Researchers at the Walter and Eliza Hall Institute for Medical Research (WEHI) in Melbourne, Australia, have used a newly developed single-cell clonal multiomics technique to gain a better understanding of the genetic programming underlying how stem cells differentiate into particular cell types.
The research team developed the new technique, known as SIS-seq (sister cells assayed in parallel for fate or RNA sequencing), in order to link the gene expression of a single cell with the particular cell types it generated.
"We invented SIS-seq in order to study 'sister' cells that descend in parallel from the mother stem cell," explained study leader Shalin Naik, laboratory head of the Division of Immunology at WEHI.
"As RNA sequencing destroys single stem cells, you can only study the genetic contents of the cell, but lose the chance to know what new cell it would have generated, with no chance of going back in time to find that out," he said.
"By letting a single stem cell divide finite times, we were able to test the sisters separately; some were tested for what they made and others for their genetic contents, [allowing us] to link the genes with the cell types that are made."
By testing the daughters of a single stem cell in different parallel tests, the WEHI researchers found 500 genes that predicted dendritic cell fate, then used CRISPR (clustered regularly interspaced short palindromic repeats) screening to discover 30 key genes that program for the antigen-presenting dendritic cells that initiate the immune response.
"CRISPR screening is the process whereby the genes that control a particular process are tested in one large experiment, by testing lots of single cells, each of which has had just one gene deleted," explained Naik.
"The 30 new genes thus identified have never been described in dendritic cell development, so may prove to be treatment targets for boosting dendritic cell numbers in vitro, prior to their injection into patients," he told BioWorld Science.
Naik and his WEHI research team intend to expand use of the clonal multiomics technique to identify the initiation of cancer development, in order to identify new cancer drug targets, they reported in the April 16, 2021, edition of Immunity.
The researchers hope that by clarifying this process, they may be able to find new immunotherapies for cancer, and plan to expand the technique for discovering new drug targets for the prevention of tumor initiation.
"We know that only a few cells that develop a cancer mutation are the ones that drive it to grow. Therefore, if we could find that proverbial 'needle in a haystack,' using our newly modified technique, we would know the genetic components that correlate with tumor outgrowth," noted Naik.
"Having the knowledge concerning those unique genes in that clone means that we could then custom-design approaches to target those genes for cancer therapy."
Naik and his research team initially investigated the processes involved in initiating generation of dendritic cells driven by the hormone Flt3 ligand, which represents an emerging new strategy in immunotherapy.
"Clinical trials are already underway, in which the Ftl3 ligand is being injected directly into patients in order to boost dendritic cell numbers," Naik said. "This is a very exciting approach to immunotherapy, because it is the dendritic cells that educate the cancer-killing T lymphocytes."
"Indeed, preclinical data exist showing that by increasing dendritic cell numbers even further, or by boosting numbers of particular dendritic cell subtypes, we may be able to kill tumors more effectively."
Looking forward, "our next step in this research area will be to apply this technique to the study of human blood cell generation, so as to identity the programming factors that generate different immune cells," said Naik.
"We will also be investigating which genes allow some clones in cancer to metastasize or to resist cancer drug treatment, which will initially be done in breast cancer and leukemia."