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Dan Landau: Splice splice baby! New paper just out in Cell Stem Cell

Photo of Dan Landau from Weill Cornell Medicine/Twitter

Aug 16, 2023, 19:51

Dan Landau: Splice splice baby! New paper just out in Cell Stem Cell

Quoting Dan Landau, Core Faculty Member at the New York Genome Center, on Twitter:

“Splice splice baby! New paper just out in Cell Stem Cell integrating Oxford Nanopore long read single-cell isoform mapping into our broader genotype-phenotype vision for clonal mosaicism!

We first applied GoT (nature.com/articles/s4158) to MDS with mutated SF3B1, adding CITE-seq for surface proteins. Single-cell mapping showed distinct differentiation biases, protein and mRNA expression differences between mutated and wild type cells within the same bone marrow.

BUT, as SF3B1 is a splice factor, we reasoned that the link between genotype and phenotype would go through altered splicing. We therefore developed a method to add high-depth long-read single-cell sequencing, uncovering the 3′ cryptic splicing signal known from bulk RNAseq

Single cell data allowed us to see that mis-splicing events were far more enriched in mutated cells (as expected), but also that different bone marrow progenitors have distinct mis-splicing patterns.

Tracking the continuum of erythroid differentiation shows a wave of mis-splicing where some genes are affects early and some late, with rough correspondence to expression. We did see some discrepancies, which in part may relate to NMD….

One of the most interesting mis-splicing events affects BAX, a critical apoptosis regulator downstream of BCL2. It was thought that this isoform turns BAX from pro- to anti-apoptotic, a finding validated by Abdel Wahablab lab, with potential implication to venetoclax treatment.

We also looked at clonal hematopoiesis (CH) samples from Irene Ghobrial lab, and saw that many of the transcriptional and differentiation biases were already there prior to over MDS.

Interestingly, many of the mis-splicing changes were also there in CH, with a good overlap with MDS samples. These data show that in some cases, CH vs. overt disease is a quantitative rather than qualitative change, related to clone size.

We are excited about this work! – Moving beyond mRNA counts to isoform profiling – Better understanding of splice factor mutations in hematopoiesis – Expanding multi-omics in genotype-phenotype mapping of clonal mosaicism.”

For the article click here

Source: Dan Landau/Twitter