Monocyte, neutrophil, and whole blood transcriptome dynamics following ischemic stroke

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.

White matter injury, cholesterol dysmetabolism, and APP/Abeta dysmetabolism interact to produce Alzheimer's disease (AD) neuropathology: A hypothesis and review

We postulate that myelin injury contributes to cholesterol release from myelin and cholesterol dysmetabolism which contributes to Abeta dysmetabolism, and combined with genetic and AD risk factors, leads to increased Abeta and amyloid plaques. Increased Abeta damages myelin to form a vicious injury cycle. Thus, white matter injury, cholesterol dysmetabolism and Abeta dysmetabolism interact to produce or worsen AD neuropathology. The amyloid cascade is the leading hypothesis for the cause of Alzheimer's disease (AD). The failure of clinical trials based on this hypothesis has raised other possibilities. Even with a possible new success (Lecanemab), it is not clear whether this is a cause or a result of the disease. With the discovery in 1993 that the apolipoprotein E type 4 allele (APOE4) was the major risk factor for sporadic, late-onset AD (LOAD), there has been increasing interest in cholesterol in AD since APOE is a major cholesterol transporter. Recent studies show that cholesterol metabolism is intricately involved with Abeta (Aβ)/amyloid transport and metabolism, with cholesterol down-regulating the Aβ LRP1 transporter and upregulating the Aβ RAGE receptor, both of which would increase brain Aβ. Moreover, manipulating cholesterol transport and metabolism in rodent AD models can ameliorate pathology and cognitive deficits, or worsen them depending upon the manipulation. Though white matter (WM) injury has been noted in AD brain since Alzheimer's initial observations, recent studies have shown abnormal white matter in every AD brain. Moreover, there is age-related WM injury in normal individuals that occurs earlier and is worse with the APOE4 genotype. Moreover, WM injury precedes formation of plaques and tangles in human Familial Alzheimer's disease (FAD) and precedes plaque formation in rodent AD models. Restoring WM in rodent AD models improves cognition without affecting AD pathology. Thus, we postulate that the amyloid cascade, cholesterol dysmetabolism and white matter injury interact to produce and/or worsen AD pathology. We further postulate that the primary initiating event could be related to any of the three, with age a major factor for WM injury, diet and APOE4 and other genes a factor for cholesterol dysmetabolism, and FAD and other genes for Abeta dysmetabolism.

Abstract 103: Isomir Diversity Is Increased In Peripheral Blood Following Ischemic Stroke And May Represent Shifts In Regulation Of Neuroinflammatory Response

MicroRNA (miRNA) expression is altered following ischemic stroke. Advances in RNA sequencing and bioinformatic tools allow study of isomiRs, isoforms of miRNA, which can have altered regulatory actions from canonical parent miRNA due to base modifications within the molecule or on the flanking regions. Here, we characterize isomiRs in the blood of ischemic stroke patients compared to vascular risk factor controls (VRFCs) and elucidate diversity of the post-stroke miRNA environment. Total RNA was isolated from peripheral blood of 47 ischemic stroke patients and 31 VRFCs using PAXgene protocol. Small RNA libraries were prepared using QIAseq miRNA Library Kit and sequenced to 14±2 M 1x75 bp reads. Raw sequence reads were trimmed, de-duplicated, and profiled using isomiRmap , which separates isomiRs from canonical miRNA sequences based on 3’ and 5’ miRNA modifications. Analysis of differentially expressed isomiRs was performed with DESeq2. A total of 74,562 unique isomiRs were identified, the majority expressed at very low level. Filtering for low abundance left 2,133 isomiRs (from 335 canonical miRNA) expressed in all subjects. Of these, 505 isomiRs (from 129 canonical miRNA) were differentially expressed (LFC > |0.5|, p adj < 0.05) between stroke and VRFCs. These isomiRs represent significant elevations in 3’ modifications (68.3% of DE isomiRs), 5’ modifications (20.2%) and non-template additions (34.3%). miRNA previously implicated in stroke had diverse isomiR profiles including cases where all isomiRs within a miRNA group were differentially expressed (e.g. let-7i) and cases where multiple isomiRs were present but not differentially expressed (e.g. miR-363). Four of 28 differentially expressed let-7i isomiRs have changes to the seed region that interacts with mRNA. Thus, miRNA-mRNA interactions distinct from the canonical let-7i seed may exist and play an altered role in stroke pathology and neuroinflammation. Analysis of small noncoding RNA sensitive to base-specific variations detects many differentially expressed isomiRs and highlights the complexity of the post-stroke miRNA environment. Further study of these isomiRs within mRNA regulatory networks will deepen our understanding of stroke related neuroinflammation and neural repair.

Abstract WP229: Hub Genes Drive Specific Gene Expression Changes Seen In Intracerebral Hemorrhage And Ischemic Stroke

Gene expression changes in peripheral leukocytes display distinctive profiles after intracerebral hemorrhage (ICH) and ischemic stroke (IS), differentiating both conditions at the molecular level. The breadth of data produced by high-throughput transcriptomic analyses can identify groups of genes and main gene expression drivers that have meaningful functional associations with the disease. This can help prioritize the investigation of key genes for diagnosis and treatment. Thus, we performed whole transcriptome analyses on ICH and IS samples and constructed gene networks from a genome-wide perspective. RNA-seq was performed on peripheral blood (WB) and isolated monocytes (MON) and neutrophils (NEU) (n=6 ICH, n=33 IS and n=9 vascular risk factors control (VRFC) subjects). Gene expression results were used to construct separate co-expression networks for all datasets analyzed (ICH + VRFCs, and IS + VRFCs, for MON, NEU and WB) using Weighted Gene Co-expression Network Analysis. Modules of genes significantly associated with ICH in the ICH + VRFCs network, and with IS in the IS + VRFCs network, were identified. The most highly interconnected genes in each of these modules were identified, representing hub genes that are potential master regulators. Functional annotation of the modules and hubs were done using gene ontology. From the significantly associated modules for ICH and IS in all sample types analyzed, there was little overlap in genes between diagnoses (≤2% in MON, ≤21 % in NEU and ≤16% in WB), and no overlap of ICH or IS hub genes from MON and NEU. In WB, ≤2% of the hubs were common to ICH and IS. It is plausible that these potential master regulators drive diagnosis-specific gene expression profiles. ICH hubs were associated with RNA splicing and mRNA processing (MON), cell adhesion (NEU) and NF-κβ signaling (WB). IS hubs were associated with cell migration (MON), T cell chemotaxis (NEU) and transcription factor activity (WB). In addition, most hubs in IS MON were noncoding RNA. The gene networks and their respective hub genes provide novel cell-specific pathophysiological insights and could represent potential key pharmacological targets and biomarkers.

Abstract WP230: Human Peripheral Blood Gene Expression Associated With 90day Ischemic Stroke Outcomes

Objective: Identifying the molecular underpinnings associated with long-term functional outcome after ischemic stroke (IS) could guide search for treatments for improved outcome. Thus, we identified early peripheral immune gene expression (GE) responses associated with 90-day IS outcome, as measured by the Barthel Index (BI).

Methods: RNA from 108 samples from three peripheral blood draws (≤3h – before thrombolytic treatment; 5h and 24h - post-treatment) from 36 CLEAR-trial subjects was analyzed on Affymetrix arrays. We performed Analysis of Covariance accounting for treatment (tPA or tPA+eptifibatide), hypercholesterolemia, hypertension, diabetes, age, sex and BI. Genes whose partial correlation with BI was significant ( P <0.005) were identified.

