Distinct peripheral blood monocyte and neutrophil transcriptional programs following intracerebral hemorrhage and different etiologies of ischemic stroke

Understanding cell-specific transcriptome responses following intracerebral hemorrhage (ICH) and ischemic stroke (IS) will improve knowledge of the immune response to brain injury. Transcriptomic profiles of 141 samples from 48 subjects with ICH, different IS etiologies, and vascular risk factor controls were characterized using RNA-seq in isolated neutrophils, monocytes and whole blood. In both IS and ICH, monocyte genes were down-regulated, whereas neutrophil gene expression changes were generally up-regulated. The monocyte down-regulated response to ICH included innate, adaptive immune, dendritic, NK cell and atherosclerosis signaling. Neutrophil responses to ICH included tRNA charging, mitochondrial dysfunction, and ER stress pathways. Common monocyte and neutrophil responses to ICH included interferon signaling, neuroinflammation, death receptor signaling, and NFAT pathways. Suppressed monocyte responses to IS included interferon and dendritic cell maturation signaling, phagosome formation, and IL-15 signaling. Activated neutrophil responses to IS included oxidative phosphorylation, mTOR, BMP, growth factor signaling, and calpain proteases-mediated blood-brain barrier (BBB) dysfunction. Common monocyte and neutrophil responses to IS included JAK1, JAK3, STAT3, and thrombopoietin signaling. Cell-type and cause-specific approaches will assist the search for future IS and ICH biomarkers and treatments.

Alternative Splicing of Putative Stroke/Vascular Risk Factor Genes Expressed in Blood Following Ischemic Stroke Is Sexually Dimorphic and Cause-Specific

Genome-wide association studies have identified putative ischemic stroke risk genes, yet, their expression after stroke is unexplored in spite of growing interest in elucidating their specific role and identifying candidate genes for stroke treatment. Thus, we took an exploratory approach to investigate sexual dimorphism, alternative splicing, and etiology in putative risk gene expression in blood following cardioembolic, atherosclerotic large vessel disease and small vessel disease/lacunar causes of ischemic stroke in each sex compared to controls. Whole transcriptome arrays assessed 71 putative stroke/vascular risk factor genes for blood RNA expression at gene-, exon-, and alternative splicing-levels. Male (n = 122) and female (n = 123) stroke and control volunteers from three university medical centers were matched for race, age, vascular risk factors, and blood draw time since stroke onset. Exclusion criteria included: previous stroke, drug abuse, subarachnoid or intracerebral hemorrhage, hemorrhagic transformation, infection, dialysis, cancer, hematological abnormalities, thrombolytics, anticoagulants or immunosuppressants. Significant differential gene expression (fold change > |1.2|, p < 0.05, partial correlation > |0.4|) and alternative splicing (false discovery rate p < 0.3) were assessed. At gene level, few were differentially expressed: ALDH2, ALOX5AP, F13A1, and IMPA2 (males, all stroke); ITGB3 (females, cardioembolic); ADD1 (males, atherosclerotic); F13A1, IMPA2 (males, lacunar); and WNK1 (females, lacunar). GP1BA and ITGA2B were alternatively spliced in both sexes (all patients vs. controls). Six genes in males, five in females, were alternatively spliced in all stroke compared to controls. Alternative splicing and exon-level analyses associated many genes with specific etiology in either sex. Of 71 genes, 70 had differential exon-level expression in stroke patients compared to control subjects. Among stroke patients, 24 genes represented by differentially expressed exons were male-specific, six were common between sexes, and two were female-specific. In lacunar stroke, expression of 19 differentially expressed exons representing six genes (ADD1, NINJ2, PCSK9, PEMT, SMARCA4, WNK1) decreased in males and increased in females. Results demonstrate alternative splicing and sexually dimorphic expression of most putative risk genes in stroke patients' blood. Since expression was also often cause-specific, sex, and etiology are factors to consider in stroke treatment trials and genetic association studies as society trends toward more personalized medicine.

