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1.
Cell ; 187(15): 4061-4077.e17, 2024 Jul 25.
Article in English | MEDLINE | ID: mdl-38878777

ABSTRACT

NLRs constitute a large, highly conserved family of cytosolic pattern recognition receptors that are central to health and disease, making them key therapeutic targets. NLRC5 is an enigmatic NLR with mutations associated with inflammatory and infectious diseases, but little is known about its function as an innate immune sensor and cell death regulator. Therefore, we screened for NLRC5's role in response to infections, PAMPs, DAMPs, and cytokines. We identified that NLRC5 acts as an innate immune sensor to drive inflammatory cell death, PANoptosis, in response to specific ligands, including PAMP/heme and heme/cytokine combinations. NLRC5 interacted with NLRP12 and PANoptosome components to form a cell death complex, suggesting an NLR network forms similar to those in plants. Mechanistically, TLR signaling and NAD+ levels regulated NLRC5 expression and ROS production to control cell death. Furthermore, NLRC5-deficient mice were protected in hemolytic and inflammatory models, suggesting that NLRC5 could be a potential therapeutic target.


Subject(s)
Inflammation , Intracellular Signaling Peptides and Proteins , NAD , Animals , Mice , Inflammation/metabolism , Intracellular Signaling Peptides and Proteins/metabolism , Intracellular Signaling Peptides and Proteins/genetics , NAD/metabolism , Humans , Immunity, Innate , Mice, Inbred C57BL , Reactive Oxygen Species/metabolism , Mice, Knockout , Signal Transduction , HEK293 Cells , Inflammasomes/metabolism , Apoptosis Regulatory Proteins/metabolism , Apoptosis Regulatory Proteins/genetics , Toll-Like Receptors/metabolism , Male , Cytokines/metabolism , Calcium-Binding Proteins
2.
Cell ; 187(2): 276-293.e23, 2024 01 18.
Article in English | MEDLINE | ID: mdl-38171360

ABSTRACT

During development, morphogens pattern tissues by instructing cell fate across long distances. Directly visualizing morphogen transport in situ has been inaccessible, so the molecular mechanisms ensuring successful morphogen delivery remain unclear. To tackle this longstanding problem, we developed a mouse model for compromised sonic hedgehog (SHH) morphogen delivery and discovered that endocytic recycling promotes SHH loading into signaling filopodia called cytonemes. We optimized methods to preserve in vivo cytonemes for advanced microscopy and show endogenous SHH localized to cytonemes in developing mouse neural tubes. Depletion of SHH from neural tube cytonemes alters neuronal cell fates and compromises neurodevelopment. Mutation of the filopodial motor myosin 10 (MYO10) reduces cytoneme length and density, which corrupts neuronal signaling activity of both SHH and WNT. Combined, these results demonstrate that cytoneme-based signal transport provides essential contributions to morphogen dispersion during mammalian tissue development and suggest MYO10 is a key regulator of cytoneme function.


Subject(s)
Cell Membrane Structures , Myosins , Neural Tube , Signal Transduction , Animals , Mice , Biological Transport , Cell Membrane Structures/metabolism , Hedgehog Proteins/metabolism , Myosins/metabolism , Pseudopodia/metabolism , Neural Tube/cytology , Neural Tube/metabolism
3.
Cell ; 185(21): 3877-3895.e21, 2022 10 13.
Article in English | MEDLINE | ID: mdl-36152627

ABSTRACT

Williams-Beuren syndrome (WBS) is a rare disorder caused by hemizygous microdeletion of ∼27 contiguous genes. Despite neurodevelopmental and cognitive deficits, individuals with WBS have spared or enhanced musical and auditory abilities, potentially offering an insight into the genetic basis of auditory perception. Here, we report that the mouse models of WBS have innately enhanced frequency-discrimination acuity and improved frequency coding in the auditory cortex (ACx). Chemogenetic rescue showed frequency-discrimination hyperacuity is caused by hyperexcitable interneurons in the ACx. Haploinsufficiency of one WBS gene, Gtf2ird1, replicated WBS phenotypes by downregulating the neuropeptide receptor VIPR1. VIPR1 is reduced in the ACx of individuals with WBS and in the cerebral organoids derived from human induced pluripotent stem cells with the WBS microdeletion. Vipr1 deletion or overexpression in ACx interneurons mimicked or reversed, respectively, the cellular and behavioral phenotypes of WBS mice. Thus, the Gtf2ird1-Vipr1 mechanism in ACx interneurons may underlie the superior auditory acuity in WBS.