Results: There were 206, 865, and 209 genes that significantly correlated with 90-day BI at ≤3h, 5h and 24h post ictus , respectively. The gene lists at all three time-points were enriched in B-cell specific genes (hypergeometric probability p<0.05), while the 5h gene list was also enriched in neutrophil-specific genes, and the 24h gene list was also enriched in monocyte-specific genes. B Cell Receptor Signaling pathway was predicted activated in subjects with better 90-day outcome at the ≤3h time-point, while ICOS-ICOSL Signaling in T Helper Cells and Role of NFAT in Regulation of the Immune Response were predicted activated at the 24h time-point.Immune-related pathways were enriched at three time-points including B cell-related, IL-7, and T cell signaling pathways. Apoptosis was suppressed in patients with better 90-day outcome at 3h and 24h post ictus . Among the genes associated with the 90-day BI were genes important for stroke and repair after stroke, such as KCNG1 , Potassium voltage-gated channel subfamily G member 1, which like other potassium channels could modulate stroke outcome. KCNG1 expression was positively correlated with 90-day BI at ≤3h and 5h. TERML4 , implicated in inflammatory response and human coronary arterial calcification had expression that positively correlated with BI at all three time-points.

Conclusion: The findings expand our understanding of the early molecular biology associated with long-term stroke outcome and may serve as potential targets to improve outcome.

Abstract TP210: Small Extracellular Vesicle-derived Micrornas Differentiate Ischemic Stroke And Intracerebral Hemorrhage: A Pilot Study

Investigating the short and long-term signaling mechanisms via small extracellular vesicles (sEVs) in peripheral blood following human Ischemic Stroke (IS) and Intracerebral Hemorrhage (ICH) is of great interest. The sEV’s cargo can induce distant responses which can be used to derive potential novel therapeutic targets and biomarkers to differentiate the two brain pathologies. Thus, we sequenced the miRNA cargo derived from peripheral blood sEVs in IS (n=3), ICH (n=3), and Vascular Risk Factor-matched Control (VRFC; n=3) subjects. Subjects were divided into contrast groups (IS vs VRFC, ICH vs VRFC, ICH vs IS), and log2 transformed expression underwent Kruskal-Wallis tests to identify differentially expressed (DE; p<0.05) miRNAs. We found 55 DE miRNAs in IS vs VRFC, 38 in ICH vs VRFC, and 45 in ICH vs IS ( Fig. 1A ). The combination of these miRNAs differentiated the three groups on Principal Components Analysis ( Fig. 1B ). IS associated miRNA included miR-30a, miR-30b, and miR-144. miR-30a is involved in hematopoietic stem cell self-renewal and can impair B cell differentiation. miR-30b may be an immune suppressor via Notch1. In male mice, miR-144 is protective against atherosclerosis. ICH associated miRNA included miR-195, miR-1-3p, and miR-20b-5p. miR-195 can inhibit the pro-inflammatory roles of macrophages. miR-1-3p is involved in cardiomyocyte development, can target TLR1 (Toll-Like Receptor 1), and may regulate autophagy. miR-20b-5p reduces Amyloid Precursor Protein (APP) mRNA and protein levels; vascular accumulation of APP is one cause of Lobar ICH. We show differential expression of sEV-derived miRNAs in peripheral blood of human IS and ICH patients that are involved in relevant signaling processes. sEV cargo profiles pose a largely underexplored intercellular signaling mechanism in IS and ICH with the potential to better characterize long distance signaling from injured brain to peripheral blood leukocytes in these brain disorders.

Early peripheral blood gene expression associated with good and poor 90-day ischemic stroke outcomes

BACKGROUND

This study identified early immune gene responses in peripheral blood associated with 90-day ischemic stroke (IS) outcomes.

METHODS

Peripheral blood samples from the CLEAR trial IS patients at ≤ 3 h, 5 h, and 24 h after stroke were compared to vascular risk factor matched controls. Whole-transcriptome analyses identified genes and networks associated with 90-day IS outcome assessed using the modified Rankin Scale (mRS) and the NIH Stroke Scale (NIHSS).

RESULTS

The expression of 467, 526, and 571 genes measured at ≤ 3, 5 and 24 h after IS, respectively, were associated with poor 90-day mRS outcome (mRS ≥ 3), while 49, 100 and 35 genes at ≤ 3, 5 and 24 h after IS were associated with good mRS 90-day outcome (mRS ≤ 2). Poor outcomes were associated with up-regulated genes or pathways such as IL-6, IL-7, IL-1, STAT3, S100A12, acute phase response, P38/MAPK, FGF, TGFA, MMP9, NF-kB, Toll-like receptor, iNOS, and PI3K/AKT. There were 94 probe sets shared for poor outcomes vs. controls at all three time-points that correlated with 90-day mRS; 13 probe sets were shared for good outcomes vs. controls at all three time-points; and 46 probe sets were shared for poor vs. good outcomes at all three time-points that correlated with 90-day mRS. Weighted Gene Co-Expression Network Analysis (WGCNA) revealed modules significantly associated with 90-day outcome for mRS and NIHSS. Poor outcome modules were enriched with up-regulated neutrophil genes and with down-regulated T cell, B cell and monocyte-specific genes; and good outcome modules were associated with erythroblasts and megakaryocytes. Finally, genes identified by genome-wide association studies (GWAS) to contain significant stroke risk loci or loci associated with stroke outcome including ATP2B, GRK5, SH3PXD2A, CENPQ, HOXC4, HDAC9, BNC2, PTPN11, PIK3CG, CDK6, and PDE4DIP were significantly differentially expressed as a function of stroke outcome in the current study.

CONCLUSIONS

This study suggests the immune response after stroke may impact functional outcomes and that some of the early post-stroke gene expression markers associated with outcome could be useful for predicting outcomes and could be targets for improving outcomes.

Gene expression changes implicate specific peripheral immune responses to Deep and Lobar Intracerebral Hemorrhages in humans

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.

Sustained ICP Elevation Is a Driver of Spatial Memory Deficits After Intraventricular Hemorrhage and Leads to Activation of Distinct Microglial Signaling Pathways

The mechanisms of cognitive decline after intraventricular hemorrhage (IVH) in some patients continue to be poorly understood. Multiple rodent models of intraventricular or subarachnoid hemorrhage have only shown mild or even no cognitive impairment on subsequent behavioral testing. In this study, we show that intraventricular hemorrhage only leads to a significant spatial memory deficit in the Morris water maze if it occurs in the setting of an elevated intracranial pressure (ICP). Histopathological analysis of these IVH + ICP animals did not show evidence of neuronal degeneration in the hippocampal formation after 2 weeks but instead showed significant microglial activation measured by lacunarity and fractal dimensions. RNA sequencing of the hippocampus showed distinct enrichment of genes in the IVH + ICP group but not in IVH alone having activated microglial signaling pathways. The most significantly activated signaling pathway was the classical complement pathway, which is used by microglia to remove synapses, followed by activation of the Fc receptor and DAP12 pathways. Thus, our study lays the groundwork for identifying signaling pathways that could be targeted to ameliorate behavioral deficits after IVH.

