1
|
Horisberger A, Griffith A, Keegan J, Arazi A, Pulford J, Murzin E, Howard K, Hancock B, Fava A, Sasaki T, Ghosh T, Inamo J, Beuschel R, Cao Y, Preisinger K, Gutierrez-Arcelus M, Eisenhaure TM, Guthridge J, Hoover PJ, Dall'Era M, Wofsy D, Kamen DL, Kalunian KC, Furie R, Belmont M, Izmirly P, Clancy R, Hildeman D, Woodle ES, Apruzzese W, McMahon MA, Grossman J, Barnas JL, Payan-Schober F, Ishimori M, Weisman M, Kretzler M, Berthier CC, Hodgin JB, Demeke DS, Putterman C, Brenner MB, Anolik JH, Raychaudhuri S, Hacohen N, James JA, Davidson A, Petri MA, Buyon JP, Diamond B, Zhang F, Lederer JA, Rao DA. Blood immunophenotyping identifies distinct kidney histopathology and outcomes in patients with lupus nephritis. bioRxiv 2024:2024.01.14.575609. [PMID: 38293222 PMCID: PMC10827101 DOI: 10.1101/2024.01.14.575609] [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: 02/01/2024]
Abstract
Lupus nephritis (LN) is a frequent manifestation of systemic lupus erythematosus, and fewer than half of patients achieve complete renal response with standard immunosuppressants. Identifying non-invasive, blood-based pathologic immune alterations associated with renal injury could aid therapeutic decisions. Here, we used mass cytometry immunophenotyping of peripheral blood mononuclear cells in 145 patients with biopsy-proven LN and 40 healthy controls to evaluate the heterogeneity of immune activation in patients with LN and to identify correlates of renal parameters and treatment response. Unbiased analysis identified 3 immunologically distinct groups of patients with LN that were associated with different patterns of histopathology, renal cell infiltrates, urine proteomic profiles, and treatment response at one year. Patients with enriched circulating granzyme B+ T cells at baseline showed more severe disease and increased numbers of activated CD8 T cells in the kidney, yet they had the highest likelihood of treatment response. A second group characterized primarily by a high type I interferon signature had a lower likelihood of response to therapy, while a third group appeared immunologically inactive by immunophenotyping at enrollment but with chronic renal injuries. Main immune profiles could be distilled down to 5 simple cytometric parameters that recapitulate several of the associations, highlighting the potential for blood immune profiling to translate to clinically useful non-invasive metrics to assess immune-mediated disease in LN.
Collapse
|
2
|
Lake BB, Menon R, Winfree S, Hu Q, Melo Ferreira R, Kalhor K, Barwinska D, Otto EA, Ferkowicz M, Diep D, Plongthongkum N, Knoten A, Urata S, Mariani LH, Naik AS, Eddy S, Zhang B, Wu Y, Salamon D, Williams JC, Wang X, Balderrama KS, Hoover PJ, Murray E, Marshall JL, Noel T, Vijayan A, Hartman A, Chen F, Waikar SS, Rosas SE, Wilson FP, Palevsky PM, Kiryluk K, Sedor JR, Toto RD, Parikh CR, Kim EH, Satija R, Greka A, Macosko EZ, Kharchenko PV, Gaut JP, Hodgin JB, Eadon MT, Dagher PC, El-Achkar TM, Zhang K, Kretzler M, Jain S. An atlas of healthy and injured cell states and niches in the human kidney. Nature 2023; 619:585-594. [PMID: 37468583 PMCID: PMC10356613 DOI: 10.1038/s41586-023-05769-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 63.0] [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: 07/31/2021] [Accepted: 01/30/2023] [Indexed: 07/21/2023]
Abstract
Understanding kidney disease relies on defining the complexity of cell types and states, their associated molecular profiles and interactions within tissue neighbourhoods1. Here we applied multiple single-cell and single-nucleus assays (>400,000 nuclei or cells) and spatial imaging technologies to a broad spectrum of healthy reference kidneys (45 donors) and diseased kidneys (48 patients). This has provided a high-resolution cellular atlas of 51 main cell types, which include rare and previously undescribed cell populations. The multi-omic approach provides detailed transcriptomic profiles, regulatory factors and spatial localizations spanning the entire kidney. We also define 28 cellular states across nephron segments and interstitium that were altered in kidney injury, encompassing cycling, adaptive (successful or maladaptive repair), transitioning and degenerative states. Molecular signatures permitted the localization of these states within injury neighbourhoods using spatial transcriptomics, while large-scale 3D imaging analysis (around 1.2 million neighbourhoods) provided corresponding linkages to active immune responses. These analyses defined biological pathways that are relevant to injury time-course and niches, including signatures underlying epithelial repair that predicted maladaptive states associated with a decline in kidney function. This integrated multimodal spatial cell atlas of healthy and diseased human kidneys represents a comprehensive benchmark of cellular states, neighbourhoods, outcome-associated signatures and publicly available interactive visualizations.
