary researchers bridging gaps and fostering collaborations between immunologists, epidemiologists, virologists, clinicians and clinical laboratories, social and behavioral scientists, policy makers, data scientists, and community members. In total, 49 institutions form the SeroNet consortium to study individuals with cancer, autoimmune disease, inflammatory bowel diseases, cardiovascular diseases, HIV, transplant recipients, as well as otherwise healthy pregnant women, children, college students, and high-risk occupational workers (including health care workers and first responders). Several studies focus on underrepresented populations, including ethnic minorities and rural communities. To support integrative data analyses across SeroNet studies, efforts are underway to define common data elements for standardized serology measurements, cellular and molecular assays, self-reported data, treatment, and clinical outcomes. In this paper, we discuss the overarching framework for SeroNet epidemiology studies, critical research questions under investigation, and data accessibility for the worldwide scientific community. Lessons learned will help inform preparedness and responsiveness to future emerging diseases.
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Affiliation(s)
- Jane C Figueiredo
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Fred R Hirsch
- Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lawrence H Kushi
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Wendy N Nembhard
- Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - James M Crawford
- Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Nicholas Mantis
- Division of Infectious Diseases Wadsworth Center, New York State Department of Health, New York, NY, USA
| | - Laurel Finster
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Noah M Merin
- Division of Hematology and Cellular Therapy, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Akil Merchant
- Division of Hematology and Cellular Therapy, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Karen L Reckamp
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Gil Y Melmed
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Los Angeles, CA, USA
| | - Jonathan Braun
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Los Angeles, CA, USA
| | - Dermot McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Los Angeles, CA, USA
| | - Samir Parekh
- Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Douglas A Corley
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Namvar Zohoori
- Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Benjamin C Amick
- Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Ruofei Du
- Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Peter K Gregersen
- Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Betty Diamond
- Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Emanuela Taioli
- Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carlos Sariol
- Unit of Comparative Medicine, University of Puerto Rico, Medical Sciences, San Juan, PR
| | - Ana Espino
- Unit of Comparative Medicine, University of Puerto Rico, Medical Sciences, San Juan, PR
| | | | - Alba Gifoni
- La Jolla Institute of Immunology, La Jolla CA, USA
| | - James Brien
- Department of Molecular Microbiology & Immunology, Saint Louis University, St. Louis MI, USA
| | - William Hanege
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Bethesda, MD, USA
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Bethesda, MD, USA
| | - David A Zidar
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Ann Scheck McAlearney
- Department of Family and Community Medicine, Ohio State University College of Medicine, Columbus, OH, USA
| | - Ania Wajnberg
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joshua LaBaer
- Biodesign Virginia G. Piper Center for Personalized Diagnostics, Arizona State University, Tempe AZ, USA
| | - E Yvonne Lewis
- Department of Public Health, Michigan State University, Flint, MI, USA
| | - Raquel A Binder
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Ann M Moormann
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Catherine Forconi
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Sarah Forrester
- Department of Population and Quantitative Health Sciences, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jennifer Batista
- Department of Population and Quantitative Health Sciences, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - John Schieffelin
- Department of Pediatrics, Tulane University School of Medicine, New Orleans, LA, USA
| | - Dongjoo Kim
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Giulia Biancon
- Section of Hematology, Department of Internal Medicine and Yale Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Jennifer VanOudenhove
- Section of Hematology, Department of Internal Medicine and Yale Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Stephanie Halene
- Section of Hematology, Department of Internal Medicine and Yale Cancer Center, Yale University School of Medicine, New Haven, CT, USA
- Yale Cancer Center, New Haven, CT, USA
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Yale Cancer Center, New Haven, CT, USA
| | - Dan H Barouch
- The Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Galit Alter
- Ragon Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Swetha Pinninti
- Department of Pediatrics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Suresh B Boppana
- Department of Pediatrics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Sunil K Pati
- Department of Pediatrics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Misty Latting
- Department of Pediatrics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Andrew H Karaba
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University, Baltimore, MD, USA
| | - John Roback
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Rafick Sekaly
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Andrew Neish
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Ahnalee M Brincks
- Department of Human Development and Family Studies, College of Social Science, Michigan State University, East Lansing, MI, USA
| | - Douglas A Granger
- Institute for Interdisciplinary Salivary Bioscience Research, University of California at Irvine; Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Amy B Karger
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Bharat Thyagarajan
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Stefani N Thomas
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Sabra L Klein
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Andrea L Cox
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University, Baltimore, MD, USA
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Todd Lucas
- Division of Public Health, College of Human Medicine, Michigan State University, East Lansing, MI, USA
| | - Debra Furr-Holden
- Division of Public Health, College of Human Medicine, Michigan State University, East Lansing, MI, USA
| | - Kent Key
- Division of Public Health, College of Human Medicine, Michigan State University, East Lansing, MI, USA
| | - Nicole Jones
- Division of Public Health, College of Human Medicine, Michigan State University, East Lansing, MI, USA
| | - Jens Wrammerr
- Department of Pediatrics, Division of Infectious Disease, Emory University, Atlanta, GA, USA
| | - Mehul Suthar
- Department of Pediatrics, Division of Infectious Disease, Emory University, Atlanta, GA, USA
| | - Serre Yu Wong
- The Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Natalie M Bowman
- University of North Carolina School of Medicine, Division of Infectious Diseases, Chapel Hill, NC, USA
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lynne D Richardson
- Institute for Health Equity Research and Department of Emergency Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Russell McBride
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Meenakshi Rana
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joshua Kennedy
- Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Karl Boehme
- Department of Microbiology and Immunology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Craig Forrest
- Department of Microbiology and Immunology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | | | - Christopher D Heaney
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Maria Knight Lapinski
- Department of Communication, Michigan AgBio Research, Michigan State University, East Lansing, MI, USA
| | - Shannon Wallet
- School of Dentistry, Department of Oral and Craniofacial Health Sciences, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Ralph S Baric
- Gillings School of Global Public Health, Department of Epidemiology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Luca Schifanella
- Division of Surgical Outcomes and Precision Medicine Research, Department of Surgery, University of Minnesota, Minneapolis, MN, USA
| | - Marcos Lopez
- Puerto Rico Public Health Trust, Puerto Rico Science, Technology and Research Trust and University of Puerto Rico at Humacao, Medical Sciences, San Juan, PR, USA
| | - Soledad Fernández
- Department of Biomedical Informatics, Center for Biostatistics, Ohio State University College of Medicine, Columbus, OH, USA
| | - Eben Kenah
- Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, OH, USA
| | - Ashish R Panchal
- Department of Emergency Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - William J Britt
- Department of Immunology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Iñaki Sanz
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Madhav Dhodapkar
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Rafi Ahmed
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Luther A Bartelt
- Department of Medicine, Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Alena J Markmann
- Department of Medicine, Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Jessica T Lin
- Department of Medicine, Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Robert S Hagan
- Department of Medicine, Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Matthew C Wolfgang
- Marsico Lung Institute and Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Jacek Skarbinski
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
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28
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Abstract
Myelodysplastic syndromes (MDS) are a heterogeneous group of clonal bone-marrow diseases with ineffective hematopoiesis resulting in cytopenias and morphologic dysplasia of hematopoietic cells. MDS carry a wide spectrum of genetic abnormalities, ranging from chromosomal abnormalities such as deletions/additions, to recurrent mutations affecting the spliceosome, epigenetic modifiers, or transcription factors. As opposed to AML, research in MDS has been hindered by the lack of preclinical models that faithfully replicate the complexity of the disease and capture the heterogeneity. The complex molecular landscape of the disease poses a unique challenge when creating transgenic mouse-models. In addition, primary MDS cells are difficult to manipulate ex vivo limiting in vitro studies and resulting in a paucity of cell lines and patient derived xenograft models. In recent years, progress has been made in the development of both transgenic and xenograft murine models advancing our understanding of individual contributors to MDS pathology as well as the complex primary interplay of genetic and microenvironment aberrations. We here present a comprehensive review of these transgenic and xenograft models for MDS and future directions.