Multi-ancestry GWAS reveals excitotoxicity associated with outcome after ischaemic stroke

During the first hours after stroke onset, neurological deficits can be highly unstable: some patients rapidly improve, while others deteriorate. This early neurological instability has a major impact on long-term outcome. Here, we aimed to determine the genetic architecture of early neurological instability measured by the difference between the National Institutes of Health Stroke Scale (NIHSS) within 6 h of stroke onset and NIHSS at 24 h. A total of 5876 individuals from seven countries (Spain, Finland, Poland, USA, Costa Rica, Mexico and Korea) were studied using a multi-ancestry meta-analyses. We found that 8.7% of NIHSS at 24 h of variance was explained by common genetic variations, and also that early neurological instability has a different genetic architecture from that of stroke risk. Eight loci (1p21.1, 1q42.2, 2p25.1, 2q31.2, 2q33.3, 5q33.2, 7p21.2 and 13q31.1) were genome-wide significant and explained 1.8% of the variability suggesting that additional variants influence early change in neurological deficits. We used functional genomics and bioinformatic annotation to identify the genes driving the association from each locus. Expression quantitative trait loci mapping and summary data-based Mendelian randomization indicate that ADAM23 (log Bayes factor = 5.41) was driving the association for 2q33.3. Gene-based analyses suggested that GRIA1 (log Bayes factor = 5.19), which is predominantly expressed in the brain, is the gene driving the association for the 5q33.2 locus. These analyses also nominated GNPAT (log Bayes factor = 7.64) ABCB5 (log Bayes factor = 5.97) for the 1p21.1 and 7p21.1 loci. Human brain single-nuclei RNA-sequencing indicates that the gene expression of ADAM23 and GRIA1 is enriched in neurons. ADAM23, a presynaptic protein and GRIA1, a protein subunit of the AMPA receptor, are part of a synaptic protein complex that modulates neuronal excitability. These data provide the first genetic evidence in humans that excitotoxicity may contribute to early neurological instability after acute ischaemic stroke.

Abstract WP251: Long Term Outcome Prediction After Ischemic Stroke Using Gene Expression

Objective: Prediction of the long-term outcome in Ischemic Stroke (IS) patients can have a significant impact on design of clinical trials and on patients’ care. We studied gene expression (GE) as a novel biomarker to provide an accurate prediction of 90-day outcome in IS patients.

Methods: RNA from 72 samples from 2 peripheral blood draws (at ≤3 and 24 hrs post IS onset) was analyzed on Affymetrix U133 Plus 2.0 microarrays. These represented samples from 36 CLEAR trial IS patients that had blood drawn within 3 hrs of stroke onset and were then treated with tPA with or without eptifibatide. The samples were split into derivation (n=25) and validation (n=11) sets. We identified the differential GE in blood at 24 hrs and the difference in GE between 24 hrs and 3 hrs post IS that was associated with 90-day post stroke outcome using the model: GE = μ + NIHSS_24hr+mRS_90day+ ε. Good outcome was defined as mRS 0-2; Poor - as mRS 3-5. Logistic regression was used to derive a biomarker classifier.

Results: Using 24 hrs GE, we identified 14 probesets (12 genes) with the highest discriminative power for predicting outcome. The model achieved recall (the probability of correctly identifying the patients with Good outcome) of 0.88 and specificity (the probability of correctly identifying the patients with Poor outcome) of 0.67 in the validation set (The AUC-ROC = 0.88). The biomarker genes were enriched in immune responses such as IL and cytokine signaling. Among the predictors were genes important for stroke and repair after stroke (e.g., MACC1 , GDF11 ). MACC1 has been considered as a potential treatment target for IS with a protective role in hypoxia-induced human brain microvascular endothelial cells. GDF11 plays a role in brain repair after IS. We also determined how the change of GE from 3 hrs to 24 hrs would predict the 90-day outcome. A panel of ten genes was able to predict outcome in the validation set (recall= 1, specificity = 0.67, AUC-ROC=0.88). These included AVPR1A , which mediates platelet aggregation and release of coagulation factors and exacerbates brain inflammatory response to injury.

Conclusion: This pilot study suggests gene expression can be used to predict stroke outcome. Some of the genes may serve as potential therapeutic targets.

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

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>

Abstract WP133: Sex Differences In The Human Intracerebral Hemorrhage Peripheral Blood Transcriptome Implicate Differential Immune And Inflammatory Responses

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.

Lipopolysaccharide, Identified Using an Antibody and by PAS Staining, Is Associated With Corpora amylacea and White Matter Injury in Alzheimer's Disease and Aging Brain

Corpora amylacea (CA) increase in number and size with aging. Their origins and functions remain unknown. Previously, we found that Alzheimer's disease (AD) brains have more CA in the periventricular white matter (PVWM) compared to aging controls. In addition, CA is associated with neurodegeneration as indicated by colocalization of degraded myelin basic protein (dMBP) with periodic acid-Schiff (PAS), a CA marker. We also found that bacterial lipopolysaccharide is present in aging brains, with more LPS in AD compared with controls. Periodic acid-Schiff staining is used to identify CA by virtue of their high polysaccharide content. Despite the growing knowledge of CA as a contributor to AD pathology, the molecules that contribute to the polysaccharides in CA are not known. Notably, lipopolysaccharides (LPS) are important cell-surface polysaccharides found in all Gram-negative bacteria. However, it is unknown whether PAS could detect LPS, whether the LPS found in aging brains contribute to the polysaccharide found in CA, and whether LPS associate with myelin injury. In this study, we found that aging brains had a myelin deficit zone (MDZ) adjacent to the ventricles in PVWM. The MDZ contained vesicles, most of which were CA. LPS and dMBP levels were higher in AD than in control brains. LPS was colocalized with dMBP in the vesicles/CA, linking white matter injury with a bacterial pro-inflammatory molecule. The vesicles also contained oxidized fibers, C-reactive protein, NG2, and GALC, markers of oligodendrocyte precursor cells (OPCs) and oligodendrocyte cells (OLs), respectively. The vesicles/CA were surrounded by dense astrocyte processes in control and AD brains. LPS was co-localized with CA by double staining of PAS with LPS in aging brains. The relationship of LPS with PAS staining was confirmed by PAS staining of purified LPS on nitrocellulose membranes. These findings reveal that LPS is one of the polysaccharides found in CA which can be stained with PAS. In addition, vesicles/CA are associated with oxidized and damaged myelin. The LPS in these vesicles/CA may have contributed to this oxidative myelin damage and may have contributed to oxidative stress to OPCs and OLs which could impair the ability to repair damaged myelin in AD and control brains.

mRNA Expression Profiles from Whole Blood Associated with Vasospasm in Patients with Subarachnoid Hemorrhage

Background

Though there are many biomarker studies of plasma and serum in patients with aneurysmal subarachnoid hemorrhage (SAH), few have examined blood cells that might contribute to vasospasm. In this study, we evaluated inflammatory and prothrombotic pathways by examining mRNA expression in whole blood of SAH patients with and without vasospasm.

Methods

Adult SAH patients with vasospasm (n = 29) and without vasospasm (n = 21) were matched for sex, race/ethnicity, and aneurysm treatment method. Diagnosis of vasospasm was made by angiography. mRNA expression was measured by Affymetrix Human Exon 1.0 ST Arrays. SAH patients with vasospasm were compared to those without vasospasm by ANCOVA to identify differential gene, exon, and alternatively spliced transcript expression. Analyses were adjusted for age, batch, and time of blood draw after SAH.

