Cancer patients with neurotrophic tyrosine receptor kinase (NTRK) gene fusions who took Larotrectinib (Vitrakviï) and Entrectinib (Rozlytrekï) lived significantly longer without disease progression, regardless of the disease origin and its gene fusion partners. Currently, detection of NTRK fusions is recommended by multiple National Comprehensive Cancer Network (NCCN) guidelines, including those for colon, non- small cell lung, breast, central nervous system, pancreatic, thyroid, gastric, hepatobiliary, and ovarian cancers. However, current diagnostic assays for NTRK gene fusions require highly invasive tissue samples, which are often limited by tumor position, patient compliance, sample amount, and tumor inaccessibility in cancers such as lung cancer, gliomas, and pancreatic cancers. Liquid biopsy allows for minimally invasive molecular profiling when tissue biopsies are scarce or unreachable. This means that patients' tumors can be molecularly profiled for precision medicine with a simple blood draw instead of a surgical procedure. The significant clinical benefit of targeted, tropomyosin receptor kinase (TRKs) inhibitor therapies towards cancer patients bearing NTRK fusions bolsters the urgent unmet need for a liquid biopsy method to screen pathological NTRK fusions to identify the TRK inhibitor responders. Extracellular vesicles (EVs) in the blood plasma of cancer patients encapsulate the entire cancer transcriptome via long and high-quality mRNA fragments up to 20 kbp. EVs harbor cancer-associated mRNA transcripts, therefore perfectly for NTRK fusion detection. To meet the urgent, unmet, clinical challenge of detecting NTRK fusions, we propose to vertically integrate our proprietary, one-component lipid nanoprobe (1C-LNP) technology for isolating total EV from plasma, a new wild-type blocker amplification (wtBA) technology to NTRK fusions in EV RNA from a high background of wildtype RNA, and the Oxford Nanopore Technologies' long-read sequencing platform for reading NTRK fusions. We will develop a minimally invasive NTRK fusion detection technology with two Aims. In Aim 1, we will optimize the 1C-LNP technology for total EV isolation in plasma. In Aim 2, we will develop and integrate 1C-LNP and wtBA to isolate high-molecular weight tumor mRNA from EVs, enrich mRNA sequence with NTRK fusions, perform single-molecule long-reads sequencing analysis using the Oxford Nanopore Flongle device, and further validate the feasibility of NTRK fusion variants detection using samples isolated from tissue and plasma EV. We anticipate significant impacts in two areas of molecular diagnostics and liquid biopsy: (1) We will create the most sensitive, state-of-the-art method to identify NTRK fusions at low variant allele frequencies; (2) We will create a minimally invasive NTRK fusion screening assay for plasma, which identifies NTRK inhibitors responders and can have an incredible impact on the patient outcomes. Phase II activities will focus on expanding this 1C-LNP integrated wtBA technology platform to other clinical actionable gene fusions such as ROS1, ALK, NRG1, RET, ETS, EWS, FGFR, ABL1 and subsequently perform the clinical validation of the gene fusion panel. Upon completion of clinical validation, we will launch this minimally invasive NTRK fusion screening test service through the Clinical Laboratory Improvement Amendments (CLIA) laboratory for oncologists.
Public Health Relevance Statement: Narrative Pan-tropomyosin receptor kinase (TRK) inhibitors, larotrectinib (Vitrakvi) and entrectinib (Rozlytrek), have dramatically transformed the therapeutic landscape for cancer patients harboring NTRK gene fusion. We propose to develop a fast, blood-based NTRK fusion screening assay to find NTRK inhibitor responders.
