Browsing by Author "Zhang, Bin"
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Item An atlas of substrate specificities for the human serine/threonine kinome(Springer Nature, 2023) Johnson, Jared L.; Yaron, Tomer M.; Huntsman, Emily M.; Kerelsky, Alexander; Song, Junho; Regev, Amit; Lin, Ting-Yu; Liberatore, Katarina; Cizin, Daniel M.; Cohen, Benjamin M.; Vasan, Neil; Ma, Yilun; Krismer, Konstantin; Torres Robles, Jaylissa; van de Kooij, Bert; van Vlimmeren, Anne E.; Andrée-Busch, Nicole; Käufer, Norbert F.; Dorovkov, Maxim V.; Ryazanov, Alexey G.; Takagi, Yuichiro; Kastenhuber, Edward R.; Goncalves, Marcus D.; Hopkins, Benjamin D.; Elemento, Olivier; Taatjes, Dylan J.; Maucuer, Alexandre; Yamashita, Akio; Degterev, Alexei; Uduman, Mohamed; Lu, Jingyi; Landry, Sean D.; Zhang, Bin; Cossentino, Ian; Linding, Rune; Blenis, John; Hornbeck, Peter V.; Turk, Benjamin E.; Yaffe, Michael B.; Cantley, Lewis C.; Biochemistry and Molecular Biology, School of MedicineProtein phosphorylation is one of the most widespread post-translational modifications in biology (1,2). With advances in mass-spectrometry-based phosphoproteomics, 90,000 sites of serine and threonine phosphorylation have so far been identified, and several thousand have been associated with human diseases and biological processes (3,4). For the vast majority of phosphorylation events, it is not yet known which of the more than 300 protein serine/threonine (Ser/Thr) kinases encoded in the human genome are responsible (3). Here we used synthetic peptide libraries to profile the substrate sequence specificity of 303 Ser/Thr kinases, comprising more than 84% of those predicted to be active in humans. Viewed in its entirety, the substrate specificity of the kinome was substantially more diverse than expected and was driven extensively by negative selectivity. We used our kinome-wide dataset to computationally annotate and identify the kinases capable of phosphorylating every reported phosphorylation site in the human Ser/Thr phosphoproteome. For the small minority of phosphosites for which the putative protein kinases involved have been previously reported, our predictions were in excellent agreement. When this approach was applied to examine the signalling response of tissues and cell lines to hormones, growth factors, targeted inhibitors and environmental or genetic perturbations, it revealed unexpected insights into pathway complexity and compensation. Overall, these studies reveal the intrinsic substrate specificity of the human Ser/Thr kinome, illuminate cellular signalling responses and provide a resource to link phosphorylation events to biological pathways.Item Artificial intelligence framework identifies candidate targets for drug repurposing in Alzheimer’s disease(BMC, 2022-01-10) Fang, Jiansong; Zhang, Pengyue; Wang, Quan; Chiang, Chien‑Wei; Zhou, Yadi; Hou, Yuan; Xu, Jielin; Chen, Rui; Zhang, Bin; Lewis, Stephen J.; Leverenz, James B.; Pieper, Andrew A.; Li, Bingshan; Li, Lang; Cummings, Jeffrey; Cheng, Feixiong; Biostatistics and Health Data Science, School of MedicineBackground: Genome-wide association studies (GWAS) have identified numerous susceptibility loci for Alzheimer's disease (AD). However, utilizing GWAS and multi-omics data to identify high-confidence AD risk genes (ARGs) and druggable targets that can guide development of new therapeutics for patients suffering from AD has heretofore not been successful. Methods: To address this critical problem in the field, we have developed a network-based artificial intelligence framework that is capable of integrating multi-omics data along with human protein-protein interactome networks to accurately infer accurate drug targets impacted by GWAS-identified variants to identify new therapeutics. When applied to AD, this approach integrates GWAS findings, multi-omics data from brain samples of AD patients and AD transgenic animal models, drug-target networks, and