Results

At the gene level, there were 259 differentially expressed genes between SAH patients with vasospasm compared to patients without (false discovery rate < 0.05, |fold change| ≥ 1.2). At the exon level, 1210 exons representing 1093 genes were differentially regulated between the two groups (P < 0.005, ≥ 1.2 |fold change|). Principal components analysis segregated SAH patients with and without vasospasm. Signaling pathways for the 1093 vasospasm-related genes included adrenergic, P2Y, ET-1, NO, sildenafil, renin–angiotensin, thrombin, CCR3, CXCR4, MIF, fMLP, PKA, PKC, CRH, PPARα/RXRα, and calcium. Genes predicted to be alternatively spliced included IL23A, RSU1, PAQR6, and TRIP6.

Conclusions

This is the first study to demonstrate that mRNA expression in whole blood distinguishes SAH patients with vasospasm from those without vasospasm and supports a role of coagulation and immune systems in vasospasm.

Electronic supplementary material

The online version of this article (10.1007/s12028-019-00861-x) contains supplementary material, which is available to authorized users.

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.

Bacterial lipopolysaccharide is associated with stroke

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.

Abstract P787: Sexually Dimorphic Gene Expression Molecular Correlates of Improvement in Human Ischemic Stroke

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.

Abstract P646: The Aging Immune Transcriptome is Linked to Ischemic Stroke Outcome

Background: Advancing age is associated with changes to the immune system, which affect stroke outcome. We previously demonstrated an age-associated alteration in leukocyte gene expression in patients with ischemic stroke. The aim of this study is to validate these findings in an independent stroke cohort and assess the relationship to stroke outcome.

Methods: Genes associated with age were identified in a cohort of 57 patients with acute ischemic stroke. Peripheral blood RNA was measured using whole genome microarrays and genes associated with advancing age identified (FDR-corrected p < 0.05, partial correlation coefficient r > |0.3|); age-associated gene expression differences in patients with poor 90-day outcome (mRS < 2) were also compared. Genes were functionally characterized by pathway and enrichment analysis and verified against age-associated genes from two additional stroke cohorts containing a total of 173 patients.

Results: There were 536 genes associated with age in the new stroke cohort, of which 286 decreased and 253 increased with age. Thirty-nine (39) of the age-associated genes were present in previous stroke cohorts analyzed, including a decrease in CCR6, CXCR5, BLNK and NT5E. A decrease in CXCR5 and CD79B was also identified in patients with poor outcome. Pathways and enriched terms relating to the humoral adaptive system immune system, including B-cell and lymphocyte activation, were among those represented in age-associated genes.

Conclusions: Age-related changes in leukocyte gene expression were validated in an independent cohort of patients with ischemic stroke. Verified changes include alterations to the humoral immune system and a relationship to stroke outcome. Further investigation of the aging immune system in stroke is warranted.

Abstract P745: Whole Blood MicroRNA and Their Target Messenger RNA Reveal Distinct Transcriptional Changes in Ischemic Stroke Patients With and Without Comorbid Cancer

Introduction: One-tenth of patients with stroke have cancer. We previously identified mRNA profiles differentiating patients with stroke and cancer, stroke only, and cancer only. In this study, we investigated mRNA and microRNA (miRNA) transcriptomes to identify potential miRNA regulators that underlie the observed mRNA changes.

Methods: We prospectively enrolled 4 groups of subjects at 3 centers from 2009-2020. This analysis included 41 subjects with ischemic stroke plus cancer, 42 subjects with ischemic stroke only, 28 subjects with cancer only, and 30 vascular risk factor controls. Stroke-only and cancer-only subjects were matched to stroke-plus-cancer subjects by age, sex, and cancer type. We performed miRNA and mRNA sequencing on blood drawn 72-120 hours after stroke. ANCOVA estimated differential expression of miRNA and mRNA between groups (FDR p<0.05, |fold-change|>1.2). Analyses were adjusted for time from stroke onset, sex, age, vascular risk factors and batch.

Results: We identified differential expression in 36 miRNA and 264 corresponding mRNA targets between the stroke-plus-cancer and stroke-only groups after accounting for cancer-only expression (Fig 1). Immune and coagulation pathways, including complement, platelet glycoproteins, TGF-β, and mTOR signaling, were overrepresented in stroke-plus-cancer vs stroke-only subjects. T cell, B cell and platelet precursor-specific genes were also overrepresented in stroke-plus-cancer subjects. When compared to other groups, stroke-plus-cancer subjects had 230 unique mRNA encoding for transcriptional regulators, including those involving splicing, epigenetics, and mediator complex genes bridging transcription factors and RNA transcriptional machinery.

Conclusion: Patients with stroke and cancer had distinct signatures of miRNA and target mRNA compared to stroke patients without cancer, supporting the hypothesis that cancer-related stroke is a unique subgroup of ischemic stroke.

Abstract P576: Plasma Bacterial Lipopolysaccharide Associates With Carotid Atherosclerosis, a Cause of Large Vessel Stroke

Introduction: Inflammation and infection are associated with cerebrovascular diseases including stroke due to carotid atherosclerotic plaques. C-reactive protein (CRP), an acute-phase protein, is upregulated in the plasma of patients with carotid atherosclerotic plaques. However, little is known about whether bacterial molecules trigger inflammation or play a role in patients with carotid atherosclerotic plaques. Recently, it has been recognized that inflammation associated with atherosclerosis and morbidity and mortality in cardiovascular diseases may be due to lipopolysaccharide (LPS) that is found in the outer wall of all Gram-negative bacteria. These findings prompted this study to explore whether plasma levels of LPS and LPS-binding protein (LBP) are elevated and correlated with CRP levels in patients with asymptomatic carotid plaques (ACP). We also compared LBP levels in patients with ACP to large vessel (LV) strokes due to carotid plaques and to matched controls.

Methods: Patients (n = 30) with ACP, LV stroke due to carotid atherosclerosis and age-, sex- matched healthy controls gave consent and had their blood drawn. Plasma was processed for LPS, LBP and CRP detection using separate ELISA for each.

Results: Plasma LBP level in ACP (22.7 ± 2.92 μg/ml) was similar to LV stroke (21.6 ± 1.56 μg/ml, p = 0.74, ACP vs LV) but greater than controls (13.6 ± 1.43 μg/ml, p = 0.011, ACP vs controls). In ACP patients, plasma LPS level (159.5 ± 30.5 μg/ml) was greater than controls (42.6 ± 11.7 μg/ml, p = 0.001); plasma CRP levels (20.2 ± 6.2 μg/ml) was higher than controls (5.3 ± 2.1 μg/ml, p = 0.011). There was a positive correlation between LPS levels and LBP levels (r = 0.86, p < 0.00001), LPS levels and CRP levels (r = 0.82, p = 0.00001), and LBP levels and CRP levels (r = 0.89, p < 0.00001) in ACP cases.

Conclusions: Plasma LPS, LBP and CRP associate with asymptomatic carotid plaques suggesting a pro-inflammatory state exists in patients with asymptomatic carotid plaques, a cause of large vessel stroke. LPS is postulated to directly upregulate both CRP and LBP. Elevated LBP in large vessel stroke patients suggests a Gram-negative bacteria associated post-stroke inflammatory state.

Aging Immune System in Acute Ischemic Stroke: A Transcriptomic Analysis

[Figure: see text].

Abstract P744: Gene Transcript Clusters Distinguish Time-Dependent Expression Patterns in Monocytes, Neutrophils and Whole Blood After Ischemic Stroke Injury

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.

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.

Genetic variation contributes to gene expression response in ischemic stroke: an eQTL study

Objective

Single nucleotide polymorphisms (SNPs) contribute to complex disorders such as ischemic stroke (IS). Since SNPs could affect IS by altering gene expression, we studied the association of common SNPs with changes in mRNA expression (i.e. expression quantitative trait loci; eQTL) in blood after IS.