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Affiliation(s)
- Wei Liu
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, United States
| | - Patric Teodorescu
- Department of Oncology, The Johns Hopkins Hospital, Johns Hopkins Medicine, Baltimore, MD, United States
| | - Stephanie Halene
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, United States
| | - Gabriel Ghiaur
- Department of Oncology, The Johns Hopkins Hospital, Johns Hopkins Medicine, Baltimore, MD, United States
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29
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Liu Y, DiStasio M, Su G, Asashima H, Enninful A, Qin X, Deng Y, Bordignon P, Cassano M, Tomayko M, Xu M, Halene S, Craft JE, Hafler D, Fan R. Spatial-CITE-seq: spatially resolved high-plex protein and whole transcriptome co-mapping. Res Sq 2022:rs.3.rs-1499315. [PMID: 35378748 PMCID: PMC8978952 DOI: 10.21203/rs.3.rs-1499315/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We present spatial-CITE-seq for high-plex protein and whole transcriptome co-mapping, which was firstly demonstrated for profiling 198 proteins and transcriptome in multiple mouse tissue types. It was then applied to human tissues to measure 283 proteins and transcriptome that revealed spatially distinct germinal center reaction in tonsil and early immune activation in skin at the COVID-19 mRNA vaccine injection site. Spatial-CITE-seq may find a range of applications in biomedical research.
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Affiliation(s)
- Yang Liu
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Marcello DiStasio
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Graham Su
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Hiromitsu Asashima
- Department of Neurology, Yale School of Medicine, New Haven, CT 06520, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Archibald Enninful
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Xiaoyu Qin
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Yanxiang Deng
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Pino Bordignon
- Lunaphore Technologies SA, Route de Lully 5c, 1131 Tolochenaz, Switzerland
| | - Marco Cassano
- Lunaphore Technologies SA, Route de Lully 5c, 1131 Tolochenaz, Switzerland
| | - Mary Tomayko
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
- Department of Dermatology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Mina Xu
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Stephanie Halene
- Department of Medicine, Yale School of Medicine, New Haven, CT 06520, USA
| | - Joseph E. Craft
- Department of Medicine, Yale School of Medicine, New Haven, CT 06520, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
- Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT 06520, USA
| | - David Hafler
- Department of Neurology, Yale School of Medicine, New Haven, CT 06520, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
- Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT 06520, USA
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
- Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT 06520, USA
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30
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Biancon G, Joshi P, Zimmer JT, Hunck T, Gao Y, Lessard MD, Courchaine E, Barentine AES, Machyna M, Botti V, Qin A, Gbyli R, Patel A, Song Y, Kiefer L, Viero G, Neuenkirchen N, Lin H, Bewersdorf J, Simon MD, Neugebauer KM, Tebaldi T, Halene S. Precision analysis of mutant U2AF1 activity reveals deployment of stress granules in myeloid malignancies. Mol Cell 2022; 82:1107-1122.e7. [PMID: 35303483 PMCID: PMC8988922 DOI: 10.1016/j.molcel.2022.02.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [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: 06/29/2021] [Revised: 12/21/2021] [Accepted: 02/15/2022] [Indexed: 12/13/2022]
Abstract
Splicing factor mutations are common among cancers, recently emerging as drivers of myeloid malignancies. U2AF1 carries hotspot mutations in its RNA-binding motifs; however, how they affect splicing and promote cancer remain unclear. The U2AF1/U2AF2 heterodimer is critical for 3' splice site (3'SS) definition. To specifically unmask changes in U2AF1 function in vivo, we developed a crosslinking and immunoprecipitation procedure that detects contacts between U2AF1 and the 3'SS AG at single-nucleotide resolution. Our data reveal that the U2AF1 S34F and Q157R mutants establish new 3'SS contacts at -3 and +1 nucleotides, respectively. These effects compromise U2AF2-RNA interactions, resulting predominantly in intron retention and exon exclusion. Integrating RNA binding, splicing, and turnover data, we predicted that U2AF1 mutations directly affect stress granule components, which was corroborated by single-cell RNA-seq. Remarkably, U2AF1-mutant cell lines and patient-derived MDS/AML blasts displayed a heightened stress granule response, pointing to a novel role for biomolecular condensates in adaptive oncogenic strategies.
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Affiliation(s)
- Giulia Biancon
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA.
| | - Poorval Joshi
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Joshua T Zimmer
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT, USA
| | - Torben Hunck
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Yimeng Gao
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Mark D Lessard
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Edward Courchaine
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - Andrew E S Barentine
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA; Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Martin Machyna
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - Valentina Botti
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - Ashley Qin
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Rana Gbyli
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Amisha Patel
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Yuanbin Song
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA; Department of Hematologic Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Lea Kiefer
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | | | - Nils Neuenkirchen
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA
| | - Haifan Lin
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA; Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA; Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA; Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA; Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Toma Tebaldi
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA; Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy.
| | - Stephanie Halene
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA; Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT, USA; Department of Pathology, Yale University School of Medicine, New Haven, CT, USA.
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31
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Gbyli R, Song Y, Liu W, Gao Y, Biancon G, Chandhok NS, Wang X, Fu X, Patel A, Sundaram R, Tebaldi T, Mamillapalli P, Zeidan AM, Flavell RA, Prebet T, Bindra RS, Halene S. In vivo anti-tumor effect of PARP inhibition in IDH1/2 mutant MDS/AML resistant to targeted inhibitors of mutant IDH1/2. Leukemia 2022; 36:1313-1323. [PMID: 35273342 PMCID: PMC9103411 DOI: 10.1038/s41375-022-01536-x] [Citation(s) in RCA: 2] [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: 08/09/2021] [Revised: 02/11/2022] [Accepted: 02/17/2022] [Indexed: 11/25/2022]
Abstract
Treatment options for patients with relapsed/ refractory acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS) are scarce. Recurring mutations, such as mutations in isocitrate dehydrogenase-1 and −2 (IDH1/2) are found in subsets of AML and MDS, are therapeutically targeted by mutant enzyme-specific small molecule inhibitors (IDHmi). IDH mutations induce diverse metabolic and epigenetic changes that drive malignant transformation. IDHmi alone are not curative and resistance commonly develops, underscoring the importance of alternate therapeutic options. We were first to report that IDH1/2 mutations induce a homologous recombination (HR) defect which confers sensitivity to poly (ADP)-ribose polymerase inhibitors (PARPi). Here, we show that the PARPi olaparib is effective against primary patient-derived IDH1/2-mutant AML/ MDS xeno-grafts (PDXs). Olaparib efficiently reduced overall engraftment and leukemia-initiating cell frequency as evident in serial transplantation assays in IDH1/2-mutant but not -wildtype AML/MDS PDXs. Importantly, we show that olaparib is effective in both IDHmi-naïve and -resistant AML PDXs, critical given the high relapse and refractoriness rates to IDHmi. Our pre-clinical studies provide a strong rationale for the translation of PARP inhibition to patients with IDH1/2-mutant AML/ MDS, providing an additional line of therapy for patients who do not respond to or relapse after targeted mutant IDH inhibition.
