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Archer M, Begemann D, Gonzalez-Kozlova E, Nepali PR, Labanca E, Shepherd P, Dogra N, Navone N, Kyprianou N. Kinesin Facilitates Phenotypic Targeting of Therapeutic Resistance in Advanced Prostate Cancer. Mol Cancer Res 2024:743192. [PMID: 38648082 DOI: 10.1158/1541-7786.mcr-23-1047] [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] [Received: 12/15/2023] [Revised: 02/16/2024] [Accepted: 04/16/2024] [Indexed: 04/25/2024]
Abstract
Understanding the mechanisms underlying resistance is critical to improving therapeutic outcomes in patients with metastatic castration-resistant prostate cancer (mCRPC). Previous work showed dynamic interconversions between epithelial-mesenchymal transition (EMT) to mesenchymal-epithelial transition (MET) defines the phenotypic landscape of prostate tumors, as a potential driver of emergence of therapeutic resistance. In this study, we use in vitro and in vivo preclinical MDA PCa PDX models of resistant human prostate cancer to determine molecular mechanisms of cross-resistance between anti-androgen therapy and taxane chemotherapy, underlying the therapeutically resistant phenotype. Transcriptomic profiling revealed that resistant and sensitive prostate cancer C4-2B cells have a unique differential gene signature response to cabazitaxel. Gene pathway analysis showed that sensitive cells exhibit increase in DNA damage, while resistant cells express genes associated with protein regulation in response to cabazitaxel. These PDX specimens are from patients who have metastatic lethal CRPC, treated with androgen-deprivation therapy (ADT), antiandrogens and chemotherapy including 2nd line taxane chemotherapy, cabazitaxel. Immunohistochemistry revealed high expression of E-cadherin and low expression of vimentin resulting in re-differentiation toward an epithelial phenotype. Furthermore, the mitotic kinesin-related protein (HSET) involved in microtubule binding and the SLCO1B3 transporter (implicated in cabazitaxel intracellular transport), associated with resistance in these prostate tumors. Combinational targeting of kinesins (ispinesib) with cabazitaxel was more effective than single monotherapies in inducing cell death in resistant prostate tumors. Implications: Our findings are of translational significance in identifying kinesin as a novel target of cross-resistance, towards enhancing therapeutic vulnerability and improved clinical outcomes in patients with advanced prostate cancer.
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Affiliation(s)
- Maddison Archer
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | | | | | - Prerna R Nepali
- Icahn School of Medicine at Mount Sinai, New York, United States
| | - Estefania Labanca
- University of Texas MD Anderson Cancer Center, Houston, Texas, United States
| | - Peter Shepherd
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Navneet Dogra
- Icahn School of Medicine at Mount Sinai, NYC, United States
| | - Nora Navone
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Natasha Kyprianou
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
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2
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Parra ER, Zhang J, Duose DY, Gonzalez-Kozlova E, Redman MW, Chen H, Manyam GC, Kumar G, Zhang J, Song X, Lazcano R, Marques-Piubelli ML, Laberiano-Fernandez C, Rojas F, Zhang B, Taing L, Jhaveri A, Geisberg J, Altreuter J, Michor F, Provencher J, Yu J, Cerami E, Moravec R, Kannan K, Luthra R, Alatrash G, Huang HH, Xie H, Patel M, Nie K, Harris J, Argueta K, Lindsay J, Biswas R, Van Nostrand S, Kim-Schulze S, Gray JE, Herbst RS, Wistuba II, Gettinger S, Kelly K, Bazhenova L, Gnjatic S, Lee JJ, Zhang J, Haymaker C. Multi-omics Analysis Reveals Immune Features Associated with Immunotherapy Benefit in Patients with Squamous Cell Lung Cancer from Phase III Lung-MAP S1400I Trial. Clin Cancer Res 2024; 30:1655-1668. [PMID: 38277235 PMCID: PMC11016892 DOI: 10.1158/1078-0432.ccr-23-0251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 05/06/2023] [Accepted: 01/24/2024] [Indexed: 01/28/2024]
Abstract
PURPOSE Identifying molecular and immune features to guide immune checkpoint inhibitor (ICI)-based regimens remains an unmet clinical need. EXPERIMENTAL DESIGN Tissue and longitudinal blood specimens from phase III trial S1400I in patients with metastatic squamous non-small cell carcinoma (SqNSCLC) treated with nivolumab monotherapy (nivo) or nivolumab plus ipilimumab (nivo+ipi) were subjected to multi-omics analyses including multiplex immunofluorescence (mIF), nCounter PanCancer Immune Profiling Panel, whole-exome sequencing, and Olink. RESULTS Higher immune scores from immune gene expression profiling or immune cell infiltration by mIF were associated with response to ICIs and improved survival, except regulatory T cells, which were associated with worse overall survival (OS) for patients receiving nivo+ipi. Immune cell density and closer proximity of CD8+GZB+ T cells to malignant cells were associated with superior progression-free survival and OS. The cold immune landscape of NSCLC was associated with a higher level of chromosomal copy-number variation (CNV) burden. Patients with LRP1B-mutant tumors had a shorter survival than patients with LRP1B-wild-type tumors. Olink assays revealed soluble proteins such as LAMP3 increased in responders while IL6 and CXCL13 increased in nonresponders. Upregulation of serum CXCL13, MMP12, CSF-1, and IL8 were associated with worse survival before radiologic progression. CONCLUSIONS The frequency, distribution, and clustering of immune cells relative to malignant ones can impact ICI efficacy in patients with SqNSCLC. High CNV burden may contribute to the cold immune microenvironment. Soluble inflammation/immune-related proteins in the blood have the potential to monitor therapeutic benefit from ICI treatment in patients with SqNSCLC.
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Affiliation(s)
- Edwin Roger Parra
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jiexin Zhang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Dzifa Yawa Duose
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Edgar Gonzalez-Kozlova
- Department of Oncological Sciences, Mount Sinai, New York, New York
- Tisch Cancer Institute, Mount Sinai, New York, New York
- Precision Immunology Institute, Mount Sinai, New York, New York
- Icahn School of Medicine at Mount Sinai, New York, New York
| | - Mary W. Redman
- SWOG Statistical Center, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Hong Chen
- Department of Thoracic-Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ganiraju C. Manyam
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gayatri Kumar
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xingzhi Song
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rossana Lazcano
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Mario L. Marques-Piubelli
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Caddie Laberiano-Fernandez
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Frank Rojas
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Baili Zhang
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Len Taing
- CIMAC-CIDC Network, Pipeline Development and Portal Integration, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Aashna Jhaveri
- CIMAC-CIDC Network, Pipeline Development and Portal Integration, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jacob Geisberg
- CIMAC-CIDC Network, Pipeline Development and Portal Integration, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jennifer Altreuter
- CIMAC-CIDC Network, Pipeline Development and Portal Integration, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Franziska Michor
- CIMAC-CIDC Network, Pipeline Development and Portal Integration, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - James Provencher
- CIMAC-CIDC Network, Pipeline Development and Portal Integration, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Joyce Yu
- CIMAC-CIDC Network, Pipeline Development and Portal Integration, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ethan Cerami
- CIMAC-CIDC Network, Pipeline Development and Portal Integration, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Radim Moravec
- Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, NCI, Bethesda, Maryland
| | - Kasthuri Kannan
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rajyalakshmi Luthra
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gheath Alatrash
- Department of Stem Cell Transplantation, The University of Texas MD Anderson Cancer, Houston, Texas
| | - Hsin-Hui Huang
- Precision Immunology Institute, Mount Sinai, New York, New York
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Hui Xie
- Precision Immunology Institute, Mount Sinai, New York, New York
| | | | - Kai Nie
- Precision Immunology Institute, Mount Sinai, New York, New York
| | - Jocelyn Harris
- Precision Immunology Institute, Mount Sinai, New York, New York
| | | | - James Lindsay
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Roshni Biswas
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Stephen Van Nostrand
- CIMAC-CIDC Network, Pipeline Development and Portal Integration, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Seunghee Kim-Schulze
- Department of Oncological Sciences, Mount Sinai, New York, New York
- Tisch Cancer Institute, Mount Sinai, New York, New York
- Precision Immunology Institute, Mount Sinai, New York, New York
- Icahn School of Medicine at Mount Sinai, New York, New York
| | | | - Roy S. Herbst
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - Ignacio I. Wistuba
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Karen Kelly
- International Association for the Study of Lung Cancer, Denver, Colorado
| | - Lyudmila Bazhenova
- University of California San Diego Moores Cancer Center, La Jolla, California
| | - Sacha Gnjatic
- Department of Oncological Sciences, Mount Sinai, New York, New York
- Tisch Cancer Institute, Mount Sinai, New York, New York
- Precision Immunology Institute, Mount Sinai, New York, New York
- Icahn School of Medicine at Mount Sinai, New York, New York
| | - J. Jack Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jianjun Zhang
- Department of Thoracic-Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Cara Haymaker
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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3
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Galsky MD, Daneshmand S, Izadmehr S, Gonzalez-Kozlova E, Chan KG, Lewis S, Achkar BE, Dorff TB, Cetnar JP, Neil BO, D'Souza A, Mamtani R, Kyriakopoulos C, Jun T, Gogerly-Moragoda M, Brody R, Xie H, Nie K, Kelly G, Horowitz A, Kinoshita Y, Ellis E, Nose Y, Ioannou G, Cabal R, Del Valle DM, Haines GK, Wang L, Mouw KW, Samstein RM, Mehrazin R, Bhardwaj N, Yu M, Zhao Q, Kim-Schulze S, Sebra R, Zhu J, Gnjatic S, Sfakianos J, Pal SK. Author Correction: Gemcitabine and cisplatin plus nivolumab as organ-sparing treatment for muscle-invasive bladder cancer: a phase 2 trial. Nat Med 2024; 30:1211. [PMID: 38242983 PMCID: PMC11031387 DOI: 10.1038/s41591-024-02814-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2024]
Affiliation(s)
- Matthew D Galsky
- Division of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Siamak Daneshmand
- Department of Urology, Keck School of Medicine of USC, Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Sudeh Izadmehr
- Division of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edgar Gonzalez-Kozlova
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kevin G Chan
- Department of Urology, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Sara Lewis
- Department of Radiology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bassam El Achkar
- Department of Radiology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tanya B Dorff
- Department of Medical Oncology & Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Jeremy Paul Cetnar
- Division of Hematology and Medical Oncology, Oregon Health and Science University, Portland, OR, USA
| | - Brock O Neil
- Department of Urology, University of Utah, Salt Lake City, UT, USA
| | - Anishka D'Souza
- Division of Hematology and Medical Oncology, Keck School of Medicine of USC, Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Ronac Mamtani
- Division of Hematology and Medical Oncology, University of Pennsylvania Abramson Cancer Center, Philadelphia, PA, USA
| | - Christos Kyriakopoulos
- Division of Hematology and Medical Oncology, University of Wisconsin Carbone Cancer Center, Madison, WI, USA
| | - Tomi Jun
- Genentech, South San Francisco, CA, USA
- Formerly with the Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mahalya Gogerly-Moragoda
- Division of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rachel Brody
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hui Xie
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kai Nie
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Geoffrey Kelly
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Amir Horowitz
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yayoi Kinoshita
- Department of Pathology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ethan Ellis
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yohei Nose
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Giorgio Ioannou
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rafael Cabal
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Diane M Del Valle
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - G Kenneth Haines
- Department of Pathology, Molecular and Cell-based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Li Wang
- Division of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Gene Dx, Stamford, CT, USA
| | - Kent W Mouw
- Department of Radiation Oncology, Dana-Farber Cancer Institute/Brigham & Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Robert M Samstein
- Department of Radiation Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Reza Mehrazin
- Department of Urology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nina Bhardwaj
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Menggang Yu
- Department of Biostatistics and Medical Informatics, University of Wisconsin Carbone Cancer Center, Madison, WI, USA
| | - Qianqian Zhao
- Department of Biostatistics and Medical Informatics, University of Wisconsin Carbone Cancer Center, Madison, WI, USA
| | - Seunghee Kim-Schulze
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert Sebra
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jun Zhu
- Division of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Gene Dx, Stamford, CT, USA
| | - Sacha Gnjatic
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John Sfakianos
- Department of Urology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sumanta K Pal
- Department of Medical Oncology & Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
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4
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LaMarche NM, Hegde S, Park MD, Maier BB, Troncoso L, Le Berichel J, Hamon P, Belabed M, Mattiuz R, Hennequin C, Chin T, Reid AM, Reyes-Torres I, Nemeth E, Zhang R, Olson OC, Doroshow DB, Rohs NC, Gomez JE, Veluswamy R, Hall N, Venturini N, Ginhoux F, Liu Z, Buckup M, Figueiredo I, Roudko V, Miyake K, Karasuyama H, Gonzalez-Kozlova E, Gnjatic S, Passegué E, Kim-Schulze S, Brown BD, Hirsch FR, Kim BS, Marron TU, Merad M. An IL-4 signalling axis in bone marrow drives pro-tumorigenic myelopoiesis. Nature 2024; 625:166-174. [PMID: 38057662 DOI: 10.1038/s41586-023-06797-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 10/30/2023] [Indexed: 12/08/2023]
Abstract
Myeloid cells are known to suppress antitumour immunity1. However, the molecular drivers of immunosuppressive myeloid cell states are not well defined. Here we used single-cell RNA sequencing of human and mouse non-small cell lung cancer (NSCLC) lesions, and found that in both species the type 2 cytokine interleukin-4 (IL-4) was predicted to be the primary driver of the tumour-infiltrating monocyte-derived macrophage phenotype. Using a panel of conditional knockout mice, we found that only deletion of the IL-4 receptor IL-4Rα in early myeloid progenitors in bone marrow reduced tumour burden, whereas deletion of IL-4Rα in downstream mature myeloid cells had no effect. Mechanistically, IL-4 derived from bone marrow basophils and eosinophils acted on granulocyte-monocyte progenitors to transcriptionally programme the development of immunosuppressive tumour-promoting myeloid cells. Consequentially, depletion of basophils profoundly reduced tumour burden and normalized myelopoiesis. We subsequently initiated a clinical trial of the IL-4Rα blocking antibody dupilumab2-5 given in conjunction with PD-1/PD-L1 checkpoint blockade in patients with relapsed or refractory NSCLC who had progressed on PD-1/PD-L1 blockade alone (ClinicalTrials.gov identifier NCT05013450 ). Dupilumab supplementation reduced circulating monocytes, expanded tumour-infiltrating CD8 T cells, and in one out of six patients, drove a near-complete clinical response two months after treatment. Our study defines a central role for IL-4 in controlling immunosuppressive myelopoiesis in cancer, identifies a novel combination therapy for immune checkpoint blockade in humans, and highlights cancer as a systemic malady that requires therapeutic strategies beyond the primary disease site.