Methods

RNA and DNA were isolated from 137 patients with acute IS and 138 vascular risk factor controls (VRFC). Gene expression was measured using Affymetrix HTA 2.0 microarrays and SNP variants were assessed with Axiom Biobank Genotyping microarrays. A linear model with a genotype (SNP) × diagnosis (IS and VRFC) interaction term was fit for each SNP‐gene pair.

Results

The eQTL interaction analysis revealed significant genotype × diagnosis interaction for four SNP‐gene pairs as cis‐eQTL and 70 SNP‐gene pairs as trans‐eQTL. Cis‐eQTL involved in the inflammatory response to IS included rs56348411 which correlated with neurogranin expression (NRGN), rs78046578 which correlated with CXCL10 expression, rs975903 which correlated with SMAD4 expression, and rs62299879 which correlated with CD38 expression. These four genes are important in regulating inflammatory response and BBB stabilization. SNP rs148791848 was a strong trans‐eQTL for anosmin‐1 (ANOS1) which is involved in neural cell adhesion and axonal migration and may be important after stroke.

Interpretation

This study highlights the contribution of genetic variation to regulating gene expression following IS. Specific inflammatory response to stroke is at least partially influenced by genetic variation. This has implications for progressing toward personalized treatment strategies. Additional research is required to investigate these genes as therapeutic targets.

MicroRNA and their target mRNAs change expression in whole blood of patients after intracerebral hemorrhage

Previous studies showed changes in mRNA levels in whole blood of rats and humans, and in miRNA in whole blood of rats following intracerebral hemorrhage (ICH). Thus, this study assessed miRNA and their putative mRNA targets in whole blood of humans following ICH. Whole transcriptome profiling identified altered miRNA and mRNA levels in ICH patients compared to matched controls. Target mRNAs of the differentially expressed miRNAs were identified, and functional analysis of the miRNA-mRNA targets was performed. Twenty-nine miRNAs (22 down, 7 up) and 250 target mRNAs (136 up, 114 down), and 7 small nucleolar RNA changed expression after ICH compared to controls (FDR < 0.05, and fold change ≥ |1.2|). These included Let7i, miR-146a-5p, miR210-5p, miR-93-5p, miR-221, miR-874, miR-17-3p, miR-378a-5p, miR-532-5p, mir-4707, miR-4450, mir-1183, Let-7d-3p, miR-3937, miR-4288, miR-4741, miR-92a-1-3p, miR-4514, mir-4658, mir-3689d-1, miR-4760-3p, and mir-3183. Pathway analysis showed regulated miRNAs/mRNAs were associated with toll-like receptor, natural killer cell, focal adhesion, TGF-β, phagosome, JAK-STAT, cytokine-cytokine receptor, chemokine, apoptosis, vascular smooth muscle, and RNA degradation signaling. Many of these pathways have been implicated in ICH. The differentially expressed miRNA and their putative mRNA targets and associated pathways may provide diagnostic biomarkers as well as point to therapeutic targets for ICH treatments in humans.

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.

Abstract 69: Trans-eQTL Analysis of Blood After Ischemic Stroke Reveals X-Linked SNP-Gene Relationships

Objective: Single nucleotide polymorphism (SNP) is one of the most common types of genetic variation and likely has a contributing role in ischemic stroke (IS). The influence of SNPs on changes of gene expression in blood after IS remains largely unknown. Thus, we evaluated the association of genetic variants with changes in mRNA expression levels (i.e. expression quantitative trait loci;eQTL) in blood after IS.

Methods: RNA and DNA were isolated from blood samples collected from 137 IS patients and 138 vascular risk factor controls (VRFC). Gene expression of protein-coding transcripts was quantified by Affymetrix HTA 2.0 microarrays and SNP variants assessed by Axiom Biobank Genotyping microarrays. A linear model with a genotype (SNP)х diagnosis (IS or VRFC) interaction was fit for each SNP-gene pair to identify novel IS diagnosis-dependent eQTL.

Results: Our trans- eQTL interaction analysis found 70 significant SNP-gene pairs (FDR<0.01). Our observations indicated that 24 mRNAs were associated with significant genotype х diagnosis interaction. Among these genes, two X-linked genes ANOS1 and POF1B were found. Expression of ANOS1 was significantly associated with SNPs rs148791848 and rs149957475. The SNP, rs950391, was significantly associated with expression of POF1B, a gene previously shown as sexually dimorphic in stroke. Interestingly, some of the eQTL SNPs affected multiple genes in trans that are known to be altered after IS. For example, X-linked SNP rs950391, altered expression of ABCA6, CLNK, EML6, POF1B, and WNT16.

Conclusions: To our knowledge, this is the first whole-genome study to examine the effect of genotype х diagnosis on gene expression of blood after IS. Some SNP-gene pairs are X-linked and may account for aspects of sexual dimorphism in stroke. Our findings facilitate better understanding of trans effects of genetic variation on gene expression in stroke.

Cancer-Related Ischemic Stroke Has a Distinct Blood mRNA Expression Profile

Background and Purpose- Comorbid cancer is common in patients with acute ischemic stroke (AIS). As blood mRNA profiles can distinguish AIS mechanisms, we hypothesized that cancer-related AIS would have a distinctive gene expression profile. Methods- We evaluated 4 groups of 10 subjects prospectively enrolled at 3 centers from 2009 to 2018. This included the group of interest with active solid tumor cancer and AIS and 3 control groups with active cancer only, AIS only, or vascular risk factors only. Subjects in the AIS-only and cancer-only groups were matched to subjects in the cancer-stroke group by age, sex, and cancer type (if applicable). Subjects in the vascular risk factor group were matched to subjects in the cancer-stroke and stroke-only groups by age, sex, and vascular risk factors. Blood was drawn 72 to 120 hours after stroke. Total RNA was processed using 3' mRNA sequencing. ANOVA and Fisher least significant difference contrast methods were used to estimate differential gene expression between groups. Results- In the cancer-stroke group, 50% of strokes were cryptogenic. All groups had differentially expressed genes that could distinguish among them. Comparing the cancer-stroke group to the stroke-only group and after accounting for cancer-only genes, 438 genes were differentially expressed, including upregulation of multiple genes/pathways implicated in autophagy signaling, immunity/inflammation, and gene regulation, including IL (interleukin)-1, interferon, relaxin, mammalian target of rapamycin signaling, SQSTMI1 (sequestosome-1), and CREB1 (cAMP response element binding protein-1). Conclusions- This study provides evidence for a distinctive molecular signature in blood mRNA expression profiles of patients with cancer-related AIS. Future studies should evaluate whether blood mRNA can predict detection of occult cancer in patients with AIS. Clinical Trial Registration- URL: https://clinicaltrials.gov. Unique identifier: NCT02604667.

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.

Smoking affects gene expression in blood of patients with ischemic stroke

OBJECTIVE

Though cigarette smoking (CS) is a well-known risk factor for ischemic stroke (IS), there is no data on how CS affects the blood transcriptome in IS patients.

METHODS

We recruited IS-current smokers (IS-SM), IS-never smokers (IS-NSM), control-smokers (C-SM), and control-never smokers (C-NSM). mRNA expression was assessed on HTA-2.0 microarrays and unique as well as commonly expressed genes identified for IS-SM versus IS-NSM and C-SM versus C-NSM.

