Pathway Mapping Research Articles

Structural Mapping of Action Potential Propagation Pathways through Healthy and Diseased Heart

Structural Mapping of Action Potential Propagation Pathways through Healthy and Diseased Heart

Transcriptional trajectories of anther development provide candidates for engineering male fertility in sorghum

Sorghum is a self-pollinated crop with multiple economic uses as cereal, forage, and biofuel feedstock. Hybrid breeding is a cornerstone for sorghum improvement strategies that currently relies on cytoplasmic male sterile lines. To engineer genic male sterility, it is imperative to examine the genetic components regulating anther/pollen development in sorghum. To this end, we have performed transcriptomic analysis from three temporal stages of developing anthers that correspond to meiotic, microspore and mature pollen stages. A total of 5286 genes were differentially regulated among the three anther stages with 890 of them exhibiting anther-preferential expression. Differentially expressed genes could be clubbed into seven distinct developmental trajectories using K-means clustering. Pathway mapping revealed that genes involved in cell cycle, DNA repair, regulation of transcription, brassinosteroid and auxin biosynthesis/signalling exhibit peak expression in meiotic anthers, while those regulating abiotic stress, carbohydrate metabolism, and transport were enriched in microspore stage. Conversely, genes associated with protein degradation, post-translational modifications, cell wall biosynthesis/modifications, abscisic acid, ethylene, cytokinin and jasmonic acid biosynthesis/signalling were highly expressed in mature pollen stage. High concurrence in transcriptional dynamics and cis-regulatory elements of differentially expressed genes in rice and sorghum confirmed conserved developmental pathways regulating anther development across species. Comprehensive literature survey in conjunction with orthology analysis and anther-preferential accumulation enabled shortlisting of 21 prospective candidates for in-depth characterization and engineering male fertility in sorghum.

Repository of proposed pathways and protein\u2013protein interaction networks in age-related macular degeneration

Age-related macular degeneration (AMD) is one of the commonest causes of sight loss in the elderly population and to date there is no intervention that slows or prevents early AMD disease progressing to blinding neovascularization or geographic atrophy. AMD is a complex disease and factors proposed to contribute to the development and progression of disease include aging, genetics, epigenetics, oxidative stress, pro-inflammatory state, and life-style factors such as smoking, alcohol, and high fat diet. Here, we generate a knowledge repository of pathways and protein–protein interaction (PPI) networks likely to be implicated in AMD pathogenesis, such as complement activation, lipid trafficking and metabolism, vitamin A cycle, oxidative stress, proteostasis, bioenergetics, autophagy/mitophagy, extracellular matrix (ECM) turnover, and choroidal vascular dropout. Two disctinct clusters ermerged from the networks for parainflamation and ECM homeostasis, which may represent two different disease modules underlying AMD pathology. Our analyses also suggest that the disease manifests primarily in RPE/choroid and less in neural retina. The use of standardized syntax when generating maps of these biological processes (SBGN standard) and networks (PSI standard) enables visualization of complex information in graphical programs such as CellDesigner and Cytoscape and enhances reusability and extension of data. The ability to focus onto subnetworks, multiple visualizations and simulation options will enable the AMD research community to computationally model subnetworks or to test experimentally new hypotheses arising from connectivities in the AMD pathway map.

Transcriptomic profiling identifies a critical role of Nrf2 in regulating the inflammatory response to fly ash particles in mouse lung.

Exposure to combustion-derived nanoparticles is recognized as a major health hazard, but the molecular responses are still insufficiently described. The transcription factor erythroid 2-related factor 2 (Nrf2, also known as NFE2L2) is a master regulator of the pulmonary defense system against insults by particulate matter. However, its downstream molecular processes are not fully characterized. In the current study, BALB/c wild-type (WT) and Nrf2-/- mice were exposed by intranasal administration to fly ash particles (F3-S; 20mg/kg BW), which were collected from a municipal waste incinerator in China, for three consecutive days. Using a comparative transcriptomics approach, the pulmonary global gene expression profiles to F3-S exposure were characterized for both genotypes. The preponderance of the differentially-expressed genes (DEGs) in WT mice induced by the fly ash particles, was related to inflammation. Functional enrichment and molecular pathway mapping of the DEGs specific to Nrf2-/- mice exposed to the particles revealed that all of the top 10 perturbed molecular pathways were associated with the inflammatory response. Our study identified a transcriptional signature related to the initial pulmonary injury in mouse upon fly ash exposure, and suggests an anti-inflammatory role of Nrf2 in protecting the lung against such exposure.