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Affiliation(s)
- Rana Gbyli
- Section of Hematology, Department of Internal Medicine and Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Yuanbin Song
- Section of Hematology, Department of Internal Medicine and Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, 06520, USA. .,Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510062, China.
| | - Wei Liu
- Section of Hematology, Department of Internal Medicine and Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Yimeng Gao
- Section of Hematology, Department of Internal Medicine and Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Giulia Biancon
- Section of Hematology, Department of Internal Medicine and Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Namrata S Chandhok
- Section of Hematology, Department of Internal Medicine and Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, 06520, USA.,Section of Hematology, Department of Internal Medicine, University of Miami, Sylvester Comprehensive Cancer Center, Miami, FL, USA
| | - Xiaman Wang
- Section of Hematology, Department of Internal Medicine and Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, 06520, USA.,Department of Hematology, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, P. R. of China
| | - Xiaoying Fu
- Section of Hematology, Department of Internal Medicine and Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, 06520, USA.,Department of Laboratory Medicine, Shenzhen Children's Hospital, Shenzhen, P. R. of China
| | - Amisha Patel
- Section of Hematology, Department of Internal Medicine and Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Ranjini Sundaram
- Department of Therapeutic Radiology, Yale University, New Haven, CT, 06520, USA
| | - Toma Tebaldi
- Section of Hematology, Department of Internal Medicine and Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, 06520, USA.,Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, 38121, Italy
| | - Padmavathi Mamillapalli
- Section of Hematology, Department of Internal Medicine and Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Amer M Zeidan
- Section of Hematology, Department of Internal Medicine and Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.,Howard Hughes Medical Institute, Yale University, New Haven, Connecticut, USA
| | - Thomas Prebet
- Section of Hematology, Department of Internal Medicine and Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Ranjit S Bindra
- Department of Therapeutic Radiology, Yale University, New Haven, CT, 06520, USA.,Department of Pathology, Yale University, New Haven, CT, 06520, USA
| | - Stephanie Halene
- Section of Hematology, Department of Internal Medicine and Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, 06520, USA. .,Department of Pathology, Yale University, New Haven, CT, 06520, USA. .,Yale Stem Cell Center and Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT, 06520, USA.
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32
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Kwan J, Vanoudenhove J, Halder S, Biancon G, Jain K, Chakraborty R, Lustberg M, Pusztai L, Campbell S, Zhao H, Halene S, Hwa J. MYOCARDIAL IMPACT OF CLONAL HEMATOPOIESIS OF INDETERMINATE POTENTIAL (CHIP) SECRETOMES IN CARDIO-ONCOLOGY PATIENTS. J Am Coll Cardiol 2022. [DOI: 10.1016/s0735-1097(22)02903-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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33
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Jawad M, Afkhami M, Ding Y, Zhang X, Li P, Young K, Xu ML, Cui W, Zhao Y, Halene S, Al-Kali A, Viswanatha D, Chen D, He R, Zheng G. DNMT3A R882 Mutations Confer Unique Clinicopathologic Features in MDS Including a High Risk of AML Transformation. Front Oncol 2022; 12:849376. [PMID: 35296003 PMCID: PMC8918526 DOI: 10.3389/fonc.2022.849376] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 01/31/2022] [Indexed: 01/14/2023] Open
Abstract
DNMT3A mutations play a prominent role in clonal hematopoiesis and myeloid neoplasms with arginine (R)882 as a hotspot, however the clinical implications of R882 vs. non-R882 mutations in myeloid neoplasms like myelodysplastic syndrome (MDS) is unclear. By data mining with publicly accessible cancer genomics databases and a clinical genomic database from a tertiary medical institution, DNMT3A R882 mutations were found to be enriched in AML (53% of all DNMT3A mutations) but decreased in frequency in clonal hematopoiesis of indeterminate potential (CHIP) (10.6%) or other myeloid neoplasms including MDS (27%) (p<.001). Next with the largest cohort of patients with DNMT3A R882 mutant MDS known to date from multiple institutions, DNMT3A R882 mutant MDS cases were shown to have more severe leukopenia, enriched SRSF2 and IDH2 mutations, increased cases with excess blasts (47% vs 22.5%, p=.004), markedly increased risk of AML transformation (25.8%, vs. 1.7%, p=.0001) and a worse progression-free survival (PFS) (median 20.3, vs. >50 months, p=.009) than non-R882 mutant MDS cases. DNMT3A R882 mutation is an independent risk factor for worse PFS, and importantly the differences in the risk of AML transformation between R882 vs. non-R882 mutant patients cannot be explained by different treatment approaches. Interestingly the higher risk of AML transformation and the worse PFS in DNMT3A R882 mutant MDS cases are mitigated by coexisting SF3B1 or SRSF2 mutations. The unique clinicopathologic features of DNMT3A R882 mutant MDS shed light on the prognostic and therapeutic implications of DNMT3A R882 mutations.
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Affiliation(s)
- Majd Jawad
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Michelle Afkhami
- Division of Molecular Pathology and Therapy Biomarkers, Department of Pathology, City of Hope Comprehensive Cancer Center, Duarte, CA, United States
- Division of Hematopathology, Department of Pathology, City of Hope Comprehensive Cancer Center, Duarte, CA, United States
| | - Yi Ding
- Department of Laboratory Medicine, Geisinger Health, Danville, PA, United States
| | - Xiaohui Zhang
- Department of Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Peng Li
- Department of Pathology, Associated Regional and University Pathologists (ARUP) Laboratories, Salt Lake City, UT, United States
| | - Kim Young
- Division of Hematopathology, Department of Pathology, City of Hope Comprehensive Cancer Center, Duarte, CA, United States
| | - Mina Luqing Xu
- Department of Pathology, Yale School of Medicine, New Haven, CT, United States
| | - Wei Cui
- Department of Pathology & Laboratory Medicine, The University of Kansas Medical Center, Kansas City, KS, United States
| | - Yiqing Zhao
- Department of Preventive Medicine, Northwestern University, Chicago, IL, United States
| | - Stephanie Halene
- Department of Internal Medicine, Division of Hematology, Yale School of Medicine, New Haven, CT, United States
| | - Aref Al-Kali
- Division of Hematology, Mayo Clinic, Rochester, MN, United States
| | - David Viswanatha
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Dong Chen
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Rong He
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Gang Zheng
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
- Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, United States
- *Correspondence: Gang Zheng,
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34
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Chupp G, Spichler-Moffarah A, Søgaard OS, Esserman D, Dziura J, Danzig L, Chaurasia R, Patra KP, Salovey A, Nunez A, May J, Astorino L, Patel A, Halene S, Wang J, Hui P, Patel P, Lu J, Li F, Gan G, Parziale S, Katsovich L, Desir GV, Vinetz JM. A Phase 2 Randomized, Double-Blind, Placebo-controlled Trial of Oral Camostat Mesylate for Early Treatment of COVID-19 Outpatients Showed Shorter Illness Course and Attenuation of Loss of Smell and Taste. medRxiv 2022:2022.01.28.22270035. [PMID: 35132421 PMCID: PMC8820673 DOI: 10.1101/2022.01.28.22270035] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Importance Early treatment of mild SARS-CoV-2 infection might lower the risk of clinical deterioration in COVID-19. Objective To determine whether oral camostat mesylate would reduce upper respiratory SARS-CoV-2 viral load in newly diagnosed outpatients with mild COVID-19, and would lead to improvement in COVID-19 symptoms. Design From June, 2020 to April, 2021, we conducted a randomized, double-blind, placebo-controlled phase 2 trial. Setting Single site, academic medical center, outpatient setting in Connecticut, USA. Participants Of 568 COVID-19 positive potential adult participants diagnosed within 3 days of study entry and assessed for eligibility, 70 were randomized and 498 were excluded (198 did not meet eligibility criteria, 37 were not interested, 265 were excluded for unknown or other reasons). The primary inclusion criteria were a positive SARS-CoV-2 nucleic acid amplification result in adults within 3 days of screening regardless of COVID-19 symptoms. Intervention Treatment was 7 days of oral camostat mesylate, 200 mg po four times a day, or placebo. Main Outcomes and Measures The primary outcome was reduction of 4-day log10 nasopharyngeal swab viral load by 0.5 log10 compared to placebo. The main prespecified secondary outcome was reduction in symptom scores as measured by a quantitative Likert scale instrument, Flu-PRO-Plus modified to measure changes in smell/taste measured using FLU-PRO-Plus. Results Participants receiving camostat had statistically significant lower quantitative symptom scores (FLU-Pro-Plus) at day 6, accelerated overall symptom resolution and notably improved taste/smell, and fatigue beginning at onset of intervention in the camostat mesylate group compared to placebo. Intention-to-treat analysis demonstrated that camostat mesylate was not associated with a reduction in 4-day log10 NP viral load compared to placebo. Conclusions and relevance The camostat group had more rapid resolution of COVID-19 symptoms and amelioration of the loss of taste and smell. Camostat compared to placebo was not associated with reduction in nasopharyngeal SARS-COV-2 viral load. Additional clinical trials are warranted to validate the role of camostat mesylate on SARS-CoV-2 infection in the treatment of mild COVID-19. Trial registration Clinicaltrials.gov, NCT04353284 (04/20/20)(https://clinicaltrials.gov/ct2/show/NCT04353284?term=camostat+%2C+yale&draw=2&rank=1).
