An integrative analysis of reprogramming in human isogenic system identified a clone selection criterion

Area of Science:

• Stem cell biology
• Epigenetics
• Genomics

Background:

• Human induced pluripotent stem cells (iPSCs) are typically assessed by physiological pluripotency markers.
• Molecular comparisons between iPSCs and embryonic stem cells (ESCs) often reveal distinct gene expression and methylation patterns.
• Understanding factors influencing iPSC molecular signatures is crucial for their reliable application.

Purpose of the Study:

• To investigate the influence of reprogramming process, parental cell type, and stochasticity on human iPSC molecular signatures.
• To establish an isogenic system for comprehensive molecular comparison of iPSCs and ESCs.
• To develop criteria for selecting optimal iPSC lines for research.

Main Methods:

• Development of a complete isogenic reprogramming system.
• Genome-wide transcriptome and methylome analysis.
• Comparison of human isogenic ESCs, ESC-derived somatic cells, and derived iPSC lines.

Main Results:

• iPSC molecular signatures are largely determined by stochasticity, independent of parental cell type or reprogramming method.
• Five iPSC clones are sufficient to achieve 95% confidence in finding a clone indistinguishable from isogenic ESCs.
• A method for selecting the "best" iPSC line based on a core set of characteristic genes was developed and validated.

Conclusions:

• The molecular identity of human iPSCs is primarily shaped by random events rather than the reprogramming process or cell origin.
• Isogenic systems are valuable for dissecting molecular variations in iPSCs.
• A robust method for selecting high-quality iPSC lines can improve their utility in regenerative medicine and disease modeling.