/ Extrachromosomal circular DNA (eccDNA) elements are physically and topologically distinct components of eukaryotic genomes that can contribute to intercellular copy-number variation, environmental adaptations, and functional genomic diversity. Recently, high-throughput sequencing has made extensive genomic mapping of eccDNA sequences possible. Notwithstanding this major advance, information regarding biogenesis of these circular DNAs and causal connections between these DNA elements and human pathologies, remains extremely limited. The sequences, structure, and biological properties of eccDNA molecules constitute a major knowledge gap, information about which can lead to strategies targeting disease-specific eccDNA structure and function. eccDNAs represent a large range of molecules (~100 bp to >1 Mbp) and coexist with eccDNAs found in normal somatic cells; isolating and characterizing different classes of eccDNA comes with their own host of unique challenges. To address these knowledge gaps, methods that can directly interrogate all circular DNA species in the cell are critically needed. In this FastTrack SBIR proposal, Phinomics, Inc. is developing is developing an innovative urine-based test that will isolate eccDNA molecules in an intact state suitable for next-generation sequencing and epigenetic characterization, and is complemented by a suite of biophysical and novel bioinformatic methods to identify and define these molecules. In Phase I, Phinomics will 1) Demonstrate the capability of Phinomics' proprietary technology to isolate comprehensive/unbiased eccDNA repertoires (circulomes) from human cell lines; and 2) Demonstrate the capability of Phinomics' technology to robustly sequence, map, assemble, and informatically profile the isolated circulome. Upon meeting Phase I Go/No-Go milestones, in Phase II Phinomics will 3) Validate Phinomics' technology as a molecular platform for bladder cancer diagnostic applications; 4) Extend the application of Phinomics' technologies to biological fluid samples; and 5) Develop a PCR test to detect circular DNA species in non-muscle invasive bladder cancer to enable CLIA certification. Preliminary data has begun to illuminate the circulome in normal somatic cell lines and tissues, glioblastoma tumor samples, and plasma, potentiating the use of eccDNA as a valuable biomarker in both solid- and liquid- biopsy applications. Surveillance based on eccDNA biomarkers is aimed at a minimally invasive strategy to determine the immune response to therapies, predict recurrence likelihood, and monitor residual disease.
Public Health Relevance Statement: NARRATIVE Extrachromosomal circular DNA (eccDNA) elements are known to play a role in a variety of normal and pathological cellular processes; however, isolating and characterizing different classes of eccDNA to determine their role in these processes is a unique challenge. To address this, Phinomics is developing an innovative, unbiased technology that provides a comprehensive toolkit to isolate every size of eccDNA molecules in an intact state suitable for next-generation sequencing together with a suite of biophysical and novel bioinformatic methods to characterize these molecules. Surveillance based on eccDNA biomarkers is aimed at a minimally invasive strategy to determine the immune response to therapies, predict recurrence likelihood, and monitor residual disease.
Project Terms: Antibiotic Agents; Antibiotic Drugs; Miscellaneous Antibiotic; Antibiotics; Biogenesis; Origin of Life; Biophysics; biophysical foundation; biophysical principles; biophysical sciences; Biopsy; Malignant neoplasm of urinary bladder; Bladder Cancer; Malignant Bladder Neoplasm; Malignant Tumor of the Bladder; Urinary Bladder Cancer; Urinary Bladder Malignant Tumor; Bladder Neoplasm; Bladder Tumors; Urinary Bladder Neoplasm; Urinary Bladder Tumor; Malignant Neoplasms; Cancers; Malignant Tumor; malignancy; neoplasm/cancer; Cell Line; CellLine; Strains Cell Lines; cultured cell line; Cell physiology; Cell Function; Cell Process; Cellular Function; Cellular Physiology; Cellular Process; Subcellular Process; Cells; Cell Body; Complement; Complement Proteins; Disease; Disorder; DNA; Deoxyribonucleic Acid; Circular DNA; Drug resistance; drug resistant; resistance to Drug; resistant to Drug; Elements; Genome; Glioblastoma; Grade IV Astrocytic Neoplasm; Grade IV Astrocytic Tumor; Grade IV Astrocytoma; glioblastoma multiforme; spongioblastoma multiforme; Goals; Human; Modern Man; Maps; Marketing; Methods; Muscle; Muscle Tissue; muscular; Noise; Patients; Plasma; Blood Plasma; Plasma Serum; Reticuloendothelial System, Serum, Plasma; Recurrence; Recurrent; Role; social role; Signal Transduction; Cell Communication and Signaling; Cell Signaling; Intracellular Communication and Signaling; Signal Transduction Systems; Signaling; biological signal transduction; Specificity; Technology; Testing; Tissues; Body Tissues; Urine; DNA Sequence; environmental adaptation; extrachromosomal DNA; Area; Solid; Phase; biologic; Biological; Detectable Residual Disease; Minimal Residual Disease; Residual Tumors; residual disease; Residual Neoplasm; Immunological response; host response; immune system response; immunoresponse; Immune response; fluid; liquid; Liquid substance; Diagnostic; Knowledge; meetings; meeting; molecular size; Performance; vaccine development; develop a vaccine; develop vaccines; development of a vaccine; Informatics; Peripheral Blood Mononuclear Cell; PBMC; Structure; novel; Human Cell Line; new technology; novel technologies; Somatic Cell; Sampling; Property; repository; depository; functional genomics; Genomics; cancer therapy; Cancer Treatment; Malignant Neoplasm Therapy; Malignant Neoplasm Treatment; anti-cancer therapy; anticancer therapy; cancer-directed therapy; cancer diagnosis; Bio-Informatics; Bioinformatics; Address; Copy Number Polymorphism; copy number variant; copy number variation; DNA Structure; Data; Cancer Diagnostics; Double Minutes; Human Pathology; Prediction of Response to Therapy; predict therapeutic response; predict therapy response; predict treatment response; therapy prediction; treatment prediction; treatment response prediction; Reproducibility; Epigenetic Process; Epigenetic; Epigenetic Change; Epigenetic Mechanism; epigenetically; Small Business Innovation Research Grant; SBIR; Small Business Innovation Research; Validation; validations; Pathologic; Monitor; Molecular; Process; Pathway interactions; pathway; Outcome; Cancer cell line; cost effective; Population; innovate; innovative; innovation; resistant; Resistance; human disease; prototype; commercialization; tumor; minimally invasive; bio-markers; biologic marker; biomarker; Biological Markers; NGS Method; NGS system; next gen sequencing; nextgen sequencing; next generation sequencing; High-Throughput Sequencing; High-Throughput Nucleotide Sequencing; cancer markers; cancer biomarkers; identification of biomarkers; marker identification; biomarker identification; CLIA accredited; CLIA approved; CLIA compliant; CLIA licensed; CLIA certified; liquid biopsy; analyze microbiome; microbiome analysis; non-muscle invasive bladder cancer; bio-informatics pipeline; bioinformatics pipeline; detection sensitivity; translational potential; translational opportunities; technology platform; technology system
