Expressed Barcode Libraries for Cell Lineage and Transcriptional State Profiling
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Solution Overview
Problem
Current methods fail to effectively study the mechanisms of non-genetic resistance in cancer cells, particularly in platinum-sensitive relapse, due to a lack of multi-functional tools that can de-convolute the contributing factors and trace the lineage and transcriptional state of individual cells.
Innovation Solution
The development of nucleic acid molecules with molecular barcodes linked to promoters and reporter genes, allowing for the simultaneous profiling of cell lineage and transcriptional state, and the use of vector libraries to genetically barcode cells, enabling the identification of genes associated with tumor dormancy and stem-cell like treatment-resistant cancer cells.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If traditional single-marker methods are used to study cancer cell resistance, then the study design is simple, but the ability to de-convolute multiple contributing factors and trace cell lineage is insufficient
Solution Approach 1:
The patent combines multiple functional elements into a single nucleic acid molecule: a molecular barcode for lineage tracing, a constitutive promoter-driven reporter gene for cell identification, and an inducible promoter-driven reporter gene for treatment response monitoring. This merging allows simultaneous tracking of cell lineage, proliferation status, and treatment effects within one integrated construct, enabling comprehensive study of cancer resistance mechanisms without requiring multiple separate markers.
Solution Approach 2:
The nucleic acid molecule is designed with universal applicability to study various aspects of cancer resistance simultaneously. The molecular barcode provides universal lineage tracing capability, while the dual-reporter system (constitutive and inducible) offers universal monitoring of cell identity and treatment response across different cancer types and therapeutic interventions, making the tool broadly applicable to diverse research questions.
2Measurement precision
If multiple separate markers are used to track different cell properties, then each marker can be optimized independently, but the overall system complexity increases and simultaneous profiling becomes difficult
Solution Approach 1:
The patent merges lineage tracing (molecular barcode), cell identification (constitutive reporter), and treatment response monitoring (inducible reporter) into a single integrated nucleic acid molecule. This unified design enables simultaneous measurement of multiple cell properties with high precision, as all markers are co-expressed in the same cell and can be analyzed together through single-cell sequencing, avoiding the complexity of coordinating multiple separate markers.
Solution Approach 2:
The molecular barcode is nested within the same nucleic acid molecule as the reporter genes, with the barcode sequence embedded in a context that includes promoter regions and reporter gene sequences. This nesting allows the barcode to be transcribed and sequenced alongside the reporter gene expressions, enabling coordinated measurement of lineage and functional states from a single molecular construct.
3Loss of information
If comprehensive multi-functional tools are developed to study cancer resistance mechanisms, then the ability to uncover contributing factors is enhanced, but the complexity of the tool increases
Solution Approach 1:
The patent combines information-capture functions into one molecule: the molecular barcode preserves lineage information, the constitutive reporter maintains cell identity data, and the inducible reporter captures treatment response dynamics. By merging these functions, the system retains comprehensive information about cell dynamics, proliferation, and resistance mechanisms without requiring multiple separate constructs, thus minimizing information loss while managing complexity.
Data Source
AI summary
Disclosed herein are nucleic acid molecules comprising molecular barcodes having a variable sequence operably linked to a promoter and compositions comprising such nucleic acid molecules. Further disclosed herein are methods for simultaneously mapping the lineage and the transcriptional state of a cell.