Simone Thair

All Publications

• A robust host-response-based signature distinguishes bacterial and viral infections across diverse global populations. Cell reports. Medicine Rao, A. M., Popper, S. J., Gupta, S., Davong, V., Vaidya, K., Chanthongthip, A., Dittrich, S., Robinson, M. T., Vongsouvath, M., Mayxay, M., Nawtaisong, P., Karmacharya, B., Thair, S. A., Bogoch, I., Sweeney, T. E., Newton, P. N., Andrews, J. R., Relman, D. A., Khatri, P. 2022; 3 (12): 100842

  Abstract

  Limited sensitivity and specificity of current diagnostics lead to the erroneous prescription of antibiotics. Host-response-based diagnostics could address these challenges. However, using 4,200 samples across 69 blood transcriptome datasets from 20 countries from patients with bacterial or viral infections representing a broad spectrum of biological, clinical, and technical heterogeneity, we show current host-response-based gene signatures have lower accuracy to distinguish intracellular bacterial infections from viral infections than extracellular bacterial infections. Using these 69 datasets, we identify an 8-gene signature to distinguish intracellular or extracellular bacterial infections from viral infections with an area under the receiver operating characteristic curve (AUROC) > 0.91 (85.9% specificity and 90.2% sensitivity). In prospective cohorts from Nepal and Laos, the 8-gene classifier distinguished bacterial infections from viral infections with an AUROC of 0.94 (87.9% specificity and 91% sensitivity). The 8-gene signature meets the target product profile proposed by the World Health Organization and others for distinguishing bacterial and viral infections.

  View details for DOI 10.1016/j.xcrm.2022.100842

  View details for PubMedID 36543117

• Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease NATURE MICROBIOLOGY Blauwkamp, T. A., Thair, S., Rosen, M. J., Blair, L., Lindner, M. S., Vilfan, I. D., Kawli, T., Christians, F. C., Venkatasubrahmanyam, S., Wall, G. D., Cheung, A., Rogers, Z. N., Meshulam-Simon, G., Huijse, L., Balakrishnan, S., Quinn, J., Hollemon, D., Hong, D. K., Vaughn, M., Kertesz, M., Bercovici, S., Wilber, J. C., Yang, S. 2019; 4 (4): 663–74

  View details for DOI 10.1038/s41564-018-0349-6

  View details for Web of Science ID 000461999200019

• Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease. Nature microbiology Blauwkamp, T. A., Thair, S., Rosen, M. J., Blair, L., Lindner, M. S., Vilfan, I. D., Kawli, T., Christians, F. C., Venkatasubrahmanyam, S., Wall, G. D., Cheung, A., Rogers, Z. N., Meshulam-Simon, G., Huijse, L., Balakrishnan, S., Quinn, J. V., Hollemon, D., Hong, D. K., Vaughn, M. L., Kertesz, M., Bercovici, S., Wilber, J. C., Yang, S. 2019

  Abstract

  Thousands of pathogens are known to infect humans, but only a fraction are readily identifiable using current diagnostic methods. Microbial cell-free DNA sequencing offers the potential to non-invasively identify a wide range of infections throughout the body, but the challenges of clinical-grade metagenomic testing must be addressed. Here we describe the analytical and clinical validation of a next-generation sequencing test that identifies and quantifies microbial cell-free DNA in plasma from 1,250 clinically relevant bacteria, DNA viruses, fungi and eukaryotic parasites. Test accuracy, precision, bias and robustness to a number of metagenomics-specific challenges were determined using a panel of 13 microorganisms that model key determinants of performance in 358 contrived plasma samples, as well as 2,625 infections simulated in silico and 580 clinical study samples. The test showed 93.7% agreement with blood culture in a cohort of 350 patients with a sepsis alert and identified an independently adjudicated cause of the sepsis alert more often than all of the microbiological testing combined (169 aetiological determinations versus 132). Among the 166 samples adjudicated to have no sepsis aetiology identified by any of the tested methods, sequencing identified microbial cell-free DNA in 62, likely derived from commensal organisms and incidental findings unrelated to the sepsis alert. Analysis of the first 2,000 patient samples tested in the CLIA laboratory showed that more than 85% of results were delivered the day after sample receipt, with 53.7% of reports identifying one or more microorganisms.