Collapse
Affiliation(s)
- Blue B Lake
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- San Diego Institute of Science, Altos Labs, San Diego, CA, USA
| | - Rajasree Menon
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Seth Winfree
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Qiwen Hu
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Ricardo Melo Ferreira
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kian Kalhor
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Daria Barwinska
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Edgar A Otto
- Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, MI, USA
| | - Michael Ferkowicz
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Dinh Diep
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- San Diego Institute of Science, Altos Labs, San Diego, CA, USA
| | - Nongluk Plongthongkum
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Amanda Knoten
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Sarah Urata
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Laura H Mariani
- Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, MI, USA
| | - Abhijit S Naik
- Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, MI, USA
| | - Sean Eddy
- Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, MI, USA
| | - Bo Zhang
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Yan Wu
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- San Diego Institute of Science, Altos Labs, San Diego, CA, USA
| | - Diane Salamon
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - James C Williams
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Xin Wang
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | | | - Paul J Hoover
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Evan Murray
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Teia Noel
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Anitha Vijayan
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | | | - Fei Chen
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Sushrut S Waikar
- Section of Nephrology, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Sylvia E Rosas
- Kidney and Hypertension Unit, Joslin Diabetes Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Francis P Wilson
- Department of Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Paul M Palevsky
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | - John R Sedor
- Lerner Research and Glickman Urology and Kidney Institutes, Cleveland Clinic, Cleveland, OH, USA
| | - Robert D Toto
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA
| | - Chirag R Parikh
- Division of Nephrology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Eric H Kim
- Department of Surgery, Washington University School of Medicine, St Louis, MO, USA
| | | | - Anna Greka
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Peter V Kharchenko
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- San Diego Institute of Science, Altos Labs, San Diego, CA, USA
| | - Joseph P Gaut
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Jeffrey B Hodgin
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Michael T Eadon
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Pierre C Dagher
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Tarek M El-Achkar
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Kun Zhang
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
- San Diego Institute of Science, Altos Labs, San Diego, CA, USA.
| | - Matthias Kretzler
- Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, MI, USA.
| | - Sanjay Jain
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.
| |
Collapse
|
3
|
Filbin MR, Mehta A, Schneider AM, Kays KR, Guess JR, Gentili M, Fenyves BG, Charland NC, Gonye AL, Gushterova I, Khanna HK, LaSalle TJ, Lavin-Parsons KM, Lilley BM, Lodenstein CL, Manakongtreecheep K, Margolin JD, McKaig BN, Rojas-Lopez M, Russo BC, Sharma N, Tantivit J, Thomas MF, Gerszten RE, Heimberg GS, Hoover PJ, Lieb DJ, Lin B, Ngo D, Pelka K, Reyes M, Smillie CS, Waghray A, Wood TE, Zajac AS, Jennings LL, Grundberg I, Bhattacharyya RP, Parry BA, Villani AC, Sade-Feldman M, Hacohen N, Goldberg MB. Longitudinal proteomic analysis of severe COVID-19 reveals survival-associated signatures, tissue-specific cell death, and cell-cell interactions. Cell Rep Med 2021; 2:100287. [PMID: 33969320 PMCID: PMC8091031 DOI: 10.1016/j.xcrm.2021.100287] [Citation(s) in RCA: 142] [Impact Index Per Article: 47.3] [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: 12/22/2020] [Revised: 03/08/2021] [Accepted: 04/23/2021] [Indexed: 02/06/2023]
Abstract
Mechanisms underlying severe coronavirus disease 2019 (COVID-19) disease remain poorly understood. We analyze several thousand plasma proteins longitudinally in 306 COVID-19 patients and 78 symptomatic controls, uncovering immune and non-immune proteins linked to COVID-19. Deconvolution of our plasma proteome data using published scRNA-seq datasets reveals contributions from circulating immune and tissue cells. Sixteen percent of patients display reduced inflammation yet comparably poor outcomes. Comparison of patients who died to severely ill survivors identifies dynamic immune-cell-derived and tissue-associated proteins associated with survival, including exocrine pancreatic proteases. Using derived tissue-specific and cell-type-specific intracellular death signatures, cellular angiotensin-converting enzyme 2 (ACE2) expression, and our data, we infer whether organ damage resulted from direct or indirect effects of infection. We propose a model in which interactions among myeloid, epithelial, and T cells drive tissue damage. These datasets provide important insights and a rich resource for analysis of mechanisms of severe COVID-19 disease.
