Browsing by Author "Zhang, Shijun"
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Item Comprehensive comparison of molecular portraits between cell lines and tumors in breast cancer(BioMed Central, 2016-08-22) Jiang, Guanglong; Zhang, Shijun; Yazdanparast, Aida; Li, Meng; Pawar, Aniruddha Vikram; Liu, Yunlong; Inavolu, Sai Mounika; Cheng, Lijun; Department of Medical and Molecular Genetics, IU School of MedicineBackground: Proper cell models for breast cancer primary tumors have long been the focal point in the cancer’s research. The genomic comparison between cell lines and tumors can investigate the similarity and dissimilarity and help to select right cell model to mimic tumor tissues to properly evaluate the drug reaction in vitro. In this paper, a comprehensive comparison in copy number variation (CNV), mutation, mRNA expression and protein expression between 68 breast cancer cell lines and 1375 primary breast tumors is conducted and presented. Results: Using whole genome expression arrays, strong correlations were observed between cells and tumors. PAM50 gene expression differentiated them into four major breast cancer subtypes: Luminal A and B, HER2amp, and Basal-like in both cells and tumors partially. Genomic CNVs patterns were observed between tumors and cells across chromosomes in general. High C > T and C > G trans-version rates were observed in both cells and tumors, while the cells had slightly higher somatic mutation rates than tumors. Clustering analysis on protein expression data can reasonably recover the breast cancer subtypes in cell lines and tumors. Although the drug-targeted proteins ER/PR and interesting mTOR/GSK3/TS2/PDK1/ER_P118 cluster had shown the consistent patterns between cells and tumor, low protein-based correlations were observed between cells and tumors. The expression consistency of mRNA verse protein between cell line and tumors reaches 0.7076. These important drug targets in breast cancer, ESR1, PGR, HER2, EGFR and AR have a high similarity in mRNA and protein variation in both tumors and cell lines. GATA3 and RP56KB1 are two promising drug targets for breast cancer. A total score developed from the four correlations among four molecular profiles suggests that cell lines, BT483, T47D and MDAMB453 have the highest similarity with tumors. Conclusions: The integrated data from across these multiple platforms demonstrates the existence of the similarity and dissimilarity of molecular features between breast cancer tumors and cell lines. The cell lines only mirror some but not all of the molecular properties of primary tumors. The study results add more evidence in selecting cell line models for breast cancer research.Item Correction: PhenoDEF: a corpus for annotating sentences with information of phenotype definitions in biomedical literature(BMC, 2022-07-20) Binkheder, Samar; Wu, Heng‑Yi; Quinney, Sara K.; Zhang, Shijun; Zitu, Md. Muntasir; Chiang, Chien‑Wei; Wang, Lei; Jones, Josette; Li, Lang; BioHealth Informatics, School of Informatics and ComputingPhenoDEF: a corpus for annotating sentences with information of phenotype definitions in biomedical literature. Binkheder S, Wu HY, Quinney SK, Zhang S, Zitu MM, Chiang CW, Wang L, Jones J, Li L. J Biomed Semantics. 2022 Jun 11;13(1):17. doi: 10.1186/s13326-022-00272-6. PMID: 35690873Item Exogenous Gene Transmission of Isocitrate Dehydrogenase 2 Mimics Ischemic Preconditioning Protection(American Society of Nephrology, 2018-04) Kolb, Alexander L.; Corridon, Peter R.; Zhang, Shijun; Xu, Weimin; Witzmann, Frank A.; Collett, Jason A.; Rhodes, George J.; Winfree, Seth; Bready, Devin; Pfeffenberger, Zechariah J.; Pomerantz, Jeremy M.; Hato, Takashi; Nagami, Glenn T.; Molitoris, Bruce A.; Basile, David P.; Atkinson, Simon J.; Bacallao, Robert L.; Biology, School of ScienceIschemic preconditioning confers organ-wide protection against subsequent ischemic stress. A substantial body of evidence underscores the importance of mitochondria adaptation as a critical component of cell protection from ischemia. To identify changes in mitochondria protein