Browsing by Author "Bathe, Oliver F."

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    development of a multiplexed protein biomarker assay for colorectal cancer
    (2008) Koppel, Jennifer S.; Bathe, Oliver F.; Schriemer, David C.
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    Frozen tissue coring and layered histological analysis improves cell type-specific proteogenomic characterization of pancreatic adenocarcinoma
    (2024-01-30) Savage, Sara R.; Wang, Yuefan; Chen, Lijun; Jewell, Scott; Newton, Chelsea; Dou, Yongchao; Li, Qing K.; Bathe, Oliver F.; Robles, Ana I.; Omenn, Gilbert S.; Thiagarajan, Mathangi; Zhang, Hui; Hostetter, Galen; Zhang, Bing
    Abstract Background Omics characterization of pancreatic adenocarcinoma tissue is complicated by the highly heterogeneous and mixed populations of cells. We evaluate the feasibility and potential benefit of using a coring method to enrich specific regions from bulk tissue and then perform proteogenomic analyses. Methods We used the Biopsy Trifecta Extraction (BioTExt) technique to isolate cores of epithelial-enriched and stroma-enriched tissue from pancreatic tumor and adjacent tissue blocks. Histology was assessed at multiple depths throughout each core. DNA sequencing, RNA sequencing, and proteomics were performed on the cored and bulk tissue samples. Supervised and unsupervised analyses were performed based on integrated molecular and histology data. Results Tissue cores had mixed cell composition at varying depths throughout. Average cell type percentages assessed by histology throughout the core were better associated with KRAS variant allele frequencies than standard histology assessment of the cut surface. Clustering based on serial histology data separated the cores into three groups with enrichment of neoplastic epithelium, stroma, and acinar cells, respectively. Using this classification, tumor overexpressed proteins identified in bulk tissue analysis were assigned into epithelial- or stroma-specific categories, which revealed novel epithelial-specific tumor overexpressed proteins. Conclusions Our study demonstrates the feasibility of multi-omics data generation from tissue cores, the necessity of interval H&E stains in serial histology sections, and the utility of coring to improve analysis over bulk tissue data.
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    Identification and Characterization of Different Metabolic Subtypes in Cancer
    (2020-01-07) Pervin, Jannat; Bathe, Oliver F.; Tang, Patricia A.; Wang, Edwin
    Cancer is a leading cause of death worldwide. Genomics based approaches represent a dominant approach in oncological research. However, multiple processes can modify genetic information and impact cancer’s phenotype in a non-coding manner such as epigenetic events, transcription of various splice variants, expression of non-coding RNA and miRNA, and post-translational modifications of proteins. Therefore, molecular events that are further downstream of the genome (perhaps reflected by the proteome or the metabolome) may better reflect the tumour phenotype. One feature of cancer is perturbed metabolism. Some of the aberrant metabolic pathways may enhance tumour viability and growth, and these perturbed pathways may be susceptible to pharmacologic inhibition. Thus, our overall goal is to categorize tumours by their metabolic features; to understand the biological implications of these metabolic features, and to identify pathways that could be potentially targeted with drugs. This project involves the development of a workflow to define the metabolic features of a tumour. The workflow will involve the categorization of tumours based on their metabolic features (at the transcriptome level), exploration of associated biological features of each metabolic subtype, and integration of multiple levels of molecular control (including mutation status, copy number variation, methylation, and metabolome). Our work began with breast cancer, which is already well characterized by a large cohort in The Cancer Genome Atlas (TCGA) project. Then we used the same principles to investigate a more complex tumour type, pancreatic cancer, which is characterized by a highly variable degree of stroma infiltration.
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    Identification and Verification of Differentially Methylated Regions in Cell-Free DNA as a Peripheral Biomarker for Bicuspid Aortic Valve Aortopathy
    (2020-01-08) Maredia, Ashna Karimbhai; Greenway, Steven C.; Fedak, Paul; Bathe, Oliver F.; Braun, Andrew P.
