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Article ; Online: Host Epac1 is required for cAMP-mediated invasion by Trypanosoma cruzi.

Musikant, Daniel / Ferri, Gabriel / Durante, Ignacio M / Buscaglia, Carlos A / Altschuler, Daniel L / Edreira, Martin M

2016 Volume 211, Page(s) 67–70

Abstract: Mechanistic details of the modulation by cAMP of Trypanosoma cruzi host cell invasion remain ill-defined. Here we report that activation of host's Epac1 stimulated invasion, whereas specific pharmacological inhibition or maneuvers that alter Epac1 ... ...

Abstract	Mechanistic details of the modulation by cAMP of Trypanosoma cruzi host cell invasion remain ill-defined. Here we report that activation of host's Epac1 stimulated invasion, whereas specific pharmacological inhibition or maneuvers that alter Epac1 subcellular localization significantly reduced invasion. Furthermore, while specific activation of host cell PKA showed no effect, its inhibition resulted in an increased invasion, revealing a crosstalk between the PKA and Epac signaling pathways during the process of invasion. Therefore, our data suggests that subcellular localization of Epac might be playing an important role during invasion and that specific activation of the host cell cAMP/Epac1 pathway is required for cAMP-mediated invasion.
MeSH term(s)	Animals ; Cells, Cultured ; Cyclic AMP/metabolism ; Cyclic AMP-Dependent Protein Kinases/metabolism ; Guanine Nucleotide Exchange Factors/metabolism ; Host-Parasite Interactions ; Protein Transport ; Rats ; Signal Transduction ; Trypanosoma cruzi/pathogenicity ; Trypanosoma cruzi/physiology
Chemical Substances	Guanine Nucleotide Exchange Factors ; Rapgef3 protein, rat ; Cyclic AMP (E0399OZS9N) ; Cyclic AMP-Dependent Protein Kinases (EC 2.7.11.11)
Language	English
Publishing date	2016-10-27
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	756166-0
ISSN	1872-9428 ; 0166-6851
ISSN (online)	1872-9428
ISSN	0166-6851
DOI	10.1016/j.molbiopara.2016.10.003
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Article ; Online: The relative resistance of children to sepsis mortality: from pathways to drug candidates.

Joachim, Rose B / Altschuler, Gabriel M / Hutchinson, John N / Wong, Hector R / Hide, Winston A / Kobzik, Lester

Molecular systems biology

2018 Volume 14, Issue 5, Page(s) e7998

Abstract: Attempts to develop drugs that address sepsis based on leads developed in animal models have failed. We sought to identify leads based on human data by exploiting a natural experiment: the relative resistance of children to mortality from severe ... ...

Abstract	Attempts to develop drugs that address sepsis based on leads developed in animal models have failed. We sought to identify leads based on human data by exploiting a natural experiment: the relative resistance of children to mortality from severe infections and sepsis. Using public datasets, we identified key differences in pathway activity (Pathprint) in blood transcriptome profiles of septic adults and children. To find drugs that could promote beneficial (child) pathways or inhibit harmful (adult) ones, we built an
MeSH term(s)	Adolescent ; Adult ; Aged ; Aged, 80 and over ; Animals ; Child ; Child, Preschool ; Cluster Analysis ; Computer Simulation ; Disease Models, Animal ; Disease Resistance ; Drug Discovery ; Drug Evaluation, Preclinical ; Female ; Gene Expression Profiling ; Humans ; Male ; Mice ; Mice, Inbred C57BL ; Microarray Analysis ; Middle Aged ; Reproducibility of Results ; Sensitivity and Specificity ; Sepsis/drug therapy ; Sepsis/mortality ; Transcriptome ; Young Adult
Language	English
Publishing date	2018-05-17
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1744-4292
ISSN (online)	1744-4292
DOI	10.15252/msb.20177998
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Article: Development of free-energy-based models for chaperonin containing TCP-1 mediated folding of actin.

Altschuler, Gabriel M / Willison, Keith R

Journal of the Royal Society, Interface

2008 Volume 5, Issue 29, Page(s) 1391–1408

Abstract: A free-energy-based approach is used to describe the mechanism through which chaperonin-containing TCP-1 (CCT) folds the filament-forming cytoskeletal protein actin, which is one of its primary substrates. The experimental observations on the actin ... ...

