Fat mass loss is a severe complication in cancer-associated cachexia, but its underlying mechanisms remain unclear. This study identifies the tumor-secreted chaperone clusterin (CLU) as a driver of white adipose tissue (...Fat mass loss is a severe complication in cancer-associated cachexia, but its underlying mechanisms remain unclear. This study identifies the tumor-secreted chaperone clusterin (CLU) as a driver of white adipose tissue (WAT) depletion in triple-negative breast cancer (TNBC). CLU secretion is increased in the serum of cachectic TNBC patients. Mechanistically, extracellular clusterin scavenges 14-3-3 in WAT, inhibiting nucleocytoplasmic translocation of the molecular clock activator BMAL1, and perturbing the transcriptional repression of circadian rhythm genes, including PER3. In tumors, desmosomal protein plakophilin 3 (PKP3) controls CLU stability by competitively binding to its lysosomal receptor LRP2, increasing CLU distribution in plaques and inhibiting its lysosomal degradation. In advanced TNBC patients, increased amounts of secreted CLU, PKP3 and PER3 are associated with cachectic fat loss. Finally, a targeted reduction of PKP3 or CLU in the serum restores PER3 expression rhythmicity and inhibits cachectic adipose wasting in a TNBC mouse model. Taken together, our results identify a targetable a clinically accessible PKP3-clusterin axis that disrupts circadian gene expression in fat tissue in breast cancer.
Herrle N, Malacarne PF, Warwick T
… +37 more, Cabrera-Orefice A, Chen Y, Gheisari M, Chatterjee S, Leisegang MS, Sarakpi T, Wionski S, Lopez M, Kader C, Teichmann T, Drekolia MK, Koch I, Keßler M, Klein S, Erhard Uschner F, Trebicka J, Brunst S, Proschak E, Günther S, Rosas-Lemus M, Baumgarten N, Klatt S, Speer T, Bibli SI, Segarra M, Acker-Palmer A, Wagner JUG, Wittig I, Dimmeler S, Schulz MH, Richards JB, Gilsbach R, T Denton T, Fleming I, Hannibal L, Brandes RP, Rezende F
Oxidative stress is a major driver of cardiovascular disease; however, the fast changes in cellular metabolism caused by short-lived reactive oxygen species (ROS) remain ill-defined. Here, we characterized changes in the...Oxidative stress is a major driver of cardiovascular disease; however, the fast changes in cellular metabolism caused by short-lived reactive oxygen species (ROS) remain ill-defined. Here, we characterized changes in the endothelial cell metabolome in response to acute oxidative challenges and identified novel redox-sensitive metabolic enzymes. HO selectively increased the amount of α-ketoglutaramate (αKGM), a largely uncharacterized metabolite produced by glutamine transamination and an unrecognized intermediate of endothelial glutamine catabolism. In addition, HO impaired the catalytic activity of nitrilase-like 2 ω-amidase (NIT2), the enzyme that converts αKGM to α-ketoglutarate (αKG), by the reversible oxidation of specific cysteine residues. Moreover, a NIT2 gene variant exhibited decreased expression in humans and was associated with increased plasma αKGM concentration. Endothelial-specific knockout of NIT2 in mice increased cellular αKGM levels and impaired angiogenesis. Further, NIT2 depletion impaired endothelial cell proliferation, sprouting, and induced senescence. In conclusion, we uncover NIT2 as a redox-sensitive enzyme of the glutamine transaminase-ω-amidase pathway that acts as a metabolic switch modulating endothelial glutamine metabolism in mice and humans.
