For more papers, visit a faculty member's page from the listing on Whitehead Faculty and access the PubMed link.
Elegant biochemistry, chaotic origin.
New Phytol. 2013 Nov;200(3):592-4 .
Identification and rescue of alpha-Synuclein toxicity in Parkinson patient-derived neurons.
Science. 2013 Oct 24.
Chung, C.Y.*, Khurana, V.*, Auluck, P.K.*, Tardiff, D.F.*, Mazzulli, J.R.*, Soldner, F.*, Baru, V.*, Lou, Y.*, Freyzon, Y.*, Cho, S., Mungenast, A.E., Muffat, J.*, Mitalipova, M.*, Pluth, M.D., Jui, N.T., Schüle, B., Lippard, S.J., Tsai, L.H., Krainc, D., Buchwald, S.L., Jaenisch, R.*, and Lindquist, S.*
The induced pluripotent stem (iPS) cell field holds promise for in vitro disease modeling. However, identifying innate cellular pathologies, particularly for age-related neurodegenerative diseases, has been challenging. Here, we exploited mutation correction of iPS cells and conserved proteotoxic mechanisms from yeast to humans to discover and reverse phenotypic responses to alpha-Synuclein (alphaSyn), a key protein involved in Parkinson's disease (PD). We generated cortical neurons from iPS cells of patients harboring alphaSyn mutations, who are at high risk of developing PD dementia. Genetic modifiers from unbiased screens in a yeast model of alphaSyn toxicity led to identification of early pathogenic phenotypes in patient neurons. These included nitrosative stress, accumulation of endoplasmic reticulum (ER)-associated degradation (ERAD) substrates and ER stress. A small molecule identified in a yeast screen, and the ubiquitin ligase Nedd4 it affects, reversed pathologic phenotypes in these neurons.
Yeast reveal a "druggable" Rsp5/Nedd4 network that ameliorates alpha-Synuclein toxicity in neurons.
Science. 2013 Oct 24.
Tardiff, D.F.*, Jui, N.T., Khurana, V.*, Tambe, M.A., Thompson, M.L., Chung, C.Y.*, Kamadurai, H.B., Kim, H.T., Lancaster, A.K.*, Caldwell, K.A., Rochet, J.C., Buchwald, S.L., Lindquist, S.*
alpha-Synuclein (alpha-syn) is a small lipid binding protein implicated in several neurodegenerative diseases, including Parkinson's disease, whose pathobiology is conserved from yeast to man. There are no therapies targeting these underlying cellular pathologies, or indeed those of any major neurodegenerative disease. Using unbiased phenotypic screens as an alternative to target-based approaches, we discovered an N-aryl benzimidazole (NAB) that strongly and selectively protected diverse cell-types from alpha-syn toxicity. Three chemical genetic screens in wild-type yeast cells established that NAB promoted endosomal transport events dependent on the E3 ubiquitin ligase, Rsp5/Nedd4. These same steps were perturbed by alpha-syn itself. Thus, NAB identifies a druggable node in the biology of alpha-syn that can correct multiple aspects of its underlying pathology, including dysfunctional endosomal and ER-to-Golgi vesicle trafficking.
LoQAtE--Localization and quantitation atlas of the yeast proteome: A new tool for multiparametric dissection of single-protein behavior in response to biological perturbations in yeast.
Nucleic Acids Res. 2013 Oct 22.
Breker, M., Gymrek, M.*, Moldavski, O., and Schuldiner, M.
Living organisms change their proteome dramatically to sustain a stable internal milieu in fluctuating environments. To study the dynamics of proteins during stress, we measured the localization and abundance of the Saccharomyces cerevisiae proteome under various growth conditions and genetic backgrounds using the GFP collection. We created a database (DB) called 'LoQAtE' (Localizaiton and Quantitation Atlas of the yeast proteomE), available online at http://www.weizmann.ac.il/molgen/loqate/, to provide easy access to these data. Using LoQAtE DB, users can get a profile of changes for proteins of interest as well as querying advanced intersections by either abundance changes, primary localization or localization shifts over the tested conditions. Currently, the DB hosts information on 5330 yeast proteins under three external perturbations (DTT, H2O2 and nitrogen starvation) and two genetic mutations [in the chaperonin containing TCP1 (CCT) complex and in the proteasome]. Additional conditions will be uploaded regularly. The data demonstrate hundreds of localization and abundance changes, many of which were not detected at the level of mRNA. LoQAtE is designed to allow easy navigation for non-experts in high-content microscopy and data are available for download. These data should open up new perspectives on the significant role of proteins while combating external and internal fluctuations.