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Affiliation(s)
- Geoffrey Chupp
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Anne Spichler-Moffarah
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Ole S. Søgaard
- Department of Clinical Medicine and Department of Infectious Diseases, Aarhus University, Aarhus, Denmark
| | - Denise Esserman
- Yale Center for Analytical Sciences, Yale School of Public Health, New Haven, CT, USA
| | - James Dziura
- Yale Center for Analytical Sciences, Yale School of Public Health, New Haven, CT, USA
| | | | - Reetika Chaurasia
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Kailash P. Patra
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Aryeh Salovey
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Angela Nunez
- Yale Center for Clinical Investigation, Yale School of Medicine, New Haven, CT, USA
| | - Jeanine May
- Yale Center for Clinical Investigation, Yale School of Medicine, New Haven, CT, USA
| | - Lauren Astorino
- Yale Center for Clinical Investigation, Yale School of Medicine, New Haven, CT, USA
| | - Amisha Patel
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Stephanie Halene
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Jianhui Wang
- Department of Pathology, Yale School of Medicine New Haven, CT, USA
| | - Pei Hui
- Department of Pathology, Yale School of Medicine New Haven, CT, USA
| | - Prashant Patel
- Investigation Drug Service, Yale New Haven Hospital, New Haven, CT, USA
| | - Jing Lu
- Investigation Drug Service, Yale New Haven Hospital, New Haven, CT, USA
| | - Fangyong Li
- Yale Center for Analytical Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Geliang Gan
- Yale Center for Analytical Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Stephen Parziale
- Yale Center for Analytical Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Lily Katsovich
- Yale Center for Analytical Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Gary V. Desir
- Investigation Drug Service, Yale New Haven Hospital, New Haven, CT, USA
| | - Joseph M. Vinetz
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
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35
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Li P, Biancon G, Patel T, Pan Z, Kothari S, Halene S, Prebet T, Xu ML. Comprehensive Clinicopathologic and Molecular Analysis of Mast Cell Leukemia With Associated Hematologic Neoplasm: A Report and In-Depth Study of 5 Cases. Front Oncol 2021; 11:730503. [PMID: 34589432 PMCID: PMC8474637 DOI: 10.3389/fonc.2021.730503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 06/25/2021] [Accepted: 08/17/2021] [Indexed: 12/02/2022] Open
Abstract
Mast cell leukemia with associated hematologic neoplasm (MCL-AHN) is a rare and highly aggressive entity that remains understudied due to the paucity of cases. We present a case of a 45-year-old man who was concurrently diagnosed with mast cell leukemia and acute myeloid leukemia. We identified four additional patients who had MCL-AHN in our institution and performed whole-exome sequencing of all available tumors. Our series revealed a novel and identical NR2F6 variant shared among two of the patients. This case series and sequencing results demonstrate the importance of fully characterizing rare tumors that are resistant to treatment.
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Affiliation(s)
- Philippa Li
- Department of Pathology, Yale School of Medicine, New Haven, CT, United States
| | - Giulia Biancon
- Section of Hematology, Department of Internal Medicine and Yale Comprehensive Cancer Center, Yale School of Medicine, New Haven, CT, United States
| | - Timil Patel
- Section of Hematology, Department of Internal Medicine and Yale Comprehensive Cancer Center, Yale School of Medicine, New Haven, CT, United States
| | - Zenggang Pan
- Department of Pathology, Yale School of Medicine, New Haven, CT, United States
| | - Shalin Kothari
- Section of Hematology, Department of Internal Medicine and Yale Comprehensive Cancer Center, Yale School of Medicine, New Haven, CT, United States
| | - Stephanie Halene
- Section of Hematology, Department of Internal Medicine and Yale Comprehensive Cancer Center, Yale School of Medicine, New Haven, CT, United States
| | - Thomas Prebet
- Section of Hematology, Department of Internal Medicine and Yale Comprehensive Cancer Center, Yale School of Medicine, New Haven, CT, United States
| | - Mina L Xu
- Department of Pathology, Yale School of Medicine, New Haven, CT, United States
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36
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Sefik E, Qu R, Kaffe E, Zhao J, Junqueira C, Mirza H, Brewer R, Han A, Steach H, Israelow B, Chen YG, Halene S, Iwasaki A, Meffre E, Nussenzweig M, Lieberman J, Wilen CB, Kluger Y, Flavell RA. Viral replication in human macrophages enhances an inflammatory cascade and interferon driven chronic COVID-19 in humanized mice. bioRxiv 2021. [PMID: 34611663 DOI: 10.1101/2021.09.27.461948] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Chronic COVID-19 is characterized by persistent viral RNA and sustained interferon (IFN) response which is recapitulated and required for pathology in SARS-CoV-2 infected MISTRG6-hACE2 humanized mice. As in the human disease, monocytes, and macrophages in SARS-CoV-2 infected MISTRG6-hACE2 are central to disease pathology. Here, we describe SARS-CoV-2 uptake in tissue resident human macrophages that is enhanced by virus specific antibodies. SARS-CoV-2 replicates in these human macrophages as evidenced by detection of double-stranded RNA, subgenomic viral RNA and expression of a virally encoded fluorescent reporter gene; and it is inhibited by Remdesivir, an inhibitor of viral replication. Although early IFN deficiency leads to enhanced disease, blocking either viral replication with Remdesivir or the downstream IFN stimulated cascade by injecting anti-IFNAR2 in vivo in the chronic stages of disease attenuates many aspects of the overactive immune-inflammatory response, especially the inflammatory macrophage response, and most consequentially, the chronic disease itself.