Collapse
Affiliation(s)
- Michael R. Filbin
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Emergency Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Arnav Mehta
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Alexis M. Schneider
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kyle R. Kays
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Matteo Gentili
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Bánk G. Fenyves
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Emergency Medicine, Semmelweis University, Budapest, Hungary
| | - Nicole C. Charland
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Anna L.K. Gonye
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Irena Gushterova
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Hargun K. Khanna
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Thomas J. LaSalle
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Brendan M. Lilley
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Carl L. Lodenstein
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Kasidet Manakongtreecheep
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Justin D. Margolin
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Brenna N. McKaig
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Maricarmen Rojas-Lopez
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Brian C. Russo
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Nihaarika Sharma
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jessica Tantivit
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Molly F. Thomas
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Robert E. Gerszten
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- CardioVascular Institute, Department of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Graham S. Heimberg
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Paul J. Hoover
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - David J. Lieb
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Brian Lin
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Center for Regenerative Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Debby Ngo
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Karin Pelka
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Miguel Reyes
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Christopher S. Smillie
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Avinash Waghray
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Center for Regenerative Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Thomas E. Wood
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Amanda S. Zajac
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | | | | | - Roby P. Bhattacharyya
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Blair Alden Parry
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Alexandra-Chloé Villani
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Moshe Sade-Feldman
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Nir Hacohen
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Marcia B. Goldberg
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| |
Collapse
|
4
|
Filbin MR, Mehta A, Schneider AM, Kays KR, Guess JR, Gentili M, Fenyves BG, Charland NC, Gonye ALK, Gushterova I, Khanna HK, LaSalle TJ, Lavin-Parsons KM, Lilly BM, Lodenstein CL, Manakongtreecheep K, Margolin JD, McKaig BN, Rojas-Lopez M, Russo BC, Sharma N, Tantivit J, Thomas MF, Gerszten RE, Heimberg GS, Hoover PJ, Lieb DJ, Lin B, Ngo D, Pelka K, Reyes M, Smillie CS, Waghray A, Wood TE, Zajac AS, Jennings LL, Grundberg I, Bhattacharyya RP, Parry BA, Villani AC, Sade-Feldman M, Hacohen N, Goldberg MB. Plasma proteomics reveals tissue-specific cell death and mediators of cell-cell interactions in severe COVID-19 patients. bioRxiv 2020:2020.11.02.365536. [PMID: 33173871 PMCID: PMC7654866 DOI: 10.1101/2020.11.02.365536] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
COVID-19 has caused over 1 million deaths globally, yet the cellular mechanisms underlying severe disease remain poorly understood. By analyzing several thousand plasma proteins in 306 COVID-19 patients and 78 symptomatic controls over serial timepoints using two complementary approaches, we uncover COVID-19 host immune and non-immune proteins not previously linked to this disease. Integration of plasma proteomics with nine published scRNAseq datasets shows that SARS-CoV-2 infection upregulates monocyte/macrophage, plasmablast, and T cell effector proteins. By comparing patients who died to severely ill patients who survived, we identify dynamic immunomodulatory and tissue-associated proteins associated with survival, providing insights into which host responses are beneficial and which are detrimental to survival. We identify intracellular death signatures from specific tissues and cell types, and by associating these with angiotensin converting enzyme 2 (ACE2) expression, we map tissue damage associated with severe disease and propose which damage results from direct viral infection rather than from indirect effects of illness. We find that disease severity in lung tissue is driven by myeloid cell phenotypes and cell-cell interactions with lung epithelial cells and T cells. Based on these results, we propose a model of immune and epithelial cell interactions that drive cell-type specific and tissue-specific damage in severe COVID-19.
