Guest lecture Miao-Ping Chien - Phenotype-based target cell subtyping and profiling
8 important questions on Guest lecture Miao-Ping Chien - Phenotype-based target cell subtyping and profiling
Single cell sequencing (scSeq) preserve information of an individual cell, they can capture?
Application of single-cell RNA seq
- Understand molecular mechanisms & identify target genes:
- Therapy resistance
- Cell differentiation
- Mechanisms that drive a process
- Identify new cell types
- Understanding the role of heterogeneity in biological processes and disease formation
- Clustering analysis with tSNE
Standard single-cell RNA-seq pipeline
- Quality control & feature selection
- Dimensionality reduction & clustering (!)
- Marker identification
- Interpretation
- Higher grades + faster learning
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Difficulties of subtyping cells
- Technical issues
- RNA != protein
- Similar expression profiles between subgroups of cells
Difficulties with tumor cell subtyping
- Tumor cells are highly heterogeneous
- How many subtypes?
- No robust biomarkers for each subtype pf tumor cells
- Does every subtype of tumor cells matter (in terms of tumorgenesis)?
An alternative for biomarkers to subtype tumor?
Challenges in scRNA-seq pipeline
- Feature selection: what if the cells of interest are very rare?
- Dimensionality reduction and clustering: what if the cells are transcriptomically similar?
- Marker identification: what if no usable markers are available
- Interpretation: cannot link genotypes to (functional) phenotypes
Chromosomoal instability (CIN)
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