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Carmona-Mora P, Knepp B, Jickling GC, Zhan X, Hakoupian M, Hull H, Alomar N, Amini H, Sharp FR, Stamova B, Ander BP. Monocyte, neutrophil, and whole blood transcriptome dynamics following ischemic stroke. BMC Med 2023; 21:65. [PMID: 36803375 PMCID: PMC9942321 DOI: 10.1186/s12916-023-02766-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 12/21/2022] [Indexed: 02/22/2023] Open
Abstract
BACKGROUND After ischemic stroke (IS), peripheral leukocytes infiltrate the damaged region and modulate the response to injury. Peripheral blood cells display distinctive gene expression signatures post-IS and these transcriptional programs reflect changes in immune responses to IS. Dissecting the temporal dynamics of gene expression after IS improves our understanding of immune and clotting responses at the molecular and cellular level that are involved in acute brain injury and may assist with time-targeted, cell-specific therapy. METHODS The transcriptomic profiles from peripheral monocytes, neutrophils, and whole blood from 38 ischemic stroke patients and 18 controls were analyzed with RNA-seq as a function of time and etiology after stroke. Differential expression analyses were performed at 0-24 h, 24-48 h, and >48 h following stroke. RESULTS Unique patterns of temporal gene expression and pathways were distinguished for monocytes, neutrophils, and whole blood with enrichment of interleukin signaling pathways for different time points and stroke etiologies. Compared to control subjects, gene expression was generally upregulated in neutrophils and generally downregulated in monocytes over all times for cardioembolic, large vessel, and small vessel strokes. Self-organizing maps identified gene clusters with similar trajectories of gene expression over time for different stroke causes and sample types. Weighted Gene Co-expression Network Analyses identified modules of co-expressed genes that significantly varied with time after stroke and included hub genes of immunoglobulin genes in whole blood. CONCLUSIONS Altogether, the identified genes and pathways are critical for understanding how the immune and clotting systems change over time after stroke. This study identifies potential time- and cell-specific biomarkers and treatment targets.
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Affiliation(s)
- Paulina Carmona-Mora
- Department of Neurology and M.I.N.D, Institute, M.I.N.D. Institute Bioscience Labs, School of Medicine, University of California at Davis, 2805 50th St, Room 2434, Sacramento, CA, 95817, USA.
| | - Bodie Knepp
- Department of Neurology and M.I.N.D, Institute, M.I.N.D. Institute Bioscience Labs, School of Medicine, University of California at Davis, 2805 50th St, Room 2434, Sacramento, CA, 95817, USA
| | - Glen C Jickling
- Division of Neurology, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, 87 Avenue & 114 Street, Edmonton, AB, T6G 2J7, Canada
| | - Xinhua Zhan
- Department of Neurology and M.I.N.D, Institute, M.I.N.D. Institute Bioscience Labs, School of Medicine, University of California at Davis, 2805 50th St, Room 2434, Sacramento, CA, 95817, USA
| | - Marisa Hakoupian
- Department of Neurology and M.I.N.D, Institute, M.I.N.D. Institute Bioscience Labs, School of Medicine, University of California at Davis, 2805 50th St, Room 2434, Sacramento, CA, 95817, USA
| | - Heather Hull
- Department of Neurology and M.I.N.D, Institute, M.I.N.D. Institute Bioscience Labs, School of Medicine, University of California at Davis, 2805 50th St, Room 2434, Sacramento, CA, 95817, USA
| | - Noor Alomar
- Department of Neurology and M.I.N.D, Institute, M.I.N.D. Institute Bioscience Labs, School of Medicine, University of California at Davis, 2805 50th St, Room 2434, Sacramento, CA, 95817, USA
| | - Hajar Amini
- Department of Neurology and M.I.N.D, Institute, M.I.N.D. Institute Bioscience Labs, School of Medicine, University of California at Davis, 2805 50th St, Room 2434, Sacramento, CA, 95817, USA
| | - Frank R Sharp
- Department of Neurology and M.I.N.D, Institute, M.I.N.D. Institute Bioscience Labs, School of Medicine, University of California at Davis, 2805 50th St, Room 2434, Sacramento, CA, 95817, USA
