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1.
Nat Immunol ; 22(6): 723-734, 2021 06.
Article in English | MEDLINE | ID: mdl-33958784

ABSTRACT

Continuous supply of immune cells throughout life relies on the delicate balance in the hematopoietic stem cell (HSC) pool between long-term maintenance and meeting the demands of both normal blood production and unexpected stress conditions. Here we identified distinct subsets of human long-term (LT)-HSCs that responded differently to regeneration-mediated stress: an immune checkpoint ligand CD112lo subset that exhibited a transient engraftment restraint (termed latency) before contributing to hematopoietic reconstitution and a primed CD112hi subset that responded rapidly. This functional heterogeneity and CD112 expression are regulated by INKA1 through direct interaction with PAK4 and SIRT1, inducing epigenetic changes and defining an alternative state of LT-HSC quiescence that serves to preserve self-renewal and regenerative capacity upon regeneration-mediated stress. Collectively, our data uncovered the molecular intricacies underlying HSC heterogeneity and self-renewal regulation and point to latency as an orchestrated physiological response that balances blood cell demands with preserving a stem cell reservoir.


Subject(s)
Cell Self Renewal/immunology , Hematopoietic Stem Cells/physiology , Immune Reconstitution , Multipotent Stem Cells/physiology , Stress, Physiological/immunology , Adult , Animals , Cell Self Renewal/genetics , Cells, Cultured , Epigenesis, Genetic/immunology , Female , Fetal Blood/cytology , Flow Cytometry , Gene Knockdown Techniques , Hematopoiesis , Hematopoietic Stem Cell Transplantation/adverse effects , Humans , Immunomagnetic Separation , Infant, Newborn , Intracellular Signaling Peptides and Proteins/genetics , Intracellular Signaling Peptides and Proteins/metabolism , Male , Mice , Middle Aged , Nectins/metabolism , Primary Cell Culture , RNA-Seq , Single-Cell Analysis , Sirtuin 1/metabolism , Stress, Physiological/genetics , Transplantation, Heterologous , p21-Activated Kinases/genetics , p21-Activated Kinases/metabolism
2.
EMBO J ; 38(14): e101109, 2019 07 15.
Article in English | MEDLINE | ID: mdl-31304627

ABSTRACT

Centriolar satellites are small electron-dense granules that cluster in the vicinity of centrosomes. Satellites have been implicated in multiple critical cellular functions including centriole duplication, centrosome maturation, and ciliogenesis, but their precise composition and assembly properties have remained poorly explored. Here, we perform in vivo proximity-dependent biotin identification (BioID) on 22 human satellite proteins, to identify 2,113 high-confidence interactions among 660 unique polypeptides. Mining this network, we validate six additional satellite components. Analysis of the satellite interactome, combined with subdiffraction imaging, reveals the existence of multiple unique microscopically resolvable satellite populations that display distinct protein interaction profiles. We further show that loss of satellites in PCM1-depleted cells results in a dramatic change in the satellite interaction landscape. Finally, we demonstrate that satellite composition is largely unaffected by centriole depletion or disruption of microtubules, indicating that satellite assembly is centrosome-independent. Together, our work offers the first systematic spatial and proteomic profiling of human centriolar satellites and paves the way for future studies aimed at better understanding the biogenesis and function(s) of these enigmatic structures.


Subject(s)
Autoantigens/genetics , Cell Cycle Proteins/genetics , Centrioles/metabolism , Proteomics/methods , Autoantigens/metabolism , Cell Cycle Proteins/metabolism , Cell Line , Gene Deletion , Humans , Microtubule-Associated Proteins/metabolism , Protein Interaction Maps , Tandem Mass Spectrometry
3.
Am J Hum Genet ; 107(4): 727-742, 2020 10 01.
Article in English | MEDLINE | ID: mdl-32891193

