The Mark Foundation Center for Advanced Genomics and Imaging at the Johns Hopkins University (JHU) brings together the tools of astronomy image analysis, pathology, computer science, cancer genomics, and immunogenomics to solve problems in oncology and find innovative solutions that can expand the number of cancer patients who benefit from immunotherapy.
Scientists from The Mark Foundation collaborate with JHU researchers as part of a joint steering committee that reviews scientific progress and facilitate the success of the center. The Mark Foundation Center for Advanced Genomics and Imaging is led by Drew Pardoll, MD, PhD, Director of the Bloomberg~Kimmel Institute for Cancer Immunotherapy and co-Director of the Cancer Immunology Program at the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, together with Janis Taube, MD, MSc, Professor of Dermatology and Pathology and Director of the Division of Dermatopathology and co-Director of the Tumor Microenvironment Laboratory of the Bloomberg~Kimmel Institute for Cancer Immunotherapy, and Alexander Szalay, PhD, a Bloomberg Distinguished Professor in the Department of Physics and Astronomy; .
Building on the MANAFEST project begun in December 2017 with support from both the Bloomberg~Kimmel Institute and The Mark Foundation for Cancer Research, the center has expanded its focus on platforms for identifying cancer immunotherapy biomarkers, leveraging innovative technologies in cancer genomics, immune cell profiling, and digital pathology. The overarching goal is to facilitate the development of biomarkers that can more accurately predict which patients will benefit from a given immunotherapy, a centerpiece of Kimmel Cancer Center’s precision therapy vision.
Astronomy accelerates pathology
One pillar of the center was the creation of a new platform called AstroPath that takes a model used in astronomy and turns into one that can be used for massively scalable, spatially resolved analysis of the tumor immune microenvironment. Using AstroPath, Taube and astrophysicist Alexander Szalay, Ph.D., a Bloomberg Distinguished Professor of Physics and Astronomy, lead ongoing research that applies the technology used to ascertain the position of galaxies to the spatial relations in the tumor microenvironment. AstroPath’s groundbreaking celestial mapping algorithms can analyze hundreds of millions of cells, so researchers receive a detailed picture of the tumor’s location in the body and how it reacts with surrounding tissues.
Towards a unified platform for cancer genomics and cancer immunology
The other pillar of the center is the MANAFEST platform, which is focused on the development of a system to identify immune responses to changes in the genomes of cancer cells that could be used as a basis for personalized immunotherapy. Mutations, which represent changes in cancer genomes, generate biochemical signatures that are recognized as foreign by the immune system. The identification of such fragments, known as mutation-associated neoantigens (MANA), and the immune cells which target them for killing, is the goal of the MANAFEST platform. To accomplish this goal, cancer genomics and immunology analyses are integrated within a single, standardized platform that enables the identification of key biological indicators of how cancer patients will respond to immunotherapies. This integration represents a collaboration between the cancer immunology and cancer genetics programs, led by Drs. Bert Vogelstein and Ken Kinzler, Professors of Oncology and co-directors of the Ludwig Center for cancer genomics.
A renewed commitment
In 2022, The Mark Foundation for Cancer Research and the Bloomberg~Kimmel Institute for Cancer Immunotherapy (BKI) announced a $10 million commitment at to continue to fund novel work and advance immunotherapy research to provide lifesaving breakthroughs to people with cancer.
“Cancer treatment is advancing every day, and immunotherapy is a big reason for that,” said Michael R. Bloomberg, founder of Bloomberg LP and Bloomberg Philanthropies and founding donor of the Bloomberg~Kimmel Institute for Cancer Immunotherapy. “By teaming up with The Mark Foundation, this new investment will build on the cutting-edge work that Johns Hopkins and its partners are leading — saving lives and bringing us closer to bigger breakthroughs.”
“In less than three years, The Mark Foundation Center at Johns Hopkins University has made outstanding progress in improving our knowledge of how tumors respond to immunotherapy,” said Ryan Schoenfeld, chief executive officer of The Mark Foundation for Cancer Research. “Our collaboration with the Bloomberg~Kimmel Institute allows us to develop the next-generation genomics and imaging platforms for cancer immunotherapy necessary to save lives. We believe that over the next five years, the number of cancer patients who will benefit will burgeon.”
Paul Rothman, MD, Dean and CEO of Johns Hopkins Medicine, and an esteemed group of scientists, bring focused leadership to the new Center: Robert Anders, MD, PhD, Associate Professor of Pathology and co-Director of the Tumor Microenvironment Laboratory of the Bloomberg-Kimmel Institute for Cancer Immunotherapy with Dr. Taube; Alan Yuille, PhD, a Bloomberg Distinguished Professor in the Departments of Cognitive Science and Computer Science; Alexander Baras, MD, PhD Associate Professor of Pathology; and Srinivasan Yegnasubramanian, MD, PhD, Associate Professor of Oncology.
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