Cancer Cell Biology Program: Bridging the Gap Between Benchwork and Bedside

The “omics” revolution is expanding exponentially. On the heels of the omics era, new paradigms are needed to harness and translate basic science advances to clinical applications. This need is being fulfilled in part by improving mechanisms for collaboration between cancer researchers and developing new knowledge-sharing tools, like the interactive Global Cancer Projects Map, a project made possible by the collaboration of several large cancer-focused groups.

Fostering collaborations that bridge the gap between benchwork discoveries and clinical practice is a core mission of the Cancer Cell Biology (CCB) Program at DF/HCC, according to Anders Naar, PhD (MGH). The program is led by Naar, along with Kornelia Polyak, MD, PhD (DFCI), and Wade Harper, PhD (HMS).

Integration of large-scale analytical methodologies, diversity of the areas of expertise of CCB members, along with an environment of cross-pollination of ideas and collaborative projects, are “enabling researchers to take the next step in getting their discoveries towards clinical translation,” Naar said.

For instance, translational science collaborations are helping make connections to medicinal chemistry for drug development. According to Naar, “Finding the molecular mechanism underlying a disease and then drugging it is sort of the Valley of Death, in terms of moving from the bench-side to bedside.”  The expertise of medicinal chemists in the program, such as Nathanael Gray, PhD (DFCI), Director of the Medicinal Chemistry Core at DF/HCC, and others, is a critical resource for drug development. Medicinal chemists can help tweak an existing FDA-approved drug with poor clinical efficacy to make the agents more clinically useful, explained Naar.

The following are some key themes in the Cancer Cell Biology program and the work being done within them.

Tumor Metabolism

An Old Player Takes Center Stage

The characteristic metabolic pattern of tumors – their reliance on glycolysis – was first described in the 1920s by Otto Warburg. Metabolic reprogramming is now recognized as a hallmark of cancer. The extent to which tumors become dependent on or “addicted” to the pathways that rewire cellular metabolism was under-appreciated. Research from CCB members, a number of whom are featured later in this story, has furthered our understanding of aberrant energy production and nutrient utilization in cancers. Their work, sometimes in unexpected or surprising ways, has uncovered molecular “linchpins in regulation of abnormal metabolism in cancer,” noted Naar.

The SIRT6 Story: Diverse Lessons in Biology from a Single Factor

Seminal studies from Raul Mostoslavsky, MD, PhD (MGH) and his colleagues provide elegant examples of SIRT6-mediated epigenetic plasticity and metabolic reprogramming in cancer.1-2 SIRT6, an NAD-dependent deacetylase, is a chromatin remodeling factor involved in ribosome biosynthesis, gene expression regulation, and tumor suppression.

Mostoslavsky and colleagues found that in colon cancer, SIRT6 suppresses the metabolic shift to glycolysis, i.e., the Warburg effect.1 Importantly, inhibition of PDK1, a glycolytic-pathway enzyme, limited colon cancer growth. SIRT6 loss promotes the dependence of colon tumors on enhanced glycolysis. 

“Pancreatic cancers, on the other hand, are already highly glycolytic,” said Mostoslavsky. Therefore, the SIRT6-loss-mediated metabolic shift is of little advantage. In a study first-authored by MGH research fellow Sita Kugel, they found that in pancreatic cancer, SIRT6 loss upregulated a developmental gene, Lin28b.2 This alternate mechanism promotes de-differentiation of pancreatic tumors. “By eliminating SIRT6, pancreatic tumors become much more aggressive, acquiring a propensity for lung metastasis not seen in the SIRT6-wild-type counterparts”, he added. 

Mostoslavsky and colleagues are collaborating with medicinal chemists to develop Lin28b inhibitors. He noted that in about 30% of patients with pancreatic cancer, tumors exhibit a low-SIRT6/high-Lin28b expression signature. Therefore, this population of patients may benefit from Lin28b-targeting therapies.