the human protein-protein interactome, along with large-scale patient database validation and in vitro mechanistic observations in human microglia cells. Results: Through this approach, we identified 103 ARGs validated by various levels of pathobiological evidence in AD. Via network-based prediction and population-based validation, we then showed that three drugs (pioglitazone, febuxostat, and atenolol) are significantly associated with decreased risk of AD compared with matched control populations. Pioglitazone usage is significantly associated with decreased risk of AD (hazard ratio (HR) = 0.916, 95% confidence interval [CI] 0.861-0.974, P = 0.005) in a retrospective case-control validation. Pioglitazone is a peroxisome proliferator-activated receptor (PPAR) agonist used to treat type 2 diabetes, and propensity score matching cohort studies confirmed its association with reduced risk of AD in comparison to glipizide (HR = 0.921, 95% CI 0.862-0.984, P = 0.0159), an insulin secretagogue that is also used to treat type 2 diabetes. In vitro experiments showed that pioglitazone downregulated glycogen synthase kinase 3 beta (GSK3β) and cyclin-dependent kinase (CDK5) in human microglia cells, supporting a possible mechanism-of-action for its beneficial effect in AD. Conclusions: In summary, we present an integrated, network-based artificial intelligence methodology to rapidly translate GWAS findings and multi-omics data to genotype-informed therapeutic discovery in AD.Item Clinical and Biological Activity of Chemoimmunotherapy in Advanced Endometrial Adenocarcinoma: A Phase II Trial of the Big Ten Cancer Research Consortium(American Association for Cancer Research, 2022) Barber, Emma L.; Chen, Siqi; Pineda, Mario Javier; Robertson, Sharon E.; Hill, Emily K.; Teoh, Deanna; Schilder, Jeanne; O’Shea, Kaitlyn L.; Kocherginsky, Masha; Zhang, Bin; Matei, Daniela; Obstetrics and Gynecology, School of MedicinePurpose: The objective of this study was to assess the efficacy and safety of pembrolizumab in combination with standard carboplatin/paclitaxel in patients with advanced endometrial cancer (EC). Patients and methods: This single-arm, open-label, multi-center phase II study enrolled patients with RECIST measurable advanced EC. Patients could have received < 1 prior platinum-based regimen and < one non-platinum chemotherapy. The primary endpoint was objective response rate (ORR). Planned sample size of 46 subjects provided 80% power to detect 15% ORR improvement compared to historical control rate of 50%. Results: 46 patients were enrolled, and 43 were evaluable for ORR. Median age was 66 (range: 43-86). Thirty-four (73.9%) patients had recurrent and 12 (26.1%) primary metastatic EC. Patients received carboplatin AUC 6, paclitaxel 175mg/m2 and pembrolizumab 200mg IV every 3 weeks for up to 6 cycles. ORR was 74.4% (32/43), higher than historic controls (p = 0.001). Median PFS was 10.6 months (95% CI 8.3-13.9 months). The most common grade 1-2 treatment related adverse event (TRAEs) included anemia (56.5%), alopecia (47.8%), fatigue (47.8%) and neuropathy (13%), while the most common grade 3-4 TRAEs were lymphopenia, leukopenia, and anemia (19.6% each). High-dimensional spectral flow cytometry (CyTEK) identified enrichment in peripheral CD8+ and CD4+ T cell populations at baseline in responders. The CD8+ T cell compartment in responders exhibited greater expression levels of PD-1 and PD-L1 and higher abundance of effector memory CD8+ cells compared to non-responders. Conclusions: Addition of pembrolizumab to carboplatin and paclitaxel for advanced EC was tolerated and improved ORR compared to historical outcomes.Item Glucocorticoid Receptor β Acts As a Co-activator of T-Cell Factor 4 and Enhances Glioma Cell Proliferation(Springer, 2015-12) Wang, Qian; Lu, Pei-Hua; Shi, Zhi-Feng; Xu, Yan-Juan; Xiang, Jie; Wang, Yan-Xia; Deng, Ling-Xiao; Xie, Ping; Yin, Ying; Zhang, Bin; Mu, Hui-Jun; Qiao, Wei-Zhen; Cui, Hua; Zou, Jian; Department