All Cancers

Current Projects
Michael E. Pacold, MD, PhD

Oxygen is a double-edged sword in pancreatic cancer biology. Pancreatic cancers require oxygen, but they are amongst the most hypoxic of cancers, with oxygen concentrations as low as 200-fold below atmospheric oxygen concentrations. Pancreatic cancers use oxygen to make molecules critical for their survival and proliferation, but they are also vulnerable to oxidative stress, which is essential for the effectiveness of cancer treatments such as radiation. Dr. Pacold has developed techniques to determine which oxygen-dependent reactions are prioritized by pancreatic cancers and enhanced by radiation treatment, with the goal of identifying new targets that can be used for pancreatic and other cancers that are treated with radiation.

Project title: "Tracing molecular oxygen in pancreatic cancer"
Institution: New York University Langone Health
Award Program: Innovator
Cancer Type: Pancreatic, All Cancers
Research Area: Biochemistry
Elli Papaemmanuil, PhD

Cancer survivors are at a higher risk of developing blood cancers than the general population due to the toxic effects of cancer treatments. Therapy-related blood cancers are often resistant to existing drugs and therefore extremely challenging to treat. Contrary to previous thought, recent studies show that the mutations causing these blood cancers can be identified in patients' blood many years before they receive therapy. Dr. Papaemmanuil has discovered that the existing mutations alone are not sufficient to cause therapy-related cancer but require the acquisition of additional mutations that affect large segments of the DNA, or "allelic imbalances." She will pursue further studies to screen patients and understand the mechanisms of therapy-related blood cancers. These findings will inform clinical strategies of early detection and targeted intervention to better treat this aggressive disease.

Project title: "Leveraging multi-modal genome profiling approaches to study disease initiation, progression, and response to therapy in TP53 mutated myeloid neoplasms"
Institution: Memorial Sloan Kettering Cancer Center
Award Program: Innovator
Cancer Type: Blood, All Cancers
Research Area: Cancer Genetics
Dylan M. Parker, PhD

Dr. Parker [HHMI Fellow] studies the role of molecular assemblies known as stress granules that form when cells are exposed to stressful conditions. The assembly of stress granules upon cellular insult is thought to regulate gene expression and modulate cell survival. Notably, stress granules are present in various cancers and many chemotherapeutic treatments lead to the formation of stress granules. Dr. Parker aims to determine the mechanisms regulating stress granule assembly and disassembly to understand how stress granule formation supports the development of cancer and chemotherapy-resistant tumors. This research has the potential to discover novel targets to treat cancers as well as sensitize chemotherapy-resistant cancers to existing treatments. Dr. Parker received his PhD from Colorado State University and his BS from the University of Oregon.

Project title: "Stress granule regulators and their roles in cancer progression"
Institution: University of Colorado Boulder
Named Award: HHMI Fellow
Award Program: Fellow
Sponsor(s) / Mentor(s): Roy R. Parker, PhD
Cancer Type: All Cancers
Research Area: Biochemistry
Titas Sengupta, PhD

An organism’s life experiences, such as exposure to bacterial pathogens, can cause sustained changes in its physiology and behavior. How these experiences are encoded in heritable RNA and DNA-associated proteins (called chromatin), and how these in turn affect the physiology of the organism itself and its progeny, are not well understood. Previous research has shown that the roundworm C. elegans can “read” small non-coding RNAs from the pathogenic bacterium Pseudomonas aeruginosa and learn and teach its progeny to avoid this bacterium. Dr. Sengupta’s [Rebecca Ridley Kry Fellow] research investigates how bacterial small RNAs taken up in the intestine can result in lifelong, multigenerational, and organism-wide changes at the epigenetic (RNA and chromatin) level to regulate brain function and behavior. She will investigate which small RNA and chromatin-associated genes are required for the learned response, where these genes function, and what changes at the epigenetic and gene expression level underlie this response. This will inform principles of epigenetic regulation of gene expression following diverse environmental stimuli, and stimuli within tissue environments, including tumor microenvironments. Dr. Sengupta received her PhD from Yale University and her MS and BS from the Indian Institute of Science Education and Research.