Antigen-specific B-cell receptor sensitizes B cells to infection by influenza virus.
Nature. 2013 Oct 20.
Dougan, S.K.*, Ashour, J.*, Karssemeijer, R.A.*, Popp, M.W.*, Avalos, A.M.*, Barisa, M.*, Altenburg, A.F.*, Ingram, J.R.*, Cragnolini, J.J.*, Guo, C., Alt, F.W., Jaenisch, R.*, and Ploegh H.L.*
Influenza A virus-specific B lymphocytes and the antibodies they produce protect against infection. However, the outcome of interactions between an influenza haemagglutinin-specific B cell via its receptor (BCR) and virus is unclear. Through somatic cell nuclear transfer we generated mice that harbour B cells with a BCR specific for the haemagglutinin of influenza A/WSN/33 virus (FluBI mice). Their B cells secrete an immunoglobulin gamma 2b that neutralizes infectious virus. Whereas B cells from FluBI and control mice bind equivalent amounts of virus through interaction of haemagglutinin with surface-disposed sialic acids, the A/WSN/33 virus infects only the haemagglutinin-specific B cells. Mere binding of virus is not sufficient for infection of B cells: this requires interactions of the BCR with haemagglutinin, causing both disruption of antibody secretion and FluBI B-cell death within 18 h. In mice infected with A/WSN/33, lung-resident FluBI B cells are infected by the virus, thus delaying the onset of protective antibody release into the lungs, whereas FluBI cells in the draining lymph node are not infected and proliferate. We propose that influenza targets and kills influenza-specific B cells in the lung, thus allowing the virus to gain purchase before the initiation of an effective adaptive response.
Analysis of in vitro insulin-resistance models and their physiological relevance to in vivo diet-induced adipose insulin resistance.
Cell Rep. 2013 Oct 17;5(1):259-70.
Lo, K.A.*, Labadorf, A., Kennedy, N.J., Han, M.S., Yap, Y.S., Matthews, B., Xin, X., Sun, L.*, Davis, R.J., Lodish, H.F.*, and Fraenkel, E.
Diet-induced obesity (DIO) predisposes individuals to insulin resistance, and adipose tissue has a major role in the disease. Insulin resistance can be induced in cultured adipocytes by a variety of treatments, but what aspects of the in vivo responses are captured by these models remains unknown. We use global RNA sequencing to investigate changes induced by TNF-alpha, hypoxia, dexamethasone, high insulin, and a combination of TNF-alpha and hypoxia, comparing the results to the changes in white adipose tissue from DIO mice. We found that different in vitro models capture distinct features of DIO adipose insulin resistance, and a combined treatment of TNF-alpha and hypoxia is most able to mimic the in vivo changes. Using genome-wide DNase I hypersensitivity followed by sequencing, we further examined the transcriptional regulation of TNF-alpha-induced insulin resistance, and we found that C/EPBbeta is a potential key regulator of adipose insulin resistance.
Super-enhancers in the control of cell identity and disease.
Cell. 2013 Oct 8.
Hnisz, D.*, Abraham, B.J.*, Lee, T.I.*, Lau, A.*, Saint-Andre, V.*, Sigova, A.A.*, Hoke, H.A.*, and Young, R.A.*
Super-enhancers are large clusters of transcriptional enhancers that drive expression of genes that define cell identity. Improved understanding of the roles that super-enhancers play in biology would be afforded by knowing the constellation of factors that constitute these domains and by identifying super-enhancers across the spectrum of human cell types. We describe here the population of transcription factors, cofactors, chromatin regulators, and transcription apparatus occupying super-enhancers in embryonic stem cells and evidence that super-enhancers are highly transcribed. We produce a catalog of super-enhancers in a broad range of human cell types and find that super-enhancers associate with genes that control and define the biology of these cells. Interestingly, disease-associated variation is especially enriched in the super-enhancers of disease-relevant cell types. Furthermore, we find that cancer cells generate super-enhancers at oncogenes and other genes important in tumor pathogenesis. Thus, super-enhancers play key roles in human cell identity in health and in disease.
