Investigating leukemia promoting processes in the bone marrow microenvironment
Understanding aging processes (e.g. senescence and inflammation) in the bone marrow microenvironment of myeloid leukemias with the goal of identifying new therapeutic targets and biomarkers of response to therapy
The Borriello Lab studies how disseminated tumor cells (DTCs) – single cells that have spread from a primary tumor to new locations - survive in a dormant state and what causes them to “awaken” and form metastases. Since most cancer deaths result from metastatic relapse, and there are no drugs to eliminate dormant cells, our goal is to uncover how the tumor microenvironment controls dormancy and awakening.
We use advanced imaging, organotypic cultures, and in vivo models to identify the signals and cell types that regulate these processes. Our research focuses on two key questions: how the primary tumor environment programs cells to become dormant, and how stromal factors—especially those from fibroblasts—reactivate them in distant organs.
By revealing these mechanisms, we aim to develop therapies that prevent metastatic recurrence by eradicating or permanently silencing dormant tumor cells.
We conduct epi-genomewide studies in colorectal cancer (CRC) and assisted reproductive technology (ART). We are interested in studying disparities (racial and age of onset) in the incidence and outcome of CRC. In the ART project, we are looking into various clinically modifiable factors that affects DNA methylation in children conceived through ART. We are also conducting longitudinal studies in the ART population.
The Golemis laboratory focuses on understanding factors contributing to the basis for aggressive tumor growth, and on evaluation of protein-targeted drugs, frequently collaborating with medical and radiation oncologists. To address these topics, the group uses bioinformatic analysis of very large genomic datasets to identify specific genetic features associated with specific patterns of therapeutic response in head and neck, lung, pancreatic and colorectal cancers. We integrate this work with use of animal models and cell-based strategies to elucidate the activity of signaling proteins and targeted therapies. We are particularly interested in investigating the Aurora-A kinase signaling axis in cancer and other pathological conditions.
Peripheral neuropathy and chronic pain are a common side effect of chemotherapy treatment for which there are no available treatments.
Our group aims to understand how neurons are damaged in response to chemotherapy. However, our research is widely applicable to other neurodegenerative conditions such as glaucoma, traumatic brain injury (TBI) or Amyotrophic Lateral Sclerosis (ALS).
To do this, we employ a wide range of molecular and biochemical techniques, including differentiation of induced pluripotent stem cells (iPSCs) into human neurons, whole genome CRISPR interference screens, RNAseq, CRISPR knock-ins/ knock-outs, and advanced microscopy.
The lab has a strong clinical focus. We are deeply interested in uncovering new molecular mechanisms that drive axon degeneration and neuron death to develop novel therapeutic strategies.
Cell cycle control in mammalian cells and its deregulation in cancer. Role of cyclins, cyclin dependent kinases (CDKs), Ser/Thr protein phosphatases and tumor suppressor genes.
Research in my laboratory focuses on the molecular mechanisms that govern the cell cycle of normal and malignant eukaryotic cells, with a particular interest in the molecular signaling that controls cell cycle specific gene expression. Our major focus is on the mechanisms that govern cell cycle entry and exit, which operate in the G1 phase of the cell cycle. When higher eukaryotic cells exit the cell cycle they have three different fates, terminal differentiation, senescence or quiescence. While the first two fates are typically irreversible, quiescent cells can reenter the cell cycle when the environment is appropriate. Eukaryotic cells have evolved to respond to a large array of growth promoting and inhibiting signals, which are eventually integrated by a conserved protein engine consisting of distinct cyclin/CDK (Cyclin Dependent Kinase) holoenzymes. CDKs are activated at specific stages of the cell cycle and their activities are required for progression through S phase and mitosis (reviewed by Graña and Reddy, 1995; Graña et al., 1998, Sotillo and Graña, 2010). I am interested in how these regulatory pathways are disrupted in cancer cells as well as in cells transformed by small DNA viruses or infected by HIV (Graña et al., 1998, Garriga and Graña, 2004, Sotillo and Graña, 2010).
