Van Andel Institute Graduate School

Grand Rapids, MI, United States

Van Andel Institute Graduate School

Grand Rapids, MI, United States
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White Y.,University of California at San Francisco | Bagchi A.,Helen DeVos Childrens Hospital | Bagchi A.,Van Andel Institute Graduate School | Van Ziffle J.,University of California at San Francisco | And 8 more authors.
Nature Communications | Year: 2016

Oncogenic KRAS mutations introduce discrete amino acid substitutions that reduce intrinsic Ras GTPase activity and confer resistance to GTPase-activating proteins (GAPs). Here we discover a partial duplication of the switch 2 domain of K-Ras encoding a tandem repeat of amino acids G60-A66dup in a child with an atypical myeloproliferative neoplasm. K-Ras proteins containing this tandem duplication or a similar five amino acid E62-A66dup mutation identified in lung and colon cancers transform the growth of primary myeloid progenitors and of Ba/F3 cells. Recombinant K-RasG60-A66dup and K-RasE62-A66dup proteins display reduced intrinsic GTP hydrolysis rates, accumulate in the GTP-bound conformation and are resistant to GAP-mediated GTP hydrolysis. Remarkably, K-Ras proteins with switch 2 insertions are impaired for PI3 kinase binding and Akt activation, and are hypersensitive to MEK inhibition. These studies illuminate a new class of oncogenic KRAS mutations and reveal unexpected plasticity in oncogenic Ras proteins that has diagnostic and therapeutic implications.

Berger P.L.,Van Andel Research Institute | Frank S.B.,Van Andel Research Institute | Frank S.B.,Michigan State University | Schulz V.V.,Van Andel Research Institute | And 8 more authors.
Cancer Research | Year: 2014

The mechanisms by which Myc overexpression or Pten loss promotes prostate cancer development are poorly understood. We identified the chromatin remodeling protein, ING4, as a crucial switch downstream of Myc and Pten that is required for human prostate epithelial differentiation. Myc-induced transient expression of ING4 is required for the differentiation of basal epithelial cells into luminal cells, while sustained ING4 expression induces apoptosis. ING4 expression is lost in >60% of human primary prostate tumors. ING4 or Pten loss prevents epithelial cell differentiation, which was necessary for tumorigenesis. Pten loss prevents differentiation by blocking ING4 expression, which is rescued by ING4 re-expression. Pten or ING4 loss generates tumor cells that co-express basal and luminal markers, indicating prostate oncogenesis occurs through disruption of an intermediate step in the prostate epithelial differentiation program. Thus, we identified a new epithelial cell differentiation switch involving Myc, Pten, and ING4, which when disrupted leads to prostate tumorigenesis. Myc overexpression and Pten loss are common genetic abnormalities in prostate cancer, whereas loss of the tumor suppressor ING4 has not been reported. This is the first demonstration that transient ING4 expression is absolutely required for epithelial differentiation, its expression is dependent on Myc and Pten, and it is lost in the majority of human prostate cancers. This is the first demonstration that loss of ING4, either directly or indirectly through loss of Pten, promotes Myc-driven oncogenesis by deregulating differentiation. The clinical implication is that Pten/ING4 negative and ING4-only negative tumors may reflect two distinct subtypes of prostate cancer. ©2014 AACR.

Cooper J.,Van Andel Institute Graduate School | Maupin K.,Van Andel Institute Graduate School | Merrill N.,Van Andel Institute Graduate School
Genes and Cancer | Year: 2015

The sixth annual Origins of Cancer Symposium was held July 10, 2015, at the Van Andel Research Institute in Grand Rapids, MI. Its theme was Beyond the Genome, with talks focused on the various influences of posttranslational modifications in malignant transformation and the spread of cancer. This event was organized by senior Ph.D. students as part of their professional development training at the Van Andel Institute Graduate School and is a successor to the original Oncogene meetings established by the Foundation for Advanced Cancer Studies in the 1980s. The symposium featured eight world-renowned scientists who disclosed their new findings and reflected upon past work related to the array of posttranslational modifications that contribute to cancer. © 2015, Impact Journals LLC. All Rights Reserved.

