ZIA BC 011492 (ZIA) | |||
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Title | Biomarkers in Cancer Diagnosis, Prognosis and Therapeutic Outcome | ||
Institution | NCI, Bethesda, MD | ||
Principal Investigator | Harris, Curtis | NCI Program Director | N/A |
Cancer Activity | N/A | Division | CCR |
Funded Amount | $1,214,304 | Project Dates | null - null |
Fiscal Year | 2018 | Project Type | Intramural |
Research Topics w/ Percent Relevance | Cancer Types w/ Percent Relevance | ||
Cancer (100.0%) Digestive Diseases (40.0%) Inflammatory Bowel Disease (20.0%) |
Colon/Rectum (40.0%) Lung (50.0%) |
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Research Type | |||
Cancer Progression & Metastasis Technology Development and/or Marker Discovery |
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Abstract | |||
Project 1A: To investigate mucosa-associated alterations of the lung microbiome during carcinogenesis, we utilized the NCI-MD case-control study and sequenced the V3-V5 16S rRNA gene. Candidate bacterial identities were validated in lung cancer samples from The Cancer Genome Atlas. We examined the ecological diversity within samples (alpha diversity) and between samples (beta diversity) of normal healthy tissues and NCI-MD non-tumor adjacent and tumor tissues. We found increasing diversity and richness in subjects with lung cancer, which could be related to changes in the lung microenvironment, indicating acquisition of somatic mutations or alterations in the immune system. We identified two genera that were able to classify lung cancer cases from immediate autopsy controls, Variovorax and Streptococcus, and may be biomarkers of lung cancer risk or associated with cancer initiation and progression. Variovorax abundance was higher in tumor compared to non-tumor tissues from the same individual, a finding that was validated in the larger TCGA dataset. Using the Resphera Insight to speciate our 16S rRNA gene reads, we were able to putatively identify the species as V. paradoxus. Fluorescent in situ hybridization (FISH) analysis of resected lung tumors further confirmed the presence of V. paradoxus in tumor tissue. V.paradoxus was localized intracellularly in tumor cells. A higher abundance of Variovorax and lower abundance of Streptococcus was seen in Stage I lung cancer, suggesting these maybe biomarkers of cancer risk or associated with cancer initiation. Variovorax species could differentiate between histological subtypes of lung cancer, adenocarcinoma (AD) and squamous cell carcinoma (SCC). We hypothesized that SCC-associated microbial taxa would be more abundant in tumors with TP53 mutations.. We investigated the association between TP53 mutations, microbial taxa, and tumor histology. Specific microbial taxa were more abundant in SCC with TP53 mutations, whereas no pattern of association was found among AD with TP53 mutations. These data support the hypothesis that in tumors with TP53 mutations, SCC-associated taxa gain greater access to the tumor microenvironment.. Species-level validation and quantification will be achieved by droplet digital PCR (ddPCR) methods. We are developing methods to identify bacterial isolates from lung tumors and are examining the role of the mucosa-associated lung microbiome, its relationship to inflammation and the metabolome in lung cancer, and the mechanisms underlying this relationship. We will explore these mechanistic relationship between specific bacterial species using a K-ras/p53R172H mouse model in the NCI gnotobiotic mouse facility and in the antibiotic-treated SPF mice. Project 1B: We developed methylation-specific ddPCR to detect and quantify rare methylation events to investigate biomarkers in liquid biopsies. The ddPCR assay could detect as few as 30 haploid genome-equivalents of methylated promoter DNA, and count a single methylated allele present at 0.2%. Differences in methylation levels between tumors and adjacent tissues were also observed. Therefore, we have established a robust and ultrasensitive method for standardized determination of DNA promoter methylation status. We are now evaluating the potential value of the ddPCR assay for prognostic classification of lung cancer patients using FFPE tumor samples. We obtained preliminary evidence that methylated DNA is detectable in ctDNA from lung cancer patients at advanced stage, and are continuing to optimize conditions for detection in patients with Stage I lung cancer. Project 1C: Another project was to evaluate urinary and blood tumor metabolite liquid biopsy approaches for early detection of lung and liver cancer and for assessing patient outcome. In a collaboration supported by the Department of Defense (DoD) Clinical Exploration Award, we are in the process of investigating the predictive capability of urinary metabolite |