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November 30, 2022

“Single Cell Multi-omics” Opens Possibilities to Link Clonal Cell Mutations with Disease

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Scientists at Weill Cornell Medicine have finally found a way to correlate mutations with observable characteristics in human cells, taking a step towards understanding how diversified mutations in cells may lead to disease.

The researchers obtained blood stem cells from the bone marrow of patients with multiple myeloma — a cancer that forms in white blood cells and is found to have large blood cell clonal outgrowths in which each cell can have different mutations. They then mapped the gene activity and phenotypic detail to characterize a clonal outgrowth mutation, or a large population of cells with the same mutation.

Typically, all cells in the body contain the same genetic information. However, as cells divide, numerous mutations can occur, potentially leading to a massive clonal outgrowth or clonal mosaicism mutations, where replicated cells each contain different genetic information. While clonal outgrowths are commonly thought to be associated with malignant transformation, many are also linked with nonmalignant disease.

“Inflammation in the gut tends to select particular clones that are more resistant to the inflammatory environment of the gut,”explained Prof. Dan Landau, physiology and biophysics. “Metabolic disorders in the liver tend to select clones that have genes that protect them.”

These clonal outgrowth mutations undergo selection where only the most fit cells survive with their genetic composition. For some cells, this can lead to normal-appearing tissue having mutations that are likely to have a relationship not just with cancer but also with other diseases such as cardiovascular disease, Landau said.

The traditional method to characterize clonal outgrowth cells is to compare mutated cells with normal cells. However, due to the similarity of mutated cells to normal cells and the variability of mutations from person to person, it has been difficult to use these methods to study clonal mosaicism in humans.

To better understand clonal mosaicism mutations, Weill Cornell researchers developed innovative “single-cell multi-omics” techniques to detect genomic and phenotypic attributes of cells with the DNMT3A mutation in bone marrow cells that can develop into all types of blood cells. This method allows one cell with a specific mutation to be analyzed,identified, and compared with the same patient’s normal, healthy cell, providing a perfect comparison without variability between patients.

“We were able, for the first time, see these clonal mosaicism mutations and actually understand what they are doing to the cells to make them grow faster,” said Landau.

This is especially significant since DNMT3A mutant cells appear and function the same as normal healthy cells but have been thought to indicate an early stage of acute myeloid leukemia development. With this new technique, scientists were able to observe new findings.

“We found that the [DNMT3A] mutation is causing the stem cell to differentiate in a particular way. The mutation seemed to skew towards myeloid cells… and in terms of the transcriptional state, which was dysregulated, we saw signatures of inflammation,” said co-author Prof. Anna Nam, pathology and laboratory medicine.

Other breakthroughs the researchers discovered using this technology also include finding that mutant stem cells were more likely to mature into red blood cells and blood-clotting platelet-producing cells. This sheds light on the mutant cell’s correlation with cardiovascular disease.

In the future, Landau and Nam both hope that single-cell multi-omic techniques can be used to correlate molecular signatures in clonal outgrowths with various diseases.

“We’re interested to see different mutations in different genes [in clonal outgrowth cells] and how they utilize unique pathways for fitness advantage,” said Nam. “[But] we’re [also] interested in how we get rid of these clonal stem cells before they become cancerous.”