Survey of extracellular communication of systemic and organ-specific inflammatory responses through cell free messenger RNA profiling in mice
Summary: Background: Inflammatory and immune responses are essential and dynamic biological processes that protect the body against acute and chronic adverse stimuli. While conventional protein markers have been used to evaluate systemic inflammatory response, the immunological response to stimulat...
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| Format: | Article |
| Language: | English |
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Elsevier
2022-09-01
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| Series: | EBioMedicine |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2352396422004248 |
| _version_ | 1818472324231331840 |
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| author | Jiali Zhuang Arkaitz Ibarra Alexander Acosta Amy P. Karns Jonathan Aballi Michael Nerenberg John J. Sninsky Stephen R. Quake Shusuke Toden |
| author_facet | Jiali Zhuang Arkaitz Ibarra Alexander Acosta Amy P. Karns Jonathan Aballi Michael Nerenberg John J. Sninsky Stephen R. Quake Shusuke Toden |
| author_sort | Jiali Zhuang |
| collection | DOAJ |
| description | Summary: Background: Inflammatory and immune responses are essential and dynamic biological processes that protect the body against acute and chronic adverse stimuli. While conventional protein markers have been used to evaluate systemic inflammatory response, the immunological response to stimulation is complex and involves modulation of a large set of genes and interacting signalling pathways of innate and adaptive immune systems. There is a need for a non-invasive tool that can comprehensively evaluate and monitor molecular dysregulations associated with inflammatory and immune responses in circulation and in inaccessible solid organs. Methods: Here we utilized cell-free messenger RNA (cf-mRNA) RNA-Seq whole transcriptome profiling and computational biology to temporally assess lipopolysaccharide (LPS) induced and JAK inhibitor modulated inflammatory and immune responses in mouse plasma samples. Findings: Cf-mRNA profiling displayed a pattern of systemic immune responses elicited by LPS and dysregulation of associated pathways. Moreover, attenuation of several inflammatory pathways, including STAT and interferon pathways, were observed following the treatment of JAK inhibitor. We further identified the dysregulation of liver-specific transcripts in cf-mRNA which reflected changes in the gene-expression pattern in this generally inaccessible biological compartment. Interpretation: Using a preclinical mouse model, we demonstrated the potential of plasma cf-mRNA profiling for systemic and organ-specific characterization of drug-induced molecular alterations that are associated with inflammatory and immune responses. Funding: Molecular Stethoscope. |
| first_indexed | 2024-04-14T04:05:34Z |
| format | Article |
| id | doaj.art-118efc30942c4675a48ce58d03e97097 |
| institution | Directory Open Access Journal |
| issn | 2352-3964 |
| language | English |
| last_indexed | 2024-04-14T04:05:34Z |
| publishDate | 2022-09-01 |
| publisher | Elsevier |
| record_format | Article |
| series | EBioMedicine |
| spelling | doaj.art-118efc30942c4675a48ce58d03e970972022-12-22T02:13:21ZengElsevierEBioMedicine2352-39642022-09-0183104242Survey of extracellular communication of systemic and organ-specific inflammatory responses through cell free messenger RNA profiling in miceJiali Zhuang0Arkaitz Ibarra1Alexander Acosta2Amy P. Karns3Jonathan Aballi4Michael Nerenberg5John J. Sninsky6Stephen R. Quake7Shusuke Toden8Molecular Stethoscope Inc., 259 E Grand Avenue, South San Francisco, CA 94080, United StatesMolecular Stethoscope Inc., 259 E Grand Avenue, South San Francisco, CA 94080, United StatesMolecular Stethoscope Inc., 259 E Grand Avenue, South San Francisco, CA 94080, United StatesMolecular Stethoscope Inc., 259 E Grand Avenue, South San Francisco, CA 94080, United StatesMolecular Stethoscope Inc., 259 E Grand Avenue, South San Francisco, CA 94080, United StatesMolecular Stethoscope Inc., 259 E Grand Avenue, South San Francisco, CA 94080, United StatesMolecular Stethoscope Inc., 259 E Grand Avenue, South San Francisco, CA 94080, United StatesDepartment of Bioengineering and Department of Applied Physics, Stanford University and Chan Zuckerberg Biohub, Stanford, CA 94305, United StatesMolecular Stethoscope Inc., 259 E Grand Avenue, South San Francisco, CA 94080, United States; Corresponding author at: Molecular Stethoscope, 259 E Grand Avenue, South San Francisco, CA 94080, United States.Summary: Background: Inflammatory and immune responses are essential and dynamic biological processes that protect the body against acute and chronic adverse stimuli. While conventional protein markers have been used to evaluate systemic inflammatory response, the immunological response to stimulation is complex and involves modulation of a large set of genes and interacting signalling pathways of innate and adaptive immune systems. There is a need for a non-invasive tool that can comprehensively evaluate and monitor molecular dysregulations associated with inflammatory and immune responses in circulation and in inaccessible solid organs. Methods: Here we utilized cell-free messenger RNA (cf-mRNA) RNA-Seq whole transcriptome profiling and computational biology to temporally assess lipopolysaccharide (LPS) induced and JAK inhibitor modulated inflammatory and immune responses in mouse plasma samples. Findings: Cf-mRNA profiling displayed a pattern of systemic immune responses elicited by LPS and dysregulation of associated pathways. Moreover, attenuation of several inflammatory pathways, including STAT and interferon pathways, were observed following the treatment of JAK inhibitor. We further identified the dysregulation of liver-specific transcripts in cf-mRNA which reflected changes in the gene-expression pattern in this generally inaccessible biological compartment. Interpretation: Using a preclinical mouse model, we demonstrated the potential of plasma cf-mRNA profiling for systemic and organ-specific characterization of drug-induced molecular alterations that are associated with inflammatory and immune responses. Funding: Molecular Stethoscope.http://www.sciencedirect.com/science/article/pii/S2352396422004248Cell free messenger RNAInflammationSystemic inflammatory responseLiquid biopsy |
| spellingShingle | Jiali Zhuang Arkaitz Ibarra Alexander Acosta Amy P. Karns Jonathan Aballi Michael Nerenberg John J. Sninsky Stephen R. Quake Shusuke Toden Survey of extracellular communication of systemic and organ-specific inflammatory responses through cell free messenger RNA profiling in mice EBioMedicine Cell free messenger RNA Inflammation Systemic inflammatory response Liquid biopsy |
| title | Survey of extracellular communication of systemic and organ-specific inflammatory responses through cell free messenger RNA profiling in mice |
| title_full | Survey of extracellular communication of systemic and organ-specific inflammatory responses through cell free messenger RNA profiling in mice |
| title_fullStr | Survey of extracellular communication of systemic and organ-specific inflammatory responses through cell free messenger RNA profiling in mice |
| title_full_unstemmed | Survey of extracellular communication of systemic and organ-specific inflammatory responses through cell free messenger RNA profiling in mice |
| title_short | Survey of extracellular communication of systemic and organ-specific inflammatory responses through cell free messenger RNA profiling in mice |
| title_sort | survey of extracellular communication of systemic and organ specific inflammatory responses through cell free messenger rna profiling in mice |
| topic | Cell free messenger RNA Inflammation Systemic inflammatory response Liquid biopsy |
| url | http://www.sciencedirect.com/science/article/pii/S2352396422004248 |
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