    Bicuspid aortic valve (BAV) is a common congenital cardiac malformation associated with aortopathy for which the progression of aortic dilation is difficult to predict at present. BAV aortopathy has been linked to genetic factors and abnormal hemodynamic flow with regions of elevated wall shear stress (WSS) on the ascending aorta. The dying vascular smooth muscle cells release fragmented DNA into the circulation and this cell-free DNA (cfDNA) could be leveraged as a biomarker for aortopathy. Identification of tissue-specific differentially methylated regions (DMRs) in DNA provides a potential mechanism to identify cfDNA arising from the ascending aorta. The objective is to identify aorta-specific DMRs in the cfDNA of BAV patients as a biomarker for the severity of the aortopathy. We hypothesize that BAV-associated aortopathy leads to increased cell death and increased release of aorta-specific cfDNA correlating with the severity of aortopathy as defined by aortic cell death, elastin degradation and dysregulation of ECM proteins. BAV patient aortic wall samples corresponding to areas of elevated and normal WSS were collected and stained for cell death. Regions of elevated aortic WSS showed greater cell death when compared to regions of normal aortic WSS (p=0.00006). We established a bioinformatic pipeline for the identification of aorta-specific DMRs and they were verified with BAV patient cfDNA. The levels of aorta specific cfDNA of the DMRs on Chr 11, 18 and 22 of BAV patients had a significant correlation with levels of cell death in elevated aortic WSS regions. However, there was no correlation with elastin thickness, ECM concentrations of matrix metalloproteinases (MMP) types 1, 2 and 3, tissue inhibitor of metalloproteinases-1 and transforming growth factor-β1. Further work needs to be done in order to identify more specific aortic DMRs that have stronger correlation to the severity of BAV aortopathy markers with larger cohorts for biomarker validation. The identification of a peripheral biomarker that correlates with tissue disease will be an important advance in the non-invasive diagnosis of BAV-associated aortopathy and potentially help guide clinical decision-making regarding the need for surgical intervention.
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    Metabolomic Biomarkers for Colorectal Cancer
    (2016) Farshidfar, Farshad; Bathe, Oliver F.; Vogel, Hans J; Kopciuk, Karen A; Hilsden, Robert; Buie, W. Donald
    Colorectal cancer (CRC) is the second most common cancer in the North America. It is also a huge burden for society. Remarkable efforts have been and are being made to improve CRC diagnosis, to enhance the effectiveness of treatments, and to eventually improve the outcome of these patients. Metabolomic profiling, as a method for describing metabolic state and alterations in the molecular constituents and capable of yielding unique and invaluable information about tumor biology, has been employed. Using a range of spectroscopy and mass spectrometry techniques, we have sought to characterize the changes in the serum metabolome that appear as a result of malignant and pre-malignant lesions in the colon and rectum. In Chapter 2, Application of gas chromatography-mass spectrometry (GC-MS) and nuclear magnetic resonance (NMR) spectroscopy for staging CRC is described. Chapter 3 describes a larger study of 320 CRC and 31 colorectal adenoma cases as well as their matching controls by GC-MS, which led to the identification of validated metabolomic signature for identification of CRC and a proposed signature for identification of colorectal adenoma. In chapter 4, an effort for quantitative profiling of 62 CRC cases and 31 colorectal adenomas and their matching controls by tandem mass spectrometry is illustrated, and a validated quantitative signature for diagnosis of CRC is reported. Chapter 5 is dedicated to studying the prognostic value of metabolomic profiling in colorectal liver metastatic patients, and a novel workflow for estimation of recurrence risk using high-dimensional data is proposed. Challenges and pitfalls confronted in different steps of the project were addressed when possible by the use of available methods. Where no reliable method was available, we made an effort to develop one. This thesis, therefore, is focused on the metabolomic characterization of CRC and the adaptation of this knowledge for the development of clinically valuable biomarkers.
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    Metabolomics and Metallomics Analyses of Renal Cell Carcinoma and Prostate Cancer
    (2019-09-12) Falegan, Oluyemi Seuntitun; Vogel, Hans J.; Hyndman, Matthew Eric; Hollenberg, Morley Donald; Bathe, Oliver F.
