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Automated multi-scale computational pathotyping (AMSCP) of inflamed synovial tissue

by Peter K. Gregersen , Deepak A. Rao , Josh Keegan , Fumitaka Mizoguchi , Michael A. McNamara , Richard D. Bell , Judith A. James , Ellen M. Gravallese , Hayley Carr , Andrew Filer , Harris Perlman , David L. Boyle , Dana E. Orange , Fei Wang , Akiko Noma , Jennifer H. Anolik , H. Mark Kenney , Miguel Otero , Chad Nusbaum , Nida Meednu , James A. Lederer , Chamith Y. Fonseka , Maxwell A. Konnaris , A. Helena Jonsson , Jennifer P. Nguyen , William Apruzzese , Eddie A. James , Mina Rohani-Pichavant , Javier Rangel-Moreno , Gary S. Firestein , Maria Gutierrez-Arcelus , Daria M. Krenitsky , Kevin Wei , Zilong Bai , Edward DiCarlo , Justin Xiang , Christopher D. Buckley , Kamil Slowikowski , Danielle Sutherby , S. Louis Bridges , Soumya Raychaudhuri , Michael B. Brenner , Saba Nayar , Karen Salomon-Escoto , Jane H. Buckner , Jason D. Turner , Darren Tabechian , Vivian P. Bykerk , Arthur M. Mandelin , David J. Lieb , Stephen Kelly , Jack McMurray , Nir Hacohen , Jennifer Albrecht , Gerald F. M. Watts , Cristina Rozo , Edward M. Schwarz , Yvonne C. Lee , Laura B. Hughes , Paul J. Utz , Anupamaa Seshadri , Jennifer Seifert , Joel M. Guthridge , Christopher T. Ritchlin , Dagmar Scheel

in 631/114/1305 / 631/250/2503 / 692/699/1670/498 / Animals / Arthritis / Arthritis, Rheumatoid - immunology / Arthritis, Rheumatoid - pathology / Automation / Computational Biology - methods / Computer applications / Cost effectiveness / Heterogeneity / Histopathology / Humanities and Social Sciences / Humans / Inflammation - pathology / Inflammatory diseases / Mice / multidisciplinary / Phenotype / Phenotypes / Phenotyping / Q / Rheumatoid arthritis / Science / Science (multidisciplinary) / Software / Synovial Membrane - immunology / Synovial Membrane - pathology / Tissues

2024

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Automated multi-scale computational pathotyping (AMSCP) of inflamed synovial tissue

2024

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2024

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Journal Article

Automated multi-scale computational pathotyping (AMSCP) of inflamed synovial tissue

Peter K. Gregersen,

Deepak A. Rao,

Josh Keegan,

Fumitaka Mizoguchi,

Michael A. McNamara,

Richard D. Bell,

Judith A. James,

Ellen M. Gravallese,

Hayley Carr,

Andrew Filer,

Harris Perlman,

David L. Boyle,

Dana E. Orange,

Fei Wang,

Akiko Noma,

Jennifer H. Anolik,

H. Mark Kenney,

Miguel Otero,

Chad Nusbaum,

Nida Meednu,

James A. Lederer,

Chamith Y. Fonseka,

Maxwell A. Konnaris,

A. Helena Jonsson,

Jennifer P. Nguyen,

William Apruzzese,

Eddie A. James,

Mina Rohani-Pichavant,

Javier Rangel-Moreno,

Gary S. Firestein,

Maria Gutierrez-Arcelus,

Daria M. Krenitsky,

Kevin Wei,

Zilong Bai,

Edward DiCarlo,

Justin Xiang,

Christopher D. Buckley,

Kamil Slowikowski,

Danielle Sutherby,

S. Louis Bridges,

Soumya Raychaudhuri,

Michael B. Brenner,

Saba Nayar,

Karen Salomon-Escoto,

Jane H. Buckner,

Jason D. Turner,

Darren Tabechian,

Vivian P. Bykerk,

Arthur M. Mandelin,

David J. Lieb,

Stephen Kelly,

Jack McMurray,

Nir Hacohen,

Jennifer Albrecht,

Gerald F. M. Watts,

Cristina Rozo,

Edward M. Schwarz,

Yvonne C. Lee,

Laura B. Hughes,

Paul J. Utz,

Anupamaa Seshadri,

Jennifer Seifert,

Joel M. Guthridge,

Christopher T. Ritchlin,

Dagmar Scheel

2024

Overview

Rheumatoid arthritis (RA) is a complex immune-mediated inflammatory disorder in which patients suffer from inflammatory-erosive arthritis. Recent advances on histopathology heterogeneity of RA synovial tissue revealed three distinct phenotypes based on cellular composition (pauci-immune, diffuse and lymphoid), suggesting that distinct etiologies warrant specific targeted therapy which motivates a need for cost effective phenotyping tools in preclinical and clinical settings. To this end, we developed an automated multi-scale computational pathotyping (AMSCP) pipeline for both human and mouse synovial tissue with two distinct components that can be leveraged together or independently: (1) segmentation of different tissue types to characterize tissue-level changes, and (2) cell type classification within each tissue compartment that assesses change across disease states. Here, we demonstrate the efficacy, efficiency, and robustness of the AMSCP pipeline as well as the ability to discover novel phenotypes. Taken together, we find AMSCP to be a valuable cost-effective method for both pre-clinical and clinical research. Automated pathotyping of synovial tissue in arthritis is a major unmet need. Here, the authors develop and demonstrate the efficacy of an automated tissue and cellular pathotyping tool for inflammatory arthritis.

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Publisher

Springer Science and Business Media LLC,Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio

Subject

/ Animals

/ Arthritis, Rheumatoid - immunology

/ Arthritis, Rheumatoid - pathology