Methods and compositions for synthetic biomarkers
Inventors
Suhy, David • ESCARPE, Paul • Roeding, Cyriac • Lin, Justin • HARWIG, Alex • RUDINA, Shireen • HARTWELL, Leland Harrison
Assignees
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Publication Number
US-12060613-B2
Publication Date
2024-08-13
Expiration Date
Abstract
The present disclosure encompasses embodiments of nucleic acids comprising genetic elements which are useful for the detection of diseased cells.
Core Innovation
A method is provided for introducing a plurality of DNA molecules into a subject suspected of having a cancer by intravenous administration. The DNA molecules comprise a plurality of different promoters or functional fragments thereof from genes overexpressed in a tumor cell operably linked to genes encoding reporter proteins, and are provided as nanoplasmids or linear vectors comprising double-stranded DNA molecules.
The reporter proteins comprise human sodium iodide symporter, herpes simplex virus thymidine kinase or functional mutants, dopamine D2 receptor or functional mutants, or a peptide epitope tag. The plurality of different promoters is selected from BIRC5, AGR2, CST1, FAMI11B, CEP55, CEACAM5, and KIF20A, with further refinement to specified tumor cell types and nanoplasmids that include a minimized bacterial ColE1 or R6K origin of replication and a bacterial RNA-based selectable marker.
After introduction of the DNA molecules, a PET-active iodine or iodide isotope, labeled-pyrimidine reporters or labeled-pyrimidine-analog PET reporters, labeled dopamine D2 receptor binders, or a labeled binding element recognizing the peptide epitope tag is administered depending on the reporter proteins present. The method detects a visual image of reporter proteins in tissue or tissues of the subject via a PET imaging method.
Claims Coverage
The independent claim coverage centers on intravenous delivery of multiple tumor-overexpressed promoter-linked reporter constructs, matched PET-detectable tracer administration based on the reporter protein type, and PET detection of reporter expression in tumor tissue. The provided items also include dependent refinements for promoter selection, tumor cell context, nanoplasmids, covalently linked DNA ends, exact promoter count, and timing before tracer administration.
Tumor-overexpressed promoter-driven reporter DNA delivered intravenously as nanoplasmids or linear dsDNA vectors
A plurality of DNA molecules is introduced to a subject suspected of having a cancer via intravenous administration, wherein the plurality comprises different promoters or functional fragments from genes overexpressed in a tumor cell operably linked to genes encoding reporter proteins, with expression driven in a cell transfected by nanoplasmids or linear vectors comprising double-stranded DNA molecules.
Reporter proteins selected to match PET-active tracer administration
Reporter proteins comprise human sodium iodide symporter, herpes simplex virus thymidine kinase or functional mutants, dopamine D2 receptor or functional mutants, or a peptide epitope tag, and a PET-active iodine or iodide isotope, labeled-pyrimidine reporters or labeled-pyrimidine-analog PET reporters, labeled dopamine D2 receptor binders, or a labeled binding element recognizing the peptide epitope tag is administered according to the reporter protein used.
PET imaging detection of reporter expression in tumor tissue
A visual image of reporter proteins in tissue or tissues of the subject suspected of having a cancer is detected via a PET imaging method.
Selected promoter set from BIRC5, AGR2, CST1, FAMI11B, CEP55, CEACAM5, KIF20A
The plurality of different promoters from genes overexpressed in the tumor cell is selected from BIRC5, AGR2, CST1, FAMI11B, CEP55, CEACAM5, KIF20A, or functional fragments thereof.
Tumor cell context restricted to specified tumor types
The tumor cell is a liver, ovarian, pancreatic, breast, lung, smooth muscle, bladder, kidney, skin, prostate, or bone tumor cell.
Nanoplasmids with minimized bacterial origin and RNA-based selectable marker
The plurality of DNA molecules is contained in nanoplasmids that include a minimized bacterial ColE1 or R6K origin of replication and a bacterial RNA-based selectable marker.
Forward and reverse strands covalently linked at each terminal end
The forward and reverse strands of double-stranded DNA molecules are covalently linked on each terminal end.
Minimum time delay before PET-tracer administration
Step (b) is performed at least one of 8, 12, 24, 36, 48, or 72 hours after step (a).
Across the independent claim and the provided dependent-claim refinements, the inventive concept centers on linking tumor-overexpressed promoter activity to reporter protein expression via intravenous delivery of nanoplasmids or linear dsDNA vectors, administering a reporter-matched PET tracer, and visualizing reporter expression by PET in specified tumor tissue contexts. The refinements constrain promoter selection, vector structure, DNA end structure, and the timing between DNA introduction and PET detection.
Stated Advantages
Enables cancer detection or staging by PET visualization of reporter protein expression in tumor tissue in a subject suspected of having a cancer.
Enables PET imaging by detecting reporter proteins expressed in tumor tissue after administering a PET-active isotope or PET-detectable tracer matched to the reporter protein type.
Enables PET-based visual imaging of reporter protein expression in tissue or tissues of a subject suspected of having a cancer.
Documented Applications
Cancer detection or staging in a subject suspected of having a cancer by detecting a PET image of reporter proteins expressed in tissue.
PET imaging in tissue based on reporter proteins including human sodium iodide symporter, HSV-tk, dopamine D2 receptor, or a peptide epitope tag, using corresponding PET-detectable tracers or labeled binding elements.
PET imaging for a subject suspected of having a cancer, including imaging of reporter proteins in tissue or tissues of the subject suspected of having a cancer.
Cancer diagnosis/imaging in a subject suspected of having a cancer using tumor-overexpressed promoter-driven reporter proteins and PET imaging detection.
Experimental barcoding of secreted luciferase fused to peptide epitope tags and detection of tag-specific luciferase signals using antibody-coated capture and ELISA, with an example of exchanging peptide barcodes for an hCG beta subunit barcode for a lateral-flow pregnancy test-style detection concept.
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