Comparative transcriptome analysis reveals Dusp1 as a critical regulator of inflammatory response to fly ash particle exposure in mouse.

Exposure to outdoor concentrations of fine particulate matter (PM2.5) is a leading global health concern. Waste incineration emission has been recognized as a potential major contributor of ambient PM2.5. Respiratory inflammation is a central feature induced by PM2.5 exposure by inhalation. However, the molecular mechanisms are not fully understood. Dual-specificity phosphatase 1 (Dusp1) plays an instrumental role in the regulation of airway inflammation. In this study, fly ash particles (20mg/kg BW) collected from a municipal waste incinerator in China were given to BALB/c wild-type (WT) and Dusp1-/- mice by intranasal administration daily for three consecutive days. While these particles induced mild inflammation in both genotypes, a significantly higher level of serum interleukin-6 (665pg/ml) was measured in Dusp1-/- mice challenged with fly ash particles than in their WT counterparts. Genome-wide transcriptome profiling of pulmonary coding genes in response to the exposure were performed in both genotypes by RNA sequencing. We identified 487 differentially-expressed genes (DEGs) in fly ash-challenged Dusp1-/- mice versus their WT counterparts with a log2fold-change >1.5 and p<0.05. Functional enrichment and molecular pathway mapping of the DEGs specific to Dusp1-/- mice exposed to the particles revealed that the top 10 perturbed molecular pathways were associated with the immune response. Our study demonstrates the anti-inflammatory role of Dusp1 in protecting the lung against insults by fly ash particles, suggesting that Dusp1 might be a therapeutic target for the treatment of PM2.5-induced respiratory diseases.

Using Community Engagement to Map Pathways of Opioid Use and Recovery

ABSTRACTWe created a tool for use by the community of Tippecanoe County Indiana and their Opioid Task Force to guide their collaborative efforts in addressing the opioid crisis. A community-engaged research strategy led to the creation of a map of opioid pathways based in a systems thinking approach that considers key stakeholders and community members as system components and reflects local resources, supply, and demand for services, and the social ecology unique to this community. Organizations are able to visualize the importance of their interactions with other organizations within the community as they work together to address the crisis. This approach could be replicated in other communities and used to address other public health issues.

Complete mapping of energy transfer pathways in the plant light-harvesting complex Lhca4.

The Lhca4 antenna complex of plant Photosystem I (PSI) is characterized by extremely red-shifted and broadened absorption and emission bands from its low-energy chlorophylls (Chls). The mixing of a charge-transfer (CT) state with the excited state manifold causing these so-called red forms results in highly complicated multi-component excited energy transfer (EET) kinetics within the complex. The two-dimensional electronic spectroscopy experiments presented here reveal that EET towards the CT state occurs on three timescales: fast from the red Chls (within 1 ps), slower (5-7 ps) from the stromal side Chls, and very slow (100-200 ps) from a newly discovered 690 nm luminal trap. The excellent agreement between the experimental data with the previously presented Redfield-Förster exciton model of Lhca4 strongly supports the equilibration scheme of the bulk excitations with the dynamically localized CT on the stromal side. Thus, a complete picture of the energy transfer pathways leading to the population of the CT final trap within the whole Lhca4 complex is presented. In view of the environmental sensitivity of the CT contribution to the Lhca4 energy landscape, we speculate that one role of the CT states is to regulate the EET from the peripheral antenna to the PSI core.

Pathway Analysis for Targeted and Untargeted Metabolomics.