Global transcriptional and translational repression in human-embryonic-stem-cell-derived Rett syndrome neurons.
Cell Stem Cell. 2013 Oct 3;13(4):446-58.
Li, Y.*, Wang, H.*, Muffat, J.*, Cheng, A.W.*, Orlando, D.A.*, Loven, J.*, Kwok, S.M., Feldman, D.A., Bateup, H.S., Gao, Q.*, Hockemeyer, D.*, Mitalipova, M.*, Lewis, C.A., Vander Heiden, M.G., Sur, M., Young, R.A.*, and Jaenisch, R.*
Rett syndrome (RTT) is caused by mutations of MECP2, a methyl CpG binding protein thought to act as a global transcriptional repressor. Here we show, using an isogenic human embryonic stem cell model of RTT, that MECP2 mutant neurons display key molecular and cellular features of this disorder. Unbiased global gene expression analyses demonstrate that MECP2 functions as a global activator in neurons but not in neural precursors. Decreased transcription in neurons was coupled with a significant reduction in nascent protein synthesis and lack of MECP2 was manifested as a severe defect in the activity of the AKT/mTOR pathway. Lack of MECP2 also leads to impaired mitochondrial function in mutant neurons. Activation of AKT/mTOR signaling by exogenous growth factors or by depletion of PTEN boosted protein synthesis and ameliorated disease phenotypes in mutant neurons. Our findings indicate a vital function for MECP2 in maintaining active gene transcription in human neuronal cells.
The folliculin tumor suppressor is a GAP for the RagC/D GTPases that signal amino acid Levels to mTORC1.
Mol Cell. 2013 Oct 2.
Tsun, Z.Y.*, Bar-Peled, L.*, Chantranupong, L.*, Zoncu, R.*, Wang, T.*, Kim, C.*, Spooner, E.*, and Sabatini, D.M.*
The mTORC1 kinase is a master growth regulator that senses numerous environmental cues, including amino acids. The Rag GTPases interact with mTORC1 and signal amino acid sufficiency by promoting the translocation of mTORC1 to the lysosomal surface, its site of activation. The Rags are unusual GTPases in that they function as obligate heterodimers, which consist of RagA or B bound to RagC or D. While the loading of RagA/B with GTP initiates amino acid signaling to mTORC1, the role of RagC/D is unknown. Here, we show that RagC/D is a key regulator of the interaction of mTORC1 with the Rag heterodimer and that, unexpectedly, RagC/D must be GDP bound for the interaction to occur. We identify FLCN and its binding partners, FNIP1/2, as Rag-interacting proteins with GAP activity for RagC/D, but not RagA/B. Thus, we reveal a role for RagC/D in mTORC1 activation and a molecular function for the FLCN tumor suppressor.
ATR/Mec1 prevents lethal meiotic recombination initiation on partially replicated chromosomes in budding yeast.
Elife. 2013 Oct 1;2:e00844.
Blitzblau, H.G.*, and Hochwagen, A.*
During gamete formation, crossover recombination must occur on replicated DNA to ensure proper chromosome segregation in the first meiotic division. We identified a Mec1/ATR- and Dbf4-dependent replication checkpoint in budding yeast that prevents the earliest stage of recombination, the programmed induction of DNA double-strand breaks (DSBs), when pre-meiotic DNA replication was delayed. The checkpoint acts through three complementary mechanisms: inhibition of Mer2 phosphorylation by Dbf4-dependent Cdc7 kinase, preclusion of chromosomal loading of Rec114 and Mre11, and lowered abundance of the Spo11 nuclease. Without this checkpoint, cells formed DSBs on partially replicated chromosomes. Importantly, such DSBs frequently failed to be repaired and impeded further DNA synthesis, leading to a rapid loss in cell viability. We conclude that a checkpoint-dependent constraint of DSB formation to duplicated DNA is critical not only for meiotic chromosome assortment, but also to protect genome integrity during gametogenesis.
*Author affiliated with Whitehead Institute for Biomedical Research