One initial focus of this laboratory was the characterization of p130, a protein structurally and functionally related to the product of the retinoblastoma susceptibility tumor suppressor gene (reviewed in Mayol and Graña, 1997; 1998; Graña et al., 1998). We first identified phosphorylation as a major mechanism for regulation of p130 in G1 and G0 (Mayol et al., 1995; Mayol et al., 1996). We, and others, found that p130 is phosphorylated during the cell cycle by the concerted action of D-type cyclin/CDKs and cyclin E/CDK2 holoenzymes (Parreño et al., 2001, Calbo et al., 2002), and determined mechanisms by which the E1A oncogene modulates pocket protein phosphorylation (Parreño et al., 2000 and Parreño et al., 2001). In addition, we and others reported on the relationship between the protein levels and phosphorylation status of pocket proteins (Mayol et al., 1996; Garriga et al., 1998a), eventually showing that p130 protein levels are regulated by the SCFSKP2 ubiquitin ligase (Bhattacharya et al., 2003). Recently, our focus has expanded to studies dealing with the coordinated regulation of the three members of the retinoblastoma family of proteins by CDKs and Ser/Thr phosphatases in response to a variety of signals (Calbo et al., 2002 and Garriga et al., 2004). In our efforts to better understand the G0/G1 transition we have found that certain serum starved tumor cells enter the cell cycle in the absence of mitogens following ectopic expression of G1 cyclins (Calbo et al., 2002). More recently we discovered that in quiescent normal human fibroblast, deregulation of cyclin E is not sufficient to induce cell cycle entry. We have subsequently found that this is due to the inability of cyclin E to activate CDK2 in normal cells. However, this can be bypassed by co-expressing SV-40 small t antigen (st), which cooperates with cyclin E to induce phosphorylation of CDK2 at its activating residue leading to CDK2 activation. Cyclin E and st cooperate to bypass quiescence induced by multiple signals and endow cells with transformed characteristics (Sotillo et al. 2008). We subsequently identified the essential replication factor CDC6 as a target of st, whose expression appears required for activation of CDK2 and cell cycle progression when the cell cycle is driven by the oncogenic expression of st and cyclin E (Sotillo et al. 2009, reviewed in Sotillo and Graña 2010). Moreover, we are also interested in gaining a better understanding as to how Ser/Thr protein phosphatases reverse the action of CDKs during the cell cycle (Garriga et al., 2004), and have recently identified particular PP2A holoenzymes implicated in this process (Jayadeva et al, 2010), reviewed in Kurimchak and Graña (2012).
The other primary area of research in this lab deals with the functional characterization of CDK9 (formerly named, PITALRE), cloned by means of its partial sequence identity to the CDC2 kinase (Graña et al., 1994; Garriga et al., 1996a and Garriga et al., 1996b). Following the identification of CDK9 as a subunit of the Positive Transcription Elongation Factor b (P-TEFb) and HIV tat associated kinase (TAK) by Dr. David Price’s group (University of Iowa), we demonstrated that the levels of cyclin T1, one of the three cyclins that bind to and activate CDK9, is upregulated during T-cell activation. Upregulation of cyclin T1 expression correlates with phosphorylation of RNA polymerase II (RNA pol II) in vivo and HIV-1 replication (Garriga et al., 1998b). Subsequently, we have characterized the signaling pathways and mechanisms responsible for cyclin T1 upregulation during T cell activation (Marshall et al., 2005). We have also found that in primary human T cells it is possible to directly inhibit CDK9 to levels that do not affect T cell activation, but potently inhibit HIV-1 replication (Salerno et al., 2007). Moreover, we have found that, although CDK9/cyclin T1 complexes are targeted by the SCFskp2 ubiquitin ligase under certain conditions, this association does not seem to regulate CDK9 expression during the cell cycle (Garriga et al., 2003). Current efforts in the laboratory are aimed at identifying CDK9 dependent genes (Garriga et al., 2010) and understanding their regulation in a variety of human cells (Keskin et al., 2012).
