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Article: Materials design at the interface of nanoparticles and innate immunity.

Szeto, Gregory Lee / Lavik, Erin B

Journal of materials chemistry. B, Materials for biology and medicine

2016 Volume 4, Issue 9, Page(s) 1610–1618

Language	English
Publishing date	2016-03-07
Publishing country	England
Document type	Journal Article
ZDB-ID	2702241-9
ISSN	2050-7518 ; 2050-750X
ISSN (online)	2050-7518
ISSN	2050-750X
DOI	10.1039/C5TB01825K
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Persistent serum protein signatures define an inflammatory subcategory of long COVID.

Nature communications

2023 Volume 14, Issue 1, Page(s) 3417

Abstract: Long COVID or post-acute sequelae of SARS-CoV-2 (PASC) is a clinical syndrome featuring diverse symptoms that can persist for months following acute SARS-CoV-2 infection. The aetiologies may include persistent inflammation, unresolved tissue damage or ... ...

Abstract	Long COVID or post-acute sequelae of SARS-CoV-2 (PASC) is a clinical syndrome featuring diverse symptoms that can persist for months following acute SARS-CoV-2 infection. The aetiologies may include persistent inflammation, unresolved tissue damage or delayed clearance of viral protein or RNA, but the biological differences they represent are not fully understood. Here we evaluate the serum proteome in samples, longitudinally collected from 55 PASC individuals with symptoms lasting ≥60 days after onset of acute infection, in comparison to samples from symptomatically recovered SARS-CoV-2 infected and uninfected individuals. Our analysis indicates heterogeneity in PASC and identified subsets with distinct signatures of persistent inflammation. Type II interferon signaling and canonical NF-κB signaling (particularly associated with TNF), appear to be the most differentially enriched signaling pathways, distinguishing a group of patients characterized also by a persistent neutrophil activation signature. These findings help to clarify biological diversity within PASC, identify participants with molecular evidence of persistent inflammation, and highlight dominant pathways that may have diagnostic or therapeutic relevance, including a protein panel that we propose as having diagnostic utility for differentiating inflammatory and non-inflammatory PASC.
MeSH term(s)	Humans ; Post-Acute COVID-19 Syndrome ; COVID-19 ; SARS-CoV-2 ; Blood Proteins ; Disease Progression ; Inflammation
Chemical Substances	Blood Proteins
Language	English
Publishing date	2023-06-09
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-38682-4
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Correction for Rando et al., "Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure".

Rando, Halie M / MacLean, Adam L / Lee, Alexandra J / Lordan, Ronan / Ray, Sandipan / Bansal, Vikas / Skelly, Ashwin N / Sell, Elizabeth / Dziak, John J / Shinholster, Lamonica / D'Agostino McGowan, Lucy / Ben Guebila, Marouen / Wellhausen, Nils / Knyazev, Sergey / Boca, Simina M / Capone, Stephen / Qi, Yanjun / Park, YoSon / Mai, David /

Sun, Yuchen / Boerckel, Joel D / Brueffer, Christian / Byrd, James Brian / Kamil, Jeremy P / Wang, Jinhui / Velazquez, Ryan / Szeto, Gregory L / Barton, John P / Goel, Rishi Raj / Mangul, Serghei / Lubiana, Tiago / Gitter, Anthony / Greene, Casey S

mSystems

2022 Volume 7, Issue 1, Page(s) e0144721

Language	English
Publishing date	2022-01-25
Publishing country	United States
Document type	Journal Article ; Published Erratum
ISSN	2379-5077
ISSN	2379-5077
DOI	10.1128/msystems.01447-21
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Article ; Online: Persistent serum protein signatures define an inflammatory subcategory of long COVID

Nature Communications, Vol 14, Iss 1, Pp 1-

2023 Volume 16

Abstract: Abstract Long COVID or post-acute sequelae of SARS-CoV-2 (PASC) is a clinical syndrome featuring diverse symptoms that can persist for months following acute SARS-CoV-2 infection. The aetiologies may include persistent inflammation, unresolved tissue ... ...