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Affiliation(s)
- Nelson M LaMarche
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Samarth Hegde
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew D Park
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Barbara B Maier
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Leanna Troncoso
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jessica Le Berichel
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Pauline Hamon
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Meriem Belabed
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Raphaël Mattiuz
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Clotilde Hennequin
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Theodore Chin
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Amanda M Reid
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Iván Reyes-Torres
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Erika Nemeth
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ruiyuan Zhang
- Columbia Stem Cell Initiative, Department of Genetics and Development, Columbia University, New York, NY, USA
| | - Oakley C Olson
- Columbia Stem Cell Initiative, Department of Genetics and Development, Columbia University, New York, NY, USA
| | - Deborah B Doroshow
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Hematology/Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Thoracic Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nicholas C Rohs
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Hematology/Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Thoracic Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jorge E Gomez
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Hematology/Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Thoracic Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rajwanth Veluswamy
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Hematology/Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Thoracic Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nicole Hall
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Hematology/Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Thoracic Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nicholas Venturini
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), BIOPOLIS, Singapore, Singapore
- INSERM U1015, Gustave Roussy Cancer Campus, Villejuif, France
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- SingHealth Duke-NUS Academic Medical Centre, Translational Immunology Institute, Singapore, Singapore
| | - Zhaoyuan Liu
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mark Buckup
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Igor Figueiredo
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vladimir Roudko
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kensuke Miyake
- Inflammation, Infection and Immunity Laboratory, Advanced Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Hajime Karasuyama
- Inflammation, Infection and Immunity Laboratory, Advanced Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Edgar Gonzalez-Kozlova
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sacha Gnjatic
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Hematology/Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Emmanuelle Passegué
- Columbia Stem Cell Initiative, Department of Genetics and Development, Columbia University, New York, NY, USA
| | - Seunghee Kim-Schulze
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brian D Brown
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Fred R Hirsch
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Hematology/Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Thoracic Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brian S Kim
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Kimberly and Eric J. Waldman Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Mark Lebwohl Center for Neuroinflammation and Sensation, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Thomas U Marron
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Hematology/Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Thoracic Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Miriam Merad
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Division of Hematology/Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Center for Thoracic Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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5
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Galsky MD, Daneshmand S, Izadmehr S, Gonzalez-Kozlova E, Chan KG, Lewis S, Achkar BE, Dorff TB, Cetnar JP, Neil BO, D'Souza A, Mamtani R, Kyriakopoulos C, Jun T, Gogerly-Moragoda M, Brody R, Xie H, Nie K, Kelly G, Horowitz A, Kinoshita Y, Ellis E, Nose Y, Ioannou G, Cabal R, Del Valle DM, Haines GK, Wang L, Mouw KW, Samstein RM, Mehrazin R, Bhardwaj N, Yu M, Zhao Q, Kim-Schulze S, Sebra R, Zhu J, Gnjatic S, Sfakianos J, Pal SK. Gemcitabine and cisplatin plus nivolumab as organ-sparing treatment for muscle-invasive bladder cancer: a phase 2 trial. Nat Med 2023; 29:2825-2834. [PMID: 37783966 PMCID: PMC10667093 DOI: 10.1038/s41591-023-02568-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [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: 01/10/2023] [Accepted: 08/24/2023] [Indexed: 10/04/2023]
Abstract
Cystectomy is a standard treatment for muscle-invasive bladder cancer (MIBC), but it is life-altering. We initiated a phase 2 study in which patients with MIBC received four cycles of gemcitabine, cisplatin, plus nivolumab followed by clinical restaging. Patients achieving a clinical complete response (cCR) could proceed without cystectomy. The co-primary objectives were to assess the cCR rate and the positive predictive value of cCR for a composite outcome: 2-year metastasis-free survival in patients forgoing immediate cystectomy or
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Affiliation(s)
- Matthew D Galsky
- Division of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Siamak Daneshmand
- Department of Urology, Keck School of Medicine of USC, Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Sudeh Izadmehr
- Division of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edgar Gonzalez-Kozlova
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kevin G Chan
- Department of Urology, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Sara Lewis
- Department of Radiology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bassam El Achkar
- Department of Radiology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tanya B Dorff
- Department of Medical Oncology & Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Jeremy Paul Cetnar
- Division of Hematology and Medical Oncology, Oregon Health and Science University, Portland, OR, USA
| | - Brock O Neil
- Department of Urology, University of Utah, Salt Lake City, UT, USA
| | - Anishka D'Souza
- Division of Hematology and Medical Oncology, Keck School of Medicine of USC, Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Ronac Mamtani
- Division of Hematology and Medical Oncology, University of Pennsylvania Abramson Cancer Center, Philadelphia, PA, USA
| | - Christos Kyriakopoulos
- Division of Hematology and Medical Oncology, University of Wisconsin Carbone Cancer Center, Madison, WI, USA
| | - Tomi Jun
- Genentech, South San Francisco, CA, USA
- Formerly with the Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mahalya Gogerly-Moragoda
- Division of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rachel Brody
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hui Xie
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kai Nie
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Geoffrey Kelly
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Amir Horowitz
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yayoi Kinoshita
- Department of Pathology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ethan Ellis
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yohei Nose
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Giorgio Ioannou
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rafael Cabal
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Diane M Del Valle
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - G Kenneth Haines
- Department of Pathology, Molecular and Cell-based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Li Wang
- Division of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Gene Dx, Stamford, CT, USA
| | - Kent W Mouw
- Department of Radiation Oncology, Dana-Farber Cancer Institute/Brigham & Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Robert M Samstein
- Department of Radiation Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Reza Mehrazin
- Department of Urology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nina Bhardwaj
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Menggang Yu
- Department of Biostatistics and Medical Informatics, University of Wisconsin Carbone Cancer Center, Madison, WI, USA
| | - Qianqian Zhao
- Department of Biostatistics and Medical Informatics, University of Wisconsin Carbone Cancer Center, Madison, WI, USA
| | - Seunghee Kim-Schulze
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert Sebra
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jun Zhu
- Division of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Gene Dx, Stamford, CT, USA
| | - Sacha Gnjatic
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John Sfakianos
- Department of Urology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sumanta K Pal
- Department of Medical Oncology & Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
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6
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Ricciardi-Jorge T, da Rocha EL, Gonzalez-Kozlova E, Rodrigues-Luiz GF, Ferguson BJ, Sweeney T, Irigoyen N, Mansur DS. PKR-mediated stress response enhances dengue and Zika virus replication. mBio 2023; 14:e0093423. [PMID: 37732809 PMCID: PMC10653888 DOI: 10.1128/mbio.00934-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 08/01/2023] [Indexed: 09/22/2023] Open
Abstract
IMPORTANCE One of the fundamental features that make viruses intracellular parasites is the necessity to use cellular translational machinery. Hence, this is a crucial checkpoint for controlling infections. Here, we show that dengue and Zika viruses, responsible for nearly 400 million infections every year worldwide, explore such control for optimal replication. Using immunocompetent cells, we demonstrate that arrest of protein translations happens after sensing of dsRNA and that the information required to avoid this blocking is contained in viral 5'-UTR. Our work, therefore, suggests that the non-canonical translation described for these viruses is engaged when the intracellular stress response is activated.
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Affiliation(s)
- Taissa Ricciardi-Jorge
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina (UFSC), Florianópolis, Brazil
- The Pirbright Institute, Woking, United Kingdom
| | - Edroaldo Lummertz da Rocha
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina (UFSC), Florianópolis, Brazil
| | - Edgar Gonzalez-Kozlova
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina (UFSC), Florianópolis, Brazil
- Icahn School of Medicine, New York, USA
| | - Gabriela Flavia Rodrigues-Luiz
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina (UFSC), Florianópolis, Brazil
| | - Brian J. Ferguson
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | | | - Nerea Irigoyen
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Daniel Santos Mansur
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina (UFSC), Florianópolis, Brazil
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7
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Jayaraman P, Rajagopal M, Paranjpe I, Liharska L, Suarez-Farinas M, Thompson R, Del Valle DM, Beckmann N, Oh W, Gulamali FF, Kauffman J, Gonzalez-Kozlova E, Dellepiane S, Vasquez-Rios G, Vaid A, Jiang J, Chen A, Sakhuja A, Chen S, Kenigsberg E, He JC, Coca SG, Chan L, Schadt E, Merad M, Kim-Schulze S, Gnjatic S, Tsalik E, Langley R, Charney AW, Nadkarni GN. Peripheral Transcriptomics in Acute and Long-Term Kidney Dysfunction in SARS-CoV2 Infection. medRxiv 2023:2023.10.25.23297469. [PMID: 37961671 PMCID: PMC10635190 DOI: 10.1101/2023.10.25.23297469] [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
Background Acute kidney injury (AKI) is common in hospitalized patients with SARS-CoV2 infection despite vaccination and leads to long-term kidney dysfunction. However, peripheral blood molecular signatures in AKI from COVID-19 and their association with long-term kidney dysfunction are yet unexplored. Methods In patients hospitalized with SARS-CoV2, we performed bulk RNA sequencing using peripheral blood mononuclear cells(PBMCs). We applied linear models accounting for technical and biological variability on RNA-Seq data accounting for false discovery rate (FDR) and compared functional enrichment and pathway results to a historical sepsis-AKI cohort. Finally, we evaluated the association of these signatures with long-term trends in kidney function. Results Of 283 patients, 106 had AKI. After adjustment for sex, age, mechanical ventilation, and chronic kidney disease (CKD), we identified 2635 significant differential gene expressions at FDR<0.05. Top canonical pathways were EIF2 signaling, oxidative phosphorylation, mTOR signaling, and Th17 signaling, indicating mitochondrial dysfunction and endoplasmic reticulum (ER) stress. Comparison with sepsis associated AKI showed considerable overlap of key pathways (48.14%). Using follow-up estimated glomerular filtration rate (eGFR) measurements from 115 patients, we identified 164/2635 (6.2%) of the significantly differentiated genes associated with overall decrease in long-term kidney function. The strongest associations were 'autophagy', 'renal impairment via fibrosis', and 'cardiac structure and function'. Conclusions We show that AKI in SARS-CoV2 is a multifactorial process with mitochondrial dysfunction driven by ER stress whereas long-term kidney function decline is associated with cardiac structure and function and immune dysregulation. Functional overlap with sepsis-AKI also highlights common signatures, indicating generalizability in therapeutic approaches. SIGNIFICANCE STATEMENT Peripheral transcriptomic findings in acute and long-term kidney dysfunction after hospitalization for SARS-CoV2 infection are unclear. We evaluated peripheral blood molecular signatures in AKI from COVID-19 (COVID-AKI) and their association with long-term kidney dysfunction using the largest hospitalized cohort with transcriptomic data. Analysis of 283 hospitalized patients of whom 37% had AKI, highlighted the contribution of mitochondrial dysfunction driven by endoplasmic reticulum stress in the acute stages. Subsequently, long-term kidney function decline exhibits significant associations with markers of cardiac structure and function and immune mediated dysregulation. There were similar biomolecular signatures in other inflammatory states, such as sepsis. This enhances the potential for repurposing and generalizability in therapeutic approaches.
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8
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Chen TY, Mihalopoulos M, Zuluaga L, Rich J, Ganta T, Mehrazin R, Tsao CK, Tewari A, Gonzalez-Kozlova E, Badani K, Dogra N, Kyprianou N. Clinical Significance of Extracellular Vesicles in Prostate and Renal Cancer. Int J Mol Sci 2023; 24:14713. [PMID: 37834162 PMCID: PMC10573190 DOI: 10.3390/ijms241914713] [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: 07/15/2023] [Revised: 09/02/2023] [Accepted: 09/03/2023] [Indexed: 10/15/2023] Open
Abstract
Extracellular vesicles (EVs)-including apoptotic bodies, microvesicles, and exosomes-are released by almost all cell types and contain molecular footprints from their cell of origin, including lipids, proteins, metabolites, RNA, and DNA. They have been successfully isolated from blood, urine, semen, and other body fluids. In this review, we discuss the current understanding of the predictive value of EVs in prostate and renal cancer. We also describe the findings supporting the use of EVs from liquid biopsies in stratifying high-risk prostate/kidney cancer and advanced disease, such as castration-resistant (CRPC) and neuroendocrine prostate cancer (NEPC) as well as metastatic renal cell carcinoma (RCC). Assays based on EVs isolated from urine and blood have the potential to serve as highly sensitive diagnostic studies as well as predictive measures of tumor recurrence in patients with prostate and renal cancers. Overall, we discuss the biogenesis, isolation, liquid-biopsy, and therapeutic applications of EVs in CRPC, NEPC, and RCC.
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Affiliation(s)
- Tzu-Yi Chen
- Department of Pathology & Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (T.-Y.C.); (A.T.)
| | - Meredith Mihalopoulos
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (M.M.); (L.Z.); (J.R.); (R.M.); (K.B.)
| | - Laura Zuluaga
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (M.M.); (L.Z.); (J.R.); (R.M.); (K.B.)
| | - Jordan Rich
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (M.M.); (L.Z.); (J.R.); (R.M.); (K.B.)
| | - Teja Ganta
- Department of Hematology/Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (T.G.); (C.-K.T.)
| | - Reza Mehrazin
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (M.M.); (L.Z.); (J.R.); (R.M.); (K.B.)
| | - Che-Kai Tsao
- Department of Hematology/Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (T.G.); (C.-K.T.)
| | - Ash Tewari
- Department of Pathology & Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (T.-Y.C.); (A.T.)
| | - Edgar Gonzalez-Kozlova
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - Ketan Badani
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (M.M.); (L.Z.); (J.R.); (R.M.); (K.B.)
| | - Navneet Dogra
- Department of Pathology & Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (T.-Y.C.); (A.T.)
| | - Natasha Kyprianou
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (M.M.); (L.Z.); (J.R.); (R.M.); (K.B.)
- The Tisch Cancer Institute, Mount Sinai Health, New York, NY 10029, USA
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9
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Coffey DG, Maura F, Gonzalez-Kozlova E, Diaz-Mejia JJ, Luo P, Zhang Y, Xu Y, Warren EH, Dawson T, Lee B, Xie H, Smith E, Ciardiello A, Cho HJ, Rahman A, Kim-Schulze S, Diamond B, Lesokhin A, Kazandjian D, Pugh TJ, Green DJ, Gnjatic S, Landgren O. Immunophenotypic correlates of sustained MRD negativity in patients with multiple myeloma. Nat Commun 2023; 14:5335. [PMID: 37660077 PMCID: PMC10475030 DOI: 10.1038/s41467-023-40966-8] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 08/18/2023] [Indexed: 09/04/2023] Open
Abstract
The role of the immune microenvironment in maintaining disease remission in patients with multiple myeloma (MM) is not well understood. In this study, we comprehensively profile the immune system in patients with newly diagnosed MM receiving continuous lenalidomide maintenance therapy with the aim of discovering correlates of long-term treatment response. Leveraging single-cell RNA sequencing and T cell receptor β sequencing of the peripheral blood and CyTOF mass cytometry of the bone marrow, we longitudinally characterize the immune landscape in 23 patients before and one year after lenalidomide exposure. We compare patients achieving sustained minimal residual disease (MRD) negativity to patients who never achieved or were unable to maintain MRD negativity. We observe that the composition of the immune microenvironment in both the blood and the marrow varied substantially according to both MRD negative status and history of autologous stem cell transplant, supporting the hypothesis that the immune microenvironment influences the depth and duration of treatment response.