Project title: "Investigating bacterial small RNA-mediated regulation of host behavior"
Institution: Princeton University
Named Award: Rebecca Ridley Kry Fellow
Award Program: Fellow
Sponsor(s) / Mentor(s): Coleen T. Murphy, PhD
Cancer Type: All Cancers
Research Area: Epigenetics
Joshua B. Sheetz, PhD

Cancer cells adapt their metabolism to achieve rapid growth and proliferation. Much of their metabolic malleability hinges on mitochondria, subcellular hubs for energy transformation and biosynthesis. As a key means to control mitochondrial composition and meet metabolic demands, cells mark mitochondrial proteins for degradation by a process called ubiquitylation. How both cancerous and healthy cells direct and monitor mitochondrial ubiquitylation remains poorly understood. Dr. Sheetz [HHMI Fellow] aims to dissect the cellular machinery that performs mitochondrial ubiquitylation and determine how this process promotes metabolic adaptability in cancer cells. A major translational goal is to identify approaches for tuning the levels of mitochondrial ubiquitylation in tumors and in metabolic disorders that put patients at risk for cancer. Dr. Sheetz received his PhD from Yale University, New Haven and his BS from the University of North Carolina, Chapel Hill. 


Project title: "Mitochondrial ubiquitylation mechanisms to exploit metabolic vulnerabilities in cancer"
Institution: University of California, Berkeley
Named Award: HHMI Fellow
Award Program: Fellow
Sponsor(s) / Mentor(s): Michael Rape, PhD
Cancer Type: All Cancers
Research Area: Cell Biology
Youngmu (Nick) Shin, PhD

Cells in our body communicate with each other in a highly selective manner. These cell-cell interactions form the basis of numerous physiological functions, such as neuronal wiring and immune recognition. Dr. Shin plans to explore the general principles of cell-cell communication by constructing a synthetic synapse and studying its organization and functional diversity. His findings will elucidate the mechanisms that organize cell-cell interfaces involved in immune cell recognition of cancer and in the cell-type transitions associated with cancer and metastasis. This work will also provide a platform for engineering highly customized cell-cell interfaces, which may prove useful in engineering immune cell therapeutics.

This project employs the stickers-and-spacers model adapted from polymer physics. Macromolecules such as proteins and nucleic acids are described as a sequence of attractive domains called "stickers" and flexible, non-interacting domains called "spacers." Dr. Shin will  use his lab's Monte Carlo simulation engine LaSSI (Lattice simulation engine for Sticker and Spacer Interactions) to calculate the average interactions between macromolecules and analyze their mesoscopic organization and phase properties.

Project title: "Exploring phase condensation as a general mechanism for organizing cell-cell communication assemblies"
Institution: University of California, San Francisco / Washington University
Award Program: Quantitative Biology Fellow
Sponsor(s) / Mentor(s): Wendell A. Lim, PhD (University of California, San Francisco), and Rohit V. Pappu, PhD (Washington University)
Cancer Type: All Cancers
Research Area: Cell Biology
Jiao Sima, PhD

Dr. Sima [HHMI Fellow] is investigating the relationship between sleep disturbances and cancer development. She is dissecting how neurons controlling the sleep-wake cycle affect immune functions that impact cancer. Dr. Sima will also examine the complementary problem of how tumor growth and chemotherapy contribute to sleep issues by analyzing gene expression patterns in neurons that regulate the sleep-wake cycle.  Understanding the cellular mechanisms linking sleep and cancer could pave the way for drugs that help prevent cancer-induced sleep problems and therapeutic approaches that boost immune function to fight cancer.