ABSTRACT

Congenital anomalies of the kidney and urinary tract (CAKUT) constitute one of the most frequent birth defects and represent the most common cause of chronic kidney disease in the first three decades of life. Despite the discovery of dozens of monogenic causes of CAKUT, most pathogenic pathways remain elusive. We performed whole-exome sequencing (WES) in 551 individuals with CAKUT and identified a heterozygous de novo stop-gain variant in ZMYM2 in two different families with CAKUT. Through collaboration, we identified in total 14 different heterozygous loss-of-function mutations in ZMYM2 in 15 unrelated families. Most mutations occurred de novo, indicating possible interference with reproductive function. Human disease features are replicated in X. tropicalis larvae with morpholino knockdowns, in which expression of truncated ZMYM2 proteins, based on individual mutations, failed to rescue renal and craniofacial defects. Moreover, heterozygous Zmym2-deficient mice recapitulated features of CAKUT with high penetrance. The ZMYM2 protein is a component of a transcriptional corepressor complex recently linked to the silencing of developmentally regulated endogenous retrovirus elements. Using protein-protein interaction assays, we show that ZMYM2 interacts with additional epigenetic silencing complexes, as well as confirming that it binds to FOXP1, a transcription factor that has also been linked to CAKUT. In summary, our findings establish that loss-of-function mutations of ZMYM2, and potentially that of other proteins in its interactome, as causes of human CAKUT, offering new routes for studying the pathogenesis of the disorder.


Subject(s)
DNA-Binding Proteins/genetics , Epigenesis, Genetic , Forkhead Transcription Factors/genetics , Mutation , Repressor Proteins/genetics , Transcription Factors/genetics , Urinary Tract/metabolism , Urogenital Abnormalities/genetics , Amphibian Proteins/antagonists & inhibitors , Amphibian Proteins/genetics , Amphibian Proteins/metabolism , Animals , Case-Control Studies , Child , Child, Preschool , DNA-Binding Proteins/metabolism , Family , Female , Forkhead Transcription Factors/metabolism , Heterozygote , Humans , Infant , Larva/genetics , Larva/growth & development , Larva/metabolism , Male , Mice , Mice, Knockout , Morpholinos/genetics , Morpholinos/metabolism , Pedigree , Protein Binding , Repressor Proteins/metabolism , Transcription Factors/metabolism , Urinary Tract/abnormalities , Urogenital Abnormalities/metabolism , Urogenital Abnormalities/pathology , Exome Sequencing , Xenopus
4.
Palliat Support Care ; : 1-10, 2023 Jun 26.
Article in English | MEDLINE | ID: mdl-37357920

ABSTRACT

OBJECTIVES: This study aims to explore the place of the relative in these triadic consultations and how this influences communication. METHODS: A mixed-methods research strategy was used. Triadic consultations for the announcement of cancer progression were recorded and following the 3 participants completed questionnaires comprising mirror-items. Recordings and answers were further investigated in a few semi-structured interviews. Comparison of quantitative responses (questionnaires) used Wilcoxon's test for matched series. Qualitative analyses (consultations, interviews) used grounded theory. Patients were over 18, followed for cancer in palliative phase, excluding brain tumors and malignant hemopathies, and presented renewed disease progression. Relatives were over 18 and authorized by the patient to participate. RESULTS: 47 consultations (audio-recordings, answers to questionnaires) and 12 interviews conducted separately with 4 triads were collected. Half the relatives, while remaining in the background, nevertheless contributed to the discussion. For patients, the presence of a relative was considered beneficial and for oncologists it facilitated the announcement. However, symptoms perceived as intimate or private appeared difficult to express for some patients, and for relatives, prognosis was a difficult subject to broach. Although their relationship with time and their expectations may differ, patients and relatives found consultations positive. Oncologists appeared to underestimate the patient's level of understanding (P<0.001) and perceptions of the seriousness of the disease (P=0.009) but not those of relatives. They did not evaluate the relative's state of health and check what the dyad had retained. SIGNIFICANCE OF RESULTS: Training via simulation sessions should be adapted to communication involving relatives.

5.
Ecol Lett ; 25(12): 2675-2687, 2022 Dec.
Article in English | MEDLINE | ID: mdl-36223413

ABSTRACT

Dispersal is a central biological process tightly integrated into life-histories, morphology, physiology and behaviour. Such associations, or syndromes, are anticipated to impact the eco-evolutionary dynamics of spatially structured populations, and cascade into ecosystem processes. As for dispersal on its own, these syndromes are likely neither fixed nor random, but conditional on the experienced environment. We experimentally studied how dispersal propensity varies with individuals' phenotype and local environmental harshness using 15 species ranging from protists to vertebrates. We reveal a general phenotypic dispersal syndrome across studied species, with dispersers being larger, more active and having a marked locomotion-oriented morphology and a strengthening of the link between dispersal and some phenotypic traits with environmental harshness. Our proof-of-concept metacommunity model further reveals cascading effects of context-dependent syndromes on the local and regional organisation of functional diversity. Our study opens new avenues to advance our understanding of the functioning of spatially structured populations, communities and ecosystems.