    Prostate cancer and renal cell carcinoma of the kidney are the most frequently diagnosed and the most lethal male genitourinary cancers respectively. While prostate cancer screening and diagnosis using serum prostate-specific-antigen is flawed by its low sensitivity and inability to detect indolent disease, the histological diversity of renal cell carcinoma poses a clinical challenge for its identification in asymptomatic individuals. It is believed that applying new technologies such as metabolomics to the discovery of potential diagnostic and prognostic biomarkers, can enhance early detection of these cancers and improve overall patient survival while preserving a high quality of life. Considering this, the metabolome of biofluids associated with renal cell carcinoma and prostate cancer were analyzed and studied. Briefly, nuclear magnetic resonance spectroscopy and gas chromatography mass spectrometry techniques were used to analyze serum and urine samples obtained from renal cell carcinoma patients for isolating disease-specific metabolic profiles. Increased levels of lactate and pyruvate accompanied by reduced levels of specific tricarboxylic acid cycle metabolites were associated with renal cell carcinoma. Furthermore, benign oncocytomas of the kidney showed a differential metabolic profile from chromophobe renal cell carcinoma, with glycine and carnitine compounds at the center of the metabolic distinction. Our results showed that the prevalence of the Warburg effect, amino acid dysregulation and glutamine metabolism may distinguish renal cell carcinoma from benign renal lesions and thus presents a platform for identifying renal neoplastic transformations in asymptomatic individuals. On the other hand, the metabolome of seminal plasma measured by nuclear magnetic resonance spectroscopy distinguished prostate cancer Gleason grade 6 from 7, specifically increased lysine levels and reduced serine levels were significantly associated with low risk Gleason grade 6 disease. Also, the plasma and urinary metabolic pattern implicated amino acid dysregulation in bone metastasis of prostate tumors compared to low and high-risk disease. Our findings showed great potential for discriminating indolent from more aggressive prostate cancer, using a non-invasive method. Finally, our metallomics results indicate that metal ions may play a vital role in kidney cancer.
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    Neoplastic cell enrichment of tumor tissues using coring and laser microdissection for proteomic and genomic analyses of pancreatic ductal adenocarcinoma
    (2022-10-20) Li, Qing K.; Hu, Yingwei; Chen, Lijun; Schnaubelt, Michael; Cui Zhou, Daniel; Li, Yize; Lu, Rita Jui-Hsien; Thiagarajan, Mathangi; Hostetter, Galen; Newton, Chelsea J.; Jewell, Scott D.; Omenn, Gil; Robles, Ana I.; Mesri, Mehdi; Bathe, Oliver F.; Zhang, Bing; Ding, Li; Hruban, Ralph H.; Chan, Daniel W.; Zhang, Hui
    Abstract Background The identification of differentially expressed tumor-associated proteins and genomic alterations driving neoplasia is critical in the development of clinical assays to detect cancers and forms the foundation for understanding cancer biology. One of the challenges in the analysis of pancreatic ductal adenocarcinoma (PDAC) is the low neoplastic cellularity and heterogeneous composition of bulk tumors. To enrich neoplastic cells from bulk tumor tissue, coring, and laser microdissection (LMD) sampling techniques have been employed. In this study, we assessed the protein and KRAS mutation changes associated with samples obtained by these enrichment techniques and evaluated the fraction of neoplastic cells in PDAC for proteomic and genomic analyses. Methods Three fresh frozen PDAC tumors and their tumor-matched normal adjacent tissues (NATs) were obtained from three sampling techniques using bulk, coring, and LMD; and analyzed by TMT-based quantitative proteomics. The protein profiles and characterizations of differentially expressed proteins in three sampling groups were determined. These three PDACs and samples of five additional PDACs obtained by the same three sampling techniques were also subjected to genomic analysis to characterize KRAS mutations. Results The neoplastic cellularity of eight PDACs ranged from less than 10% to over 80% based on morphological review. Distinctive proteomic patterns and abundances of certain tumor-associated proteins were revealed when comparing the tumors and NATs by different sampling techniques. Coring and bulk tissues had comparable proteome profiles, while LMD samples had the most distinct proteome composition compared to bulk tissues. Further genomic analysis of bulk, cored, or LMD samples demonstrated that KRAS mutations were significantly enriched in LMD samples while coring was less effective in enriching for KRAS mutations when bulk tissues contained a relatively low neoplastic cellularity. Conclusions In addition to bulk tissues, samples from LMD and coring techniques can be used for proteogenomic studies. The greatest enrichment of neoplastic cellularity is obtained with the LMD technique.