| | - Boryana Stamova
- Department of Neurology and M.I.N.D, Institute, M.I.N.D. Institute Bioscience Labs, School of Medicine, University of California at Davis, 2805 50th St, Room 2434, Sacramento, CA, 95817, USA
| | - Bradley P Ander
- Department of Neurology and M.I.N.D, Institute, M.I.N.D. Institute Bioscience Labs, School of Medicine, University of California at Davis, 2805 50th St, Room 2434, Sacramento, CA, 95817, USA
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Knepp B, Ander BP, Jickling GC, Hull H, Yee AH, Ng K, Rodriguez F, Carmona-Mora P, Amini H, Zhan X, Hakoupian M, Alomar N, Sharp FR, Stamova B. Gene expression changes implicate specific peripheral immune responses to Deep and Lobar Intracerebral Hemorrhages in humans. Brain Hemorrhages 2022; 3:155-176. [PMID: 36936603 PMCID: PMC10019834 DOI: 10.1016/j.hest.2022.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The peripheral immune system response to Intracerebral Hemorrhage (ICH) may differ with ICH in different brain locations. Thus, we investigated peripheral blood mRNA expression of Deep ICH, Lobar ICH, and vascular risk factor-matched control subjects (n = 59). Deep ICH subjects usually had hypertension. Some Lobar ICH subjects had cerebral amyloid angiopathy (CAA). Genes and gene networks in Deep ICH and Lobar ICH were compared to controls. We found 774 differentially expressed genes (DEGs) and 2 co-expressed gene modules associated with Deep ICH, and 441 DEGs and 5 modules associated with Lobar ICH. Pathway enrichment showed some common immune/inflammatory responses between locations including Autophagy, T Cell Receptor, Inflammasome, and Neuroinflammation Signaling. Th2, Interferon, GP6, and BEX2 Signaling were unique to Deep ICH. Necroptosis Signaling, Protein Ubiquitination, Amyloid Processing, and various RNA Processing terms were unique to Lobar ICH. Finding amyloid processing pathways in blood of Lobar ICH patients suggests peripheral immune cells may participate in processes leading to perivascular/vascular amyloid in CAA vessels and/or are involved in its removal. This study identifies distinct peripheral blood transcriptome architectures in Deep and Lobar ICH, emphasizes the need for considering location in ICH studies/clinical trials, and presents potential location-specific treatment targets.
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Affiliation(s)
- Bodie Knepp
- Department of Neurology, School of Medicine, University of California at Davis, Sacramento, CA, USA
| | - Bradley P. Ander
- Department of Neurology, School of Medicine, University of California at Davis, Sacramento, CA, USA
| | - Glen C. Jickling
- Department of Medicine, Division of Neurology, University of Alberta, Edmonton, Canada
| | - Heather Hull
- Department of Neurology, School of Medicine, University of California at Davis, Sacramento, CA, USA
| | - Alan H. Yee
- Department of Neurology, School of Medicine, University of California at Davis, Sacramento, CA, USA
| | - Kwan Ng
- Department of Neurology, School of Medicine, University of California at Davis, Sacramento, CA, USA
| | - Fernando Rodriguez
- Department of Neurology, School of Medicine, University of California at Davis, Sacramento, CA, USA
| | - Paulina Carmona-Mora
- Department of Neurology, School of Medicine, University of California at Davis, Sacramento, CA, USA
| | - Hajar Amini
- Department of Neurology, School of Medicine, University of California at Davis, Sacramento, CA, USA
| | - Xinhua Zhan
- Department of Neurology, School of Medicine, University of California at Davis, Sacramento, CA, USA
| | - Marisa Hakoupian
- Department of Neurology, School of Medicine, University of California at Davis, Sacramento, CA, USA
| | - Noor Alomar
- Department of Neurology, School of Medicine, University of California at Davis, Sacramento, CA, USA
| | - Frank R. Sharp
- Department of Neurology, School of Medicine, University of California at Davis, Sacramento, CA, USA
| | - Boryana Stamova
- Department of Neurology, School of Medicine, University of California at Davis, Sacramento, CA, USA