  View details for PubMedID 30742071

• The IL20 Genetic Polymorphism Is Associated with Altered Clinical Outcome in Septic Shock JOURNAL OF INNATE IMMUNITY Nakada, T., Wacharasint, P., Russell, J. A., Boyd, J. H., Nakada, E., Thair, S. A., Shimada, T., Walley, K. R. 2018; 10 (3): 181–88

  Abstract

  The IL10 family of genes includes crucial immune regulators. We tested the hypothesis that single nucleotide polymorphisms (SNPs) in IL10, IL19, IL20, and IL24 of the IL10 family gene cluster alter the clinical outcome of septic shock.Patients with septic shock (n = 1,193) were genotyped for 13 tag SNPs of IL10, IL19, IL20, and IL24. IL20 gene expression was measured in genotyped lymphoblastoid cells in vitro. Cardiac surgical ICU patients (n = 981) were genotyped for IL20 rs2981573 A/G. The primary outcome variable was 28-day mortality.Patients with the G allele of IL20 rs2981573 had a significantly increased hazard of death over the 28-day period compared to patients with the A allele in the septic shock cohort (adjusted hazard ratio 1.27; 95% confidence interval 1.10-1.47; p = 8.0 × 10-4). Patients with the GG genotype had more organ dysfunction (p < 0.05). The GG genotype was associated with increased IL20 gene expression in stimulated lymphoblastoid cells in vitro (p < 0.05). The cardiac surgical ICU patients with the GG genotype had an increased length of ICU stay (p = 0.032).The GG genotype of IL20 rs2981573 SNP was associated with increased IL20 gene expression and increased adverse outcomes in patients with septic shock and following cardiac surgery.

  View details for DOI 10.1159/000486104

  View details for Web of Science ID 000435959200004

  View details for PubMedID 29334679

• Microbial Typing by Machine Learned DNA Melt Signatures SCIENTIFIC REPORTS Andini, N., Wang, B., Athamanolap, P., Hardick, J., Masek, B. J., Thair, S., Hu, A., Avornu, G., Peterson, S., Cogill, S., Rothman, R. E., Carroll, K. C., Gaydos, C. A., Wang, J. T., Batzoglou, S., Yang, S. 2017; 7

  Abstract

  There is still an ongoing demand for a simple broad-spectrum molecular diagnostic assay for pathogenic bacteria. For this purpose, we developed a single-plex High Resolution Melt (HRM) assay that generates complex melt curves for bacterial identification. Using internal transcribed spacer (ITS) region as the phylogenetic marker for HRM, we observed complex melt curve signatures as compared to 16S rDNA amplicons with enhanced interspecies discrimination. We also developed a novel Naïve Bayes curve classification algorithm with statistical interpretation and achieved 95% accuracy in differentiating 89 bacterial species in our library using leave-one-out cross-validation. Pilot clinical validation of our method correctly identified the etiologic organisms at the species-level in 59 culture-positive mono-bacterial blood culture samples with 90% accuracy. Our findings suggest that broad bacterial sequences may be simply, reliably and automatically profiled by ITS HRM assay for clinical adoption.

  View details for DOI 10.1038/srep42097

  View details for Web of Science ID 000393494300001

  View details for PubMedID 28165067

• TNFAIP2 Inhibits Early TNFa-Induced NF-x03BA;B Signaling and Decreases Survival in Septic Shock Patients. Journal of innate immunity Thair, S. A., Topchiy, E., Boyd, J. H., Cirstea, M., Wang, C., Nakada, T., Fjell, C. D., Wurfel, M., Russell, J. A., Walley, K. R. 2016; 8 (1): 57-66

  Abstract

  During septic shock, tumor necrosis factor alpha (TNFα) is an early response gene and induces a plethora of genes and signaling pathways. To identify robust signals in genes reliably upregulated by TNFα, we first measured microarray gene expression in vitro and searched methodologically comparable, publicly available data sets to identify concordant signals. Using tag single-nucleotide polymorphisms in the genes common to all data sets, we identified a genetic variant of the TNFAIP2 gene, rs8126, associated with decreased 28-day survival and increased organ dysfunction in an adult cohort in the Vasopressin and Septic Shock Trial. Similar to this cohort, we found that an association with rs8126 and increased organ dysfunction is replicated in a second cohort of septic shock patients in the St. Paul's Hospital Intensive Care Unit. We found that TNFAIP2 inhibits NF-x03BA;B activity, impacting the downstream cytokine interleukin (IL)-8. The minor G allele of TNFAIP2 rs8126 resulted in greater TNFAIP2 expression, decreased IL-8 production and was associated with decreased survival in patients experiencing septic shock. These data suggest that TNFAIP2 is a novel inhibitor of NF-x03BA;B that acts as an autoinhibitor of the TNFα response during septic shock.

