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Article ; Online: E-wave asymmetry elucidates diastolic ventricular stiffness-relaxation coupling: model-based prediction with in vivo validation.

Amrute, Junedh M / Zhang, David / Padovano, William M / Kovács, Sándor J

American journal of physiology. Heart and circulatory physiology

2020 Volume 320, Issue 1, Page(s) H181–H189

Abstract: Load, chamber stiffness, and relaxation are the three established determinants of global diastolic function (DF). Coupling of systolic stiffness and isovolumic relaxation has been hypothesized; however, diastolic stiffness-relaxation coupling (DSRC) ... ...

Abstract	Load, chamber stiffness, and relaxation are the three established determinants of global diastolic function (DF). Coupling of systolic stiffness and isovolumic relaxation has been hypothesized; however, diastolic stiffness-relaxation coupling (DSRC) remains unknown. The parametrized diastolic filling (PDF) formalism, a validated DF model incorporates DSRC. PDF model-predicted DSRC was validated by analysis of 159 Doppler E-waves from a published data set (22 healthy volunteers undergoing bicycle exercise). E-waves at varying (46-120 bpm) heart rates (HR) demonstrated variation in acceleration time (AT), deceleration time (DT), and E-wave peak velocity. AT, DT, and E
MeSH term(s)	Adult ; Bicycling ; Diastole ; Echocardiography, Doppler ; Exercise ; Female ; Healthy Volunteers ; Heart Rate ; Heart Ventricles/diagnostic imaging ; Humans ; Male ; Models, Cardiovascular ; Predictive Value of Tests ; Reproducibility of Results ; Retrospective Studies ; Systole ; Time Factors ; Ventricular Function, Left ; Young Adult
Language	English
Publishing date	2020-11-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Validation Study
ZDB-ID	603838-4
ISSN	1522-1539 ; 0363-6135
ISSN (online)	1522-1539
ISSN	0363-6135
DOI	10.1152/ajpheart.00650.2020
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Article ; Online: Author Correction: SVEP1 is an endogenous ligand for the orphan receptor PEAR1.

Elenbaas, Jared S / Pudupakkam, Upasana / Ashworth, Katrina J / Kang, Chul Joo / Patel, Ved / Santana, Katherine / Jung, In-Hyuk / Lee, Paul C / Burks, Kendall H / Amrute, Junedh M / Mecham, Robert P / Halabi, Carmen M / Alisio, Arturo / Di Paola, Jorge / Stitziel, Nathan O

Nature communications

2023 Volume 14, Issue 1, Page(s) 1511

Language	English
Publishing date	2023-03-17
Publishing country	England
Document type	Published Erratum
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-37005-x
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Article ; Online: Vascular smooth muscle- and myeloid cell-derived integrin α9β1 does not directly mediate the development of atherosclerosis in mice.

Jung, In-Hyuk / Elenbaas, Jared S / Burks, Kendall H / Amrute, Junedh M / Xiangyu, Zhang / Alisio, Arturo / Stitziel, Nathan O

Atherosclerosis

2022 Volume 360, Page(s) 15–20

Abstract: Background and aims: Sushi, von Willebrand factor type A, EGF pentraxin domain-containing 1 (SVEP1), an extracellular matrix protein, is a human coronary artery disease locus that promotes atherosclerosis. We previously demonstrated that SVEP1 induces ... ...