RESULTS

One hundred and fifty-eight genes were differentially expressed in IS-SM versus IS-NSM; 100 genes were differentially expressed in C-SM versus C-NSM; and 10 genes were common to both IS-SM and C-SM (P < 0.01; |fold change| ≥ 1.2). Functional pathway analysis showed the 158 IS-SM-regulated genes were associated with T-cell receptor, cytokine-cytokine receptor, chemokine, adipocytokine, tight junction, Jak-STAT, ubiquitin-mediated proteolysis, and adherens junction signaling. IS-SM showed more altered genes and functional networks than C-SM.

INTERPRETATION

We propose some of the 10 genes that are elevated in both IS-SM and C-SM (GRP15, LRRN3, CLDND1, ICOS, GCNT4, VPS13A, DAP3, SNORA54, HIST1H1D, and SCARNA6) might contribute to increased risk of stroke in current smokers, and some genes expressed by blood leukocytes and platelets after stroke in smokers might contribute to worse stroke outcomes that occur in smokers.

Cleaved β-Actin May Contribute to DNA Fragmentation Following Very Brief Focal Cerebral Ischemia

Our previous study demonstrated caspase independent DNA fragmentation after very brief cerebral ischemia, the mechanism of which was unclear. In this study, we explore whether actin is cleaved following focal cerebral ischemia, and whether these structural changes of actin might modulate DNA fragmentation observed following focal ischemia. Results showed that a cleaved β-actin fragment was identified in brains of rats 24 hours following 10-minute and 2-hour focal ischemia. Though granzyme B and caspase-3 cleaved β-actin in vitro, the fragment size of β-actin cleaved by granzyme B was the same as those found after 10-minute and 2-hour focal ischemia. This was consistent with increases of granzyme B activity after 10-minute and 2-hour ischemia compared with controls. Cerebral extracts from 10-minute and 2-hour ischemic brains degraded DNA in vitro. Adding intact β-actin to these samples completely abolished DNA degradation from the 10-minute ischemia group but not from the 2-hour ischemia group. We concluded that β-actin is likely cleaved by granzyme B by 24 hours following 10-minute and 2-hour focal cerebral ischemia. Intact β-actin inhibits DNase, and cleavage of β-actin activates DNase, which leads to DNA fragmentation observed in the brain following very brief focal ischemia.

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 46: RNA Expression Profiles From Whole Blood Associated With Vasospasm in Patients With Subarachnoid Hemorrhage

Background and Purpose: Though there are many biomarker studies of plasma and serum in patients with aneurysmal subarachnoid hemorrhage (SAH), few have examined cells in blood that might contribute to vasospasm and delayed ischemic neurological deficits (DIND). In this study we evaluate inflammatory and prothrombotic pathways by examining RNA expression in whole blood (including leukocytes, platelets) of SAH patients with vasospasm compared to those without vasospasm.

Methods: Adult patients with aneurysmal SAH admitted to UCSF from 2003 to 2010 were enrolled. Patients with vasospasm (n=29) and without vasospasm (n=21) were matched for sex, race/ethnicity and aneurysm treatment method. Diagnosis of vasospasm was made by angiography. RNA expression was measured by Affymetrix Human Exon 1.0 ST Arrays. SAH patients with vasospasm were compared to those without vasospasm by ANCOVA to identify differential gene expression, exon expression and alternatively spliced transcript expression. Analyses were adjusted for age, batch, and days after SAH.

Results: At the gene level there were 276 differentially expressed between SAH with vasospasm compared to patients without (P<0.05,

Abstract TMP117: Relationship of Cerebral White Matter Hyperintensity Progression and Leukocyte Activation

Background: Cerebral white matter hyperintensities (WMH) are an important contributor to injury in the aging brain. Progression in WMH volume is associated with cognitive decline and gait impairment. Understanding the factors associated with WMH progression may provide insight to pathogenesis and identify novel treatment targets to improve cognitive health.

Methods: In 60 patients assessed for a cognitive complaint, an MRI brain was obtained at baseline and then repeated at a median of 5.9 years (IQR 3.5-8.2 years) from start of study. WMH was measured by semi-automated segmentation protocol and rate of progression per year determined. A blood sample was acquired at baseline in a PAXgene tube and used to measure whole genome RNA expression by RNA sequencing. The relationship between rate of WMH progression over time and leukocyte RNA expression was analyzed.

Results: The mean age was 76.1 (SD 8.3) years and 61% of participants were female. The median rate of WMH progression over 5.8 years was 1.3 mm 3 /year (IQR 0.27-3.3mm 3 /year). The median WMH volume was 5.5 mL (IQR 2.2-14.2). Patients in the quartile with the highest rate of WMH progression had increased leukocyte expression of genes involved in pattern recognition receptors (INFK, NLRP3, OAS1, TGFB1), interferon signaling (IFI6, IFIT1, IFITM3), and leukocyte extravasation (CLDN5, ICAM1, ITGB3, NCF1, TIMP2). A gene model could predict patients likely to experience a high rate of WMH progression over time with >80% accuracy. This remained significant when adjusted for factors associated with WMH progression.

Conclusions: Progression of WMH over time is associated with increased expression of genes involved in leukocyte extravasation, pattern recognition receptor activation and interferon signaling. Patients at risk for WMH progression may be identified by leukocyte RNA expression. Further studies are needed to evaluate the role of peripheral inflammation in relation to rate of WMH progression and contribution to cognitive decline.

Abstract WP535: Differential Immune Activation in Patients With Acute Ischemic Stroke and Admission Blood Pressure Greater Than 185/110 mm Hg

Background: A blood pressure > 185/110 mm Hg is associated with increased risk of tPA related hemorrhagic transformation (HT). Stroke guidelines recommend blood pressure >185/110 mm Hg be lowered before tPA treatment. How high blood pressure increases blood-brain barrier disruption and risk of hemorrhagic transformation remains poorly understood. We evaluated peripheral leukocyte activation in stroke patients in relation to elevated blood pressure and their potential contribution to blood-brain barrier disruption.

Methods: Blood samples from acute ischemic stroke patients were collected within 3 hours of stroke onset, prior to treatment with thrombolytic. Patients were grouped by BP >185/110 mm Hg (n=19) and BP <185/110 mm Hg (n=46). Total blood RNA was assessed by whole genome microarray and differential gene expression analyzed by ANCOVA. Functional analysis of identified genes was performed. Correlation analysis was conducted to identify genes correlated with systolic blood pressure.

Results: Strokes with admission BP >185/110 mm Hg had 231 genes differentially expressed compared to strokes with BP <185/110 mm Hg (p <0.05, fold change ≥|1.2|). Key genes and pathways associated with BP>185/110 mm Hg included downregulation of caveolin-1 and upregulation of matrix metalloproteinases (MMPs). Several of these genes, including MMP-21, linearly correlated with increasing systolic blood pressure (r=0.25, p = 0.02).

Conclusions: A blood pressure >185/110 mm Hg is associated with differential immune activation in patients with acute ischemic stroke, including caveolin-1 and matrix metalloproteinases. These differences may contribute to blood-brain barrier disruption and risk of hemorrhagic transformation in acute stroke patients with blood pressure >185/110 mm Hg. Whether modulating immune activation could reduce blood-brain barrier disruption and risk of HT requires further study.