Recent advances in analytical techniques, particularly LC-MS, generate increasingly large and complex metabolomics datasets. Pathway analysis tools help place the experimental observations into relevant biological or disease context. This chapter provides an overview of the general concepts and common tools for pathway analysis, including Mummichog for untargeted metabolomics. Examples of pathway mapping, MetScape, and Mummichog are explained. This serves as both a practical tutorial and a timely survey of pathway analysis for label-free metabolomics data.

Nuclear magnetic resonance (NMR)-based metabolome profile evaluation in dairy cows with and without displaced abomasum

Background Displaced abomasum (DA) is a condition of dairy cows that severely impacts animal welfare and causes huge economic losses. Objective To assess the metabolic status of the disease using metabolomics in serum, urine and liver samples aimed at both water soluble and lipid soluble fractions. Methods Fifty Holstein multiparous cows with DA (42 left, 8 right) and 20 clinically healthy Holstein multiparous cows were used. Left DA was associated with concomitant ketosis in 19 animals and right in two. NMR-based metabolomics approach and hematological and biochemical analyses were performed. Statistical analysis was carried out on 1H-NMR data after they have been normalized using PQN method. Results Contrary to generated PCA score plots the OPLS-supervised method revealed differences between healthy animals and diseased ones based on serum water-soluble samples. While water and lipid soluble metabolites decreased in serum samples, fatty acid fractions and cholesterol were increased in liver samples in DA affected cows. The metabolomic and chemical profiles clearly revealed that cows with DA (especially with LDA) were at risk of ketosis and fatty liver. Serum hippuric acid concentration was significantly higher in healthy cows in comparison with LDA, whereas serum glycine concentration was reported higher for healthy when compared to RDA affected animals. Conclusion A biochemical network and pathway mapping revealed ‘valine, leucine and isoleucine biosynthesis’ and ‘phenylalanine, tyrosine and tryptophan biosynthesis’ as the most probable altered metabolic pathway in DA condition. Serum was advocated as the optimal biological matrix for the 1H-NMR analysis.

Pathway mapping reveals antiretroviral treatments' targeted cell cycle regulation in lung cancer

Abstract The human cell cycle is a tightly regulated process with checkpoints in place to ensure genomic integrity. Cyclin/cyclin dependent kinases (CDKs) complexes drive the progression of the cell cycle while CDK-inhibitors (CDKIs) halt the cell cycle. Deregulation of the cell cycle is a hallmark of lung cancer. TP53 and FOXO transcription factors share similar mechanisms in the regulation of the cell cycle. Lung carcinogenesis in the antiretroviral (ARV) era remains to be understood. This study aimed at mapping the biological pathways related to the human cell cycle that are influenced by the ARVs (Efavirenz-EFV and Lopinavir/ritonavir-LPV/r) treatment in A549 and MRC-5 lung cells. For this purpose, Reactome database was used to map these pathways. In addition, the Database for Annotation, Visualisation and Integrated Discovery (DAVID) was used for functional enrichment analysis in a set of genes and to visualise differentially expressed genes within a particular KEGG pathway, and also to perform Gene Ontology. Furthermore, the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database was used to determine the protein-protein interaction of the differentially expressed gene (DEG) targets. Reactome analysis revealed a decrease in DNA replication and an increase in response to external stimuli and DNA repair genes in both normal and adenocarcinoma lung cancer models. A further increase in apoptotic genes is observed in the cancer cells in response to ARV treatment. Interestingly, the FOXO pathway was also shown to be upregulated in the test (ARV) groups. KEGG pathway shows a reduction in cyclin/CDK activity in ARV treated models. STRING analysis illustrates a direct and strong interaction between DNA damage and response (DDR) genes upregulated by ARV exposure. Analysis from all three databases suggests the cytotoxic and anti-proliferative effects of EFV and LPV/r on lung cancer.