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Affiliation(s)
- David G Coffey
- Division of Myeloma, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA.
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
| | - Francesco Maura
- Division of Myeloma, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | | | - J Javier Diaz-Mejia
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Ping Luo
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Yong Zhang
- Office of Oncologic Diseases, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Yuexin Xu
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Edus H Warren
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Travis Dawson
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brian Lee
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hui Xie
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric Smith
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Amanda Ciardiello
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hearn J Cho
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Multiple Myeloma Research Foundation, Norwalk, USA
| | - Adeeb Rahman
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Benjamin Diamond
- Division of Myeloma, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Alexander Lesokhin
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dickran Kazandjian
- Division of Myeloma, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Damian J Green
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Sacha Gnjatic
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ola Landgren
- Division of Myeloma, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA.
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10
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Li X, La Salvia S, Liang Y, Adamiak M, Kohlbrenner E, Jeong D, Chepurko E, Ceholski D, Lopez-Gordo E, Yoon S, Mathiyalagan P, Agarwal N, Jha D, Lodha S, Daaboul G, Phan A, Raisinghani N, Zhang S, Zangi L, Gonzalez-Kozlova E, Dubois N, Dogra N, Hajjar RJ, Sahoo S. Extracellular Vesicle-Encapsulated Adeno-Associated Viruses for Therapeutic Gene Delivery to the Heart. Circulation 2023; 148:405-425. [PMID: 37409482 DOI: 10.1161/circulationaha.122.063759] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 05/16/2023] [Indexed: 07/07/2023]
Abstract
BACKGROUND Adeno-associated virus (AAV) has emerged as one of the best tools for cardiac gene delivery due to its cardiotropism, long-term expression, and safety. However, a significant challenge to its successful clinical use is preexisting neutralizing antibodies (NAbs), which bind to free AAVs, prevent efficient gene transduction, and reduce or negate therapeutic effects. Here we describe extracellular vesicle-encapsulated AAVs (EV-AAVs), secreted naturally by AAV-producing cells, as a superior cardiac gene delivery vector that delivers more genes and offers higher NAb resistance. METHODS We developed a 2-step density-gradient ultracentrifugation method to isolate highly purified EV-AAVs. We compared the gene delivery and therapeutic efficacy of EV-AAVs with an equal titer of free AAVs in the presence of NAbs, both in vitro and in vivo. In addition, we investigated the mechanism of EV-AAV uptake in human left ventricular and human induced pluripotent stem cell-derived cardiomyocytes in vitro and mouse models in vivo using a combination of biochemical techniques, flow cytometry, and immunofluorescence imaging. RESULTS Using cardiotropic AAV serotypes 6 and 9 and several reporter constructs, we demonstrated that EV-AAVs deliver significantly higher quantities of genes than AAVs in the presence of NAbs, both to human left ventricular and human induced pluripotent stem cell-derived cardiomyocytes in vitro and to mouse hearts in vivo. Intramyocardial delivery of EV-AAV9-sarcoplasmic reticulum calcium ATPase 2a to infarcted hearts in preimmunized mice significantly improved ejection fraction and fractional shortening compared with AAV9-sarcoplasmic reticulum calcium ATPase 2a delivery. These data validated NAb evasion by and therapeutic efficacy of EV-AAV9 vectors. Trafficking studies using human induced pluripotent stem cell-derived cells in vitro and mouse hearts in vivo showed significantly higher expression of EV-AAV6/9-delivered genes in cardiomyocytes compared with noncardiomyocytes, even with comparable cellular uptake. Using cellular subfraction analyses and pH-sensitive dyes, we discovered that EV-AAVs were internalized into acidic endosomal compartments of cardiomyocytes for releasing and acidifying AAVs for their nuclear uptake. CONCLUSIONS Together, using 5 different in vitro and in vivo model systems, we demonstrate significantly higher potency and therapeutic efficacy of EV-AAV vectors compared with free AAVs in the presence of NAbs. These results establish the potential of EV-AAV vectors as a gene delivery tool to treat heart failure.
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Affiliation(s)
- Xisheng Li
- Cardiovascular Research Institute (X.L., S.L.S., M.A., E.C., D.C., E.L.-G., S.Y., N.A., D.J., S.L., A.P., N.R., S.Z., L.Z., S.S.), Icahn School of Medicine at Mount Sinai, New York, NY
| | - Sabrina La Salvia
- Cardiovascular Research Institute (X.L., S.L.S., M.A., E.C., D.C., E.L.-G., S.Y., N.A., D.J., S.L., A.P., N.R., S.Z., L.Z., S.S.), Icahn School of Medicine at Mount Sinai, New York, NY
| | - Yaxuan Liang
- Center for Biological Science and Technology, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, China (Y.L.)
| | - Marta Adamiak
- Cardiovascular Research Institute (X.L., S.L.S., M.A., E.C., D.C., E.L.-G., S.Y., N.A., D.J., S.L., A.P., N.R., S.Z., L.Z., S.S.), Icahn School of Medicine at Mount Sinai, New York, NY
| | - Erik Kohlbrenner
- Cardiovascular Research Institute (X.L., S.L.S., M.A., E.C., D.C., E.L.-G., S.Y., N.A., D.J., S.L., A.P., N.R., S.Z., L.Z., S.S.), Icahn School of Medicine at Mount Sinai, New York, NY
- Spark Therapeutics, Philadelphia, PA (E.K.)
| | - Dongtak Jeong
- Department of Molecular and Life Science, College of Science and Convergence Technology, Hanyang University-ERICA, Ansan, South Korea (D.J.)
| | - Elena Chepurko
- Cardiovascular Research Institute (X.L., S.L.S., M.A., E.C., D.C., E.L.-G., S.Y., N.A., D.J., S.L., A.P., N.R., S.Z., L.Z., S.S.), Icahn School of Medicine at Mount Sinai, New York, NY
| | - Delaine Ceholski
- Cardiovascular Research Institute (X.L., S.L.S., M.A., E.C., D.C., E.L.-G., S.Y., N.A., D.J., S.L., A.P., N.R., S.Z., L.Z., S.S.), Icahn School of Medicine at Mount Sinai, New York, NY
| | - Estrella Lopez-Gordo
- Cardiovascular Research Institute (X.L., S.L.S., M.A., E.C., D.C., E.L.-G., S.Y., N.A., D.J., S.L., A.P., N.R., S.Z., L.Z., S.S.), Icahn School of Medicine at Mount Sinai, New York, NY
| | - Seonghun Yoon
- Cardiovascular Research Institute (X.L., S.L.S., M.A., E.C., D.C., E.L.-G., S.Y., N.A., D.J., S.L., A.P., N.R., S.Z., L.Z., S.S.), Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Neha Agarwal
- Cardiovascular Research Institute (X.L., S.L.S., M.A., E.C., D.C., E.L.-G., S.Y., N.A., D.J., S.L., A.P., N.R., S.Z., L.Z., S.S.), Icahn School of Medicine at Mount Sinai, New York, NY
| | - Divya Jha
- Cardiovascular Research Institute (X.L., S.L.S., M.A., E.C., D.C., E.L.-G., S.Y., N.A., D.J., S.L., A.P., N.R., S.Z., L.Z., S.S.), Icahn School of Medicine at Mount Sinai, New York, NY
| | - Shweta Lodha
- Cardiovascular Research Institute (X.L., S.L.S., M.A., E.C., D.C., E.L.-G., S.Y., N.A., D.J., S.L., A.P., N.R., S.Z., L.Z., S.S.), Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Anh Phan
- Cardiovascular Research Institute (X.L., S.L.S., M.A., E.C., D.C., E.L.-G., S.Y., N.A., D.J., S.L., A.P., N.R., S.Z., L.Z., S.S.), Icahn School of Medicine at Mount Sinai, New York, NY
| | - Nikhil Raisinghani
- Cardiovascular Research Institute (X.L., S.L.S., M.A., E.C., D.C., E.L.-G., S.Y., N.A., D.J., S.L., A.P., N.R., S.Z., L.Z., S.S.), Icahn School of Medicine at Mount Sinai, New York, NY
| | - Shihong Zhang
- Cardiovascular Research Institute (X.L., S.L.S., M.A., E.C., D.C., E.L.-G., S.Y., N.A., D.J., S.L., A.P., N.R., S.Z., L.Z., S.S.), Icahn School of Medicine at Mount Sinai, New York, NY
| | - Lior Zangi
- Cardiovascular Research Institute (X.L., S.L.S., M.A., E.C., D.C., E.L.-G., S.Y., N.A., D.J., S.L., A.P., N.R., S.Z., L.Z., S.S.), Icahn School of Medicine at Mount Sinai, New York, NY
| | - Edgar Gonzalez-Kozlova
- Department of Oncological Sciences (E.G.-K.), Icahn School of Medicine at Mount Sinai, New York, NY
| | - Nicole Dubois
- Department of Cell, Developmental and Regenerative Biology (N. Dubois), Icahn School of Medicine at Mount Sinai, New York, NY
- Mindich Child Health and Development Institute (N. Dubois), Icahn School of Medicine at Mount Sinai, New York, NY
| | - Navneet Dogra
- Department of Pathology and Laboratory Medicine (N. Dogra), Icahn School of Medicine at Mount Sinai, New York, NY
- Icahn Genomics Institute (N.Dogra), Icahn School of Medicine at Mount Sinai, New York, NY
| | - Roger J Hajjar
- Gene and Cell Therapy Institute, Massachusetts General Brigham, Boston (R.J.H.)
| | - Susmita Sahoo
- Cardiovascular Research Institute (X.L., S.L.S., M.A., E.C., D.C., E.L.-G., S.Y., N.A., D.J., S.L., A.P., N.R., S.Z., L.Z., S.S.), Icahn School of Medicine at Mount Sinai, New York, NY
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11
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Paranjpe I, Jayaraman P, Su CY, Zhou S, Chen S, Thompson R, Del Valle DM, Kenigsberg E, Zhao S, Jaladanki S, Chaudhary K, Ascolillo S, Vaid A, Gonzalez-Kozlova E, Kauffman J, Kumar A, Paranjpe M, Hagan RO, Kamat S, Gulamali FF, Xie H, Harris J, Patel M, Argueta K, Batchelor C, Nie K, Dellepiane S, Scott L, Levin MA, He JC, Suarez-Farinas M, Coca SG, Chan L, Azeloglu EU, Schadt E, Beckmann N, Gnjatic S, Merad M, Kim-Schulze S, Richards B, Glicksberg BS, Charney AW, Nadkarni GN. Proteomic characterization of acute kidney injury in patients hospitalized with SARS-CoV2 infection. Commun Med (Lond) 2023; 3:81. [PMID: 37308534 PMCID: PMC10258469 DOI: 10.1038/s43856-023-00307-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 05/18/2023] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND Acute kidney injury (AKI) is a known complication of COVID-19 and is associated with an increased risk of in-hospital mortality. Unbiased proteomics using biological specimens can lead to improved risk stratification and discover pathophysiological mechanisms. METHODS Using measurements of ~4000 plasma proteins in two cohorts of patients hospitalized with COVID-19, we discovered and validated markers of COVID-associated AKI (stage 2 or 3) and long-term kidney dysfunction. In the discovery cohort (N = 437), we identified 413 higher plasma abundances of protein targets and 30 lower plasma abundances of protein targets associated with COVID-AKI (adjusted p < 0.05). Of these, 62 proteins were validated in an external cohort (p < 0.05, N = 261). RESULTS We demonstrate that COVID-AKI is associated with increased markers of tubular injury (NGAL) and myocardial injury. Using estimated glomerular filtration (eGFR) measurements taken after discharge, we also find that 25 of the 62 AKI-associated proteins are significantly associated with decreased post-discharge eGFR (adjusted p < 0.05). Proteins most strongly associated with decreased post-discharge eGFR included desmocollin-2, trefoil factor 3, transmembrane emp24 domain-containing protein 10, and cystatin-C indicating tubular dysfunction and injury. CONCLUSIONS Using clinical and proteomic data, our results suggest that while both acute and long-term COVID-associated kidney dysfunction are associated with markers of tubular dysfunction, AKI is driven by a largely multifactorial process involving hemodynamic instability and myocardial damage.
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Affiliation(s)
- Ishan Paranjpe
- Department of Medicine, Stanford University, Stanford, CA, USA
| | - Pushkala Jayaraman
- The Charles Bronfman Institute for Personalized Medicine (CBIPM), Division of Data Driven and Digital Medicine (D3M), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Chen-Yang Su
- Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
- Department of Computer Science, Quantitative Life Sciences, McGill University, Montreal, QC, Canada
| | - Sirui Zhou
- Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Steven Chen
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ryan Thompson
- The Charles Bronfman Institute for Personalized Medicine (CBIPM), Division of Data Driven and Digital Medicine (D3M), Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mount Sinai Clinical Intelligence Center (MSCIC), The Charles Bronfman Institute for Personalized Medicine (CBIPM), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Diane Marie Del Valle
- The Mount Sinai Clinical Intelligence Center (MSCIC), The Charles Bronfman Institute for Personalized Medicine (CBIPM), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ephraim Kenigsberg
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shan Zhao
- Department of Anesthesiology, Perioperative and Pain Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Suraj Jaladanki
- The Mount Sinai Clinical Intelligence Center (MSCIC), The Charles Bronfman Institute for Personalized Medicine (CBIPM), Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kumardeep Chaudhary
- Clinical Informatics, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Steven Ascolillo
- The Mount Sinai Clinical Intelligence Center (MSCIC), The Charles Bronfman Institute for Personalized Medicine (CBIPM), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Akhil Vaid
- The Mount Sinai Clinical Intelligence Center (MSCIC), The Charles Bronfman Institute for Personalized Medicine (CBIPM), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edgar Gonzalez-Kozlova
- The Mount Sinai Clinical Intelligence Center (MSCIC), The Charles Bronfman Institute for Personalized Medicine (CBIPM), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Justin Kauffman
- The Mount Sinai Clinical Intelligence Center (MSCIC), The Charles Bronfman Institute for Personalized Medicine (CBIPM), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Arvind Kumar
- The Mount Sinai Clinical Intelligence Center (MSCIC), The Charles Bronfman Institute for Personalized Medicine (CBIPM), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Manish Paranjpe
- Division of Health Sciences and Technology, Harvard Medical School, Boston, MA, USA
| | - Ross O Hagan
- The Mount Sinai Clinical Intelligence Center (MSCIC), The Charles Bronfman Institute for Personalized Medicine (CBIPM), Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Samir Kamat
- The Mount Sinai Clinical Intelligence Center (MSCIC), The Charles Bronfman Institute for Personalized Medicine (CBIPM), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Faris F Gulamali
- The Mount Sinai Clinical Intelligence Center (MSCIC), The Charles Bronfman Institute for Personalized Medicine (CBIPM), Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hui Xie
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joceyln Harris
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Manishkumar Patel
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kimberly Argueta
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Craig Batchelor
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kai Nie
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sergio Dellepiane
- Department of Medicine, Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Leisha Scott
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew A Levin
- The Mount Sinai Clinical Intelligence Center (MSCIC), The Charles Bronfman Institute for Personalized Medicine (CBIPM), Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Anesthesiology, Perioperative and Pain Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John Cijiang He
- Department of Medicine, Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mayte Suarez-Farinas
- Department of Biostatistics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Steven G Coca
- Department of Medicine, Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lili Chan
- Department of Medicine, Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Evren U Azeloglu
- Department of Medicine, Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Noam Beckmann
- The Mount Sinai Clinical Intelligence Center (MSCIC), The Charles Bronfman Institute for Personalized Medicine (CBIPM), Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sacha Gnjatic
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Miram Merad
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Seunghee Kim-Schulze
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brent Richards
- Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
- Department of Computer Science, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Department of Twin Research, King's College London, London, GB, UK
| | | | - Alexander W Charney
- Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Charles Bronfman Institute for Personalized Medicine (CBIPM), Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Girish N Nadkarni
- The Charles Bronfman Institute for Personalized Medicine (CBIPM), Division of Data Driven and Digital Medicine (D3M), Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada.