  View details for DOI 10.1159/000437330

  View details for PubMedID 26347487

• VPS13D Gene Variant Is Associated with Altered IL-6 Production and Mortality in Septic Shock. Journal of innate immunity Nakada, T. A., Boyd, J. H., Russell, J. A., Aguirre-Hernández, R., Wilkinson, M. D., Thair, S. A., Nakada, E., McConechy, M. K., Fjell, C. D., Walley, K. R. 2015

  Abstract

  Genetic variations contribute to septic shock mortality. To discover a novel locus, we performed in vitro genome-wide association studies (GWAS) and further tested the result in a cohort of septic shock patients.Two in vitro GWAS using a quantitative trait locus analysis of stimulated IL-6 production in lymphoblastoid cells from 60 individuals of European ancestry were performed. VPS13D rs6685273 was genotyped in European ancestry patients (n = 498). The VPS13D gene was silenced in vitro.Two GWAS using lymphoblastoid cells identified the locus of VPS13D rs6685273 that was significant in the same direction in both GWAS. The VPS13D rs6685273 C allele was associated with increased IL-6 production. Patients with septic shock who had the VPS13D rs6685273 CC genotype had an increased 28-day mortality (p = 0.023) and more organ failure (p < 0.05) compared to the CT/TT genotypes. VPS13D in vitro gene silencing in the HeLa cell line increased IL-6 production. Furthermore, the rs6685273 genotype was associated with differential VPS13D splice variant expression.The VPS13D rs6685273 C allele was associated with increased IL-6 production in vitro. The patients with the VPS13D rs6685273 CC genotype had increased 28-day mortality and increased organ failure. VPS13D appears to regulate IL-6 production. © 2015 S. Karger AG, Basel.

  View details for DOI 10.1159/000381265

  View details for PubMedID 25896417

• Identification of a Nonsynonymous Polymorphism in the SVEP1 Gene Associated With Altered Clinical Outcomes in Septic Shock CRITICAL CARE MEDICINE Nakada, T., Russell, J. A., Boyd, J. H., Thair, S. A., Walley, K. R. 2015; 43 (1): 101-108

  Abstract

  Mortality from septic shock is highly heritable. The identification of causal genetic factors is insufficient. To discover key contributors, we first identified nonsynonymous single-nucleotide polymorphisms in conserved genomic regions that are predicted to have significant effects on protein function. We then test the hypothesis that these nonsynonymous single-nucleotide polymorphisms across the genome alter clinical outcome of septic shock.Genetic-association study plus in vitro experiment using primary cells plus in silico analysis using genomic DNA and protein database.Twenty-seven ICUs at academic teaching centers in Canada, Australia, and the United States.Patients with septic shock of European ancestry (n = 520).Patients with septic shock were genotyped for 843 nonsynonymous single-nucleotide polymorphisms in conserved regions of the genome and are predicted to have damaging effects from the protein sequence.The primary outcome variable was 28-day mortality. Secondary outcome variables were organ dysfunction. Productions of adhesion molecules including interleukin-8, growth-regulated oncogene-α, monocyte chemoattractant protein-1, and monocyte chemoattractant protein-3 were measured in human umbilical vein endothelial cells after SVEP1 gene silencing by RNA interference. Patients with septic shock having the SVEP1 C allele of nonsynonymous single-nucleotide polymorphism, SVEP1 c.2080A>C (p. Gln581His, rs10817033), had a significant increase in the hazard of death over the 28 days (hazard ratio, 1.72; 95% CI, 1.31-2.26; p = 9.7 × 10-5) and increased organ dysfunction and needed more organ support (p < 0.05). Silencing SVEP1 significantly increased interleukin-8, growth-regulated oncogene-α, monocyte chemoattractant protein-1, monocyte chemoattractant protein-3 production in human umbilical vein endothelial cells under lipopolysaccharide stimulation (p < 0.01).C allele of SVEP1 c.2080A>C (p. Gln581His) single-nucleotide polymorphism, a non-synonymous single-nucleotide polymorphism in conserved regions and predicted to have damaging effects on protein structure, was associated with increased 28-day mortality and organ dysfunction of septic shock. SVEP1 appears to regulate molecules of the leukocyte adhesion pathway.

