1
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Cui A, Li B, Wallace MS, Gonye ALK, Oetheimer C, Patel H, Tonnerre P, Holmes JA, Lieb D, Yao BS, Ma A, Roberts K, Damasio M, Chen JH, Piou D, Carlton-Smith C, Brown J, Mylvaganam R, Hon Fung JM, Sade-Feldman M, Aneja J, Gustafson J, Epstein ET, Salloum S, Brisac C, Thabet A, Kim AY, Lauer GM, Hacohen N, Chung RT, Alatrakchi N. Single-cell atlas of the liver myeloid compartment before and after cure of chronic viral hepatitis. J Hepatol 2024; 80:251-267. [PMID: 36972796 DOI: 10.1016/j.jhep.2023.02.040] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 01/22/2023] [Accepted: 02/14/2023] [Indexed: 03/29/2023]
Abstract
BACKGROUND & AIMS Chronic viral infections present serious public health challenges; however, direct-acting antivirals (DAAs) are now able to cure nearly all patients infected with hepatitis C virus (HCV), representing the only cure of a human chronic viral infection to date. DAAs provide a valuable opportunity to study immune pathways in the reversal of chronic immune failures in an in vivo human system. METHODS To leverage this opportunity, we used plate-based single-cell RNA-seq to deeply profile myeloid cells from liver fine needle aspirates in patients with HCV before and after DAA treatment. We comprehensively characterised liver neutrophils, eosinophils, mast cells, conventional dendritic cells, plasmacytoid dendritic cells, classical monocytes, non-classical monocytes, and macrophages, and defined fine-grained subpopulations of several cell types. RESULTS We discovered cell type-specific changes post-cure, including an increase in MCM7+STMN1+ proliferating CD1C+ conventional dendritic cells, which may support restoration from chronic exhaustion. We observed an expected downregulation of interferon-stimulated genes (ISGs) post-cure as well as an unexpected inverse relationship between pre-treatment viral load and post-cure ISG expression in each cell type, revealing a link between viral loads and sustained modifications of the host's immune system. We found an upregulation of PD-L1/L2 gene expression in ISG-high neutrophils and IDO1 expression in eosinophils, pinpointing cell subpopulations crucial for immune regulation. We identified three recurring gene programmes shared by multiple cell types, distilling core functions of the myeloid compartment. CONCLUSIONS This comprehensive single-cell RNA-seq atlas of human liver myeloid cells in response to cure of chronic viral infections reveals principles of liver immunity and provides immunotherapeutic insights. CLINICAL TRIAL REGISTRATION This study is registered at ClinicalTrials.gov (NCT02476617). IMPACT AND IMPLICATIONS Chronic viral liver infections continue to be a major public health problem. Single-cell characterisation of liver immune cells during hepatitis C and post-cure provides unique insights into the architecture of liver immunity contributing to the resolution of the first curable chronic viral infection of humans. Multiple layers of innate immune regulation during chronic infections and persistent immune modifications after cure are revealed. Researchers and clinicians may leverage these findings to develop methods to optimise the post-cure environment for HCV and develop novel therapeutic approaches for other chronic viral infections.
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Affiliation(s)
- Ang Cui
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Bo Li
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard University Virology Program, Harvard Medical School, Boston, MA, USA
| | - Michael S Wallace
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Anna L K Gonye
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Christopher Oetheimer
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Hailey Patel
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Pierre Tonnerre
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Institut de Recherche Saint-Louis, Université Paris Cité, Inserm U976 (HIPI), Team ATIP-Avenir, Paris, France
| | - Jacinta A Holmes
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Department of Gastroenterology, St Vincent's Hospital Melbourne, Melbourne, VIC, Australia
| | - David Lieb
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Brianna S Yao
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aileen Ma
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kela Roberts
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Marcos Damasio
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jonathan H Chen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Daphnee Piou
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Charles Carlton-Smith
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Joelle Brown
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ravi Mylvaganam
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | | | - Moshe Sade-Feldman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jasneet Aneja
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Division of Infectious Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jenna Gustafson
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Eliana T Epstein
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Shadi Salloum
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Cynthia Brisac
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ashraf Thabet
- Department of Interventional Radiology, Massachusetts General Hospital, Boston, MA, USA
| | - Arthur Y Kim
- Division of Infectious Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Georg M Lauer
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | - Raymond T Chung
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
| | - Nadia Alatrakchi
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
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2
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Tian J, Chen JH, Chao SX, Pelka K, Giannakis M, Hess J, Burke K, Jorgji V, Sindurakar P, Braverman J, Mehta A, Oka T, Huang M, Lieb D, Spurrell M, Allen JN, Abrams TA, Clark JW, Enzinger AC, Enzinger PC, Klempner SJ, McCleary NJ, Meyerhardt JA, Ryan DP, Yurgelun MB, Kanter K, Van Seventer EE, Baiev I, Chi G, Jarnagin J, Bradford WB, Wong E, Michel AG, Fetter IJ, Siravegna G, Gemma AJ, Sharpe A, Demehri S, Leary R, Campbell CD, Yilmaz O, Getz GA, Parikh AR, Hacohen N, Corcoran RB. Combined PD-1, BRAF and MEK inhibition in BRAF V600E colorectal cancer: a phase 2 trial. Nat Med 2023; 29:458-466. [PMID: 36702949 PMCID: PMC9941044 DOI: 10.1038/s41591-022-02181-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [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: 06/12/2022] [Accepted: 12/12/2022] [Indexed: 01/27/2023]
Abstract
While BRAF inhibitor combinations with EGFR and/or MEK inhibitors have improved clinical efficacy in BRAFV600E colorectal cancer (CRC), response rates remain low and lack durability. Preclinical data suggest that BRAF/MAPK pathway inhibition may augment the tumor immune response. We performed a proof-of-concept single-arm phase 2 clinical trial of combined PD-1, BRAF and MEK inhibition with sparatlizumab (PDR001), dabrafenib and trametinib in 37 patients with BRAFV600E CRC. The primary end point was overall response rate, and the secondary end points were progression-free survival, disease control rate, duration of response and overall survival. The study met its primary end point with a confirmed response rate (24.3% in all patients; 25% in microsatellite stable patients) and durability that were favorable relative to historical controls of BRAF-targeted combinations alone. Single-cell RNA sequencing of 23 paired pretreatment and day 15 on-treatment tumor biopsies revealed greater induction of tumor cell-intrinsic immune programs and more complete MAPK inhibition in patients with better clinical outcome. Immune program induction in matched patient-derived organoids correlated with the degree of MAPK inhibition. These data suggest a potential tumor cell-intrinsic mechanism of cooperativity between MAPK inhibition and immune response, warranting further clinical evaluation of optimized targeted and immune combinations in CRC. ClinicalTrials.gov registration: NCT03668431.