Subject(s)
Auditory Cortex/physiology , Williams Syndrome/physiopathology , Animals , Auditory Cortex/cytology , Disease Models, Animal , Humans , Induced Pluripotent Stem Cells , Interneurons/cytology , Interneurons/physiology , Mice , Phenotype , Trans-Activators/genetics , Williams Syndrome/genetics
4.
Nature ; 628(8007): 442-449, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38538798

ABSTRACT

Whereas oncogenes can potentially be inhibited with small molecules, the loss of tumour suppressors is more common and is problematic because the tumour-suppressor proteins are no longer present to be targeted. Notable examples include SMARCB1-mutant cancers, which are highly lethal malignancies driven by the inactivation of a subunit of SWI/SNF (also known as BAF) chromatin-remodelling complexes. Here, to generate mechanistic insights into the consequences of SMARCB1 mutation and to identify vulnerabilities, we contributed 14 SMARCB1-mutant cell lines to a near genome-wide CRISPR screen as part of the Cancer Dependency Map Project1-3. We report that the little-studied gene DDB1-CUL4-associated factor 5 (DCAF5) is required for the survival of SMARCB1-mutant cancers. We show that DCAF5 has a quality-control function for SWI/SNF complexes and promotes the degradation of incompletely assembled SWI/SNF complexes in the absence of SMARCB1. After depletion of DCAF5, SMARCB1-deficient SWI/SNF complexes reaccumulate, bind to target loci and restore SWI/SNF-mediated gene expression to levels that are sufficient to reverse the cancer state, including in vivo. Consequently, cancer results not from the loss of SMARCB1 function per se, but rather from DCAF5-mediated degradation of SWI/SNF complexes. These data indicate that therapeutic targeting of ubiquitin-mediated quality-control factors may effectively reverse the malignant state of some cancers driven by disruption of tumour suppressor complexes.


Subject(s)
Multiprotein Complexes , Mutation , Neoplasms , SMARCB1 Protein , Animals , Female , Humans , Male , Mice , Cell Line, Tumor , CRISPR-Cas Systems , Gene Editing , Neoplasms/genetics , Neoplasms/metabolism , SMARCB1 Protein/deficiency , SMARCB1 Protein/genetics , SMARCB1 Protein/metabolism , Tumor Suppressor Proteins/deficiency , Tumor Suppressor Proteins/genetics , Tumor Suppressor Proteins/metabolism , Multiprotein Complexes/chemistry , Multiprotein Complexes/metabolism , Proteolysis , Ubiquitin/metabolism
5.
Mol Cell ; 82(13): 2472-2489.e8, 2022 07 07.
Article in English | MEDLINE | ID: mdl-35537449

ABSTRACT

Disruption of antagonism between SWI/SNF chromatin remodelers and polycomb repressor complexes drives the formation of numerous cancer types. Recently, an inhibitor of the polycomb protein EZH2 was approved for the treatment of a sarcoma mutant in the SWI/SNF subunit SMARCB1, but resistance occurs. Here, we performed CRISPR screens in SMARCB1-mutant rhabdoid tumor cells to identify genetic contributors to SWI/SNF-polycomb antagonism and potential resistance mechanisms. We found that loss of the H3K36 methyltransferase NSD1 caused resistance to EZH2 inhibition. We show that NSD1 antagonizes polycomb via cooperation with SWI/SNF and identify co-occurrence of NSD1 inactivation in SWI/SNF-defective cancers, indicating in vivo relevance. We demonstrate that H3K36me2 itself has an essential role in the activation of polycomb target genes as inhibition of the H3K36me2 demethylase KDM2A restores the efficacy of EZH2 inhibition in SWI/SNF-deficient cells lacking NSD1. Together our data expand the mechanistic understanding of SWI/SNF and polycomb interplay and identify NSD1 as the key for coordinating this transcriptional control.


Subject(s)
Enhancer of Zeste Homolog 2 Protein , F-Box Proteins , Histone-Lysine N-Methyltransferase , Jumonji Domain-Containing Histone Demethylases , Polycomb-Group Proteins , SMARCB1 Protein , Chromatin/genetics , Chromatin/metabolism , Enhancer of Zeste Homolog 2 Protein/antagonists & inhibitors , Enhancer of Zeste Homolog 2 Protein/genetics , Enhancer of Zeste Homolog 2 Protein/metabolism , F-Box Proteins/genetics , F-Box Proteins/metabolism , Histone-Lysine N-Methyltransferase/genetics , Histone-Lysine N-Methyltransferase/metabolism , Histones/genetics , Histones/metabolism , Humans , Jumonji Domain-Containing Histone Demethylases/genetics , Jumonji Domain-Containing Histone Demethylases/metabolism , Polycomb-Group Proteins/genetics , Polycomb-Group Proteins/metabolism , Rhabdoid Tumor/genetics , Rhabdoid Tumor/metabolism , Rhabdoid Tumor/pathology , SMARCB1 Protein/genetics , SMARCB1 Protein/metabolism , Transcription Factors/genetics , Transcription Factors/metabolism , Transcriptional Activation/genetics , Tumor Cells, Cultured/metabolism
6.
Nature ; 624(7990): 154-163, 2023 Dec.
Article in English | MEDLINE | ID: mdl-37968405

