Unlocking immune-mediated disease mechanisms with transcriptomics

被引：23

作者：

de Jong, Emma ^{[1
]}

Bosco, Anthony ^{[1
]}

机构：

[1] Univ Western Australia, Ctr Hlth Res, Telethon Kids Inst, Nedlands, WA, Australia

来源：

BIOCHEMICAL SOCIETY TRANSACTIONS | 2021年 / 49卷 / 02期

关键词：

EXPRESSION; ASTHMA; NETWORKS; RECONSTRUCTION; COMMUNICATION; MUTATIONS; INFERENCE; THERAPY; BLOOD;

D O I：

10.1042/BST20200652

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The transcriptome represents the entire set of RNA transcripts expressed in a cell, reflecting both the underlying genetic and epigenetic landscape and environmental influences, providing a comprehensive view of functional cellular states at any given time. Recent technological advances now enable the study of the transcriptome at the resolution of individual cells, providing exciting opportunities to characterise cellular and molecular events that underpin immune-medicated diseases. Here, we draw on recent examples from the literature to highlight the application of advanced bioinformatics tools to extract mechanistic insight and disease biology from bulk and single-cell transcriptomic profiles. Key considerations for the use of available analysis techniques are presented throughout.

引用

页码：705 / 714

页数：10

共 59 条

[1] Functional characterization of somatic mutations in cancer using network-based inference of protein activity [J].

Alvarez, Mariano J. ;

Shen, Yao ;

Giorgi, Federico M. ;

Lachmann, Alexander ;

Ding, B. Belinda ;

Ye, B. Hilda ;

Califano, Andrea .

NATURE GENETICS, 2016, 48 (08) :838-+

[2] xCell: digitally portraying the tissue cellular heterogeneity landscape [J].

Aran, Dvir ;

Hu, Zicheng ;

Butte, Atul J. .

GENOME BIOLOGY, 2017, 18

[3] Deciphering cell-cell interactions and communication from gene expression [J].

Armingol, Erick ;

Officer, Adam ;

Harismendy, Olivier ;

Lewis, Nathan E. .

NATURE REVIEWS GENETICS, 2021, 22 (02) :71-88

[4] Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1 [J].

Barbie, David A. ;

Tamayo, Pablo ;

Boehm, Jesse S. ;

Kim, So Young ;

Moody, Susan E. ;

Dunn, Ian F. ;

Schinzel, Anna C. ;

Sandy, Peter ;

Meylan, Etienne ;

Scholl, Claudia ;

Froehling, Stefan ;

Chan, Edmond M. ;

Sos, Martin L. ;

Michel, Kathrin ;

Mermel, Craig ;

Silver, Serena J. ;

Weir, Barbara A. ;

Reiling, Jan H. ;

Sheng, Qing ;

Gupta, Piyush B. ;

Wadlow, Raymond C. ;

Le, Hanh ;

Hoersch, Sebastian ;

Wittner, Ben S. ;

Ramaswamy, Sridhar ;

Livingston, David M. ;

Sabatini, David M. ;

Meyerson, Matthew ;

Thomas, Roman K. ;

Lander, Eric S. ;

Mesirov, Jill P. ;

Root, David E. ;

Gilliland, D. Gary ;

Jacks, Tyler ;

Hahn, William C. .

NATURE, 2009, 462 (7269) :108-U122

[5] A Severe Asthma Disease Signature from Gene Expression Profiling of Peripheral Blood from U-BIOPRED Cohorts [J].

Bigler, Jeannette ;

Boedigheimer, Michael ;

Schofield, James P. R. ;

Skipp, Paul J. ;

Corfield, Julie ;

Rowe, Anthony ;

Sousa, Ana R. ;

Timour, Martin ;

Twehues, Lori ;

Hu, Xuguang ;

Roberts, Graham ;

Welcher, Andrew A. ;

Yu, Wen ;

Lefaudeux, Diane ;

De Meulder, Bertrand ;

Auffray, Charles ;

Chung, Kian F. ;

Adcock, Ian M. ;

Sterk, Peter J. ;

Djukanovic, Ratko .

AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, 2017, 195 (10) :1311-1320

[6] A cellular census of human lungs identifies novel cell states in health and in asthma [J].

Braga, Felipe A. Vieira ;

Kar, Gozde ;

Berg, Marijn ;

Carpaij, Orestes A. ;

Polanski, Krzysztof ;

Simon, Lukas M. ;

Brouwer, Sharon ;

Gomes, Tomas ;

Hesse, Laura ;

Jiang, Jian ;

Fasouli, Eirini S. ;

Efremova, Mirjana ;

Vento-Tormo, Roser ;

Talavera-Lopez, Carlos ;

Jonker, Marnix R. ;

Affleck, Karen ;

Palit, Subarna ;

Strzelecka, Paulina M. ;

Firth, Helen V. ;

Mahbubani, Krishnaa T. ;

Cvejic, Ana ;

Meyer, Kerstin B. ;

Saeb-Parsy, Kourosh ;

Luinge, Marjan ;

Brandsma, Corry-Anke ;

Timens, Wim ;

Angelidis, Ilias ;

Strunz, Maximilian ;

Koppelman, Gerard H. ;

van Oosterhout, Antoon J. ;

Schiller, Herbert B. ;

Theis, Fabian J. ;

van den Berge, Maarten ;

Nawijn, Martijn C. ;

Teichmann, Sarah A. .

NATURE MEDICINE, 2019, 25 (07) :1153-+

[7] NicheNet: modeling intercellular communication by linking ligands to target genes [J].

Browaeys, Robin ;

Saelens, Wouter ;

Saeys, Yvan .

NATURE METHODS, 2020, 17 (02) :159-+

[8] From 'differential expression' to 'differential networking' - identification of dysfunctional regulatory networks in diseases [J].

de la Fuente, Alberto .

TRENDS IN GENETICS, 2010, 26 (07) :326-333

[9] Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows [J].

Denisenko, Elena ;

Guo, Belinda B. ;

Jones, Matthew ;

Hou, Rui ;

de Kock, Leanne ;

Lassmann, Timo ;

Poppe, Daniel ;

Clement, Olivier ;

Simmons, Rebecca K. ;

Lister, Ryan ;

Forrest, Alistair R. R. .

GENOME BIOLOGY, 2020, 21 (01)

[10] Tubular cell and keratinocyte single-cell transcriptomics applied to lupus nephritis reveal type I IFN and fibrosis relevant pathways [J].

Der, Evan ;

Suryawanshi, Hemant ;

Morozov, Pavel ;

Kustagi, Manjunath ;

Goilav, Beatrice ;

Ranabathou, Saritha ;

Izmirly, Peter ;

Clancy, Robert ;

Belmont, H. Michael ;

Koenigsberg, Mordecai ;

Mokrzycki, Michele ;

Rominieki, Helen ;

Graham, Jay A. ;

Rocca, Juan P. ;

Bornkamp, Nicole ;

Jordan, Nicole ;

Schulte, Emma ;

Wu, Ming ;

Pullman, James ;

Slowikowski, Kamil ;

Raychaudhuri, Soumya ;

Guthridge, Joel ;

James, Judith ;

Buyon, Jill ;

Tuschl, Thomas ;

Putterman, Chaim ;

Anolik, Jennifer ;

Apruzzese, William ;

Arazi, Arnon ;

Berthier, Celine ;

Brenner, Michael ;

Connery, Sean ;

Cunningham, Melissa ;

Dall'Era, Maria ;

Davidson, Anne ;

Fava, Andrea ;

Fonseka, Chamith ;

Furie, Richard ;

Goldman, Dan ;

Gupta, Rohit ;

Guthridge, Joel ;

Hacohen, Nir ;

Hildeman, David ;

Hoover, Paul ;

Hsu, Raymond ;

Kado, Ruba ;

Kalunian, Kenneth ;

Kamen, Diane ;

Kretzler, Mattias ;

Maecker, Holden .

NATURE IMMUNOLOGY, 2019, 20 (07) :915-+

← 1 2 3 4 5 6 →