  View details for DOI 10.1097/CCM.0000000000000604

  View details for Web of Science ID 000346409100033

  View details for PubMedID 25188548

• PCSK9 is a critical regulator of the innate immune response and septic shock outcome SCIENCE TRANSLATIONAL MEDICINE Walley, K. R., Thain, K. R., Russell, J. A., Reilly, M. P., Meyer, N. J., Ferguson, J. F., Christie, J. D., Nakada, T., Fjell, C. D., Thair, S. A., Cirstea, M. S., Boyd, J. H. 2014; 6 (258)

  Abstract

  A decrease in the activity of proprotein convertase subtilisin/kexin type 9 (PCSK9) increases the amount of low-density lipoprotein (LDL) receptors on liver cells and, therefore, LDL clearance. The clearance of lipids from pathogens is related to endogenous lipid clearance; thus, PCSK9 may also regulate removal of pathogen lipids such as lipopolysaccharide (LPS). Compared to controls, Pcsk9 knockout mice displayed decreases in inflammatory cytokine production and in other physiological responses to LPS. In human liver cells, PCSK9 inhibited LPS uptake, a necessary step in systemic clearance and detoxification. Pharmacological inhibition of PCSK9 improved survival and inflammation in murine polymicrobial peritonitis. Human PCSK9 loss-of-function genetic variants were associated with improved survival in septic shock patients and a decrease in inflammatory cytokine response both in septic shock patients and in healthy volunteers after LPS administration. The PCSK9 effect was abrogated in LDL receptor (LDLR) knockout mice and in humans who are homozygous for an LDLR variant that is resistant to PCSK9. Together, our results show that reduced PCSK9 function is associated with increased pathogen lipid clearance via the LDLR, a decreased inflammatory response, and improved septic shock outcome.

  View details for DOI 10.1126/scitranslmed.3008782

  View details for Web of Science ID 000343318000010

  View details for PubMedID 25320235

• A Multibiomarker-Based Outcome Risk Stratification Model for Adult Septic Shock CRITICAL CARE MEDICINE Wong, H. R., Lindsell, C. J., Pettilae, V., Meyer, N. J., Thair, S. A., Karlsson, S., Russell, J. A., Fjell, C. D., Boyd, J. H., Ruokonen, E., Shashaty, M. G., Christie, J. D., Hart, K. W., Lahni, P., Walley, K. R. 2014; 42 (4): 781-789

  Abstract

  Clinical trials in septic shock continue to fail due, in part, to inequitable and sometimes unknown distribution of baseline mortality risk between study arms. Investigators advocate that interventional trials in septic shock require effective outcome risk stratification. We derived and tested a multibiomarker-based approach to estimate mortality risk in adults with septic shock.Previous genome-wide expression studies identified 12 plasma proteins as candidates for biomarker-based risk stratification. The current analysis used banked plasma samples and clinical data from existing studies. Biomarkers were assayed in plasma samples obtained from 341 subjects with septic shock within 24 hours of admission to the ICU. Classification and regression tree analysis was used to generate a decision tree predicting 28-day mortality based on a combination of both biomarkers and clinical variables. The derived tree was first tested in an independent cohort of 331 subjects, then calibrated using all subjects (n = 672), and subsequently validated in another independent cohort (n = 209).Multiple ICUs in Canada, Finland, and the United States.Eight hundred eighty-one adults with septic shock or severe sepsis.None.The derived decision tree included five candidate biomarkers, admission lactate concentration, age, and chronic disease burden. In the derivation cohort, sensitivity for mortality was 94% (95% CI, 87-97), specificity was 56% (50-63), positive predictive value was 50% (43-57), and negative predictive value was 95% (89-98). Performance was comparable in the test cohort. The calibrated decision tree had the following test characteristics in the validation cohort: sensitivity 85% (76-92), specificity 60% (51-69), positive predictive value 61% (52-70), and negative predictive value 85% (75-91).We have derived, tested, calibrated, and validated a risk stratification tool and found that it reliably estimates the probability of mortality in adults with septic shock.

  View details for DOI 10.1097/CCM.0000000000000106

  View details for Web of Science ID 000332839700019

  View details for PubMedID 24335447

• Cytokines and Signaling Molecules Predict Clinical Outcomes in Sepsis PLOS ONE Fjell, C. D., Thair, S., Hsu, J. L., Walley, K. R., Russell, J. A., Boyd, J. 2013; 8 (11)