ABSTRACT

CD8+ cytotoxic T cells (CTLs) orchestrate antitumour immunity and exhibit inherent heterogeneity1,2, with precursor exhausted T (Tpex) cells but not terminally exhausted T (Tex) cells capable of responding to existing immunotherapies3-7. The gene regulatory network that underlies CTL differentiation and whether Tex cell responses can be functionally reinvigorated are incompletely understood. Here we systematically mapped causal gene regulatory networks using single-cell CRISPR screens in vivo and discovered checkpoints for CTL differentiation. First, the exit from quiescence of Tpex cells initiated successive differentiation into intermediate Tex cells. This process is differentially regulated by IKAROS and ETS1, the deficiencies of which dampened and increased mTORC1-associated metabolic activities, respectively. IKAROS-deficient cells accumulated as a metabolically quiescent Tpex cell population with limited differentiation potential following immune checkpoint blockade (ICB). Conversely, targeting ETS1 improved antitumour immunity and ICB efficacy by boosting differentiation of Tpex to intermediate Tex cells and metabolic rewiring. Mechanistically, TCF-1 and BATF are the targets for IKAROS and ETS1, respectively. Second, the RBPJ-IRF1 axis promoted differentiation of intermediate Tex to terminal Tex cells. Accordingly, targeting RBPJ enhanced functional and epigenetic reprogramming of Tex cells towards the proliferative state and improved therapeutic effects and ICB efficacy. Collectively, our study reveals that promoting the exit from quiescence of Tpex cells and enriching the proliferative Tex cell state act as key modalities for antitumour effects and provides a systemic framework to integrate cell fate regulomes and reprogrammable functional determinants for cancer immunity.


Subject(s)
Cell Differentiation , Clustered Regularly Interspaced Short Palindromic Repeats , Gene Editing , Mutagenesis , Neoplasms , Single-Cell Analysis , T-Lymphocytes, Cytotoxic , Humans , Cell Differentiation/drug effects , Cell Differentiation/genetics , Clustered Regularly Interspaced Short Palindromic Repeats/genetics , Immune Checkpoint Inhibitors/immunology , Immune Checkpoint Inhibitors/pharmacology , Neoplasms/genetics , Neoplasms/immunology , Single-Cell Analysis/methods , T-Lymphocytes, Cytotoxic/cytology , T-Lymphocytes, Cytotoxic/drug effects , T-Lymphocytes, Cytotoxic/immunology , T-Lymphocytes, Cytotoxic/metabolism
7.
Nature ; 607(7917): 135-141, 2022 07.
Article in English | MEDLINE | ID: mdl-35732731

ABSTRACT

The identification of mechanisms to promote memory T (Tmem) cells has important implications for vaccination and anti-cancer immunotherapy1-4. Using a CRISPR-based screen for negative regulators of Tmem cell generation in vivo5, here we identify multiple components of the mammalian canonical BRG1/BRM-associated factor (cBAF)6,7. Several components of the cBAF complex are essential for the differentiation of activated CD8+ T cells into T effector (Teff) cells, and their loss promotes Tmem cell formation in vivo. During the first division of activated CD8+ T cells, cBAF and MYC8 frequently co-assort asymmetrically to the two daughter cells. Daughter cells with high MYC and high cBAF display a cell fate trajectory towards Teff cells, whereas those with low MYC and low cBAF preferentially differentiate towards Tmem cells. The cBAF complex and MYC physically interact to establish the chromatin landscape in activated CD8+ T cells. Treatment of naive CD8+ T cells with a putative cBAF inhibitor during the first 48 h of activation, before the generation of chimeric antigen receptor T (CAR-T) cells, markedly improves efficacy in a mouse solid tumour model. Our results establish cBAF as a negative determinant of Tmem cell fate and suggest that manipulation of cBAF early in T cell differentiation can improve cancer immunotherapy.