Subject(s)
Biological Evolution , Ecosystem , Animals , Syndrome , Phenotype
6.
J Immunol ; 205(5): 1419-1432, 2020 09 01.
Article in English | MEDLINE | ID: mdl-32747500

ABSTRACT

Maturation of lymphoid cells is controlled by the action of stage and lineage-restricted transcription factors working in concert with the general transcription and chromatin remodeling machinery to regulate gene expression. To better understand this functional interplay, we used Biotin Identification in human embryonic kidney cells to identify proximity interaction partners for GATA3, TCF7 (TCF1), SPI1, HLF, IKZF1, PAX5, ID1, and ID2. The proximity interaction partners shared among the lineage-restricted transcription factors included ARID1a, a BRG1-associated factor complex component. CUT&RUN analysis revealed that ARID1a shared binding with TCF7 and GATA3 at a substantial number of putative regulatory elements in mouse T cell progenitors. In support of an important function for ARID1a in lymphocyte development, deletion of Arid1a in early lymphoid progenitors in mice resulted in a pronounced developmental arrest in early T cell development with a reduction of CD4+CD8+ cells and a 20-fold reduction in thymic cellularity. Exploring gene expression patterns in DN3 cells from Wt and Arid1a-deficient mice suggested that the developmental block resided in the DN3a to DN3b transition, indicating a deficiency in ß-selection. Our work highlights the critical importance of functional interactions between stage and lineage-restricted factors and the basic transcription machinery during lymphocyte differentiation.


Subject(s)
CD4-Positive T-Lymphocytes/immunology , CD8-Positive T-Lymphocytes/immunology , DNA-Binding Proteins/genetics , DNA-Binding Proteins/immunology , Lymphocytes/immunology , Transcription Factors/genetics , Transcription Factors/immunology , Animals , Cell Differentiation/genetics , Cell Differentiation/immunology , Cell Line , Cell Lineage/genetics , Cell Lineage/immunology , Chromatin/genetics , Chromatin/immunology , GATA3 Transcription Factor/genetics , GATA3 Transcription Factor/immunology , Gene Expression/genetics , Gene Expression/immunology , HEK293 Cells , Humans , Lymphocyte Activation/genetics , Lymphocyte Activation/immunology , Mice , Mice, Inbred C57BL , Transcription, Genetic/genetics , Transcription, Genetic/immunology
7.
Nucleic Acids Res ; 48(14): 7864-7882, 2020 08 20.
Article in English | MEDLINE | ID: mdl-32324228

ABSTRACT

It has been recently shown that many proteins are lacking from reference databases used in mass spectrometry analysis, due to their translation templated on alternative open reading frames. This questions our current understanding of gene annotation and drastically expands the theoretical proteome complexity. The functions of these alternative proteins (AltProts) still remain largely unknown. We have developed a large-scale and unsupervised approach based on cross-linking mass spectrometry (XL-MS) followed by shotgun proteomics to gather information on the functional role of AltProts by mapping them back into known signalling pathways through the identification of their reference protein (RefProt) interactors. We have identified and profiled AltProts in a cancer cell reprogramming system: NCH82 human glioma cells after 0, 16, 24 and 48 h Forskolin stimulation. Forskolin is a protein kinase A activator inducing cell differentiation and epithelial-mesenchymal transition. Our data show that AltMAP2, AltTRNAU1AP and AltEPHA5 interactions with tropomyosin 4 are downregulated under Forskolin treatment. In a wider perspective, Gene Ontology and pathway enrichment analysis (STRING) revealed that RefProts associated with AltProts are enriched in cellular mobility and transfer RNA regulation. This study strongly suggests novel roles of AltProts in multiple essential cellular functions and supports the importance of considering them in future biological studies.


Subject(s)
Cellular Reprogramming , Cyclic AMP-Dependent Protein Kinases/metabolism , Protein Interaction Mapping , Cell Line, Tumor , Cellular Reprogramming/drug effects , Colforsin/pharmacology , Enzyme Activation , Humans , Mass Spectrometry , Microtubule-Associated Proteins/metabolism , Nuclear Proteins/metabolism , Proteomics , RNA-Binding Proteins/metabolism , Receptor, EphA5/metabolism , Signal Transduction , Tropomyosin/metabolism
8.
Mol Cell Proteomics ; 18(11): 2285-2297, 2019 11.
Article in English | MEDLINE | ID: mdl-31519766