Abstract TP327: Major Inflammatory Pathways in Peripheral Blood Associate With Intracerebral Hemorrhage Volume in Human

Objectives: Intracerebral hemorrhage (ICH) volume is a major determinant of functional outcome. The peripheral immune system plays a critical role in post-ICH damage and repair. Identifying potential modulators of ICH volume may guide the search for therapeutic targets. We performed a whole genome expression study in peripheral blood to examine the immune response following ICH with respect to ICH volume.

Methods: Whole-genome RNA expression from 18 ICH subjects (14M/4F) was assessed on Affymetrix HTA 2.0 microarrays. Volumetric measurements were conducted on CT images using AnalyzePro. Multiple Regression including ICH volume while accounting for time from ICH onset to blood draw and interval between scan time and blood draw, was performed. A partial correlation between gene expression and ICH volume was calculated, with FDR p<0.3 (nominal p<0.005) and Pearson Correlation coefficient r>|0.6| considered significant. Pathway analysis and activation/suppression prediction of over-represented pathways was performed (Benjamini-Hochberg p<0.05, pathway activation/suppression Z-score >|2|).

Results: Gene expression levels of 281 genes, including coding (mRNA) and non-coding RNA (i.e. several miRNAs) were associated with ICH volume. Major pathways, such as Neuroinflammation Signaling, were predicted to be activated in subjects with larger ICH volumes. So were Inflammasome Pathway, Toll-like Receptor, Leukocyte Extravasation, NF-kB signaling and FC? Receptor-Mediated Phagocytosis – some of which have been associated with poor clinical outcomes. Scavenger mechanisms, such as FC? Receptor-Mediated Phagocytosis, have been implicated in hematoma resolution. Thrombin Signaling, involved in coagulation, was also activated in subjects with larger ICH volumes. Peroxisome Proliferator-Activated Receptor (PPAR) Signaling was predicted to be suppressed in subjects with larger ICH volumes. PPAR pathway activation may have a neuroprotective effect following experimental ICH.

Conclusions: We provide human data on genes and pathways associated with ICH volume. The results reveal major inflammatory pathways associated with ICH volume, which may be therapeutic targets for human ICH.

Abstract WP416: Specific Transcriptome Response in Neutrophils, Monocytes and Whole Blood in Human Intracerebral Hemorrhage and Ischemic Stroke of Different Etiologies

Understanding transcriptome changes following intracerebral hemorrhage (ICH) and ischemic stroke (IS) of different etiologies, can lead to a better understanding of the molecular and cellular pathways involved in the response to acute brain injury caused by ICH and IS. We characterized the transcriptomic profiles from ICH and different IS etiologies to identify acute molecular changes in isolated monocytes, neutrophils and in whole blood. Peripheral blood was drawn from ICH (6) and IS (33) cases (cardioembolic, large vessel and lacunar) in the first 30 ± 20 hours post-onset of symptoms. We performed whole-genome RNA sequencing of whole blood (WB), and isolated neutrophils and monocytes. Control cases (10) with vascular risk factors (diabetes and/or hypertension and/or hypercholesterolemia) were also included (VRFC). A linear regression model including the interaction diagnosis x sample subtype with p<0.05 and overlap with FDR<0.2, (fold-change>1.2) was used for identifying differentially expressed (DE) genes. Gene ontology and pathway enrichment were performed for investigating the biological context of the DE. We observed specific transcriptional responses for ICH and IS, and within IS etiologies in monocytes, neutrophils and WB. Neutrophils’ response was the strongest with highest number of DE genes in both ICH and IS and its etiologies when compared to VRFC. Most of the changes were cell-type specific and involved immune response and signal transduction pathways. For example, in ICH compared to VRFC, about half of the over-represented pathways were unique to either monocytes or neutrophils. Many pathways over-represented in WB were not over-represented in monocytes or neutrophils, signifying the importance of additional blood cell types in the immune response to ICH and IS. A T-cell receptor gene was DE in WB only, and in opposite directions in ICH and IS when compared to VRFC, thus is a good biomarker candidate. The unique expression changes in neutrophils and monocytes after ICH and IS and its subtypes underscore their involvement in IS and ICH pathophysiology. The large number of unique genes and pathways in whole blood not detected in monocytes or neutrophils signify the contribution of other peripheral blood cell types to the ICH and IS responses.

