Proteogenomic reprogramming to a functional human blastomere-like stem cell state via a PARP-DUX4 regulatory axis

Area of Science:

• Developmental Biology
• Stem Cell Biology
• Proteogenomics

Background:

• Human pluripotent stem cells (hPSCs) are crucial for developmental studies.
• Understanding early human embryogenesis requires models that recapitulate key developmental stages.
• Tankyrase and PARP1 are enzymes involved in DNA repair and gene regulation.

Purpose of the Study:

• To investigate the reprogramming of hPSCs into a naive, blastomere-like state.
• To assess the developmental potential of reprogrammed cells in interspecific chimeras.
• To elucidate the proteogenomic mechanisms underlying this reprogramming.

Main Methods:

• Culture of hPSCs with tankyrase-PARP1 inhibitors.
• Induction of DUX4 expression.
• Injection of reprogrammed cells into murine embryos.
• Proteome-ubiquitinome analysis.
• Chromatin immunoprecipitation sequencing (ChIP-seq).

Main Results:

• Reprogrammed cells, termed TIRN-SCs, exhibit blastomere-like characteristics and express pioneer factors.
• TIRN-SCs contribute to both embryonic and extra-embryonic lineages in human-mouse chimeras.
• Enhanced chimeric contribution observed with ectopic E-Cadherin expression.
• Placental chimeras were generated from TIRN-SC-derived trophoblast stem cells.
• Proteomic analysis revealed altered TNKS/PARP1 levels and a hyper-ubiquitinated proteome.
• A DUX4-NANOG-SOX2-OCT4-PARP1 (NSOP) axis was identified, regulating lineage plasticity.

Conclusions:

• Tankyrase/PARP1 inhibition reprograms hPSCs into developmentally plastic TIRN-SCs.
• TIRN-SCs offer a novel model for studying early human embryogenesis and proteogenomic regulation.
• These findings advance the potential for creating interspecific chimeras for developmental research.