ABSTRACT

The Golgi-specific Brefeldin-A resistance factor 1 (GBF1) is the only large GEF that regulates Arf activation at the cis-Golgi and is actively recruited to membranes on an increase in Arf-GDP. Recent studies have revealed that GBF1 recruitment requires one or more heat-labile and protease-sensitive protein factor(s) (Quilty et al., 2018, J. Cell Science, 132). Proximity-dependent biotinylation (BioID) and mass spectrometry from enriched Golgi fractions identified GBF1 proximal proteins that may regulate its recruitment. Knockdown studies revealed C10orf76 to be involved in Golgi maintenance. We find that C10orf76 interacts with GBF1 and rapidly cycles on and off GBF1-positive Golgi structures. More importantly, its depletion causes Golgi fragmentation, alters GBF1 recruitment, and impairs secretion. Homologs were identified in most species, suggesting its presence in the last eukaryotic common ancestor.


Subject(s)
Carrier Proteins/metabolism , Golgi Apparatus/metabolism , Guanine Nucleotide Exchange Factors/metabolism , Intracellular Membranes/metabolism , Biotinylation , HeLa Cells , Humans , Protein Binding , Protein Interaction Domains and Motifs , Protein Transport
9.
Proc Natl Acad Sci U S A ; 115(47): 11988-11993, 2018 11 20.
Article in English | MEDLINE | ID: mdl-30397109

ABSTRACT

Limited dispersal is classically considered as a prerequisite for ecological specialization to evolve, such that generalists are expected to show greater dispersal propensity compared with specialists. However, when individuals choose habitats that maximize their performance instead of dispersing randomly, theory predicts dispersal with habitat choice to evolve in specialists, while generalists should disperse more randomly. We tested whether habitat choice is associated with thermal niche specialization using microcosms of the ciliate Tetrahymena thermophila, a species that performs active dispersal. We found that thermal specialists preferred optimal habitats as predicted by theory, a link that should make specialists more likely to track suitable conditions under environmental changes than expected under the random dispersal assumption. Surprisingly, generalists also performed habitat choice but with a preference for suboptimal habitats. Since this result challenges current theory, we developed a metapopulation model to understand under which circumstances such a preference for suboptimal habitats should evolve. We showed that competition between generalists and specialists may favor a preference for niche margins in generalists under environmental variability. Our results demonstrate that the behavioral dimension of dispersal-here, habitat choice-fundamentally alters our predictions of how dispersal evolve with niche specialization, making dispersal behaviors crucial for ecological forecasting facing environmental changes.


Subject(s)
Biota/physiology , Competitive Behavior/physiology , Tetrahymena thermophila/physiology , Animals , Biological Evolution , Ciliophora/physiology , Ecosystem , Specialization , Species Specificity , Temperature , Territoriality
10.
J Biol Chem ; 294(44): 16172-16185, 2019 11 01.
Article in English | MEDLINE | ID: mdl-31515271

ABSTRACT

Connections between deficient autophagy and insulin resistance have emerged, however, the mechanism through which reduced autophagy impairs insulin-signaling remains unknown. We examined mouse embryonic fibroblasts lacking Atg16l1 (ATG16L1 KO mouse embryonic fibroblasts (MEFs)), an essential autophagy gene, and observed deficient insulin and insulin-like growth factor-1 signaling. ATG16L1 KO MEFs displayed reduced protein content of insulin receptor substrate-1 (IRS1), pivotal to insulin signaling, whereas IRS1myc overexpression recovered downstream insulin signaling. Endogenous IRS1 protein content and insulin signaling were restored in ATG16L1 KO mouse embryonic fibroblasts (MEF) upon proteasome inhibition. Through proximity-dependent biotin identification (BioID) and co-immunoprecipitation, we found that Kelch-like proteins KLHL9 and KLHL13, which together form an E3 ubiquitin (Ub) ligase complex with cullin 3 (CUL3), are novel IRS1 interactors. Expression of Klhl9 and Klhl13 was elevated in ATG16L1 KO MEFs and siRNA-mediated knockdown of Klhl9, Klhl13, or Cul3 recovered IRS1 expression. Moreover, Klhl13 and Cul3 knockdown increased insulin signaling. Notably, adipose tissue of high-fat fed mice displayed lower Atg16l1 mRNA expression and IRS1 protein content, and adipose tissue KLHL13 and CUL3 expression positively correlated to body mass index in humans. We propose that ATG16L1 deficiency evokes insulin resistance through induction of Klhl9 and Klhl13, which, in complex with Cul3, promote proteasomal IRS1 degradation.