of Neurological Surgery, IU School of MedicineWe previously reported that glucocorticoid receptor β (GRβ) regulates injury-mediated astrocyte activation and contributes to glioma pathogenesis via modulation of β-catenin/T-cell factor/lymphoid enhancer factor (TCF/LEF) transcriptional activity. The aim of this study was to characterize the mechanism behind cross-talk between GRβ and β-catenin/TCF in the progression of glioma. Here, we reported that GRβ knockdown reduced U118 and Shg44 glioma cell proliferation in vitro and in vivo. Mechanistically, we found that GRβ knockdown decreased TCF/LEF transcriptional activity without affecting β-catenin/TCF complex. Both GRα and GRβ directly interact with TCF-4, while only GRβ is required for sustaining TCF/LEF activity under hormone-free condition. GRβ bound to the N-terminus domain of TCF-4 its influence on Wnt signaling required both ligand- and DNA-binding domains (LBD and DBD, respectively). GRβ and TCF-4 interaction is enough to maintain the TCF/LEF activity at a high level in the absence of β-catenin stabilization. Taken together, these results suggest a novel cross-talk between GRβ and TCF-4 which regulates Wnt signaling and the proliferation in gliomas.Item Identification and transcriptomic assessment of latent profile pediatric septic shock phenotypes(Springer Nature, 2024-07-17) Atreya, Mihir R.; Huang, Min; Moore, Andrew R.; Zheng, Hong; Hasin-Brumshtein, Yehudit; Fitzgerald, Julie C.; Weiss, Scott L.; Cvijanovich, Natalie Z.; Bigham, Michael T.; Jain, Parag N.; Schwarz, Adam J.; Lutfi, Riad; Nowak, Jeffrey; Thomas, Neal J.; Quasney, Michael; Dahmer, Mary K.; Baines, Torrey; Haileselassie, Bereketeab; Lautz, Andrew J.; Stanski, Natalja L.; Standage, Stephen W.; Kaplan, Jennifer M.; Zingarelli, Basilia; Sahay, Rashmi; Zhang, Bin; Sweeney, Timothy E.; Khatri, Purvesh; Sanchez-Pinto, L. Nelson; Kamaleswaran, Rishikesan; Pediatrics, School of MedicineBackground: Sepsis poses a grave threat, especially among children, but treatments are limited owing to heterogeneity among patients. We sought to test the clinical and biological relevance of pediatric septic shock subclasses identified using reproducible approaches. Methods: We performed latent profile analyses using clinical, laboratory, and biomarker data from a prospective multi-center pediatric septic shock observational cohort to derive phenotypes and trained a support vector machine model to assign phenotypes in an internal validation set. We established the clinical relevance of phenotypes and tested for their interaction with common sepsis treatments on patient outcomes. We conducted transcriptomic analyses to delineate phenotype-specific biology and inferred underlying cell subpopulations. Finally, we compared whether latent profile phenotypes overlapped with established gene-expression endotypes and compared survival among patients based on an integrated subclassification scheme. Results: Among 1071 pediatric septic shock patients requiring vasoactive support on day 1 included, we identified two phenotypes which we designated as Phenotype 1 (19.5%) and Phenotype 2 (80.5%). Membership in Phenotype 1 was associated with ~ fourfold adjusted odds of complicated course relative to Phenotype 2. Patients belonging to Phenotype 1 were characterized by relatively higher Angiopoietin-2/Tie-2 ratio, Angiopoietin-2, soluble thrombomodulin (sTM), interleukin 8 (IL-8), and intercellular adhesion molecule 1 (ICAM-1) and lower Tie-2 and Angiopoietin-1 concentrations compared to Phenotype 2. We did not identify significant interactions between phenotypes, common treatments, and clinical outcomes. Transcriptomic analysis revealed overexpression of genes implicated in the innate immune response and driven primarily by developing neutrophils among patients designated as Phenotype 1. There was no statistically significant overlap between established