The subcellular localization of many mRNAs to neuronal projections allows neurons to efficiently and rapidly react to spatially restricted external cues. However, for most of these RNAs, the mechanisms that govern their...The subcellular localization of many mRNAs to neuronal projections allows neurons to efficiently and rapidly react to spatially restricted external cues. However, for most of these RNAs, the mechanisms that govern their localization are unknown. Here, using subcellular fractionation and single-molecule RNA FISH, we found that loss of TDP-43 results in increased accumulation of hundreds of mRNAs in neurites. Using high-throughput functional assays in cells and high-throughput binding assays in vitro, we subsequently identified specific regions within these mRNAs that mediate their TDP-43-dependent localization and interaction with TDP-43. We found that the same regions also mediated TDP-43-dependent mRNA instability, suggesting a mechanism by which TDP-43 regulates mRNA localization. ALS-associated mutations in TDP-43 resulted in similar mRNA mislocalization phenotypes as did TDP-43 loss in mouse dorsal root ganglia and human iPS-derived motor neurons. These findings establish TDP-43 as a direct negative regulator of mRNA abundance in neurites and suggest that mislocalization of specific transcripts may occur in ALS patients.
Proximity labeling has emerged as a powerful approach for identifying protein-protein interaction networks within living systems, particularly those involving weak or transient associations. Here, we present a comprehens...Proximity labeling has emerged as a powerful approach for identifying protein-protein interaction networks within living systems, particularly those involving weak or transient associations. Here, we present a comprehensive revised proximity labeling workflow, integrating TurboID labeling of endogenously expressed fusion proteins and data-independent acquisition (DIA) mass spectrometry (MS). We benchmark this pipeline with a study of five conserved Caenorhabditis elegans proteins-NEKL-2, NEKL-3, MLT-2, MLT-3, and MLT-4- that form two NEKL-MLT kinase-scaffold subcomplexes involved in membrane trafficking and actin regulation. Profiling of NEKL-MLT interactomes across 23 experiments validated our approach through the identification of known NEKL-MLT binding partners and conserved nekl-mlt genetic interactors, including the discovery of several novel functional interactors. Importantly, inclusion of methodological variations, stringent controls, and filtering strategies enhanced sensitivity and reproducibility, defining a set of intuitive quantitative metrics for routine assessment of experimental quality. We show that DIA-based interactome workflows produce physiologically relevant findings, even in the presence of experimental noise and variability across biological replicates. Our study underscores the utility of DIA mass spectrometry in proximity labeling applications and highlights the value of incorporating internal controls, quantitative metrics, and biological validation to enhance confidence in candidate interactors.
The Golgi apparatus is the central hub of secretory and endosomal pathways in a eukaryotic cell. Despite having a conserved basic organization, the Golgi varies greatly in structure and operation mode between different c...The Golgi apparatus is the central hub of secretory and endosomal pathways in a eukaryotic cell. Despite having a conserved basic organization, the Golgi varies greatly in structure and operation mode between different cell types, ranging from dispersed cisternae in the budding yeast to the ribbon of cisternae stacks in most mammalian cells. Cell shape and secretory demands dictate structural and functional properties of the Golgi. Neurons are a particularly interesting type of secretory cells that have a highly polarized architecture and a large and diverse secretome. The neuronal Golgi complex evolved into an elaborate set of compartmentalized organelles that process and sort diverse neuronal cargos, including synaptic proteins, neuropeptides, and neurotrophic factors. In this review, we describe the structural adaptations of the Golgi to neuronal architecture and discuss the principles of neuronal cargo sorting. We also highlight structural rearrangements of the neuronal Golgi in neurodegenerative diseases and discuss the role of mutations in Golgi-related proteins in neurodevelopment.
Somatic hypermutation (SHM) in variable regions of immunoglobulin genes by activation-induced deaminase (AID) is essential for the maturation of protective antibodies against pathogen and vaccine antigens. AID preferenti...Somatic hypermutation (SHM) in variable regions of immunoglobulin genes by activation-induced deaminase (AID) is essential for the maturation of protective antibodies against pathogen and vaccine antigens. AID preferentially mutates cytosines within WRCH motifs (wherein W = A/T, R = A/G, and H = A/C/T) in single-stranded DNA, yet these motifs show large but reproducible variation in mutation frequency, suggesting a crucial role for sequences flanking the WRCH motifs (i.e., a sequence grammar) in determining mutational outcomes. However, the nature of this sequence grammar is poorly understood. Here, we demonstrate that identical sequence contexts can exert significantly varying effects on the mutagenesis of different WRCH motifs. Molecular dynamics simulations reveal that both the sequence context and the specific WRCH motif modulate AID activity by altering the mode and strength of AID's interactions with single-stranded DNA. Repositioning a motif and its context within the variable region significantly alters its mutability. Therefore, the mutability of AID target cytosines is determined by a motif-specific sequence grammar that determines, in part, how activation-induced deaminase binds single-stranded DNA, as well as the motif position.