Subject(s)
Autophagy-Related Proteins/deficiency , Insulin Receptor Substrate Proteins/metabolism , Insulin Resistance , Animals , Autophagy/physiology , Autophagy-Related Proteins/genetics , Autophagy-Related Proteins/metabolism , Cullin Proteins/metabolism , Fibroblasts/metabolism , Genes, Regulator , HEK293 Cells , Humans , Insulin/metabolism , Male , Mice , Mice, Inbred C57BL , Proteins/metabolism , Signal Transduction , Ubiquitin-Protein Ligase Complexes/metabolism
11.
Proc Biol Sci ; 287(1919): 20192818, 2020 01 29.
Article in English | MEDLINE | ID: mdl-31992166

ABSTRACT

Habitat fragmentation is expected to reduce dispersal movements among patches as a result of increased inter-patch distances. Furthermore, since habitat fragmentation is expected to raise the costs of moving among patches in the landscape, it should hamper the ability or tendency of organisms to perform informed dispersal decisions. Here, we used microcosms of the ciliate Tetrahymena thermophila to test experimentally whether habitat fragmentation, manipulated through the length of corridors connecting patches differing in temperature, affects habitat choice. We showed that a twofold increase of inter-patch distance can as expected hamper the ability of organisms to choose their habitat at immigration. Interestingly, it also increased their habitat choice at emigration, suggesting that organisms become choosier in their decision to either stay or leave their patch when obtaining information about neighbouring patches gets harder. This study points out that habitat fragmentation might affect not only dispersal rate but also the level of non-randomness of dispersal, with emigration and immigration decisions differently affected. These consequences of fragmentation might considerably modify ecological and evolutionary dynamics of populations facing environmental changes.


Subject(s)
Ciliophora/physiology , Ecosystem , Temperature , Territoriality
12.
Mol Cell Proteomics ; 17(11): 2242-2255, 2018 11.
Article in English | MEDLINE | ID: mdl-30037810

ABSTRACT

Zika virus (ZIKV) is a membrane enveloped Flavivirus with a positive strand RNA genome, transmitted by Aedes mosquitoes. The geographical range of ZIKV has dramatically expanded in recent decades resulting in increasing numbers of infected individuals, and the spike in ZIKV infections has been linked to significant increases in both Guillain-Barré syndrome and microcephaly. Although a large number of host proteins have been physically and/or functionally linked to other Flaviviruses, very little is known about the virus-host protein interactions established by ZIKV. Here we map host cell protein interaction profiles for each of the ten polypeptides encoded in the ZIKV genome, generating a protein topology network comprising 3033 interactions among 1224 unique human polypeptides. The interactome is enriched in proteins with roles in polypeptide processing and quality control, vesicle trafficking, RNA processing and lipid metabolism. >60% of the network components have been previously implicated in other types of viral infections; the remaining interactors comprise hundreds of new putative ZIKV functional partners. Mining this rich data set, we highlight several examples of how ZIKV may usurp or disrupt the function of host cell organelles, and uncover an important role for peroxisomes in ZIKV infection.


Subject(s)
Organelles/virology , Protein Interaction Maps , Zika Virus/physiology , HEK293 Cells , HeLa Cells , Host-Pathogen Interactions , Humans , Models, Biological , Peroxisomes/metabolism , Viral Proteins/metabolism , Zika Virus Infection/metabolism , Zika Virus Infection/virology
13.
Proteomics ; 19(24): e1900139, 2019 12.
Article in English | MEDLINE | ID: mdl-31617661

ABSTRACT

A number of unique proteases localize to specific sub-compartments of the mitochondria, but the functions of these enzymes are poorly defined. Here, in vivo proximity-dependent biotinylation (BioID) is used to map the interactomes of seven proteases localized to the mitochondrial intermembrane space (IMS). In total, 802 high confidence proximity interactions with 342 unique proteins are identified. While all seven proteases co-localized with the IMS markers OPA1 and CLPB, 230 of the interacting partners are unique to just one or two protease bait proteins, highlighting the ability of BioID to differentiate unique interactomes within the confined space of the IMS. Notably, high-temperature requirement peptidase 2 (HTRA2) interacts with eight of 13 components of the mitochondrial intermembrane space bridging (MIB) complex, a multiprotein assembly essential for the maintenance of mitochondrial cristae structure. Knockdown of HTRA2 disrupts cristae in HEK 293 and OCI-AML2 cells, and leads to increased intracellular levels of the MIB subunit IMMT. Using a cell-free assay it is demonstrated that HTRA2 can degrade recombinant IMMT but not two other core MIB complex subunits, SAMM50 and CHCHD3. The IMS protease interactome thus represents a rich dataset that can be mined to uncover novel IMS protease biology.