Abstract	Background and aims: Sushi, von Willebrand factor type A, EGF pentraxin domain-containing 1 (SVEP1), an extracellular matrix protein, is a human coronary artery disease locus that promotes atherosclerosis. We previously demonstrated that SVEP1 induces vascular smooth muscle cell (VSMC) proliferation and an inflammatory phenotype in the arterial wall to enhance the development of atherosclerotic plaque. The only receptor known to interact with SVEP1 is integrin α9β1, a cell surface receptor that is expressed by VSMCs and myeloid lineage-derived monocytes and macrophages. Our previous in vitro studies suggested that integrin α9β1 was necessary for SVEP1-induced VSMC proliferation and inflammation; however, the underlying mechanisms mediated by integrin α9β1 in these cell types during the development of atherosclerosis remain poorly understood. Methods and results: Here, using cell-specific gene targeting, we investigated the effects of the integrin α9β1 receptor on VSMCs and myeloid cells in mouse models of atherosclerosis. Interestingly, we found that depleting integrin α9β1 in either VSMCs or myeloid cells did not affect the formation or complexity of atherosclerotic plaque in vessels after either 8 or 16 weeks of high fat diet feeding. Conclusions: Our results indicate that integrin α9β1 in these two cell types does not mediate the in vivo effect of SVEP1 in the development of atherosclerosis. Instead, our results suggest either the presence of other potential receptor(s) or alternative integrin α9β1-expressing cell types responsible for SVEP1 induced signaling in the development of atherosclerosis.
MeSH term(s)	Mice ; Humans ; Animals ; Muscle, Smooth, Vascular/metabolism ; Plaque, Atherosclerotic/metabolism ; von Willebrand Factor/metabolism ; Epidermal Growth Factor ; Atherosclerosis/genetics ; Atherosclerosis/metabolism ; Macrophages/metabolism ; Extracellular Matrix Proteins/metabolism ; Myocytes, Smooth Muscle/metabolism ; Cell Proliferation ; Cells, Cultured
Chemical Substances	integrin alpha 9 beta 1 ; von Willebrand Factor ; Epidermal Growth Factor (62229-50-9) ; Extracellular Matrix Proteins
Language	English
Publishing date	2022-10-04
Publishing country	Ireland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	80061-2
ISSN	1879-1484 ; 0021-9150
ISSN (online)	1879-1484
ISSN	0021-9150
DOI	10.1016/j.atherosclerosis.2022.09.015
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Article ; Online: B cells mediate lung ischemia/reperfusion injury by recruiting classical monocytes via synergistic B cell receptor/TLR4 signaling.

Farahnak, Khashayar / Bai, Yun Zhu / Yokoyama, Yuhei / Morkan, Deniz B / Liu, Zhiyi / Amrute, Junedh M / De Filippis Falcon, Alejandro / Terada, Yuriko / Liao, Fuyi / Li, Wenjun / Shepherd, Hailey M / Hachem, Ramsey R / Puri, Varun / Lavine, Kory J / Gelman, Andrew E / Bharat, Ankit / Kreisel, Daniel / Nava, Ruben G

The Journal of clinical investigation

2024 Volume 134, Issue 6

Abstract: Ischemia/reperfusion injury-mediated (IRI-mediated) primary graft dysfunction (PGD) adversely affects both short- and long-term outcomes after lung transplantation, a procedure that remains the only treatment option for patients suffering from end-stage ... ...

Abstract	Ischemia/reperfusion injury-mediated (IRI-mediated) primary graft dysfunction (PGD) adversely affects both short- and long-term outcomes after lung transplantation, a procedure that remains the only treatment option for patients suffering from end-stage respiratory failure. While B cells are known to regulate adaptive immune responses, their role in lung IRI is not well understood. Here, we demonstrated by intravital imaging that B cells are rapidly recruited to injured lungs, where they extravasate into the parenchyma. Using hilar clamping and transplant models, we observed that lung-infiltrating B cells produce the monocyte chemokine CCL7 in a TLR4-TRIF-dependent fashion, a critical step contributing to classical monocyte (CM) recruitment and subsequent neutrophil extravasation, resulting in worse lung function. We found that synergistic BCR-TLR4 activation on B cells is required for the recruitment of CMs to the injured lung. Finally, we corroborated our findings in reperfused human lungs, in which we observed a correlation between B cell infiltration and CM recruitment after transplantation. This study describes a role for B cells as critical orchestrators of lung IRI. As B cells can be depleted with currently available agents, our study provides a rationale for clinical trials investigating B cell-targeting therapies.
MeSH term(s)	Humans ; Monocytes ; Toll-Like Receptor 4/genetics ; Lung ; Reperfusion Injury ; Ischemia ; Receptors, Antigen, B-Cell
Chemical Substances	Toll-Like Receptor 4 ; Receptors, Antigen, B-Cell ; TLR4 protein, human
Language	English
Publishing date	2024-01-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	3067-3
ISSN	1558-8238 ; 0021-9738
ISSN (online)	1558-8238
ISSN	0021-9738
DOI	10.1172/JCI170118
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Article ; Online: CellTagging: combinatorial indexing to simultaneously map lineage and identity at single-cell resolution.