Microbial translation arrest peptides monitor intracellular environments and feedback-regulate downstream gene expression. Previous studies have identified a class of bacterial arrest peptides with C-terminal RAPP-like s...Microbial translation arrest peptides monitor intracellular environments and feedback-regulate downstream gene expression. Previous studies have identified a class of bacterial arrest peptides with C-terminal RAPP-like sequences, encoded upstream of genes involved in protein localization. In this study, we found that among RAPP-like sequences, RAPP (Arg-Ala-Pro-Pro) and RGPP (Arg-Gly-Pro-Pro) could more readily evolve into translation-impeding sequences with a particularly robust arrest that is refractory to EF-P. RAPP-like motifs were found to be strongly excluded from bacterial proteomes, likely reflecting the risk of disrupting the cellular translation system. Meanwhile, these motifs tended to occur near the C-terminus of relatively small secretory and membrane proteins. Notably, they were encoded upstream of genes with diverse functions beyond protein localization. Indeed, we identified seven RAPP/RGPP-containing arrest peptides from Streptomyces lividans encoded upstream of genes with diverse functions. These findings illustrate the bidirectional evolution of RAPP-containing proteins: their elimination from bacterial proteomes and their adaptation into arrest peptides with various regulatory roles.
Post-meiotic development of spermatids is under the control of a sophisticated RNA metabolic network, wherein the N6-methyladenosine (mA) modification of mRNA, and proteins that bind to it, exert crucial functions in reg...Post-meiotic development of spermatids is under the control of a sophisticated RNA metabolic network, wherein the N6-methyladenosine (mA) modification of mRNA, and proteins that bind to it, exert crucial functions in regulating sperm development from spermatogonia to spermatocytes. However, which mA recognition proteins are involved in male post-meiotic spermiogenesis, and via which regulatory mechanisms, remains largely unknown. Here, we uncover the involvement of the mA reader protein IGF2BP3 in the regulation of post-meiotic spermatid development. Genetic ablation of Igf2bp3 results in spermatogenesis defects, leading to male sub-fertility or even infertility. Mechanistically, IGF2BP3 loss-of-function leads to the excessive translation of its target RNAs associated with histone-to-protamine replacement, particularly Dot1l and Hdac11. IGF2BP3 translationally represses these targets through its mA-binding property and through its interaction with its binding partner YBX2. Sperm developmental defects of IGF2BP3 knockout mouse can be rescued by siRNAs targeting Dot1l and Hdac11. Collectively, our findings define the essential role of IGF2BP3-dependent regulation of protein biosynthesis in histone-to-protamine replacement during spermiogenesis, helping to understand the functions of mA RNA modification in sperm development and male fertility.
Protein quality control (PQC) in the secretory pathway, a process critically linked to numerous human diseases, begins in the endoplasmic reticulum (ER) and involves ER-associated degradation (ERAD) of terminally misfold...Protein quality control (PQC) in the secretory pathway, a process critically linked to numerous human diseases, begins in the endoplasmic reticulum (ER) and involves ER-associated degradation (ERAD) of terminally misfolded proteins. In this study, we conducted genome-wide screens in baker's yeast (Saccharomyces cerevisiae) to investigate the degradation of Gas1*, a misfolded version of an O-mannosylated, glycosylphosphatidylinositol (GPI)-anchored protein. In combination with detailed biochemical and genetic analyses, these screens revealed an unexpected bifunctionality of the evolutionarily conserved heteromeric enzyme complex Pbn1-Gpi14: while it has been previously recognized as a GPI-mannosyltransferase, we here find that it catalyzes the O-mannosylation of misfolded proteins, thereby promoting their ERAD. This process is particularly relevant for misfolded proteins that lack N-glycans. Our results suggest that protein O-mannosylation constitutes a distinct type of glycan-dependent mechanism for promoting ERAD.