Subject(s)
ATP-Dependent Proteases/metabolism , High-Temperature Requirement A Serine Peptidase 2/metabolism , Mitochondria/metabolism , Mitochondrial Membranes/metabolism , Mitochondrial Proteins/metabolism , Proteome/metabolism , High-Temperature Requirement A Serine Peptidase 2/antagonists & inhibitors , High-Temperature Requirement A Serine Peptidase 2/genetics , Humans , Membrane Proteins/metabolism , Mitochondrial Precursor Protein Import Complex Proteins , Protein Interaction Maps , RNA, Small Interfering/genetics
14.
Mol Cell Proteomics ; 16(10): 1864-1888, 2017 10.
Article in English | MEDLINE | ID: mdl-28794006

ABSTRACT

Lung cancer is the leading cause of cancer mortality worldwide, with squamous cell carcinoma (SQCC) being the second most common form. SQCCs are thought to originate in bronchial basal cells through an injury response to smoking, which results in this stem cell population committing to hyperplastic squamous rather than mucinous and ciliated fates. Copy number gains in SOX2 in the region of 3q26-28 occur in 94% of SQCCs, and appear to act both early and late in disease progression by stabilizing the initial squamous injury response in stem cells and promoting growth of invasive carcinoma. Thus, anti-SOX2 targeting strategies could help treat early and/or advanced disease. Because SOX2 itself is not readily druggable, we sought to characterize SOX2 binding partners, with the hope of identifying new strategies to indirectly interfere with SOX2 activity. We now report the first use of proximity-dependent biotin labeling (BioID) to characterize the SOX2 interactome in vivo We identified 82 high confidence SOX2-interacting partners. An interaction with the coactivator EP300 was subsequently validated in both basal cells and SQCCs, and we demonstrate that EP300 is necessary for SOX2 activity in basal cells, including for induction of the squamous fate. We also report that EP300 copy number gains are common in SQCCs and that growth of lung cancer cell lines with 3q gains, including SQCC cells, is dependent on EP300. Finally, we show that EP300 inhibitors can be combined with other targeted therapeutics to achieve more effective growth suppression. Our work supports the use of BioID to identify interacting protein partners of nondruggable oncoproteins such as SOX2, as an effective strategy to discover biologically relevant, druggable targets.


Subject(s)
Biotin/metabolism , Carcinoma, Squamous Cell/metabolism , E1A-Associated p300 Protein/metabolism , Lung Neoplasms/metabolism , SOXB1 Transcription Factors/metabolism , Aminopyridines/pharmacology , Animals , Benzimidazoles/pharmacology , Biotin/genetics , Bronchi/cytology , Bronchi/pathology , Disease Progression , E1A-Associated p300 Protein/antagonists & inhibitors , E1A-Associated p300 Protein/genetics , HEK293 Cells , Humans , Isoxazoles/pharmacology , Mice , Mice, Inbred NOD , Mice, SCID , Morpholines/pharmacology , Primary Cell Culture , SOXB1 Transcription Factors/genetics , Stem Cells , Tumor Cells, Cultured
15.
Mol Cell Proteomics ; 14(7): 1781-95, 2015 Jul.
Article in English | MEDLINE | ID: mdl-25900982

ABSTRACT

The identification of ubiquitin E3 ligase substrates has been challenging, due in part to low-affinity, transient interactions, the rapid degradation of targets and the inability to identify proteins from poorly soluble cellular compartments. SCF(ß-TrCP1) and SCF(ß-TrCP2) are well-studied ubiquitin E3 ligases that target substrates for proteasomal degradation, and play important roles in Wnt, Hippo, and NFκB signaling. Combining 26S proteasome inhibitor (MG132) treatment with proximity-dependent biotin labeling (BioID) and semiquantitative mass spectrometry, here we identify SCF(ß-TrCP1/2) interacting partners. Based on their enrichment in the presence of MG132, our data identify over 50 new putative SCF(ß-TrCP1/2) substrates. We validate 12 of these new substrates and reveal previously unsuspected roles for ß-TrCP in the maintenance of nuclear membrane integrity, processing (P)-body turnover and translational control. Together, our data suggest that ß-TrCP is an important hub in the cellular stress response. The technique presented here represents a complementary approach to more standard IP-MS methods and should be broadly applicable for the identification of substrates for many ubiquitin E3 ligases.