Subject(s)
CD8-Positive T-Lymphocytes , Cell Differentiation , DNA Helicases , Multiprotein Complexes , Nuclear Proteins , Proto-Oncogene Proteins c-myc , Transcription Factors , Animals , CD8-Positive T-Lymphocytes/cytology , DNA Helicases/metabolism , Disease Models, Animal , Immunologic Memory , Immunotherapy , Memory T Cells/cytology , Mice , Multiprotein Complexes/chemistry , Multiprotein Complexes/metabolism , Neoplasms , Nuclear Proteins/metabolism , Proto-Oncogene Proteins c-myc/metabolism , Receptors, Chimeric Antigen , Transcription Factors/metabolism
8.
Mol Cell ; 77(6): 1206-1221.e7, 2020 03 19.
Article in English | MEDLINE | ID: mdl-31980388

ABSTRACT

Alternative polyadenylation (APA) contributes to transcriptome complexity by generating mRNA isoforms with varying 3' UTR lengths. APA leading to 3' UTR shortening (3' US) is a common feature of most cancer cells; however, the molecular mechanisms are not understood. Here, we describe a widespread mechanism promoting 3' US in cancer through ubiquitination of the mRNA 3' end processing complex protein, PCF11, by the cancer-specific MAGE-A11-HUWE1 ubiquitin ligase. MAGE-A11 is normally expressed only in the male germline but is frequently re-activated in cancers. MAGE-A11 is necessary for cancer cell viability and is sufficient to drive tumorigenesis. Screening for targets of MAGE-A11 revealed that it ubiquitinates PCF11, resulting in loss of CFIm25 from the mRNA 3' end processing complex. This leads to APA of many transcripts affecting core oncogenic and tumor suppressors, including cyclin D2 and PTEN. These findings provide insights into the molecular mechanisms driving APA in cancer and suggest therapeutic strategies.


Subject(s)
3' Untranslated Regions/genetics , Antigens, Neoplasm/metabolism , Lung Neoplasms/pathology , Neoplasm Proteins/metabolism , Ovarian Neoplasms/pathology , RNA, Messenger/metabolism , Ubiquitin/metabolism , mRNA Cleavage and Polyadenylation Factors/metabolism , Animals , Antigens, Neoplasm/genetics , Apoptosis , Biomarkers, Tumor , Carcinogenesis , Carcinoma, Squamous Cell/genetics , Carcinoma, Squamous Cell/metabolism , Carcinoma, Squamous Cell/pathology , Cell Proliferation , Cleavage And Polyadenylation Specificity Factor/genetics , Cleavage And Polyadenylation Specificity Factor/metabolism , Female , Gene Expression Regulation, Neoplastic , Humans , Lung Neoplasms/genetics , Lung Neoplasms/metabolism , Male , Mice , Mice, Inbred NOD , Mice, SCID , Neoplasm Proteins/genetics , Ovarian Neoplasms/genetics , Ovarian Neoplasms/metabolism , Polyadenylation , RNA Splicing , RNA, Messenger/genetics , Tumor Cells, Cultured , Tumor Suppressor Proteins/genetics , Tumor Suppressor Proteins/metabolism , Ubiquitin-Protein Ligases/genetics , Ubiquitin-Protein Ligases/metabolism , Ubiquitination , Xenograft Model Antitumor Assays , mRNA Cleavage and Polyadenylation Factors/genetics
9.
Mol Cell ; 79(4): 645-659.e9, 2020 08 20.
Article in English | MEDLINE | ID: mdl-32692974

ABSTRACT

Stress granules (SGs) are membrane-less ribonucleoprotein condensates that form in response to various stress stimuli via phase separation. SGs act as a protective mechanism to cope with acute stress, but persistent SGs have cytotoxic effects that are associated with several age-related diseases. Here, we demonstrate that the testis-specific protein, MAGE-B2, increases cellular stress tolerance by suppressing SG formation through translational inhibition of the key SG nucleator G3BP. MAGE-B2 reduces G3BP protein levels below the critical concentration for phase separation and suppresses SG initiation. Knockout of the MAGE-B2 mouse ortholog or overexpression of G3BP1 confers hypersensitivity of the male germline to heat stress in vivo. Thus, MAGE-B2 provides cytoprotection to maintain mammalian spermatogenesis, a highly thermosensitive process that must be preserved throughout reproductive life. These results demonstrate a mechanism that allows for tissue-specific resistance against stress and could aid in the development of male fertility therapies.


Subject(s)
Cytoplasmic Granules/genetics , DNA Helicases/genetics , Poly-ADP-Ribose Binding Proteins/genetics , Protein Biosynthesis , RNA Helicases/genetics , RNA Recognition Motif Proteins/genetics , Stress, Physiological/genetics , 5' Untranslated Regions , Animals , Antigens, Neoplasm/genetics , Antigens, Neoplasm/metabolism , Cytoplasmic Granules/metabolism , Cytoplasmic Granules/pathology , DEAD-box RNA Helicases/genetics , DEAD-box RNA Helicases/metabolism , DNA Helicases/metabolism , Female , HCT116 Cells , HeLa Cells , Humans , Male , Mice, Inbred C57BL , Mice, Knockout , Mice, Transgenic , Neoplasm Proteins/genetics , Neoplasm Proteins/metabolism , Poly-ADP-Ribose Binding Proteins/metabolism , RNA Helicases/metabolism , RNA Recognition Motif Proteins/metabolism , Spermatogonia/cytology , Spermatogonia/pathology , Testis/cytology , Testis/metabolism
10.
Nature ; 600(7888): 308-313, 2021 12.
Article in English | MEDLINE | ID: mdl-34795452