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Medicine, Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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12
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Magen A, Hamon P, Fiaschi N, Soong BY, Park MD, Mattiuz R, Humblin E, Troncoso L, D'souza D, Dawson T, Kim J, Hamel S, Buckup M, Chang C, Tabachnikova A, Schwartz H, Malissen N, Lavin Y, Soares-Schanoski A, Giotti B, Hegde S, Ioannou G, Gonzalez-Kozlova E, Hennequin C, Le Berichel J, Zhao Z, Ward SC, Fiel I, Kou B, Dobosz M, Li L, Adler C, Ni M, Wei Y, Wang W, Atwal GS, Kundu K, Cygan KJ, Tsankov AM, Rahman A, Price C, Fernandez N, He J, Gupta NT, Kim-Schulze S, Gnjatic S, Kenigsberg E, Deering RP, Schwartz M, Marron TU, Thurston G, Kamphorst AO, Merad M. Intratumoral dendritic cell-CD4 + T helper cell niches enable CD8 + T cell differentiation following PD-1 blockade in hepatocellular carcinoma. Nat Med 2023; 29:1389-1399. [PMID: 37322116 PMCID: PMC11027932 DOI: 10.1038/s41591-023-02345-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 04/10/2023] [Indexed: 06/17/2023]
Abstract
Despite no apparent defects in T cell priming and recruitment to tumors, a large subset of T cell rich tumors fail to respond to immune checkpoint blockade (ICB). We leveraged a neoadjuvant anti-PD-1 trial in patients with hepatocellular carcinoma (HCC), as well as additional samples collected from patients treated off-label, to explore correlates of response to ICB within T cell-rich tumors. We show that ICB response correlated with the clonal expansion of intratumoral CXCL13+CH25H+IL-21+PD-1+CD4+ T helper cells ("CXCL13+ TH") and Granzyme K+ PD-1+ effector-like CD8+ T cells, whereas terminally exhausted CD39hiTOXhiPD-1hiCD8+ T cells dominated in nonresponders. CD4+ and CD8+ T cell clones that expanded post-treatment were found in pretreatment biopsies. Notably, PD-1+TCF-1+ (Progenitor-exhausted) CD8+ T cells shared clones mainly with effector-like cells in responders or terminally exhausted cells in nonresponders, suggesting that local CD8+ T cell differentiation occurs upon ICB. We found that these Progenitor CD8+ T cells interact with CXCL13+ TH within cellular triads around dendritic cells enriched in maturation and regulatory molecules, or "mregDC". These results suggest that discrete intratumoral niches that include mregDC and CXCL13+ TH control the differentiation of tumor-specific Progenitor exhasuted CD8+ T cells following ICB.
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Affiliation(s)
- Assaf Magen
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Pauline Hamon
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nathalie Fiaschi
- Department of Oncology & Angiogenesis, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Brian Y Soong
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew D Park
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Raphaël Mattiuz
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Etienne Humblin
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Leanna Troncoso
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Darwin D'souza
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Travis Dawson
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joel Kim
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Steven Hamel
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mark Buckup
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Christie Chang
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexandra Tabachnikova
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hara Schwartz
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nausicaa Malissen
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yonit Lavin
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alessandra Soares-Schanoski
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bruno Giotti
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Samarth Hegde
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Giorgio Ioannou
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edgar Gonzalez-Kozlova
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Clotilde Hennequin
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jessica Le Berichel
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zhen Zhao
- The Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stephen C Ward
- The Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Isabel Fiel
- The Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Baijun Kou
- Department of Oncology & Angiogenesis, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Michael Dobosz
- Department of Oncology & Angiogenesis, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Lianjie Li
- Department of Oncology & Angiogenesis, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Christina Adler
- Molecular Profiling & Data Science, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Min Ni
- Molecular Profiling & Data Science, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Yi Wei
- Molecular Profiling & Data Science, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Wei Wang
- Molecular Profiling & Data Science, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Gurinder S Atwal
- Molecular Profiling & Data Science, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Kunal Kundu
- VI NEXT, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Kamil J Cygan
- VI NEXT, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Alexander M Tsankov
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adeeb Rahman
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | | | - Namita T Gupta
- Molecular Profiling & Data Science, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Seunghee Kim-Schulze
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sacha Gnjatic
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ephraim Kenigsberg
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Raquel P Deering
- Department of Oncology & Angiogenesis, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Myron Schwartz
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Division of Hematology/Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Thomas U Marron
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Division of Hematology/Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Gavin Thurston
- Department of Oncology & Angiogenesis, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA.
| | - Alice O Kamphorst
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Miriam Merad
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Institute for Thoracic Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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13
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Soleymani T, Chen TY, Gonzalez-Kozlova E, Dogra N. The human neurosecretome: extracellular vesicles and particles (EVPs) of the brain for intercellular communication, therapy, and liquid-biopsy applications. Front Mol Biosci 2023; 10:1156821. [PMID: 37266331 PMCID: PMC10229797 DOI: 10.3389/fmolb.2023.1156821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/25/2023] [Indexed: 06/03/2023] Open
Abstract
Emerging evidence suggests that brain derived extracellular vesicles (EVs) and particles (EPs) can cross blood-brain barrier and mediate communication among neurons, astrocytes, microglial, and other cells of the central nervous system (CNS). Yet, a complete understanding of the molecular landscape and function of circulating EVs & EPs (EVPs) remain a major gap in knowledge. This is mainly due to the lack of technologies to isolate and separate all EVPs of heterogeneous dimensions and low buoyant density. In this review, we aim to provide a comprehensive understanding of the neurosecretome, including the extracellular vesicles that carry the molecular signature of the brain in both its microenvironment and the systemic circulation. We discuss the biogenesis of EVPs, their function, cell-to-cell communication, past and emerging isolation technologies, therapeutics, and liquid-biopsy applications. It is important to highlight that the landscape of EVPs is in a constant state of evolution; hence, we not only discuss the past literature and current landscape of the EVPs, but we also speculate as to how novel EVPs may contribute to the etiology of addiction, depression, psychiatric, neurodegenerative diseases, and aid in the real time monitoring of the "living brain". Overall, the neurosecretome is a concept we introduce here to embody the compendium of circulating particles of the brain for their function and disease pathogenesis. Finally, for the purpose of inclusion of all extracellular particles, we have used the term EVPs as defined by the International Society of Extracellular Vesicles (ISEV).
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Affiliation(s)
- Taliah Soleymani
- Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Tzu-Yi Chen
- Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Edgar Gonzalez-Kozlova
- Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Navneet Dogra
- Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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14
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Su CY, Zhou S, Gonzalez-Kozlova E, Butler-Laporte G, Brunet-Ratnasingham E, Nakanishi T, Jeon W, Morrison DR, Laurent L, Afilalo J, Afilalo M, Henry D, Chen Y, Carrasco-Zanini J, Farjoun Y, Pietzner M, Kimchi N, Afrasiabi Z, Rezk N, Bouab M, Petitjean L, Guzman C, Xue X, Tselios C, Vulesevic B, Adeleye O, Abdullah T, Almamlouk N, Moussa Y, DeLuca C, Duggan N, Schurr E, Brassard N, Durand M, Del Valle DM, Thompson R, Cedillo MA, Schadt E, Nie K, Simons NW, Mouskas K, Zaki N, Patel M, Xie H, Harris J, Marvin R, Cheng E, Tuballes K, Argueta K, Scott I, Greenwood CMT, Paterson C, Hinterberg MA, Langenberg C, Forgetta V, Pineau J, Mooser V, Marron T, Beckmann ND, Kim-Schulze S, Charney AW, Gnjatic S, Kaufmann DE, Merad M, Richards JB. Circulating proteins to predict COVID-19 severity. Sci Rep 2023; 13:6236. [PMID: 37069249 PMCID: PMC10107586 DOI: 10.1038/s41598-023-31850-y] [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: 06/02/2022] [Accepted: 03/17/2023] [Indexed: 04/19/2023] Open
Abstract
Predicting COVID-19 severity is difficult, and the biological pathways involved are not fully understood. To approach this problem, we measured 4701 circulating human protein abundances in two independent cohorts totaling 986 individuals. We then trained prediction models including protein abundances and clinical risk factors to predict COVID-19 severity in 417 subjects and tested these models in a separate cohort of 569 individuals. For severe COVID-19, a baseline model including age and sex provided an area under the receiver operator curve (AUC) of 65% in the test cohort. Selecting 92 proteins from the 4701 unique protein abundances improved the AUC to 88% in the training cohort, which remained relatively stable in the testing cohort at 86%, suggesting good generalizability. Proteins selected from different COVID-19 severity were enriched for cytokine and cytokine receptors, but more than half of the enriched pathways were not immune-related. Taken together, these findings suggest that circulating proteins measured at early stages of disease progression are reasonably accurate predictors of COVID-19 severity. Further research is needed to understand how to incorporate protein measurement into clinical care.
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Affiliation(s)
- Chen-Yang Su
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
- Department of Computer Science, McGill University, Montréal, QC, Canada
- Quantitative Life Sciences Program, McGill University, Montreal, Quebec, Canada
| | - Sirui Zhou
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | | | - Guillaume Butler-Laporte
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | | | - Tomoko Nakanishi
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Graduate School of Medicine, McGill International Collaborative School in Genomic Medicine, Kyoto University, Kyoto, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | - Wonseok Jeon
- Department of Computer Science, McGill University, Montréal, QC, Canada
| | - David R Morrison
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Laetitia Laurent
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Jonathan Afilalo
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Marc Afilalo
- Department of Emergency Medicine, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Danielle Henry
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Yiheng Chen
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Julia Carrasco-Zanini
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Yossi Farjoun
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Maik Pietzner
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Computational Medicine, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Nofar Kimchi
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Zaman Afrasiabi
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Nardin Rezk
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Meriem Bouab
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Louis Petitjean
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Charlotte Guzman
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Xiaoqing Xue
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Chris Tselios
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Branka Vulesevic
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Olumide Adeleye
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Tala Abdullah
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Noor Almamlouk
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Yara Moussa
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Chantal DeLuca
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Naomi Duggan
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Erwin Schurr
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, QC, Canada
| | - Nathalie Brassard
- Research Centre of the Centre Hospitalier de L'Université de Montréal, Montreal, QC, Canada
| | - Madeleine Durand
- Research Centre of the Centre Hospitalier de L'Université de Montréal, Montreal, QC, Canada
| | - Diane Marie Del Valle
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ryan Thompson
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mario A Cedillo
- Department of Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric Schadt
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kai Nie
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nicole W Simons
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Konstantinos Mouskas
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nicolas Zaki
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Manishkumar Patel
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hui Xie
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jocelyn Harris
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert Marvin
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Esther Cheng
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kevin Tuballes
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kimberly Argueta
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ieisha Scott
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Celia M T Greenwood
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | | | | | - Claudia Langenberg
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Computational Medicine, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Vincenzo Forgetta
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Joelle Pineau
- Department of Computer Science, McGill University, Montréal, QC, Canada
| | - Vincent Mooser
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Thomas Marron
- Immunotherapy and Phase 1 Trials, Mount Sinai Hospital, New York, NY, USA
| | - Noam D Beckmann
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Seunghee Kim-Schulze
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexander W Charney
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sacha Gnjatic
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniel E Kaufmann
- Research Centre of the Centre Hospitalier de L'Université de Montréal, Montreal, QC, Canada
- Department of Medicine, Université de Montréal, Montreal, QC, Canada
- Division of Infectious Diseases, Department of Medicine, University Hospital of Lausanne and University of Lausanne, Lausanne, Switzerland
| | - Miriam Merad
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - J Brent Richards
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada.
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada.
- Department of Human Genetics, McGill University, Montreal, QC, Canada.
- Department of Twin Research, King's College London, London, UK.
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15
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Nadkarni G, Paranjpe I, Jayaraman P, Su CY, Zhou S, Chen S, Valle DD, Thompson R, Kenigsberg E, Zhao S, Jaladanki S, Chaudhary K, Ascolillo S, Vaid A, Gonzalez-Kozlova E, Kumar A, Paranjpe M, O'Hagan R, Kamat S, Gulamali F, Kauffman J, Xie H, Harris J, Patel M, Argueta K, Batchelor C, Nie K, Dellepiane S, Scott L, Levin M, He J, Suárez-Fariñas M, Coca S, Chan L, Azeloglu E, Schadt E, Beckmann N, Gnjatic S, Merad M, Kim-Schulze S, Richards JB, Glicksberg B, Charney A. Proteomic Characterization of Acute Kidney Injury in Patients Hospitalized with SARS-CoV2 Infection. Res Sq 2023:rs.3.rs-2379226. [PMID: 36993735 PMCID: PMC10055503 DOI: 10.21203/rs.3.rs-2379226/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
Background Acute kidney injury (AKI) is a known complication of COVID-19 and is associated with an increased risk of in-hospital mortality. Unbiased proteomics using biological specimens can lead to improved risk stratification and discover pathophysiological mechanisms. Methods Using measurements of ~4000 plasma proteins in two cohorts of patients hospitalized with COVID-19, we discovered and validated markers of COVID-associated AKI (stage 2 or 3) and long-term kidney dysfunction. In the discovery cohort (N= 437), we identified 413 higher plasma abundances of protein targets and 40 lower plasma abundances of protein targets associated with COVID-AKI (adjusted p <0.05). Of these, 62 proteins were validated in an external cohort (p <0.05, N =261). Results We demonstrate that COVID-AKI is associated with increased markers of tubular injury ( NGAL ) and myocardial injury. Using estimated glomerular filtration (eGFR) measurements taken after discharge, we also find that 25 of the 62 AKI-associated proteins are significantly associated with decreased post-discharge eGFR (adjusted p <0.05). Proteins most strongly associated with decreased post-discharge eGFR included desmocollin-2 , trefoil factor 3 , transmembrane emp24 domain-containing protein 10 , and cystatin-C indicating tubular dysfunction and injury. Conclusions Using clinical and proteomic data, our results suggest that while both acute and long-term COVID-associated kidney dysfunction are associated with markers of tubular dysfunction, AKI is driven by a largely multifactorial process involving hemodynamic instability and myocardial damage.
