EP-4741795-A2 - SYSTEMS AND METHODS FOR PRE-ANALYTICAL SUBSTRATE PROCESSING

Abstract

Some embodiments presented in this disclosure concern an Automated Tissue Dissection (ATD) System. An ATD system is a one stop, and potentially low-cost, system to perform dissections on a substrate from pathologist digital mark or pen mark on the substrate using non-contact and/or mechanical method to extract a Formalin-Fixed Paraffin-Embedded (FFPE) tissue sample with: (a) only the ROI or ROIs as area to be saved; and (b) remove or decompose nucleic acid content in the region of no interest (RONI) and collect all tissue sample from a standard microscope substrate into a specific container.

Inventors

• YEUNG, HUBERT
• YUAN, Amy Lee Hsieh
• LEE, CHUN WAI
• MORALEDA, Gabriel Jesus Samuel Perlas
• CASSEL, JONATHAN M.

Assignees

• Genomic Health, Inc.

Dates

Publication Date

20260513

Application Date

20190621

Claims (15)

1. A bioanalytical system comprising (a) a first component for contacting a biological sample or a region therein with a contact medium comprising a particulate substance and pressurized air under conditions sufficient to effectuate at least a partial transfer of a component in the biological sample to the contact medium; (b) a second component for removing the contact medium from the biological sample; and (c) optionally a third component for analyzing the component in the contact medium or the processed biological sample or both the contact medium and the processed biological sample.
2. The bioanalytical system of claim 1, wherein the first component comprises a pressurized particle micro-blaster (PMB) containing the contact medium.
3. The bioanalytical system of claim 1 or 2, wherein the second component comprises a vacuum, pressure differential or gradient, a medium for transporting the particulate substance (e.g., liquid or aerosol), or a transfer medium selected from magnetic field or electric field.
4. The bioanalytical system of any preceding claim, wherein the optional third component comprises an instrument selected from polymerase chain reaction (PCR), quantitative PCR (qPCR), reverse transcriptase PCR (RT-PCR), nucleic acid sequence based amplification (NASBA), loop mediated isothermal amplification (LAMP), rolling circle amplification (RCA), immunoassay, immunoPCR (iPCR), enzyme activity assay, staining, imaging, whole genome amplification (WGA), in situ PCR, in situ WGA, polony formation, sequencing, single-molecule sequencing, nanopore analysis, nanopore sequencing, single-molecule imaging, DNA ball formation, electrophoresis, microelectromechanical systems (MEMS) electrophoresis, mass spectrometry, chromatography (e.g., HPLC), proximity ligation assay, electrochemical detection, plasmon resonance (SPR), hybridization assay (e.g., in situ hybridization assay such as fluorescence in situ hybridization (FISH)) FRET, cell sorting (e.g., FACS), electrochemiluminescence ELISA, and chemiluminescence ELISA.
5. The bioanalytical system of any preceding claim, wherein: a. the first component selectively contacts a region of non-interest (RONI) in the biological sample with the contact medium under conditions sufficient to effectuate at least partial transfer of the RONI in the biological sample to the contact medium; or b. the first component selective contacts a region of interest (ROI) in the biological sample with the contact medium under conditions sufficient to effectuate at least partial transfer of the ROI in the biological sample to the contact medium.
6. A method of assaying for an analyte in a biological sample comprising processing the biological sample by (a) contacting the biological sample with a contact medium comprising a particulate substance and pressurized air under conditions sufficient to effectuate at least partial transfer of a component in the biological sample to the contact medium; and (b) removing the contact medium from the biological sample to obtain a processed biological sample; and assaying for the analyte in the processed biological sample or the removed contact medium.
7. The method of claim 6, wherein: a. a RONI in the biological sample is contacted with the contact medium under conditions sufficient to effectuate at least partial transfer of the RONI in the biological sample to the contact medium; or b. a ROI in the biological sample is contacted with the contact medium under conditions sufficient to effectuate at least partial transfer of the ROI in the biological sample to the contact medium.
8. The method of claim 6 or 7, wherein assaying for the analyte in the processed biological sample or the removed contact medium comprises polymerase chain reaction (PCR), quantitative PCR (qPCR), reverse transcriptase PCR (RT-PCR), nucleic acid sequence based amplification (NASBA), loop mediated isothermal amplification (LAMP), rolling circle amplification (RCA), immunoassay, immunoPCR (iPCR), enzyme activity assay, staining, imaging, whole genome amplification (WGA), in situ PCR, in situ WGA, polony formation, sequencing, single-molecule sequencing, nanopore analysis, nanopore sequencing, single-molecule imaging, DNA ball formation, electrophoresis, microelectromechanical systems (MEMS) electrophoresis, mass spectrometry, chromatography (e.g., HPLC), proximity ligation assay, electrochemical detection, plasmon resonance (SPR), hybridization assay (e.g., in situ hybridization assay such as fluorescence in situ hybridization (FISH)) FRET, cell sorting (e.g., FACS), electrochemiluminescence ELISA, or chemiluminescence ELISA.
9. The biological system or method of any one of the preceding claims, wherein the biological sample is processed for analysis of one or more analytes of interest.
10. The biological system or method of any one of the preceding claims, wherein the biological sample comprises punch biopsy specimens, needle biopsy specimens, fresh tissues, tissue cultures, frozen tissue specimen, neutral formalin-treated tissues, organs, organelles, formalin fixed paraffin embedded (FFPE) tissues, ethanol-fixed paraffin-embedded (EFPE) tissues, hematoxylin and eosin (H&E) stained tissues, or glutaraldehyde fixed tissues.
11. The biological system or method of any one of the preceding claims, wherein the biological sample comprises at least one analyte of diagnostic interest selected from genomic DNA (gDNA), methylated DNA, specific methylated DNA, messenger RNA (mRNA), fragmented DNA, fragmented RNA, fragmented mRNA, mitochondrial DNA (mtDNA), chloroplast DNA (ctDNA), viral RNA or viral DNA, microRNA, ribosomal RNA, in situ PCR product, polyA mRNA, RNA/DNA hybrid, lipid, carbohydrate, protein, glycoprotein, lipoprotein, phosphoprotein, specific phosphorylated or acetylated variant of a protein, or viral coat proteins; preferably nucleic acids selected from mRNA, gDNA, viral DNA or viral RNA.