ABSTRACT

Nutrients are emerging regulators of adaptive immunity1. Selective nutrients interplay with immunological signals to activate mechanistic target of rapamycin complex 1 (mTORC1), a key driver of cell metabolism2-4, but how these environmental signals are integrated for immune regulation remains unclear. Here we use genome-wide CRISPR screening combined with protein-protein interaction networks to identify regulatory modules that mediate immune receptor- and nutrient-dependent signalling to mTORC1 in mouse regulatory T (Treg) cells. SEC31A is identified to promote mTORC1 activation by interacting with the GATOR2 component SEC13 to protect it from SKP1-dependent proteasomal degradation. Accordingly, loss of SEC31A impairs T cell priming and Treg suppressive function in mice. In addition, the SWI/SNF complex restricts expression of the amino acid sensor CASTOR1, thereby enhancing mTORC1 activation. Moreover, we reveal that the CCDC101-associated SAGA complex is a potent inhibitor of mTORC1, which limits the expression of glucose and amino acid transporters and maintains T cell quiescence in vivo. Specific deletion of Ccdc101 in mouse Treg cells results in uncontrolled inflammation but improved antitumour immunity. Collectively, our results establish epigenetic and post-translational mechanisms that underpin how nutrient transporters, sensors and transducers interplay with immune signals for three-tiered regulation of mTORC1 activity and identify their pivotal roles in licensing T cell immunity and immune tolerance.


Subject(s)
CRISPR-Cas Systems , Gene Editing , Nutrients , Protein Interaction Maps , T-Lymphocytes, Regulatory , Animals , Female , Male , Mice , Carrier Proteins/metabolism , CRISPR-Cas Systems/genetics , Forkhead Transcription Factors/metabolism , Genome/genetics , Homeostasis , Immune Tolerance , Inflammation/pathology , Mechanistic Target of Rapamycin Complex 1/metabolism , Neoplasms/immunology , Nuclear Proteins/metabolism , Nutrients/metabolism , Proteasome Endopeptidase Complex/metabolism , Proteolysis , S-Phase Kinase-Associated Proteins/metabolism , T-Lymphocytes, Regulatory/immunology , T-Lymphocytes, Regulatory/metabolism , Trans-Activators/metabolism
11.
Nature ; 595(7866): 295-302, 2021 07.
Article in English | MEDLINE | ID: mdl-34079130

ABSTRACT

Sickle cell disease (SCD) is caused by a mutation in the ß-globin gene HBB1. We used a custom adenine base editor (ABE8e-NRCH)2,3 to convert the SCD allele (HBBS) into Makassar ß-globin (HBBG), a non-pathogenic variant4,5. Ex vivo delivery of mRNA encoding the base editor with a targeting guide RNA into haematopoietic stem and progenitor cells (HSPCs) from patients with SCD resulted in 80% conversion of HBBS to HBBG. Sixteen weeks after transplantation of edited human HSPCs into immunodeficient mice, the frequency of HBBG was 68% and hypoxia-induced sickling of bone marrow reticulocytes had decreased fivefold, indicating durable gene editing. To assess the physiological effects of HBBS base editing, we delivered ABE8e-NRCH and guide RNA into HSPCs from a humanized SCD mouse6 and then transplanted these cells into irradiated mice. After sixteen weeks, Makassar ß-globin represented 79% of ß-globin protein in blood, and hypoxia-induced sickling was reduced threefold. Mice that received base-edited HSPCs showed near-normal haematological parameters and reduced splenic pathology compared to mice that received unedited cells. Secondary transplantation of edited bone marrow confirmed that the gene editing was durable in long-term haematopoietic stem cells and showed that HBBS-to-HBBG editing of 20% or more is sufficient for phenotypic rescue. Base editing of human HSPCs avoided the p53 activation and larger deletions that have been observed following Cas9 nuclease treatment. These findings point towards a one-time autologous treatment for SCD that eliminates pathogenic HBBS, generates benign HBBG, and minimizes the undesired consequences of double-strand DNA breaks.