Collapse
|
5
|
Arazi A, Rao DA, Berthier CC, Davidson A, Liu Y, Hoover PJ, Chicoine A, Eisenhaure TM, Jonsson AH, Li S, Lieb DJ, Zhang F, Slowikowski K, Browne EP, Noma A, Sutherby D, Steelman S, Smilek DE, Tosta P, Apruzzese W, Massarotti E, Dall'Era M, Park M, Kamen DL, Furie RA, Payan-Schober F, Pendergraft WF, McInnis EA, Buyon JP, Petri MA, Putterman C, Kalunian KC, Woodle ES, Lederer JA, Hildeman DA, Nusbaum C, Raychaudhuri S, Kretzler M, Anolik JH, Brenner MB, Wofsy D, Hacohen N, Diamond B. The immune cell landscape in kidneys of patients with lupus nephritis. Nat Immunol 2019; 20:902-914. [PMID: 31209404 PMCID: PMC6726437 DOI: 10.1038/s41590-019-0398-x] [Citation(s) in RCA: 415] [Impact Index Per Article: 83.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 04/05/2019] [Indexed: 02/07/2023]
Abstract
Lupus nephritis is a potentially fatal autoimmune disease for which the
current treatment is ineffective and often toxic. To develop mechanistic
hypotheses of disease, we analyzed kidney samples from patients with lupus
nephritis and from healthy control subjects using single-cell RNA sequencing.
Our analysis revealed 21 subsets of leukocytes active in disease, including
multiple populations of myeloid cells, T cells, natural killer cells and B cells
that demonstrated both pro-inflammatory responses and inflammation-resolving
responses. We found evidence of local activation of B cells correlated with an
age-associated B-cell signature and evidence of progressive stages of monocyte
differentiation within the kidney. A clear interferon response was observed in
most cells. Two chemokine receptors, CXCR4 and
CX3CR1, were broadly expressed, implying a potentially
central role in cell trafficking. Gene expression of immune cells in urine and
kidney was highly correlated, which would suggest that urine might serve as a
surrogate for kidney biopsies.
Collapse
Affiliation(s)
- Arnon Arazi
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Deepak A Rao
- Division of Rheumatology, Immunology, Allergy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Celine C Berthier
- Internal Medicine, Department of Nephrology, University of Michigan, Ann Arbor, MI, USA
| | - Anne Davidson
- Center for Autoimmune and Musculoskeletal Diseases, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Yanyan Liu
- Division of Rheumatology, Immunology, Allergy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Paul J Hoover
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Adam Chicoine
- Division of Rheumatology, Immunology, Allergy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - A Helena Jonsson
- Division of Rheumatology, Immunology, Allergy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Shuqiang Li
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David J Lieb
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Fan Zhang
- Division of Rheumatology, Immunology, Allergy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kamil Slowikowski
- Division of Rheumatology, Immunology, Allergy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Edward P Browne
- UNC HIV Cure Center and Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Akiko Noma
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Dawn E Smilek
- Lupus Nephritis Trials Network, University of California San Francisco, San Francisco, CA, USA.,Immune Tolerance Network, University of California San Francisco, San Francisco, CA, USA
| | - Patti Tosta
- Lupus Nephritis Trials Network, University of California San Francisco, San Francisco, CA, USA.,Immune Tolerance Network, University of California San Francisco, San Francisco, CA, USA
| | - William Apruzzese
- Division of Rheumatology, Immunology, Allergy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Elena Massarotti
- Division of Rheumatology, Immunology, Allergy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Maria Dall'Era
- Rheumatology Division, University of California San Francisco, San Francisco, CA, USA
| | - Meyeon Park
- Division of Nephrology, University of California San Francisco, San Francisco, CA, USA
| | - Diane L Kamen
- Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC, USA
| | - Richard A Furie
- Division of Rheumatology, Northwell Health, Great Neck, NY, USA
| | - Fernanda Payan-Schober
- Department of Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX, USA
| | | | - Elizabeth A McInnis
- University of North Carolina Kidney Center, Division of Nephrology and Hypertension, Department of Medicine, UNC School of Medicine, Chapel Hill, NC, USA
| | - Jill P Buyon
- Department of Medicine, Division of Rheumatology, New York University School of Medicine, New York, NY, USA
| | - Michelle A Petri
- Division of Rheumatology, Johns Hopkins University, Baltimore, MD, USA
| | - Chaim Putterman
- Division of Rheumatology and Department of Microbiology and Immunology, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY, USA
| | - Kenneth C Kalunian
- University of California San Diego School of Medicine, La Jolla, CA, USA
| | - E Steve Woodle
- Division of Transplantation, Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - James A Lederer
- Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - David A Hildeman
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA.,Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | | | - Soumya Raychaudhuri
- Division of Rheumatology, Immunology, Allergy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Matthias Kretzler
- Internal Medicine, Department of Nephrology, University of Michigan, Ann Arbor, MI, USA
| | - Jennifer H Anolik
- Department of Medicine, Division of Allergy, Immunology, and Rheumatology, University of Rochester Medical Center, Rochester, NY, USA
| | - Michael B Brenner
- Division of Rheumatology, Immunology, Allergy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - David Wofsy
- Rheumatology Division, University of California San Francisco, San Francisco, CA, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Betty Diamond
- Center for Autoimmune and Musculoskeletal Diseases, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, USA.
