Scientists at the Children’s National Hospital in Washington D.C., have successfully merged two scientific fields that led to a novel multi-targeted T-cell immunotherapy. As part of their research, they discovered unique proteins in an individual tumor’s cells, which then helped scientists generate personalized T-cells to target and kill tumors.
The results of their pre-clinical study research were published in Nature Communications. 
This effort is the first to create a new workflow for neoantigen identification that incorporates both genetic sequencing and protein identification to create a personalized treatment for medulloblastoma in children, a common, very fast-growing, malignant primary central nervous system (CNS) tumor.
In children, medulloblastoma accounts for 15 to 20% of all brain tumors. The disease generally occurs in children between the ages of three and eight but can be seen in children and adults of any age. On average, there are about 350 cases of medulloblastoma diagnosed each year in the United States. The overall survival rates are between 25 and 75% depending on the molecular subgroup, metastatic status, and age at diagnosis.
Today, effective therapy requires intensive chemo- and radiation therapies, including post-operative craniospinal irradiation, considered the cornerstone of potentially curative therapy for most patients with medulloblastoma, and systemic chemotherapy. However, late toxicities related to endocrine function, growth and bone development, life-altering neurocognitive deficits, ototoxicity, gynecological toxicity and health of the offspring, cardiac toxicity, and pulmonary toxicity, are considered major problems, significantly affecting long term health-related Quality of Life (hrQoL) of survivors.
If, after chemoradiotherapy, medulloblastoma recurs, there are no standard effective therapies and virtually no long-term survivors. Hence, there is an urgent medical need to develop novel therapeutics that can combat this cancer and augment the current standard of care therapies without increasing the burden of the late effects. 
Neoantigens exclusively expressed on tumor cells, are one of the main targets of an effective antitumor T-cell response. The ideal target antigen is abundantly expressed by tumor cells but not by normal tissues, in order to limit off-target effects.
Using a novel proteogenomic approach to identify tumor-restricted peptides the scientists at the Children’s National Hospital were able to select and expand T-cells capable of mounting a tumor-specific cytotoxic immune response, with no off-target effects for patients with medulloblastoma.
Based on the potential of this promising personalized T-cells strategy, the researchers are now designing a phase I clinical trial slated to open in 12-18 months.
“This work is an incredibly exciting advancement in personalized medicine. It will allow us to treat patients with a novel T cell therapy that is developed for each individual patient to specifically attack and kill their tumor,” said Catherine Bollard, M.D., M.B.Ch.B., director of the Center for Cancer and Immunology Research at Children’s National and co-senior author on the paper.
“This treatment will offer a potential option for children with hard-to-treat brain tumors for which all other therapeutic options have been exhausted,” Bollard added.
Low-input proteogenomic approach
First, the researchers sequenced the DNA of small tissue samples while studying its complete set of proteins that influence cancer biology — also named a “low-input proteogenomic approach” by the authors. After analyzing the empirical data, which shies away from the commonly used predictive models, the researchers developed a T-cell immunotherapy that targets the tumor’s unique proteins and allows the T-cells to distinguish between healthy cells and tumor cells. This means that Rivero-Hinojosa et al. managed to merge two research fields, proteogenomics, and immunotherapy, and lay the groundwork for personalized, targeted T cell therapies to treat children with brain tumors.
“Neoantigen discovery techniques have either been dependent upon in silico prediction algorithms or have required a significant amount of tumor tissue, making them inappropriate for most brain tumors,” said Brian Rood, M.D., medical director of Neuro-oncology and the Brain Tumor Institute at Children’s National.
“This neoantigen identification pipeline creates a new opportunity to expand the repertoire of T cell-based immunotherapies,” he added.
Tumor cells have damaged DNA that creates mutations during the repair process because they do not do a good job at maintaining their DNA fidelity. The repairs, therefore, create aberrant DNA that codes for proteins that were never intended by the genetic code and, consequently, they are unique to the individual’s tumor cells.
“We developed a new filtering pipeline to remove non-annotated normal peptides. Targeting antigens that are completely specific to the tumor, and expressed nowhere else in the body, will potentially increase the strength of tumor antigen-specific T-cell products while decreasing the toxicity,” said Samuel Rivero- Hinojosa, Ph.D., staff scientist at Children’s National and first author of the study.
Once the experts identified these unique peptides, they used them to select and expand T-cells, which showed specificity for the tumor-specific neoantigens and the ability to kill tumor cells. The next step is to conduct a clinical trial in which a patient’s own T-cells are trained to recognize their tumor’s unique neoantigens and then reinfused back into the patient.
From an immunotherapy standpoint, tumor specificity is important because when clinicians treat patients with T-cell therapies, they want to make sure that the T-cells directly target and kill the tumor and will not cause devastating harm to healthy cells. This paper demonstrated that it may be possible to create a better efficacy and safety margin with this new approach.
In the past five years, under the leadership of Bollard, the Center for Cancer and Immunology Research at Children’s National has advanced scientific knowledge in preclinical and clinical settings. The center discovered a signaling pathway that can be hijacked to prevent brain tumor development and further advanced translational research with several key first-in-human studies that utilized novel cell therapies to treat cancer and life-threatening viral infections.
 Rivero-Hinojosa S, Grant M, Panigrahi A, Zhang H, Caisova V, Bollard CM, Rood BR. Proteogenomic discovery of neoantigens facilitates personalized multi-antigen targeted T cell immunotherapy for brain tumors. Nature Communications 10.1038/s41467-021-26936-y [Article]
 Shih DJ, Northcott PA, Remke M, Korshunov A, Ramaswamy V, Kool M, Luu B, Yao Y, Wang X, Dubuc AM, Garzia L, Peacock J, Mack SC, et al. Cytogenetic prognostication within medulloblastoma subgroups. J Clin Oncol. 2014 Mar 20;32(9):886-96. doi: 10.1200/JCO.2013.50.9539. Epub 2014 Feb 3. PMID: 24493713; PMCID: PMC3948094.
 Fossati P, Ricardi U, Orecchia R. Pediatric medulloblastoma: toxicity of current treatment and potential role of protontherapy. Cancer Treat Rev. 2009 Feb;35(1):79-96. doi: 10.1016/j.ctrv.2008.09.002. Epub 2008 Oct 30. PMID: 18976866.
 Rivero-Hinojosa S, Grant M, Panigrahi A, Zhang H, Caisova V, Bollard CM, Rood BR Proteogenomic discovery of novel tumor proteins as neoantigens for personalized T cell immunotherapy in pediatric medulloblastoma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1067.
Featured image: A researcher at Children’s National Hospital in Washington D.C. Photo Courtesy: © 2016 – 2021 Children’s National Hospital. Used with permission