Subject(s)
Adenine/metabolism , Anemia, Sickle Cell/genetics , Anemia, Sickle Cell/therapy , Gene Editing , Hematopoietic Stem Cell Transplantation , Hematopoietic Stem Cells/metabolism , beta-Globins/genetics , Animals , Antigens, CD34/metabolism , CRISPR-Associated Protein 9/metabolism , Disease Models, Animal , Female , Genetic Therapy , Genome, Human/genetics , Hematopoietic Stem Cells/cytology , Hematopoietic Stem Cells/pathology , Humans , Male , Mice
12.
Mol Cell ; 74(4): 742-757.e8, 2019 05 16.
Article in English | MEDLINE | ID: mdl-30979586

ABSTRACT

Disturbances in autophagy and stress granule dynamics have been implicated as potential mechanisms underlying inclusion body myopathy (IBM) and related disorders. Yet the roles of core autophagy proteins in IBM and stress granule dynamics remain poorly characterized. Here, we demonstrate that disrupted expression of the core autophagy proteins ULK1 and ULK2 in mice causes a vacuolar myopathy with ubiquitin and TDP-43-positive inclusions; this myopathy is similar to that caused by VCP/p97 mutations, the most common cause of familial IBM. Mechanistically, we show that ULK1/2 localize to stress granules and phosphorylate VCP, thereby increasing VCP's activity and ability to disassemble stress granules. These data suggest that VCP dysregulation and defective stress granule disassembly contribute to IBM-like disease in Ulk1/2-deficient mice. In addition, stress granule disassembly is accelerated by an ULK1/2 agonist, suggesting ULK1/2 as targets for exploiting the higher-order regulation of stress granules for therapeutic intervention of IBM and related disorders.


Subject(s)
Autophagy-Related Protein-1 Homolog/genetics , Lysosomal Storage Diseases/genetics , Muscular Diseases/genetics , Protein Serine-Threonine Kinases/genetics , Valosin Containing Protein/genetics , Adenosine Triphosphatases/genetics , Animals , Autophagy/genetics , DNA-Binding Proteins/genetics , Disease Models, Animal , Humans , Inclusion Bodies/genetics , Inclusion Bodies/pathology , Lysosomal Storage Diseases/metabolism , Lysosomal Storage Diseases/pathology , Mice , Muscular Diseases/metabolism , Muscular Diseases/pathology , Phosphorylation/genetics , Stress, Physiological/genetics , Ubiquitin/genetics
14.
Proc Natl Acad Sci U S A ; 119(38): e2206147119, 2022 09 20.
Article in English | MEDLINE | ID: mdl-36095192

ABSTRACT

The neocortex, the center for higher brain function, first emerged in mammals and has become massively expanded and folded in humans, constituting almost half the volume of the human brain. Primary microcephaly, a developmental disorder in which the brain is smaller than normal at birth, results mainly from there being fewer neurons in the neocortex because of defects in neural progenitor cells (NPCs). Outer radial glia (oRGs), NPCs that are abundant in gyrencephalic species but rare in lissencephalic species, are thought to play key roles in the expansion and folding of the neocortex. However, how oRGs expand, whether they are necessary for neocortical folding, and whether defects in oRGs cause microcephaly remain important questions in the study of brain development, evolution, and disease. Here, we show that oRG expansion in mice, ferrets, and human cerebral organoids requires cyclin-dependent kinase 6 (CDK6), the mutation of which causes primary microcephaly via an unknown mechanism. In a mouse model in which increased Hedgehog signaling expands oRGs and intermediate progenitor cells and induces neocortical folding, CDK6 loss selectively decreased oRGs and abolished neocortical folding. Remarkably, this function of CDK6 in oRG expansion did not require its kinase activity, was not shared by the highly similar CDK4 and CDK2, and was disrupted by the mutation causing microcephaly. Therefore, our results indicate that CDK6 is conserved to promote oRG expansion, that oRGs are necessary for neocortical folding, and that defects in oRG expansion may cause primary microcephaly.


Subject(s)
Cyclin-Dependent Kinase 6 , Ependymoglial Cells , Microcephaly , Neocortex , Animals , Cyclin-Dependent Kinase 6/genetics , Cyclin-Dependent Kinase 6/metabolism , Ependymoglial Cells/cytology , Ependymoglial Cells/enzymology , Ferrets , Hedgehog Proteins/metabolism , Humans , Mice , Microcephaly/genetics , Neocortex/abnormalities , Neocortex/enzymology , Neural Stem Cells/cytology , Neural Stem Cells/enzymology , Organoids/embryology
15.
BMC Biol ; 22(1): 122, 2024 May 29.
Article in English | MEDLINE | ID: mdl-38807188