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Affiliation(s)
- Jun Tian
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA, USA
| | - Jonathan H Chen
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA, USA
- The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Sherry X Chao
- The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Karin Pelka
- The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Gladstone-UCSF Institute of Genomic Immunology, Gladstone Institutes Department of Microbiology and Immunology, UCSF, San Francisco, CA, USA
| | - Marios Giannakis
- Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Julian Hess
- The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Kelly Burke
- Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Vjola Jorgji
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA, USA
| | - Princy Sindurakar
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA, USA
| | - Jonathan Braverman
- The Koch Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Arnav Mehta
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA, USA
- The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Tomonori Oka
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA, USA
| | - Mei Huang
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA, USA
| | - David Lieb
- The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Maxwell Spurrell
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA, USA
| | - Jill N Allen
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA, USA
| | - Thomas A Abrams
- Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Jeffrey W Clark
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA, USA
| | - Andrea C Enzinger
- Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Peter C Enzinger
- Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Samuel J Klempner
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA, USA
| | - Nadine J McCleary
- Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | | | - David P Ryan
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA, USA
| | - Matthew B Yurgelun
- Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Katie Kanter
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA, USA
| | - Emily E Van Seventer
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA, USA
| | - Islam Baiev
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA, USA
| | - Gary Chi
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA, USA
| | - Joy Jarnagin
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA, USA
| | - William B Bradford
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA, USA
| | - Edmond Wong
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA, USA
| | - Alexa G Michel
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA, USA
| | - Isobel J Fetter
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA, USA
| | - Giulia Siravegna
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA, USA
| | - Angelo J Gemma
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA, USA
| | - Arlene Sharpe
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Shadmehr Demehri
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA, USA
| | - Rebecca Leary
- Novartis Institute for Biomedical Research, Cambridge, MA, USA
| | | | - Omer Yilmaz
- The Koch Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gad A Getz
- The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Aparna R Parikh
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA, USA
| | - Nir Hacohen
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA, USA.
- The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
| | - Ryan B Corcoran
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA, USA.
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3
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Tonnerre P, Wolski D, Subudhi S, Aljabban J, Hoogeveen RC, Damasio M, Drescher HK, Bartsch LM, Tully DC, Sen DR, Bean DJ, Brown J, Torres-Cornejo A, Robidoux M, Kvistad D, Alatrakchi N, Cui A, Lieb D, Cheney JA, Gustafson J, Lewis-Ximenez LL, Massenet-Regad L, Eisenhaure T, Aneja J, Haining WN, Chung RT, Hacohen N, Allen TM, Kim AY, Lauer GM. Differentiation of exhausted CD8 + T cells after termination of chronic antigen stimulation stops short of achieving functional T cell memory. Nat Immunol 2021; 22:1030-1041. [PMID: 34312544 PMCID: PMC8323980 DOI: 10.1038/s41590-021-00982-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 06/22/2021] [Indexed: 12/13/2022]
Abstract
T cell exhaustion is associated with failure to clear chronic infections and malignant cells. Defining the molecular mechanisms of T cell exhaustion and reinvigoration is essential to improving immunotherapeutic modalities. Here we confirmed pervasive phenotypic, functional, and transcriptional differences between memory and exhausted antigen-specific CD8+ T cells in human hepatitis C virus (HCV) infection before and after treatment. After viral cure, phenotypic changes in clonally stable exhausted T cell populations suggested differentiation towards a memory-like profile. However, functionally, the cells showed little improvement and critical transcriptional regulators remained in the exhaustion state. Notably, T cells from chronic HCV infection that were exposed to antigen for less time because of viral escape mutations were functionally and transcriptionally more similar to memory T cells from spontaneously resolved HCV infection. Thus, T cell stimulation duration impacts exhaustion recovery, with antigen removal after long-term exhaustion being insufficient for development of functional T cell memory.