  Abstract

  Inflammatory response during sepsis is incompletely understood due to small sample sizes and variable timing of measurements following the onset of symptoms. The vasopressin in septic shock trial (VASST) compared the addition of vasopressin to norepinephrine alone in patients with septic shock. During this study plasma was collected and 39 cytokines measured in a 363 patients at both baseline (before treatment) and 24 hours. Clinical features relating to both underlying health and the acute organ dysfunction induced by the severe infection were collected during the first 28 days of admission.Cluster analysis of cytokines identifies subgroups of patients at differing risk of death and organ failure.Circulating cytokines and other signaling molecules were measured using a Luminex multi-bead analyte detection system. Hierarchical clustering was performed on plasma values to create patient subgroups. Enrichment analysis identified clinical outcomes significantly different according to these chemically defined patient subgroups. Logistic regression was performed to assess the importance of cytokines for predicting patient subgroups.Plasma levels at baseline produced three subgroups of patients, while 24 hour levels produced two subgroups. Using baseline cytokine data, one subgroup of 47 patients showed a high level of enrichment for severe septic shock, coagulopathy, renal failure, and risk of death. Using data at 24 hours, a larger subgroup of 81 patients that largely encompassed the 47 baseline subgroup patients had a similar enrichment profile. Measurement of two cytokines, IL2 and CSF2 and their product were sufficient to classify patients into these subgroups that defined clinical risks.A distinct pattern of cytokine levels measured early in the course of sepsis predicts disease outcome. Subpopulations of patients have differing clinical outcomes that can be predicted accurately from small numbers of cytokines. Design of clinical trials and interventions may benefit from consideration of cytokine levels.

  View details for DOI 10.1371/journal.pone.0079207

  View details for Web of Science ID 000327143800041

  View details for PubMedID 24244449

  View details for PubMedCentralID PMC3828333

• Noncanonical Nuclear Factor Kappa B (NF-kappa B) Signaling and Potential for Therapeutics in Sepsis CURRENT INFECTIOUS DISEASE REPORTS Thair, S., Russell, J. A. 2013; 15 (5): 364-371

  Abstract

  NF-κB signaling plays a central role in the pathophysiology of severe sepsis and septic shock. Despite tremendous and missed efforts, novel therapeutics for severe sepsis and septic shock are still needed. Many drugs have been designed to target the canonical NF-κB signaling pathway with limited success, potentially due to the nonspecificity of the drugs for other kinases and the interaction of canonical signaling with other pathways. Here, we review the canonical and noncanonical signaling pathways of NF-κB, the cross talk and negative regulation of the two pathways, and the potential for therapeutics arising from the noncanonical NF-κB pathway in relation to the pathophysiology of septic shock.

  View details for DOI 10.1007/s11908-013-0362-0

  View details for Web of Science ID 000338287200003

  View details for PubMedID 23975688

• Vasopressin Compared with Norepinephrine Augments the Decline of Plasma Cytokine Levels in Septic Shock AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE Russell, J. A., Fjell, C., Hsu, J. L., Lee, T., Boyd, J., Thair, S., Singer, J., Patterson, A. J., Walley, K. R. 2013; 188 (3): 356-364

  Abstract

  Changes in plasma cytokine levels may predict mortality, and therapies (vasopressin versus norepinephrine) could change plasma cytokine levels in early septic shock.Our hypotheses were that changes in plasma cytokine levels over 24 hours differ between survivors and nonsurvivors, and that there are different effects of vasopressin and norepinephrine on plasma cytokine levels in septic shock.We studied 394 patients in a randomized, controlled trial of vasopressin versus norepinephrine in septic shock. We used hierarchical clustering and principal components analysis of the baseline cytokine concentrations to subgroup cytokines; we then compared survivors to nonsurvivors (28 d) and compared vasopressin- versus norepinephrine-induced changes in cytokine levels over 24 hours.A total of 39 plasma cytokines were measured at baseline and at 24 hours. Hierarchical clustering and principal components analysis grouped cytokines similarly. Survivors (versus nonsurvivors) had greater decreases of overall cytokine levels (P < 0.001). Vasopressin decreased overall 24-hour cytokine concentration compared with norepinephrine (P = 0.037). In less severe septic shock, the difference in plasma cytokine reduction over 24 hours between survivors and nonsurvivors was less pronounced than that seen in more severe septic shock. Furthermore, vasopressin decreased interferon-inducible protein 10 and granulocyte colony-stimulating factor more than did norepinephrine in less severe septic shock, whereas vasopressin decreased granulocyte-macrophage colony-stimulating factor in patients who had more severe shock.Survivors of septic shock had greater decreases of cytokines, chemokines and growth factors in early septic shock. Vasopressin decreased 24-hour plasma cytokine levels more than did norepinephrine. The vasopressin-associated decrease of cytokines differed according to severity of shock. Clinical trial registered with www.controlled-trials.com (ISRCTN94845869).