ABSTRACT

BACKGROUND: The innate immune system serves as the first line of host defense. Transforming growth factor-ß-activated kinase 1 (TAK1) is a key regulator of innate immunity, cell survival, and cellular homeostasis. Because of its importance in immunity, several pathogens have evolved to carry TAK1 inhibitors. In response, hosts have evolved to sense TAK1 inhibition and induce robust lytic cell death, PANoptosis, mediated by the RIPK1-PANoptosome. PANoptosis is a unique innate immune inflammatory lytic cell death pathway initiated by an innate immune sensor and driven by caspases and RIPKs. While PANoptosis can be beneficial to clear pathogens, excess activation is linked to pathology. Therefore, understanding the molecular mechanisms regulating TAK1 inhibitor (TAK1i)-induced PANoptosis is central to our understanding of RIPK1 in health and disease. RESULTS: In this study, by analyzing results from a cell death-based CRISPR screen, we identified protein phosphatase 6 (PP6) holoenzyme components as regulators of TAK1i-induced PANoptosis. Loss of the PP6 enzymatic component, PPP6C, significantly reduced TAK1i-induced PANoptosis. Additionally, the PP6 regulatory subunits PPP6R1, PPP6R2, and PPP6R3 had redundant roles in regulating TAK1i-induced PANoptosis, and their combined depletion was required to block TAK1i-induced cell death. Mechanistically, PPP6C and its regulatory subunits promoted the pro-death S166 auto-phosphorylation of RIPK1 and led to a reduction in the pro-survival S321 phosphorylation. CONCLUSIONS: Overall, our findings demonstrate a key requirement for the phosphatase PP6 complex in the activation of TAK1i-induced, RIPK1-dependent PANoptosis, suggesting this complex could be therapeutically targeted in inflammatory conditions.


Subject(s)
Phosphoprotein Phosphatases , Receptor-Interacting Protein Serine-Threonine Kinases , Receptor-Interacting Protein Serine-Threonine Kinases/metabolism , Receptor-Interacting Protein Serine-Threonine Kinases/genetics , Humans , Phosphoprotein Phosphatases/metabolism , Phosphoprotein Phosphatases/genetics , MAP Kinase Kinase Kinases/metabolism , MAP Kinase Kinase Kinases/genetics , Necroptosis , Immunity, Innate
16.
Blood ; 139(7): 1039-1051, 2022 02 17.
Article in English | MEDLINE | ID: mdl-34767620

ABSTRACT

Human telomere biology disorders (TBD)/short telomere syndromes (STS) are heterogeneous disorders caused by inherited loss-of-function mutations in telomere-associated genes. Here, we identify 3 germline heterozygous missense variants in the RPA1 gene in 4 unrelated probands presenting with short telomeres and varying clinical features of TBD/STS, including bone marrow failure, myelodysplastic syndrome, T- and B-cell lymphopenia, pulmonary fibrosis, or skin manifestations. All variants cluster to DNA-binding domain A of RPA1 protein. RPA1 is a single-strand DNA-binding protein required for DNA replication and repair and involved in telomere maintenance. We showed that RPA1E240K and RPA1V227A proteins exhibit increased binding to single-strand and telomeric DNA, implying a gain in DNA-binding function, whereas RPA1T270A has binding properties similar to wild-type protein. To study the mutational effect in a cellular system, CRISPR/Cas9 was used to knock-in the RPA1E240K mutation into healthy inducible pluripotent stem cells. This resulted in severe telomere shortening and impaired hematopoietic differentiation. Furthermore, in patients with RPA1E240K, we discovered somatic genetic rescue in hematopoietic cells due to an acquired truncating cis RPA1 mutation or a uniparental isodisomy 17p with loss of mutant allele, coinciding with stabilized blood counts. Using single-cell sequencing, the 2 somatic genetic rescue events were proven to be independently acquired in hematopoietic stem cells. In summary, we describe the first human disease caused by germline RPA1 variants in individuals with TBD/STS.


Subject(s)
Bone Marrow Failure Disorders/pathology , Gain of Function Mutation , Heterozygote , Myelodysplastic Syndromes/pathology , Replication Protein A/genetics , Telomere Shortening , Telomere/genetics , Adolescent , Adult , Bone Marrow Failure Disorders/etiology , Bone Marrow Failure Disorders/metabolism , Cell Differentiation , Child , Female , Humans , Infant, Newborn , Male , Middle Aged , Myelodysplastic Syndromes/etiology , Myelodysplastic Syndromes/metabolism , Young Adult
17.
PLoS Biol ; 19(6): e3001281, 2021 06.
Article in English | MEDLINE | ID: mdl-34077419

ABSTRACT

Nutrient-responsive protein kinases control the balance between anabolic growth and catabolic processes such as autophagy. Aberrant regulation of these kinases is a major cause of human disease. We report here that the vertebrate nonreceptor tyrosine kinase Src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristylation sites (SRMS) inhibits autophagy and promotes growth in a nutrient-responsive manner. Under nutrient-replete conditions, SRMS phosphorylates the PHLPP scaffold FK506-binding protein 51 (FKBP51), disrupts the FKBP51-PHLPP complex, and promotes FKBP51 degradation through the ubiquitin-proteasome pathway. This prevents PHLPP-mediated dephosphorylation of AKT, causing sustained AKT activation that promotes growth and inhibits autophagy. SRMS is amplified and overexpressed in human cancers where it drives unrestrained AKT signaling in a kinase-dependent manner. SRMS kinase inhibition activates autophagy, inhibits cancer growth, and can be accomplished using the FDA-approved tyrosine kinase inhibitor ibrutinib. This illuminates SRMS as a targetable vulnerability in human cancers and as a new target for pharmacological induction of autophagy in vertebrates.