Westrate L.M.,Van Andel Research Institute | Westrate L.M.,Van Andel Institute Graduate School | Drocco J.A.,Los Alamos National Laboratory | Drocco J.A.,Lawrence Livermore National Laboratory | And 4 more authors.
PLoS ONE | Year: 2014

Mitochondria are dynamic organelles that undergo constant remodeling through the regulation of two opposing processes, mitochondrial fission and fusion. Although several key regulators and physiological stimuli have been identified to control mitochondrial fission and fusion, the role of mitochondrial morphology in the two processes remains to be determined. To address this knowledge gap, we investigated whether morphological features extracted from time-lapse live-cell images of mitochondria could be used to predict mitochondrial fate. That is, we asked if we could predict whether a mitochondrion is likely to participate in a fission or fusion event based on its current shape and local environment. Using live-cell microscopy, image analysis software, and supervised machine learning, we characterized mitochondrial dynamics with single-organelle resolution to identify features of mitochondria that are predictive of fission and fusion events. A random forest (RF) model was trained to correctly classify mitochondria poised for either fission or fusion based on a series of morphological and positional features for each organelle. Of the features we evaluated, mitochondrial perimeter positively correlated with mitochondria about to undergo a fission event. Similarly mitochondrial solidity (compact shape) positively correlated with mitochondria about to undergo a fusion event. Our results indicate that fission and fusion are positively correlated with mitochondrial morphological features; and therefore, mitochondrial fission and fusion may be influenced by the mechanical properties of mitochondrial membranes. © 2014 Westrate et al.

Westrate L.M.,Van Andel Research Institute | Westrate L.M.,Van Andel Institute Graduate School | Sayfie A.D.,Van Andel Research Institute | Burgenske D.M.,Van Andel Research Institute | And 3 more authors.
PLoS ONE | Year: 2014

Cancer cells have several hallmarks that define their neoplastic behavior. One is their unabated replicative potential that allows cells to continually proliferate, and thereby contribute to increasing tumor burden. The progression of a cell through the cell cycle is regulated by a series of checkpoints that ensures successful transmission of genetic information, as well as various cellular components, including organelles and protein complexes to the two resulting daughter cells. The mitochondrial reticulum undergoes coordinated changes in shape to correspond with specific stages of the cell cycle, the most dramatic being complete mitochondrial fragmentation prior to cytokinesis. To determine whether mitochondrial fission is a required step to ensure proper mitochondrial segregation into two daughter cells, we investigated the importance of mitochondrial dynamics to cell cycle progression. We found that mitochondrial hyperfusion promotes a defect in cell cycle progression characterized by an inability for cells to exit G2/M. Additionally, extended periods of persistent mitochondrial fusion led to robust caspase-dependent cell death. The cell death signals were coordinated through activation and cleavage of caspase-8, promoting a potent death response. These results demonstrate the importance of mitochondrial dynamics in cell cycle progression, and that inhibiting mitochondrial fission regulators may provide a therapeutic strategy to target the replicative potential of cancer cells. © 2014 Westrate et al.

Niemi N.M.,Van Andel Research Institute | Niemi N.M.,Van Andel Institute Graduate School | Lanning N.J.,Van Andel Research Institute | Westrate L.M.,Van Andel Research Institute | MacKeigan J.P.,Van Andel Research Institute
PLoS ONE | Year: 2013

Protein Tyrosine Phosphatase localized to the Mitochondrion 1 (PTPMT1) is a dual specificity phosphatase exclusively localized to the mitochondria, and has recently been shown to be a critical component in the cardiolipin biosynthetic pathway. The downregulation of PTPMT1 in pancreatic beta cells has been shown to increase cellular ATP levels and insulin production, however, the generalized role of PTPMT1 in cancer cells has not been characterized. Here we report that downregulation of PTPMT1 activity is sufficient to induce apoptosis of cancer cells. Additionally, the silencing of PTPMT1 decreases cardiolipin levels in cancer cells, while selectively increasing ATP levels in glycolytic media. Additionally, sublethal downregulation of PTPMT1 synergizes with low doses of paclitaxel to promote cancer cell death. Our data suggest that inhibition of PTPMT1 causes a metabolic crisis in cancer cells that induces cell death, and may be a mechanism by which cancer cells can be sensitized to currently available therapies. © 2013 Niemi et al.