The intracerebral hemorrhage blood transcriptome in humans differs from the ischemic stroke and vascular risk factor control blood transcriptomes

Understanding how the blood transcriptome of human intracerebral hemorrhage (ICH) differs from ischemic stroke (IS) and matched controls (CTRL) will improve understanding of immune and coagulation pathways in both disorders. This study examined RNA from 99 human whole-blood samples using GeneChip® HTA 2.0 arrays to assess differentially expressed transcripts of alternatively spliced genes between ICH, IS and CTRL. We used a mixed regression model with FDR-corrected p(Dx) < 0.2 and p < 0.005 and |FC| > 1.2 for individual comparisons. For time-dependent analyses, subjects were divided into four time-points: 0(CTRL), <24 h, 24-48 h, >48 h; 489 transcripts were differentially expressed between ICH and CTRL, and 63 between IS and CTRL. ICH had differentially expressed T-cell receptor and CD36 genes, and iNOS, TLR, macrophage, and T-helper pathways. IS had more non-coding RNA. ICH and IS both had angiogenesis, CTLA4 in T lymphocytes, CD28 in T helper cells, NFAT regulation of immune response, and glucocorticoid receptor signaling pathways. Self-organizing maps revealed 4357 transcripts changing expression over time in ICH, and 1136 in IS. Understanding ICH and IS transcriptomes will be useful for biomarker development, treatment and prevention strategies, and for evaluating how well animal models recapitulate human ICH and IS.

Inflammatory, regulatory, and autophagy co-expression modules and hub genes underlie the peripheral immune response to human intracerebral hemorrhage

BACKGROUND

Intracerebral hemorrhage (ICH) has a high morbidity and mortality. The peripheral immune system and cross-talk between peripheral blood and brain have been implicated in the ICH immune response. Thus, we delineated the gene networks associated with human ICH in the peripheral blood transcriptome. We also compared the differentially expressed genes in blood following ICH to a prior human study of perihematomal brain tissue.

METHODS

We performed peripheral blood whole-transcriptome analysis of ICH and matched vascular risk factor control subjects (n = 66). Gene co-expression network analysis identified groups of co-expressed genes (modules) associated with ICH and their most interconnected genes (hubs). Mixed-effects regression identified differentially expressed genes in ICH compared to controls.

RESULTS

Of seven ICH-associated modules, six were enriched with cell-specific genes: one neutrophil module, one neutrophil plus monocyte module, one T cell module, one Natural Killer cell module, and two erythroblast modules. The neutrophil/monocyte modules were enriched in inflammatory/immune pathways; the T cell module in T cell receptor signaling genes; and the Natural Killer cell module in genes regulating alternative splicing, epigenetic, and post-translational modifications. One erythroblast module was enriched in autophagy pathways implicated in experimental ICH, and NRF2 signaling implicated in hematoma clearance. Many hub genes or module members, such as IARS, mTOR, S1PR1, LCK, FYN, SKAP1, ITK, AMBRA1, NLRC4, IL6R, IL17RA, GAB2, MXD1, PIK3CD, NUMB, MAPK14, DDX24, EVL, TDP1, ATG3, WDFY3, GSK3B, STAT3, STX3, CSF3R, PIP4K2A, ANXA3, DGAT2, LRP10, FLOT2, ANK1, CR1, SLC4A1, and DYSF, have been implicated in neuroinflammation, cell death, transcriptional regulation, and some as experimental ICH therapeutic targets. Gene-level analysis revealed 1225 genes (FDR p < 0.05, fold-change > |1.2|) have altered expression in ICH in peripheral blood. There was significant overlap of the 1225 genes with dysregulated genes in human perihematomal brain tissue (p = 7 × 10-3). Overlapping genes were enriched for neutrophil-specific genes (p = 6.4 × 10-08) involved in interleukin, neuroinflammation, apoptosis, and PPAR signaling.

