Evidence map›Paper›PMID 29996944›Full record

ArticleArthritis research & therapy2018

Methods for high-dimensional analysis of cells dissociated from cryopreserved synovial tissue

Laura T Donlin, Deepak A Rao, Kevin Wei, Kamil Slowikowski, Mandy J McGeachy, Jason D Turner, Nida Meednu, Fumitaka Mizoguchi, Maria Gutierrez-Arcelus, David J Lieb and 34 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Arthritis research & therapy, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
82citing papers in PubMed, 1 pooled it
11.9field-weighted citation impact, top 1% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

82 citing papers in PubMed, 1 synthesis or guideline pooled it, 127 citations in OpenAlex.

  1. Pooled it
  2. Trial
  3. Review
  4. Article
  5. Article
  6. Article
  7. Article
  8. Article
  9. Article
  10. Article
  11. Article
  12. TScience immunology · 2025
    Article
  13. Review
  14. Review
  15. Review
  16. Article
  17. Review
  18. Article
  19. Article
  20. Article

22 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

44 authors at 11 institutions in 2 countries.

Laura T DonlinHospital for Special Surgery, New York, NY, 10021, USA.
Deepak A RaoBrigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
Kevin WeiBrigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
Kamil SlowikowskiBrigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
Mandy J McGeachyUniversity of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA.
Jason D TurnerUniversity of Birmingham, Queen Elizabeth Hospital, B15 2WB, Birmingham, UK.
Nida MeednuUniversity of Rochester Medical Center, Rochester, NY, 14642, USA.
Fumitaka MizoguchiBrigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
Maria Gutierrez-ArcelusBrigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
David J LiebBroad Institute of MIT and Harvard University, Cambridge, MA, 02142, USA.
Joshua KeeganBrigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
Kaylin MuskatUniversity of California San Diego School of Medicine, La Jolla, CA, 92093, USA.
Joshua HillmanUniversity of California San Diego School of Medicine, La Jolla, CA, 92093, USA.
Cristina RozoHospital for Special Surgery, New York, NY, 10021, USA.
Edd RickerHospital for Special Surgery, New York, NY, 10021, USA.
Thomas M EisenhaureBroad Institute of MIT and Harvard University, Cambridge, MA, 02142, USA.
Shuqiang LiBroad Institute of MIT and Harvard University, Cambridge, MA, 02142, USA.
Edward P BrowneBroad Institute of MIT and Harvard University, Cambridge, MA, 02142, USA.
Adam ChicoineBrigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
Danielle SutherbyBroad Institute of MIT and Harvard University, Cambridge, MA, 02142, USA.
Akiko NomaBroad Institute of MIT and Harvard University, Cambridge, MA, 02142, USA.
Accelerating Medicines Partnership RA/SLE Network
Chad NusbaumBroad Institute of MIT and Harvard University, Cambridge, MA, 02142, USA.
Stephen KellyMile End Hospital, Barts Health NHS Trust, E1 1BB, London, UK.
Alessandra B PernisHospital for Special Surgery, New York, NY, 10021, USA.
Lionel B IvashkivHospital for Special Surgery, New York, NY, 10021, USA.
Susan M GoodmanHospital for Special Surgery, New York, NY, 10021, USA.
William H RobinsonStanford University School of Medicine, Stanford, CA, 94305, USA.
Paul J UtzStanford University School of Medicine, Stanford, CA, 94305, USA.
James A LedererBrigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
Ellen M GravalleseUniversity of Massachusetts Medical School, Worcester, MA, 01605, USA.
Brendan F BoyceUniversity of Rochester Medical Center, Rochester, NY, 14642, USA.
Nir HacohenBroad Institute of MIT and Harvard University, Cambridge, MA, 02142, USA.
Costantino PitzalisQueen Mary University of London, E1 4NS, London, UK.
Peter K GregersenThe Feinstein Institute for Medical Research, Manhasset, NY, 11030, USA.
Gary S FiresteinUniversity of California San Diego School of Medicine, La Jolla, CA, 92093, USA.
Soumya RaychaudhuriBrigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
Larry W MorelandUniversity of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA.
V Michael HolersUniversity of Colorado of Denver School of Medicine, Aurora, CO, 80045, USA.
Vivian P BykerkHospital for Special Surgery, New York, NY, 10021, USA.
Andrew FilerUniversity of Birmingham, Queen Elizabeth Hospital, B15 2WB, Birmingham, UK.
David L BoyleUniversity of California San Diego School of Medicine, La Jolla, CA, 92093, USA.
Michael B BrennerBrigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
Jennifer H AnolikUniversity of Rochester Medical Center, Rochester, NY, 14642, USA. jennifer_anolik@urmc.rochester.edu.
Broad Institute · USBrigham and Women's Hospital · USHospital for Special Surgery · USFeinstein Institute for Medical Research · USQueen Elizabeth Hospital Birmingham · GBUniversity of Pittsburgh · USHarvard University · USStanford University · USUniversity of California San Diego · USUniversity of Massachusetts Chan Medical School · USUniversity of Rochester Medical Center · US

