Single-Cell Chromosome Structure and Gene Expression Detection

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Solution Overview

Problem

Current methods for studying chromosome structure and gene expression are limited by the inability to simultaneously measure genetic structure and function at the single cell level, with existing techniques either focusing on single loci or providing indirect, population-based measurements that do not account for spatial organization or gene expression variability.

Innovation Solution

A method involving fluorescence in situ hybridization (FISH) that allows for the simultaneous determination of chromosome structural conformation and gene expression by hybridizing fluorescently labeled oligonucleotide probes with target RNA sequences, enabling the visualization of multiple genes and their expression levels within a single cell, using a barcoding scheme to distinguish between different probes and quantify gene expression profiles.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Measurement precision

If conventional imaging assays focus on the position of one or two loci at a time, then measurement precision for specific loci is improved, but the ability to obtain global chromosome structure information and gene expression data simultaneously deteriorates

Engineering Contradiction:

Improvelocus position measurement precisionVSAvoidsimultaneous measurement capability

Core Design Contradiction:

Measurement precisionVSAdaptability or versatility

Solution Approach 1:

The patent divides the chromosome into multiple loci, each targeted by specific fluorescent probes. Multiple loci can be simultaneously visualized using different fluorophores, enabling both precise locus measurement and global chromosome structure analysis in the same experiment

Inventive Principle:

Principle #1Segmentation

Solution Approach 2:

The imaging assay is designed to simultaneously perform multiple functions: visualizing chromosome structure, measuring locus positions, and detecting gene expression at multiple loci at once. The same assay protocol handles all these measurements without requiring separate experiments

Inventive Principle:

Principle #6Universality (Multi-functionality)

2Adaptability or versatility

If global biochemical approaches are used, then comprehensive chromosome structure information is obtained, but measurement precision at the single cell level deteriorates due to averaging over populations

Engineering Contradiction:

Improveglobal information coverageVSAvoidsingle cell measurement precision

Core Design Contradiction:

Adaptability or versatilityVSMeasurement precision

Solution Approach 1:

Instead of averaging data from many cells, the patent creates visual copies of individual chromosomes and gene expressions through fluorescence microscopy. Each fluorescent signal represents a specific molecule or locus in a single cell, preserving individual cell variability while providing global structural context

Inventive Principle:

Principle #26Copying

3Adaptability or versatility

If multiple fluorescent probes are used to target different RNA sequences, then gene expression profiling capability is improved, but device complexity increases due to the need for multiple fluorophores and probe sets

Engineering Contradiction:

Improvegene expression profiling capabilityVSAvoidprobe and fluorophore system complexity

Core Design Contradiction:

Adaptability or versatilityVSDevice complexity

Solution Approach 1:

The patent segments the chromosome into distinct loci, each with its own probe set and fluorophore assignment. This modular approach allows systematic multiplication of probe sets without creating unmanageable complexity, as each segment can be independently designed and analyzed

Inventive Principle:

Principle #1Segmentation

Solution Approach 2:

Different fluorophores with distinct emission wavelengths (colors) are assigned to different probe sets. This color-coding system enables simultaneous visualization of multiple gene expressions and chromosome structures without signal interference, simplifying the analysis of complex multi-target data

Inventive Principle:

Principle #32Color changes

Applied Scientific Principles

This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.

Function Achieved in This Case

Enables detailed, real-time visualization and measurement of chromosome structure and gene expression in living cells, providing a comprehensive understanding of spatial organization and its role in gene expression, which can be applied to disease diagnosis and clinical research.

Implementation Method 1

hybridizing a plurality of target sequences of RNA in the cell with members of at least one set of fluorescently labeled oligonucleotide probes

Methodology Applied

Scientific EffectHybridization:

Implementation Method 2

fluorescently labeled oligonucleotide probes... pattern of fluorescently labeled probes hybridized to the target sequences of RNA

Methodology Applied

Scientific EffectFluorescence: Fluorescence

Data Source

PatentUS10308983B2Method for detecting chromosome structure and gene expression simultaneously in single cells

Publication Date: 2019.06.04 THE TRUSTEES OF THE UNIV OF PENNSYLVANIA

AI summary

The present invention relates to systems and methods for measuring chromosome structure and gene expression. In one embodiment, the present invention includes an assay for determining the spatial organization of gene expression in the nucleus. The present invention also includes a method based on fluorescence in situ hybridization (FISH) that simultaneously yields information on the physical position and expression of individual genes. By lighting up a large number of targets on a particular chromosome using a bar-coding scheme, the large scale structure of an entire chromosome can be determined.