Small noncoding RNAs (sncRNAs) are subject to 3'-end trimming and tailing activities that impact maturation versus degradation decisions during biogenesis. To investigate the dynamics of human sncRNA 3'-end processing at...Small noncoding RNAs (sncRNAs) are subject to 3'-end trimming and tailing activities that impact maturation versus degradation decisions during biogenesis. To investigate the dynamics of human sncRNA 3'-end processing at a global level, we performed genome-wide 3'-end sequencing of newly transcribed and steady-state sncRNAs. This revealed widespread post-transcriptional adenylation of newly transcribed sncRNAs, which came in two distinct varieties. One is characterized by oligoadenylation, which is transient, promoted by TENT4A/4B polymerases, and most commonly observed on unstable small nucleolar RNAs that are not fully processed at their 3'-ends. The other is characterized by monoadenylation, which is broadly catalyzed by TENT2 and, in contrast to oligoadenylation, stably accumulates at the 3'-end of sncRNAs, including Polymerase-III-transcribed (Pol-III) RNAs and a subset of small nuclear RNAs. Monoadenylation inhibits Pol-III RNA post-transcriptional 3'-uridine trimming and extension and, in the case of 7SL RNAs, prevents their accumulation with nuclear La protein and promotes their biogenesis towards assembly into cytoplasmic signal recognition particles. Thus, the biogenesis of human sncRNAs involves widespread mono- or oligoadenylation with divergent impacts on sncRNA fates.
Localization of lysosomes influences their properties, e.g., perinuclear lysosomes are more acidic but less mobile compared with the peripheral ones. Furthermore, the endoplasmic reticulum (ER) can actively regulate the...Localization of lysosomes influences their properties, e.g., perinuclear lysosomes are more acidic but less mobile compared with the peripheral ones. Furthermore, the endoplasmic reticulum (ER) can actively regulate the dynamics and functions of lysosomes via membrane contact sites. In this study, we find that ER-resident apoptosis-resistant E3 ubiquitin protein ligase 1 (AREL1) establishes membrane contacts with lysosomes by directly interacting with the Va subunit of V-ATPase. AREL1 also catalyzes K33-linked polyubiquitylation of V-ATPase VB2 subunit, inducing its binding to UBAC2 localized in the perinuclear ER. Depletion of AREL1 or UBAC2 increases the number of peripheral lysosomes that possess partially assembled V-ATPase, elevated luminal pH, and attenuated degradative capacity. Knockdown of ZRANB1, the deubiquitylating enzyme that antagonizes AREL1-mediated VB2 ubiquitylation, promotes perinuclear clustering of lysosomes and increases lysosomal acidity and degradation. Mice lacking Arel1 exhibit age-dependent Purkinje cell loss, an ataxic phenotype, and motor impairment. Lipofuscin accumulation in the residual Purkinje cells of Arel1 mice indicates lysosomal dysfunction. Orchestration of lysosomal positioning and function by the AREL1-UBAC2-V-ATPase axis underscores the physiological significance of ER-regulated perinuclear lysosomal positioning in neurons.