| | | |
Collapse
|
6
|
Leatherwood C, Speyer CB, Feldman CH, D'Silva K, Gómez-Puerta JA, Hoover PJ, Waikar SS, McMahon GM, Rennke HG, Costenbader KH. Clinical characteristics and renal prognosis associated with interstitial fibrosis and tubular atrophy (IFTA) and vascular injury in lupus nephritis biopsies. Semin Arthritis Rheum 2019; 49:396-404. [PMID: 31277928 DOI: 10.1016/j.semarthrit.2019.06.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 05/21/2019] [Accepted: 06/05/2019] [Indexed: 12/21/2022]
Abstract
BACKGROUND Interstitial fibrosis and tubular atrophy (IFTA) and vascular injury are frequent histologic features of lupus nephritis renal biopsies, but their clinical correlates and prognostic value are not well understood. This cohort study investigated demographic, clinical and laboratory characteristics, and outcomes, associated with IFTA and vascular injury in lupus nephritis. METHODS Reports of all renal biopsies performed at an academic medical center (1990-2017) with WHO/ISN/RPS Class II-V lupus nephritis were reviewed. Demographics, clinical variables and labs at biopsy, treatment, and date of death were collected. Additional data from the U.S. Renal Data System (USRDS) provided dates of ESRD and death after ESRD. Multivariable regression analyses identified demographic and clinical factors associated with each histologic finding. Cumulative incidence functions and multivariable Cox proportional hazard models estimated the risk of progression to ESRD and death. RESULTS Within 202 initial biopsies, IFTA was associated with the patient's SLICC/ACR damage index (without renal domain) and serum creatinine, and vascular injury was associated with serum creatinine in multivariable models. In Cox regression models adjusting for age, sex, race, serum creatinine, calendar year, and biopsy class, moderate/severe IFTA was associated with elevated ESRD (HRSD 5.18, 95% CI 2.53, 10.59) and death (HR 4.19, 95%CI 1.27, 13.81). After adjustment for age, sex and race, moderate/severe vascular injury was associated with ESRD (HRSD 2.13, 95% CI 1.21, 3.75) and but this relationship was not significant after adjustment for serum creatinine and calendar year. CONCLUSIONS IFTA is a strong predictor of ESRD and death, even in proliferative nephritis, and a risk factor for poor outcomes independent of class. Vascular injury is a strong predictor of prognosis, but not independent of serum creatinine and class. The prognostic value of these lesions calls for consideration when determining treatment for lupus nephritis.
Collapse
Affiliation(s)
- Cianna Leatherwood
- Division of Rheumatology, Immunology and Allergy, Department of Medicine, Brigham and Women's Hospital, Boston, MA
| | - Cameron B Speyer
- Division of Rheumatology, Immunology and Allergy, Department of Medicine, Brigham and Women's Hospital, Boston, MA
| | - Candace H Feldman
- Division of Rheumatology, Immunology and Allergy, Department of Medicine, Brigham and Women's Hospital, Boston, MA
| | - Kristin D'Silva
- General Internal Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA
| | | | - Paul J Hoover
- Division of Rheumatology, Immunology and Allergy, Department of Medicine, Brigham and Women's Hospital, Boston, MA
| | - Sushrut S Waikar
- Renal Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA
| | - Gearoid M McMahon
- Renal Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA
| | - Helmut G Rennke
- Renal Service, Department of Pathology, Brigham and Women's Hospital, Boston, MA
| | - Karen H Costenbader
- Division of Rheumatology, Immunology and Allergy, Department of Medicine, Brigham and Women's Hospital, Boston, MA.