MicroRNA-122 Mimic Improves Stroke Outcomes and Indirectly Inhibits NOS2 After Middle Cerebral Artery Occlusion in Rats

Aim: Our previous study demonstrated miR-122 mimic decreased NOS2 expression in blood leucocytes and improved stroke outcomes when given immediately after middle cerebral artery occlusion (MCAO) in rats. Since NOS2 is associated with neuro-inflammation in stroke and decreasing NOS2 expression alone in leucocytes is insufficient to improve stroke outcomes, we hypothesized that miR-122 mimic may also decrease NOS2 expression in brain microvascular endothelial cells (BMVECs) even at extended time windows.

Methods: We administered PEG-liposome wrapped miR-122 mimic (2.4 mg/kg, i.v.) 0 or 6 h after MCAO, and assessed stroke volume and NOS2 expression in BMVECs 24 h following MCAO in rats. Luciferase reporter assays were used to determine if miR-122 binds to 3′ untranslated regions (3′UTR) of NOS2.

Results: The data showed that miR-122 mimic decreased infarct volumes and decreased MCAO-induced NOS2 over-expression in BMVECs. However, miR-122 did not bind to 3′UTR of NOS2 in the luciferase assays.

Conclusion: The data show the 6-h period of therapeutic efficacy of miR-122 mimic which could relate to indirect knockdown of NOS2 in both BMVECs and leucocytes.

MicroRNA-based therapeutics in central nervous system injuries

Central nervous system (CNS) injuries, such as stroke, traumatic brain injury (TBI) and spinal cord injury (SCI), are important causes of death and long-term disability worldwide. MicroRNA (miRNA), small non-coding RNA molecules that negatively regulate gene expression, can serve as diagnostic biomarkers and are emerging as novel therapeutic targets for CNS injuries. MiRNA-based therapeutics include miRNA mimics and inhibitors (antagomiRs) to respectively decrease and increase the expression of target genes. In this review, we summarize current miRNA-based therapeutic applications in stroke, TBI and SCI. Administration methods, time windows and dosage for effective delivery of miRNA-based drugs into CNS are discussed. The underlying mechanisms of miRNA-based therapeutics are reviewed including oxidative stress, inflammation, apoptosis, blood-brain barrier protection, angiogenesis and neurogenesis. Pharmacological agents that protect against CNS injuries by targeting specific miRNAs are presented along with the challenges and therapeutic potential of miRNA-based therapies.

Lipopolysaccharide Associates with Amyloid Plaques, Neurons and Oligodendrocytes in Alzheimer's Disease Brain: A Review

This review proposes that lipopolysaccharide (LPS, found in the wall of all Gram-negative bacteria) could play a role in causing sporadic Alzheimer’s disease (AD). This is based in part upon recent studies showing that: Gram-negative E. coli bacteria can form extracellular amyloid; bacterial-encoded 16S rRNA is present in all human brains with over 70% being Gram-negative bacteria; ultrastructural analyses have shown microbes in erythrocytes of AD patients; blood LPS levels in AD patients are 3-fold the levels in control; LPS combined with focal cerebral ischemia and hypoxia produced amyloid-like plaques and myelin injury in adult rat cortex. Moreover, Gram-negative bacterial LPS was found in aging control and AD brains, though LPS levels were much higher in AD brains. In addition, LPS co-localized with amyloid plaques, peri-vascular amyloid, neurons, and oligodendrocytes in AD brains. Based upon the postulate LPS caused oligodendrocyte injury, degraded Myelin Basic Protein (dMBP) levels were found to be much higher in AD compared to control brains. Immunofluorescence showed that the dMBP co-localized with β amyloid (Aβ) and LPS in amyloid plaques in AD brain, and dMBP and other myelin molecules were found in the walls of vesicles in periventricular White Matter (WM). These data led to the hypothesis that LPS acts on leukocyte and microglial TLR4-CD14/TLR2 receptors to produce NFkB mediated increases of cytokines which increase Aβ levels, damage oligodendrocytes and produce myelin injury found in AD brain. Since Aβ_1–42 is also an agonist for TLR4 receptors, this could produce a vicious cycle that accounts for the relentless progression of AD. Thus, LPS, the TLR4 receptor complex, and Gram-negative bacteria might be treatment or prevention targets for sporadic AD.

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.

Abstract TP134: HDAC9 Polymorphisms Alter Blood Gene Expression in Patients With Large Vessel Atherosclerotic Stroke

Background and Purpose: HDAC9 polymorphisms rs2107595 and rs11984041 are associated with large vessel atherosclerotic stroke. HDAC9 regulates gene expression and is expressed in circulating leukocytes involved in atherosclerosis. In this study, we sought to determine whether HDAC9 single nucleotide polymorphisms (SNPs) rs2107595 or rs11984041 influence gene expression in blood of patients with large vessel atherosclerotic stroke (LVAS).

Methods: In 155 patients (43 LVAS and 112 vascular risk factor control) HDAC9 was genotyped for SNPs rs2107595 and rs11984041. RNA was isolated from whole blood and gene expression differences between HDAC9 risk allele positive and risk allele negative LVAS and control patients identified using human transcriptome microarrays. Pathway analysis was performed to identify canonical pathways and molecular functions associated with HDAC9 SNPs in LVAS.

Results: In rs2107595 risk allele positive LVAS patients there were 155 genes differentially expressed compared to SNP negative patients (fold change > |1.2|, p<0.05). Over represented pathways corresponded to IL6 signaling, cholesterol efflux and platelet aggregation. In rs11984041 risk allele positive LVAS patients there were 419 genes differentially expressed genes compared to risk allele negative patients (fold change > |1.2|, p<0.05). Over represented pathways included NF-?B signaling, T cell response and macrophage activation.

Conclusions: Polymorphisms in HDAC9 are associated with differences in gene expression in blood cells of patients with LVAS. The risk alleles in HDAC9 may contribute to functional differences in peripheral immune cells involved in stroke related atherosclerosis, plaque stability, and inflammation.

Inhibition of Src family kinases improves cognitive function after intraventricular hemorrhage or intraventricular thrombin

Intraventricular hemorrhage causes spatial memory loss, but the mechanism remains unknown. Our recent studies demonstrated that traumatic brain injury activates Src family kinases, which cause spatial memory loss. To test whether the spatial memory loss was due to blood in the ventricles, which activated Src family kinases, we infused autologous whole blood or thrombin into the lateral ventricles of adult rats to model non-traumatic intraventricular hemorrhage. Hippocampal neuron loss was examined 1 day to 5 weeks later. Spatial memory function was assessed 29 to 33 days later using the Morris water maze. Five weeks after the ventricular injections of blood or thrombin, there was death of most hippocampal neurons and significant memory deficits compared with sham operated controls. These data show that intraventricular thrombin is sufficient to kill hippocampal neurons and produce spatial memory loss. In addition, systemic administration of the non-specific Src family kinase inhibitor PP2 or intraventricular injection of siRNA-Fyn, a Src family kinase family member, prevented hippocampal neuronal loss and spatial memory deficits following intraventricular hemorrhage. The data support the conclusions that thrombin mediates the hippocampal neuronal cell death and spatial memory deficits produced by intraventricular blood and that these can be blocked by non-specific inhibition of Src family kinases or by inhibiting Fyn.