Project Terms: 21+ years old; Adult Human; adulthood; Adult; Biological Assay; Assay; Bioassay; Biologic Assays; Biopsy; Blood; Blood Reticuloendothelial System; Western Blotting; Immunoblotting; Western Immunoblotting; protein blotting; Breast; Malignant Neoplasms; Cancers; Malignant Tumor; malignancy; neoplasm/cancer; Malignant neoplasm of thyroid; Malignant Thyroid Gland Neoplasm; Malignant Tumor of the Thyroid; Malignant Tumor of the Thyroid Gland; Thyroid Cancer; Cell Line; CellLine; Strains Cell Lines; cultured cell line; Cells; Cell Body; Colon; Disease; Disorder; DNA; Deoxyribonucleic Acid; Enzyme-Linked Immunosorbent Assay; ELISA; enzyme linked immunoassay; Gene Frequency; Allele Frequency; allelic frequency; Gene Fusion; Genes; Glioma; Glial Cell Tumors; Glial Neoplasm; Glial Tumor; Neuroglial Neoplasm; Neuroglial Tumor; glial-derived tumor; neuroglia neoplasm; neuroglia tumor; Goals; Introns; Intervening Sequences; Laboratories; Lipids; High Density Lipoproteins; HDL; HDL Lipoproteins; Heavy Lipoproteins; High density lipoprotein; alpha-Lipoproteins; Low-Density Lipoproteins; LDL; LDL Lipoproteins; beta-Lipoproteins; Very low density lipoprotein; Prebeta-Lipoproteins; VLDL; VLDL Lipoproteins; Lung; Lung Respiratory System; pulmonary; malignant stomach neoplasm; Gastric Body Cancer; Gastric Cancer; Gastric Cardia Cancer; Gastric Fundus Cancer; Gastric Pylorus Cancer; Malignant Gastric Neoplasm; Malignant Gastric Tumor; Stomach Cancer; gastric malignancy; malignant stomach tumor; stomach fundus cancer; stomach pylorus cancer; Membrane Lipids; Cell Membrane Lipids; Methods; Molecular Weight; Patients; Plasma; Blood Plasma; Plasma Serum; Reticuloendothelial System, Serum, Plasma; Plasma Proteins; Proteins; Reading; Recommendation; Ribonucleases; RNA Nucleases; RNase; Ribonuclease Family Protein; RNA; Non-Polyadenylated RNA; RNA Gene Products; Ribonucleic Acid; Messenger RNA; mRNA; Technology; Time; Tissues; Body Tissues; Tropomyosin; Ultracentrifugation; Fibroblast Growth Factor Receptors; FGF Receptors; FGF-R; FGFR; Fibroblast Growth Factor Receptor Family; Point Mutation; Guidelines; fusion gene; Label; Area; Surface; Clinical; Encapsulated; Phase; PTK Receptors; Receptor Tyrosine Kinase Gene; Transmembrane Receptor Protein Tyrosine Kinase; Tyrosine Kinase Linked Receptors; Tyrosine Kinase Receptors; Receptor Protein-Tyrosine Kinases; Malignant Tumor of the Lung; Pulmonary Cancer; Pulmonary malignant Neoplasm; lung cancer; Malignant neoplasm of lung; Disease Progression; Oncologist; Solid Tumor; Solid Neoplasm; Therapeutic; Malignant neoplasm of pancreas; Malignant Pancreatic Neoplasm; Pancreas Cancer; Pancreatic Cancer; pancreatic malignancy; Diagnostic; Knowledge; Operative Surgical Procedures; Operative Procedures; Surgical; Surgical Interventions; Surgical Procedure; surgery; Magnetism; magnetic; particle; Performance; receptor; Receptor Protein; hybrid gene; cohort; Modality; Devices; Excision; Abscission; Extirpation; Removal; Surgical Removal; resection; Positioning Attribute; Position; ROS1 gene; MCF3; ROS1; v-ROS Avian UR2 Sarcoma Virus Oncogene Homolog 1; Modeling; Sampling; response; Nanotechnology; nano tech; nano technology; nano-technological; nanotech; nanotechnological; single molecule; Central Nervous System; CNS Nervous System; Neuraxis; Malignant Ovarian Neoplasm; Malignant Ovarian Tumor; Malignant Tumor of the Ovary; Ovary Cancer; ovarian cancer; Malignant neoplasm of ovary; kinase inhibitor; RNA Degradation; nano sphere; Nanosphere; Tissue Sample; Tumor Weights; Patient Compliance; patient adherence; patient cooperation; therapy compliance; therapy cooperation; treatment compliance; compliance behavior; NRG1 gene; GGF; GGF2; HGL; HRGA; Heregulin Gene; NEU Differentiation Factor Gene; NRG1; ABL1 gene; ABL1; Abelson Murine Leukemia Viral Oncogene Homolog 1; JTK7; c-Abl; c-abl Genes; c-abl Proto-Oncogenes; Length; Detection; Molecular Profiling; Molecular Fingerprinting; molecular profile; molecular signature; National Comprehensive Cancer Network; NCCN; Cancer Patient; Patient-Focused Outcomes; Patient outcome; Patient-Centered Outcomes; patient oriented outcomes; Transcript; Tumor-Derived; Validation; validations; Pathologic; Development; developmental; cost; Gene variant; allele variant; allelic variant; genomic variant; genetic variant; nanoprobe; nano pore; nanopore; cost effective; innovate; innovative; innovation; tumor; minimally invasive; operations; operation; screenings; screening; hepatobiliary cancer; precision-based medicine; precision medicine; targeted drug therapy; targeted drug treatments; targeted therapeutic; targeted therapeutic agents; targeted therapy; targeted treatment; child patients; pediatric patients; clinically actionable; diagnostic assay; global gene expression; global transcription profile; transcriptome; sequencing platform; molecular diagnostics; extracellular vesicles; liquid biopsy; testing services; preservation; Clinical Laboratory Improvement Amendments; variant detection; detection limit; detection sensitivity; screening services; inhibitor therapy; inhibitor drug; inhibitor therapeutic; Diameter; Non-Invasive Detection; Noninvasive Detection; technology platform; technology system