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37
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Kwan J, Lee S, Tao W, Wei W, Simonov M, Halene S, Hwa J, Baldassarre L. CARDIOVASCULAR AND MORTALITY OUTCOMES IN ONCOLOGY PATIENTS HOSPITALIZED WITH COVID-19. J Am Coll Cardiol 2021. [PMCID: PMC8091382 DOI: 10.1016/s0735-1097(21)04648-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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38
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Song Y, Shan L, Gbyli R, Liu W, Strowig T, Patel A, Fu X, Wang X, Xu ML, Gao Y, Qin A, Bruscia EM, Tebaldi T, Biancon G, Mamillapalli P, Urbonas D, Eynon E, Gonzalez DG, Chen J, Krause DS, Alderman J, Halene S, Flavell RA. Combined liver-cytokine humanization comes to the rescue of circulating human red blood cells. Science 2021; 371:1019-1025. [PMID: 33674488 DOI: 10.1126/science.abe2485] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 02/01/2021] [Indexed: 12/13/2022]
Abstract
In vivo models that recapitulate human erythropoiesis with persistence of circulating red blood cells (RBCs) have remained elusive. We report an immunodeficient murine model in which combined human liver and cytokine humanization confer enhanced human erythropoiesis and RBC survival in the circulation. We deleted the fumarylacetoacetate hydrolase (Fah) gene in MISTRG mice expressing several human cytokines in place of their murine counterparts. Liver humanization by intrasplenic injection of human hepatocytes (huHep) eliminated murine complement C3 and reduced murine Kupffer cell density. Engraftment of human sickle cell disease (SCD)-derived hematopoietic stem cells in huHepMISTRGFah -/- mice resulted in vaso-occlusion that replicated acute SCD pathology. Combined liver-cytokine-humanized mice will facilitate the study of diseases afflicting RBCs, including bone marrow failure, hemoglobinopathies, and malaria, and also preclinical testing of therapies.
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Affiliation(s)
- Yuanbin Song
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, and Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT, USA.,Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA.,Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Liang Shan
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA. .,Department of Medicine, Pathology and Immunology, Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | - Rana Gbyli
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, and Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT, USA.,Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA
| | - Wei Liu
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, and Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT, USA.,Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA
| | - Till Strowig
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.,Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Amisha Patel
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, and Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT, USA.,Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA
| | - Xiaoying Fu
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, and Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT, USA.,Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA.,Department of Laboratory Medicine, Shenzhen Children's Hospital, Shenzhen, People's Republic of China
| | - Xiaman Wang
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, and Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT, USA.,Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA.,Department of Hematology, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Mina L Xu
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Yimeng Gao
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, and Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT, USA.,Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA
| | - Ashley Qin
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, and Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT, USA.,Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA
| | - Emanuela M Bruscia
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Toma Tebaldi
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, and Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT, USA.,Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA.,Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Giulia Biancon
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, and Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT, USA.,Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA
| | - Padmavathi Mamillapalli
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, and Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT, USA.,Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA
| | - David Urbonas
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Elizabeth Eynon
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - David G Gonzalez
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Jie Chen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Diane S Krause
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA.,Department of Pathology, Yale University School of Medicine, New Haven, CT, USA.,Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Jonathan Alderman
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Stephanie Halene
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, and Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT, USA. .,Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA. .,Howard Hughes Medical Institute, Yale University, New Haven, CT, USA
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39
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Abstract
Double-stranded RNAs (dsRNAs) are abundantly present in cells, playing multiple regulatory functions. dsRNAs of viral origin activate innate immune responses. Since RNA editing and modifications affect the structure and recognition of RNAs, their alteration can result in the accumulation of aberrant endogenous dsRNAs inducing a deleterious innate immune response. Here, we present a complete protocol for the measurement of dsRNAs in a live mouse tissue using dsRNA immunoprecipitation and sequencing (dsRIP-Seq). This protocol focuses on tissue isolation, dsRNA immunoprecipitation and downstream computational analysis. For complete details on the use and execution of this protocol, please refer to Gao et al. (2020). Purification and sequencing of double-stranded RNAs (dsRNAs) in live tissues Open-source computational framework for the quantification and comparison of dsRNAs
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Affiliation(s)
- Yimeng Gao
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA.,Yale Stem Cell Center and Yale RNA Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Shirui Chen
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Stephanie Halene
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA.,Yale Stem Cell Center and Yale RNA Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Toma Tebaldi
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA.,Yale Stem Cell Center and Yale RNA Center, Yale University School of Medicine, New Haven, CT 06520, USA.,Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento 38123, Italy
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40
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Sefik E, Israelow B, Zhao J, Qu R, Song E, Mirza H, Kaffe E, Halene S, Meffre E, Kluger Y, Nussenzweig M, Wilen CB, Iwasaki A, Flavell RA. A humanized mouse model of chronic COVID-19 to evaluate disease mechanisms and treatment options. Res Sq 2021:rs.3.rs-279341. [PMID: 33758831 PMCID: PMC7987100 DOI: 10.21203/rs.3.rs-279341/v1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Coronavirus-associated acute respiratory disease, called coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). More than 90 million people have been infected with SARS-CoV-2 and more than 2 million people have died of complications due to COVID-19 worldwide. COVID-19, in its severe form, presents with an uncontrolled, hyperactive immune response and severe immunological injury or organ damage that accounts for morbidity and mortality. Even in the absence of complications, COVID-19 can last for several months with lingering effects of an overactive immune system. Dysregulated myeloid and lymphocyte compartments have been implicated in lung immunopathology. Currently, there are limited clinically-tested treatments of COVID-19 with disparities in the apparent efficacy in patients. Accurate model systems are essential to rapidly evaluate promising discoveries but most currently available in mice, ferrets and hamsters do not recapitulate sustained immunopathology described in COVID19 patients. Here, we present a comprehensively humanized mouse COVID-19 model that faithfully recapitulates the innate and adaptive human immune responses during infection with SARS-CoV-2 by adapting recombinant adeno-associated virus (AAV)-driven gene therapy to deliver human ACE2 to the lungs 1 of MISTRG6 mice. Our unique model allows for the first time the study of chronic disease due to infection with SARS-CoV-2 in the context of patient-derived antibodies to characterize in real time the potential culprits of the observed human driving immunopathology; most importantly this model provides a live view into the aberrant macrophage response that is thought to be the effector of disease morbidity and ARDS in patients. Application of therapeutics such as patient-derived antibodies and steroids to our model allowed separation of the two aspects of the immune response, infectious viral clearance and immunopathology. Inflammatory cells seeded early in infection drove immune-patholgy later, but this very same early anti-viral response was also crucial to contain infection.
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Affiliation(s)
- Esen Sefik
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
| | - Ben Israelow
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
| | - Jun Zhao
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Rihao Qu
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Eric Song
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
| | - Haris Mirza
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
| | - Eleanna Kaffe
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
| | - Stephanie Halene
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT
| | - Eric Meffre
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
| | - Yuval Kluger
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Michel Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Craig B Wilen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT,USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
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41
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Meizlish ML, Pine AB, Bishai JD, Goshua G, Nadelmann ER, Simonov M, Chang CH, Zhang H, Shallow M, Bahel P, Owusu K, Yamamoto Y, Arora T, Atri DS, Patel A, Gbyli R, Kwan J, Won CH, Dela Cruz C, Price C, Koff J, King BA, Rinder HM, Wilson FP, Hwa J, Halene S, Damsky W, van Dijk D, Lee AI, Chun HJ. A neutrophil activation signature predicts critical illness and mortality in COVID-19. Blood Adv 2021; 5:1164-1177. [PMID: 33635335 PMCID: PMC7908851 DOI: 10.1182/bloodadvances.2020003568] [Citation(s) in RCA: 196] [Impact Index Per Article: 65.3] [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: 10/16/2020] [Accepted: 01/13/2021] [Indexed: 12/29/2022] Open
Abstract
Pathologic immune hyperactivation is emerging as a key feature of critical illness in COVID-19, but the mechanisms involved remain poorly understood. We carried out proteomic profiling of plasma from cross-sectional and longitudinal cohorts of hospitalized patients with COVID-19 and analyzed clinical data from our health system database of more than 3300 patients. Using a machine learning algorithm, we identified a prominent signature of neutrophil activation, including resistin, lipocalin-2, hepatocyte growth factor, interleukin-8, and granulocyte colony-stimulating factor, which were the strongest predictors of critical illness. Evidence of neutrophil activation was present on the first day of hospitalization in patients who would only later require transfer to the intensive care unit, thus preceding the onset of critical illness and predicting increased mortality. In the health system database, early elevations in developing and mature neutrophil counts also predicted higher mortality rates. Altogether, these data suggest a central role for neutrophil activation in the pathogenesis of severe COVID-19 and identify molecular markers that distinguish patients at risk of future clinical decompensation.