Project title: "Cellular mechanisms linking sleep disturbance and cancer development"
Institution: University of California, Berkeley
Named Award: HHMI Fellow
Award Program: Fellow
Sponsor(s) / Mentor(s): Yang Dan, PhD
Cancer Type: All Cancers
Research Area: Neuroscience
Sukrit Singh, PhD

Kinase proteins, which regulate the activity of other proteins, are a major class of cancer therapy targets, with over 65 FDA-approved drugs targeted against them. However, tumors can evolve resistance to kinase-targeting therapies, and it remains difficult to predict whether a specific tumor will resist a particular kinase-targeting drug. Dr. Singh will use protein structural models and biophysical predictions to analyze how kinase mutations cause cancers to resist therapy. As these computationally intensive calculations could require decades on a single desktop computer, he will use a computing platform called Folding@home, which harnesses idle computer time donated by citizen scientists around the world to run the calculations. By developing new algorithms to predict whether a known mutation will resist a kinase-targeting drug, Dr. Singh hopes to advance precision oncology to allow clinicians to predict a treatment's chance of success given a patient's tumor profile. While his work primarily focuses on resistance to the drug crizotinib, used to treat non-small-cell lung carcinomas, his approaches can be extrapolated to other tumors and cancer targets. Dr. Singh received his BA and his PhD in computational and molecular biophysics from Washington University in St. Louis.

Molecular dynamics (MD) simulations are computational microscopes that model and capture atomically detailed protein motions. To analyze MD simulations, Dr. Singh will construct Markov State Models, network representations of a protein's conformational landscape, and couple them with information theoretic measures of communication between mutated residues and drug binding sites. Alchemical Free Energy calculations will predict the impact of mutation on a drug's binding energy using artificial "alchemical" intermediates to measure the energetic cost of mutating a residue.

Project title: "Physics-driven prediction of drug-resistant clinical mutations to improve precision oncology"
Institution: Memorial Sloan Kettering Cancer Center / Stony Brook University
Award Program: Quantitative Biology Fellow
Sponsor(s) / Mentor(s): John D. Chodera, PhD (Memorial Sloan Kettering Cancer Center), and Markus A. Seeliger, PhD (Stony Brook University)
Cancer Type: Blood, Kidney and Bladder, Lung, All Cancers
Research Area: Biophysics
Marie R. Siwicki, PhD

Neutrophils are important anti-microbial cells within the innate immune system. Recently, it has been shown that neutrophils can perform diverse functions, taking on both pro-inflammatory and pro-healing roles in response to tissue injury or insult. Dr. Siwicki's [Dale F. and Betty Ann Frey Fellow] goal is to understand how different neutrophil subtypes or states function to balance inflammatory versus regenerative processes, ultimately influencing tissue health and cancer. This work has the potential to uncover the basis of neutrophils' pro-tumor versus anti-tumor functions and could open the door to therapeutic targeting of specific neutrophil behaviors in order to improve clinical outcomes in cancer. Dr. Siwicki received her PhD from Harvard Medical School, Boston and ScB from Brown University, Providence.


Project title: "Investigating neutrophil functional heterogeneity in wound healing and cancer"
Institution: University of Calgary
Named Award: Dale F. and Betty Ann Frey Fellow
Award Program: Fellow
Sponsor(s) / Mentor(s): Paul Kubes, PhD
Cancer Type: Other Cancer, Colorectal, All Cancers
Research Area: Basic Immunology
Jamie B. Spangler, PhD

Groundbreaking advances in immunotherapy have revolutionized the treatment of cancer. In particular, new antibody drugs that block immunosuppressive pathways have achieved remarkable success in reawakening the immune system to clear tumor cells, leading to lasting cures in patients whose cancers do not respond to any other therapies. Unfortunately, the majority of patients (>70%) do not respond to immunotherapy treatment. It is difficult to predict which patients will benefit, creating an urgent demand for novel immunotherapy drugs that act through alternative mechanisms. Dr. Spangler is working to develop a class of antibody therapeutics that target cancer-promoting pathways in a different way than all current immunotherapies, with the goal of drastically expanding the percentage of cancer patients who benefit from them.

Project title: "Engineered multispecific down-regulating antibodies to advance cancer immunotherapy"
Institution: Johns Hopkins University
Award Program: Innovator
Cancer Type: Breast, Colorectal, All Cancers
Research Area: Immunotherapy
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