Cell Pathology Revealed by Single-Cell Genotype-Phenotype Mapping

Explore a 33-minute webinar on cell pathology revealed through single-cell genotype-phenotype mapping. Delve into the complexities of cancer genetics, focusing on how somatic mutations drive disease progression and serve as prognostic markers. Learn about the challenges of linking genotypes to phenotypes in polyclonal tissues and discover how single-cell resolution methods address these issues. Examine the application of droplet microfluidics and single-cell sequencing techniques in resolving tumor heterogeneity. Investigate the process of single-cell genotyping and immunophenotyping, including DNA barcoding of antibodies for sequencing readouts. Analyze high-dimensional data visualization techniques and their application in understanding clonal diversity and disease progression. Explore case studies demonstrating the method's effectiveness in complex patient samples. Finally, consider the potential applications of this technology in studying HIV latency and identifying distinct T cell subcompartments affected by the virus.

Intro
Cell pathology revealed by single cell genotype- phenotype mapping
The genetic cause of most cancers is known
Tumor heterogeneity masks mutation co-occurrence
Droplet microfluidics provides scalability and cost efficiency
Single cell sequencing resolves tissue heterogeneity
DNA is the gold standard for genotyping
Single cell DNA sequencing requires harsh cell lysis
Proteinase K digestion of chromatin releases DNA and can be heat inactivated
Multiplexed PCR in droplets selects for the regions of interest
Uniform target amplification ensures low allele dropout
Single cell genotyping allows deconvoluting clonal heterogeneity
To link the genotype to the phenotype we need both
Single cell immunophenotyping is well established
Attaching DNA barcodes to antibodies allows for a sequencing readout
A genotype vector and an antibody count vector is measured for each cell
To visualize high dimensional data 2D projections are used
A synthetic cell mixture proves that the method works
How does a lengthy disease history affect clonal diversity?
The phenotype maps into a tight compartment
A patient with atypical blasts, what drives it?
Divergent differentiation response hints at unchartered variability
Partnering with Mission Bio helps adopting of method by other labs
New questions
HIV remains an incurable disease due to the latent reservoir
What is special about cells with latent HIV?
Can we make an assay that exploits this marker?
The HIV provirus is a perfect biomarker - can DAb-seq exploit it?
Integrated HIV genomes can reliably be detected in complex samples
Distinct T cell subcompartments are resolved
Strong tropism for distinct CD4+ T cell compartments
Concluding remarks