The mission of the Nuclear Dynamics and Cancer (NDC) program is to tackle mechanistic problems controlling nuclear function, while devising strategies to translate basic science findings into biomarker studies and/or clinical trials. The NDC program faculty members address key concepts about how proper packaging and regulation of DNA impacts genome integrity, gene regulation and epigenetic mechanisms in normal and cancer cells, while establishing how these insights are impacting therapeutic opportunities.
Even in the HAART era where the viral load is below detection levels, the prevalence of HIV-1 associated neurocognitive disorders (HAND) remains high due to many reasons such as latent virus reactivation and drugs' inability to efficiently cross the blood brain barrier (BBB). Therefore, it is important to understand the mechanisms leading to neuronal deregulation in HIV-1-infected patients in the HAART era. The lack of productive infection of neurons by HIV-1 suggests that viral and cellular proteins with neurotoxic activities that are released from HIV-1 infected target cells, or reservoirs cells for latent active virus, cause this neuronal deregulation. The viral proteins Tat, Vpr and gp120 have been shown to alter the expression of various important cytokines and inflammatory proteins in infected and uninfected cells. The mechanisms and the cellular factors used by these proteins to cause neuronal damage remain unclear. Therefore, research in the Molecular Studies of Neurodegenerative Diseases (MSND) lab mainly focuses on the identification of these mechanisms utilizing molecular, virological, and cellular approaches to determine the cellular factors used by the viral proteins as well as their interplay with microRNAs to cause neuronal dysfunction.
The outcome of these studies will advance the understanding of HIV-1 pathogenesis and will decipher the mechanisms used by HIV-1 Tat, Vpr and gp120 proteins that lead to neuronal degeneration.
The Schultz lab focuses on developing better treatments for small cell lung cancer (SCLC), a fast-growing and hard-to-treat form of lung cancer.
Our lab focuses on how these cancer cells grow and survive, how they move through a key phase in the cell cycle (called the G1/S transition) and how they rely on energy from their mitochondria. We are exploring the cellular function of approved drugs that target these processes, to potentially allow repurposing of existing agents for use in cancer.
We also test new drug combinations that might work better than alone. One idea we’re studying is “Population Synergy.” That means not just targeting cancer cells but also the nearby healthy cells that they closely interact with.
Our goal is to generate new clinical trials using these insights.
Our laboratory studies how cancer cells keep their DNA stable when it is under stress—either from within the cell, or from outside sources such as radiation or chemotherapy.
We investigate how the packaging of DNA inside the nucleus and certain chemical changes on proteins help cancer cells manage DNA damage and continue growing at the same time. By using powerful tools like quantitative imaging, genomics, and protein analysis, we aim to find new players, mechanisms, and pathways that protect the genome.
Our long-term goal is to use these discoveries to guide the development of better treatments for cancers marked by inherently high DNA damage and replication stress.
My laboratory focuses on determination of the role of DNA repair mechanisms in acute (AML, ALL) and chronic (CML) leukemias including the potential of therapeutic interventions. We found that acute and chronic leukemia stem cells (LSCs) accumulate potentially lethal DNA double strand breaks (DSBs), but homologous recombination (HR) and nonhomologous endjoining (NHEJ) protect their survival. Normal cells use BRAC1/2dependent HR and DNAPK –mediated NHEJ to prevent DSBtriggered apoptosis. However, leukemia cells may employ RAD52 mediated HR and PARP1mediated NHEJ. These changes may be driven by genetic and epigenetic aberrations. Individual patients with leukemias displaying deficiencies in specific DSB repair pathway are identified by Gene Expression and Mutation Analysis (GEMA). We explore these differences to target tumorspecific DNA repair mechanisms to achieve “synthetic lethality” in leukemia cells, with negligible effects on normal cells. These studies will lead to novel therapeutic approaches based on induction of personalized medicineguided synthetic lethality in leukemias from individual patients. We were first to demonstrate that targeting RAD52 can be successfully applied in individual leukemias identified by GEMA.