Learning Progressions, Paradigms, and Geographic Thinking in the Anthropocene

Learning progression research has the capability to connect thinking in the education sciences and geography. Learning progressions provide a map of the various pathways that students take to master a topic. The aim of this paper is to illustrate significant conceptual ties between learning progressions and disciplinary geography. Two construct paradigms overlap to form an entryway between educational and geographic thought: constructivism from education and possibilism within geography. The learning progression method can form a bridge between the two paradigms. Learning progression research in geography depends on being able to answer two questions. First, which geographic concepts should be tracked? Given the ongoing changes in global human-environmental systems, priority could be dedicated to the topics that stimulate synthesis thinking about the human-environment relationship in the Anthropocene, or “Age of Humans.” Second, how should geographers track advancement in learning about human-environment concepts? Learning progression research provides a method to document multiple aspects of advancement in student learning. But, geographic learning does not exist solely in the confines of the classroom. Furthermore, school districts vary in the amount and quality of geography that they allow. New understandings would come from a mixed-methods approach that addresses geographic understandings by the lifelong learner in the context of both formal and informal geography education.

A comprehensive pathway map of IL-18-mediated signalling.

Interleukin-18 (IL-18) is a member of the IL-1 family of cytokines and was initially described as an IFN-γ-inducing factor derived from anti-CD3-stimulated T-helper (Th)1 cells. IL-18 plays a significant role in the activation of hematopoietic cell types mediating both Th1 and Th2 responses and is the primary inducer of interferon-γ in these cells. The biological activity of IL-18 is mediated through its binding to the IL-18 receptor complex and activation of nuclear factor-κB (NF-κB), culminating in the production and release of several cytokines, chemokines, and cellular adhesion molecules. In certain cell types, IL-18 also activates mitogen-activated protein kinases (MAPKs) and phosphoinositide 3-kinase/ AKT serine/threonine kinase (PI3K/AKT) signaling modules leading to the production and release of proinflammatory cytokines. IL-18-mediated signaling acts as one of the vital components of the immunomodulatory cytokine networks involved in host defense, inflammation, and tissue regeneration. Albeit its biomedical importance, a comprehensive resource of IL-18 mediated signaling pathway is currently lacking. In this study, we report on the development of an integrated pathway map of IL-18/IL-18R signaling. The pathway map was developed through literature mining from published literature based on manual curation guidelines adapted from NetPath and includes information on 16 protein-protein interaction events, 38 enzyme-catalysis events, 12 protein translocation events, 26 activations/inhibition events, transcriptional regulators, 230 gene regulation events and 84 induced protein expression events. The IL-18 signaling pathway can be freely accessed through the WikiPathways database (https://www.wikipathways.org/index.php/Pathway:WP4754).

Abstract LB-A03: Molecular systems-guided imaging of multicellular in situ adaptation to targeted therapy in BRAF-mutant cancer

Abstract Adaptive signaling through receptor tyrosine kinases (RTKs) has been highly implicated in the resistance to drugs targeting constitutive RAS/RAF/MEK/ERK signaling, particularly in malignancies with constitutive V600 BRAF mutation. However, it has been difficult to systematically understand how such RTK-mediated bypass signaling is influenced by dynamic and localized interactions between tumor cells and neighboring stromal and immune populations. Here we present a pipeline that combines single-cell and bulk transcriptomic analysis from patients, with systems-level mapping of phosphosignaling pathways in co-cultures, to guide the longitudinal in vivo confocal (intravital) microscopy of adaptive bypass signaling in mouse models of BRAF-mutant cancer. This pipeline prioritizes key myeloid populations and phosphosignaling activities (including of ERK) to image in vivo. Intravital microscopy reveals how therapy-induced myeloid accumulation simultaneously shapes the local activity of multiple co-regulated signaling pathways in neighboring cancer cells, in a RTK-dependent manner. Overall, this work offers an integrative approach to quantitating multiple single-cell signaling pathway activities in the tumor microenvironment, and directly images the dynamics with which known cancer-cell autonomous mechanisms of targeted therapy resistance can be locally amplified by neighboring immune cell populations. Citation Format: Stephanie Wang, Ralph Weissleder, Douglas Lauffenburger, Miles Miller. Molecular systems-guided imaging of multicellular in situ adaptation to targeted therapy in BRAF-mutant cancer [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr LB-A03. doi:10.1158/1535-7163.TARG-19-LB-A03