Subject(s)
Biotin/metabolism , Protein Phosphatase 1/metabolism , SKP Cullin F-Box Protein Ligases/metabolism , Ubiquitin-Protein Ligases/metabolism , beta-Transducin Repeat-Containing Proteins/metabolism , Eukaryotic Initiation Factor-2/metabolism , Gene Knockdown Techniques , HeLa Cells , Humans , Intracellular Signaling Peptides and Proteins/metabolism , Membrane Proteins/metabolism , Multiprotein Complexes/metabolism , Nuclear Envelope/metabolism , Phosphorylation , Protein Stability , Reproducibility of Results , Substrate Specificity , Ubiquitin/metabolism
16.
Bull Cancer ; 111(5): 505-512, 2024 May.
Article in English | MEDLINE | ID: mdl-38553287

ABSTRACT

INTRODUCTION: Given the current global cancer epidemic across the world, the need for healthcare professionals in this field is crucial. Little is known about the factors that drive medical students toward oncology. METHOD: We conducted a systematic review of the literature (from 1980 to the present), using several search equations and selecting original articles written in English based on qualitative or quantitative surveys, to understand what motivates medical students to choose oncology. RESULTS: We identified only seven articles that reported quantitative surveys; no qualitative surveys were found. These seven surveys are composed of closed-ended questions and are pragmatic questionnaires based on field knowledge, but without an underlying theory. These studies most often interrogate students already oriented towards oncology. The following five concepts associated with the choice of oncology had the highest recurrence among these seven surveys, which had been conducted in different countries and at various times: interest in cancer management, initiation of the specialty during the 2nd cycle, job opportunities, low working hours, and quality of life. DISCUSSION: The literature on this topic is particularly scarce. No qualitative studies have been published in the English language. The limited data in the literature do not allow us to fully comprehend the problem.


Subject(s)
Career Choice , Medical Oncology , Motivation , Students, Medical , Humans , Students, Medical/psychology , Medical Oncology/education , Quality of Life , Surveys and Questionnaires , Neoplasms
17.
Cell Rep ; 43(2): 113713, 2024 Feb 27.
Article in English | MEDLINE | ID: mdl-38306274

ABSTRACT

R2TP is a chaperone complex consisting of the AAA+ ATPases RUVBL1 and RUVBL2, as well as RPAP3 and PIH1D1 proteins. R2TP is responsible for the assembly of macromolecular complexes mainly acting through different adaptors. Using proximity-labeling mass spectrometry, we identified deleted in primary ciliary dyskinesia (DPCD) as an adaptor of R2TP. Here, we demonstrate that R2TP-DPCD influences ciliogenesis initiation through a unique mechanism by interaction with Akt kinase to regulate its phosphorylation levels rather than its stability. We further show that DPCD is a heart-shaped monomeric protein with two domains. A highly conserved region in the cysteine- and histidine-rich domains-containing proteins and SGT1 (CS) domain of DPCD interacts with the RUVBL2 DII domain with high affinity to form a stable R2TP-DPCD complex both in cellulo and in vitro. Considering that DPCD is one among several CS-domain-containing proteins found to associate with RUVBL1/2, we propose that RUVBL1/2 are CS-domain-binding proteins that regulate complex assembly and downstream signaling.


Subject(s)
Proto-Oncogene Proteins c-akt , Signal Transduction , Phosphorylation , ATPases Associated with Diverse Cellular Activities , Cognition
18.
Nat Commun ; 15(1): 3120, 2024 Apr 10.
Article in English | MEDLINE | ID: mdl-38600106

ABSTRACT

Salmonella utilizes a type 3 secretion system to translocate virulence proteins (effectors) into host cells during infection1. The effectors modulate host cell machinery to drive uptake of the bacteria into vacuoles, where they can establish an intracellular replicative niche. A remarkable feature of Salmonella invasion is the formation of actin-rich protuberances (ruffles) on the host cell surface that contribute to bacterial uptake. However, the membrane source for ruffle formation and how these bacteria regulate membrane mobilization within host cells remains unclear. Here, we show that Salmonella exploits membrane reservoirs for the generation of invasion ruffles. The reservoirs are pre-existing tubular compartments associated with the plasma membrane (PM) and are formed through the activity of RAB10 GTPase. Under normal growth conditions, membrane reservoirs contribute to PM homeostasis and are preloaded with the exocyst subunit EXOC2. During Salmonella invasion, the bacterial effectors SipC, SopE2, and SopB recruit exocyst subunits from membrane reservoirs and other cellular compartments, thereby allowing exocyst complex assembly and membrane delivery required for bacterial uptake. Our findings reveal an important role for RAB10 in the establishment of membrane reservoirs and the mechanisms by which Salmonella can exploit these compartments during host cell invasion.