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Affiliation(s)
| | | | - Jason D Bishai
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, and
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT
| | - George Goshua
- Section of Hematology, Department of Internal Medicine
| | | | - Michael Simonov
- Clinical and Translational Research Accelerator, Department of Internal Medicine
- Department of Dermatology, and
| | - C-Hong Chang
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, and
| | - Hanming Zhang
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, and
| | - Marcus Shallow
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, and
| | - Parveen Bahel
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
| | - Kent Owusu
- Department of Pharmacy, Yale New Haven Health System, New Haven, CT
| | - Yu Yamamoto
- Clinical and Translational Research Accelerator, Department of Internal Medicine
| | - Tanima Arora
- Clinical and Translational Research Accelerator, Department of Internal Medicine
| | - Deepak S Atri
- Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, MA; and
| | - Amisha Patel
- Section of Hematology, Department of Internal Medicine
| | - Rana Gbyli
- Section of Hematology, Department of Internal Medicine
| | - Jennifer Kwan
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, and
| | - Christine H Won
- Section of Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, and
| | - Charles Dela Cruz
- Section of Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, and
| | - Christina Price
- Section of Immunology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - Jonathan Koff
- Section of Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, and
| | - Brett A King
- Section of Immunology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - Henry M Rinder
- Section of Hematology, Department of Internal Medicine
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
| | - F Perry Wilson
- Clinical and Translational Research Accelerator, Department of Internal Medicine
| | - John Hwa
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, and
| | | | | | - David van Dijk
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, and
| | - Alfred I Lee
- Section of Hematology, Department of Internal Medicine
| | - Hyung J Chun
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, and
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42
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Gu SX, Tyagi T, Jain K, Gu VW, Lee SH, Hwa JM, Kwan JM, Krause DS, Lee AI, Halene S, Martin KA, Chun HJ, Hwa J. Thrombocytopathy and endotheliopathy: crucial contributors to COVID-19 thromboinflammation. Nat Rev Cardiol 2021; 18:194-209. [PMID: 33214651 PMCID: PMC7675396 DOI: 10.1038/s41569-020-00469-1] [Citation(s) in RCA: 246] [Impact Index Per Article: 82.0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/19/2020] [Indexed: 02/06/2023]
Abstract
The core pathology of coronavirus disease 2019 (COVID-19) is infection of airway cells by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that results in excessive inflammation and respiratory disease, with cytokine storm and acute respiratory distress syndrome implicated in the most severe cases. Thrombotic complications are a major cause of morbidity and mortality in patients with COVID-19. Patients with pre-existing cardiovascular disease and/or traditional cardiovascular risk factors, including obesity, diabetes mellitus, hypertension and advanced age, are at the highest risk of death from COVID-19. In this Review, we summarize new lines of evidence that point to both platelet and endothelial dysfunction as essential components of COVID-19 pathology and describe the mechanisms that might account for the contribution of cardiovascular risk factors to the most severe outcomes in COVID-19. We highlight the distinct contributions of coagulopathy, thrombocytopathy and endotheliopathy to the pathogenesis of COVID-19 and discuss potential therapeutic strategies in the management of patients with COVD-19. Harnessing the expertise of the biomedical and clinical communities is imperative to expand the available therapeutics beyond anticoagulants and to target both thrombocytopathy and endotheliopathy. Only with such collaborative efforts can we better prepare for further waves and for future coronavirus-related pandemics.
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Affiliation(s)
- Sean X Gu
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Tarun Tyagi
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Kanika Jain
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Vivian W Gu
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Seung Hee Lee
- Division of Cardiovascular Diseases, Center for Biomedical Sciences, National Institute of Health, Cheongju, Chungbuk, Korea
| | - Jonathan M Hwa
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Jennifer M Kwan
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Diane S Krause
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Alfred I Lee
- Section of Hematology, Department of Internal Medicine and Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Stephanie Halene
- Section of Hematology, Department of Internal Medicine and Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Kathleen A Martin
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Hyung J Chun
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - John Hwa
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA.
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43
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Shallis RM, Bewersdorf JP, Swoboda DM, Wei W, Gowda L, Prebet T, Halene S, Pillai MM, Parker T, Neparidze N, Podoltsev NA, Seropian S, Sallman DA, Gore SD, Zeidan AM. Challenges in the Evaluation and Management of Toxicities Arising From Immune Checkpoint Inhibitor Therapy for Patients With Myeloid Malignancies. Clin Lymphoma Myeloma Leuk 2021; 21:e483-e487. [PMID: 33551344 DOI: 10.1016/j.clml.2021.01.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 12/28/2020] [Accepted: 01/05/2021] [Indexed: 11/30/2022]
Affiliation(s)
- Rory M Shallis
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine and Yale Cancer Center, New Haven, CT
| | - Jan Philipp Bewersdorf
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine and Yale Cancer Center, New Haven, CT
| | - David M Swoboda
- Department of Hematology and Oncology, H. Lee Moffitt Cancer Center, Tampa, FL
| | - Wei Wei
- Department of Biostatistics, Yale School of Public Health, New Haven, CT
| | - Lohith Gowda
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine and Yale Cancer Center, New Haven, CT
| | - Thomas Prebet
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine and Yale Cancer Center, New Haven, CT
| | - Stephanie Halene
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine and Yale Cancer Center, New Haven, CT
| | - Manoj M Pillai
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine and Yale Cancer Center, New Haven, CT
| | - Terri Parker
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine and Yale Cancer Center, New Haven, CT
| | - Natalia Neparidze
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine and Yale Cancer Center, New Haven, CT
| | - Nikolai A Podoltsev
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine and Yale Cancer Center, New Haven, CT
| | - Stuart Seropian
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine and Yale Cancer Center, New Haven, CT
| | - David A Sallman
- Department of Hematology and Oncology, H. Lee Moffitt Cancer Center, Tampa, FL
| | - Steven D Gore
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine and Yale Cancer Center, New Haven, CT
| | - Amer M Zeidan
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine and Yale Cancer Center, New Haven, CT.
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44
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Pine AB, Meizlish ML, Goshua G, Chang CH, Zhang H, Bishai J, Bahel P, Patel A, Gbyli R, Kwan JM, Won CH, Price C, Dela Cruz CS, Halene S, van Dijk D, Hwa J, Lee AI, Chun HJ. Circulating markers of angiogenesis and endotheliopathy in COVID-19. Pulm Circ 2020; 10:2045894020966547. [PMID: 33282193 PMCID: PMC7691906 DOI: 10.1177/2045894020966547] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 09/23/2020] [Indexed: 11/15/2022] Open
Abstract
Increase in thrombotic and microvascular complications is emerging to be a key
feature of patients with critical illness associated with COVID-19 infection.