gene-expression endotypes, reflective of the host adaptive response, and the newly derived phenotypes, reflective of the host innate response including microvascular endothelial dysfunction. However, an integrated subclassification scheme demonstrated varying survival probabilities when comparing patient endophenotypes. Conclusions: Our research underscores the reproducibility of latent profile analyses to identify pediatric septic shock phenotypes with high prognostic relevance. Pending validation, an integrated subclassification scheme, reflective of the different facets of the host response, holds promise to inform targeted intervention among those critically ill.Item Integrative metabolomics-genomics approach reveals key metabolic pathways and regulators of Alzheimer's disease(Wiley, 2022) Horgusluoglu, Emrin; Neff, Ryan; Song, Won-Min; Wang, Minghui; Wang, Qian; Arnold, Matthias; Krumsiek, Jan; Galindo-Prieto, Beatriz; Ming, Chen; Nho, Kwangsik; Kastenmüller, Gabi; Han, Xianlin; Baillie, Rebecca; Zeng, Qi; Andrews, Shea; Cheng, Haoxiang; Hao, Ke; Goate, Alison; Bennett, David A.; Saykin, Andrew J.; Kaddurah-Daouk, Rima; Zhang, Bin; Alzheimer's Disease Neuroimaging Initiative (ADNI); Alzheimer Disease Metabolomics Consortium; Radiology and Imaging Sciences, School of MedicineMetabolites, the biochemical products of the cellular process, can be used to measure alterations in biochemical pathways related to the pathogenesis of Alzheimer's disease (AD). However, the relationships between systemic abnormalities in metabolism and the pathogenesis of AD are poorly understood. In this study, we aim to identify AD‐specific metabolomic changes and their potential upstream genetic and transcriptional regulators through an integrative systems biology framework for analyzing genetic, transcriptomic, metabolomic, and proteomic data in AD. Metabolite co‐expression network analysis of the blood metabolomic data in the Alzheimer's Disease Neuroimaging Initiative (ADNI) shows short‐chain acylcarnitines/amino acids and medium/long‐chain acylcarnitines are most associated with AD clinical outcomes, including episodic memory scores and disease severity. Integration of the gene expression data in both the blood from the ADNI and the brain from the Accelerating Medicines Partnership Alzheimer's Disease (AMP‐AD) program reveals ABCA1 and CPT1A are involved in the regulation of acylcarnitines and amino acids in AD. Gene co‐expression network analysis of the AMP‐AD brain RNA‐seq data suggests the CPT1A‐ and ABCA1‐centered subnetworks are associated with neuronal system and immune response, respectively. Increased ABCA1 gene expression and adiponectin protein, a regulator of ABCA1, correspond to decreased short‐chain acylcarnitines and amines in AD in the ADNI. In summary, our integrated analysis of large‐scale multiomics data in AD systematically identifies novel metabolites and their potential regulators in AD and the findings pave a way for not only developing sensitive and specific diagnostic biomarkers for AD but also identifying novel molecular mechanisms of AD pathogenesis.Item Interobserver Agreement for CT and MRI Findings of Chronic Pancreatitis in Children: A Multicenter Ancillary Study Under the INSPPIRE Consortium(American Roentgen Ray Society, 2022) Trout, Andrew T.; Abu-El-Haija, Maisam; Anupindi, Sudha A.; Marine, Megan B.; Murati, Michael; Phelps, Andrew S.; Rees, Mitchell A.; Squires, Judy H.; Ellery, Kate M.; Gariepy, Cheryl E.; Maqbool, Asim; McFerron, Brian A.; Perito, Emily R.; Schwarzenberg, Sarah J.; Zhang, Bin; Andersen, Dana K.; Lowe, Mark E.; Uc, Aliye; Consortium for the Study of Chronic Pancreatitis, Diabetes and Pancreatic Cancer (CPDPC); Radiology and Imaging Sciences, School of MedicineBackground: Imaging findings represent key criteria for diagnosing chronic pancreatitis in children. Understanding radiologists’ agreement for imaging findings is critical to standardizing and