Funding

Tracking and Evaluation CoreU54GM104938 · NIGMS · UNIVERSITY OF OKLAHOMA HLTH SCIENCES CTR · PI PAUL G SPICER · 2013 to 2026
$68.2M
Research BaseP30DK063720 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI KRUMMEL, MATTHEW F · 2003 to 2019
$21.8M
Training Program in Bioinformatics and Integrative GenomicsT32HG002295 · NHGRI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI Peter J Park · 2001 to 2026
$15.8M
STEROID THERAPY AND CYTOKINES IN RHEUMATIC DISEASESR01AI046712 · NIAID · HOSPITAL FOR SPECIAL SURGERY · PI IVASHKIV, LIONEL B · 2000 to 2025
$12.5M
CYTOKINE REGULATION OF RA SYNOVIOCYTE PHENOTYPER01AR046713 · NIAMS · HOSPITAL FOR SPECIAL SURGERY · PI IVASHKIV, LIONEL B · 1999 to 2025
$8.3M
Tissue Acquisition Research GroupUM2AR067678 · NIAMS · STANFORD UNIVERSITY · PI HOLERS, VERNON MICHAEL, UTZ, PAUL JOSEPH · 2014 to 2020
$8.2M
Rochester Resource-Based Center for Bone, Muscle and Orthopaedic Research (ROCSTARR) (Overall Application)P30AR069655 · NIAMS · UNIVERSITY OF ROCHESTER · PI Edward M. Schwarz · 2016 to 2026
$7.8M
Cellular Dynamics at the Synovium-Bone interface in RAUH2AR067690 · NIAMS · UNIVERSITY OF ROCHESTER · PI ANOLIK, JENNIFER HOWITT · 2014 to 2020
$3.0M
Macrophage Modulation of Lung FibrosisR01HL134375 · NHLBI · NORTHWESTERN UNIVERSITY AT CHICAGO · PI PERLMAN, HARRIS R · 2017 to 2020
$2.9M
Macrophage and Fibroblast Crosstalk in the RA SynoviumK01AR066063 · NIAMS · HOSPITAL FOR SPECIAL SURGERY · PI DONLIN, LAURA T. · 2014 to 2018
$527k
Laser Capture as a Novel Tool to Dissect B Cell Roles in Rheumatoid ArthritisR21AR071670 · NIAMS · UNIVERSITY OF ROCHESTER · PI ANOLIK, JENNIFER HOWITT · 2017 to 2018
$367k
Transcriptomics in synoviocytes defines pathogenesis of rheumatoid arthritisF31AR070582 · NIAMS · HARVARD MEDICAL SCHOOL · PI SLOWIKOWSKI, KAMIL · 2016 to 2017
$63k
NHGRI NIH HHS T32 HG002295NHLBI NIH HHS R01 HL134375NIAID NIH HHS R01 AI046712NIAMS NIH HHS F31 AR070582NIAMS NIH HHS K01 AR066063NIAMS NIH HHS P30 AR069655NIAMS NIH HHS R01 AR046713NIAMS NIH HHS R21 AR071670NIAMS NIH HHS UH2 AR067690NIAMS NIH HHS UM2 AR067678NIDDK NIH HHS P30 DK063720NIGMS NIH HHS U54 GM104938
6 · The paper itself

Abstract

backgroundDetailed molecular analyses of cells from rheumatoid arthritis (RA) synovium hold promise in identifying cellular phenotypes that drive tissue pathology and joint damage. The Accelerating Medicines Partnership RA/SLE Network aims to deconstruct autoimmune pathology by examining cells within target tissues through multiple high-dimensional assays. Robust standardized protocols need to be developed before cellular phenotypes at a single cell level can be effectively compared across patient samples.

methodsMultiple clinical sites collected cryopreserved synovial tissue fragments from arthroplasty and synovial biopsy in a 10% DMSO solution. Mechanical and enzymatic dissociation parameters were optimized for viable cell extraction and surface protein preservation for cell sorting and mass cytometry, as well as for reproducibility in RNA sequencing (RNA-seq). Cryopreserved synovial samples were collectively analyzed at a central processing site by a custom-designed and validated 35-marker mass cytometry panel. In parallel, each sample was flow sorted into fibroblast, T-cell, B-cell, and macrophage suspensions for bulk population RNA-seq and plate-based single-cell CEL-Seq2 RNA-seq.

resultsUpon dissociation, cryopreserved synovial tissue fragments yielded a high frequency of viable cells, comparable to samples undergoing immediate processing. Optimization of synovial tissue dissociation across six clinical collection sites with ~ 30 arthroplasty and ~ 20 biopsy samples yielded a consensus digestion protocol using 100 μg/ml of Liberase™ TL enzyme preparation. This protocol yielded immune and stromal cell lineages with preserved surface markers and minimized variability across replicate RNA-seq transcriptomes. Mass cytometry analysis of cells from cryopreserved synovium distinguished diverse fibroblast phenotypes, distinct populations of memory B cells and antibody-secreting cells, and multiple CD4

conclusionsWe have established a robust protocol to acquire viable cells from cryopreserved synovial tissue with intact transcriptomes and cell surface phenotypes. A centralized pipeline to generate multiple high-dimensional analyses of synovial tissue samples collected across a collaborative network was developed. Integrated analysis of such datasets from large patient cohorts may help define molecular heterogeneity within RA pathology and identify new therapeutic targets and biomarkers.

Indexed as

Arthritis, RheumatoidCryopreservationFlow CytometryHigh-Throughput Screening AssaysHumansSynovial MembraneAccelerating Medicines PartnershipArthroplastyCyTOFMass cytometryRheumatoid arthritisRNA sequencingSynovial biopsySynovial tissue

Identifiers

PMID29996944
PMCPMC6042350
OpenAlexW2872432516

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.