Following cell entry, HIV-1 capsids enter the nucleus by passage through nuclear pores and reach nuclear speckles with subsequent uncoating of the reverse-transcribed genome and its integration into speckle-associated ch...Following cell entry, HIV-1 capsids enter the nucleus by passage through nuclear pores and reach nuclear speckles with subsequent uncoating of the reverse-transcribed genome and its integration into speckle-associated chromatin domains. Here, we characterized the ultrastructure of HIV-1 subviral complexes in nuclei of primary monocyte-derived macrophages and cell lines using live-cell imaging, super-resolution microscopy, and correlative light and electron tomography in the absence and presence of capsid-targeting inhibitors Lenacapavir and PF74. Capsid-like structures containing viral DNA, as well as broken capsids, clustered in nuclear speckles and were displaced from speckles by drug treatment. This was accompanied by alteration of the nuclear capsid structure, with electron-dense protrusions emanating from the narrow end of capsid cones and exposure of integration-competent genomic HIV-1 DNA. Our data indicate that synthesis of genomic dsDNA can be completed inside the closed HIV-1 capsid, and speckle-associated factors could regulate genome uncoating. This may ensure that genome uncoating occurs at optimal sites for integration into transcriptionally active chromatin. The results also shed further light on the mechanism of action of Lenacapavir.
Zhao H, Wei Q, Luo Z
… +18 more, Liu X, Yang C, Chen N, Wang Y, Luo X, Zuo X, Luo Q, Yang Y, Zhou Y, Liu J, Zhang T, Yang D, Long Y, Mobet Y, Xu J, Wang W, Liu T, Yi P
The role of epigenetic regulation of RNAs in the tumorigenesis remains incompletely understood. This study uncovers a critical function of the 5-methylcytosine (mC) RNA modification reader protein ALYREF (also termed, AL...The role of epigenetic regulation of RNAs in the tumorigenesis remains incompletely understood. This study uncovers a critical function of the 5-methylcytosine (mC) RNA modification reader protein ALYREF (also termed, ALY; BEF) in ovarian cancer. ALYREF is elevated in ovarian cancer patient samples, and its depletion reduces ovarian tumorigenesis and metastasis in mice in a mC-dependent manner. Mechanistically, ALYREF binds to the mC-modified mRNA of ADP-ribosyltransferase PARP10, competing with exosome complex component MTR4, and enhancing the stability and nuclear export of PARP10 mRNA. Further, ALYREF forms condensates in the nucleus of ovarian cancer cells, and depletion or mutation of ALYREF's intrinsically disordered regions rescues its control on PARP10 mRNA nucleoplasmic distribution and stability, reduces tumor growth and is required for promotion of ovarian cancer aggressiveness and proliferation. Finally, ALYREF and PARP10 expression correlate with poor prognosis in ovarian cancer patients. Together, these findings suggest that ALYREF phase separation facilitates the malignant progression of ovarian cancer by promoting PARP10 expression and thereby enhancing PARP10-dependent proliferative pathways in a mC-dependent manner.
ADP-ribosylation is an important protein post-translational modification catalysed by a family of PARP enzymes in humans and is involved in DNA damage and immunity among other processes. While poly-ADP-ribosylation has b...ADP-ribosylation is an important protein post-translational modification catalysed by a family of PARP enzymes in humans and is involved in DNA damage and immunity among other processes. While poly-ADP-ribosylation has been established as a protein degradation signal in several cases, the role of mono-ADP-ribosylation in protein turnover has remained elusive and mostly relies on overexpression systems. Here, we describe a way to visualise high levels of endogenous ADP-ribosylation by inhibiting the ubiquitin pathway. By blocking ubiquitylation/proteasome, we found that ADP-ribosylation by at least three different PARPs (PARP7, PARP1 and TNKS) can be greatly induced. We discovered that specific activation of the aryl hydrocarbon receptor (AHR) pathway in combination with the ubiquitin pathway inhibition promotes quantitative ADP-ribosylation of PARP7 targets, including the mono-ADP-ribosyltransferase PARP7 itself and AHR. We found that DTX2 is the E3 ligase responsible for degrading ADP-ribosylated PARP7, AHR and other PARP7 substrates. This PARP7-DTX2 crosstalk establishes a mechanism to rapidly shut down AHR-mediated transcription by decreasing its protein levels. Taken together, our findings uncover a paradigm where mono-ADP-ribosylation acts as a degradation mark.