optimizing diagnostic criteria. Objective: To evaluate the interobserver agreement among experienced pediatric radiologists for subjective, quantitative, and semi-quantitative imaging findings of chronic pancreatitis in children. Methods: In this retrospective study, CT or MRI examinations performed in children with chronic pancreatitis were submitted by six sites participating in the INSPPIRE consortium. One pediatric radiologist from each of the six sites reviewed examinations; three of the radiologists independently reviewed all CT examinations, and the other three radiologists independently reviewed all MRI examinations. Reviewers recorded 13 categorical imaging findings of chronic pancreatitis and measured pancreas thickness and duct diameter. Agreement was assessed using kappa coefficients for the categorical variables and intraclass correlation coefficients (ICC) for the continuous measures. Results: A total of 76 CT and 80 MRI examinations performed in 110 children (mean age, 11.3±4.6 years; 65 girls, 45 boys) were reviewed. For CT, kappa coefficients for categorical findings ranged from −0.01 to 0.81, with relatively high kappa coefficients for parenchymal calcification (κ=0.81), main pancreatic duct dilation (κ=0.63), and atrophy (κ=0.52). ICCs for parenchymal thickness measurements ranged from 0.57 in the pancreas head to 0.80 in the body and tail. ICC for duct diameter was 0.85. For MRI, kappa coefficients for categorical findings ranged from −0.01 to 0.74, with relatively high kappa coefficients for main duct irregularity (κ=0.74), side branch dilation (κ=0.70), number of dilated side branches (κ=0.65), and main duct dilation (κ=0.64); kappa coefficient for atrophy was 0.52. ICCs for parenchymal thickness measurements ranged from 0.59 in the pancreas head to 0.68 in the tail. ICC for duct diameter was 0.77. Conclusion: Interobserver agreement was fair to moderate for most CT and MRI findings of chronic pancreatitis in children. Clinical Impact: This study highlights challenges for the imaging diagnosis of pediatric chronic pancreatitis. Standardized and/or objective criteria are needed given the importance of imaging in diagnosis.Item Osteocyte-Intrinsic TGF-β Signaling Regulates Bone Quality through Perilacunar/Canalicular Remodeling(Elsevier, 2017-11-28) Dole, Neha S.; Mazur, Courtney M.; Acevedo, Claire; Lopez, Justin P.; Monteiro, David A.; Fowler, Tristan W.; Gludovatz, Bernd; Walsh, Flynn; Regan, Jenna N.; Messina, Sara; Evans, Daniel S.; Lang, Thomas F.; Zhang, Bin; Ritchie, Robert O.; Mohammad, Khalid S.; Alliston, Tamara; Medicine, School of MedicineSummary Poor bone quality contributes to bone fragility in diabetes, aging, and osteogenesis imperfecta. However, the mechanisms controlling bone quality are not well understood, contributing to the current lack of strategies to diagnose or treat bone quality deficits. Transforming growth factor beta (TGF-β) signaling is a crucial mechanism known to regulate the material quality of bone, but its cellular target in this regulation is unknown. Studies showing that osteocytes directly remodel their perilacunar/canalicular matrix led us to hypothesize that TGF-β controls bone quality through perilacunar/canalicular remodeling (PLR). Using inhibitors and mice with an osteocyte-intrinsic defect in TGF-β signaling (TβRIIocy−/−), we show that TGF-β regulates PLR in a cell-intrinsic manner to control bone quality. Altogether, this study emphasizes that osteocytes are key in executing the biological control of bone quality through PLR, thereby highlighting the fundamental role of osteocyte-mediated PLR in bone homeostasis and fragility.Item Revisiting Post-ICU Admission Fluid Balance Across Pediatric Sepsis Mortality Risk Strata: A Secondary Analysis of a Prospective Observational Cohort Study(Wolters Kluwer, 2024-01-16) Atreya, Mihir R.; Cvijanovich, Natalie Z.; Fitzgerald, Julie C.; Weiss, Scott L.; Bigham, Michael