| |
Collapse
|
7
|
Sade-Feldman M, Yizhak K, Bjorgaard SL, Ray JP, de Boer CG, Jenkins RW, Lieb DJ, Chen JH, Frederick DT, Barzily-Rokni M, Freeman SS, Reuben A, Hoover PJ, Villani AC, Ivanova E, Portell A, Lizotte PH, Aref AR, Eliane JP, Hammond MR, Vitzthum H, Blackmon SM, Li B, Gopalakrishnan V, Reddy SM, Cooper ZA, Paweletz CP, Barbie DA, Stemmer-Rachamimov A, Flaherty KT, Wargo JA, Boland GM, Sullivan RJ, Getz G, Hacohen N. Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma. Cell 2019; 176:404. [PMID: 30633907 DOI: 10.1016/j.cell.2018.12.034] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
8
|
Sade-Feldman M, Yizhak K, Bjorgaard SL, Ray JP, de Boer CG, Jenkins RW, Lieb DJ, Chen JH, Frederick DT, Barzily-Rokni M, Freeman SS, Reuben A, Hoover PJ, Villani AC, Ivanova E, Portell A, Lizotte PH, Aref AR, Eliane JP, Hammond MR, Vitzthum H, Blackmon SM, Li B, Gopalakrishnan V, Reddy SM, Cooper ZA, Paweletz CP, Barbie DA, Stemmer-Rachamimov A, Flaherty KT, Wargo JA, Boland GM, Sullivan RJ, Getz G, Hacohen N. Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma. Cell 2018; 175:998-1013.e20. [PMID: 30388456 PMCID: PMC6641984 DOI: 10.1016/j.cell.2018.10.038] [Citation(s) in RCA: 998] [Impact Index Per Article: 166.3] [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: 01/17/2018] [Revised: 07/07/2018] [Accepted: 10/15/2018] [Indexed: 02/07/2023]
Abstract
Treatment of cancer has been revolutionized by immune checkpoint blockade therapies. Despite the high rate of response in advanced melanoma, the majority of patients succumb to disease. To identify factors associated with success or failure of checkpoint therapy, we profiled transcriptomes of 16,291 individual immune cells from 48 tumor samples of melanoma patients treated with checkpoint inhibitors. Two distinct states of CD8+ T cells were defined by clustering and associated with patient tumor regression or progression. A single transcription factor, TCF7, was visualized within CD8+ T cells in fixed tumor samples and predicted positive clinical outcome in an independent cohort of checkpoint-treated patients. We delineated the epigenetic landscape and clonality of these T cell states and demonstrated enhanced antitumor immunity by targeting novel combinations of factors in exhausted cells. Our study of immune cell transcriptomes from tumors demonstrates a strategy for identifying predictors, mechanisms, and targets for enhancing checkpoint immunotherapy.
Collapse
MESH Headings
- Animals
- Antibodies, Monoclonal, Humanized/immunology
- Antibodies, Monoclonal, Humanized/pharmacology
- Antigens, CD/immunology
- Antineoplastic Agents, Immunological/immunology
- Antineoplastic Agents, Immunological/pharmacology
- Apyrase/antagonists & inhibitors
- Apyrase/immunology
- CD8-Positive T-Lymphocytes/immunology
- Cell Line, Tumor
- Humans
- Immunotherapy/methods
- Leukocyte Common Antigens/antagonists & inhibitors
- Leukocyte Common Antigens/immunology
- Melanoma/immunology
- Melanoma/therapy
- Mice
- Mice, Inbred BALB C
- Mice, Inbred C57BL
- T Cell Transcription Factor 1/metabolism
- Transcriptome
Collapse
Affiliation(s)
- Moshe Sade-Feldman
- Massachusetts General Hospital Cancer Center, Harvard Medical School (HMS), Boston, MA, USA; Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA; Department of Medicine, Massachusetts General Hospital, HMS, Boston, MA, USA
| | - Keren Yizhak
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Stacey L Bjorgaard
- Massachusetts General Hospital Cancer Center, Harvard Medical School (HMS), Boston, MA, USA; Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - John P Ray
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Carl G de Boer
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Russell W Jenkins
- Massachusetts General Hospital Cancer Center, Harvard Medical School (HMS), Boston, MA, USA; Department of Medicine, Massachusetts General Hospital, HMS, Boston, MA, USA; Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA
| | - David J Lieb