Abstract	A free-energy-based approach is used to describe the mechanism through which chaperonin-containing TCP-1 (CCT) folds the filament-forming cytoskeletal protein actin, which is one of its primary substrates. The experimental observations on the actin folding and unfolding pathways are collated and then re-examined from this perspective, allowing us to determine the position of the CCT intervention on the actin free-energy folding landscape. The essential role for CCT in actin folding is to provide a free-energy contribution from its ATP cycle, which drives actin to fold from a stable, trapped intermediate I3, to a less stable but now productive folding intermediate I2. We develop two hypothetical mechanisms for actin folding founded upon concepts established for the bacterial type I chaperonin GroEL and extend them to the much more complex CCT system of eukaryotes. A new model is presented in which CCT facilitates free-energy transfer through direct coupling of the nucleotide hydrolysis cycle to the phases of actin substrate maturation.
MeSH term(s)	Actins/metabolism ; Chaperonin 60/metabolism ; Chaperonin Containing TCP-1 ; Chaperonins/metabolism ; Models, Chemical ; Models, Molecular ; Protein Folding
Chemical Substances	Actins ; Chaperonin 60 ; Chaperonin Containing TCP-1 (EC 3.6.1.-) ; Chaperonins (EC 3.6.1.-)
Language	English
Publishing date	2008-08-15
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2156283-0
ISSN	1742-5662 ; 1742-5689
ISSN (online)	1742-5662
ISSN	1742-5689
DOI	10.1098/rsif.2008.0185
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Article: Host Epac1 is required for cAMP-mediated invasion by Trypanosoma cruzi

Musikant, Daniel / Carlos A. Buscaglia / Daniel L. Altschuler / Gabriel Ferri / Ignacio M. Durante / Martin M. Edreira

Molecular and biochemical parasitology. 2016,

2016

Abstract: Mechanistic details of the modulation by cAMP of Trypanosoma cruzi host cell invasion remain ill-defined. Here we report that activation of hostâs Epac1 stimulated invasion, whereas specific pharmacological inhibition or maneuvers that alter Epac1 ... ...

Abstract	Mechanistic details of the modulation by cAMP of Trypanosoma cruzi host cell invasion remain ill-defined. Here we report that activation of hostâs Epac1 stimulated invasion, whereas specific pharmacological inhibition or maneuvers that alter Epac1 subcellular localization significantly reduced invasion. Furthermore, while specific activation of host cell PKA showed no effect, its inhibition resulted in an increased invasion, revealing a crosstalk between the PKA and Epac signaling pathways during the process of invasion. Therefore, our data suggests that subcellular localization of Epac might be playing an important role during invasion and that specific activation of the host cell cAMP/Epac1 pathway is required for cAMP-mediated invasion.
Keywords	cAMP-dependent protein kinase ; cell invasion ; cyclic AMP ; signal transduction ; Trypanosoma cruzi
Language	English
Size	p. .
Publishing place	Elsevier B.V.
Document type	Article
Note	Pre-press version
ZDB-ID	756166-0
ISSN	1872-9428 ; 0166-6851
ISSN (online)	1872-9428
ISSN	0166-6851
DOI	10.1016/j.molbiopara.2016.10.003
Database	NAL-Catalogue (AGRICOLA)

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Article: Unfolding energetics of G-alpha-actin: a discrete intermediate can be re-folded to the native state by CCT.

Altschuler, Gabriel M / Klug, David R / Willison, Keith R

Journal of molecular biology

2005 Volume 353, Issue 2, Page(s) 385–396

Abstract: Nascent actin requires interactions with the highly conserved and essential eukaryotic chaperonin-containing TCP-1 (CCT) for its correct folding to the native state in vivo. Biochemical and structural analysis of the interaction between actin and CCT has ...

