Systems and methods for sample preparation, data generation, and protein corona analysis
Inventors
Manning, William • Kim, Young • Kwan-Leong, Brandon • Liou, Hope • Zhao, Xiaoyan • Hornburg, Daniel • Goldberg, Martin
Assignees
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Publication Number
US-12241899-B2
Publication Date
2025-03-04
Expiration Date
Abstract
Systems and methods for automated sample preparation and processing of protein corona are described herein, as well as its application in the discovery of advanced diagnostic tools as well as therapeutic agents.
Core Innovation
The invention provides an automated system for distinguishing states of a biological sample using a plurality of magnetic particles and a sensor array. The sensor array includes a magnetic support and a magnetic sensor array removably coupled to the magnetic support, with partitions that comprise the biological sample, a diluent comprising a buffer, and the plurality of magnetic particles. The magnetic particles have a carboxyl functionalized silica surface and are configured to bind to at least 300 different proteins from the biological sample.
The system uses a fluid transfer unit with a multichannel fluid transfer instrument comprising a plurality of pipettes to transfer fluids between units within the system, supported by reagent storage, waste storage, and a consumable storage with pipette tips. Reagents stored include a buffer, a wash solution, a resuspension solution, and a denaturing solution comprising a protease, where the protease comprises trypsin. Under control of a processor executing program steps, the biological sample is contacted with at least one partition of the plurality of partitions and incubated with the plurality of magnetic particles of the magnetic sensor array.
The controlled steps further prepare a population of proteins for mass spectrometry by adding the resuspension solution and the denaturing solution to the partition, thereby desorbing and digesting a plurality of proteins in the biological sample to generate the population of proteins. The described workflow is directed to generating proteomic data suitable for distinguishing biological states and assigning biological-state results based on protein/biomolecule signatures derived from the corona-bound proteins.
The document further outlines that the resulting biomolecule fingerprint signatures can be used to distinguish biological states, including disease stages, using computer processors and machine-executable code and certainty thresholds for analysis and classification.
Claims Coverage
The independent claim is directed to an automated system for distinguishing states of a biological sample. The independent claim includes three inventive features covering partitioned sensor-array contact with magnetic particles configured to bind proteins, automated multichannel fluid transfer with reagent and waste handling, and generating a population of proteins for mass spectrometry via resuspension and protease denaturing (trypsin).
Partitioned magnetic sensor array with carboxyl-functionalized particles
A sensor array comprising a magnetic support and a magnetic sensor array removably coupled to the magnetic support, with partitions comprising a biological sample, a diluent comprising a buffer, and a plurality of magnetic particles having a carboxyl functionalized silica surface, configured to bind to at least 300 different proteins from the biological sample.
Automated multichannel fluid transfer system for reagent handling
A fluid transfer unit comprising a multichannel fluid transfer instrument with a plurality of pipettes for transferring fluids between units within the system, together with reagent storage for storing buffer, wash solution, resuspension solution, and a denaturing solution comprising a protease that comprises trypsin, and a waste unit for storing a reagent to be disposed of.
Resuspension and trypsin-based desorption and digestion for mass spectrometry
Programmed control steps contacting and incubating the biological sample with at least one partition and the plurality of magnetic particles, followed by preparing a population of proteins for mass spectrometry by adding the resuspension solution and the denaturing solution to desorb and digest a plurality of proteins in the biological sample, thereby generating the population of proteins.
Independent claim coverage centers on a partitioned magnetic sensor array using carboxyl-functionalized magnetic particles that bind at least 300 proteins, an automated multichannel fluid transfer architecture with reagent and waste handling, and programmed preparation of desorbed and trypsin-digested proteins for mass spectrometry to support distinguishing biological states.
Stated Advantages
Distinguishes states of a biological sample using protein-binding biomolecule corona behavior and derived protein populations for mass spectrometry-based biomolecule fingerprinting.
Can generate biomolecule corona signatures that distinguish healthy, pre-disease, and disease states, including early/intermediate/late disease stages.
Enables combining biomolecule corona signatures across sensor elements, separately combined or concurrently assayed.
Demonstrates dynamic-range compression of plasma protein measurements by particle coronas, including improved low-abundance protein detection.
Enables distinguishing states of a biological sample.
Generates a population of proteins for mass spectrometry by desorbing and digesting proteins in the biological sample.
Supports biomolecule fingerprint signatures for assigning a biological state and distinguishing disease stages.
Documented Applications
Disease detection and biological-state distinction using sensor-element particle panels forming biomolecule corona signatures, including healthy, pre-disease, and disease states such as early/intermediate/late cancer and other disorders.
Cancer study example using non-small cell lung cancer (NSCLC), comparing Stage IV NSCLC vs matched controls with differential protein feature groups identified by mass spectrometry.
Protein-fingerprint classification workflows using supervised/unsupervised machine learning on proteomic data derived from mass spectrometry analysis, including distinguishing biological states based on biomolecule fingerprints.
Plasma protein measurements using dynamic-range compression by particle coronas to improve detection of low-abundance proteins.
Distinguishing states of a biological sample, including assigning biological state results and distinguishing disease stages (e.g., cancer stages) based on biomolecule fingerprint signatures.
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