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16
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Aranda CJ, Gonzalez-Kozlova E, Saunders SP, Fernandes-Braga W, Ota M, Narayanan S, He JS, Del Duca E, Swaroop B, Gnjatic S, Shattner G, Reibman J, Soter NA, Guttman-Yassky E, Curotto de Lafaille MA. IgG memory B cells expressing IL4R and FCER2 are associated with atopic diseases. Allergy 2023; 78:752-766. [PMID: 36445014 PMCID: PMC9991991 DOI: 10.1111/all.15601] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [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: 07/02/2022] [Revised: 10/25/2022] [Accepted: 11/17/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND Atopic diseases are characterized by IgE antibody responses that are dependent on cognate CD4 T cell help and T cell-produced IL-4 and IL-13. Current models of IgE cell differentiation point to the role of IgG memory B cells as precursors of pathogenic IgE plasma cells. The goal of this work was to identify intrinsic features of memory B cells that are associated with IgE production in atopic diseases. METHODS Peripheral blood B lymphocytes were collected from individuals with physician diagnosed asthma or atopic dermatitis (AD) and from non-atopic individuals. These samples were analyzed by spectral flow cytometry, single cell RNA sequencing (scRNAseq), and in vitro activation assays. RESULTS We identified a novel population of IgG memory B cells characterized by the expression of IL-4/IL-13 regulated genes FCER2/CD23, IL4R, IL13RA1, and IGHE, denoting a history of differentiation during type 2 immune responses. CD23+ IL4R+ IgG+ memory B cells had increased occurrence in individuals with atopic disease. Importantly, the frequency of CD23+ IL4R+ IgG+ memory B cells correlated with levels of circulating IgE. Consistently, in vitro stimulated B cells from atopic individuals generated more IgE+ cells than B cells from non-atopic subjects. CONCLUSIONS These findings suggest that CD23+ IL4R+ IgG+ memory B cells transcribing IGHE are potential precursors of IgE plasma cells and are linked to pathogenic IgE production.
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Affiliation(s)
- Carlos J Aranda
- Division of Allergy and Immunology, Department of Pediatrics, Jaffe Food Allergy Institute, Icahn School of Medicine at Mount Sinai (ISMMS), New York, New York, USA
- Precision Immunology Institute (PrIISM), ISMMS, New York, New York, USA
| | | | - Sean P Saunders
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine (NYUSM), New York, New York, USA
| | - Weslley Fernandes-Braga
- Division of Allergy and Immunology, Department of Pediatrics, Jaffe Food Allergy Institute, Icahn School of Medicine at Mount Sinai (ISMMS), New York, New York, USA
- Precision Immunology Institute (PrIISM), ISMMS, New York, New York, USA
| | - Miyo Ota
- Division of Allergy and Immunology, Department of Pediatrics, Jaffe Food Allergy Institute, Icahn School of Medicine at Mount Sinai (ISMMS), New York, New York, USA
- Precision Immunology Institute (PrIISM), ISMMS, New York, New York, USA
| | - Sriram Narayanan
- Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
| | - Jin-Shu He
- Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
| | - Ester Del Duca
- Department of Dermatology, ISMMS, New York, New York, USA
| | - Bose Swaroop
- Department of Dermatology, ISMMS, New York, New York, USA
| | - Sacha Gnjatic
- Precision Immunology Institute (PrIISM), ISMMS, New York, New York, USA
- Tisch Cancer Institute, ISMMS, New York, New York, USA
| | - Gail Shattner
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine (NYUSM), New York, New York, USA
| | - Joan Reibman
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine (NYUSM), New York, New York, USA
| | | | | | - Maria A Curotto de Lafaille
- Division of Allergy and Immunology, Department of Pediatrics, Jaffe Food Allergy Institute, Icahn School of Medicine at Mount Sinai (ISMMS), New York, New York, USA
- Precision Immunology Institute (PrIISM), ISMMS, New York, New York, USA
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17
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Pilcher W, Thomas BE, Bhasin SS, Jayasinghe RG, Yao L, Gonzalez-Kozlova E, Dasari S, Kim-Schulze S, Rahman A, Patton J, Fiala M, Cheloni G, Kourelis T, Dhodapkar MV, Vij R, Mehr S, Hamilton M, Cho HJ, Auclair D, Avigan DE, Kumar SK, Gnjatic S, Ding L, Bhasin M. Cross center single-cell RNA sequencing study of the immune microenvironment in rapid progressing multiple myeloma. NPJ Genom Med 2023; 8:3. [PMID: 36702834 PMCID: PMC9879959 DOI: 10.1038/s41525-022-00340-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 11/18/2022] [Indexed: 01/27/2023] Open
Abstract
Despite advancements in understanding the pathophysiology of Multiple Myeloma (MM), the cause of rapid progressing disease in a subset of patients is still unclear. MM's progression is facilitated by complex interactions with the surrounding bone marrow (BM) cells, forming a microenvironment that supports tumor growth and drug resistance. Understanding the immune microenvironment is key to identifying factors that promote rapid progression of MM. To accomplish this, we performed a multi-center single-cell RNA sequencing (scRNA-seq) study on 102,207 cells from 48 CD138- BM samples collected at the time of disease diagnosis from 18 patients with either rapid progressing (progression-free survival (PFS) < 18 months) or non-progressing (PFS > 4 years) disease. Comparative analysis of data from three centers demonstrated similar transcriptome profiles and cell type distributions, indicating subtle technical variation in scRNA-seq, opening avenues for an expanded multicenter trial. Rapid progressors depicted significantly higher enrichment of GZMK+ and TIGIT+ exhausted CD8+ T-cells (P = 0.022) along with decreased expression of cytolytic markers (PRF1, GZMB, GNLY). We also observed a significantly higher enrichment of M2 tolerogenic macrophages in rapid progressors and activation of pro-proliferative signaling pathways, such as BAFF, CCL, and IL16. On the other hand, non-progressive patients depicted higher enrichment for immature B Cells (i.e., Pre/Pro B cells), with elevated expression for markers of B cell development (IGLL1, SOX4, DNTT). This multi-center study identifies the enrichment of various pro-tumorigenic cell populations and pathways in those with rapid progressing disease and further validates the robustness of scRNA-seq data generated at different study centers.
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Affiliation(s)
- William Pilcher
- Aflac Cancer and Blood Disorders Center, Atlanta, GA USA ,grid.189967.80000 0001 0941 6502Coulter Department of Biomedical Engineering, Emory University, Atlanta, GA USA
| | - Beena E. Thomas
- Aflac Cancer and Blood Disorders Center, Atlanta, GA USA ,grid.189967.80000 0001 0941 6502Department of Pediatrics, Emory School of Medicine, Atlanta, GA USA
| | - Swati S. Bhasin
- Aflac Cancer and Blood Disorders Center, Atlanta, GA USA ,grid.189967.80000 0001 0941 6502Department of Pediatrics, Emory School of Medicine, Atlanta, GA USA
| | - Reyka G. Jayasinghe
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University School of Medicine, Saint Louis, MO USA
| | - Lijun Yao
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University School of Medicine, Saint Louis, MO USA
| | - Edgar Gonzalez-Kozlova
- grid.59734.3c0000 0001 0670 2351Human Immune Monitoring Center, Icahn School of Medicine at Mt. Sinai, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Surendra Dasari
- grid.66875.3a0000 0004 0459 167XDivision of Biomedical Statistics & Informatics, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN USA
| | - Seunghee Kim-Schulze
- grid.59734.3c0000 0001 0670 2351Human Immune Monitoring Center, Icahn School of Medicine at Mt. Sinai, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Adeeb Rahman
- grid.59734.3c0000 0001 0670 2351Human Immune Monitoring Center, Icahn School of Medicine at Mt. Sinai, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | | | - Mark Fiala
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University School of Medicine, Saint Louis, MO USA
| | - Giulia Cheloni
- grid.38142.3c000000041936754XBeth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA USA
| | - Taxiarchis Kourelis
- grid.66875.3a0000 0004 0459 167XMayo Clinic Rochester, Division of Hematology, Rochester, MN USA
| | - Madhav V. Dhodapkar
- grid.189967.80000 0001 0941 6502Department of Hematology/Medical Oncology Emory University School of Medicine, Atlanta, GA USA ,grid.189967.80000 0001 0941 6502Winship Cancer Institute, Emory University, Atlanta, GA USA
| | - Ravi Vij
- grid.4367.60000 0001 2355 7002Washington University School of Medicine, St Louis, MO USA
| | - Shaadi Mehr
- grid.429426.f0000 0000 9350 5788Multiple Myeloma Research Foundation (MMRF), Norwalk, CT USA
| | - Mark Hamilton
- grid.429426.f0000 0000 9350 5788Multiple Myeloma Research Foundation (MMRF), Norwalk, CT USA
| | - Hearn Jay Cho
- grid.59734.3c0000 0001 0670 2351Human Immune Monitoring Center, Icahn School of Medicine at Mt. Sinai, New York, NY USA ,grid.429426.f0000 0000 9350 5788Multiple Myeloma Research Foundation (MMRF), Norwalk, CT USA
| | - Daniel Auclair
- grid.429426.f0000 0000 9350 5788Multiple Myeloma Research Foundation (MMRF), Norwalk, CT USA
| | - David E. Avigan
- grid.38142.3c000000041936754XBeth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA USA
| | - Shaji K. Kumar
- grid.66875.3a0000 0004 0459 167XMayo Clinic Rochester, Division of Hematology, Rochester, MN USA
| | - Sacha Gnjatic
- grid.59734.3c0000 0001 0670 2351Human Immune Monitoring Center, Icahn School of Medicine at Mt. Sinai, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Li Ding
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University School of Medicine, Saint Louis, MO USA
| | - Manoj Bhasin
- Aflac Cancer and Blood Disorders Center, Atlanta, GA USA ,grid.189967.80000 0001 0941 6502Coulter Department of Biomedical Engineering, Emory University, Atlanta, GA USA ,grid.189967.80000 0001 0941 6502Department of Pediatrics, Emory School of Medicine, Atlanta, GA USA ,grid.189967.80000 0001 0941 6502Winship Cancer Institute, Emory University, Atlanta, GA USA ,grid.189967.80000 0001 0941 6502Department of Biomedical Informatics, Emory School of Medicine, Atlanta, GA USA
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18
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Thompson RC, Simons NW, Wilkins L, Cheng E, Del Valle DM, Hoffman GE, Cervia C, Fennessy B, Mouskas K, Francoeur NJ, Johnson JS, Lepow L, Le Berichel J, Chang C, Beckmann AG, Wang YC, Nie K, Zaki N, Tuballes K, Barcessat V, Cedillo MA, Yuan D, Huckins L, Roussos P, Marron TU, Glicksberg BS, Nadkarni G, Heath JR, Gonzalez-Kozlova E, Boyman O, Kim-Schulze S, Sebra R, Merad M, Gnjatic S, Schadt EE, Charney AW, Beckmann ND. Molecular states during acute COVID-19 reveal distinct etiologies of long-term sequelae. Nat Med 2023; 29:236-246. [PMID: 36482101 PMCID: PMC9873574 DOI: 10.1038/s41591-022-02107-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 10/25/2022] [Indexed: 12/13/2022]
Abstract
Post-acute sequelae of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are debilitating, clinically heterogeneous and of unknown molecular etiology. A transcriptome-wide investigation was performed in 165 acutely infected hospitalized individuals who were followed clinically into the post-acute period. Distinct gene expression signatures of post-acute sequelae were already present in whole blood during acute infection, with innate and adaptive immune cells implicated in different symptoms. Two clusters of sequelae exhibited divergent plasma-cell-associated gene expression patterns. In one cluster, sequelae associated with higher expression of immunoglobulin-related genes in an anti-spike antibody titer-dependent manner. In the other, sequelae associated independently of these titers with lower expression of immunoglobulin-related genes, indicating lower non-specific antibody production in individuals with these sequelae. This relationship between lower total immunoglobulins and sequelae was validated in an external cohort. Altogether, multiple etiologies of post-acute sequelae were already detectable during SARS-CoV-2 infection, directly linking these sequelae with the acute host response to the virus and providing early insights into their development.