  View details for DOI 10.1164/rccm.201302-0355OC

  View details for Web of Science ID 000322617800017

  View details for PubMedID 23796235

• Sepsis in transit: from clinical to molecular classification CRITICAL CARE Thair, S. A., Russell, J. A. 2012; 16 (6)

  Abstract

  In the previous issue of Critical Care, Maslove and colleagues studied circulating neutrophil transcriptional expression to discover and validate a molecular subclassification of adult patients with sepsis. The authors divided patients into small derivation (n = 55) and validation (n = 71) cohorts. Their complex methodology included partitioning around medoid and hierarchical clustering methods to define two transcriptionally distinct subtypes of sepsis. Pathway analysis found that chemokine and cytokine pathways as well as Toll-like receptor signaling were enhanced. Investigation of specific drug target genes relevant to sepsis found significantly different expression levels between the two molecular subtypes. Interestingly, most patient characteristics did not differ between groups, except for an increase in the proportion of severe sepsis in molecular subtype 1. Possible confounders of this study were the small sample size, population stratification, and lack of information regarding drug interventions, all of which support the need for more studies with larger cohorts that include transcriptional profiles. This thought-provoking hypothesis-generating study could lead to a new neutrophil expression-based molecular classification of adult sepsis.

  View details for DOI 10.1186/cc11813

  View details for Web of Science ID 000317566500032

  View details for PubMedID 23151274

• Association of angiotensin II type 1 receptor-associated protein gene polymorphism with increased mortality in septic shock CRITICAL CARE MEDICINE Nakada, T., Russell, J. A., Boyd, J. H., McLaughlin, L., Nakada, E., Thair, S. A., Hirasawa, H., Oda, S., Walley, K. R. 2011; 39 (7): 1641-1648

  Abstract

  Angiotensin II and its postreceptor signaling are crucial in regulating vasomotor tone. The objective of this study was to test the hypothesis that single nucleotide polymorphisms in angiotensin II pathway genes alter outcome of septic shock.Genetic association study and in vitro experiment.Intensive care units at academic teaching centers.Derivation and validation septic shock cohorts (n = 589 and n = 616, respectively) and a coronary artery bypass surgery cohort (n = 551).Patients with septic shock in the derivation cohort were genotyped for tag single nucleotide polymorphisms: angiotensin-converting enzyme (six single nucleotide polymorphisms), angiotensin II receptor type 1 (five single nucleotide polymorphisms), and angiotensin II type 1 receptor-associated protein (three single nucleotide polymorphisms), which is a negative regulator of angiotensin II receptor type 1. Patients in the septic shock replication cohort and the coronary artery bypass graft cohort were genotyped for the angiotensin II type 1 receptor-associated protein rs11121816.The primary outcome variable was 28-day mortality. Secondary outcome variables were blood pressure and heart rate. Angiotensin II type 1 receptor-associated protein messenger RNA expression was measured in genotyped lymphoblastoid cells in vitro. Patients with septic shock patients the GG genotype of angiotensin II type 1 receptor-associated protein rs11121816 had increased 28-day mortality in the derivation cohort (54.8% vs. 41.4%; adjusted hazard ratio, 1.46; 95% confidence interval, 1.09-1.93; p = .010 [all ethnicities]; p = .050 [white]) and in the replication cohort (43.8% vs. 32.3%; hazard ratio, 1.42; 95% confidence interval, 1.03-1.98; p = .035 [all ethnicities]; p = .037 [white]). Patients having the GG genotype had decreased mean arterial pressure (98.3% of other genotype, p = .058 [derivation cohort]; 97.7%, p = .00060 [replication cohort]) and increased heart rate (104.1%, p = .023 [derivation cohort], 102.9%, p = nonsignificant [replication cohort]). GG genotype patients undergoing coronary artery bypass grafting had decreased postoperative mean arterial pressure and increased postoperative heart rate (p < .05). GG genotype lymphoblastoid cells had 2.0-fold higher angiotensin II type 1 receptor-associated protein messenger RNA expression (p < .05).For angiotensin II type 1 receptor-associated protein, the negative regulator of angiotensin II receptor type 1, the GG genotype of rs11121816 was associated with increased angiotensin II type 1 receptor-associated protein expression, decreased blood pressure, and increased heart rate as well as increased 28-day mortality in septic shock.

  View details for DOI 10.1097/CCM.0b013e318218665a

  View details for Web of Science ID 000291721800006

  View details for PubMedID 21423001

• Leucyl/Cystinyl Aminopeptidase Gene Variants in Septic Shock CHEST Nakada, T., Russell, J. A., Wellman, H., Boyd, J. H., Nakada, E., Thain, K. R., Thair, S. A., Hirasawa, H., Oda, S., Walley, K. R. 2011; 139 (5): 1042-1049