- Corresponding author at: Department of Neurology, UC Davis School of Medicine, MIND Bioscience Labs Room 2415, 2805 50th Street, Sacramento, CA 95817, USA. (B. Stamova)
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Carmona-Mora P, Knepp B, Jickling G, Zhan X, Hakoupian M, Hull H, Alomar N, Amini H, Sharp FR, Stamova B, Ander B. Abstract TMP114: Time-based Dynamic Analyses Of Gene Expression In Monocytes, Neutrophils And Whole Blood Identify Key Hub Genes And Functional Processes Following Acute Ischemic Stroke. Stroke 2022. [DOI: 10.1161/str.53.suppl_1.tmp114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Gene expression changes in peripheral blood reflect injury and repair processes occurring post ischemic stroke (IS). Our study explored the dynamic time-dependent expression of key genes involved in the immune response after IS to better understand the biology and to identify specific diagnostic biomarkers. Using RNA-sequencing, we analyzed gene expression profiles of 38 IS patients and 18 controls with at least one vascular risk factor (VRFC) including diabetes and/or hypertension and/or hypercholesterolemia in isolated monocytes, neutrophils and whole blood. We used two approaches: Weighted Gene Co-expression Network Analysis (WGCNA) with respect to time after stroke onset; and differential expression analyses with subject samples split into time points (TPs) from stroke onset (TP0=VRFC; TP1=0-24 h; TP2=24-48 h; and TP3≥48 h). In WGCNA, highly interconnected “hub” genes were identified for modules significant to time (p<0.05). Differentially expressed genes (DEGs) with diagnosisхTP p<0.02 and fold-change>
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Affiliation(s)
| | | | | | - Xinhua Zhan
- MIND INSTITUTE UNIVERSITY CA DAVIS, Sacramento, CA
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Knepp B, Rodriguez F, Yee AH, Ng K, Jickling G, Zhan X, Amini H, Carmona P, Hull H, Alomar N, Hakoupian M, Sharp FR, Ander B, Stamova B. Abstract WP133: Sex Differences In The Human Intracerebral Hemorrhage Peripheral Blood Transcriptome Implicate Differential Immune And Inflammatory Responses. Stroke 2022. [DOI: 10.1161/str.53.suppl_1.wp133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Sex differences in immune and inflammatory pathways have been shown in health and disease. However, little research has been done on sex differences following human Intracerebral Hemorrhage (ICH). We sought to unveil transcriptome differences in blood between Male (M) and Female (F) ICH responses. We evaluated 33 ICH patients and 33 vascular risk factor matched controls (VRFC), 9F and 24M each. Peripheral blood expression of 21,175 genes was analyzed at the co-expression network level with WGCNA - separate F (F-ICH and F-VRFC) and M (M-ICH and M-VRFC) networks generated; and per gene level (ANCOVA: Age, Time, and Sex*Dx (Diagnosis)). Five F (F-6, F-20, F-21, F-19, F-5) and 2 M (M-32, M-26) WGCNA modules were significant to Dx (p < 0.05) (Fig 1A). 105 genes were significant for the direct comparison (F-ICH vs M-ICH p < 0.05, |FC| > 1.2; Sex*Dx FDR < 0.2), which separated Sex*Dx groups (Fig 1B). 1,425 genes were differentially expressed in F-ICH (F-ICH vs F-VRFC p < 0.05, |FC| > 1.2; Sex*Dx FDR < 0.2) and 421 in M-ICH (M-ICH vs M-VRFC p < 0.05, |FC| > 1.2; Sex*Dx FDR < 0.2) (Fig 1C). F-ICH response was enriched in Monocyte and T Cell Specific genes and M-ICH in B Cell and Erythroblast specific genes; both were enriched in Neutrophil specific genes (Fig 1A). Overall, F modules and gene lists were significantly enriched in 236 GO terms (FDR < 0.1) and M modules in 55; 20 were common (Fig 1D). The ICH response unique to F-ICH included Inflammatory Response, T Cell Activation, Autophagy, Apoptotic Process, and RNA Splicing. M-ICH unique included B Cell Receptor Signaling, Immunoglobulin Receptor Binding, Antigen Binding, Complement Activation, and Receptor Mediated Endocytosis. Common responses included Innate Immune Response, Blood Coagulation, and Fc-ã Receptor Signaling Involved in Phagocytosis (Fig 1E). We found sex differences in ICH transcriptome responses in human peripheral blood. These implicate specific cell types in each sex that could represent novel sex-specific treatment targets.