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Jonathan H Chen
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA; Department of Pathology, Massachusetts General Hospital, HMS, Boston, MA, USA
| | - Dennie T Frederick
- Massachusetts General Hospital Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
| | - Michal Barzily-Rokni
- Massachusetts General Hospital Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
| | - Samuel S Freeman
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA; Department of Biomedical Informatics, HMS, Boston, MA, USA
| | - Alexandre Reuben
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Paul J Hoover
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA; Brigham & Women's Hospital, Division of Rheumatology, Immunology and Allergy, Boston, MA, USA
| | - Alexandra-Chloé Villani
- Massachusetts General Hospital Cancer Center, Harvard Medical School (HMS), Boston, MA, USA; Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA; Department of Medicine, Massachusetts General Hospital, HMS, Boston, MA, USA
| | - Elena Ivanova
- Department of Medicine, Massachusetts General Hospital, HMS, Boston, MA, USA; Belfer Center for Applied Cancer Science, Dana Farber Cancer Institute, Boston, MA, USA
| | - Andrew Portell
- Department of Medicine, Massachusetts General Hospital, HMS, Boston, MA, USA; Belfer Center for Applied Cancer Science, Dana Farber Cancer Institute, Boston, MA, USA
| | - Patrick H Lizotte
- Department of Medicine, Massachusetts General Hospital, HMS, Boston, MA, USA; Belfer Center for Applied Cancer Science, Dana Farber Cancer Institute, Boston, MA, USA
| | - Amir R Aref
- Department of Medicine, Massachusetts General Hospital, HMS, Boston, MA, USA; Belfer Center for Applied Cancer Science, Dana Farber Cancer Institute, Boston, MA, USA
| | - Jean-Pierre Eliane
- Department of Pathology, Massachusetts General Hospital, HMS, Boston, MA, USA
| | - Marc R Hammond
- Massachusetts General Hospital Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
| | - Hans Vitzthum
- Massachusetts General Hospital Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
| | - Shauna M Blackmon
- Massachusetts General Hospital Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
| | - Bo Li
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA; Department of Virology, Harvard Medical School, Boston, MA, USA
| | | | - Sangeetha M Reddy
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zachary A Cooper
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cloud P Paweletz
- Department of Medicine, Massachusetts General Hospital, HMS, Boston, MA, USA; Belfer Center for Applied Cancer Science, Dana Farber Cancer Institute, Boston, MA, USA
| | - David A Barbie
- Department of Medicine, Massachusetts General Hospital, HMS, Boston, MA, USA
| | | | - Keith T Flaherty
- Massachusetts General Hospital Cancer Center, Harvard Medical School (HMS), Boston, MA, USA; Department of Medicine, Massachusetts General Hospital, HMS, Boston, MA, USA
| | - Jennifer A Wargo
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Genevieve M Boland
- Massachusetts General Hospital Cancer Center, Harvard Medical School (HMS), Boston, MA, USA; Department of Surgery, Massachusetts General Hospital, HMS, Boston, MA, USA
| | - Ryan J Sullivan
- Massachusetts General Hospital Cancer Center, Harvard Medical School (HMS), Boston, MA, USA; Department of Medicine, Massachusetts General Hospital, HMS, Boston, MA, USA
| | - Gad Getz
- Massachusetts General Hospital Cancer Center, Harvard Medical School (HMS), Boston, MA, USA; Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA; Department of Pathology, Massachusetts General Hospital, HMS, Boston, MA, USA; Department of Pathology, Harvard Medical School, Boston, MA, USA.
| | - Nir Hacohen
- Massachusetts General Hospital Cancer Center, Harvard Medical School (HMS), Boston, MA, USA; Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA; Department of Medicine, Massachusetts General Hospital, HMS, Boston, MA, USA.
