Understanding Human Autoimmunity and Autoinflammation Through Transcriptomics

被引：64

作者：

Banchereau, Romain ^{[1
]}

Cepika, Alma-Martina ^{[1
]}

Banchereau, Jacques ^{[2
]}

Pascual, Virginia ^{[1
]}

机构：

[1] Baylor Inst Immunol Res, Dallas, TX 75204 USA

[2] Jackson Lab Genom Med, Farmington, CT 06030 USA

来源：

ANNUAL REVIEW OF IMMUNOLOGY, VOL 35 | 2017年 / 35卷

关键词：

autoimmunity; autoinflammation; transcriptomics; mechanisms; patient stratification; therapeutic targets; SYSTEMIC-LUPUS-ERYTHEMATOSUS; JUVENILE IDIOPATHIC ARTHRITIS; PERIPHERAL-BLOOD CELLS; ALPHA MONOCLONAL-ANTIBODY; GENE-EXPRESSION PATTERNS; PLACEBO-CONTROLLED TRIAL; I INTERFERON SIGNATURE; REGULATORY FACTOR 5; ZETA MESSENGER-RNA; RHEUMATOID-ARTHRITIS;

D O I：

10.1146/annurev-immunol-051116-052225

中图分类号：

R392 [医学免疫学]; Q939.91 [免疫学];

学科分类号：

100102 ;

摘要：

Transcriptomics, the high-throughput characterization of RNAs, has been instrumental in defining pathogenic signatures in human autoimmunity and autoinflammation. It enabled the identification of new therapeutic targets in IFN-, IL-1- and IL-17-mediated diseases. Applied to immunomonitoring, transcriptomics is starting to unravel diagnostic and prognostic signatures that stratify patients, track molecular changes associated with disease activity, define personalized treatment strategies, and generally inform clinical practice. Herein, we review the use of transcriptomics to define mechanistic, diagnostic, and predictive signatures in human autoimmunity and autoinflammation. We discuss some of the analytical approaches applied to extract biological knowledge from high-dimensional data sets. Finally, we touch upon emerging applications of transcriptomics to study eQTLs, B and T cell repertoire diversity, and isoform usage.

引用

页码：337 / 370

页数：34

共 241 条

[31]

Buenrostro JD, 2013, NAT METHODS, V10, P1213, DOI [10.1038/NMETH.2688, 10.1038/nmeth.2688]

[32] Molecular classification of Crohn's disease and ulcerative colitis patients using transcriptional profiles in peripheral blood mononuclear cells [J].

Burczynski, ME ;

Peterson, RL ;

Twine, NC ;

Zuberek, KA ;

Brodeur, BJ ;

Casciotti, L ;

Maganti, V ;

Reddy, PS ;

Strahs, A ;

Immermann, F ;

Spinelli, W ;

Schwertschlag, U ;

Slager, AM ;

Cotreau, MM ;

Dorner, AJ .

JOURNAL OF MOLECULAR DIAGNOSTICS, 2006, 8 (01) :51-61

[33] Gene expression analysis in RA: towards personalized medicine [J].

Burska, A. N. ;

Roget, K. ;

Blits, M. ;

Gomez, L. Soto ;

van de Loo, F. ;

Hazelwood, L. D. ;

Verweij, C. L. ;

Rowe, A. ;

Goulielmos, G. N. ;

van Baarsen, L. G. M. ;

Ponchel, F. .

PHARMACOGENOMICS JOURNAL, 2014, 14 (02) :93-106

[34] Oxidized mitochondrial nucleoids released by neutrophils drive type I interferon production in human lupus [J].

Caielli, Simone ;

Athale, Shruti ;

Domic, Bojana ;

Murat, Elise ;

Chandra, Manjari ;

Banchereau, Romain ;

Baisch, Jeanine ;

Phelps, Kate ;

Clayton, Sandra ;

Gong, Mei ;

Wright, Tracey ;

Punaro, Marilynn ;

Palucka, Karolina ;

Guiducci, Cristiana ;

Banchereau, Jacques ;

Pascual, Virginia .

JOURNAL OF EXPERIMENTAL MEDICINE, 2016, 213 (05) :697-713

[35] Characterizing immune repertoires by high throughput sequencing: strategies and applications [J].

Calis, Jorg J. A. ;

Rosenberg, Brad R. .

TRENDS IN IMMUNOLOGY, 2014, 35 (12) :581-590

[36] A network-based analysis of systemic inflammation in humans [J].

Calvano, SE ;

Xiao, WZ ;

Richards, DR ;

Felciano, RM ;

Baker, HV ;

Cho, RJ ;

Chen, RO ;

Brownstein, BH ;

Cobb, JP ;

Tschoeke, SK ;

Miller-Graziano, C ;

Moldawer, LL ;

Mindrinos, MN ;

Davis, RW ;

Tompkins, RG ;

Lowry, SF .

NATURE, 2005, 437 (7061) :1032-1037

[37] An activating NLRC4 inflammasome mutation causes autoinflammation with recurrent macrophage activation syndrome [J].

Canna, Scott W. ;

de Jesus, Adriana A. ;

Gounil, Sushanth ;

Brooks, Stephen R. ;

Marrero, Bernadette ;

Liu, Yin ;

DiMattia, Michael A. ;

Zaal, Kristien J. M. ;

Sanchez, Gina A. Montealegre ;

Kim, Hanna ;

Chapelle, Dawn ;

Plass, Nicole ;

Huang, Yan ;

Villarinol, Alejandro V. ;

Biancotto, Angelique ;

Fleisher, Thomas A. ;

Duncan, Joseph A. ;

O'Shea, John J. ;

Benseler, Susanne ;

Grom, Alexei ;

Deng, Zuoming ;

Laxer, Ronald M. ;

Goldbach-Mansky, Raphaela .

NATURE GENETICS, 2014, 46 (10) :1140-1146

[38] Treating rheumatological diseases and co-morbidities with interleukin-1 blocking therapies [J].

Cavalli, Giulio ;

Dinarello, Charles A. .

RHEUMATOLOGY, 2015, 54 (12) :2134-2144

[39] The Noncoding RNA Revolution-Trashing Old Rules to Forge New Ones [J].

Cech, Thomas R. ;

Steitz, Joan A. .

CELL, 2014, 157 (01) :77-94

[40] A modular analysis framework for blood genomics studies: Application to systemic lupus erythematosus [J].

Chaussabel, Damien ;

Quinn, Charles ;

Shen, Jing ;

Patel, Pinakeen ;

Glaser, Casey ;

Baldwin, Nicole ;

Stichweh, Dorothee ;

Blankenship, Derek ;

Li, Lei ;

Munagala, Indira ;

Bennett, Lynda ;

Allantaz, Florence ;

Mejias, Asuncion ;

Ardura, Monica ;

Kaizer, Ellen ;

Monnet, Laurence ;

Allman, Windy ;

Randall, Henry ;

Johnson, Diane ;

Lanier, Aimee ;

Punaro, Marilynn ;

Wittkowski, Knut M. ;

White, Perrin ;

Fay, Joseph ;

Klintmalm, Goran ;

Ramilo, Octavio ;

Palucka, A. Karolina ;

Banchereau, Jacques ;

Pascual, Virginia .

IMMUNITY, 2008, 29 (01) :150-164

← 1 2 3 4 5 6 7 8 9 10 →