Uncovering complex molecular networks in host-pathogen interactions using systems biology

被引：2

作者：

Peters, Joshua M. ^{[1
,2
]}

Solomon, Sydney L. ^{[1
,2
]}

Itoh, Christopher Y. ^{[1
,2
]}

Bryson, Bryan D. ^{[1
,2
]}

机构：

[1] MIT, Dept Biol Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA

[2] MGH MIT & Harvard, Ragon Inst, Cambridge, MA 02139 USA

来源：

EMERGING TOPICS IN LIFE SCIENCES | 2019年 / 3卷 / 04期

关键词：

MYCOBACTERIUM-TUBERCULOSIS; RESPONSES; CELLS; MECHANISMS; SCREEN;

D O I：

10.1042/ETLS20180174

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：

Interactions between pathogens and their hosts can induce complex changes in both host and pathogen states to privilege pathogen survival or host clearance of the pathogen. To determine the consequences of specific host-pathogen interactions, a variety of techniques in microbiology, cell biology, and immunology are available to researchers. Systems biology that enables unbiased measurements of transcriptomes, proteomes, and other biomolecules has become increasingly common in the study of host-pathogen interactions. These approaches can be used to generate novel hypotheses or to characterize the effects of particular perturbations across an entire biomolecular network. With proper experimental design and complementary data analysis tools, high-throughput omics techniques can provide novel insights into the mechanisms that underlie processes from phagocytosis to pathogen immune evasion. Here, we provide an overview of the suite of biochemical approaches for high-throughput analyses of host-pathogen interactions, analytical frameworks for understanding the resulting datasets, and a vision for the future of this exciting field.

引用

页码：371 / 378

页数：8

共 47 条

[31] Mycobacterium tuberculosis and the environment within the phagosome [J].

Rohde, Kyle ;

Yates, Robin M. ;

Purdy, Georgiana E. ;

Russell, David G. .

IMMUNOLOGICAL REVIEWS, 2007, 219 :37-54

[32] Proteome analysis of host-pathogen interactions: Investigation of pathogen responses to the host cell environment [J].

Schmidt, Frank ;

Voelker, Uwe .

PROTEOMICS, 2011, 11 (15) :3203-3211

[33] Dynamic Changes in Chromatin Accessibility Occur in CD8+ T Cells Responding to Viral Infection [J].

Scott-Browne, James P. ;

Lopez-Moyado, Isaac F. ;

Trifari, Sara ;

Wong, Victor ;

Chavez, Lukas ;

Rao, Anjana ;

Pereira, Renata M. .

IMMUNITY, 2016, 45 (06) :1327-1340

[34] Innate immune reconstitution with suppression of HIV-1 [J].

Scully, Eileen P. ;

Lockhart, Ainsley ;

Garcia-Beltran, Wilfredo ;

Palmer, Christine D. ;

Musante, Chelsey ;

Rosenberg, Eric ;

Allen, Todd M. ;

Chang, J. Judy ;

Bosch, Ronald J. ;

Altfeld, Marcus .

JCI INSIGHT, 2016, 1 (03)

[35] Single cell mass cytometry reveals remodeling of human T cell phenotypes by varicella zoster virus [J].

Sen, Nandini ;

Mukherjee, Gourab ;

Arvin, Ann M. .

METHODS, 2015, 90 :85-94

[36] Comparative Flavivirus-Host Protein Interaction Mapping Reveals Mechanisms of Dengue and Zika Virus Pathogenesis [J].

Shah, Priya S. ;

Link, Nichole ;

Jang, Gwendolyn M. ;

Sharp, Phillip P. ;

Zhu, Tongtong ;

Swaney, Danielle L. ;

Johnson, Jeffrey R. ;

Von Dollen, John ;

Ramage, Holly R. ;

Satkamp, Laura ;

Newton, Billy ;

Huttenhain, Ruth ;

Petit, Marine J. ;

Baum, Tierney ;

Everitt, Amanda ;

Laufman, Orly ;

Tassetto, Michel ;

Shales, Michael ;

Stevenson, Erica ;

Iglesias, Gabriel N. ;

Shokat, Leila ;

Tripathi, Shashank ;

Balasubramaniam, Vinod ;

Webb, Laurence G. ;

Aguirre, Sebastian ;

Willsey, A. Jeremy ;

Garcia-Sastre, Adolfo ;

Pollard, Katherine S. ;

Cherry, Sara ;

Gamarnik, Andrea V. ;

Marazzi, Ivan ;

Taunton, Jack ;

Fernandez-Sesma, Ana ;

Bellen, Hugo J. ;

Andino, Raul ;

Krogan, Nevan J. .

CELL, 2018, 175 (07) :1931-+

[37] A Physical and Regulatory Map of Host-Influenza Interactions Reveals Pathways in H1N1 Infection [J].

Shapira, Sagi D. ;

Gat-Viks, Irit ;

Shum, Bennett O. V. ;

Dricot, Amelie ;

de Grace, Marciela M. ;

Wu, Liguo ;

Gupta, Piyush B. ;

Hao, Tong ;

Silver, Serena J. ;

Root, David E. ;

Hill, David E. ;

Regev, Aviv ;

Hacohen, Nir .

CELL, 2009, 139 (07) :1255-1267

[38] CRISPR-based genomic tools for the manipulation of genetically intractable microorganisms [J].

Shapiro, Rebecca S. ;

Chavez, Alejandro ;

Collins, James J. .

NATURE REVIEWS MICROBIOLOGY, 2018, 16 (06) :333-339

[39] A Genome-wide CRISPR Screen in Toxoplasma Identifies Essential Apicomplexan Genes [J].

Sidik, Saima M. ;

Huet, Diego ;

Ganesan, Suresh M. ;

Huynh, My-Hang ;

Wang, Tim ;

Nasamu, Armiyaw S. ;

Thiru, Prathapan ;

Saeij, Jeroen P. J. ;

Carruthers, Vern B. ;

Niles, Jacquin C. ;

Lourido, Sebastian .

CELL, 2016, 166 (06) :1423-+

[40] Tracking a Hospital Outbreak of Carbapenem-Resistant Klebsiella pneumoniae with Whole-Genome Sequencing [J].

Snitkin, Evan S. ;

Zelazny, Adrian M. ;

Thomas, Pamela J. ;

Stock, Frida ;

Henderson, David K. ;

Palmore, Tara N. ;

Segre, Julia A. .

SCIENCE TRANSLATIONAL MEDICINE, 2012, 4 (148)

← 1 2 3 4 5 →