Abstract	Nascent actin requires interactions with the highly conserved and essential eukaryotic chaperonin-containing TCP-1 (CCT) for its correct folding to the native state in vivo. Biochemical and structural analysis of the interaction between actin and CCT has been studied extensively but the underlying energetics and kinetics of the CCT-dependent actin folding process are not understood. We investigated the unfolding and folding pathways of actin, using stopped flow fluorescence and biochemical techniques. By using very low concentrations of actin, taking account of temperature and ATP concentration dependences we were able to determine accurately the activation energy of unfolding to a stable intermediate, I(3). Use of the fluorescent calcium chelator Quin-2 and consideration of the ATP concentration dependence on the unfolding rate has allowed the intrinsic kinetics to be linked to the accepted reaction scheme for actin denaturation. A free energy of -28.7(+/-0.2) kJ mol(-1) was determined for the loss of ATP from Ca-free G-actin, in good agreement with previous studies. Understanding the K(eq) value for this step then allowed the temperature dependence of the unfolding reaction of co-factor-free actin to be evaluated, yielding an activation energy for the unfolding of G-actin of 81.3(+/-3.3) kJ mol(-1). By chemical coupling of the extrinsic probe, Alexa Fluor 488 to cysteine 374 of native alpha-actin, we were able to follow the binding and folding of I(3) by CCT, observing for the first time, in vitro re-folding of EDTA-denatured G-actin. The high value of the activation energy between native actin and a non-native folding intermediate (I(3)) is characteristic of a partially folded, molten globule state expected to contain partial secondary structure.
MeSH term(s)	Actins/chemistry ; Adenosine Triphosphate/metabolism ; Animals ; Chaperonins/chemistry ; Chaperonins/metabolism ; Chelating Agents/chemistry ; Edetic Acid/chemistry ; Fluorescent Dyes/chemistry ; Models, Molecular ; Protein Binding ; Protein Denaturation ; Protein Folding ; Protein Renaturation ; Rabbits ; Temperature
Chemical Substances	Actins ; Chelating Agents ; Fluorescent Dyes ; Adenosine Triphosphate (8L70Q75FXE) ; Edetic Acid (9G34HU7RV0) ; Chaperonins (EC 3.6.1.-)
Language	English
Publishing date	2005-10-21
Publishing country	England
Document type	Journal Article
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2005.07.062
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Article ; Online: Yeast phosducin-like protein 2 acts as a stimulatory co-factor for the folding of actin by the chaperonin CCT via a ternary complex.

McCormack, Elizabeth A / Altschuler, Gabriel M / Dekker, Carien / Filmore, Heather / Willison, Keith R

Journal of molecular biology

2009 Volume 391, Issue 1, Page(s) 192–206

Abstract: The eukaryotic chaperonin-containing TCP-1 (CCT) folds the cytoskeletal protein actin. The folding mechanism of this 16-subunit, 1-MDa machine is poorly characterised due to the absence of quantitative in vitro assays. We identified phosducin-like ... ...

Abstract	The eukaryotic chaperonin-containing TCP-1 (CCT) folds the cytoskeletal protein actin. The folding mechanism of this 16-subunit, 1-MDa machine is poorly characterised due to the absence of quantitative in vitro assays. We identified phosducin-like protein 2, Plp2p (=PLP2), as an ATP-elutable binding partner of yeast CCT while establishing the CCT interactome. In a novel in vitro CCT-ACT1 folding assay that is functional under physiological conditions, PLP2 is a stimulatory co-factor. In a single ATP-driven cycle, PLP2-CCT-ACT1 complexes yield 30-fold more native actin than CCT-ACT1 complexes. PLP2 interacts directly with ACT1 through the C-terminus of its thioredoxin fold and the CCT-binding subdomain 4 of actin. The in vitro CCT-ACT1-PLP2 folding cycle of the preassembled complex takes 90 s at 30 degrees C, several times slower than the canonical chaperonin GroEL. The specific interactions between PLP2, CCT and ACT1 in the yeast-component in vitro system and the pronounced stimulatory effect of PLP2 on actin folding are consistent with in vivo genetic approaches demonstrating an essential and positive role for PLP2 in cellular processes involving actin in Saccharomyces cerevisiae. In mammalian systems, however, several members of the PLP family, including human PDCL3, the orthologue of PLP2, have been shown to be inhibitory toward CCT-mediated folding of actin in vivo and in vitro. Here, using a rabbit-reticulocyte-derived in vitro translation system, we found that inhibition of beta-actin folding by PDCL3 can be relieved by exchanging its acidic C-terminal extension for that of PLP2. It seems that additional levels of regulatory control of CCT activity by this PLP have emerged in higher eukaryotes.
MeSH term(s)	Actins/metabolism ; Adenosine Triphosphate/metabolism ; Carrier Proteins/metabolism ; Chaperonin Containing TCP-1 ; Chaperonins/metabolism ; Kinetics ; Protein Binding ; Protein Folding ; Protein Multimerization ; Saccharomyces cerevisiae Proteins/metabolism ; Temperature
Chemical Substances	Act1 protein, S cerevisiae ; Actins ; Carrier Proteins ; Saccharomyces cerevisiae Proteins ; phosducin-like protein 2, S cerevisiae ; Adenosine Triphosphate (8L70Q75FXE) ; Chaperonin Containing TCP-1 (EC 3.6.1.-) ; Chaperonins (EC 3.6.1.-)
Language	English
Publishing date	2009-08-07
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2009.06.003
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Article ; Online: Divergent LIN28-mRNA associations result in translational suppression upon the initiation of differentiation.