Our laboratory studies non-small cell lung cancer (NSCLC), and head and neck squamous cell carcinoma. Standard treatments for these two cancers include chemoradiotherapy, often combined with immunotherapy. A subset of patients also benefits from targeted therapies, which specifically “target” cancer cells and are generally less toxic than conventional chemotherapy. However, despite advances in these treatments, long-term benefit remains poor due to limited treatment efficacy or the emergence of therapy resistance.
Our research focuses on protein kinases, which represent one of the most promising avenues for targeted therapy development. We investigate how specific protein kinases drive cancer cell growth and survival. We also study the role of these protein kinases in cellular state changes (plasticity) and the interactions of cancer cells with their surrounding microenvironment, which enable cancer cells to adapt and resist treatment.
Our goal is to identify new molecular targets that support cancer cell survival and plasticity to aid in the development of targeted therapy strategies to improve outcomes and quality of life for patients with lung and head and neck cancers.
Esophageal squamous epithelium exhibits a defined proliferation-differentiation equilibrium that supports barrier function, a primary defense against luminal contents, which may include food allergens and carcinogens. Esophageal pathology often features impaired squamous differentiation and barrier dysfunction, suggesting that mucosal defense mechanisms beyond mechanical barrier exist. We have identified autophagy as a critical cytoprotective mechanism in esophageal epithelia exposed to stressors relevant to esophageal squamous cell carcinoma (ESCC; one of the most deadly forms of human cancer), Eosinophilic Esophagitis (EoE; an emerging food allergy-associated inflammatory disorder) and Barrett’s Esophagus (BE; a precursor to esophageal adenocarcinoma). Using these studies as a foundation, we now aim to define the precise functional roles of autophagy in epithelial mucosal defense under conditions of health and disease. We utilize a multi-disciplinary approach coupling molecular biology and biochemical techniques with innovative murine disease models, 3D organoid culture and patient-derived specimens with associated clinical data to uncover fundamental mechanisms contributing to epithelial homeostasis and then apply this knowledge toward the development of novel translational avenues for prevention, prognosis and therapy in benign and malignant human diseases.
The overarching goal of my research program is to elucidate the molecular mechanisms of ultraviolet radiation (UVR)-induced melanomagenesis.
The major etiological risk factor for the majority of melanomas has long been known to be UVR, yet the underlying mechanisms largely remain elusive. The hunt for melanoma-initiating genes has remained focused on UVR-induced DNA mutations. However, several studies have fueled the notion that mechanisms other than direct DNA damage are also important for UVR-induced initiation and progression of melanoma. To find clues to these mechanisms, we profiled the melanocytic gene expression response to UVR exposure while in their normal skin microenvironment (Nature 469:548). To circumvent the considerable challenge of studying a cell type in vivo that constitutes a tiny fraction of the mammalian skin, we developed a mouse model in which melanocytes can be both imaged in vivo and highly purified by virtue of tetracycline-inducible, melanocyte-specific GFP expression (iDct-GFP mice). This novel mouse model provides an invaluable tool to explore melanocyte and melanoma biology while residing within their natural microenvironment.
We have shown that the role of UVR in melanomagenesis involves not only UVR-induced DNA damage, but also how altered gene expression in exposed melanocytes drives interactions with elements of the microenvironment to escape destruction. Our results suggest that UV insult stimulates an intricate interplay between melanocytes and the skin microenvironment. It is clear that the alterations in melanocytic gene expression profile following UVR exposure stem from a combination of the direct UVR-induced effects on melanocytes and microenvironmental cues. We intend to tease out these intrinsic and extrinsic mechanisms to delineate the important molecular players in UVR-induced melanomagenesis.
Project 1: Role of the microenvironmental cytokine Interferon-gamma in initiation and progression of UV-induced melanoma
Project 2: The genomic and epigenomic mechanisms of UV-induced melanomagenesis