Biomarkers of Acute Stroke Etiology (BASE) Study Methodology

Acute ischemic stroke affects over 800,000 US adults annually, with hundreds of thousands more experiencing a transient ischemic attack. Emergent evaluation, prompt acute treatment, and identification of stroke or TIA (transient ischemic attack) etiology for specific secondary prevention are critical for decreasing further morbidity and mortality of cerebrovascular disease. The Biomarkers of Acute Stroke Etiology (BASE) study is a multicenter observational study to identify serum markers defining the etiology of acute ischemic stroke. Observational trial of patients presenting to the hospital within 24 h of stroke onset. Blood samples are collected at arrival, 24, and 48 h later, and RNA gene expression is utilized to identify stroke etiology marker candidates. The BASE study began January 2014. At the time of writing, there are 22 recruiting sites. Enrollment is ongoing, expected to hit 1000 patients by March 2017. The BASE study could potentially aid in focusing the initial diagnostic evaluation to determine stroke etiology, with more rapidly initiated targeted evaluations and secondary prevention strategies.Clinical Trial Registration Clinicaltrials.gov NCT02014896 https://clinicaltrials.gov/ct2/show/NCT02014896?term=biomarkers+of+acute+stroke+etiology&rank=1.

Blood transcriptomic comparison of individuals with and without autism spectrum disorder: A combined-samples mega-analysis

Blood-based microarray studies comparing individuals affected with autism spectrum disorder (ASD) and typically developing individuals help characterize differences in circulating immune cell functions and offer potential biomarker signal. We sought to combine the subject-level data from previously published studies by mega-analysis to increase the statistical power. We identified studies that compared ex vivo blood or lymphocytes from ASD-affected individuals and unrelated comparison subjects using Affymetrix or Illumina array platforms. Raw microarray data and clinical meta-data were obtained from seven studies, totaling 626 affected and 447 comparison subjects. Microarray data were processed using uniform methods. Covariate-controlled mixed-effect linear models were used to identify gene transcripts and co-expression network modules that were significantly associated with diagnostic status. Permutation-based gene-set analysis was used to identify functionally related sets of genes that were over- and under-expressed among ASD samples. Our results were consistent with diminished interferon-, EGF-, PDGF-, PI3K-AKT-mTOR-, and RAS-MAPK-signaling cascades, and increased ribosomal translation and NK-cell related activity in ASD. We explored evidence for sex-differences in the ASD-related transcriptomic signature. We also demonstrated that machine-learning classifiers using blood transcriptome data perform with moderate accuracy when data are combined across studies. Comparing our results with those from blood-based studies of protein biomarkers (e.g., cytokines and trophic factors), we propose that ASD may feature decoupling between certain circulating signaling proteins (higher in ASD samples) and the transcriptional cascades which they typically elicit within circulating immune cells (lower in ASD samples). These findings provide insight into ASD-related transcriptional differences in circulating immune cells. © 2016 Wiley Periodicals, Inc.

Possible sexually dimorphic role of miRNA and other sncRNA in ASD brain

Background

Autism spectrum disorder (ASD) is sexually dimorphic in brain structure, genetics, and behaviors. In studies of brain tissue, the age of the population is clearly a factor in interpreting study outcome, yet sex is rarely considered. To begin to address this issue, we extend our previously published microarray analyses to examine expression of small noncoding RNAs (sncRNAs), including microRNAs (miRNAs), in ASD and in the control temporal cortex in males and females. Predicted miRNA targets were identified as well as the pathways they overpopulate.

Findings

After considering age, sexual dimorphism in ASD sncRNA expression persists in the temporal cortex and in the patterning that distinguishes regions. Among the sexually dimorphic miRNAs are miR-219 and miR-338, which promote oligodendrocyte differentiation, miR-125, implicated in neuronal differentiation, and miR-488, implicated in anxiety. Putative miRNA targets are significantly over-represented in immune and nervous system pathways in both sexes, consistent with previous mRNA studies. Even for common pathways, the specific target mRNAs are often sexually dimorphic. For example, both male and female target genes significantly populate the Axonal Guidance Signaling pathway, yet less than a third of the targets are common to both sexes.

Conclusions

Our findings of sexual dimorphism in sncRNA levels underscore the importance of considering sex, in addition to age, when interpreting molecular findings on ASD brain.

Electronic supplementary material

The online version of this article (doi:10.1186/s13229-017-0117-0) contains supplementary material, which is available to authorized users.

Abstract WP424: Let7i Microrna Regulates Immune Response in Patients with Ischemic Stroke

Background and Purpose: The immune system responds rapidly following ischemic brain injury and can contribute to the final extent of brain damage. microRNA are differentially expressed in leukocytes following ischemic stroke and may regulate the immune response to ischemic brain injury. In this study we evaluate microRNA let7i-5p in ischemic stroke and its regulation of leukocytes.

Methods: A total of 212 patients were studied; 106 with acute ischemic stroke and 106 risk factor matched controls. . RNA from circulating leukocytes was isolated from blood collected in PaxGene tubes. Let7i-5p miRNA expression was assessed by Taqman qRT-PCR. Given microRNAs act to destabilize and degrade their target mRNA, mRNA that inversely correlated with let7i were identified. To demonstrate let7i post-transcriptional regulation of target genes, a 3’UTR luciferase assay was performed. Target protein expression was assessed by ELISA.

Results: Let7i was decreased in patients with acute ischemic stroke (fold change -1.70, p<0.00001). A modest inverse correlation between let7i and NIH Stroke Scale at admission (r= -0.32, p=0.02), infarct volume (r= -0.21, p=0.04) and plasma MMP9 (r= -0.46, p=0.01) was identified. The decrease in let7i was associated with increased expression of several of its messenger RNA targets including CD86, CXCL8 and HMGB1. In vitro studies confirm let7i post-transcriptional regulation of target genes CD86, CXCL8 and HMGB1. Functional analysis predicted let7i regulates pathways involved in leukocyte activation, recruitment, and proliferation including canonical pathways CD86 signaling in T helper cells, HMGB1 signaling, and CXCL8 signaling.

Conclusions: Let7i is decreased in circulating leukocytes of patients with acute ischemic stroke. Mechanisms by which let7i regulates inflammatory response post-stroke include targeting CD86, CXCL8 and HMGB1.

Abstract TP81: MiR122 Modulates Nos2 to Improve Stroke Outcomes After Middle Cerebral Artery Occlusion in Rats

Based upon our previous findings that microRNA-122 (miR-122) was decreased in peripheral blood of both humans and rats after ischemic stroke, we hypothesized that elevating miR-122 in blood might improve outcomes after ischemic stroke.

Using the in vivo polyethylene glycol 2000 (PEG)-liposome based miRNA transfection system and the rat middle cerebral artery occlusion (MCAO) model, we recently demonstrated that intravenous (i.v.) miR-122 mimic, given immediately after MCAO, elevated miR-122 in peripheral blood, prevented neurological impairments, and reduced brain infarction volume up to 93% after MCAO in rats. Using Taqman PCR based assays, we demonstrate fourteen direct miR-122 target genes (e.g. Nos2, Vcam1, Clic4, Ucp2, Dlg2, and others) were decreased in blood leukocytes following miR-122 mimic treatment after MCAO in rats. Focusing on ONE miR-122 target gene (Nos2), we demonstrated that miR-122 binds to the complementary sequence within three prime untranslated regions (3’UTRs) of Nos2 using luciferase reporter assay, and that miR-122 mimic decreases Nos2 expression in brain microvascular endothelial cells (BMVECs) after MCAO in rats.

These results show that Nos2 is decreased in leukocytes and BMVECs following miR-122 mimic treatment after MCAO, which likely contributes to miR-122 induced protection after MCAO in rats.

Acknowledgements: This study was supported by NIH grants R01NS089901 (DZL) and NS054652 (FRS). There were no conflicts of interest.