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Affiliation(s)
- Pierre Tonnerre
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. .,Inserm U976, Université de Paris, Institut de Recherche Saint-Louis, Paris, France.
| | - David Wolski
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Sonu Subudhi
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jihad Aljabban
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ruben C Hoogeveen
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Marcos Damasio
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Hannah K Drescher
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Lea M Bartsch
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Damien C Tully
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Debattama R Sen
- Division of Medical Sciences, Harvard Medical School, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David J Bean
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Joelle Brown
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Almudena Torres-Cornejo
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Maxwell Robidoux
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Daniel Kvistad
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Nadia Alatrakchi
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ang Cui
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Harvard-MIT Division of Health Sciences and Technology, MIT, Cambridge, MA, USA
| | - David Lieb
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - James A Cheney
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jenna Gustafson
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | | | | | - Jasneet Aneja
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Division of Infectious Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - W Nicholas Haining
- Division of Medical Sciences, Harvard Medical School, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Raymond T Chung
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Todd M Allen
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Arthur Y Kim
- Division of Infectious Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Georg M Lauer
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
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4
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Hoover P, Peters M, Lieb D, Jones T, Mishra R, Hacohen N, Davidson A. Kidney macrophages in human lupus nephritis and mouse models express conserved inflammatory and remodeling gene programs and localize to the same anatomic sub-compartments. The Journal of Immunology 2021. [DOI: 10.4049/jimmunol.206.supp.52.05] [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] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Abstract
Tissue macrophages promote kidney homeostasis through tightly regulated initiation, maintenance, and resolution of tissue repair. In lupus nephritis (LN), kidney macrophages may drive damage in glomeruli and other kidney sub-compartments leading to proteinuria and fibrosis. Recent single-cell RNA sequencing work uncovered 4 novel kidney macrophage subsets in LN patient biopsies: M2-like “reparative”, “inflammatory”, “phagocytic”, and “resident” subsets. But how macrophage gene programs translate into cellular functions driving proximal tissue damage has been difficult to study because we do not fully understand how mouse models recapitulate human LN. Here, we used single cell RNA sequencing to identify kidney macrophage subsets conserved in human and mouse models of LN. We compared the transcriptomes of macrophages collected from human LN patients at peak clinical disease to those from 4 mouse strains at early and peak clinical disease. We discovered that human “reparative”, “inflammatory”, “phagocytic” subsets were conserved across species. In particular, human “reparative” and mouse resident macrophages shared inflammatory and remodeling programs, expressed interferon stimulated genes, and localized to the same kidney sub-compartments. In nephritic mice, this subset converted to a mixed M1-inflammatory/M2-repair phenotype also observed in humans, thus identifying potential conserved programs driving tissue damage in mice and humans. These findings strongly support shared roles for conserved human and mouse macrophages. Critically, they open a new path utilizing mice to study how conserved programs translate into cellular functions driving proximal tissue damage.
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Affiliation(s)
- Paul Hoover
- 1Brigham and Women’s Hosp. and Harvard Med. Sch
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5
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Mehta A, Rucevic M, Sprecher E, Rosenberg LH, Lieb D, Kasumova G, Kim MS, Bai X, Frederick DT, Flaherty K, Sullivan RJ, Hacohen N, Boland G. Abstract LB-260: The use of blood-based protein biomarkers to uncover determinants of immunotherapy response in melanoma. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-lb-260] [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
Background: Despite recent successes with immune checkpoint blockade (ICB) in melanoma, the prognosis for most patients remains dire. Whereas a small fraction of patients are able to achieve disease control, most do not respond or are limited by immune-related adverse events. Robust non-invasive predictors of ICB response have the potential to guide clinical decision making and alter management of patients, however, no such predictors currently exist. Methods: We applied a highly-multiplex proximity extension assay (Olink Proteomics) to simultaneously detect >1000 proteins in the plasma of metastatic melanoma patients treated with anti-PD-1 antibodies. Our training cohort comprised of 116 patients, 66 of whom were classified as having treatment benefit (responders, R) and 50 having no benefit (non-responders, NR). An additional 58 patients comprised a validation cohort, including 44 R and 14 NR. Plasma samples were collected at baseline, and at 6-weeks and 6-months after starting treatment. A subset of patients additionally had single-cell RNA-seq performed on tumor tissue. Group differences and treatment effects were evaluated using a linear model with maximum likelihood estimation for model parameters and Benjamini and Hochberg multiple hypothesis correction. Results: At the baseline, 6 significantly differentially expressed (DE) proteins were identified between R and NR. In particular, we found elevated expression of ST2 and IL-6, two key immunoregulatory proteins, in NR. At the 6-week on-treatment time point, more dynamic changes occurred and 79 significantly DE proteins were identified between R and NR, including proteins implicated in primary or acquired resistance, such as IL-8, MIA, TNFR1 and potential novel targets as MCP-4/CCL13, ICOSLG and VEGF. Proteomic changes identified at baseline and 6-weeks were more profound at 6-months post-treatment, and moreover 238 DE proteins were confirmed significant between R and NR at this later time-point. Importantly, we were able to leverage these differences to build classifiers of R and NR subsets. We next looked at the mRNA expression of DE proteins within the tumor microenvironment by leveraging scRNAseq data from a subset of these patients. We uncovered enriched expression of these genes in certain myeloid and exhausted T cell subsets, thus shedding insight into the potential role of these cell subsets in ICB response. Conclusions: Whole plasma proteomic profiling of anti-PD1 treated patients identified important tumor and immune changes associated with R and NR. Advanced proteomic technologies enabling an easy and non-invasive means for the discovery of circulatory protein biomarkers may predict sensitivity to immunotherapy and uncover biological insights underlying primary resistance.
Citation Format: Arnav Mehta, Marijana Rucevic, Emmett Sprecher, Lina H. Rosenberg, David Lieb, Gyulnara Kasumova, Michelle S. Kim, Xue Bai, Dennie T. Frederick, Keith Flaherty, Ryan J. Sullivan, Nir Hacohen, Genevieve Boland. The use of blood-based protein biomarkers to uncover determinants of immunotherapy response in melanoma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr LB-260.