CONCLUSIONS

This study delineates key processes underlying ICH pathophysiology, complements experimental ICH findings, and the hub genes significantly expand the list of novel ICH therapeutic targets. The overlap between blood and brain gene responses underscores the importance of examining blood-brain interactions in human ICH.

Abstract TP421: Immune, Autophagy and Regulatory Co-Expression Modules Underlie the Peripheral Immune Response to Human Intracerebral Hemorrhage

Background: The peripheral immune system is involved in the damage and repair following intracerebral hemorrhage (ICH). Nevertheless, little is known about the transcriptional response following human ICH. Thus, we aimed to define the co-expression networks in the peripheral blood transcriptome of ICH patients compared to controls and identified the genes with highest connectivity which are potential immune response master-regulators.

Methods: We performed transcriptomic analysis on 66 human peripheral whole-blood samples (33 ICH, 33 vascular risk factor controls) using GeneChip® HTA 2.0 arrays. Weighted gene co-expression network analysis (WGCNA) of ICH compared to matched controls identified groups of co-expressed genes (modules) associated with ICH and their most interconnected genes (hubs).

Results: We identified seven modules of co-expressed genes associated with ICH. Six modules were enriched with cell-specific genes including one neutrophil module, one neutrophil plus monocyte module, one T-cell module, one natural killer cell module and two erythroblast modules. The neutrophil / monocyte modules were enriched in inflammatory / immune pathways, while the T-cell module was enriched for T-cell receptor and other T-cell signaling genes. The natural killer cell module was enriched in genes that regulate alternative splicing, and epigenetic regulation. One erythroblast module was enriched in autophagy pathways implicated in experimental ICH, and in NRF2 signaling implicated in hematoma clearance. Many hub and module genes such as MTOR, S1PR1, LCK, FYN, SKAP1, ITK, AMBRA1, NLRC4, IL6R, IL17RA, GAB2, MXD1, PIK3CD, NUMB, MAPK14, DDX24, EVL, TDP1, ATG3, WDFY3, GSK3B, STAT3, STX3, CSF3R, PIP4K2A, ANXA3, DGAT2, LRP10, FLOT2, ANK1, CR1, SLC4A1 and DYSF, have been implicated in neuroinflammation, cell death, transcriptional and translational regulation, and some as experimental ICH therapeutic targets.

Conclusion: This study defined coordinately expressed modules of genes in the peripheral immune response underlying ICH pathophysiology. Some of the results

complement experimental ICH findings. The identified hub genes and their networks may help guide the search for novel therapeutic targets for ICH.

Abstract TP274: HMGB1 is Regulated by Microrna in Patients With Ischemic Stroke

Background: High mobility group box 1 (HMGB1) is a strong inducer of inflammatory pathways in ischemic stroke, and a marker of worse neurological outcome at 1 year. As such HMGB1 may contribute to secondary brain injury and decline in ischemic stroke. We sought to understand the regulation of HMGB1 by microRNA in patients with ischemic stroke and the relationship to stroke severity.

Methods: In 106 ischemic stroke patients and 106 vascular risk factor controls levels of HMGB1 were compared in relationship to levels of microRNA. HMGB1 in plasma was measured by ELISA. microRNA isolated from circulating leukocytes were measured by microarray and confirmed by RT-PCR. HMGB1 regulation by identified microRNA were assessed both in-silico and in-vitro by luciferase assay.

Results: HMGB1 is increased in ischemic stroke patients compared to controls (p<0.05) in a manner that is related to severity of stroke. An increase in admission NIHSS is associated with an increase in HMGB1. The increase in HMGB1 corresponded with a decreased in microRNA let7i. Direct regulation of HMGB1 was shown for microRNA let7i. When HMGB1 levels were adjusted for let7i, the association with NIHSS was no longer present.

Conclusions: HMGB1 is increased in patients with stroke and correlates with stroke severity. microRNA regulate HMGB1 in patients with stroke and may be an important mediator of immune activation associated with secondary ischemic brain injury.