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Affiliation(s)
- Ryan C Thompson
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | - Esther Cheng
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Diane Marie Del Valle
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gabriel E Hoffman
- Department of Genetics and Genomic Sciences, Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carlo Cervia
- Department of Immunology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Brian Fennessy
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Konstantinos Mouskas
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Susan and Leonard Feinstein Inflammatory Bowel Disease Clinical Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nancy J Francoeur
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Lauren Lepow
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jessica Le Berichel
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Christie Chang
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Ying-Chih Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kai Nie
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nicholas Zaki
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kevin Tuballes
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vanessa Barcessat
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mario A Cedillo
- Department of Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dan Yuan
- Institute for Systems Biology, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Laura Huckins
- Department of Genetics and Genomic Sciences, Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Panos Roussos
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mental Illness Research Education and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, Bronx, NY, USA
- Center for Dementia Research, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY, USA
| | - Thomas U Marron
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Hematology and Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Benjamin S Glicksberg
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Girish Nadkarni
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Data Driven and Digital Medicine (D3M), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - James R Heath
- Institute for Systems Biology, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Edgar Gonzalez-Kozlova
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Onur Boyman
- Department of Immunology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Seunghee Kim-Schulze
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Sema4, a Mount Sinai venture, Stamford, CT, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Miriam Merad
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sacha Gnjatic
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Hematology and Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Sema4, a Mount Sinai venture, Stamford, CT, USA
| | - Alexander W Charney
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Noam D Beckmann
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Medicine, Division of Data Driven and Digital Medicine (D3M), Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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19
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Butler-Laporte G, Gonzalez-Kozlova E, Su CY, Zhou S, Nakanishi T, Brunet-Ratnasingham E, Morrison D, Laurent L, Afilalo J, Afilalo M, Henry D, Chen Y, Carrasco-Zanini J, Farjoun Y, Pietzner M, Kimchi N, Afrasiabi Z, Rezk N, Bouab M, Petitjean L, Guzman C, Xue X, Tselios C, Vulesevic B, Adeleye O, Abdullah T, Almamlouk N, Moussa Y, DeLuca C, Duggan N, Schurr E, Brassard N, Durand M, Del Valle DM, Thompson R, Cedillo MA, Schadt E, Nie K, Simons NW, Mouskas K, Zaki N, Patel M, Xie H, Harris J, Marvin R, Cheng E, Tuballes K, Argueta K, Scott I, Greenwood CMT, Paterson C, Hinterberg M, Langenberg C, Forgetta V, Mooser V, Marron T, Beckmann N, Kenigsberg E, Charney AW, Kim-schulze S, Merad M, Kaufmann DE, Gnjatic S, Richards JB. The dynamic changes and sex differences of 147 immune-related proteins during acute COVID-19 in 580 individuals. Clin Proteomics 2022; 19:34. [PMID: 36171541 PMCID: PMC9516500 DOI: 10.1186/s12014-022-09371-z] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 08/21/2022] [Indexed: 02/02/2023] Open
Abstract
INTRODUCTION Severe COVID-19 leads to important changes in circulating immune-related proteins. To date it has been difficult to understand their temporal relationship and identify cytokines that are drivers of severe COVID-19 outcomes and underlie differences in outcomes between sexes. Here, we measured 147 immune-related proteins during acute COVID-19 to investigate these questions. METHODS We measured circulating protein abundances using the SOMAscan nucleic acid aptamer panel in two large independent hospital-based COVID-19 cohorts in Canada and the United States. We fit generalized additive models with cubic splines from the start of symptom onset to identify protein levels over the first 14 days of infection which were different between severe cases and controls, adjusting for age and sex. Severe cases were defined as individuals with COVID-19 requiring invasive or non-invasive mechanical respiratory support. RESULTS 580 individuals were included in the analysis. Mean subject age was 64.3 (sd 18.1), and 47% were male. Of the 147 proteins, 69 showed a significant difference between cases and controls (p < 3.4 × 10-4). Three clusters were formed by 108 highly correlated proteins that replicated in both cohorts, making it difficult to determine which proteins have a true causal effect on severe COVID-19. Six proteins showed sex differences in levels over time, of which 3 were also associated with severe COVID-19: CCL26, IL1RL2, and IL3RA, providing insights to better understand the marked differences in outcomes by sex. CONCLUSIONS Severe COVID-19 is associated with large changes in 69 immune-related proteins. Further, five proteins were associated with sex differences in outcomes. These results provide direct insights into immune-related proteins that are strongly influenced by severe COVID-19 infection.
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Affiliation(s)
- Guillaume Butler-Laporte
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada ,grid.14709.3b0000 0004 1936 8649Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec Canada
| | - Edgar Gonzalez-Kozlova
- grid.59734.3c0000 0001 0670 2351Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Chen-Yang Su
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada ,grid.14709.3b0000 0004 1936 8649Department of Computer Science, McGill University, Montréal, Québec Canada
| | - Sirui Zhou
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada ,grid.14709.3b0000 0004 1936 8649Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec Canada
| | - Tomoko Nakanishi
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada ,grid.14709.3b0000 0004 1936 8649Department of Human Genetics, McGill University, Montréal, Québec Canada ,grid.258799.80000 0004 0372 2033Graduate School of Medicine, McGill International Collaborative School in Genomic Medicine, Kyoto University, KyotoKyoto, Japan ,grid.54432.340000 0001 0860 6072Japan Society for the Promotion of Science, Tokyo, Japan
| | - Elsa Brunet-Ratnasingham
- grid.410559.c0000 0001 0743 2111Research Centre of the Centre Hospitalier de L’Université de Montréal, Montréal, Québec Canada
| | - David Morrison
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Laetitia Laurent
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Jonathan Afilalo
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada ,grid.14709.3b0000 0004 1936 8649Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec Canada
| | - Marc Afilalo
- grid.414980.00000 0000 9401 2774Department of Emergency Medicine, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Danielle Henry
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Yiheng Chen
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada ,grid.14709.3b0000 0004 1936 8649Department of Human Genetics, McGill University, Montréal, Québec Canada
| | - Julia Carrasco-Zanini
- grid.5335.00000000121885934MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Yossi Farjoun
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Maik Pietzner
- grid.5335.00000000121885934MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK ,grid.484013.a0000 0004 6879 971XComputational Medicine, Berlin Institute of Health at Charité—Universitätsmedizin Berlin, Berlin, Germany
| | - Nofar Kimchi
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Zaman Afrasiabi
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Nardin Rezk
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Meriem Bouab
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Louis Petitjean
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Charlotte Guzman
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Xiaoqing Xue
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Chris Tselios
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Branka Vulesevic
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Olumide Adeleye
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Tala Abdullah
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Noor Almamlouk
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Yara Moussa
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Chantal DeLuca
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Naomi Duggan
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Erwin Schurr
- grid.63984.300000 0000 9064 4811Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Québec Canada
| | - Nathalie Brassard
- grid.410559.c0000 0001 0743 2111Research Centre of the Centre Hospitalier de L’Université de Montréal, Montréal, Québec Canada
| | - Madeleine Durand
- grid.410559.c0000 0001 0743 2111Research Centre of the Centre Hospitalier de L’Université de Montréal, Montréal, Québec Canada
| | - Diane Marie Del Valle
- grid.59734.3c0000 0001 0670 2351Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Ryan Thompson
- grid.59734.3c0000 0001 0670 2351Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Mario A. Cedillo
- grid.59734.3c0000 0001 0670 2351Department of Radiology, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Eric Schadt
- grid.59734.3c0000 0001 0670 2351Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Kai Nie
- grid.59734.3c0000 0001 0670 2351Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Nicole W. Simons
- grid.59734.3c0000 0001 0670 2351Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Konstantinos Mouskas
- grid.59734.3c0000 0001 0670 2351Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Nicolas Zaki
- grid.59734.3c0000 0001 0670 2351Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Manishkumar Patel
- grid.59734.3c0000 0001 0670 2351Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Hui Xie
- grid.59734.3c0000 0001 0670 2351Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Jocelyn Harris
- grid.59734.3c0000 0001 0670 2351Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Robert Marvin
- grid.59734.3c0000 0001 0670 2351Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Esther Cheng
- grid.59734.3c0000 0001 0670 2351Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Kevin Tuballes
- grid.59734.3c0000 0001 0670 2351Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Kimberly Argueta
- grid.59734.3c0000 0001 0670 2351Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Ieisha Scott
- grid.59734.3c0000 0001 0670 2351Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | | | - Celia M. T. Greenwood
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada ,grid.14709.3b0000 0004 1936 8649Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec Canada
| | - Clare Paterson
- grid.437866.80000 0004 0625 700XSomaLogic Inc, Boulder, CO USA
| | | | - Claudia Langenberg
- grid.5335.00000000121885934MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK ,grid.437866.80000 0004 0625 700XSomaLogic Inc, Boulder, CO USA
| | - Vincenzo Forgetta
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Vincent Mooser
- grid.14709.3b0000 0004 1936 8649Department of Human Genetics, McGill University, Montréal, Québec Canada
| | - Thomas Marron
- grid.59734.3c0000 0001 0670 2351Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA ,grid.416167.30000 0004 0442 1996Early Phase Trials Unit, Mount Sinai Hospital, New York, NY USA
| | - Noam Beckmann
- grid.59734.3c0000 0001 0670 2351Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Ephraim Kenigsberg
- grid.59734.3c0000 0001 0670 2351Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Alexander W. Charney
- grid.59734.3c0000 0001 0670 2351Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Seunghee Kim-schulze
- grid.59734.3c0000 0001 0670 2351Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Miriam Merad
- grid.59734.3c0000 0001 0670 2351Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Daniel E. Kaufmann
- grid.410559.c0000 0001 0743 2111Research Centre of the Centre Hospitalier de L’Université de Montréal, Montréal, Québec Canada ,grid.14848.310000 0001 2292 3357Department of Medicine, Université de Montréal, Montréal, Québec Canada
| | - Sacha Gnjatic
- grid.59734.3c0000 0001 0670 2351Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - J Brent Richards
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada ,grid.14709.3b0000 0004 1936 8649Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec Canada ,grid.14709.3b0000 0004 1936 8649Department of Human Genetics, McGill University, Montréal, Québec Canada ,grid.13097.3c0000 0001 2322 6764Department of Twin Research, King’s College London, London, UK ,5 Prime Sciences, Montreal, Québec Canada ,grid.14709.3b0000 0004 1936 8649McGill University, King’s College London (Honorary), Jewish General Hospital, Pavilion H-4133755 Côte-Ste-Catherine, Montréal, Québec H3T 1E2 Canada
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20
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Yao L, Jayasinghe RG, Lee BH, Bhasin SS, Pilcher W, Doxie DB, Gonzalez-Kozlova E, Dasari S, Fiala MA, Pita-Juarez Y, Strausbauch M, Kelly G, Thomas BE, Kumar SK, Cho HJ, Anderson E, Wendl MC, Dawson T, D'Souza D, Oh ST, Cheloni G, Li Y, DiPersio JF, Rahman AH, Dhodapkar KM, Kim-Schulze S, Vij R, Vlachos IS, Mehr S, Hamilton M, Auclair D, Kourelis T, Avigan D, Dhodapkar MV, Gnjatic S, Bhasin MK, Ding L. Comprehensive characterization of the multiple myeloma immune microenvironment using integrated scRNA-seq, CyTOF, and CITE-seq analysis. Cancer Research Communications 2022; 2:1255-1265. [PMID: 36969740 PMCID: PMC10035369 DOI: 10.1158/2767-9764.crc-22-0022] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 06/09/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022]
Abstract
Abstract
As part of the Multiple Myeloma Research Foundation (MMRF) immune atlas pilot project, we compared immune cells of Multiple Myeloma (MM) bone marrow samples from 18 patients assessed by single-cell RNA-seq (scRNA-seq), mass cytometry (CyTOF), and Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) to understand the concordance of measurements among single-cell techniques. Cell type abundances are relatively consistent across the three approaches, while variations are observed in T cells, macrophages, and monocytes. Concordance and correlation analysis of cell type marker gene expression across different modalities highlighted the importance of choosing cell type marker genes best suited to particular modalities. By integrating data from these three assays, we found International Staging System (ISS) stage 3 patients exhibited decreased CD4+ T/ CD8+ T cells ratio. Moreover, we observed upregulation of RAC2 and PSMB9, in NK cells of fast progressors (FP) compared to those of non-progressors (NP), as revealed by both scRNA-seq and CITE-seq RNA measurement. This detailed examination of the immune microenvironment in MM using multiple single cell technologies revealed markers associated with MM rapid progression which will be further characterized by the full-scale immune atlas project.
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Affiliation(s)
- Lijun Yao
- Washington University, St. Louis University School of Medicine, St. Louis, Mo, United States
| | - Reyka G Jayasinghe
- Washington University in St. Louis School of Medicine, Saint Louis, MO, United States
| | - Brian H. Lee
- Icahn School of Medicine at Mt. Sinai, New York, United States
| | - Swati S. Bhasin
- Emory University School of Medicine, Atlanta, GA, United States
| | | | | | | | | | - Mark A Fiala
- Washington University in St. Louis School of Medicine, St. Louis, United States
| | | | | | - Geoffrey Kelly
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Beena E Thomas
- Emory University School of Medicine, Atlanta, Ga, United States
| | | | - Hearn Jay Cho
- Multiple Myeloma Research Foundation, Norwalk, CT, United States
| | | | - Michael C. Wendl
- Washington University, St. Louis University School of Medicine, St. Louis, Mo, United States
| | - Travis Dawson
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Darwin D'Souza
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Stephen T Oh
- Washington University in St. Louis School of Medicine, St. Louis, United States
| | - Giulia Cheloni
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Ying Li
- Mayo Clinic, Rochester, Minnesota, United States
| | | | - Adeeb H. Rahman
- Icahn School of Medicine at Mt. Sinai, New York, United States
| | | | | | - Ravi Vij
- Washington University in St. Louis, Saint Louis, MO, United States
| | | | - Shaadi Mehr
- Multiple Myeloma Research Foundation, Norwalk, CT, United States
| | - Mark Hamilton
- Multiple Myeloma Research Foundation, Norwalk, CT, United States
| | | | | | - David Avigan
- Harvard Medical School, Boston, MA, United States
| | | | - Sacha Gnjatic
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Manoj K. Bhasin
- Beth Israel Deaconess Medical Center, Boston, MA, United States
| | - Li Ding
- Washington University School of Medicine in St. Louis, St Louis, MO, United States
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21
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Carbonell G, Del Valle DM, Gonzalez-Kozlova E, Marinelli B, Klein E, El Homsi M, Stocker D, Chung M, Bernheim A, Simons NW, Xiang J, Nirenberg S, Kovatch P, Lewis S, Merad M, Gnjatic S, Taouli B. Quantitative chest computed tomography combined with plasma cytokines predict outcomes in COVID-19 patients. Heliyon 2022; 8:e10166. [PMID: 35958514 PMCID: PMC9356575 DOI: 10.1016/j.heliyon.2022.e10166] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 03/08/2022] [Accepted: 07/27/2022] [Indexed: 01/29/2023] Open
Abstract
Despite extraordinary international efforts to dampen the spread and understand the mechanisms behind SARS-CoV-2 infections, accessible predictive biomarkers directly applicable in the clinic are yet to be discovered. Recent studies have revealed that diverse types of assays bear limited predictive power for COVID-19 outcomes. Here, we harness the predictive power of chest computed tomography (CT) in combination with plasma cytokines using a machine learning and k-fold cross-validation approach for predicting death during hospitalization and maximum severity degree in COVID-19 patients. Patients (n = 152) from the Mount Sinai Health System in New York with plasma cytokine assessment and a chest CT within five days from admission were included. Demographics, clinical, and laboratory variables, including plasma cytokines (IL-6, IL-8, and TNF-α), were collected from the electronic medical record. We found that CT quantitative alone was better at predicting severity (AUC 0.81) than death (AUC 0.70), while cytokine measurements alone better-predicted death (AUC 0.70) compared to severity (AUC 0.66). When combined, chest CT and plasma cytokines were good predictors of death (AUC 0.78) and maximum severity (AUC 0.82). Finally, we provide a simple scoring system (nomogram) using plasma IL-6, IL-8, TNF-α, ground-glass opacities (GGO) to aerated lung ratio and age as new metrics that may be used to monitor patients upon hospitalization and help physicians make critical decisions and considerations for patients at high risk of death for COVID-19.
