Personalized Immunomonitoring Uncovers Molecular Networks that Stratify Lupus Patients

Romain Banchereau, Seunghee Hong, Brandi Cantarel, Nicole Baldwin, Jeanine Baisch, Michelle Edens, Alma Martina Cepika, Peter Acs, Jacob Turner, Esperanza Anguiano, Parvathi Vinod, Shaheen Kahn, Gerlinde Obermoser, Derek Blankenship, Edward Wakeland, Lorien Nassi, Alisa Gotte, Marilynn Punaro, Yong Jun Liu, Jacques BanchereauJose Rossello-Urgell, Tracey Wright, Virginia Pascual

Research output: Contribution to journalArticlepeer-review

262 Citations (Scopus)

Abstract

Summary Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by loss of tolerance to nucleic acids and highly diverse clinical manifestations. To assess its molecular heterogeneity, we longitudinally profiled the blood transcriptome of 158 pediatric patients. Using mixed models accounting for repeated measurements, demographics, treatment, disease activity (DA), and nephritis class, we confirmed a prevalent IFN signature and identified a plasmablast signature as the most robust biomarker of DA. We detected gradual enrichment of neutrophil transcripts during progression to active nephritis and distinct signatures in response to treatment in different nephritis subclasses. Importantly, personalized immunomonitoring uncovered individual correlates of disease activity that enabled patient stratification into seven groups, supported by patient genotypes. Our study uncovers the molecular heterogeneity of SLE and provides an explanation for the failure of clinical trials. This approach may improve trial design and implementation of tailored therapies in genetically and clinically complex autoimmune diseases.

Original languageEnglish
Pages (from-to)551-565
Number of pages15
JournalCell
Volume165
Issue number3
DOIs
Publication statusPublished - 2016 Apr 21

Bibliographical note

Funding Information:
This work was supported by the National Institute of Arthritis and Musculoskeletal and Skin Diseases (P50 AR054083-01), the National Institute of Allergy and Infectious Diseases (U19 AI082715), the Alliance for Lupus Research, and the Baylor-Scott & White Health Care Research Foundation and is dedicated to the memory of Dr. J. Donald Capra. We thank members of the sample, genomics, and flow cytometry cores at BIIR for research support. We thank Dr. Anna Lisa Lucido for her critical review of the manuscript and Drs. Katie Stewart, Julie Fuller, and Ashley Cooper for their clinical expertise. Jacques Banchereau is a member of the Board of Directors and the chairman of the Scientific Advisory Board of Neovacs, a French biotechnology company focused on the development of Kinoids, therapeutic vaccines for the treatment of autoimmune and inflammatory diseases (in particular SLE) and cancer. Yong-Jun Liu is an employee of Medimmune, which is involved in the development of drugs to treat SLE.

Publisher Copyright:
© 2016 Elsevier Inc.

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)

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