Abstract	Abstract Long COVID or post-acute sequelae of SARS-CoV-2 (PASC) is a clinical syndrome featuring diverse symptoms that can persist for months following acute SARS-CoV-2 infection. The aetiologies may include persistent inflammation, unresolved tissue damage or delayed clearance of viral protein or RNA, but the biological differences they represent are not fully understood. Here we evaluate the serum proteome in samples, longitudinally collected from 55 PASC individuals with symptoms lasting ≥60 days after onset of acute infection, in comparison to samples from symptomatically recovered SARS-CoV-2 infected and uninfected individuals. Our analysis indicates heterogeneity in PASC and identified subsets with distinct signatures of persistent inflammation. Type II interferon signaling and canonical NF-κB signaling (particularly associated with TNF), appear to be the most differentially enriched signaling pathways, distinguishing a group of patients characterized also by a persistent neutrophil activation signature. These findings help to clarify biological diversity within PASC, identify participants with molecular evidence of persistent inflammation, and highlight dominant pathways that may have diagnostic or therapeutic relevance, including a protein panel that we propose as having diagnostic utility for differentiating inflammatory and non-inflammatory PASC.
Keywords	Science ; Q
Subject code	610
Language	English
Publishing date	2023-06-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Modeling collective cell behavior in cancer: Perspectives from an interdisciplinary conversation.

Adler, Frederick R / Anderson, Alexander R A / Bhushan, Abhinav / Bogdan, Paul / Bravo-Cordero, Jose Javier / Brock, Amy / Chen, Yun / Cukierman, Edna / DelGiorno, Kathleen E / Denis, Gerald V / Ferrall-Fairbanks, Meghan C / Gartner, Zev Jordan / Germain, Ronald N / Gordon, Deborah M / Hunter, Ginger / Jolly, Mohit Kumar / Karacosta, Loukia Georgiou / Mythreye, Karthikeyan / Katira, Parag /

Cell systems

2023 Volume 14, Issue 4, Page(s) 252–257

Abstract: Collective cell behavior contributes to all stages of cancer progression. Understanding how collective behavior emerges through cell-cell interactions and decision-making will advance our understanding of cancer biology and provide new therapeutic ... ...

Abstract	Collective cell behavior contributes to all stages of cancer progression. Understanding how collective behavior emerges through cell-cell interactions and decision-making will advance our understanding of cancer biology and provide new therapeutic approaches. Here, we summarize an interdisciplinary discussion on multicellular behavior in cancer, draw lessons from other scientific disciplines, and identify future directions.
MeSH term(s)	Humans ; Mass Behavior ; Neoplasms ; Communication
Language	English
Publishing date	2023-04-20
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2854138-8
ISSN	2405-4720 ; 2405-4712
ISSN (online)	2405-4720
ISSN	2405-4712
DOI	10.1016/j.cels.2023.03.002
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Article: Longitudinal immune dynamics of mild COVID-19 define signatures of recovery and persistence.

Talla, Aarthi / Vasaikar, Suhas V / Lemos, Maria P / Moodie, Zoe / Lee Pebworth, Mark-Phillip / Henderson, Kathy E / Cohen, Kristen W / Czartoski, Julie L / Lai, Lilin / Suthar, Mehul S / Heubeck, Alexander T / Genge, Palak C / Roll, Charles R / Weiss, Morgan / Reading, Julian / Kondza, Nina / MacMillan, Hugh / Fong, Olivia C / Thomson, Zachary James /

Graybuck, Lucas T / Okada, Lauren Y / Newell, Evan W / Coffey, Ernest M / Meijer, Paul / Becker, Lynne A / De Rosa, Stephen C / Skene, Peter J / Torgerson, Troy R / Li, Xiao-Jun / Szeto, Gregory Lee / McElrath, M Juliana / Bumol, Thomas F

bioRxiv : the preprint server for biology

2021

Abstract: SARS-CoV-2 has infected over 200 million and caused more than 4 million deaths to date. Most individuals (>80%) have mild symptoms and recover in the outpatient setting, but detailed studies of immune responses have focused primarily on moderate to ... ...