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Affiliation(s)
- Guillermo Carbonell
- Department of Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA,BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Radiology, Universidad de Murcia, Spain,Instituto Murciano de Investigación Biosanitaria, Spain
| | - Diane Marie Del Valle
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edgar Gonzalez-Kozlova
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brett Marinelli
- Department of Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Emma Klein
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Maria El Homsi
- Department of Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel Stocker
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Institute of Diagnostic and Interventional Radiology, University Hospital Zurich, Switzerland
| | - Michael Chung
- Department of Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adam Bernheim
- Department of Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nicole W. Simons
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jiani Xiang
- Scientific Computing; Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sharon Nirenberg
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Scientific Computing; Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Patricia Kovatch
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Scientific Computing; Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sara Lewis
- Department of Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA,BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Miriam Merad
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sacha Gnjatic
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Oncological Sciences; Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bachir Taouli
- Department of Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA,BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Corresponding author.
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22
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Chen TY, Gonzalez-Kozlova E, Soleymani T, La Salvia S, Kyprianou N, Sahoo S, Tewari AK, Cordon-Cardo C, Stolovitzky G, Dogra N. Extracellular vesicles carry distinct proteo-transcriptomic signatures that are different from their cancer cell of origin. iScience 2022; 25:104414. [PMID: 35663013 PMCID: PMC9157216 DOI: 10.1016/j.isci.2022.104414] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 09/23/2021] [Revised: 12/22/2021] [Accepted: 05/12/2022] [Indexed: 12/11/2022] Open
Abstract
Circulating extracellular vesicles (EVs) contain molecular footprints-lipids, proteins, RNA, and DNA-from their cell of origin. Consequently, EV-associated RNA and proteins have gained widespread interest as liquid-biopsy biomarkers. Yet, an integrative proteo-transcriptomic landscape of EVs and comparison with their cell of origin remains obscure. Here, we report that EVs enrich distinct proteo-transcriptome that does not linearly correlate with their cell of origin. We show that EVs enrich endosomal and extracellular proteins, small RNA (∼13-200 nucleotides) associated with cell differentiation, development, and Wnt signaling. EVs cargo specific RNAs (RNY3, vtRNA, and MIRLET-7) and their complementary proteins (YBX1, IGF2BP2, and SRSF1/2). To ensure an unbiased and independent analyses, we studied 12 cancer cell lines, matching EVs (inhouse and exRNA database), and serum EVs of patients with prostate cancer. Together, we show that EV-RNA-protein complexes may constitute a functional interaction network to protect and regulate molecular access until a function is achieved.
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Affiliation(s)
- Tzu-Yi Chen
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York 10029, USA
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York 10029, USA
| | - Edgar Gonzalez-Kozlova
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Taliah Soleymani
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York 10029, USA
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York 10029, USA
| | - Sabrina La Salvia
- Department of Cardiology, Icahn School of Medicine at Mount Sinai, New York 10029, USA
| | - Natasha Kyprianou
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York 10029, USA
| | - Susmita Sahoo
- Department of Cardiology, Icahn School of Medicine at Mount Sinai, New York 10029, USA
| | - Ashutosh K. Tewari
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York 10029, USA
| | - Carlos Cordon-Cardo
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York 10029, USA
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Gustavo Stolovitzky
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York 10029, USA
- IBM T. J. Watson Research Center, Yorktown Heights, New York 10598, USA
- Sema4, Stamford, CT 06902, USA
| | - Navneet Dogra
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York 10029, USA
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York 10029, USA
- IBM T. J. Watson Research Center, Yorktown Heights, New York 10598, USA
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23
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Gonzalez-Kozlova E, Huang HH, Redman M, Herbst R, Gettinger S, Bazhenova L, Xie H, Patel M, Nie K, Harris J, Argueta K, Kelly K, Cerami E, Lindsay J, Yu J, Biswas R, Van Nostrand S, Moravec R, Valle DMD, Kim-schulze S, Gnjatic S. Abstract 5026: Dynamic changes in circulating protein levels reveal an association between ipilimumab and nivolumab combination treatment (SWOG Lung-MAP S1400I trial) with outcomes in squamous cell lung cancer. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-5026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Squamous cell lung cancer (SqCLC) is a type of non-small cell lung cancer strongly associated with cigarette smoking and with known targetable mutations, however some patients do not have matching targeted drugs. The S1400I Phase III randomized LungMap sub-study of nivo+ipi versus nivo accrued 275 (252 eligible) previously-treated patients with stage IV SqCLC and absence of matched mutations (NCT02154490).Here, to investigate the longitudinal (baseline, C2 week 3, C4 week 7, C5 week 9) serum protein changes associated with treatment or response, we performed Olink proximity extension assay in 160 patients (561 samples) using an immuno-oncology panel of 92 analytes. We utilized mixed linear and joint models to identify differentially expressed proteins between treatment arms (nivo vs. nivo+ipi), response and quantify the effect of other potential prognostic factors. This approach quantifies the effect of covariates such as smoking status, demographics, prior radiation therapy, and metastases. We jointly modeled expression and survival to identify changes in proteins over time. The thresholds for significance in differentially expression tests were a log fold change of at least 0.5 and a false discovery rate of under 0.05 (FDR as a multiple testing adjustment method). The joint models used thresholds of log fold change of more than 1 and hazard ratio of more than 1. Results revealed increases in 40 serum proteins after treatment with either nivo alone or combined with ipi, including CXCL9, CXCL10, CXCL11, CXCL13, IL6, IL8, IL10, IFNg, and soluble PD-L1 and PDCD1. nivo+ipi treatment showed greater increases in IL8 and CXCL13 post-treatment compared to nivo alone. In addition, circulating IL6, CXCL13, and MIC-A/B were higher in patients with stable or progressive disease compared to those with objective response after treatment. The joint model revealed a worse hazard ratio with increases in 10 soluble proteins, including IL6, IL8, and CXCL13. Finally, for patients with similar values of IL8, those treated by combination had a better survival outcome than those treated by nivo alone. Using a data-modeling approach, we identified significant longitudinal changes in 40 serum proteins out of 92 tested in patients with SqCLC treated with nivo or nivo+ipi. Increases in serum inflammatory markers IL6 and CXCL13 were associated with worse disease. Although overall survival was not statistically different between arms, our modeling approaches suggested that IL-8 monitoring may help identify patients benefiting more from the combination vs. nivo alone.
Citation Format: Edgar Gonzalez-Kozlova, Hsin-Hui Huang, Mary Redman, Roy Herbst, Scott Gettinger, Luda Bazhenova, Hui Xie, Manishkumar Patel, Kai Nie, Jocelyn Harris, Kimberly Argueta, Karen Kelly, Ethan Cerami, James Lindsay, Joyce Yu, Roshni Biswas, Stephen Van Nostrand, Radim Moravec, Diane Marie Del Valle, Seunghee Kim-schulze, Sacha Gnjatic. Dynamic changes in circulating protein levels reveal an association between ipilimumab and nivolumab combination treatment (SWOG Lung-MAP S1400I trial) with outcomes in squamous cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5026.
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Affiliation(s)
| | | | - Mary Redman
- 2SWOG Statistical Center; Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Roy Herbst
- 3The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Hui Xie
- 1Icahn School of Medicine, New York, NY
| | | | - Kai Nie
- 1Icahn School of Medicine, New York, NY
| | | | | | | | | | | | - Joyce Yu
- 5Dana-Farber Cancer Institute, Boston, MA
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24
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Gonzalez-Kozlova E, Huang HH, Redman MW, Herbst RS, Gettinger SN, Bazhenova L, Xie H, Patel M, Nie K, Harris J, Argueta K, Cerami E, Hong J, Biswas R, Van Nostrand S, Kelly K, Moravec R, Del Valle D, Kim-Schulze S, Gnjatic S. Dynamic changes in serum analyte levels associated with clinical outcome in squamous cell lung cancer trial SWOG Lung-MAP S1400I of nivolumab ± ipilimumab. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.9044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
9044 Background: While Immune checkpoint blockade (ICB) is standard treatment for lung cancer there are limited biomarkers that predict benefit, pharmacokinetic on-treatment activity or explain progression. S1400I was a randomized Phase III trial of nivolumab(N)+ipilimumab(I) versus N (NCT02154490, PMID 34264316) for ICB naïve, previously treated stage IV or recurrent squamous cell lung cancer. We performed circulating serum protein analysis of serial blood specimens from patients enrolled in S1400I to evaluate if serum proteins levels changed over time, changes differed by treatment arm, and if they were associated with overall survival. Methods: 561 serial blood specimens (baseline, weeks (wk) 3, 7, 9, and progression [PD]) from 160 of 252 eligible patients enrolled to S1400I were analyzed for 92 immuno-oncology analytes with the Olink proximity extension assay. Protein levels were normalized with use of internal controls and quantified as log2 protein expression (denoted as NPX). Linear mixed models evaluated change in expression from baseline at each time point (wks 3,7,9 and PD), and NPX differences at baseline, wk3, and PD depending on best objective response. A Cox model was used to evaluate the association between baseline NPX and survival. Overall survival and longitudinal cytokine expression were jointly modeled using a linear mixed model to estimate dynamic biomarker changes in NPX and a Cox model for survival. The joint models for time-varying NPX values included a random intercept and modeled time using a natural spline with three knots. Significance was defined as P < 0.05. Results: Serum proteins PCDC1, CXCL9, and CXCL10 were increased from baseline at wks 3,7,9 and at PD. CCL19 was increased at wks 3 and 7 but not at wk 9 and PD. IL10 and IFNγ were increased at wk 3 but subsequently returned to baseline. Change in CXCL13 from baseline to PD was larger for N+I versus N. Baseline CCL23, CSF-1, IL6, and MUC-16 were associated with shorter survival (HR > 1). Joint modeling of survival with cytokines showed an increased risk of death (HR > 1) with higher longitudinal serum levels of CXCL13, MMP12, CSF-1, and IL8. Patients achieving objective response had higher IL4 and LAMP3 and lower IL6 and IL8 at baseline and wk 3 compared to non-responders. Conclusions: Measurements of blood circulating soluble proteins represent easily accessible biomarkers that may be useful as indicators of outcome, and that will need to be prospectively confirmed. Clinical trial information: NCT02154490.
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Affiliation(s)
| | | | - Mary Weber Redman
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | - Scott N. Gettinger
- Yale School of Medicine and Smilow Cancer Center, Yale New Haven Hospital, New Haven, CT
| | | | - Hui Xie
- Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Kai Nie
- Icahn School of Medicine at Mount Sinai, New York, NY
| | | | | | | | - Joyce Hong
- Dana Farber Cancer Institute, Boston, MA
| | | | | | - Karen Kelly
- University of California Davis Comprehensive Cancer Center, Sacramento, CA
| | | | | | - Seunghee Kim-Schulze
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Sacha Gnjatic
- Icahn School of Medicine at Mount Sinai, New York, NY
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25
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Carbonell G, Del Valle DM, Gonzalez-kozlova E, Marinelli B, Klein E, Homsi ME, Stocker D, Chung M, Bernheim A, Simons NW, Xiang J, Nirenberg S, Kovatch P, Lewis S, Merad M, Gnjatic S, Taouli B. Quantitative chest CT combined with plasma cytokines predict outcomes in COVID-19 patients.. [PMID: 34671777 PMCID: PMC8528085 DOI: 10.1101/2021.10.11.21264709] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Despite extraordinary international efforts to dampen the spread and understand the mechanisms behind SARS-CoV-2 infections, accessible predictive biomarkers directly applicable in the clinic are yet to be discovered. Recent studies have revealed that diverse types of assays bear limited predictive power for COVID-19 outcomes. Here, we harness the predictive power of chest CT in combination with plasma cytokines using a machine learning approach for predicting death during hospitalization and maximum severity degree in COVID-19 patients. Patients (n=152) from the Mount Sinai Health System in New York with plasma cytokine assessment and a chest CT within 5 days from admission were included. Demographics, clinical, and laboratory variables, including plasma cytokines (IL-6, IL-8, and TNF-α) were collected from the electronic medical record. We found that chest CT combined with plasma cytokines were good predictors of death (AUC 0.78) and maximum severity (AUC 0.82), whereas CT quantitative was better at predicting severity (AUC 0.81 vs 0.70) while cytokine measurements better predicted death (AUC 0.70 vs 0.66). Finally, we provide a simple scoring system using plasma IL-6, IL-8, TNF-α, GGO to aerated lung ratio and age as novel metrics that may be used to monitor patients upon hospitalization and help physicians make critical decisions and considerations for patients at high risk of death for COVID-19.
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26
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Thompson RC, Simons NW, Wilkins L, Cheng E, Del Valle DM, Hoffman GE, Fennessy B, Mouskas K, Francoeur NJ, Johnson JS, Lepow L, Le Berichel J, Chang C, Beckmann AG, Wang YC, Nie K, Zaki N, Tuballes K, Barcessat V, Cedillo MA, Huckins L, Roussos P, Marron TU, Glicksberg BS, Nadkarni G, Gonzalez-Kozlova E, Kim-Schulze S, Sebra R, Merad M, Gnjatic S, Schadt EE, Charney AW, Beckmann ND. Acute COVID-19 gene-expression profiles show multiple etiologies of long-term sequelae. medRxiv 2021:2021.10.04.21264434. [PMID: 34642700 PMCID: PMC8509101 DOI: 10.1101/2021.10.04.21264434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 12/13/2022]
Abstract
Two years into the SARS-CoV-2 pandemic, the post-acute sequelae of infection are compounding the global health crisis. Often debilitating, these sequelae are clinically heterogeneous and of unknown molecular etiology. Here, a transcriptome-wide investigation of this new condition was performed in a large cohort of acutely infected patients followed clinically into the post-acute period. Gene expression signatures of post-acute sequelae were already present in whole blood during the acute phase of infection, with both innate and adaptive immune cells involved. Plasma cells stood out as driving at least two distinct clusters of sequelae, one largely dependent on circulating antibodies against the SARS-CoV-2 spike protein and the other antibody-independent. Altogether, multiple etiologies of post-acute sequelae were found concomitant with SARS-CoV-2 infection, directly linking the emergence of these sequelae with the host response to the virus.
