Our research
Our lab seeks to understand how changes in intra- and extra-cellular metabolites affect chromatin biology. We are interested in:
- 1) how metabolic rewiring arises; and
- 2) how metabolic rewiring drives changes in cellular phenotypes in normal physiology (e.g., influencing cell fates); and in cancer, in particular in colorectal cancer.
We use a combination of classic tissue culture and molecular biology techniques, patient-derived biopsies and xenografts, epigenetic mapping tools and bioinformatics approaches to understand metabolism and epigenetics and to discover novel treatments for cancer.
From Krebs to Weintraub, or how to go from metabolism to gene expression
DNA is not a simple linear molecule with protein-coding instructions; the secondary and tertiary structures of DNA play a large role in which genes are turned on or off. A key player in changing whether chromatin is ‘open’ or ‘closed’ is the structure of the core component of chromatin, the nucleosome. Histone tails on nucleosome particles can be covalently modified by metabolic enzymes, ultimately leading to increased or decreased compaction between adjacent nucleosomes. Thus, histone acetyl-transferases (HATs) transfer acetyl moieties from acetyl-CoA to histone lysine residues, increasing accessibility. Conversely, histone methyl-transferases (HMTs) transfer methyl moieties from S-adenosyl methionine to histone lysine residues, most commonly decreasing accessibility. This ‘histone code’ is also dependent on ‘eraser’ enzymes, histone deacetylases (HDACs) and histone demethylases (KDMs), enzymes that use NAD and alpha-ketoglutarate and O2, respectively, to remove acetyl marks and methyl marks. This complex interplay between metabolism and chromatin carries an important prediction, that the availability of metabolic substrates dictates the chromatin landscape of a cell.
The majority of cells in our body never divide. They have instead committed to carrying out a specialized function. This specialization is dependent on a stable supply of nutrients that permit anabolic metabolism, and a stable removal of waste products that permit catabolic metabolism. Hence, as opposed to the cells of unicellular organisms, cells in metazoan organisms assume an unchanging environment and ‘double-down’ on reading a very small fraction of their genome to differentiate and carry out a very specialized function.
The metabolic wiring diagrams that are monolithically represented in biochemistry textbooks are much more flexible in multicellular organisms. In fact, metabolic rewiring is a hallmark of cancer. Some cells require enormous amounts of ATP and rewire their metabolism to extract as much energy as possible from energy-rich nutrients (e.g. myofibers or neurons). Other cells have less of a need for ATP and a much more dire need for synthesizing the building blocks required to double their biomass (proliferating cells). These cells conserve multicarbon precursors (rather than burning them for energy) and require NAD+ regeneration to maintain glycolysis. Yet other groups of cells require metabolic intermediates for committing to cell fate decisions. Each of these unique metabolic needs determines the availability of nutrients for chromatin-modifying reactions. Two key questions in my lab are 1) how does metabolic rewiring arise? And 2) why is metabolic rewiring implemented? What are its consequences?
Cellular homeostasis is not universal; many biological phenomena take place when blood supply is interrupted, tissue barriers break, or demand exceeds supply. These processes are at the core of pathologies like cancer, where increased demand for nutrients to facilitate proliferation clashes with impaired or altered blood supply. Some of the broad questions we ask in the lab are:
- Is cell fate driven by metabolic rewiring?
- Why is differentiation a generally irreversible process?
- Can we change the state of a cell by changing flux through metabolic pathways? Conversely, can the extra cellular environment coax a cell to de-differentiate?
- How do pre-cancerous cells learn to ignore differentiation cues to continue dividing?
- How do altered metabolic environments like ischemia influence these signals?
- How do cancer cells continue to divide (a huge anabolic undertaking) despite the harsh metabolic environments present in solid tumors? Are cancer cells that develop under metabolic restrictions selectively sensitive to insults that normal cells are immune to (e.g. synthetic lethalities)?
The two main metabolic pathways we currently focus on are:
Polyamines regulate cell fate by altering the accessibility of histone tails
Polyamines are polycationic alkyl-amines abundant in proliferating stem and cancer cells. How these metabolites influence numerous cellular processes remains unclear. We have recently shown that polyamine levels decrease during differentiation and that inhibiting polyamine synthesis leads to a differentiated-like cell state. Polyamines are enriched in the nucleus, where their loss drives changes in chromatin accessibility and histone post-translational modifications. Polyamines interact electrostatically with DNA on the nucleosome core, freeing histone tails to conformations accessible to chromatin-modifying enzymes. Consistent with their role in increasing histone-tail accessibility, polyamines are able to replace MYC’s role in reprogramming to pluripotency. These data reveal a mechanism by which an abundant metabolite influences chromatin structure and function in a direct but sequence independent manner, facilitating chromatin remodeling during reprogramming and limiting it during fate commitment.
Ongoing projects in the lab aim to understand whether and how polyamines might regulate specific chromatin regions, RNA molecules, nuclear condensate structure/function, how these processes influence pluripotency and reprogramming, oncogenesis and aging, and whether modulating polyamine levels in vivo might be an effective treatment in a variety of cancers.
A gradient of hypoxia in the colon sets up polarized differentiation of enterocytes
Colorectal cancer (CRC) is the third most common malignancy in the US and therapeutic advances over the last30 years have been insufficient. Metabolic rewiring is a hallmark of cancer that is commonly driven by onco-genic mutations. However, how limiting concentrations of physiological nutrients (metabolic bottlenecks) lead to metabolic rewiring is poorly understood. Hypoxia, low oxygen levels, is a metabolic limitation or bottleneck that is intrinsic to the normal colon. Hypoxia, through effects on altering nucleotide metabolism, can lead to replicative stress. Replicative stress has been shown in the hematopoietic system to trigger differentiation of proliferating precursors and to sensitize tumor cells to an array of therapeutic agents. We hypothesize that hypoxia is a metabolic bottleneck that drives cellular differentiation in the normal colon, and that this bottleneck generates therapeutic vulnerabilities in CRC. We use 2D and 3D models of normal colon differentiation and colorectal cancer to probe how hypoxic gradients impact cell state through effects on replication stress, cell cycle, and epigenetic landscape. We also use a 3D-printed tissue culture system (MEMIC, Metabolic Microenvironment Chamber; adapted from the Carmofon lab) that recapitulates the gradient of oxygen levels seen in the normal colon. This work provides a physiologic framework to understand the effects of metabolic bottlenecks like hypoxia on normal differentiation of the colon and the acquisition ofmalignant cell states in CRC.
We are also looking to identify targetable pathways that arise from the interplay between metabolic and epigenetic alterations in human CRC. We believe these approaches and insights can be extrapolated to other tissues and their respective malignancies.