  Abstract

  Vasopressin is an essential peptide hormone regulating cardiovascular homeostasis and an adjunctive vasopressor therapy for septic shock.We tested for association between single nucleotide polymorphisms (SNPs) in vasopressin pathway genes and altered outcome in derivation (n = 589) and replication (n = 616) cohorts of patients with septic shock. The primary outcome was 28-day mortality and the secondary outcome was vasopressin clearance. In a third cardiac surgical cohort (n = 977), we tested for locus-specific heritability of serum sodium concentrations.Of 17 tested tag SNPs in five vasopressin pathway genes (arginine vasopressin [AVP], arginine vasopressin receptor 1A and 1B [AVPR1A, AVPR1B], leucyl/cystinyl aminopeptidase [LNPEP], and oxytocin receptor [OXTR]), rs18059 in LNPEP (also known as vasopressinase) was associated with 28-day mortality in the derivation cohort (P = .037). Therefore, we resequenced the 160-kb haplotype block encompassing the LNPEP gene, including rs18059, and genotyped the 230 identified SNPs in the derivation cohort. The strongest signal was found for LNPEP rs4869317 (adjusted P = .044). The rs4869317 TT genotype was associated with increased 28-day mortality in the derivation cohort (51.0% [TT] vs 34.5% [AA/AT]; adjusted hazard ratio [HR], 1.58; 95% CI, 1.21-2.06; P = .00073) and the replication cohort (38.6% vs 29.6%; HR, 1.36; 95% CI, 1.03-1.80; P = .030). We found that the TT genotype was associated with increased plasma vasopressin clearance (P = .028), and the rs4869317 genotype accounted for 80% of the variance of serum sodium concentrations (locus-specific heritability) in cardiac surgical patients.The genetic variation in LNPEP (vasopressinase) is associated with 28-day mortality in septic shock and is associated with biologic effects on vasopressin clearance and serum sodium regulation. Further confirmation in additional cohorts is required.

  View details for DOI 10.1378/chest.10-2517

  View details for Web of Science ID 000290554300012

  View details for PubMedID 21330387

• A Single Nucleotide Polymorphism in NF-kappa B Inducing Kinase Is Associated with Mortality in Septic Shock JOURNAL OF IMMUNOLOGY Thair, S. A., Walley, K. R., Nakada, T., McConechy, M. K., Boyd, J. H., Wellman, H., Russell, J. A. 2011; 186 (4): 2321-2328

  Abstract

  We tested the hypothesis that single nucleotide polymorphisms (SNPs) within genes of the NF-κB pathway are associated with altered clinical outcome of septic shock patients. We genotyped 59 SNPs in the NF-κB pathway in a discovery cohort of septic shock patients (St. Paul's Hospital [SPH], N = 589), which identified the C allele of rs7222094 T/C within MAP3K14 (NF-κB inducing kinase; NIK) associated with increased 28-d mortality (uncorrected p = 0.00024, Bonferroni corrected p = 0.014). This result was replicated in a second cohort of septic shock patients (Vasopressin and Septic Shock Trial [VASST; N = 616]) in which the CC genotype of rs7222094 was associated with increased 28-d mortality (Cox regression: SPH cohort hazard ratio [HR], 1.35; 95% confidence interval [CI], 1.12-1.64; p = 0.002 Caucasian only; and VASST cohort HR, 1.24; 95% CI, 1.00-1.52; p = 0.048 Caucasian only). Patients having the CC genotype of rs7222094 in SPH experienced more renal and hematological dysfunction (p = 0.003 and p = 0.011), while patients of the VASST cohort with the rs7222094 CC genotype showed the same trend toward more renal dysfunction. In lymphoblastoid cell lines, we found the rs7222094 genotype most strongly associated with mRNA expression of CXCL10, a chemokine regulated by NF-κB. Accordingly, we measured CXCL10 protein levels and found that the CC genotype of rs7222094 was associated with significantly lower levels than those of the TT genotype in lymphoblastoid cell lines (p < 0.05) and in septic shock patients (p = 0.017). This suggests that the CC genotype of NIK rs7222094 is associated with increased mortality and organ dysfunction in septic shock patients, perhaps due to altered regulation of NF-κB pathway genes, including CXCL10.

  View details for DOI 10.4049/jimmunol.1002864

  View details for Web of Science ID 000286882700052

  View details for PubMedID 21257964

• Molecular mechanisms of sepsis. Contributions to microbiology Russell, J. A., Boyd, J., Nakada, T., Thair, S., Walley, K. R. 2011; 17: 48-85

  Abstract

  In cancer, therapies are targeted at 6 important pathways. In sepsis, there is ongoing controversy regarding the number and relative roles of pathways that are activated or repressed and which are important in the progression from health to death. Adding to complexity, there is interaction of pathways, there are differences in temporal pattern of up and down-regulation of pathways and there are different responses of pathways to therapies of sepsis. In this review, we define four key pathways of sepsis: (1) inflammation and immunity, (2) coagulation and fibrinolysis, (3) apoptosis, and (4) endocrine. Each of these pathways can impair endothelial function, a unifying aspect of the pathophysiology of sepsis. There are few studies of interactions of pathways except for the interacttion of inflammation/immunity with coagulation/fibrinolysis. Successful treatment of cancer requires that cancer therapies interrupt several key pathways of cancer. Accordingly, we suggest that successful treatment of sepsis will require therapies that interrupt several key pathways of sepsis. Perhaps the paucity of approved therapies for sepsis is related in part to the underevaluation of novel pathways, to lack of understanding of interactions of pathways and to lack of interruption of key pathways of sepsis.