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Affiliation(s)
- Ryan C. Thompson
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Nicole W. Simons
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lillian Wilkins
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Esther Cheng
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Diane Marie Del Valle
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Precision Immunology Institute, Mount Sinai, New York, NY 10029, USA
| | - Gabriel E. Hoffman
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Brian Fennessy
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Konstantinos Mouskas
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Susan and Leonard Feinstein Inflammatory Bowel Disease Clinical Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nancy J. Francoeur
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Lauren Lepow
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Christie Chang
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Precision Immunology Institute, Mount Sinai, New York, NY 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Ying-chih Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kai Nie
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Nicholas Zaki
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kevin Tuballes
- Precision Immunology Institute, Mount Sinai, New York, NY 10029, USA
| | - Vanessa Barcessat
- Precision Immunology Institute, Mount Sinai, New York, NY 10029, USA
| | - Mario A. Cedillo
- Department of Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laura Huckins
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Panagiotis Roussos
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Thomas U. Marron
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Precision Immunology Institute, Mount Sinai, New York, NY 10029, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Medicine, Mount Sinai, New York, NY 10029, USA
- Department of Medicine, Division of Hematology and Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Benjamin S. Glicksberg
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY 10065, USA
| | - Girish Nadkarni
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Division of Data Driven and Digital Medicine (D3M), Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10065, USA
| | - Edgar Gonzalez-Kozlova
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Seunghee Kim-Schulze
- Precision Immunology Institute, Mount Sinai, New York, NY 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Mount Sinai, New York, NY 10029, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Sema4, a Mount Sinai venture, Stamford CT, 06902, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Miriam Merad
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Precision Immunology Institute, Mount Sinai, New York, NY 10029, USA
- Department of Oncological Sciences, Mount Sinai, New York, NY 10029, USA
| | - Sacha Gnjatic
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Precision Immunology Institute, Mount Sinai, New York, NY 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Medicine, Division of Hematology and Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Mount Sinai, New York, NY 10029, USA
| | - Eric E. Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Sema4, a Mount Sinai venture, Stamford CT, 06902, USA
| | - Alexander W. Charney
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Noam D. Beckmann
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
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27
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von Felden J, Garcia-Lezana T, Dogra N, Gonzalez-Kozlova E, Ahsen ME, Craig A, Gifford S, Wunsch B, Smith JT, Kim S, Diaz JEL, Chen X, Labgaa I, Haber P, Olsen R, Han D, Restrepo P, D'Avola D, Hernandez-Meza G, Allette K, Sebra R, Saberi B, Tabrizian P, Asgharpour A, Dieterich D, Llovet JM, Cordon-Cardo C, Tewari A, Schwartz M, Stolovitzky G, Losic B, Villanueva A. Unannotated small RNA clusters associated with circulating extracellular vesicles detect early stage liver cancer. Gut 2021; 71:gutjnl-2021-325036. [PMID: 34321221 PMCID: PMC8795201 DOI: 10.1136/gutjnl-2021-325036] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 07/15/2021] [Indexed: 01/30/2023]
Abstract
OBJECTIVE Surveillance tools for early cancer detection are suboptimal, including hepatocellular carcinoma (HCC), and biomarkers are urgently needed. Extracellular vesicles (EVs) have gained increasing scientific interest due to their involvement in tumour initiation and metastasis; however, most extracellular RNA (exRNA) blood-based biomarker studies are limited to annotated genomic regions. DESIGN EVs were isolated with differential ultracentrifugation and integrated nanoscale deterministic lateral displacement arrays (nanoDLD) and quality assessed by electron microscopy, immunoblotting, nanoparticle tracking and deconvolution analysis. Genome-wide sequencing of the largely unexplored small exRNA landscape, including unannotated transcripts, identified and reproducibly quantified small RNA clusters (smRCs). Their key genomic features were delineated across biospecimens and EV isolation techniques in prostate cancer and HCC. Three independent exRNA cancer datasets with a total of 479 samples from 375 patients, including longitudinal samples, were used for this study. RESULTS ExRNA smRCs were dominated by uncharacterised, unannotated small RNA with a consensus sequence of 20 nt. An unannotated 3-smRC signature was significantly overexpressed in plasma exRNA of patients with HCC (p<0.01, n=157). An independent validation in a phase 2 biomarker case-control study revealed 86% sensitivity and 91% specificity for the detection of early HCC from controls at risk (n=209) (area under the receiver operating curve (AUC): 0.87). The 3-smRC signature was independent of alpha-fetoprotein (p<0.0001) and a composite model yielded an increased AUC of 0.93. CONCLUSION These findings directly lead to the prospect of a minimally invasive, blood-only, operator-independent clinical tool for HCC surveillance, thus highlighting the potential of unannotated smRCs for biomarker research in cancer.
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Affiliation(s)
- Johann von Felden
- Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Medicine, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Teresa Garcia-Lezana
- Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Navneet Dogra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- IBM Thomas J Watson Research Center, Yorktown Heights, New York, USA
| | - Edgar Gonzalez-Kozlova
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Mehmet Eren Ahsen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Amanda Craig
- Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Stacey Gifford
- IBM Thomas J Watson Research Center, Yorktown Heights, New York, USA
| | - Benjamin Wunsch
- IBM Thomas J Watson Research Center, Yorktown Heights, New York, USA
| | - Joshua T Smith
- IBM Thomas J Watson Research Center, Yorktown Heights, New York, USA
| | - Sungcheol Kim
- IBM Thomas J Watson Research Center, Yorktown Heights, New York, USA
| | - Jennifer E L Diaz
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Xintong Chen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ismail Labgaa
- Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Visceral Surgery, Lausanne University Hospital, Lausanne, Switzerland
| | - Philipp Haber
- Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Reena Olsen
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Dan Han
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Paula Restrepo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Delia D'Avola
- Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Liver Unit and Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Clínica Universidad de Navarra, Pamplona, Spain
| | - Gabriela Hernandez-Meza
- Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Kimaada Allette
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Sema4, Stamford, Connecticut, USA
| | - Behnam Saberi
- Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Parissa Tabrizian
- Recanati/Miller Transplantation Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Surgery, Mount Sinai School of Medicine, New York, New York, USA
| | - Amon Asgharpour
- Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Douglas Dieterich
- Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Josep M Llovet
- Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Liver Cancer Translational Research Laboratory, BCLC Group, IDIBAPS, CIBEREHD, Hospital Clinic, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Catalonia, Spain
| | - Carlos Cordon-Cardo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ash Tewari
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Myron Schwartz
- Department of Surgery, Mount Sinai School of Medicine, New York, New York, USA
| | - Gustavo Stolovitzky
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- IBM Thomas J Watson Research Center, Yorktown Heights, New York, USA
| | - Bojan Losic
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Diabetes, Obesity and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Augusto Villanueva
- Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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28
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Comella PH, Gonzalez-Kozlova E, Kosoy R, Charney AW, Peradejordi IF, Chandrasekar S, Tyler SR, Wang W, Losic B, Zhu J, Hoffman GE, Kim-Schulze S, Qi J, Patel M, Kasarskis A, Suarez-Farinas M, Gümüş ZH, Argmann C, Merad M, Becker C, Beckmann ND, Schadt EE. A Molecular network approach reveals shared cellular and molecular signatures between chronic fatigue syndrome and other fatiguing illnesses. medRxiv 2021:2021.01.29.21250755. [PMID: 33564792 PMCID: PMC7872387 DOI: 10.1101/2021.01.29.21250755] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 12/27/2022]
Abstract
IntroThe molecular mechanisms of chronic fatigue syndrome (CFS, or Myalgic encephalomyelitis), a disease defined by extreme, long-term fatigue, remain largely uncharacterized, and presently no molecular diagnostic test and no specific treatments exist to diagnose and treat CFS patients. While CFS has historically had an estimated prevalence of 0.1-0.5% [1], concerns of a “long hauler” version of Coronavirus disease 2019 (COVID-19) that symptomatically overlaps CFS to a significant degree(Supplemental Table-1)and appears to occur in 10% of COVID-19 patients[2], has raised concerns of a larger spike in CFS [3]. Here, we established molecular signatures of CFS and a corresponding network-based disease context from RNA-sequencing data generated on whole blood and FACs sorted specific peripheral blood mononuclear cells (PBMCs) isolated from CFS cases and non-CFS controls. The immune cell type specific molecular signatures of CFS we identified, overlapped molecular signatures from other fatiguing illnesses, demonstrating a common molecular etiology. Further, after constructing a probabilistic causal model of the CFS gene expression data, we identified master regulator genes modulating network states associated with CFS, suggesting potential therapeutic targets for CFS.
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Affiliation(s)
- Phillip H. Comella
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Edgar Gonzalez-Kozlova
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Roman Kosoy
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Alexander W. Charney
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Irene Font Peradejordi
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
- Cornell Tech at Cornell University, New York, NY, 10044, USA
| | - Shreya Chandrasekar
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
- Cornell Tech at Cornell University, New York, NY, 10044, USA
| | - Scott R. Tyler
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Wenhui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bojan Losic
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jun Zhu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Gabriel E. Hoffman
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Seunghee Kim-Schulze
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jingjing Qi
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Manishkumar Patel
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Andrew Kasarskis
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
- Department of Population Health Science and Policy at the Icahn School of Medicine at Mount Sinai
| | - Mayte Suarez-Farinas
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Zeynep H. Gümüş
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Carmen Argmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Miriam Merad
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Noam D. Beckmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Eric E. Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
- Sema4, a Mount Sinai venture, Stamford CT, 06902, USA
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29
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Vivas-Ruiz DE, Sandoval GA, Gonzalez-Kozlova E, Zarria-Romero J, Lazo F, Rodríguez E, Magalhães HPB, Chávez-Olortegui C, Oliveira LS, Alvarenga VG, Urra FA, Toledo J, Yarlequé A, Eble JA, Sanchez EF. Fibrinogen-clotting enzyme, pictobin, from Bothrops pictus snake venom. Structural and functional characterization. Int J Biol Macromol 2020; 153:779-795. [PMID: 32169454 DOI: 10.1016/j.ijbiomac.2020.03.055] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 11/12/2019] [Revised: 03/09/2020] [Accepted: 03/09/2020] [Indexed: 12/14/2022]
Abstract
A thrombin-like enzyme, pictobin, was purified from Bothrops pictus snake venom. It is a 41-kDa monomeric glycoprotein as showed by mass spectrometry and contains approx. 45% carbohydrate by mass which could be removed with N-glycosidase. Pictobin coagulates plasma and fibrinogen, releasing fibrinopeptide A and induces the formation of a friable/porous fibrin network as visualized by SEM. The enzyme promoted platelet aggregation in human PRP and defibrination in mouse model and showed catalytic activity on chromogenic substrates S-2266, S-2366, S-2160 and S-2238. Pictobin interacts with the plasma inhibitor α2-macroglobulin, which blocks its interaction with fibrinogen but not with the small substrate BApNA. Heparin does not affect its enzymatic activity. Pictobin cross reacted with polyvalent bothropic antivenom, and its deglycosylated form reduced its catalytic action and antivenom reaction. In breast and lung cancer cells, pictobin inhibits the fibronectin-stimulated migration. Moreover, it produces strong NADH oxidation, mitochondrial depolarization, ATP decrease and fragmentation of mitochondrial network. These results suggest by first time that a snake venom serinprotease produces mitochondrial dysfunction by affecting mitochondrial dynamics and bioenergetics. Structural model of pictobin reveals a conserved chymotrypsin fold β/β hydrolase. These data indicate that pictobin has therapeutic potential in the treatment of cardiovascular disorders and metastatic disease.
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Affiliation(s)
- Dan E Vivas-Ruiz
- Laboratorio de Biología Molecular, Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Perú, Av. Venezuela Cdra 34 S/N, Ciudad Universitaria, Lima 01, Lima, Peru.
| | - Gustavo A Sandoval
- Laboratorio de Biología Molecular, Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Perú, Av. Venezuela Cdra 34 S/N, Ciudad Universitaria, Lima 01, Lima, Peru
| | - Edgar Gonzalez-Kozlova
- Department of Genetics and Genomic Sciences, Icahn School for Data Science and Genomic Technology, New York, NYC, USA
| | - Jacquelyne Zarria-Romero
- Laboratorio de Reproducción y Biología del Desarrollo, Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Perú, Av. Venezuela ra 34 S/N, Ciudad Universitaria, Lima 01, Lima, Peru
| | - Fanny Lazo
- Laboratorio de Biología Molecular, Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Perú, Av. Venezuela Cdra 34 S/N, Ciudad Universitaria, Lima 01, Lima, Peru
| | - Edith Rodríguez
- Laboratorio de Biología Molecular, Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Perú, Av. Venezuela Cdra 34 S/N, Ciudad Universitaria, Lima 01, Lima, Peru
| | - Henrique P B Magalhães
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil
| | - Carlos Chávez-Olortegui
- Departamento de Bioquímica-Inmunología, Instituto de Ciências Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil
| | - Luciana S Oliveira
- Research and Development Center, Ezequiel Dias Foundation, 30510-010 Belo Horizonte, MG, Brazil
| | - Valeria G Alvarenga
- Research and Development Center, Ezequiel Dias Foundation, 30510-010 Belo Horizonte, MG, Brazil
| | - Félix A Urra
- Programa de Farmacología Clínica y Molecular, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Independencia 1027, Casilla 7, Santiago 7800003, Chile
| | - Jorge Toledo
- Instituto de Neurociencia Biomédica, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago 8380453, Chile; Facultad de Ciencias de la Salud, Universidad San Sebastián, Lota 2465, Providencia, Santiago 7510157, Chile
| | - Armando Yarlequé
- Laboratorio de Biología Molecular, Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Perú, Av. Venezuela Cdra 34 S/N, Ciudad Universitaria, Lima 01, Lima, Peru
| | - Johannes A Eble
- Institute for Physiological Chemistry and Pathobiochemistry, University of Münster, 48149 Münster, Germany
| | - Eladio F Sanchez
- Research and Development Center, Ezequiel Dias Foundation, 30510-010 Belo Horizonte, MG, Brazil
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Bubie A, Gonzalez-Kozlova E, Akers N, Villanueva A, Losic B. Tumor fitness, immune exhaustion and clinical outcomes: impact of immune checkpoint inhibitors. Sci Rep 2020; 10:5062. [PMID: 32193450 PMCID: PMC7081289 DOI: 10.1038/s41598-020-61992-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 11/06/2019] [Accepted: 03/06/2020] [Indexed: 12/25/2022] Open
Abstract
Recently proposed tumor fitness measures, based on profiling neoepitopes for reactive viral epitope similarity, have been proposed to predict response to immune checkpoint inhibitors in melanoma and small-cell lung cancer. Here we applied these checkpoint based fitness measures to the matched checkpoint treatment naive Cancer Genome Atlas (TCGA) samples where cytolytic activity (CYT) imparts a known survival benefit. We observed no significant survival predictive power beyond that of overall patient tumor mutation burden, and furthermore, found no association between checkpoint based fitness and tumor T-cell infiltration, cytolytic activity, and abundance (tumor infiltrating lymphocyte, TIL, burden). In addition, we investigated the key assumption of viral epitope similarity driving immune response in the hepatitis B virally infected liver cancer TCGA cohort, and uncovered suggestive evidence that tumor neoepitopes actually dominate viral epitopes in putative immunogenicity and plausibly drive immune response and recruitment.
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Affiliation(s)
- Adrian Bubie
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Edgar Gonzalez-Kozlova
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Nicholas Akers
- Adaptive biotechnologies, 1551 Eastlake Avenue E, Suite 200, Seattle, WA, 98102, USA
| | - Augusto Villanueva
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Bojan Losic
- Department of Genetics and Genomic Sciences, Tisch Cancer Institute, Cancer Immunology, Diabetes, Obesity and Metabolism Institute, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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