In colon and skin cancer models, Mostoslavsky’s group found that tumor-propagating cells are highly glycolytic. “It was initially surprising to us,” he said, “that the metabolic adaptation that we thought occurred in the bulk of the tumor, occurs in this unique population of tumor-propagating cells, which are more resistant to therapy, and [the adaptation] is established so early in the process of tumor formation.”

Unusual Diets of Tumors: Fat? Yes Please! Ammonia? Sure!

Recent work from Marcia Haigis, PhD (HMS), revealed two unexpected ways in which tumor cells utilize metabolic reprogramming to survive and thrive in harsh physiological conditions.

Haigis, William Kaelin, MD (DFCI) and colleagues discovered a mechanism through which tumors burn fat.3 They set out to identify binding partners for the prolyl hydroxylase-domain containing protein, PHD3. “We identified a new binding partner for PHD3 that associates with the outer mitochondrial membrane called acetyl-CoA carboxylase 2 (ACC2). ACC2 controls the entry of fat into the mitochondria, whereby once the fat enters the mitochondria it is burned for energy production,” explained Haigis. PHD3 hydroxylates a proline residue in ACC.

“Of more significance in cancer, the PHD3 axis is highly dysregulated, especially in AML and subsets of prostate cancer. We could stratify the tumor response to pharmacological inhibitors of fat oxidation based on their PHD3 expression profile,” she added, “it’s an interesting twist”.

The Haigis lab made another surprising discovery  – tumor cells utilize ammonia as fuel.4 A remarkable finding, as ammonia is considered a highly toxic molecule generated as a “metabolic byproduct” of amino acid metabolism. They found high levels of ammonia in and around tumors. Normal cells use glutamine dehydrogenase to convert glutamine to alpha-keto-glutarate and ammonia, which is then removed through the urea cycle. “But in tumor cells, there is such an excess of ammonia that the enzyme runs in reverse and uses ammonia to synthesize amino acids,” said Haigis.

Haigis and colleagues are now seeking to decipher the mechanisms through which fat and ammonia utilization promotes tumor survival and proliferation. They are also interested in developing therapeutic strategies for targeting these metabolic liabilities.

Cell Cycle Regulators Orchestrate Metabolic Reprogramming

Cyclins and their associated cyclin-dependent kinases (CDKs) play pivotal roles in cell cycle regulation. Peter Sicinski, MD, PhD (DFCI) and colleagues have discovered new functions for these canonical cell cycle regulators. 

His group, along with those of Nicholas Dyson, PhD (MGH), Tom Roberts, PhD (DFCI) and Kornelia Polyak, MD, PhD (DFCI), discovered that the cyclin D3-CDK6 complex regulates cellular metabolism in T-cell acute lymphoblastic leukemia (T-ALL).5 The complex inhibits glycolytic pathway enzymes, redirecting metabolic intermediates to alternate pathways that generate antioxidants. Inhibition of the D3-CDK6 complex in T-ALL attenuates the protective effect, promoting tumor cell cycle arrest as well as death.

They used the Human Cancer Cell Line Encyclopedia to identify the top 20 D3-CDK6-expressing non-leukemia cancer cells. They found that, akin to T-ALL cells, CDK inhibition induced cell death in these, but not low D3-CDK6-expressing, tumor cells. Mouse xenograft studies with primary human melanoma cells reiterated the sensitivity of high-D3-CDK6-expressing cancers to CDK inhibition. “We hypothesize that one can use high D3-CDK6 expression in cancer therapy as a predictor of response. These tumors might respond to CDK4/6 inhibition by undergoing tumor cell death,” said Sicinski.

In more recent work, the Sicinski, Wenyi Wei, PhD (BIDMC) and Gordon Freeman, PhD (DFCI) labs uncovered a role for the cyclin D-CDK4 complex in modulating anti-tumor immune responses. The cyclin D-CDK4 complex regulates levels of the immune checkpoint protein programmed cell death protein ligand (PD-L1).6 In mouse tumor models, the anti-tumor effect of  anti-PD-1 immunotherapy could be boosted by concurrent treatment with CDK4/6 inhibitors.