  View details for DOI 10.1159/000324009

  View details for PubMedID 21659747

• beta(2)-Adrenergic Receptor Gene Polymorphism Is Associated with Mortality in Septic Shock AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE Nakada, T., Russell, J. A., Boyd, J. H., Aguirre-Hernandez, R., Thain, K. R., Thair, S. A., Nakada, E., McConechy, M., Walley, K. R. 2010; 181 (2): 143-149

  Abstract

  The CysGlyGln haplotype of the beta(2)-adrenergic receptor gene (ADRB2) is functional and associated with altered responses to adrenergic agonists in patients with asthma. Whether this functional haplotype alters outcome in patients receiving adrenergic agonists in septic shock is unknown.To determine whether genetic variation of ADRB2 influences outcome in septic shock.Two cohorts of patients with septic shock were studied: a single center (St. Paul's Hospital [SPH]) cohort (n = 589) and the Vasopressin and Septic Shock Trial (VASST) cohort (n = 616). The A allele of the rs1042717 G/A polymorphism is in complete linkage disequilibrium with the CysGlyGln haplotype of ADRB2; therefore, rs1042717 was genotyped. Modulation by norepinephrine and salbutamol of IL-6 production by stimulated in vitro lymphoblastoid cells was measured by genotype.Patients who had the AA genotype of rs1042717 displayed increased 28-day mortality in SPH (adjusted hazard ratio, 2.23; 95% confidence interval, 1.33-3.72; P = 0.0022), and this result was replicated in VASST (adjusted hazard ratio 2.82; 95% confidence interval, 1.56-5.09; P = 0.0006). This genotypic effect was eliminated in patients treated with acute low-dose corticosteroids. In all patients, the AA genotype was associated with more organ dysfunction. Patients with the AA genotype had a higher heart rate (SPH; P < 0.05; VASST; P < 0.05) and required a higher norepinephrine dose over Days 1 through 3 (VASST; P < 0.05). The AA genotype was associated with decreased norepinephrine and salbutamol inhibition of IL-6 production by stimulated lymphoblastoid cells in vitro (P < 0.05).The AA genotype of ADRB2 rs1042717, identifying homozygotes for the CysGlyGln haplotype, was associated with increased mortality and more organ dysfunction in septic shock.

  View details for DOI 10.1164/rccm.200903-0332OC

  View details for Web of Science ID 000273539800008

  View details for PubMedID 19850944

• Exploiting the Therapeutic Potential of MicroRNAs in Viral Diseases Expectations and Limitations MOLECULAR DIAGNOSIS & THERAPY Hemida, M. G., Ye, X., Thair, S., Yang, D. 2010; 14 (5): 271-282

  Abstract

  New therapeutic approaches are urgently needed for serious diseases, including cancer, cardiovascular diseases, viral infections, and others. A recent direction in drug development is the utilization of nucleic acid-based therapeutic molecules, such as antisense oligonucleotides, ribozymes, short interfering RNA (siRNA), and microRNA (miRNA). miRNAs are endogenous, short, non-coding RNA molecules. Some viruses encode their own miRNAs, which play pivotal roles in viral replication and immune evasion strategies. Conversely, viruses that do not encode miRNAs may manipulate host cell miRNAs for the benefits of their replication. miRNAs have therefore become attractive tools for the study of viral pathogenesis. Lately, novel therapeutic strategies based on miRNA technology for the treatment of viral diseases have been progressing rapidly. Although this new generation of molecular therapy is promising, there are still several challenges to face, such as targeting delivery to specific tissues, avoiding off-target effects of miRNAs, reducing the toxicity of the drugs, and overcoming mutations and drug resistance. In this article, we review the current knowledge of the role and therapeutic potential of miRNAs in viral diseases, and discuss the limitations of these therapies, as well as strategies to overcome them to provide safe and effective clinical applications of these new therapeutics.

  View details for Web of Science ID 000284677900001

  View details for PubMedID 21053993