Improving the accuracy of sentinel node detection in sentinel node biopsy for head and neck cutaneous malignancy

Introduction Recent advances in mapping of cutaneous lymphatic pathways shows that individuals have discreet and specific drainage patterns. These are most complex in the head and neck. SNB is shown to be most accurate (i.e there are fewer eventual false negatives) when individual nodes which are both hot and blue are harvested. However, the injection of labelled radiocolloid is not usually given by the same person as gives the blue dye, and we became aware that this could give rise to the injections being given in different peri-scar/perilesional positions, and thus give rise to the colloid and the blue dye not entering the same lymphatic channels, both as each other, and as any previously metastasising melanoma cells.

Immunoinformatics design of a novel multi-epitope peptide vaccine to combat multi-drug resistant infections caused by Vibrio vulnificus

Multi-drug resistant Vibrio vulnificus is a Gram-negative bacillus responsible for diseases, such as: sepsis, septicemia, gastroenteritis, and fatal necrotizing fasciitis in humans. The treatment and prevention of V. vulnificus infections are challenging because of resistance to antibiotics and the non-availability of a licensed vaccine. Considering this, an in-silico based approach comprising subtractive proteomics, immunoinformatics, molecular docking, and dynamics simulation studies is applied herein to identify potential epitope vaccine candidates for the mentioned pathogen. Two potential vaccine candidates: vibC and flgL are filtered based on essentiality, outer membrane localization, virulence, antigenic, pathway mapping, and cellular protein-protein network analysis. Using immunoinformatic tools, 9-mer B-cell derived T-cell antigenic epitopes are predicted for the said shortlisted two proteins that are demonstrating excellent affinity for predominant HLA allele (DRB1*0101) in human population. Screened peptides are used further in multi-epitope peptide designing and linked to an adjuvant to enhance the immunogenic properties of the designed construct. Furthermore, the construct was docked blindly to TLR4 immune receptor, and analyzed in conformational dynamics simulation to decipher the complex affinity and understand time dependent behavior, respectively. We expect this designed in silico construct to be useful for vaccinologists to evaluate its immune protective efficacy in in vivo animal models.

Susceptibility-weighted imaging for metabolic pathway mapping of low-dosage nanoparticles in organisms

Accurate and noninvasive monitoring of nanoparticles' (NPs) distribution and metabolism in organism is important, especially for NPs at low-dosage, but remains challenging due to the insufficient sensitivity and resolution of the existing imaging techniques. Herein, Fe3O4 NPs with different sizes were synthesized for low-dosage NPs' metabolism study with susceptibility weighted imaging (SWI) technique. SWI, as a functional MRI technique with phase postprocessing, can sensitively detect the differences of magnetic susceptibilities between tissues, so can measure the Fe3O4 contents even at low dosage in tissues. After in vivo intravenous injection, Fe3O4 NPs could be visually distinguished in major organs (kidney, liver, spleen) by SWI, and the corresponding content changes over time were also sensitively detected, but cannot be achieved via the conventional T2-weighted imaging (T2WI). With the SWI technique, the metabolic pathways of Fe3O4 NPs in body were mapped, revealing the critical dependence on the sizes of NPs. This is significant for the assessment of NPs’ metabolic time, toxicity risk, and application potentiality. Undoubtedly, SWI is a powerful tool for real-time metabolism low-dose NPs with designed characteristics (shapes, sizes, surface properties, etc.), and noninvasive detection of targets with magnetic nano-sensors in vivo.

Single-Cell Mapping of Stress Response and Cell Death Pathways in Acute Myeloid Leukemia Reveals Stressor-Specific Alterations and Distinct Response Patterns

Single-Cell Mapping of Stress Response and Cell Death Pathways in Acute Myeloid Leukemia Reveals Stressor-Specific Alterations and Distinct Response Patterns

Macular ganglion cell complex thinning in children with visual field defects due to central nervous system pathology.