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Affiliation(s)
| | | | | | | | - David Lieb
- 3Broad Institute of MIT and Harvard, Cambridge, MA
| | | | | | - Xue Bai
- 1Massachusetts General Hospital, Boston, MA
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6
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Marigo I, Trovato R, Hofer F, Ingangi V, Desantis G, Leone K, De Sanctis F, Ugel S, Canè S, Simonelli A, Lamolinara A, Iezzi M, Fassan M, Rugge M, Boschi F, Borile G, Eisenhaure T, Sarkizova S, Lieb D, Hacohen N, Azzolin L, Piccolo S, Lawlor R, Scarpa A, Carbognin L, Bria E, Bicciato S, Murray PJ, Bronte V. Disabled Homolog 2 Controls Prometastatic Activity of Tumor-Associated Macrophages. Cancer Discov 2020; 10:1758-1773. [PMID: 32651166 DOI: 10.1158/2159-8290.cd-20-0036] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 06/08/2020] [Accepted: 07/06/2020] [Indexed: 11/16/2022]
Abstract
Tumor-associated macrophages (TAM) are regulators of extracellular matrix (ECM) remodeling and metastatic progression, the main cause of cancer-associated death. We found that disabled homolog 2 mitogen-responsive phosphoprotein (DAB2) is highly expressed in tumor-infiltrating TAMs and that its genetic ablation significantly impairs lung metastasis formation. DAB2-expressing TAMs, mainly localized along the tumor-invasive front, participate in integrin recycling, ECM remodeling, and directional migration in a tridimensional matrix. DAB2+ macrophages escort the invasive dissemination of cancer cells by a mechanosensing pathway requiring the transcription factor YAP. In human lobular breast and gastric carcinomas, DAB2+ TAMs correlated with a poor clinical outcome, identifying DAB2 as potential prognostic biomarker for stratification of patients with cancer. DAB2 is therefore central for the prometastatic activity of TAMs. SIGNIFICANCE: DAB2 expression in macrophages is essential for metastasis formation but not primary tumor growth. Mechanosensing cues, activating the complex YAP-TAZ, regulate DAB2 in macrophages, which in turn controls integrin recycling and ECM remodeling in 3-D tissue matrix. The presence of DAB2+ TAMs in patients with cancer correlates with worse prognosis.This article is highlighted in the In This Issue feature, p. 1611.
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Affiliation(s)
- Ilaria Marigo
- Veneto Institute of Oncology IOV-IRCCS, Padova, Italy.
| | - Rosalinda Trovato
- Department of Medicine, Section of Immunology, University of Verona, Verona, Italy.
| | - Francesca Hofer
- Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
| | | | | | - Kevin Leone
- Veneto Institute of Oncology IOV-IRCCS, Padova, Italy
| | - Francesco De Sanctis
- Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
| | - Stefano Ugel
- Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
| | - Stefania Canè
- Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
| | - Anna Simonelli
- Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
| | - Alessia Lamolinara
- Department of Medicine and Aging Science, Center for Advanced Studies and Technology (CAST), University G. D'Annunzio of Chieti-Pescara, Chieti, Italy
| | - Manuela Iezzi
- Department of Medicine and Aging Science, Center for Advanced Studies and Technology (CAST), University G. D'Annunzio of Chieti-Pescara, Chieti, Italy
| | - Matteo Fassan
- Department of Medicine-DIMED, University of Padova, Padova, Italy
| | - Massimo Rugge
- Department of Medicine-DIMED, University of Padova, Padova, Italy
| | - Federico Boschi
- Department of Computer Science, University of Verona, Verona, Italy
| | - Giulia Borile
- Department of Physics and Astronomy "G. Galilei," University of Padova, Padova, Italy.,Institute of Pediatric Research Città della Speranza, Padova, Italy
| | | | | | - David Lieb
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Luca Azzolin
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Stefano Piccolo
- Department of Molecular Medicine, University of Padova, Padova, Italy.,IFOM, The FIRC Institute for Molecular Oncology, Padova, Italy
| | - Rita Lawlor
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, Italy
| | - Aldo Scarpa
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, Italy.,Department of Diagnostic and Public Health, University of Verona, Verona, Italy
| | - Luisa Carbognin
- Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Università Cattolica Del Sacro Cuore, Roma, Italy
| | - Emilio Bria
- Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Università Cattolica Del Sacro Cuore, Roma, Italy
| | - Silvio Bicciato
- Department of Life Sciences, Center for Genome Research, University of Modena and Reggio Emilia, Modena, Italy
| | - Peter J Murray
- Max Planck Institute for Biochemistry, Martinsried, Germany
| | - Vincenzo Bronte
- Department of Medicine, Section of Immunology, University of Verona, Verona, Italy.
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7
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Mehta A, Rucevic M, Sprecher E, Hultin Rosenberg L, Lieb D, Kasumova GG, Kim MS, Bai X, Frederick DT, Flaherty K, Sullivan RJ, Hacohen N, Boland GM. The use of plasma proteomic markers to understand the biology of immunotherapy response. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.10062] [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
10062 Background: Despite recent successes with immune checkpoint blockade (ICB) in melanoma, the prognosis for most patients remains dire. Whereas small fraction of patients are able to achieve disease control, most do not respond or are limited by immune-related toxicities. Robust non-invasive predictors of ICB response have the potential to guide clinical decision and alter management of patients, however, no such predictors currently exist. Methods: We applied a highly-multiplex Proximity Extension Assay to simultaneously detect > 1000 proteins in the plasma of anti-PD-1 treated melanoma patients. Our cohort comprised 116 patients, 66 responders (R) and 50 non-responders (NR). Additional 65 patients comprised a validation cohort with 30 R and 35 NR, and included 50 patients who developed treatment-related toxicities. Plasma samples were collected at baseline, 6-weeks and 6-months after starting the treatment. A subset of patients had single-cell RNA-seq performed on tumor tissue. Group differences and treatment effects were evaluated by linear model with maximum likelihood estimation for model parameters and Benjamini and Hochberg multiple hypothesis correction. Results: At baseline, 6 significantly differentially expressed (DE) proteins were identified between R and NR. Elevated expression of ST2 and IL-6, two key immunoregulatory proteins were found in NR. At 6-weeks, more dynamic changes occurred and 79 significantly DE proteins were identified between R and NR, including proteins implicated in primary or acquired resistance as IL-8, MIA, TNFR1 and potential novel targets as MCP-4/CCL13, ICOSLG and VEGF. Proteomic changes identified at baseline and 6-weeks were more profound at 6-months, and moreover 238 proteins were confirmed significant between R and NR. Importantly, we were able to leverage these differences to build classifiers of R and NR subsets. We compared mRNA expression of DE proteins within the tumor microenvironment by leveraging scRNAseq data from a subset of these patients. Enriched expression of these genes was uncovered in certain myeloid and exhausted T cell subsets, thus shedding insight into the potential role of these cell subsets in ICB response. Conclusions: Plasma proteomic profiling of anti-PD1 treated patients identified important tumor and immune changes associated with response. Non-invasive means discovery of circulatory protein biomarkers may predict sensitivity to immunotherapy and uncover biological insights underlying primary resistance.
