intestinal epithelia

Cancer Metabolism and Signaling Networks Program

Cancer overruns cell programs, allowing tumors to take root.

Overview

We are researching the pathways and signals that tumors use to reprogram their metabolism to escape normal cell death. Understanding these pathways helps identify therapeutic targets and is critical for the design of tumor-specific, less toxic therapies.

What is the focus of our program — what questions are we asking?

We are identifying and characterizing the signaling molecules that control the interphase between cell survival and death cascades. The main emphasis is to study how cancer cells reprogram their metabolism and protein homeostasis to survive nutrient stress conditions associated to tumor progression and how they might use processes such as autophagy and macropinocytosis to prevent various forms of cell death, including apoptosis and necrosis, and to keep growing. We address these fundamental biological questions at the organismal level, utilizing relevant models of human cancer, and at a cellular and detailed molecular structural level. This interdisciplinary approach positions our program at the leading edge of discovering new cancer pathways allowing us the translation of our findings into better medicines.

Director's Statement


How will our research help patients?

One of the fundamental weaknesses in the present treatment of cancer is the ability of tumor cells to endure stress under conditions of metabolic deprivation or chemotherapy. Understanding these pathways, and the identification of the key proteins that control the ability of cancer cells to reprogram their metabolism through biochemical, and epigenetic or genetic alterations that make them resistant to therapies, is of paramount importance for the design of more targeted and therefore less toxic therapies. Our program constitutes a highly interdisciplinary group addressing these important questions, which results in the identification of new and more selective therapeutic targets not only for cancer but also for other pathologies. 


Recent Scientific Accomplishments
 

The family of RING-In between-RING (RBR) ubiquitin ligases represents an intriguing family of E3 ligases that encompass the prominent factor parkin. Additionally, the RBR protein HOIP forms the central unit of the linear ubiquitin chain–assembly complex (LUBAC), which has emerged as key regulator of the NF-κB pathway. The laboratory of Dr. Riedl solved the structure of HOIP in complex with an ubiquitin linked e2 (UBCH5~ubiquitin) and an additional ubiquitin representing the first structure of an RBR in its active conformation. Importantly, this work ultimately resolves the mechanism of RBR type E3 ligases and provides for the first time detailed insight into their catalytic mechanism. This work, published in Nature (PMID: 26789245  [PubMed - in process]), reveals that RBR proteins must utilize a covalent intermediate because the E2 binding site overlaps with the binding site for the acceptor ubiquitin of the future linear ubiquitin chain.

In the past year, the laboratory of Dr. Marassi made significant progress on the understanding of the mechanism of apoptosis regulation by BCL-2 family proteins, and in the development of robust computational methods that enable membrane protein structure calculations in physically realistic environments. Marassi’s lab developed methods for reconstituting BCL-2 proteins in lipid bilayer nanodiscs that mimic the mitochondrial outer membrane. These samples are useful for both structural studies and ligand binding assays. Dr. Marassi’s studies are focusing on BCL-XL, a dominant inhibitor of apoptosis and a significant anti-cancer drug target. The structures of membrane-bound BCL-2 proteins have been long sought-after because they hold the keys for understanding the mechanistic basis of activity and for the development of selective drugs free of off-target effects. These very interesting studies have been published in The Journal of Molecular Biology (PMC4457587), and Biophysical Journal. (PMC4572468).

Dr. Hansen’s group focused on investigating the molecular mechanisms by which the nutrient sensor TOR modulates aging, using the nematode C. elegans as her primary model organism. One mechanism is protein synthesis by key regulators such as S6 kinase (S6K). Her group published a manuscript in Cell Reports (in press) in which they carried out a proteomic analysis and identified the arginine kinase ARGK-1, an intracellular energy regulator, as a novel and selective longevity effector of S6K in C. elegans. ARGK-1 functions together with another energy regulator AAK-2/AMPK, and the mammalian ortholog creatine kinase is elevated in S6K1-deficient mice. Another TOR-regulated process is autophagy, a cellular recycling process. In a study led by Hansen’s former trainee Dr. Louis Lapierre, now an assistant professor at Brown University, identified a novel link between lipoprotein biogenesis, autophagy, and aging; this study was published in Autophagy (PMID: 26671266 [PubMed - in process]).