Abstract	SARS-CoV-2 has infected over 200 million and caused more than 4 million deaths to date. Most individuals (>80%) have mild symptoms and recover in the outpatient setting, but detailed studies of immune responses have focused primarily on moderate to severe COVID-19. We deeply profiled the longitudinal immune response in individuals with mild COVID-19 beginning with early time points post-infection (1-15 days) and proceeding through convalescence to >100 days after symptom onset. We correlated data from single cell analyses of peripheral blood cells, serum proteomics, virus-specific cellular and humoral immune responses, and clinical metadata. Acute infection was characterized by vigorous coordinated innate and adaptive immune activation that differed in character by age (young vs. old). We then characterized signals associated with recovery and convalescence to define and validate a new signature of inflammatory cytokines, gene expression, and chromatin accessibility that persists in individuals with post-acute sequelae of SARS-CoV-2 infection (PASC).
Language	English
Publishing date	2021-08-19
Publishing country	United States
Document type	Preprint
DOI	10.1101/2021.05.26.442666
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Article ; Online: Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure.

Rando, Halie M / MacLean, Adam L / Lee, Alexandra J / Lordan, Ronan / Ray, Sandipan / Bansal, Vikas / Skelly, Ashwin N / Sell, Elizabeth / Dziak, John J / Shinholster, Lamonica / McGowan, Lucy D'Agostino / Guebila, Marouen Ben / Wellhausen, Nils / Knyazev, Sergey / Boca, Simina M / Capone, Stephen / Qi, Yanjun / Park, YoSon / Sun, Yuchen /

Mai, David / Boerckel, Joel D / Brueffer, Christian / Byrd, James Brian / Kamil, Jeremy P / Wang, Jinhui / Velazquez, Ryan / Szeto, Gregory L / Barton, John P / Goel, Rishi Raj / Mangul, Serghei / Lubiana, Tiago / Gitter, Anthony / Greene, Casey S

ArXiv

2021

Abstract: The novel coronavirus SARS-CoV-2, which emerged in late 2019, has since spread around the world and infected hundreds of millions of people with coronavirus disease 2019 (COVID-19). While this viral species was unknown prior to January 2020, its ... ...

Abstract	The novel coronavirus SARS-CoV-2, which emerged in late 2019, has since spread around the world and infected hundreds of millions of people with coronavirus disease 2019 (COVID-19). While this viral species was unknown prior to January 2020, its similarity to other coronaviruses that infect humans has allowed for rapid insight into the mechanisms that it uses to infect human hosts, as well as the ways in which the human immune system can respond. Here, we contextualize SARS-CoV-2 among other coronaviruses and identify what is known and what can be inferred about its behavior once inside a human host. Because the genomic content of coronaviruses, which specifies the virus's structure, is highly conserved, early genomic analysis provided a significant head start in predicting viral pathogenesis and in understanding potential differences among variants. The pathogenesis of the virus offers insights into symptomatology, transmission, and individual susceptibility. Additionally, prior research into interactions between the human immune system and coronaviruses has identified how these viruses can evade the immune system's protective mechanisms. We also explore systems-level research into the regulatory and proteomic effects of SARS-CoV-2 infection and the immune response. Understanding the structure and behavior of the virus serves to contextualize the many facets of the COVID-19 pandemic and can influence efforts to control the virus and treat the disease.
Language	English
Publishing date	2021-02-01
Publishing country	United States
Document type	Preprint
ISSN	2331-8422
ISSN (online)	2331-8422
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure.

mSystems

2021 Volume 6, Issue 5, Page(s) e0009521

Abstract	The novel coronavirus SARS-CoV-2, which emerged in late 2019, has since spread around the world and infected hundreds of millions of people with coronavirus disease 2019 (COVID-19). While this viral species was unknown prior to January 2020, its similarity to other coronaviruses that infect humans has allowed for rapid insight into the mechanisms that it uses to infect human hosts, as well as the ways in which the human immune system can respond. Here, we contextualize SARS-CoV-2 among other coronaviruses and identify what is known and what can be inferred about its behavior once inside a human host. Because the genomic content of coronaviruses, which specifies the virus's structure, is highly conserved, early genomic analysis provided a significant head start in predicting viral pathogenesis and in understanding potential differences among variants. The pathogenesis of the virus offers insights into symptomatology, transmission, and individual susceptibility. Additionally, prior research into interactions between the human immune system and coronaviruses has identified how these viruses can evade the immune system's protective mechanisms. We also explore systems-level research into the regulatory and proteomic effects of SARS-CoV-2 infection and the immune response. Understanding the structure and behavior of the virus serves to contextualize the many facets of the COVID-19 pandemic and can influence efforts to control the virus and treat the disease.
Language	English
Publishing date	2021-10-26
Publishing country	United States
Document type	Journal Article
ISSN	2379-5077
ISSN	2379-5077
DOI	10.1128/mSystems.00095-21
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Article ; Online: A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages.