Kong, Wenjun / Biddy, Brent A / Kamimoto, Kenji / Amrute, Junedh M / Butka, Emily G / Morris, Samantha A

Nature protocols

2020 Volume 15, Issue 3, Page(s) 750–772

Abstract: Single-cell technologies are offering unparalleled insight into complex biology, revealing the behavior of rare cell populations that are masked in bulk population analyses. One current limitation of single-cell approaches is that lineage relationships ... ...

Abstract	Single-cell technologies are offering unparalleled insight into complex biology, revealing the behavior of rare cell populations that are masked in bulk population analyses. One current limitation of single-cell approaches is that lineage relationships are typically lost as a result of cell processing. We recently established a method, CellTagging, permitting the parallel capture of lineage information and cell identity via a combinatorial cell indexing approach. CellTagging integrates with high-throughput single-cell RNA sequencing, where sequential rounds of cell labeling enable the construction of multi-level lineage trees. Here, we provide a detailed protocol to (i) generate complex plasmid and lentivirus CellTag libraries for labeling of cells; (ii) sequentially CellTag cells over the course of a biological process; (iii) profile single-cell transcriptomes via high-throughput droplet-based platforms; and (iv) generate a CellTag expression matrix, followed by clone calling and lineage reconstruction. This lentiviral-labeling approach can be deployed in any organism or in vitro culture system that is amenable to viral transduction to simultaneously profile lineage and identity at single-cell resolution.
MeSH term(s)	Animals ; Cell Line ; Cell Lineage ; Cell Tracking/methods ; Escherichia coli ; Fibroblasts/physiology ; Gene Expression Regulation ; Humans ; Mice
Language	English
Publishing date	2020-02-12
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2244966-8
ISSN	1750-2799 ; 1754-2189
ISSN (online)	1750-2799
ISSN	1754-2189
DOI	10.1038/s41596-019-0247-2
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Article ; Online: SVEP1 is an endogenous ligand for the orphan receptor PEAR1.

Nature communications

2023 Volume 14, Issue 1, Page(s) 850

Abstract: Sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1 (SVEP1) is an extracellular matrix protein that causally promotes vascular disease and associates with platelet reactivity in humans. Here, using a human genomic and proteomic ... ...

Abstract	Sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1 (SVEP1) is an extracellular matrix protein that causally promotes vascular disease and associates with platelet reactivity in humans. Here, using a human genomic and proteomic approach, we identify a high affinity, disease-relevant, and potentially targetable interaction between SVEP1 and the orphan receptor Platelet and Endothelial Aggregation Receptor 1 (PEAR1). This interaction promotes PEAR1 phosphorylation and disease associated AKT/mTOR signaling in vascular cells and platelets. Mice lacking SVEP1 have reduced platelet activation, and exogenous SVEP1 induces PEAR1-dependent activation of platelets. SVEP1 and PEAR1 causally and concordantly relate to platelet phenotypes and cardiovascular disease in humans, as determined by Mendelian Randomization. Targeting this receptor-ligand interaction may be a viable therapeutic strategy to treat or prevent cardiovascular and thrombotic disease.
MeSH term(s)	Humans ; Animals ; Mice ; Blood Platelets/metabolism ; Ligands ; Proteomics ; Receptors, Cell Surface/metabolism ; Platelet Aggregation ; Cell Adhesion Molecules/metabolism
Chemical Substances	Ligands ; Receptors, Cell Surface ; PEAR1 protein, human ; SVEP1 protein, human ; Cell Adhesion Molecules
Language	English
Publishing date	2023-02-15
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/s41467-023-36486-0
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Article ; Online: Cell specific peripheral immune responses predict survival in critical COVID-19 patients