T.; Jain, Parag N.; Abulebda, Kamal; Lutfi, Riad; Nowak, Jeffrey; Thomas, Neal J.; Baines, Torrey; Quasney, Michael; Haileselassie, Bereketeab; Sahay, Rashmi; Zhang, Bin; Alder, Matthew N.; Stanski, Natalja L.; Goldstein, Stuart L.; Pediatrics, School of MedicineOBJECTIVES: Post-ICU admission cumulative positive fluid balance (PFB) is associated with increased mortality among critically ill patients. We sought to test whether this risk varied across biomarker-based risk strata upon adjusting for illness severity, presence of severe acute kidney injury (acute kidney injury), and use of continuous renal replacement therapy (CRRT) in pediatric septic shock. DESIGN: Ongoing multicenter prospective observational cohort. SETTING: Thirteen PICUs in the United States (2003–2023). PATIENTS: Six hundred and eighty-one children with septic shock. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: Cumulative percent PFB between days 1 and 7 (days 1–7 %PFB) was determined. Primary outcome of interest was complicated course defined as death or persistence of greater than or equal to two organ dysfunctions by day 7. Pediatric Sepsis Biomarker Risk Model (PERSEVERE)-II biomarkers were used to assign mortality probability and categorize patients into high mortality (n = 91), intermediate mortality (n = 134), and low mortality (n = 456) risk strata. Cox proportional hazard regression models with adjustment for PERSEVERE-II mortality probability, presence of sepsis-associated acute kidney injury on day 3, and use of CRRT, demonstrated that time-dependent variable days 1–7%PFB was independently associated with an increased hazard of complicated course. Risk-stratified analyses revealed that each 10% increase in days 1–7 %PFB was associated with increased hazard of complicated course only among patients with high mortality risk strata (adjusted hazard ratio 1.24 (95% CI, 1.08–1.43), p = 0.003). However, this association was not causally mediated by PERSEVERE-II biomarkers. CONCLUSIONS: Our data demonstrate the influence of cumulative %PFB on the risk of complicated course in pediatric septic shock. Contrary to our previous report, this risk was largely driven by patients categorized as having a high mortality risk based on PERSEVERE-II biomarkers. Incorporation of such prognostic enrichment tools in randomized trials of restrictive fluid management or early initiation of de-escalation strategies may inform targeted application of such interventions among at-risk patients.Item Systems modeling of white matter microstructural abnormalities in Alzheimer's disease(Elsevier, 2020-02-04) Horgusluoglu-Moloch, Emrin; Xiao, Gaoyu; Wang, Minghui; Wang, Qian; Zhou, Xianxiao; Nho, Kwangsik; Saykin, Andrew J.; Schadt, Eric; Zhang, Bin; Alzheimer's Disease Neuroimaging Initiative (ADNI); Radiology and Imaging Sciences, School of MedicineINTRODUCTION: Microstructural abnormalities in white matter (WM) are often reported in Alzheimer's disease (AD). However, it is unclear which brain regions have the strongest WM changes in presymptomatic AD and what biological processes underlie WM abnormality during disease progression. METHODS: We developed a systems biology framework to integrate matched diffusion tensor imaging (DTI), genetic and transcriptomic data to investigate regional vulnerability to AD and identify genetic risk factors and gene subnetworks underlying WM abnormality in AD. RESULTS: We quantified regional WM abnormality and identified most vulnerable brain regions. A SNP rs2203712 in CELF1 was most significantly associated with several DTI-derived features in the hippocampus, the top ranked brain region. An immune response gene subnetwork in the blood was most correlated with DTI features across all the brain regions. DISCUSSION: Incorporation of image analysis with gene network analysis enhances our understanding of disease progression and facilitates identification of novel therapeutic strategies for AD.