expression in response to ischemic preconditioning, we isolated mitochondria from ischemic preconditioned kidneys and sham-treated kidneys as a basis for comparison. The proteomic screen identified highly upregulated proteins, including NADP+-dependent isocitrate dehydrogenase 2 (IDH2), and we confirmed the ability of this protein to confer cellular protection from injury in murine S3 proximal tubule cells subjected to hypoxia. To further evaluate the role of IDH2 in cell protection, we performed detailed analysis of the effects of Idh2 gene delivery on kidney susceptibility to ischemia-reperfusion injury. Gene delivery of IDH2 before injury attenuated the injury-induced rise in serum creatinine (P<0.05) observed in controls and increased the mitochondria membrane potential (P<0.05), maximal respiratory capacity (P<0.05), and intracellular ATP levels (P<0.05) above those in controls. This communication shows that gene delivery of Idh2 can confer organ-wide protection against subsequent ischemia-reperfusion injury and mimics ischemic preconditioning.Item Hydrodynamic delivery for prevention of acute kidney injury(2015) Zhang, Shijun; Atkinson, Simon; Bacallao, Robert; Blazer-Yost, BonnieThe young field of gene therapy offers the promises of significant progress towards the treatment of many different types of human diseases. Gene therapy has been proposed as an innovative way to treat Acute Kidney Injury (AKI). Through proteomic analysis, the upregulation of two enzymes, IDH2 and SULT1C2, within the mitochondrial fraction has been identified following ischemic preconditioning, a treatment by which rat kidneys are protected from ischemia. Using the hydrodynamic fluid gene delivery technique, we were able to upregulate the expression of IDH2 and SULT1C2 in the kidney. We found that the delivery of IDH2 plasmid through hydrodynamic fluid delivery to the kidney resulted in increased mitochondrial oxygen respiration compared with injured kidneys without gene delivery. We also found that renal ischemic preconditioning altered the membrane fluidity of mitochondria. In conclusion, our study supports the idea that upregulated expression of IDH2 in mitochondria can protect the kidney against AKI, while the protective function of upregulated SULT1C2 needs to be further studied.Item PhenoDEF: a corpus for annotating sentences with information of phenotype definitions in biomedical literature(Springer, 2022) Binkheder, Samar; Wu, Heng-Yi; Quinney, Sara K.; Zhang, Shijun; Zitu, Md. Muntasir; Chiang, Chien-Wei; Wang, Lei; Jones, Josette; Li, Lang; BioHealth Informatics, School of Informatics and ComputingBackground Adverse events induced by drug-drug interactions are a major concern in the United States. Current research is moving toward using electronic health record (EHR) data, including for adverse drug events discovery. One of the first steps in EHR-based studies is to define a phenotype for establishing a cohort of patients. However, phenotype definitions are not readily available for all phenotypes. One of the first steps of developing automated text mining tools is building a corpus. Therefore, this study aimed to develop annotation guidelines and a gold standard corpus to facilitate building future automated approaches for mining phenotype definitions contained in the literature. Furthermore, our aim is to improve the understanding of how these published phenotype definitions are presented in the literature and how we annotate them for future text mining tasks. Results Two annotators manually annotated the corpus on a sentence-level for the presence of evidence for phenotype definitions. Three major categories (inclusion, intermediate, and exclusion) with a total of ten dimensions were proposed characterizing major contextual patterns and cues for presenting phenotype definitions in published literature. The developed annotation guidelines were used to annotate the corpus that contained 3971 sentences: 1923 out of 3971 (48.4%) for the inclusion category, 1851 out of 3971 (46.6%) for the intermediate category, and 2273 out of 3971 (57.2%) for exclusion category. The highest number of annotated sentences was 1449 out of 3971 (36.5%) for the “Biomedical & Procedure” dimension. The lowest number of annotated sentences was 49 out of 3971 (1.2%) for “The use of NLP”. The overall percent inter-annotator agreement was 97.8%. Percent and Kappa statistics also showed high inter-annotator agreement across all dimensions. Conclusions The corpus and annotation guidelines can serve as a foundational informatics approach for annotating and mining phenotype definitions in literature, and can be used later for text mining applications.Item Subpathway Analysis of Transcriptome Profiles Reveals New Molecular Mechanisms of Acquired Chemotherapy Resistance in Breast Cancer(MDPI, 2022-10-05) Huo, Yang; Shao, Shuai; Liu, Enze; Li, Jin; Tian, Zhen; Wu, Xue; Zhang, Shijun; Stover, Daniel; Wu, Huanmei; Cheng, Lijun; Li, Lang; Biostatistics and Health Data Science, Richard M. Fairbanks School of Public HealthChemoresistance has been a major challenge in the treatment of patients with breast cancer. The diverse omics platforms and small sample sizes reported in the current studies of chemoresistance in breast cancer limit the consensus regarding the underlying molecular mechanisms of chemoresistance and the applicability of these study findings. Therefore, we built two transcriptome datasets for patients with chemotherapy-resistant breast cancers—one comprising paired transcriptome samples from 40 patients before and after chemotherapy and the second including unpaired samples from 690 patients before and 45 patients after chemotherapy. Subsequent conventional pathway analysis and new subpathway analysis using these cohorts uncovered 56 overlapping upregulated genes (false discovery rate [FDR], 0.018) and 36 downregulated genes (FDR, 0.016). Pathway analysis revealed the activation of several pathways in the chemotherapy-resistant tumors, including those of drug metabolism, MAPK, ErbB, calcium, cGMP-PKG, sphingolipid, and PI3K-Akt, as well as those activated by Cushing’s syndrome, human papillomavirus (HPV) infection, and proteoglycans in cancers, and subpathway analysis identified the activation of several more, including fluid shear stress, Wnt, FoxO, ECM-receptor interaction, RAS signaling, Rap1, mTOR focal adhesion, and cellular senescence (FDR < 0.20). Among these pathways, those associated with Cushing’s syndrome, HPV infection, proteoglycans in cancer, fluid shear stress, and focal adhesion have not yet been reported in breast cancer chemoresistance. Pathway and subpathway analysis of a subset of triple-negative breast cancers from the two cohorts revealed activation of the identical chemoresistance pathways.Item Translational high-dimensional drug Interaction discovery and validation using health record databases and pharmacokinetics models(Wiley, 2017) Chiang, Chien-Wei; Zhang, Pengyue; Wang, Xueying; Wang, Lei; Zhang, Shijun; Ning, Xia; Shen, Li; Quinney, Sara K.; Li, Lang; Medical and Molecular Genetics, School of MedicinePolypharmacy increases the risk of drug-drug interactions (DDI's). Combining epidemiological studies with pharmacokinetic modeling, we detected and evaluated high-dimensional DDI's among thirty frequent drugs. Multi-drug combinations that increased risk of myopathy were identified in the FDA Adverse Event Reporting System (FAERS) and electronic medical record (EMR) databases by a mixture drug-count response model. CYP450 inhibition was estimated among the 30 drugs in the presence of 1 to 4 inhibitors using in vitro in vivo extrapolation. Twenty-eight 3-way and 43 4-way DDI's had significant myopathy risk in both databases and predicted increases in the area under the concentration time curve ratio (AUCR) >2-fold. The HD-DDI of omeprazole, fluconazole and clonidine was associated with a 6.41-fold (FAERS) and 18.46-fold (EMR) increase risk of myopathy (LFDR<0.005); the AUCR of omeprazole in this combination was 9.35.The combination of health record informatics and pharmacokinetic modeling is a powerful translational approach to detect high-dimensional DDI's.