Junedh M. Amrute / Alexandra M. Perry / Gautam Anand / Carlos Cruchaga / Karl G. Hock / Christopher W. Farnsworth / Gwendalyn J. Randolph / Kory J. Lavine / Ashley L. Steed

Nature Communications, Vol 13, Iss 1, Pp 1-

2022 Volume 11

Abstract: Infection with SARS-CoV-2 results in activation of multiple immune cell types in situ but also in the peripheral blood compartment. Here the authors apply single cell sequencing and machine learning to characterise the response and link this to confer ... ...

Abstract	Infection with SARS-CoV-2 results in activation of multiple immune cell types in situ but also in the peripheral blood compartment. Here the authors apply single cell sequencing and machine learning to characterise the response and link this to confer prognostic indicators in critically ill COVID-19 patients.
Keywords	Science ; Q
Language	English
Publishing date	2022-02-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
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Article ; Online: Derivation of extra-embryonic and intra-embryonic macrophage lineages from human pluripotent stem cells.

Bredemeyer, Andrea L / Amrute, Junedh M / Koenig, Andrew L / Idol, Rachel A / He, Li / Luff, Stephanie A / Dege, Carissa / Leid, Jamison M / Schilling, Joel D / Hinson, J Travis / Dinauer, Mary C / Sturgeon, Christopher M / Lavine, Kory J

Development (Cambridge, England)

2022 Volume 149, Issue 8

Abstract: Tissue-resident macrophages are increasingly recognized as important determinants of organ homeostasis, tissue repair, remodeling and regeneration. Although the ontogeny and function of tissue-resident macrophages has been identified as distinct from ... ...

Abstract	Tissue-resident macrophages are increasingly recognized as important determinants of organ homeostasis, tissue repair, remodeling and regeneration. Although the ontogeny and function of tissue-resident macrophages has been identified as distinct from postnatal hematopoiesis, the inability to specify, in vitro, similar populations that recapitulate these developmental waves has limited our ability to study their function and potential for regenerative applications. We took advantage of the concept that tissue-resident macrophages and monocyte-derived macrophages originate from distinct extra-embryonic and definitive hematopoietic lineages to devise a system to generate pure cultures of macrophages that resemble tissue-resident or monocyte-derived subsets. We demonstrate that human pluripotent stem cell-derived extra-embryonic-like and intra-embryonic-like hematopoietic progenitors differentiate into morphologically, transcriptionally and functionally distinct macrophage populations. Single-cell RNA sequencing of developing and mature cultures uncovered distinct developmental trajectories and gene expression programs of macrophages derived from extra-embryonic-like and intra-embryonic-like hematopoietic progenitors. These findings establish a resource for the generation of human tissue resident-like macrophages to study their specification and function under defined conditions and to explore their potential use in tissue engineering and regenerative medicine applications.
MeSH term(s)	Cell Differentiation/genetics ; Hematopoiesis ; Homeostasis ; Humans ; Macrophages/metabolism ; Pluripotent Stem Cells
Language	English
Publishing date	2022-05-03
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	90607-4
ISSN	1477-9129 ; 0950-1991
ISSN (online)	1477-9129
ISSN	0950-1991
DOI	10.1242/dev.200016
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Article ; Online: Cell specific peripheral immune responses predict survival in critical COVID-19 patients.

Amrute, Junedh M / Perry, Alexandra M / Anand, Gautam / Cruchaga, Carlos / Hock, Karl G / Farnsworth, Christopher W / Randolph, Gwendalyn J / Lavine, Kory J / Steed, Ashley L

Nature communications

2022 Volume 13, Issue 1, Page(s) 882

Abstract: SARS-CoV-2 triggers a complex systemic immune response in circulating blood mononuclear cells. The relationship between immune cell activation of the peripheral compartment and survival in critical COVID-19 remains to be established. Here we use single- ... ...