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Affiliation(s)
- Bodie Knepp
- Neurology, Univ of California Davis Sch of Medicine, Sacramento, CA
| | | | - Alan H Yee
- Univ of California Davis Sch of Medicine, Sacramento, CA
| | - Kwan Ng
- Neurology, Univ of California Davis Sch of Medicine, Sacramento, CA
| | | | - Xinhua Zhan
- Neurology, Univ of California Davis Sch of Medicine, Sacramento, CA
| | - Hajar Amini
- Neurology, Univ of California Davis Sch of Medicine, Sacramento, CA
| | - Paulina Carmona
- Neurology, Univ of California Davis Sch of Medicine, Sacramento, CA
| | - Heather Hull
- Neurology, Univ of California Davis Sch of Medicine, Sacramento, CA
| | - Noor Alomar
- Neurology, Univ of California Davis Sch of Medicine, Sacramento, CA
| | - Marisa Hakoupian
- Neurology, Univ of California Davis Sch of Medicine, Sacramento, CA
| | - Frank R Sharp
- Neurology, Univ of California Davis Sch of Medicine, Sacramento, CA
| | - Bradley Ander
- Neurology, Univ of California Davis Sch of Medicine, Sacramento, CA
| | - Boryana Stamova
- Neurology, Univ of California Davis Sch of Medicine, Sacramento, CA
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Hakoupian M, Ferino E, Jickling GC, Amini H, Stamova B, Ander BP, Alomar N, Sharp FR, Zhan X. Bacterial lipopolysaccharide is associated with stroke. Sci Rep 2021; 11:6570. [PMID: 33753837 PMCID: PMC7985504 DOI: 10.1038/s41598-021-86083-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 03/08/2021] [Indexed: 01/22/2023] Open
Abstract
We aimed to determine if plasma levels of bacterial lipopolysaccharide (LPS) and lipoteichoic acid (LTA) are associated with different causes of stroke and correlate with C-reactive protein (CRP), LPS-binding protein (LBP), and the NIH stroke scale (NIHSS). Ischemic stroke (cardioembolic (CE), large artery atherosclerosis (LAA), small vessel occlusion (SVO)), intracerebral hemorrhage (ICH), transient ischemic attack (TIA) and control subjects were compared (n = 205). Plasma LPS, LTA, CRP, and LBP levels were quantified by ELISA. LPS and CRP levels were elevated in ischemic strokes (CE, LAA, SVO) and ICH compared to controls. LBP levels were elevated in ischemic strokes (CE, LAA) and ICH. LTA levels were increased in SVO stroke compared to TIA but not controls. LPS levels correlated with CRP and LBP levels in stroke and TIA. LPS, LBP and CRP levels positively correlated with the NIHSS and WBC count but negatively correlated with total cholesterol. Plasma LPS and LBP associate with major causes of ischemic stroke and with ICH, whereas LPS/LBP do not associate with TIAs. LTA only associated with SVO stroke. LPS positively correlated with CRP, LBP, and WBC but negatively correlated with cholesterol. Higher LPS levels were associated with worse stroke outcomes.
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Affiliation(s)
- Marisa Hakoupian
- Department of Neurology, University of California Davis School of Medicine, Sacramento, CA, USA
| | - Eva Ferino
- Department of Neurology, University of California Davis School of Medicine, Sacramento, CA, USA
| | - Glen C Jickling
- Department of Neurology, University of California Davis School of Medicine, Sacramento, CA, USA.,Division of Neurology, Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Hajar Amini
- Department of Neurology, University of California Davis School of Medicine, Sacramento, CA, USA
| | - Boryana Stamova
- Department of Neurology, University of California Davis School of Medicine, Sacramento, CA, USA
| | - Bradley P Ander
- Department of Neurology, University of California Davis School of Medicine, Sacramento, CA, USA
| | - Noor Alomar
- Department of Neurology, University of California Davis School of Medicine, Sacramento, CA, USA
| | - Frank R Sharp
- Department of Neurology, University of California Davis School of Medicine, Sacramento, CA, USA
| | - Xinhua Zhan
- Department of Neurology, University of California Davis School of Medicine, Sacramento, CA, USA. .,Department of Neurology and MIND Institute, University of California Davis Medical Center, 2805 50th Street, Sacramento, CA, 95817, USA.
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Amini H, Knepp B, Hull H, Carmona-Mora P, Hakoupian M, Alomar N, Jickling G, Zhan X, Khoury J, Pancioli A, Broderick J, Ander BP, Stamova B, Sharp FR. Abstract P787: Sexually Dimorphic Gene Expression Molecular Correlates of Improvement in Human Ischemic Stroke. Stroke 2021. [DOI: 10.1161/str.52.suppl_1.p787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Objective:
Ischemic stroke (IS) is sexually dimorphic for risk factors, age, heritability, causes, treatment, and outcome. We identified transcriptional correlates with 90-day outcome that differed between male and female IS subjects.
Methods:
RNA from 72 samples from 2 peripheral blood draws (at ≤3 and 24h post IS onset) was analyzed on Affymetrix U133 Plus 2 microarrays. These represented samples from 36 CLEAR trial IS patients treated with tPA with or without eptifibatide after the first blood sample within 3 hours of stroke onset. Changes in gene expression levels (deltaGE) between 3h and 24h were calculated and the association with percent NIH Stroke Scale (NIHSS) improvement from 3h to 90 days (% Improvement) examined. We used mixed-effects linear regression, including Treatment, Age, Sex, Vascular Risk Factors, 3h NIHSS, % Improvement, and a Sex * % Improvement interaction. Sex differences in association of gene expression with % Improvement were determined by examining the Sex * % Improvement interaction term, p<0.005 was considered statistically significant.