PurposeTo study the relationship between macular ganglion cell complex (GCC) thickness and visual field defects (VFD) caused by central nervous system (CNS) lesions in children and evaluate the possibility of predicting VFD according to GCC maps.MethodsThe GCC maps of a group of children with VFD due to CNS lesions with respect of the vertical meridian in at least one eye (study group), as well as of children with other neuro-ophthalmological problems and healthy children were presented to two masked evaluators, who were asked to predict the patients’ VFD on the basis of GCC damage: the evaluators classified VFD as normal, hemianopia (homonymous or heteronymous) or diffuse.ResultsSeventeen patients were included in the study group, with a median age of 12 years. Fifteen had brain tumours and two epilepsy. The mean MD of the affected hemifields was −26.00 dB (SD 7.89 dB) versus −5.51 dB (SD 3.52 dB) for the nonaffected hemifields, p < 0.001. The mean GCC thickness was of 56.04 μm (SD 11.95 μm) in the affected hemiretinas versus 74.31 μm (SD 10.64 μm) for the non-affected, p < 0.001. Kappa coefficients between VFD and those estimated by the evaluators were 0.705 and 0.658 (p < 0.001) for evaluators 1 and 2.ConclusionsGCC thickness can reflect damage to the visual pathway and GCC maps may be useful to identify chiasmal and retrochiasmal lesions, since GCC atrophy in most of these cases respects the vertical meridian. GCC maps might be used as a surrogate marker for visual damage in patients unable to perform perimetry.

Integrated Multi-Level Omics to Characterize Bortezomib Resistance in Multiple Myeloma

Introduction The use of proteasome inhibitors (PIs), such as bortezomib (BTZ), in multiple myeloma (MM) has markedly increased the survival of newly diagnosed patients. Although advancements in therapeutic regimens in the past decade have improved prognosis, we lack knowledge of the mechanisms that lead to drug resistance. To assess the contributors to BTZ-resistance, we integrated steady-state metabolomics, proteomics and gene expression from two naïve and BTZ-resistant cell line models. In addition, gene expression associated with ex vivo PI resistance has been analyzed. Potential predictive biomarkers of PI-resistance and novel targets for combination therapy will be investigated. Methods Parental cell lines, RPMI 8226 and U266, were acquired from ATCC. 8226-B25 and U266-PSR (kind gift from Dr. S. Grant) BTZ-resistant derivatives were selected from their respective parental naïve cell lines by chronic drug exposure. Untargeted metabolomics, activity-based protein profiling (ABPP), and expression proteomics data were acquired using liquid chromatography-mass spectrometry. Gene expression profiles of both cell lines and ex vivo patient specimens were derived from RNAseq. Metabolomics and proteomics data were normalized with iterative rank order normalization. Significantly different genes, proteins, and metabolites were integrated for pathway mapping and identification of biomarkers for PI resistance. Results Consistent with previous findings, kynurenine, a product of tryptophan catabolism, is significantly altered in both of our cell line models. In the 8226 and 8226-B25 pair, PI resistance was associated with increased kynurenine and positively correlated with TDO2 and IDO1 overexpression consistent with published literature (Li et al. Nature Medicine, 2019, 25, 850-60). As expected, PSMB2, a subunit of the proteasome, is overexpressed and has a higher activity in both 8226-B25 and U266-PSR in the ABPP and expression proteomics, and higher expression in 8226-B25 RNAseq data. PSMB2 is also overexpressed and significant in the RNAseq patient data, increasingly from newly diagnosed/pre-treatment to early relapse (p-value 2E-4) and late relapse (p-value 0.0052). In addition, CD38 is an enzyme responsible for conversion of NAD+ to nicotinamide and ADP-ribose. It has increased expression in MM cells and is significantly downregulated in ABPP (log2 ratio -4.25, p-value 2E-13), expression proteomics (log2 ratio -2.5), and RNAseq (log2 ratio -2.6, p-value 5E-6) in the 8226-B25 BTZ-resistant cells. In the steady-state metabolomics of the 8226-B25 cells, ADP-ribose (log2 ratio 4.11, p-value 2E-5) is the most upregulated known metabolite. This change suggests a downstream result of resistance within this interaction and a potential biomarker of PI resistance. However, gene expression of CD38 in patient samples was relatively unchanged. CD38 was not detected in the U266-PSR proteomics or RNAseq data and ADP-ribose (log2 ratio -0.63, p-value 0.06) was not significantly altered, suggesting a different mechanism of resistance in this cell line. Conclusions Though common mechanisms of PI resistance were identified, our data clearly show that BTZ-resistance arises by heterogeneous means in the two cell line models, promoting the need for biomarkers that can determine resistance and predict response in individual patients (or cohorts). Decreased expression of CD38 in 8226-B25 could elucidate mechanisms of PI resistance and immune response evasion strategies of MM cells. Further investigation of CD38 expression as a BTZ-resistance biomarker could lead to improving combination therapies with monoclonal antibodies, such as daratumumab, and PIs in newly diagnosed MM patients by predicting response prior to treatment. Further examination of ADP-ribose metabolism may lead to the mechanism of synergy between PARP inhibitors and proteasome inhibitors. Ultimately, we plan to integrate and utilize these multi-omics approaches in patient specimens and improve MM patient care by identifying PI resistance biomarkers to predict patient response. Disclosures Shain: Adaptive Biotechnologies: Consultancy; Janssen: Membership on an entity's Board of Directors or advisory committees; AbbVie: Research Funding; Celgene: Membership on an entity's Board of Directors or advisory committees; Sanofi Genzyme: Membership on an entity's Board of Directors or advisory committees; Takeda: Membership on an entity's Board of Directors or advisory committees; Amgen: Membership on an entity's Board of Directors or advisory committees; Bristol-Myers Squibb: Membership on an entity's Board of Directors or advisory committees.