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    Serum metabolomic profile as a means to distinguish stage of colorectal cancer
    (BioMed Central, 2012-05-14) Bathe, Oliver F.; Farshidfar, Farshad; Weljie, Aalim M.; Kopciuk, Karen; Buie, W Don; MacLean, Anthony; Dixon, Elijah; Sutherland, Francis R; Molckovsky, Andrea; Vogel, Hans J
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    Serum metabolomics: development and validation of a new diagnostic test for pancreatic cancer
    (2012) McConnell, Yarrow Jean; Bathe, Oliver F.; Weljie, Aalim
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    Spontaneous Regression of Hepatocellular Carcinoma and Review of Reports in the Published English Literature
    (2019-03-31) Chohan, Moaz B. Y.; Taylor, Nick; Coffin, Carla; Burak, Kelly W.; Bathe, Oliver F.
    Background. Spontaneous regression of hepatocellular carcinoma (HCC) is a rare event, although it has been described by numerous groups. The long-term fate of individuals experiencing an SR is not well described, and the underlying mechanism(s) of SR are unknown. Case Presentation: A 79-year-old Asian female with metastatic HCC taking only valsartan for hypertension had a marked reduction in tumor dimension in the primary tumor and the pulmonary metastases. Serum alpha-fetoprotein (AFP) decreased from 17,833 μg/L to 26 μg/L. Her disease progressed after 71 months, and she died shortly after. In a review of 66 patients with SR reported in the English literature, median survival was 83 months. Median survival in 37 cases that underwent resection after SR was 108 months. Conclusions. The case and a review of the literature illustrate that SR is often durable and associated with an excellent prognosis. Understanding the underlying mechanism of SR may point to novel therapeutic strategies.
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    Tumor endothelial marker 8 (TEM8) expression in tumor and endothelial cells
    (2008) Opoku-Darko, Michael; Bathe, Oliver F.
    Tumor endothelial marker 8 (TEM8) is highly expressed in tumor vasculature, but not in other endothelial cells including those involved in normal physiological angiogenesis such as wound healing and corpus luteum formation. It has not been reported whether this is due to some intrinsic characteristic of the tumor endothelium or secondary to tumor microenvironmental factors. Screening of TEM8 levels in various cancer and endothelial cell lines used in this project revealed variable transcript level. Changes in level of expression of TEM8 transcripts in human umbilical vein endothelial cells (HUVECs) were examined under the influence of such microenvironmental factors as hypoxia and vascular endothelial growth factor (VEGF), the most potent pro-angiogenic agent. While hypoxia dramatically increased the levels of TEM8 in HUVECs, VEGF seemed to do so only moderately. TEM8 mRNA levels were elevated in HUVECs co­cultured with some breast cancer cell lines including, Hs578T, MDA MB 468, MDA MB 453s, MDA MB 231 and MDA MB 436. Contrary to that however, HUVECs co-cultured with the breast cancer cell lines, SKBR3, MCF-7 and BT-474 had no significant changes in TEM8 transcription. Induction of TEM8 was due to direct cell-cell contact rather than to secretion of soluble factors by the tumor cells. Interestingly, the TEM8 inducing breast cancer cell lines have a more aggressive phenotype than the non-inducing group. TEM8 may therefore be a marker of aggressiveness in breast cancer. Overexpression of TEM8 in HUVECs led to more rapid endothelial cell growth and, in contrast down-regulating the gene by AdshRNA resulted in reduced cell growth. Together, these data suggest that endothelial cell expression of TEM8 is a function of the tumor microenvironment. Its up­regulation in tumor-associated endothelial cells encourages their growth.