Tan, Shen Mynn / Altschuler, Gabriel / Zhao, Tian Yun / Ang, Haw Siang / Yang, Henry / Lim, Bing / Vardy, Leah / Hide, Winston / Thomson, Andrew M / Lareu, Ricky R

Nucleic acids research

2014 Volume 42, Issue 12, Page(s) 7997–8007

Abstract: LIN28 function is fundamental to the activity and behavior of human embryonic stem cells (hESCs) and induced pluripotent stem cells. Its main roles in these cell types are the regulation of translational efficiency and let-7 miRNA maturation. However, ... ...

Abstract	LIN28 function is fundamental to the activity and behavior of human embryonic stem cells (hESCs) and induced pluripotent stem cells. Its main roles in these cell types are the regulation of translational efficiency and let-7 miRNA maturation. However, LIN28-associated mRNA cargo shifting and resultant regulation of translational efficiency upon the initiation of differentiation remain unknown. An RNA-immunoprecipitation and microarray analysis protocol, eRIP, that has high specificity and sensitivity was developed to test endogenous LIN28-associated mRNA cargo shifting. A combined eRIP and polysome analysis of early stage differentiation of hESCs with two distinct differentiation cues revealed close similarities between the dynamics of LIN28 association and translational modulation of genes involved in the Wnt signaling, cell cycle, RNA metabolism and proteasomal pathways. Our data demonstrate that change in translational efficiency is a major contributor to early stages of differentiation of hESCs, in which LIN28 plays a central role. This implies that eRIP analysis of LIN28-associated RNA cargoes may be used for rapid functional quality control of pluripotent stem cells under manufacture for therapeutic applications.
MeSH term(s)	Cell Differentiation/genetics ; Cells, Cultured ; Embryonic Stem Cells/cytology ; Embryonic Stem Cells/metabolism ; Humans ; Polyribosomes/metabolism ; Protein Biosynthesis ; RNA, Messenger/metabolism ; RNA-Binding Proteins/metabolism
Chemical Substances	Lin28A protein, human ; RNA, Messenger ; RNA-Binding Proteins
Language	English
Publishing date	2014-05-23
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gku430
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Article: Pathprinting: An integrative approach to understand the functional basis of disease.

Altschuler, Gabriel M / Hofmann, Oliver / Kalatskaya, Irina / Payne, Rebecca / Ho Sui, Shannan J / Saxena, Uma / Krivtsov, Andrei V / Armstrong, Scott A / Cai, Tianxi / Stein, Lincoln / Hide, Winston A

Genome medicine

2013 Volume 5, Issue 7, Page(s) 68

Abstract: New strategies to combat complex human disease require systems approaches to biology that integrate experiments from cell lines, primary tissues and model organisms. We have developed Pathprint, a functional approach that compares gene expression ... ...

Abstract	New strategies to combat complex human disease require systems approaches to biology that integrate experiments from cell lines, primary tissues and model organisms. We have developed Pathprint, a functional approach that compares gene expression profiles in a set of pathways, networks and transcriptionally regulated targets. It can be applied universally to gene expression profiles across species. Integration of large-scale profiling methods and curation of the public repository overcomes platform, species and batch effects to yield a standard measure of functional distance between experiments. We show that pathprints combine mouse and human blood developmental lineage, and can be used to identify new prognostic indicators in acute myeloid leukemia. The code and resources are available at http://compbio.sph.harvard.edu/hidelab/pathprint.
Language	English
Publishing date	2013-07-26
Publishing country	England
Document type	Journal Article
ZDB-ID	2484394-5
ISSN	1756-994X
ISSN	1756-994X
DOI	10.1186/gm472
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Article ; Online: A data-driven approach links microglia to pathology and prognosis in amyotrophic lateral sclerosis.

Cooper-Knock, Johnathan / Green, Claire / Altschuler, Gabriel / Wei, Wenbin / Bury, Joanna J / Heath, Paul R / Wyles, Matthew / Gelsthorpe, Catherine / Highley, J Robin / Lorente-Pons, Alejandro / Beck, Tim / Doyle, Kathryn / Otero, Karel / Traynor, Bryan / Kirby, Janine / Shaw, Pamela J / Hide, Winston

Acta neuropathologica communications

2017 Volume 5, Issue 1, Page(s) 23

Abstract: Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease that lacks a predictive and broadly applicable biomarker. Continued focus on mutation-specific upstream mechanisms has yet to predict disease progression in the clinic. ... ...