While endotheliopathy is thought to be a key factor of COVID-19-associated
coagulopathy, markers indicative of this process that are prognostic of disease
severity have not been well-established in this patient population. Using plasma
profiling of patients with COVID-19, we identified circulating markers that
segregated with disease severity: markers of angiogenesis (VEGF-A, PDGF-AA and
PDGF-AB/BB) were elevated in hospitalized patients with non-critical COVID-19
infection, while markers of endothelial injury (angiopoietin-2, FLT-3L, PAI-1)
were elevated in patients with critical COVID-19 infection. In survival
analysis, elevated markers of endothelial injury (angiopoietin-2, follistatin,
PAI-1) were strongly predictive of in-hospital mortality. Our findings
demonstrate that non-critical and critical phases of COVID-19 disease may be
driven by distinct mechanisms involving key aspects of endothelial cell
function, and identify drivers of COVID-19 pathogenesis and potential targets
for future therapies.
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Affiliation(s)
- Alexander B Pine
- Section of Hematology, Yale School of Medicine, New Haven, CT, USA
| | | | - George Goshua
- Section of Hematology, Yale School of Medicine, New Haven, CT, USA
| | - C-Hong Chang
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Hanming Zhang
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Jason Bishai
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Parveen Bahel
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | | | - Rana Gbyli
- Yale School of Medicine, New Haven, CT, USA
| | - Jennifer M Kwan
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Christine H Won
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Christina Price
- Section of Immunology, Yale School of Medicine, New Haven, CT, USA
| | - Charles S Dela Cruz
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | | | - David van Dijk
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Yale School of Medicine, New Haven, CT, USA
| | - John Hwa
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Alfred I Lee
- Section of Hematology, Yale School of Medicine, New Haven, CT, USA
| | - Hyung J Chun
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Yale School of Medicine, New Haven, CT, USA
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45
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Liu Y, Yang M, Deng Y, Su G, Enninful A, Guo CC, Tebaldi T, Zhang D, Kim D, Bai Z, Norris E, Pan A, Li J, Xiao Y, Halene S, Fan R. High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue. Cell 2020; 183:1665-1681.e18. [PMID: 33188776 DOI: 10.1016/j.cell.2020.10.026] [Citation(s) in RCA: 322] [Impact Index Per Article: 80.5] [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: 09/21/2019] [Revised: 07/31/2020] [Accepted: 10/14/2020] [Indexed: 12/21/2022]
Abstract
We present deterministic barcoding in tissue for spatial omics sequencing (DBiT-seq) for co-mapping of mRNAs and proteins in a formaldehyde-fixed tissue slide via next-generation sequencing (NGS). Parallel microfluidic channels were used to deliver DNA barcodes to the surface of a tissue slide, and crossflow of two sets of barcodes, A1-50 and B1-50, followed by ligation in situ, yielded a 2D mosaic of tissue pixels, each containing a unique full barcode AB. Application to mouse embryos revealed major tissue types in early organogenesis as well as fine features like microvasculature in a brain and pigmented epithelium in an eye field. Gene expression profiles in 10-μm pixels conformed into the clusters of single-cell transcriptomes, allowing for rapid identification of cell types and spatial distributions. DBiT-seq can be adopted by researchers with no experience in microfluidics and may find applications in a range of fields including developmental biology, cancer biology, neuroscience, and clinical pathology.
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Affiliation(s)
- Yang Liu
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Mingyu Yang
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Yanxiang Deng
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Graham Su
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Archibald Enninful
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Cindy C Guo
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Toma Tebaldi
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA; Section of Hematology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA
| | - Di Zhang
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Dongjoo Kim
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Zhiliang Bai
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Eileen Norris
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Alisia Pan
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Jiatong Li
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Yang Xiao
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Stephanie Halene
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA; Section of Hematology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA; Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT 06520, USA.
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46
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Taylor J, Mi X, North K, Binder M, Penson A, Lasho T, Knorr K, Haddadin M, Liu B, Pangallo J, Benbarche S, Wiseman D, Tefferi A, Halene S, Liang Y, Patnaik MM, Bradley RK, Abdel-Wahab O. Single-cell genomics reveals the genetic and molecular bases for escape from mutational epistasis in myeloid neoplasms. Blood 2020; 136:1477-1486. [PMID: 32640014 PMCID: PMC7515689 DOI: 10.1182/blood.2020006868] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [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: 05/06/2020] [Accepted: 07/06/2020] [Indexed: 12/13/2022] Open
Abstract
Large-scale sequencing studies of hematologic malignancies have revealed notable epistasis among high-frequency mutations. One of the most striking examples of epistasis occurs for mutations in RNA splicing factors. These lesions are among the most common alterations in myeloid neoplasms and generally occur in a mutually exclusive manner, a finding attributed to their synthetic lethal interactions and/or convergent effects. Curiously, however, patients with multiple-concomitant splicing factor mutations have been observed, challenging our understanding of one of the most common examples of epistasis in hematologic malignancies. In this study, we performed bulk and single-cell analyses of patients with myeloid malignancy who were harboring ≥2 splicing factor mutations, to understand the frequency and basis for the coexistence of these mutations. Although mutations in splicing factors were strongly mutually exclusive across 4231 patients (q < .001), 0.85% harbored 2 concomitant bona fide splicing factor mutations, ∼50% of which were present in the same individual cells. However, the distribution of mutations in patients with double mutations deviated from that in those with single mutations, with selection against the most common alleles, SF3B1K700E and SRSF2P95H/L/R, and selection for less common alleles, such as SF3B1 non-K700E mutations, rare amino acid substitutions at SRSF2P95, and combined U2AF1S34/Q157 mutations. SF3B1 and SRSF2 alleles enriched in those with double-mutations had reduced effects on RNA splicing and/or binding compared with the most common alleles. Moreover, dual U2AF1 mutations occurred in cis with preservation of the wild-type allele. These data highlight allele-specific differences as critical in regulating the molecular effects of splicing factor mutations as well as their cooccurrences/exclusivities with one another.
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Affiliation(s)
- Justin Taylor
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY
- University of Miami Miller School of Medicine, Miami, FL
| | - Xiaoli Mi
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Khrystyna North
- Division of Public Health Sciences and
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
- Department of Genome Sciences, University of Washington, Seattle, WA
| | | | - Alexander Penson
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY
| | | | - Katherine Knorr
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Michael Haddadin
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Bo Liu
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Joseph Pangallo
- Division of Public Health Sciences and
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Salima Benbarche
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Daniel Wiseman
- Division of Cancer Sciences, University of Manchester, Manchester, United Kingdom
| | | | - Stephanie Halene
- Section of Hematology, Department of Internal Medicine and
- Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT; and
| | - Yang Liang
- State Key Laboratory of Oncology in South China, Department of Hematologic Oncology, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Peoples Republic of China
| | | | - Robert K Bradley
- Division of Public Health Sciences and
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY
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47
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Meizlish ML, Pine AB, Bishai JD, Goshua G, Nadelmann ER, Simonov M, Chang CH, Zhang H, Shallow M, Bahel P, Owusu K, Yamamoto Y, Arora T, Atri DS, Patel A, Gbyli R, Kwan J, Won CH, Dela Cruz C, Price C, Koff J, King BA, Rinder HM, Wilson FP, Hwa J, Halene S, Damsky W, van Dijk D, Lee AI, Chun H. A neutrophil activation signature predicts critical illness and mortality in COVID-19. medRxiv 2020. [PMID: 32908988 DOI: 10.1101/2020.09.01.20183897] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Pathologic immune hyperactivation is emerging as a key feature of critical illness in COVID-19, but the mechanisms involved remain poorly understood. We carried out proteomic profiling of plasma from cross-sectional and longitudinal cohorts of hospitalized patients with COVID-19 and analyzed clinical data from our health system database of over 3,300 patients. Using a machine learning algorithm, we identified a prominent signature of neutrophil activation, including resistin, lipocalin-2, HGF, IL-8, and G-CSF, as the strongest predictors of critical illness. Neutrophil activation was present on the first day of hospitalization in patients who would only later require transfer to the intensive care unit, thus preceding the onset of critical illness and predicting increased mortality. In the health system database, early elevations in developing and mature neutrophil counts also predicted higher mortality rates. Altogether, we define an essential role for neutrophil activation in the pathogenesis of severe COVID-19 and identify molecular neutrophil markers that distinguish patients at risk of future clinical decompensation.