The Cosford lab employs medicinal chemistry and chemical biology approaches to probe cellular pathways that regulate cell survival pathways in deadly tumors. This lab, in collaboration with the lab of Ruben Shaw at the Salk Institute, recently identified SBI-0206965, the first potent and selective small molecule inhibitor of ULK1, a serine/threonine kinase that is a critical regulator of autophagy. In a very interesting paper published in Molecular Cell (PMC4530630) they showed that SBI-0206965 inhibits autophagy and activates cell death in tumor cells resistant to mTOR inhibitors. These are critical observations that will allow the field of autophagy to move beyond the utilization of lysosomal inhibitors for the pharmacological treatment of cancer by targeting autophagy.

A major focus of the laboratory of Dr. Diaz-Meco is to understand how cancer cells respond to nutrient availability. Her previous work identified the scaffold protein p62 as a critical component of the mTORC1 nutrient-sensing signaling complex. The mTORC1 complex is central to the cellular response to changes in nutrient availability. However, the signal initiating these p62-driven processes was previously unknown. During this year, the Diaz-Meco laboratory has further studied the molecular underpinnings of this critical pathway in cancer.  Dr. Diaz-Meco and her colleagues identified and reported in a paper published in Cell Reports (PMC4551582) that p62 is phosphorylated via a cascade that includes MEK3/6 and p38d and that is driven by the PB1-containing kinase MEKK3. This phosphorylation results in the activation of mTORC1, and the regulation of autophagy and cell proliferation. Genetic inactivation of MEKK3 or p38d mimics that of p62 in that it leads to inhibited growth of PTEN-deficient prostate organoids. The translational relevance of this study is supported by the analysis of human prostate cancer samples that showed upregulation of these three components of the pathway, which correlated with enhanced mTORC1 activation. The work of Dr. Diaz-Meco in this area is being pursued further from that drug discovery point of view in a project in collaboration with the SBP Chemical Genomics group, and structural biologist at Scripps, with the goal of identifying potentially new therapeutic approaches to the selective inhibition of mTORC1 in cancer.

During this year the major area of research in the laboratory of Dr. Moscat has been the study of the molecular basis of hepatocellular carcinoma. Large scale genomic and transcriptomic interrogation of cancer has confirmed the incredible variability of the genomic landscape of many tumors including hepatocellular carcinoma (HCC), in which more than 28,000 different somatic mutations have been identified. This makes the design of better therapeutic strategies based on cancer-linked genetic alterations extremely challenging. However, inflammation and metabolic stress caused by components of the tumor epithelium can result in non-genetic vulnerabilities that can be potentially exploited for the design of innovative therapeutic approaches. Dr. Moscat’s laboratory, in collaboration with that of Dr. Karin at UCSD, has established for the fist time that p62 is necessary and sufficient for HCC induction in mice and that its high expression level in non-tumor human liver predicts rapid HCC recurrence after curative ablation. These studies, shown in a paper in Cancer Cell (in press) demonstrate that high p62 expression is needed for activation of NRF2 and mTORC1, for c-Myc induction and protection of HCC-initiating cells from oxidative stress-induced death. These important observations were complemented with studies shown in a paper in Cell (PMID: 26919428) that p62 is a critical negative regulator for mitochondrial-mediated activation of the inflammasome. Therefore, p62 regulates two essential and antagonistic functions in the tumor microenvironment. On the one hand, it regulates progression from premalignancy to malignancy, most likely by preventing oxidative stress-induced death of HCC-initiating cells, thereby allowing such cells to accumulate multiple oncogenic mutations, while promoting their growth through mTORC1. On the other, it represses macrophage-driven inflammation in the tumor microenvironment.


Publications

Huang J, Duran A, Reina-Campos M, Valencia T, Castilla EA, Müller TD, Tschöp MH, Moscat J, Diaz-Meco MT
Cancer Cell 2018 Apr 9;33(4):770-784.e6
Ekanayake V, Nisan D, Ryzhov P, Yao Y, Marassi FM
Biophys J 2018 Aug 7;115(3):533-542
Lundquist MR, Goncalves MD, Loughran RM, Possik E, Vijayaraghavan T, Yang A, Pauli C, Ravi A, Verma A, Yang Z, Johnson JL, Wong JCY, Ma Y, Hwang KS, Weinkove D, Divecha N, Asara JM, Elemento O, Rubin MA, Kimmelman AC, Pause A, Cantley LC, Emerling BM
Mol Cell 2018 May 3;70(3):531-544.e9