| |
Collapse
|
9
|
Hoover PJ, Lewis RS. Stoichiometric Requirements for Trapping and Activation of CRAC Channels by STIM1 At ER-Plasma Membrane Junctions. Biophys J 2011. [DOI: 10.1016/j.bpj.2010.12.1209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
|
10
|
Park CY, Hoover PJ, Mullins FM, Bachhawat P, Covington ED, Raunser S, Walz T, Garcia KC, Dolmetsch RE, Lewis RS. STIM1 clusters and activates CRAC channels via direct binding of a cytosolic domain to Orai1. Cell 2009; 136:876-90. [PMID: 19249086 DOI: 10.1016/j.cell.2009.02.014] [Citation(s) in RCA: 753] [Impact Index Per Article: 50.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2008] [Revised: 01/06/2009] [Accepted: 02/09/2009] [Indexed: 12/25/2022]
Abstract
Store-operated Ca(2+) channels activated by the depletion of Ca(2+) from the endoplasmic reticulum (ER) are a major Ca(2+) entry pathway in nonexcitable cells and are essential for T cell activation and adaptive immunity. After store depletion, the ER Ca(2+) sensor STIM1 and the CRAC channel protein Orai1 redistribute to ER-plasma membrane (PM) junctions, but the fundamental issue of how STIM1 activates the CRAC channel at these sites is unresolved. Here, we identify a minimal, highly conserved 107-aa CRAC activation domain (CAD) of STIM1 that binds directly to the N and C termini of Orai1 to open the CRAC channel. Purified CAD forms a tetramer that clusters CRAC channels, but analysis of STIM1 mutants reveals that channel clustering is not sufficient for channel activation. These studies establish a molecular mechanism for store-operated Ca(2+) entry in which the direct binding of STIM1 to Orai1 drives the accumulation and the activation of CRAC channels at ER-PM junctions.
Collapse
Affiliation(s)
- Chan Young Park
- Department of Neurobiology, Stanford University School of Medicine, CA 94305, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Reed C, Sturbaum GD, Hoover PJ, Sterling CR. Cryptosporidium parvum mixed genotypes detected by PCR-restriction fragment length polymorphism analysis. Appl Environ Microbiol 2002; 68:427-9. [PMID: 11772657 PMCID: PMC126566 DOI: 10.1128/aem.68.1.427-429.2002] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Combinations of 10 Cryptosporidium parvum oocysts, with various ratios of genotype I to genotype II, were isolated and subjected to PCR-restriction fragment length polymorphism analysis. Amplification of both genotypes in these samples ranged from 31 to 74% and yielded no information about the genotype proportions. In addition, since both genotypes were not always detected, amplification of a single genotype is not conclusive evidence that the sample contains only a single genotype.
Collapse
Affiliation(s)
- Carrie Reed
- Department of Veterinary Science and Microbiology, University of Arizona, Tucson, Arizona 85721, USA
| | | | | | | |
Collapse
|
12
|
Sturbaum GD, Reed C, Hoover PJ, Jost BH, Marshall MM, Sterling CR. Species-specific, nested PCR-restriction fragment length polymorphism detection of single Cryptosporidium parvum oocysts. Appl Environ Microbiol 2001; 67:2665-8. [PMID: 11375178 PMCID: PMC92922 DOI: 10.1128/aem.67.6.2665-2668.2001] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Concurrent with recent advances seen with Cryptosporidium parvum detection in both treated and untreated water is the need to properly evaluate these advances. A micromanipulation method by which known numbers of C. parvum oocysts, even a single oocyst, can be delivered to a test matrix for detection sensitivity is presented. Using newly developed nested PCR-restriction fragment length polymorphism primers, PCR sensitivity was evaluated with 1, 2, 3, 4, 5, 7, or 10 oocysts. PCR detection rates (50 samples for each number of oocysts) ranged from 38% for single oocysts to 92% for 5 oocysts, while 10 oocysts were needed to achieve 100% detection. The nested PCR conditions amplified products from C. parvum, Cryptosporidium baileyi, and Cryptosporidium serpentis but no other Cryptosporidium sp. or protozoan tested. Restriction enzyme digestion with VspI distinguished between C. parvum genotypes 1 and 2. Restriction enzyme digestion with DraII distinguished C. parvum from C. baileyi and C. serpentis. Use of known numbers of whole oocysts encompasses the difficulty of liberating DNA from the oocyst and eliminates the standard deviation inherent within a dilution series. To our knowledge this is the first report in which singly isolated C. parvum oocysts were used to evaluate PCR sensitivity. This achievement illustrates that PCR amplification of a single oocyst is feasible, yet sensitivity remains an issue, thereby illustrating the difficulty of dealing with low oocyst numbers when working with environmental water samples.
Collapse
Affiliation(s)
- G D Sturbaum
- Department of Veterinary Science and Microbiology, University of Arizona, Tucson, Arizona 85721, USA
| | | | | | | | | | | |
Collapse
|