In another unexpected twist, his group uncovered a kinase activity-independent role for cyclin E in liver tumor development. The “addictions” of different cancers to specific cyclin-CDK complexes, and their amenability to therapeutic intervention, will continue to be a focus of his research.

Tumor Proteolysis

Cancer cells are more dependent on the protein “quality control” carried out through the ubiquitin-proteasome system, due to their rapid cycling and higher rates of protein synthesis. Regulation of proteolysis has emerged as another focal theme in the CCB program.  

Wenyi Wei, PhD (BIDMC), William Kaelin, MD (DFCI),  Alex Toker, PhD (BIDMC), Sabina Signoretti, MD (BWH), and John Asara, PhD (BIDMC) discovered a novel role for VHL, a ubiquitin ligase, in negative regulation of the oncogenic factor Akt.7

A team led by Peter Sicinski (DFCI), Kornelia Polyak (DFCI), Wade Harper (HMS), Wenyi Wei (BIDMC), Keith Ligon, MD, PhD (DFCI), and Roderick Bronson, DVM (HMS) discovered the role of G1 cyclin/CDK complexes in regulation of pluripotency.8 CDK inhibition abrogates phosphorylation of pluripotency factors, promoting their proteolytic degradation. The loss of pluripotency can attenuate “stem-cell-like” properties of tumor-initiating cells, providing a CDK-inhibitor-based therapeutic strategy.

Looking Ahead: Upcoming Symposia

A CCB program-sponsored day-long symposium, organized by Anders Naar (MGH) and Nika Danial, PhD (DFCI), will be held at DFCI on May 23, 2018. This symposium will highlight recent advances in cancer metabolism and metabolic reprogramming to foster increased inter-programmatic and cross-institutional interactions and collaborations.

Another symposium, spearheaded by Kornelia Polyak (DFCI), is slated for Fall 2018. Tumor evolution and single-cell detection and analysis methodologies, major interests of the CCB community, are the themes for this symposium. Keep an eye on for more information about both symposia.

Cancer is a multi-faceted disease; so should be the approach to eradicating cancer.

“The cross-institutional [CCB] program has over 100 members from 7 institutions, and [it] continues to grow,” said Naar. Over the past year, CCB members have published 518 papers, many of which directly impact the prevention, diagnosis or treatment of cancer.

A theme common to the narratives from CCB members is that unexpected results may yield profound lessons in biology. Their scientific journeys took them on roads less traveled, with surprising twists, but they also uncovered bolder and more potent solutions for tackling cancer.


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  2. Kugel S, Sebastián C, Fitamant J, et al. SIRT6 Suppresses Pancreatic Cancer through Control of Lin28b. Cell. 2016;165(6):1401-1415.
  3. German NJ, Yoon H, Yusuf RZ, et al. PHD3 Loss in Cancer Enables Metabolic Reliance on Fatty Acid Oxidation via Deactivation of ACC2. Mol Cell. 2016;63(6):1006-20.
  4. Spinelli JB, Yoon H, Ringel AE, Jeanfavre S, Clish CB, Haigis MC. Metabolic recycling of ammonia via glutamate dehydrogenase supports breast cancer biomass. Science. 2017;358(6365):941-946.
  5. Wang H, Nicolay BN, Chick JM, et al. The metabolic function of cyclin D3-CDK6 kinase in cancer cell survival. Nature. 2017;546(7658):426-430.
  6. Zhang J, Bu X, Wang H, et al. Cyclin D-CDK4 kinase destabilizes PD-L1 via cullin 3-SPOP to control cancer immune surveillance. Nature. 2018;553(7686):91-95.
  7. Guo J, Chakraborty AA, Liu P, et al. pVHL suppresses kinase activity of Akt in a proline-hydroxylation-dependent manner. Science. 2016 353:929-32.
  8. Liu L, Michowski W, Inuzuka H, et al. G1 cyclins link proliferation, pluripotency and differentiation of embryonic stem cells. Nat Cell Biol. 2017;19(3):177-188.