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48
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Bewersdorf JP, Shallis RM, Boddu PC, Wood B, Radich J, Halene S, Zeidan AM. The minimal that kills: Why defining and targeting measurable residual disease is the “Sine Qua Non” for further progress in management of acute myeloid leukemia. Blood Rev 2020; 43:100650. [DOI: 10.1016/j.blre.2019.100650] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 12/04/2019] [Accepted: 12/13/2019] [Indexed: 12/13/2022]
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49
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Meizlish ML, Pine AB, Goshua G, Chang CH, Zhang H, Bishai J, Bahel P, Patel A, Gbyli R, Kwan J, Price C, Cruz CSD, Halene S, van Dijk D, Hwa J, Lee AI, Chun HJ. Circulating Markers of Angiogenesis and Endotheliopathy in COVID-19. medRxiv 2020. [PMID: 32637968 PMCID: PMC7340194 DOI: 10.1101/2020.06.29.20140376] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
| | - Alexander B Pine
- Section of Hematology, Section of Cardiovascular Medicine, New Haven, Connecticut
| | - George Goshua
- Section of Hematology, Section of Cardiovascular Medicine, New Haven, Connecticut
| | - C-Hong Chang
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, New Haven, Connecticut
| | - Hanming Zhang
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, New Haven, Connecticut
| | - Jason Bishai
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, New Haven, Connecticut
| | - Parveen Bahel
- Department of Laboratory Medicine, Critical Care, and Sleep Medicine, New Haven, Connecticut
| | - Amisha Patel
- Section of Hematology, Section of Cardiovascular Medicine, New Haven, Connecticut
| | - Rana Gbyli
- Section of Hematology, Section of Cardiovascular Medicine, New Haven, Connecticut
| | - Jennifer Kwan
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, New Haven, Connecticut
| | - Christina Price
- Section of Immunology, Critical Care, and Sleep Medicine, New Haven, Connecticut
| | - Charles S Dela Cruz
- Section of Pulmonary, Critical Care, and Sleep Medicine, New Haven, Connecticut
| | - Stephanie Halene
- Section of Hematology, Section of Cardiovascular Medicine, New Haven, Connecticut
| | - David van Dijk
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, New Haven, Connecticut
| | - John Hwa
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, New Haven, Connecticut
| | - Alfred I Lee
- Section of Hematology, Section of Cardiovascular Medicine, New Haven, Connecticut
| | - Hyung J Chun
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, New Haven, Connecticut
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50
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Goshua G, Pine AB, Meizlish ML, Chang CH, Zhang H, Bahel P, Baluha A, Bar N, Bona RD, Burns AJ, Dela Cruz CS, Dumont A, Halene S, Hwa J, Koff J, Menninger H, Neparidze N, Price C, Siner JM, Tormey C, Rinder HM, Chun HJ, Lee AI. Endotheliopathy in COVID-19-associated coagulopathy: evidence from a single-centre, cross-sectional study. Lancet Haematol 2020; 7:e575-e582. [PMID: 32619411 PMCID: PMC7326446 DOI: 10.1016/s2352-3026(20)30216-7] [Citation(s) in RCA: 719] [Impact Index Per Article: 179.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 06/12/2020] [Accepted: 06/12/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND An important feature of severe acute respiratory syndrome coronavirus 2 pathogenesis is COVID-19-associated coagulopathy, characterised by increased thrombotic and microvascular complications. Previous studies have suggested a role for endothelial cell injury in COVID-19-associated coagulopathy. To determine whether endotheliopathy is involved in COVID-19-associated coagulopathy pathogenesis, we assessed markers of endothelial cell and platelet activation in critically and non-critically ill patients admitted to the hospital with COVID-19. METHODS In this single-centre cross-sectional study, hospitalised adult (≥18 years) patients with laboratory-confirmed COVID-19 were identified in the medical intensive care unit (ICU) or a specialised non-ICU COVID-19 floor in our hospital. Asymptomatic, non-hospitalised controls were recruited as a comparator group for biomarkers that did not have a reference range. We assessed markers of endothelial cell and platelet activation, including von Willebrand Factor (VWF) antigen, soluble thrombomodulin, soluble P-selectin, and soluble CD40 ligand, as well as coagulation factors, endogenous anticoagulants, and fibrinolytic enzymes. We compared the level of each marker in ICU patients, non-ICU patients, and controls, where applicable. We assessed correlations between these laboratory results with clinical outcomes, including hospital discharge and mortality. Kaplan-Meier analysis was used to further explore the association between biochemical markers and survival. FINDINGS 68 patients with COVID-19 were included in the study from April 13 to April 24, 2020, including 48 ICU and 20 non-ICU patients, as well as 13 non-hospitalised, asymptomatic controls. Markers of endothelial cell and platelet activation were significantly elevated in ICU patients compared with non-ICU patients, including VWF antigen (mean 565% [SD 199] in ICU patients vs 278% [133] in non-ICU patients; p<0·0001) and soluble P-selectin (15·9 ng/mL [4·8] vs 11·2 ng/mL [3·1]; p=0·0014). VWF antigen concentrations were also elevated above the normal range in 16 (80%) of 20 non-ICU patients. We found mortality to be significantly correlated with VWF antigen (r = 0·38; p=0·0022) and soluble thrombomodulin (r = 0·38; p=0·0078) among all patients. In all patients, soluble thrombomodulin concentrations greater than 3·26 ng/mL were associated with lower rates of hospital discharge (22 [88%] of 25 patients with low concentrations vs 13 [52%] of 25 patients with high concentrations; p=0·0050) and lower likelihood of survival on Kaplan-Meier analysis (hazard ratio 5·9, 95% CI 1·9-18·4; p=0·0087). INTERPRETATION Our findings show that endotheliopathy is present in COVID-19 and is likely to be associated with critical illness and death. Early identification of endotheliopathy and strategies to mitigate its progression might improve outcomes in COVID-19. FUNDING This work was supported by a gift donation from Jack Levin to the Benign Hematology programme at Yale, and the National Institutes of Health.
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Affiliation(s)
| | | | | | - C-Hong Chang
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, New Haven, CT, USA
| | - Hanming Zhang
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, New Haven, CT, USA
| | - Parveen Bahel
- Department of Laboratory Medicine, New Haven, CT, USA
| | | | - Noffar Bar
- Section of Hematology, New Haven, CT, USA
| | | | | | | | | | | | - John Hwa
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, New Haven, CT, USA
| | - Jonathan Koff
- Section of Pulmonary, Critical Care, and Sleep Medicine, New Haven, CT, USA
| | | | | | | | - Jonathan M Siner
- Section of Pulmonary, Critical Care, and Sleep Medicine, New Haven, CT, USA
| | | | | | - Hyung J Chun
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, New Haven, CT, USA
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