Single-cell analysis reveals clues about promising cancer therapy

Eencellige analyse onthult aanwijzingen over veelbelovende kankertherapie

A functional landscape and activation states of CD19 CAR T pre-infusion products from patients with ALL. (A) Schematic of experimental design. MSLN, mesothelin. (B) Uniform Manifold Approximation and Projection (UMAP) plot of 97,981 single CAR T cells collected from 12 patients. Eleven clusters are identified through unattended clustering. (C) UMAP distribution of all profiled cells separated by stimulation conditions. (D) Clustering and differential expression analysis of single CAR T cells revealed three major populations, characterized by high expression levels of HMGB2, LTB and CSF2, respectively. The distribution of the three marker genes and the cell cycle expression pattern of four experimental conditions were shown. (E) Quantification of fully active CSF2 cell proportion in three response groups at the four conditions. Upon stimulation with CD19-3T3 cells or anti-CD3/CD28 beads, a large population of cells express high levels of CSF2 and other cytokines, including IFNG, IL2, IL13, CCL3/CCL4 and XCL1/XCL2. The P values ​​were calculated by the Mann-Whitney test. Credit: scientific progress (2022). DOI: 10.1126/sciaadv.abj2820

A form of cancer treatment known as CAR T therapy has shown great promise for blood cancer treatments over the past decade, but all too often patients relapse within a short period of time. Now, a team of researchers has uncovered some crucial clues as to why — potentially leading to treatments to prevent these relapses.

The study, a collaboration between researchers from Yale University and the University of Pennsylvania, was published in: scientific progress

CAR T therapy involves isolating virus-fighting T cells from a patient’s blood and genetically modifying them with chimeric antigen receptors (CAR), which target surface markers expressed on cancer cells. These CAR T cells are infused back into a patient’s bloodstream to fight cancer cells. It has been shown to be particularly effective in fighting blood cancers such as acute lymphoblastic leukemia (ALL), lymphoma and multiple myeloma. However, remissions in a significant number of subjects are short-lived and 30% to 60% of treated patients relapse within a year.

The researchers looked for the differences between patients with long-term remission and the patients with a relapse. They looked for patterns in the patients’ cells and examined 100,000 single CAR T cells from 12 pediatric ALL patients. Of these 12 patients, five had a complete remission lasting more than five years, and another five relapsed over the course of the study at a median time of 9.6 months. The other two subjects showed no objective response to therapy.

Using technologies developed in the lab of Rong Fan, professor of biomedical engineering at Yale University and pathology at Yale School of Medicine, the researchers used what’s known as a “multi-omics” approach — where data sets from the transcriptome and combine the proteome – to perform a powerful single-cell analysis. This allowed them to closely study the complete gene expression profile of each cell and identify hidden molecular mechanisms between the CAR T cells, which could play a role in the development of future treatments.

The research team identified modules of co-expressed cytokines – secreted proteins that act as messengers for the immune system and are important regulators in the orchestration of immune cells. Of these, they found that a group of cytokines representing T helper 2 (Th2) function was prominent in the cell profiles of the patients who had been in remission for five years or more. Th2 cells are a subtype of cells that mediate the activation and maintenance of our immune response. With this, said Pablo G. Camara, assistant professor of genetics at UPenn, “we can better assess differences in the functionality of CAR T cells from different patients.”

“This observation implies that Th2 function may be indispensable for maintaining long-term remission in CAR T therapy,” added the study’s lead author, Zhiliang Bai, a postdoctoral associate in the Fan lab at Yale.

Fan said the analysis provides valuable insights into the factors that determine why some patients go into permanent remission.

“It also suggests a potential biomarker to predict therapeutic outcomes prior to administering this costly and complex treatment in cancer patients,” he said.

Single-cell analysis reveals clues about promising cancer therapy

Credit: Yale School of Engineering and Applied Science

The researchers expanded the study to an additional 49 ALL patients who participated in two other CAR T studies and conducted independent evaluations. J. Joseph Melenhorst, co-author of the study and former Professor of Pathology and Laboratory Medicine at UPenn, said the experimental results at Yale and UPenn jointly confirmed that the presence of Th2 function in CAR T infusion product is indeed associated with prolonged remission during 5 years.

“With a follow-up of approximately 10 years, we have collected enough data and are now able to answer this pressing unanswered question: Why have those patients relapsed compared to highly durable responders?” he said.

Based on the current findings, the researchers expanded their single-cell multi-omics profiling to 81 patients, covering all clinical response types in CAR T treatment.

“We expect that this huge dataset can give us a more accurate and comprehensive understanding of the fundamental mechanisms,” Fan said.

Researchers seek to improve success of chimeric antigen receptor T-cell therapy in non-Hodgkin’s lymphoma

More information:
Zhiliang Bai et al, Single-cell antigen-specific landscape of CAR T infusion product identifies determinants of CD19-positive relapse in patients with ALL, scientific progress (2022). DOI: 10.1126/sciaadv.abj2820

Provided by Yale University

Quote: Single-cell analysis reveals clues about promising cancer therapy (2022, June 20) retrieved June 20, 2022 from

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