Abstract	Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease that lacks a predictive and broadly applicable biomarker. Continued focus on mutation-specific upstream mechanisms has yet to predict disease progression in the clinic. Utilising cellular pathology common to the majority of ALS patients, we implemented an objective transcriptome-driven approach to develop noninvasive prognostic biomarkers for disease progression. Genes expressed in laser captured motor neurons in direct correlation (Spearman rank correlation, p < 0.01) with counts of neuropathology were developed into co-expression network modules. Screening modules using three gene sets representing rate of disease progression and upstream genetic association with ALS led to the prioritisation of a single module enriched for immune response to motor neuron degeneration. Genes in the network module are important for microglial activation and predict disease progression in genetically heterogeneous ALS cohorts: Expression of three genes in peripheral lymphocytes - LILRA2, ITGB2 and CEBPD - differentiate patients with rapid and slowly progressive disease, suggesting promise as a blood-derived biomarker. TREM2 is a member of the network module and the level of soluble TREM2 protein in cerebrospinal fluid is shown to predict survival when measured in late stage disease (Spearman rank correlation, p = 0.01). Our data-driven systems approach has, for the first time, directly linked microglia to the development of motor neuron pathology. LILRA2, ITGB2 and CEBPD represent peripherally accessible candidate biomarkers and TREM2 provides a broadly applicable therapeutic target for ALS.
MeSH term(s)	Adult ; Aged ; Aged, 80 and over ; Amyotrophic Lateral Sclerosis/genetics ; Amyotrophic Lateral Sclerosis/metabolism ; Amyotrophic Lateral Sclerosis/pathology ; Biomarkers/metabolism ; Brain/metabolism ; Brain/pathology ; Cell Line ; Cohort Studies ; Disease Progression ; Female ; Genome-Wide Association Study ; Humans ; Lymphocytes/metabolism ; Lymphocytes/pathology ; Male ; Membrane Glycoproteins/genetics ; Membrane Glycoproteins/metabolism ; Microglia/metabolism ; Microglia/pathology ; Middle Aged ; Motor Neurons/metabolism ; Motor Neurons/pathology ; Prognosis ; Receptors, Immunologic/genetics ; Receptors, Immunologic/metabolism ; Spinal Cord/metabolism ; Spinal Cord/pathology
Chemical Substances	Biomarkers ; Membrane Glycoproteins ; Receptors, Immunologic ; TREM2 protein, human
Language	English
Publishing date	2017-03-16
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Research Support, U.S. Gov't, P.H.S. ; Research Support, Non-U.S. Gov't
ZDB-ID	2715589-4
ISSN	2051-5960 ; 2051-5960
ISSN (online)	2051-5960
ISSN	2051-5960
DOI	10.1186/s40478-017-0424-x
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Article ; Online: The Stem Cell Discovery Engine: an integrated repository and analysis system for cancer stem cell comparisons.

Ho Sui, Shannan J / Begley, Kimberly / Reilly, Dorothy / Chapman, Brad / McGovern, Ray / Rocca-Sera, Philippe / Maguire, Eamonn / Altschuler, Gabriel M / Hansen, Terah A A / Sompallae, Ramakrishna / Krivtsov, Andrei / Shivdasani, Ramesh A / Armstrong, Scott A / Culhane, Aedín C / Correll, Mick / Sansone, Susanna-Assunta / Hofmann, Oliver / Hide, Winston

Nucleic acids research

2011 Volume 40, Issue Database issue, Page(s) D984–91

Abstract: Mounting evidence suggests that malignant tumors are initiated and maintained by a subpopulation of cancerous cells with biological properties similar to those of normal stem cells. However, descriptions of stem-like gene and pathway signatures in ... ...

Abstract	Mounting evidence suggests that malignant tumors are initiated and maintained by a subpopulation of cancerous cells with biological properties similar to those of normal stem cells. However, descriptions of stem-like gene and pathway signatures in cancers are inconsistent across experimental systems. Driven by a need to improve our understanding of molecular processes that are common and unique across cancer stem cells (CSCs), we have developed the Stem Cell Discovery Engine (SCDE)-an online database of curated CSC experiments coupled to the Galaxy analytical framework. The SCDE allows users to consistently describe, share and compare CSC data at the gene and pathway level. Our initial focus has been on carefully curating tissue and cancer stem cell-related experiments from blood, intestine and brain to create a high quality resource containing 53 public studies and 1098 assays. The experimental information is captured and stored in the multi-omics Investigation/Study/Assay (ISA-Tab) format and can be queried in the data repository. A linked Galaxy framework provides a comprehensive, flexible environment populated with novel tools for gene list comparisons against molecular signatures in GeneSigDB and MSigDB, curated experiments in the SCDE and pathways in WikiPathways. The SCDE is available at http://discovery.hsci.harvard.edu.
MeSH term(s)	Animals ; Databases, Genetic ; Gene Expression Profiling ; Humans ; Mice ; Neoplastic Stem Cells/metabolism ; Systems Integration
Language	English
Publishing date	2011-11-24
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkr1051
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