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Affiliation(s)
| | | | | | | | - David Lieb
- Broad Institute of Harvard and MIT, Cambridge, MA
| | | | | | - Xue Bai
- Massachusetts General Hospital Cancer Center/Peking University Cancer Hospital, Boston, MA
| | | | - Keith Flaherty
- Dana-Farber Cancer Institute/Harvard Medical School/Massachusetts General Hospital, Boston, MA
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Mehta A, Kasumova G, Shi A, Rucevic M, Sallman-Almen M, Rosenberg LH, Sprecher E, Ohmura J, Kim M, Lieb D, Bai X, Frederick DT, Kellis M, Sullivan RJ, Flaherty KT, Hacohen N, Boland GM. Abstract 4533: Plasma and exosome proteomic profiling for prediction of immunotherapy response and toxicity. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-4533] [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
Immune checkpoint blockade (ICB) has revolutionized the treatment of many solid tumors, including metastatic melanoma. Despite recent successes, many patients fail to respond or are overcome by severe toxicities that limit further treatment. To date, there are no non-invasive predictors of response and toxicity that can guide treatment decisions. In this work, we perform whole plasma and exosome proteomic profiling to construct a predictive model of immunotherapy response and toxicity, and to glean further biologic insight into the mechanisms underlying resistance to ICB. Whole plasma was analyzed in a cohort of 150 melanoma patients receiving anti-PD1 antibodies (MGH IRB #11-181) at baseline, and on-treatment at 6 week and 6 month time-points. Exosomes were analyzed in 15 of these patients for all time-points. Proteomic analysis was performed using a multiplex proximity extension assay that enabled detection of more than 1000 proteins simultaneously. A linear mixed model with maximum likelihood estimation for model parameters was used to analyze differences between patient groups, and significant differences were determined after Benjamini and Hochberg multiple hypothesis correction. Between plasma baseline and on-treatment time-points, 67 differentially expressed proteins were identified including markers of inflammation such as PD1, CXCL9, CXCL10, CXCL11, IL10, CCL3 and TNFR2. Exosome samples had a distinct protein signature over the treatment period compared to plasma, including differential expression of CXCL16, CCL18, CCL20, and IL6, among others. 41 proteins were differentially expressed in plasma between ICB responders and non-responders including several inflammatory proteins such as CD28, TNFb, MCSFRa and IL8, and others implicated in melanoma resistance, such as MIA and ERBB2. Again, exosome samples had a distinct protein signature between responders and non-responders compared to plasma samples, consisting of CXCL9, CXCL13, CXCL16, CCL19, CD8a, GZMA and CD5 expression. Whereas plasma proteins reflected a myeloid signature, exosome proteins reflected a lymphoid signature, suggesting that the two compartments may capture elements of different immune processes. Integrating data from both plasma and exosome proteomics, we applied machine learning tools to build a predictor of response. Further analysis to look for predictors of toxicity is also currently underway. Overall, our work suggests that plasma and exosome protein signatures are distinct and may reflect unique immunological processes. Proteomic analysis of these compartments may be an effective way for non-invasive liquid biopsy to predict ICB response.
Citation Format: Arnav Mehta, Gyulnara Kasumova, Alvin Shi, Marijana Rucevic, Markus Sallman-Almen, Lina Hultin Rosenberg, Emmett Sprecher, Jacqueline Ohmura, Michelle Kim, David Lieb, Xue Bai, Dennie T. Frederick, Manolis Kellis, Ryan J. Sullivan, Keith T. Flaherty, Nir Hacohen, Genevieve M. Boland. Plasma and exosome proteomic profiling for prediction of immunotherapy response and toxicity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4533.