Kimmerling, Robert J / Lee Szeto, Gregory / Li, Jennifer W / Genshaft, Alex S / Kazer, Samuel W / Payer, Kristofor R / de Riba Borrajo, Jacob / Blainey, Paul C / Irvine, Darrell J / Shalek, Alex K / Manalis, Scott R

Nature communications

2016 Volume 7, Page(s) 10220

Abstract: We introduce a microfluidic platform that enables off-chip single-cell RNA-seq after multi-generational lineage tracking under controlled culture conditions. We use this platform to generate whole-transcriptome profiles of primary, activated murine CD8+ ... ...

Abstract	We introduce a microfluidic platform that enables off-chip single-cell RNA-seq after multi-generational lineage tracking under controlled culture conditions. We use this platform to generate whole-transcriptome profiles of primary, activated murine CD8+ T-cell and lymphocytic leukemia cell line lineages. Here we report that both cell types have greater intra- than inter-lineage transcriptional similarity. For CD8+ T-cells, genes with functional annotation relating to lymphocyte differentiation and function--including Granzyme B--are enriched among the genes that demonstrate greater intra-lineage expression level similarity. Analysis of gene expression covariance with matched measurements of time since division reveals cell type-specific transcriptional signatures that correspond with cell cycle progression. We believe that the ability to directly measure the effects of lineage and cell cycle-dependent transcriptional profiles of single cells will be broadly useful to fields where heterogeneous populations of cells display distinct clonal trajectories, including immunology, cancer, and developmental biology.
MeSH term(s)	Animals ; CD8-Positive T-Lymphocytes/metabolism ; Cell Cycle/physiology ; Cell Line, Tumor ; Mice ; Microfluidic Analytical Techniques/instrumentation ; Microfluidic Analytical Techniques/methods ; RNA/genetics ; Transcription, Genetic
Chemical Substances	RNA (63231-63-0)
Language	English
Publishing date	2016-01-06
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/ncomms10220
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Longitudinal immune dynamics of mild COVID-19 define signatures of recovery and persistence

Talla, Aarthi / Vasaikar, Suhas V / Lemos, Maria P / Moodie, Zoe / Pebworth, Mark-Phillip Lee / Henderson, Kathy E / Cohen, Kristen W / Czartoski, Julie L / Lai, Lilin / Suthar, Mehul S / Heubeck, Alexander T / Genge, Palak C / Roll, Charles M / Weiss, Morgan / Reading, Julian / Kondza, Nina / MacMillan, Hugh / Fong, Olivia C / Thomson, Zachary James /

Graybuck, Lucas T / Newell, Evan W / Coffey, Ernest M / Meijer, Paul / Becker, Lynne A / De Rosa, Stephen C / Torgerson, Troy R. / Skene, Peter J. / Li, Xiaojun / Szeto, Gregory Lee / McElrath, M Juliana / Bumol, Thomas F.

bioRxiv

Abstract: SARS-CoV-2 has infected over 160 million and caused more than 3 million deaths to date. Most individuals (>80%) have mild symptoms and recover in the outpatient setting, but detailed studies of immune responses have focused primarily on moderate to ... ...

Abstract	SARS-CoV-2 has infected over 160 million and caused more than 3 million deaths to date. Most individuals (>80%) have mild symptoms and recover in the outpatient setting, but detailed studies of immune responses have focused primarily on moderate to severe COVID-19. We deeply profiled the longitudinal immune response in individuals with mild COVID beginning with early time points post-infection (1-15 days) and proceeding through convalescence to >100 days after symptom onset. We correlated data from single cell analyses of peripheral blood cells, serum proteomics, virus-specific cellular and humoral immune responses, and clinical metadata. Acute infection was characterized by vigorous coordinated innate and adaptive activation, including an early cellular and proteomic signature that correlated with the amplitude of virus-specific humoral responses after day 30. We characterized signals associated with recovery and convalescence to define a new signature of inflammatory cytokines, gene expression, and chromatin accessibility that persists in individuals with post-acute sequelae of SARS-CoV-2 infection (PASC).
Keywords	covid19
Language	English
Publishing date	2021-05-26
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2021.05.26.442666
Database	COVID19

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