New Web-based Atlas of Mass Cytometry Profiles Includes Immunotherapy Responses

Oncologists have achieved some immune responses in patients with pancreatic cancer using various combinations of vaccines and immune checkpoint inhibitors, but it’s not always clear which therapy induces which response.

To support further study, investigators at the Johns Hopkins Kimmel Cancer Center have made available a free, web-based atlas of mass cytometry profiles from patients with metastatic pancreatic cancer. The work was supported by the Lustgarten Foundation for Pancreatic Cancer Research; the National Institutes of Health (NIH), the National Cancer Institute (NCI), SU2C/AACR, the Emerson Cancer Research Fund; an Allegheny Health Network grant, the JHU Discovery Award, and SPORE (Specialized Programs of Research Excellence).

“The atlas contains information from 260 cytometry profiles (of markers on immune cells) from blood samples from 64 patients who participated in three clinical trials of two pancreatic cancer vaccines and two checkpoint inhibitors in different permutations,” explained Won Jin Ho, M.D., an associate professor of oncology at the Johns Hopkins University School of Medicine and associate director of the Johns Hopkins Kimmel Cancer Center’s Convergence Institute, which aims to aims to leverage multi-disciplinary team science to solve cancer.

“We have a platform for immune profiling based on 40-plus protein level markers to understand immune system responses,” Ho noted.

“We also study patients before and after treatment so that we can understand longitudinal responses, or how cancer treatments induce changes in the immune system,” he added.

Access
A description of the atlas was published in in January 12, 2026 issue of Cancer Immunology Research, a publication of the American Association for Cancer Research (AACR).[1] The resource, available online through SciServer, houses fully annotated cytometry data from three trials. Enabled by collaboration with the Institute for Data Intensive Engineering and Science at Johns Hopkins, the atlas’ user interface and built-in tools simplify comparisons of cell types and expression levels. Researchers plan to add to the atlas over time, including information from tumor tissue analyses, Ho says.

“Pancreatic cancer is such a lethal disease, which was our motivation to make this public,” Ho says. The five-year survival rate is just 13%, according to the Pancreatic Cancer Action Network.

“Our group has done a lot of investigational immunotherapy trials. These are early-phase trials of smaller groups of patients, but have been very informative, even if the clinical outcomes have not met what we wanted,” he added.

Researchers applied new cytometry techniques to blood samples collected in previously completed trials to build the atlas and inform the development of new therapies. Dimitrios Sidiropoulos, Ph.D., a computational cancer immunologist at Johns Hopkins, co-led the cross-trial integration of data, identifying immune signatures in blood that are distinct for specific immunotherapies and can be projected onto tumor tissues, demonstrating the utility of the atlas. “What we’re hoping is that scientists can go to this repository, explore the data, and generate hypotheses to carry out new studies,” Ho said.

In the same issue of the journal, Ho and colleagues also reported results of a new phase 2 study of 57 patients with metastatic pancreatic cancer whose disease progressed while on chemotherapy.

The trial, led by Dung Le, M.D., the Bloomberg~Kimmel Professor of Cancer Immunotherapy, and Katie Bever, M.D., an assistant professor of oncology, randomized patients to one of two treatment groups: the vaccine CRS-207 plus the immunotherapies anti-PD1 nivolumab and anti-CTLA4 ipilimumab, with or without the vaccine GVAX, during six 21-day cycles.[2]

While response rates were not significantly different between the groups, in-depth immunologic studies co-led by Amanda Huff, Ph.D., an assistant professor of oncology, found that the vaccine-based regimens could generate T-cell clones specific for the antigen mesothelin and the KRAS mutation, and that those clones infiltrated tumors.

The findings, published as companion papers, are complementary in assessing the effects of key immunotherapeutic agents.

Adding anti-CTLA4 to the immunotherapy backbone significantly increases the infiltration of antigen-experienced T-cells and “is going to be an important part of future immunotherapy backbones,” Ho concluded.

Additional information and data

• Raw protein expression data are shared in files [Available on Zenodo]
• Analysis code (Available on the GitHub repository).

Reference
[1] Sidiropoulos DN, Zhang Z, Durham JN, Charmsaz S, Gross NE, Lee JW, Sun Y, Perikala S, Tandurella JA, Lvovs D, Mitschang A, Lemson G, Shin SM, Hernandez AG, Mitchell S, Leatherman JM, Danilova L, Wang H, Fertig EJ, Jaffee EM, Bever KM, Le DT, Ho WJ. Cytometric Atlas of Combination Immunotherapy in Pancreatic Cancer: Blood-Based Signatures Reveal Vaccine and Checkpoint Inhibitor Responses. Cancer Immunol Res. 2026 Jan 12. doi: 10.1158/2326-6066.CIR-25-1126. Epub ahead of print. PMID: 41524578.
[2] Bever KM, Huff AL, Danilova L, Wetzel M, Tandurella JA, Durham JN, Wang T, Lee JW, Coyne EM, Montagne JM, Mitchell JT, Hernandez AG, Shin SM, Anders RA, Wang H, Fertig EJ, Jaffee EM, Le DT, Ho WJ. A randomized phase II study: CRS207/GVAX plus anti-PD1 and anti-CTLA4 recruits mesothelin- and mKRAS-specific T cells into PDAC. Cancer Immunol Res. 2026 Jan 12. doi: 10.1158/2326-6066.CIR-25-0545. Epub ahead of print. PMID: 41524570.

Featured image: Members of the Won Jin Ho Laboratory within the Johns Hopkins Kimmel Cancer Center Gastrointestinal Oncology Group. Photo courtesy © 2026 Won Jin Ho Lab. Used with permission

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