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Affiliation(s)
| | | | - Alvin Shi
- 2Massachusetts Institute of Technology, Cambridge, MA
| | | | | | | | | | | | | | - David Lieb
- 4Broad Institute of Harvard and MIT, Cambridge, MA
| | - Xue Bai
- 1Massachusetts General Hospital, Boston, MA
| | | | | | | | | | - Nir Hacohen
- 4Broad Institute of Harvard and MIT, Cambridge, MA
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Narayen G, Lieb D. SAT-584 Pembrolizumab-Related Graves' Disease: A Rare Adverse Effect of an Anti-PD-1 Antibody Cancer Immunotherapy. J Endocr Soc 2019. [PMCID: PMC6552512 DOI: 10.1210/js.2019-sat-584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Garima Narayen
- Eastern Virginia Medical School, Norfolk, VA, United States
| | - David Lieb
- Eastern Virginia Medical School, Norfolk, VA, United States
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10
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Lan YY, Heather JM, Eisenhaure T, Garris CS, Lieb D, Raychowdhury R, Hacohen N. Extranuclear DNA accumulates in aged cells and contributes to senescence and inflammation. Aging Cell 2019; 18:e12901. [PMID: 30706626 PMCID: PMC6413746 DOI: 10.1111/acel.12901] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [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: 02/01/2018] [Revised: 11/19/2018] [Accepted: 11/26/2018] [Indexed: 12/19/2022] Open
Abstract
Systemic inflammation is central to aging‐related conditions. However, the intrinsic factors that induce inflammation are not well understood. We previously identified a cell‐autonomous pathway through which damaged nuclear DNA is trafficked to the cytosol where it activates innate cytosolic DNA sensors that trigger inflammation. These results led us to hypothesize that DNA released after cumulative damage contributes to persistent inflammation in aging cells through a similar mechanism. Consistent with this notion, we found that older cells harbored higher levels of extranuclear DNA compared to younger cells. Extranuclear DNA was exported by a leptomycin B‐sensitive process, degraded through the autophagosome–lysosomal pathway and triggered innate immune responses through the DNA‐sensing cGAS‐STING pathway. Patient cells from the aging diseases ataxia and progeria also displayed extranuclear DNA accumulation, increased pIRF3 and pTBK1, and STING‐dependent p16 expression. Removing extranuclear DNA in old cells using DNASE2A reduced innate immune responses and senescence‐associated (SA) β‐gal enzyme activity. Cells and tissues of Dnase2a−/− mice with defective DNA degradation exhibited slower growth, higher activity of β‐gal, or increased expression of HP‐1β and p16 proteins, while Dnase2a−/−;Sting−/− cells and tissues were rescued from these phenotypes, supporting a role for extranuclear DNA in senescence. We hypothesize a direct role for excess DNA in aging‐related inflammation and in replicative senescence, and propose DNA degradation as a therapeutic approach to remove intrinsic DNA and revert inflammation associated with aging.
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Affiliation(s)
- Yuk Yuen Lan
- Center for Cancer Research; Massachusetts General Hospital; Charlestown Massachusetts
- Broad Institute; Cambridge Massachusetts
- Department of Medicine; Harvard Medical School; Boston Massachusetts
| | - James M. Heather
- Center for Cancer Research; Massachusetts General Hospital; Charlestown Massachusetts
| | | | - Christopher Stuart Garris
- Center for Systems Biology; Massachusetts General Hospital; Boston Massachusetts
- Graduate Program in Immunology; Harvard Medical School; Boston Massachusetts
| | - David Lieb
- Broad Institute; Cambridge Massachusetts
| | | | - Nir Hacohen
- Center for Cancer Research; Massachusetts General Hospital; Charlestown Massachusetts
- Broad Institute; Cambridge Massachusetts
- Department of Medicine; Harvard Medical School; Boston Massachusetts
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11
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Mehta A, Kasumova G, Rucevic M, Sallman-Almen M, Hultin Rosenberg L, Kim MS, Lieb D, Bai X, Frederick DT, Sullivan RJ, Flaherty K, Hacohen N, Boland GM. Liquid biopsy using plasma proteomic profiling to reveal predictors of immunotherapy response. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.8_suppl.130] [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
130 Background: The response of metastatic melanoma to anti-PD1 is heterogeneous. We performed proteomic profiling of patient plasma samples to build a predictor of immunotherapy response and uncover biological insights underlying primary resistance. Methods: 58 metastatic melanoma patients receiving anti-PD1 (Pembrolizumab or Nivolumab) at MGH comprised the initial cohort, and 150 additional patients comprised a validation cohort. Plasma samples were collected (MGH IRB #11-181) at baseline and several on-treatment time-points. Samples were analyzed for 1102 proteins by a multiplex proximity extension assay (Olink Proteomics). A subset of patients had single-cell RNA-seq (Smart-Seq2 protocol) performed on tumor tissue. Group differences and treatment effects were evaluated using linear mixed models with maximum likelihood estimation for model parameters, and Benjamini and Hochberg multiple hypothesis correction. Results: 70 significantly differentially expressed (DE) proteins were identified across the treatment period, including markers of immune activation (PD1, CXCL9, CXCL10, CD25, IL-17a, among others). 38 significantly DE proteins were identified with on-treatment time points between anti-PD1 responders (R) and non-responders (NR), including several implicated in primary or acquired resistance (IL8, MIA, ERBB2, among others). Importantly, we demonstrate the relationship of these serum biomarkers to overall and progression-free survival, and employed statistical learning approaches to build classifiers of treatment response, leveraging early and late on-treatment time points. Analysis of single-cell RNA-seq data (Sade-Feldman et al, Cell, 2018) of tumor tissue from a subset of these patients revealed that gene expression of most proteins predictive of response were enriched among tumor myeloid cells, with the remainder of proteins being reflective of exhausted T cell states. Conclusions: Whole plasma proteomic profiling of anti-PD1 treated patients revealed DE proteins between R and NR that may enable a liquid biopsy to predict anti-PD1 response. These results unveil a putative role of myeloid cells within the tumor microenvironment in anti-PD1 response or primary resistance.