Abstract	SARS-CoV-2 triggers a complex systemic immune response in circulating blood mononuclear cells. The relationship between immune cell activation of the peripheral compartment and survival in critical COVID-19 remains to be established. Here we use single-cell RNA sequencing and Cellular Indexing of Transcriptomes and Epitomes by sequence mapping to elucidate cell type specific transcriptional signatures that associate with and predict survival in critical COVID-19. Patients who survive infection display activation of antibody processing, early activation response, and cell cycle regulation pathways most prominent within B-, T-, and NK-cell subsets. We further leverage cell specific differential gene expression and machine learning to predict mortality using single cell transcriptomes. We identify interferon signaling and antigen presentation pathways within cDC2 cells, CD14 monocytes, and CD16 monocytes as predictors of mortality with 90% accuracy. Finally, we validate our findings in an independent transcriptomics dataset and provide a framework to elucidate mechanisms that promote survival in critically ill COVID-19 patients. Identifying prognostic indicators among critical COVID-19 patients holds tremendous value in risk stratification and clinical management.
MeSH term(s)	Aged ; Aged, 80 and over ; COVID-19/genetics ; COVID-19/immunology ; COVID-19/mortality ; Critical Illness ; Female ; Gene Expression ; Humans ; Immunity, Cellular/genetics ; Immunity, Cellular/immunology ; Leukocytes, Mononuclear/immunology ; Longitudinal Studies ; Male ; Middle Aged ; Prognosis ; Reproducibility of Results ; SARS-CoV-2/pathogenicity ; Single-Cell Analysis ; Transcriptome/immunology
Language	English
Publishing date	2022-02-15
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/s41467-022-28505-3
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Article ; Online: Peripheral blood mononuclear cell tissue factor (F3 gene) transcript levels and circulating extracellular vesicles are elevated in severe coronavirus 2019 (COVID-19) disease.

Girard, Thomas J / Antunes, Lilian / Zhang, Nan / Amrute, Junedh M / Subramanian, Renumathi / Eldem, Irem / Remy, Kenneth E / Mazer, Monty / Erlich, Emma C / Cruchaga, Carlos / Steed, Ashley L / Randolph, Gwendalyn J / Di Paola, Jorge

Journal of thrombosis and haemostasis : JTH

2022 Volume 21, Issue 3, Page(s) 629–638

Abstract: Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is associated with excessive coagulation, thrombosis, and mortality.: Objective: To provide insight into mechanisms that contribute to excessive coagulation in ... ...

Abstract	Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is associated with excessive coagulation, thrombosis, and mortality. Objective: To provide insight into mechanisms that contribute to excessive coagulation in coronavirus 2019 (COVID-19) disease. Patients/methods: Blood from COVID-19 patients was investigated for coagulation-related gene expression and functional activities. Results: Single-cell RNA sequencing (scRNA-seq) of peripheral blood mononuclear cells from severe COVID-19 patients revealed a 5.2-fold increase in tissue factor (TF [F3 gene]) transcript expression levels (P < .05), the trigger of extrinsic coagulation; a 7.7-fold increase in C1-inhibitor (SERPING1 gene; P < .01) transcript expression levels, an inhibitor of intrinsic coagulation; and a 4.4-fold increase in anticoagulant thrombomodulin (TM [THBD gene]) transcript expression levels (P < .001). Bulk RNA-seq analysis of sorted CD14 Conclusions: Beyond local lung injury, SARS-CoV-2 infection increases systemic TF (F3) transcript levels and elevates circulating extracellular vesicles that likely contribute to disease-associated coagulation, thrombosis, and related mortality.
MeSH term(s)	Humans ; Blood Coagulation Disorders ; COVID-19 ; Extracellular Vesicles/metabolism ; Leukocytes, Mononuclear/metabolism ; SARS-CoV-2 ; Thromboplastin/metabolism ; Thrombosis
Chemical Substances	Thromboplastin (9035-58-9) ; F3 protein, human
Language	English
Publishing date	2022-12-22
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2112661-6
ISSN	1538-7836 ; 1538-7933
ISSN (online)	1538-7836
ISSN	1538-7933
DOI	10.1016/j.jtha.2022.11.033
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