Results:
577 genes correlated differently with % Improvement in IS males and females. These included matrix metalloproteinases (MMPs), which play a major role in BBB dysfunction and outcomes post IS.
MMP11
,
MMP14
and
MM17
correlated with % Improvement in opposite direction in males and females. Inflammatory genes like
IL-27
, implicated in infarct volume and stroke outcome, and ABC transporters (
ABCC9
) also had opposite correlation with % Improvement in males and females. Calmodulin 1 (
CAML1
) was also sexually dimorphic, and a SNP in
CALM1
has been implicated in IS risk and blood coagulation in female IS patients. EIF2 signaling, a major protein synthesis pathway was activated in males (adj. p = 1e-8), while suppressed in females (adj. p value = 1e-9). Protein synthesis and associated unfolded protein response cascade have previously been implicated in stroke outcome.
Conclusions:
The identified sexually dimorphic gene expression associated with 90-day improvement might relate to sex differences in blood immune and clotting pathways. The findings expand our understanding of the genomic underpinnings associated with stroke outcome and may serve as potential sex-specific treatment targets.
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Affiliation(s)
- Hajar Amini
- Neurology, UC DAVIS Sch of Medicine, Sacramento, CA
| | - Bodie Knepp
- Neurology, UC DAVIS Sch of Medicine, Sacramento, CA
| | - Heather Hull
- Neurology, UC DAVIS Sch of Medicine, Sacramento, CA
| | | | | | - Noor Alomar
- Neurology, UC DAVIS Sch of Medicine, Sacramento, CA
| | | | - Xinhua Zhan
- Neurology, UC DAVIS Sch of Medicine, Sacramento, CA
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Carmona-Mora P, Jickling GC, Zhan X, Hakoupian M, Hull H, Alomar N, Amini H, Knepp B, Sharp FR, Stamova B, Ander BP. Abstract P744: Gene Transcript Clusters Distinguish Time-Dependent Expression Patterns in Monocytes, Neutrophils and Whole Blood After Ischemic Stroke Injury. Stroke 2021. [DOI: 10.1161/str.52.suppl_1.p744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Introduction:
After ischemic stroke (IS), peripheral leukocytes infiltrate the damaged region and modulate the response to injury. We previously showed that peripheral blood cells display different gene expression profiles after IS and these transcriptional programs reflect the changes in immune processes in response to IS. Dissecting the temporal dynamics of gene expression after IS improves our understanding of the changes of molecular and cellular pathways involved in acute brain injury.
Methods:
We analyzed the transcriptomic profiles of 33 IS patients in isolated monocytes, neutrophils and whole blood. RNA-sequencing was performed on all the stroke samples as well as 12 controls with vascular risk factors (diabetes and/or hypertension and/or hypercholesterolemia). To identify differentially expressed genes, subjects were split into time points (TPs) from stroke onset (TP1= 0-24 h; TP2= 24-48 h; and TP3= > 48 h), and controls were assigned TP0. A linear regression model including time and the interaction of diagnosis x TP with cutoff of p<0.02 and fold-change>|1.2| was used. Time dependent changes were analyzed using artificial neural networks to identify clusters of genes that behave in a similar way across TPs.
Results:
Unique patterns of temporal expression were distinguished for the three sample types. These include genes not expressed in TP0 that peak only within the first 24 h, others that peak or decrease in TP2 and TP3, and more complex patterns. Genes that peak at TP1 in monocytes and neutrophils are related to cell adhesion and leukocyte differentiation/migration, respectively. Early peaks in whole blood occur in genes related to transcriptional regulation. In monocytes, interleukin pathways are enriched across all TPs, whereas there is a trend of suppression after 24 h in neutrophils. The inflammasome pathway is enriched in the earlier TPs in neutrophils, while not enriched in monocytes until over 48 hours.
Conclusion:
Our analyses on gene expression dynamics and cluster patterns allow identification of key genes and pathways at different time points following ischemic injury that are valuable as IS biomarkers and may be possible treatment targets.
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Affiliation(s)
| | | | - Xinhua Zhan
- Neurology, Univ of California-Davis, Sacramento, CA
| | | | - Heather Hull
- Neurology, Univ of California-Davis, Sacramento, CA
| | - Noor Alomar
- Neurology, Univ of California-Davis, Sacramento, CA
| | | | - Bodie Knepp
- Neurology, Univ of California-Davis, Sacramento, CA
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