Subject(s)
Salmonella Infections , Salmonella typhimurium , Humans , Salmonella typhimurium/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Salmonella Infections/microbiology , Cell Membrane/metabolism , Membranes/metabolism , HeLa Cells
19.
J Invest Dermatol ; 2024 Jun 20.
Article in English | MEDLINE | ID: mdl-38908781

ABSTRACT

Merkel cell carcinoma (MCC) is an aggressive skin cancer with a high mortality rate. MC polyomavirus (MCPyV) causes 80% of MCCs, encoding the viral oncogenes small T (sT) and truncated large T antigens (tLT). These proteins impair the Rb1-dependent G1/S checkpoint blockade and subvert the host cell epigenome to promote cancer. Whole proteome analysis and proximal interactomics identified a tLT-dependent deregulation of DNA damage response (DDR). Our investigation revealed a previously unreported interaction between tLT and the histone methyltransferase EHMT2, to our knowledge. T Antigens knockdown reduced DDR protein levels and increased levels of the DNA damage marker γH2Ax. EHMT2 normally promotes H3K9 methylation and DDR signaling. Given that inhibition of EHMT2 did not significantly change the MCC cells proteome, tLT-EHMT2 interaction could affect the DDR. With tLT, we report that EHMT2 gained DNA damage repair proximal interactors. EHMT2 inhibition rescued proliferation in MCC cells depleted for their T antigens, suggesting impaired DDR and/or lack of checkpoint efficiency. Combined tLT and EHMT2 inhibition led to altered DDR, evidenced by multiple signaling alterations. Here we show that tLT hijacks multiple components of the DNA damage machinery to enhance tolerance to DNA damage in MCC cells, which could explain the genetic stability of these cancers.

20.
Cell Death Dis ; 14(4): 237, 2023 04 04.
Article in English | MEDLINE | ID: mdl-37015912

ABSTRACT

Using multi-omics analyses including RNAseq, RT-PCR, RACE-PCR, and shotgun proteomic with enrichment strategies, we demonstrated that newborn rat astrocytes produce neural immunoglobulin constant and variable heavy chains as well as light chains. However, their edification is different from the ones found in B cells and they resemble aberrant immunoglobulins observed in several cancers. Moreover, the complete enzymatic V(D)J recombination complex has also been identified in astrocytes. In addition, the constant heavy chain is also present in adult rat astrocytes, whereas in primary astrocytes from human fetus we identified constant and variable kappa chains as well as the substitution lambda chains known to be involved in pre-B cells. To gather insights into the function of these neural IgGs, CRISPR-Cas9 of IgG2B constant heavy chain encoding gene (Igh6), IgG2B overexpression, proximal labeling of rat astrocytes IgG2B and targets identification through 2D gels were performed. In Igh6 KO astrocytes, overrepresentation of factors involved in hematopoietic cells, neural stem cells, and the regulation of neuritogenesis have been identified. Moreover, overexpression of IgG2B in astrocytes induces the CRTC1-CREB-BDNF signaling pathway known to be involved in gliogenesis, whereas Igh6 KO triggers the BMP/YAP1/TEAD3 pathway activated in astrocytes dedifferentiation into neural progenitors. Proximal labeling experiments revealed that IgG2B is N-glycosylated by the OST complex, addressed to vesicle membranes containing the ATPase complex, and behaves partially like CD98hc through its association with LAT1. These experiments also suggest that proximal IgG2B-LAT1 interaction occurs concomitantly with MACO-1 and C2CD2L, at the heart of a potentially novel cell signaling platform. Finally, we demonstrated that these chains are synthesized individually and associated to recognize specific targets. Indeed, intermediate filaments Eif4a2 and Pdia6 involved in astrocyte fate constitute targets for these neural IgGs. Taken together, we hypothese that neural aberrant IgG chains may act as gatekeepers of astrocytes' fate.


Subject(s)
Astrocytes , Neural Stem Cells , Rats , Humans , Animals , Astrocytes/metabolism , Proteomics , Neurons/metabolism , Immunoglobulin G/genetics , Transcription Factors/metabolism
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