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Affiliation(s)
| | | | | | | | | | | | - David Lieb
- Broad Institute of Harvard and MIT, Cambridge, MA
| | - Xue Bai
- Massachusetts General Hospital, Boston, MA
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12
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Gillies CE, Putler R, Menon R, Otto E, Yasutake K, Nair V, Hoover P, Lieb D, Li S, Eddy S, Fermin D, McNulty MT, Hacohen N, Kiryluk K, Kretzler M, Wen X, Sampson MG. An eQTL Landscape of Kidney Tissue in Human Nephrotic Syndrome. Am J Hum Genet 2018; 103:232-244. [PMID: 30057032 PMCID: PMC6081280 DOI: 10.1016/j.ajhg.2018.07.004] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 06/29/2018] [Indexed: 01/14/2023] Open
Abstract
Expression quantitative trait loci (eQTL) studies illuminate the genetics of gene expression and, in disease research, can be particularly illuminating when using the tissues directly impacted by the condition. In nephrology, there is a paucity of eQTL studies of human kidney. Here, we used whole-genome sequencing (WGS) and microdissected glomerular (GLOM) and tubulointerstitial (TI) transcriptomes from 187 individuals with nephrotic syndrome (NS) to describe the eQTL landscape in these functionally distinct kidney structures. Using MatrixEQTL, we performed cis-eQTL analysis on GLOM (n = 136) and TI (n = 166). We used the Bayesian "Deterministic Approximation of Posteriors" (DAP) to fine-map these signals, eQTLBMA to discover GLOM- or TI-specific eQTLs, and single-cell RNA-seq data of control kidney tissue to identify the cell type specificity of significant eQTLs. We integrated eQTL data with an IgA Nephropathy (IgAN) GWAS to perform a transcriptome-wide association study (TWAS). We discovered 894 GLOM eQTLs and 1,767 TI eQTLs at FDR < 0.05. 14% and 19% of GLOM and TI eQTLs, respectively, had >1 independent signal associated with its expression. 12% and 26% of eQTLs were GLOM specific and TI specific, respectively. GLOM eQTLs were most significantly enriched in podocyte transcripts and TI eQTLs in proximal tubules. The IgAN TWAS identified significant GLOM and TI genes, primarily at the HLA region. In this study, we discovered GLOM and TI eQTLs, identified those that were tissue specific, deconvoluted them into cell-specific signals, and used them to characterize known GWAS alleles. These data are available for browsing and download via our eQTL browser, "nephQTL."
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Affiliation(s)
- Christopher E Gillies
- Department of Pediatrics-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Rosemary Putler
- Department of Pediatrics-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Rajasree Menon
- Department of Computational Medicine and Bioinformatics, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Edgar Otto
- Department of Medicine-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Kalyn Yasutake
- Department of Pediatrics-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Viji Nair
- Department of Medicine-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Paul Hoover
- Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA; Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | - David Lieb
- Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | - Shuqiang Li
- Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | - Sean Eddy
- Department of Medicine-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Damian Fermin
- Department of Pediatrics-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Michelle T McNulty
- Department of Pediatrics-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Nir Hacohen
- Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA; Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | - Krzysztof Kiryluk
- Department of Medicine, Division of Nephrology, College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Matthias Kretzler
- Department of Computational Medicine and Bioinformatics, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA; Department of Medicine-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Xiaoquan Wen
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Matthew G Sampson
- Department of Pediatrics-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA.
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Dobrydneva Y, Periasamy M, Butcher M, Galkina E, Kuhn N, Lieb D, Fontana M, Wohlgemuth S, Nadler J. Weight‐loss surgery rapidly alleviates platelet hyperactivity in morbid obesity. FASEB J 2013. [DOI: 10.1096/fasebj.27.1_supplement.1114.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | | | | | - David Lieb
- Eastern Virginia Medical SchoolNorfolkVA
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14
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Dobrydneva Y, Periasamy M, Galkina E, Kuhn N, Lieb D, Fontana M, Wohlgemuth S, Nadler J. Weight loss surgery decreases platelet activation in morbidly obese patients. FASEB J 2012. [DOI: 10.1096/fasebj.26.1_supplement.876.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | | | - David Lieb
- Eastern Virginia Medical SchoolNorfolkVA
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15
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Dobrydneva Y, Taylor A, Galkina E, Kuhn N, Lieb D, Fontana M, Wohlgemuth S, Nadler J. Bariatric surgery decreases level of platelet‐monocyte aggregates in morbidly obese patients. FASEB J 2011. [DOI: 10.1096/fasebj.25.1_supplement.1028.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | | | - David Lieb
- Eastern Virginia Medical SchoolNorfolkVA
| | - Mark Fontana
- Sentara Metabolic and Weight Loss CenterNorfolkVA
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16
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Abstract
Pericardial cysts are rare abnormalities and usually do not cause any symptoms. Rarely, pericardial cysts cause symptoms and may lead to complications. There have been multiple case reports of rare complications of pericardial cysts including right ventricular outflow obstruction, pulmonary stenosis, pericardial tamponade, and partial erosion into the superior vena cava. We report a case of delayed presentation of a pericardial cyst following trauma causing a syndrome resembling congestive heart failure. To our knowledge there has been only one report of this complication.
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Affiliation(s)
- Themis Komodromos
- Division of Cardiology, Michael Reese Hospital, 2929 South Ellis Avenue, Chicago, IL 60616, USA.
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Affiliation(s)
- Golam Alam
- Cardiology Internal Medicine Radiology, Michael Reese Hospital, Chicago, Illinois 60616, USA.
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18
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Abstract
Infectious complications occurring after percutaneous transluminal coronary angioplasty are uncommon. We are reporting a case of bacterial pericarditis developing 1 week after coronary angioplasty and stent implantation. Treatment with appropriate antibiotics and drainage of the infected pericardial effusion was followed by a protracted hospital course and eventual control of infection and discharge of the patient.
