NEW YORK – Two new studies from researchers at Stanford University have demonstrated the utility of 10x Genomics' single-cell platform to analyze immune cells and their role in cancer therapies.
Using the 10x Chromium Single Cell Immune Profiling Solution and the Chromium Single Cell ATAC (assay for transposase-accessible chromatin) Solution, researchers led by Howard Chang, a professor at Stanford University School of Medicine, studied T cell clonal expansion and recently published papers in Nature Medicine and Nature Biotechnology, respectively.
The papers are "studying some of the very same samples, but using different kinds of single-cell technology," Chang said. "We really got a multi-modal view of the entire process of how cancer immunotherapy works." The main link between the two studies was that the clonal expansion and replacement of T cells that happens after immunotherapy is initiated is most pronounced in cells that have a particular chromatin signature.
Chang is a paid advisor to 10x Genomics and is a co-founder of Epinomics, which 10x acquired a year ago.
The Nature Medicine paper, published last month, used the 10x single-cell immune profiling assay to determine where tumor-fighting T cells come from. The study may upend the conventional wisdom that those cells, spurred by immunotherapies, come from within the tumor. Chang said his results suggest the cells are actually recruited from the blood. The finding has implications for how clinicians might predict response to treatment, he said.
The Nature Biotechnology paper, published last week, demonstrated the capabilities of 10x's new ATAC-seq assay to profile chromatin accessibility in hundreds of thousands of single cells.
"It's a beautiful, landmark paper," said Bing Ren, a single-cell researcher at the University of California, San Diego, who was not involved with either study. "They analyzed blood samples and cancer samples and demonstrated the strength of the platform. I think it's a hugely valuable resource for the community."
"This is probably their coming-out party for the 10x ATAC-seq assay," he added. "As far as I know, it's the first paper. [10x] has released a lot of data, but not in a publication."
10x's ATAC-seq assay has been available since October 2018, and the Stanford researchers posted both papers to the BioRxiv preprint server earlier this year.
As previously reported, the 10x ATAC-seq assay offers the ability to analyze 10,000 nuclei per sample and up to 80,000 nuclei per chip, with a capture efficiency of 65 percent.
Giovanna Prout, senior director of product marketing at 10x Genomics, said that while the company is growing in general, it has seen growth in sales for both the immune profiling solution and the ATAC-seq assay.
She also suggested that the Nature Medicine paper wouldn't have been possible without single-cell methods. While the researchers used bulk sequencing methods to validate their results, without the resolution afforded by 10x's platform, they wouldn't have been able to determine that tumor-infiltrating cells weren't originally found in the tumor, she said.
Chang noted that his team used immune receptor sequencing from Adaptive Biotechnologies in that study. He also praised the "robustness" and capture rate of the 10x assays. The patient biopsy samples the researchers were working with were very small and "very precious," he said, and because they were serial biopsies, "there's no way you can substitute one sample for another."
"Everything we got had to end up as data," he said. "The method can't sometimes work and sometimes not, that would destroy such a project."
The results from the Nature Medicine paper should make researchers rethink how to predict if a patient will respond to immunotherapies, he added.
"A lot of prediction is based on the tumor before treatment," and which types of T cells are present, Chang said. "Our study suggests that those [T cells] are not the ones that end up fighting the tumor. You can profile them as much as you want, but they're not what matters."
"The T cells that are going to matter are in the blood," he said. "This is actually very promising. There are many tumors where it's hard to stick a needle into them. Blood is much more accessible. And trying to [biopsy] the tumor over and over again is a challenge."
In showcasing the 10x ATAC-seq assay, the Nature Biotech paper provided what Chang called an "unbiased deconstruction of tissues without any prior hypotheses or preconceived notions."
The researchers wrote that their study looked at malignant, stromal, and immune cell types in the tumor microenvironment. "Here we can just analyze all cell types present," Chang said. "And let the data guide you as to what's interesting."
One thing the researchers picked up on was chromatin states associated with exhausted T cells, which have been repeatedly stimulated to the point where they're not as active as they were before. Chang said the study found DNA regulatory elements that are only activated in exhausted T cells and that some of the transcription factors involved were like those seen in T follicular cells. "This is perhaps one of the first studies linking T follicular cells to exhaustion, especially in cancer therapy," he said.
Chang noted that his team was able to see cell development trajectories. By clustering cells with similar chromatin signatures, they could walk backwards form a terminal cell type to the next most similar cluster of cells, all the way back to hematopoietic stem cells.
The Stanford team was able, for example, to recreate the B cell lineage, which has been well studied. But for lineages that haven't, of which there are many, "we can work out that development trajectory," Chang said.