12. The biological system or method of any one of the preceding claims, wherein the particulate substance is capable of binding to an analyte or a non-analyte in the biological sample; preferably, the particulate substance is capable of binding to the analyte via an interaction selected from ionic interaction, polar-apolar interaction, hydrophobic interaction, van der waal's interaction, chemical coupling, dielectric or zwitterion interaction or a combination thereof.
13. The biological system or method of any one of the preceding claims, wherein the contact medium comprises a pressurized inert gas selected from helium, argon, xenon, nitrogen, carbon dioxide, or a mixture thereof.
14. The biological system or method of any one of the preceding claims, wherein the biological sample is mounted on a substrate, preferably wherein the substrate is selected from glass, silicon, poly-L-lysine coated material, nitrocellulose, polystyrene, cyclic olefin copolymers (COCs), cyclic olefin polymers (COPs), polypropylene, polyethylene, and/or polycarbonate.
15. The biological system or method of any one of the preceding claims, wherein the biological sample comprises a nucleic acid analyte and the contact medium comprises a particulate substance comprising silica.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS FIELD The present disclosure generally relates to fields of histology and/or pathobiology. More specifically, the present disclosure relates to pre-analytical substrate processing systems and related methods which, in some embodiments, may be useful for separating and isolating regions of interest (ROI) and regions of non-interest (RONI) in the substrate, e.g., biological substrates such as histology specimen. BACKGROUND A variety of methods have been suggested to resolve cumbersome nature of scraping procedures for preparation and/or processing of histological samples for downstream analysis. For example, vacuum blasting techniques have been recommended; however, these are only deployable in an industrial setting and thus require expensive tools and instruments. Also, currently there is no vacuum blasting technology that is compatible with substrates mounted on microscopic glass slides. Similarly, particle-based blasting methods such as sandblasting, e.g., with silica particles, silica-coated particles or polymer-coated ferromagnetic beads, require separation of the particles from the regions of interest (ROI) prior to implementation of the downstream analytical steps. Current tissue dissection processes are completely manual, using razor blades to directly collect "S" (i.e., ROI) areas from substrates. For example, conventional workflows for substrate submissions include an entirely manual process where a user manually transfers pathologist area of interest markings on a stained slide to unstained slides using a standard off-the-shelf marking pen. The user then uses a razor blade or equivalent to scrape off the area of interest on the marked unstained substrate and collect into a container. This described manual process limits operator accuracy by completely relying on operator hand/eye coordination, which affects the consistency and accuracy of the tissue scraping. This process also introduces ergonomics/safety issues because constant force being applied to the glass surface may cause laceration and ergonomic issues (e.g., carpel tunnel) with the operator. Current implementations of digital pathology have improved many areas of histology/pathology workflows. However, there are still some important areas of unmet needs. One unmet need is that some substrate submissions cannot be processed digitally using the commercial Digital Pathology Systems. A substantial number of cases still require manual glass workflow processing. Therefore, there exists a need for a way to convert this process to achieve full digital workflow. SUMMARY Some embodiments presented in this disclosure concern an Automated Tissue Dissection (ATD) System. An ATD system is a one stop, and potentially low-cost, system to perform dissections on a substrate from pathologist digital mark or pen mark on the substrate using non-contact and/or mechanical method to extract a Formalin-Fixed Paraffin-Embedded (FFPE) tissue sample with: (a) only the ROI or ROIs as area to be saved: and (b) remove or decompose nucleic acid content in the region of no interest (RONI) and collect all tissue sample from a standard microscope substrate into a specific container. According to certain aspects of the present disclosure, ATD is merged with a digital pathology process to scrape ROI on substrates. Also disclosed are systems and methods for either collecting desirable "S" (i.e., ROI) regions or removing undesired "X" regions in feasible ways. The described systems and methods provide a low cost flexible system to digitalize slide images and simplify downstream scraping processes. The systems, in some embodiments, may be able to perform the following: (a) capture stained and unstained slide images with suitable magnification, (b) digitalize a pen marking into a digital marking, (c) perform an object based or other algorithm to match marking coordinates on a substrate to the associated substrates, (d) extract marked sample ROI into a container, (e) remove samples in RONI or decompose nucleic acid in RONI and collect all samples (e.g., tissue) into a container, and (f) lyse the sample and output lysate. This technology may be useful because current manual processes may have certain disadvantages or limitations, such as: (a) poorer quality, (b) operator limitations, (c) work hazards, (d) ergonomics, and/or (e) safety. For example, manual dissection methods completely rely on individual operator hand/eye coordination, which may affect the consistency and accuracy of the outcome. They may also require a dedicated training plan to achieve consistent accuracy. Performing manual dissection with constant force applied to the glass surface can also cause ergonomic issues with the operator over a period of time; for example, wrist injuries such as carpal tunnel syndrome. Thus, in many laboratories, operators must also limit the number of hours they spend performing manual dissections in order to help prevent injury. In terms of safe