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Affiliation(s)
- A Sankari
- Department of Cardiology, Michael Reese Hospital, Chicago, Illinois 60616, USA
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19
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Kaiser RS, Maguire MG, Grunwald JE, Lieb D, Jani B, Brucker AJ, Maguire AM, Ho AC, Fine SL. One-year outcomes of panretinal photocoagulation in proliferative diabetic retinopathy. Am J Ophthalmol 2000; 129:178-85. [PMID: 10682970 DOI: 10.1016/s0002-9394(99)00322-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
PURPOSE To describe the clinical features and complications of diabetic retinopathy, visual acuity, and number of repeat treatments after panretinal photocoagulation for proliferative diabetic retinopathy in a tertiary care center. METHODS A cohort study was conducted with data collection from medical records of patients undergoing panretinal photocoagulation between 1985 and 1995 at the Scheie Eye Institute; 297 eyes of 186 patients were eligible for study. RESULTS The presence of neovascularization of the disk at baseline, an earlier onset of diabetes, and a shorter duration of disease before panretinal photocoagulation were the strongest risk factors for needing an additional panretinal photocoagulation treatment. Sixty-two percent of eyes with poor visual acuity (< or =20/200) at baseline still had poor visual acuity at 1 year, and 76% with good visual acuity (> or =20/40) at baseline maintained good visual acuity at 1 year. Poor vision at baseline was the only risk factor for having poor vision at 1 year. Vitreous hemorrhage was present in 44% of eyes at baseline. New vitreous hemorrhage developed in 37% of eyes during the first year after panretinal photocoagulation. A traction retinal detachment was present in 4% of eyes at baseline and newly developed in 6% of eyes during follow-up. A repeat panretinal photocoagulation treatment was performed in 39% of eyes after initial treatment. A vitrectomy was performed in 10% of eyes from baseline through the 1-year follow-up visit. CONCLUSIONS The data from this study are useful for counseling patients with respect to likely visual outcome, possibility of major complications from proliferative diabetic retinopathy, and the chance of undergoing additional laser treatment after panretinal photocoagulation.
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Affiliation(s)
- R S Kaiser
- Scheie Eye Institute, Department of Ophthalmology, University of Pennsylvania, Philadelphia 19104, USA
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20
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Hussain KM, Kabins S, Lieb D, Chandna H, Denes P. Coagulase-negative staphylococcus endocarditis restricted to the normal pulmonic valve in a patient with end-stage renal disease: case report and review. Clin Infect Dis 1998; 27:1550-2. [PMID: 9868690 DOI: 10.1086/517752] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Affiliation(s)
- K M Hussain
- Division of Cardiology, Michael Reese Hospital and Medical Center, Chicago, Illinois, USA
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21
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Rios A, Silber E, Lieb D, Bavishi N, Varga P, Burton B, Clark W, Denes P. Heterogeneous response in the aortic root elastic properties to long term β-blockade in patients with the Marfan syndrome. J Am Coll Cardiol 1998. [DOI: 10.1016/s0735-1097(98)80783-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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22
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Abstract
A case of mitral valve aneurysm is presented in which infective endocarditis of the mitral valve was complicated by aneurysm formation 6 weeks later. The presence of mitral valve aneurysm was suspected on transthoracic echocardiography and confirmed by transesophageal echocardiography.
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Affiliation(s)
- M Changlani
- Department of Medicine, Humana Hospital-Michael Reese, Chicago, IL 60616
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23
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Abstract
Baffles within the lumen of the pulmonary artery are created in (1) the Aubert procedure, a variation of the arterial switch favored by some surgeons when two major coronary ostia arise close to one another or when one coronary artery has an intramural course, and (2) the Takeuchi procedure, a technique applied to patients with anomalous origin of the left coronary from the pulmonary artery. In both operations, coronary artery transplantation is avoided; instead, an aorticopulmonary window is created and aortic blood is redirected by an intrapulmonary artery baffle into the coronary circulation. We imaged five patients with Aubert and 10 patients with Takeuchi procedures by use of ultrasound to assess the sequelae of such intraarterial baffles. All five Aubert patients were < 3 weeks old; the ages of the 10 Takeuchi patients ranged from 2 to 86 months. Two patients died early after surgery; the remaining 13 patients were observed for 3 to 83 months (median 46 months). In all 15 patients, the baffle geometry was visualized and the aorticopulmonary window was identified. In the six who had serial imaging, none developed aorticopulmonary window stenosis. In no patient was any peribaffle shunting detected. Supravalvar narrowing, caused by the baffle partially obstructing the neopulmonary artery, was observed in two of five Aubert patients; in only one of these has reoperation been performed. In one of the 10 Takeuchi patients supravalvar narrowing of the pulmonary artery (related to repair of coexistent tetralogy of Fallot) has developed and the patient has since undergone reoperation.
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Affiliation(s)
- A J Chin
- Cardiac Non-Invasive Laboratories, Children's Hospital of Philadelphia, PA 19104
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24
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Fine DH, Rufeh F, Lieb D, Rounbehler DP. Description of the thermal energy analyzer (TEA) for trace determination of volatile and nonvolatile N-nitroso compounds. Anal Chem 1975; 47:1188-91. [PMID: 1147251 DOI: 10.1021/ac60357a073] [Citation(s) in RCA: 121] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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25
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26
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Fine DH, Lieb D, Rufeh F. Principle of operation of the thermal energy analyzer for the trace analysis of volatile and non-volatile N-nitroso compounds. J Chromatogr A 1975; 107:351-7. [PMID: 1169253 DOI: 10.1016/0021-9673(75)80011-2] [Citation(s) in RCA: 81] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The theoretical basis for the thermal energy analyzer is discussed. Using the principles outlined, the feasibility of selectivity detecting mug/kg levels of volatile and non-volatile N-nitroso compounds is established.
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27
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