Antifungal resistance in pathogenic fungi endanger global health and food supply. Wild-type fission yeast, Schizosaccharomyces pombe, can gain resistance to insults including caffeine and antifungal compounds through rev...Antifungal resistance in pathogenic fungi endanger global health and food supply. Wild-type fission yeast, Schizosaccharomyces pombe, can gain resistance to insults including caffeine and antifungal compounds through reversible epimutations. Resistant epimutants exhibit ectopic histone-H3K9 methylation-dependent heterochromatin islands, repressing underlying genes. Two genes whose heterochromatin island-induced repression causes resistance encode mitochondrial proteins: LYR-domain protein Cup1 and Cox1 translation regulator Ppr4. Genetic mutations, cup1-tt and ppr4Δ, that phenocopy epimutants, cause mitochondrial dysfunction, including respiratory deficiency, poor growth on non-glucose carbon sources, and elevated reactive oxygen species. Transcriptomic analyses indicate cup1-tt and ppr4Δ cells activate Pap1 transcription factor-dependent oxidative stress response and mitonuclear retrograde pathways. Pap1 nuclear localisation and recruitment to promoters of oxidoreductase and membrane transporter genes is increased, causing increased efflux activity. cup1 and ppr4 epimutants likewise show mitochondrial dysfunction phenotypes and increased efflux, explaining how heterochromatin-island epimutations cause drug resistance. Thus, wild-type cells harness epimutations that impose mitochondrial dysfunction to bypass external insults. As mitochondrial dysfunction is linked to antifungal resistance in several fungi, similar epimutations likely contribute to development of resistance in fungal pathogens.
The successes of cancer immunotherapy have inspired research aiming to increase the number of immune-responsive cancers. The first effective immunotherapeutic strategies-immune checkpoint blockade (ICB) and CAR T cells-w...The successes of cancer immunotherapy have inspired research aiming to increase the number of immune-responsive cancers. The first effective immunotherapeutic strategies-immune checkpoint blockade (ICB) and CAR T cells-were designed to overcome limitations in CD8 T cell recognition and killing of tumor cells. However, most solid tumors still do not respond to these measures and new treatment approaches are needed. Tumors evolve many strategies to avoid immune control. One way to identify immunotherapy strategies is to study what distinguishes immunotherapy-responsive and -unresponsive tumors. Another way is to identify the differences in tumors that emerge after carcinogen exposure in immunocompetent versus immunodeficient hosts. Still another way is to identify changes in gene expression in emerging tumors that enable them to escape immunosurveillance (known as tumor immunoediting). Evolving tumors suppress antigen processing and presentation to avoid triggering tumor-specific T cells but also repress key innate immune genes that transmit danger signals to immune cells. In this perspective, we discuss the roles of innate immunity in anti-tumor responses and consider how innate immunity could be harnessed to make tumors more immune-responsive.
DNA replication initiation is a tightly regulated process that requires the coordinated assembly of replication machineries throughout the genome. During the first step of initiation, origin licensing, the MCM replicativ...DNA replication initiation is a tightly regulated process that requires the coordinated assembly of replication machineries throughout the genome. During the first step of initiation, origin licensing, the MCM replicative helicase motor is loaded onto replication origins by the origin recognition complex (ORC) as a head-to-head double hexamer complex. Distinct mechanisms have been proposed to facilitate human MCM double hexamer loading, but the physiological relevance of each of them remains unclear. Here, we investigate the evolutionary conservation of these pathways using an AlphaFold-guided structural phylogenetics approach. Our analyses reveal that ORC6, a subunit of ORC previously thought to be essential for origin licensing in vivo, has been lost in multiple metazoan lineages. Despite this loss, many of these species retain an element in ORC3, the ORC3 tether, that can interact with MCM and facilitate an ORC6-independent MCM loading mechanism. AlphaFold2 Multimer predictions suggest that ORC3 tether interactions with MCM are broadly conserved across Metazoa. Our findings support the physiological relevance of ORC6-independent MCM loading, provide experimentally testable hypotheses on origin licensing mechanisms in diverse metazoan species, and highlight how AlphaFold can be leveraged to investigate protein evolution and function over large timescales.