Low free triiodothyronineis predicts worsen neurological outcome of patients with acute ischemic stroke: a retrospective study with bioinformatics analysis

BackgroudPatients with acute ischemic stroke (AIS) often experience low serum free triiodothyronine (FT3), but the association of low FT3 with stroke severity, subtype and prognosis has not yet been thoroughly studied, and the molecular events underlying these clinical observation were also unclear.MethodsWe retrospectively collected 221 cases of AIS and 182 non-AIS cases with detailed clinical data from our department. FT3 concentrations were measured on admission to predict functional outcome within 3 months using multivariable models adjusted for other risk factors. Receiver operating characteristic (ROC) curves were calculated to define the best cutoff value of FT3 of stroke severity, subtypes and neurological outcome. Gene set enrichment, pathway mapping and network analyses of deferentially expressed genes (DEGs) were performed.ResultsFT3 was significantly decreased in AIS patients with National Institutes of Health Stroke Scale (NIHSS) > 3 and 3-months modified Rankin Scale (mRS) > 2. The cut-off value of FT3 for NIHSS on admission was 4.30 pmol/L. Also, FT3 level was significantly lower in large artery atherosclerosis (LAA) group and cardioembolism (CE) group than that in small vessel occlusion (SVO). FT3 value served as an independent predictor for neurological outcomes for which the cut-off value of FT3 was 4.38 pmol/l. Gene ontology (GO) analysis showed that the biological function of DEGs was mainly enriched in multicellur organism, neuron differentiation and cellular response to hypoxia. The cellular components were involved in extracelluar region, exosome and matrix, and the molecular functions were transcriptional activator activity, DNA binding and nuclear hormone receptor binding. Signal pathways analysis was indicative of neuroactive ligand-receptor interaction, thyroid hormone signaling pathway, and protein digestion and absorption these DEGs were involved in. Six related gene were identified as hubs from the protein-protein interaction (PPI) networks. Three modules were selected from PPI, of which MMP4, ADRA2C and EIF3E were recognized as the seed genes.ConclusionsLow FT3 value on admission was associated with stroke severity, subtype and prognosis. In addition, DEGs identified from bioinformatics analysis are likely to be candidates for elucidating clinical outcomes with low FT3, and provide us with therapeutic targets for improving stroke prognosis.