Zarif J.C.,Van Andel Research Institute | Zarif J.C.,Michigan State University | Lamb L.E.,Beaumont Health System Research Institute | Schulz V.V.,Van Andel Research Institute | And 3 more authors.
Oncotarget | Year: 2015

Castration-resistant prostate cancers still depend on nuclear androgen receptor (AR) function despite their lack of dependence on exogenous androgen. Second generation anti-androgen therapies are more efficient at blocking nuclear AR; however resistant tumors still develop. Recent studies indicate Src is highly active in these resistant tumors. By manipulating AR activity in several different prostate cancer cell lines through RNAi, drug treatment, and the use of a nuclear-deficient AR mutant, we demonstrate that androgen acting on cytoplasmic AR rapidly stimulates Src tyrosine kinase via a non-genomic mechanism. Cytoplasmic AR, acting through Src enhances laminin integrin-dependent invasion. Active Matriptase, which cleaves laminin, is elevated within minutes after androgen stimulation, and is subsequently shed into the medium. Matriptase activation and shedding induced by cytoplasmic AR is dependent on Src. Concomitantly, CDCP1/gp140, a Matriptase and Src substrate that controls integrin-based migration, is activated. However, only inhibition of Matriptase, but not CDCP1, suppresses the AR/Src-dependent increase in invasion. Matriptase, present in conditioned medium from AR-stimulated cells, is sufficient to enhance invasion in the absence of androgen. Thus, invasion is stimulated by a rapid but sustained increase in Src activity, mediated non-genomically by cytoplasmic AR, leading to rapid activation and shedding of the laminin protease Matriptase.

Niemi N.M.,Van Andel Research Institute | Niemi N.M.,Van Andel Institute Graduate School | Mackeigan J.P.,Van Andel Research Institute
Antioxidants and Redox Signaling | Year: 2013

Significance: Apoptosis is a complex cellular process subject to multiple layers of regulation. One such layer of regulation includes post-translational modifications, including acetylation and phosphorylation. In particular, phosphorylation of proteins directly implicated in the apoptotic process has been extensively documented. Importantly, these phosphorylation events often have functional consequences, affecting the onset of apoptotic cell death. Recent Advances: Large-scale proteomics studies have identified multiple novel phosphorylation sites on proteins involved in the apoptotic process. The delineation of the regulation and functional consequences of these phosphorylation events will be important in understanding the regulatory complexity of apoptosis. Critical Issues: Multiple mitochondrial-localized proteins involved in apoptosis are functionally affected by phosphorylation, which can ultimately dictate whether a cell lives or dies. The dynamic interplay between these phosphorylated proteins and their regulatory enzymes is critical for understanding the complex cellular decision to undergo apoptosis. Future Directions: Detailed analysis of the kinetic and spatial regulation of phosphorylation events on apoptotic proteins, as well as how these dynamics influence the cell death process, will illuminate the complex interplay between the network of proteins that control the decision to undergo cell death. Antioxid. Redox Signal. 19, 572-582. © 2013, Mary Ann Liebert, Inc.

Martin K.R.,Van Andel Research Institute | Barua D.,Los Alamos National Laboratory | Kauffman A.L.,Van Andel Research Institute | Westrate L.M.,Van Andel Research Institute | And 5 more authors.
Autophagy | Year: 2013

Macroautophagy (autophagy) is a cellular recycling program essential for homeostasis and survival during cytotoxic stress. This process, which has an emerging role in disease etiology and treatment, is executed in four stages through the coordinated action of more than 30 proteins. An effective strategy for studying complicated cellular processes, such as autophagy, involves the construction and analysis of mathematical or computational models. When developed and refined from experimental knowledge, these models can be used to interrogate signaling pathways, formulate novel hypotheses about systems, and make predictions about cell signaling changes induced by specific interventions. Here, we present the development of a computational model describing autophagic vesicle dynamics in a mammalian system. We used time-resolved, live-cell microscopy to measure the synthesis and turnover of autophagic vesicles in single cells. The stochastically simulated model was consistent with data acquired during conditions of both basal and chemicallyinduced autophagy. The model was tested by genetic modulation of autophagic machinery and found to accurately predict vesicle dynamics observed experimentally. Furthermore, the model generated an unforeseen prediction about vesicle size that is consistent with both published findings and our experimental observations. Taken together, this model is accurate and useful and can serve as the foundation for future efforts aimed at quantitative characterization of autophagy. © 2013 Landes Bioscience.

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