Subject(s)
Autophagy , Neoplasms/metabolism , Neoplasms/pathology , Tacrolimus Binding Proteins/metabolism , src-Family Kinases/metabolism , Adenine/analogs & derivatives , Adenine/pharmacology , Animals , Autophagy/drug effects , Beclin-1/metabolism , Cell Line, Tumor , Cell Proliferation/drug effects , Cellular Senescence/drug effects , Enzyme Activation/drug effects , Mice , Nuclear Proteins/metabolism , Phosphoprotein Phosphatases/metabolism , Phosphorylation/drug effects , Phosphotyrosine/metabolism , Piperidines/pharmacology , Protein Binding/drug effects , Proto-Oncogene Proteins c-akt/metabolism , Signal Transduction/drug effects , src-Family Kinases/antagonists & inhibitors
18.
Blood ; 138(23): 2313-2326, 2021 12 09.
Article in English | MEDLINE | ID: mdl-34110416

ABSTRACT

CRLF2-rearranged (CRLF2r) acute lymphoblastic leukemia (ALL) accounts for more than half of Philadelphia chromosome-like (Ph-like) ALL and is associated with a poor outcome in children and adults. Overexpression of CRLF2 results in activation of Janus kinase (JAK)-STAT and parallel signaling pathways in experimental models, but existing small molecule inhibitors of JAKs show variable and limited efficacy. Here, we evaluated the efficacy of proteolysis-targeting chimeras (PROTACs) directed against JAKs. Solving the structure of type I JAK inhibitors ruxolitinib and baricitinib bound to the JAK2 tyrosine kinase domain enabled the rational design and optimization of a series of cereblon (CRBN)-directed JAK PROTACs utilizing derivatives of JAK inhibitors, linkers, and CRBN-specific molecular glues. The resulting JAK PROTACs were evaluated for target degradation, and activity was tested in a panel of leukemia/lymphoma cell lines and xenograft models of kinase-driven ALL. Multiple PROTACs were developed that degraded JAKs and potently killed CRLF2r cell lines, the most active of which also degraded the known CRBN neosubstrate GSPT1 and suppressed proliferation of CRLF2r ALL in vivo, e.g. compound 7 (SJ988497). Although dual JAK/GSPT1-degrading PROTACs were the most potent, the development and evaluation of multiple PROTACs in an extended panel of xenografts identified a potent JAK2-degrading, GSPT1-sparing PROTAC that demonstrated efficacy in the majority of kinase-driven xenografts that were otherwise unresponsive to type I JAK inhibitors, e.g. compound 8 (SJ1008030). Together, these data show the potential of JAK-directed protein degradation as a therapeutic approach in JAK-STAT-driven ALL and highlight the interplay of JAK and GSPT1 degradation activity in this context.


Subject(s)
Janus Kinases/antagonists & inhibitors , Precursor Cell Lymphoblastic Leukemia-Lymphoma/drug therapy , Protein Kinase Inhibitors/pharmacology , Proteolysis/drug effects , Receptors, Cytokine/genetics , Animals , Cell Line, Tumor , Drug Discovery , Female , Gene Expression Regulation, Leukemic/drug effects , Humans , Janus Kinases/metabolism , Mice, Inbred NOD , Models, Molecular , Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics , Precursor Cell Lymphoblastic Leukemia-Lymphoma/metabolism , Protein Kinase Inhibitors/chemistry , Protein Kinase Inhibitors/therapeutic use
19.
Blood ; 137(2): 155-167, 2021 01 14.
Article in English | MEDLINE | ID: mdl-33156908

ABSTRACT

The histone mark H3K27me3 and its reader/writer polycomb repressive complex 2 (PRC2) mediate widespread transcriptional repression in stem and progenitor cells. Mechanisms that regulate this activity are critical for hematopoietic development but are poorly understood. Here we show that the E3 ubiquitin ligase F-box only protein 11 (FBXO11) relieves PRC2-mediated repression during erythroid maturation by targeting its newly identified substrate bromo adjacent homology domain-containing 1 (BAHD1), an H3K27me3 reader that recruits transcriptional corepressors. Erythroblasts lacking FBXO11 are developmentally delayed, with reduced expression of maturation-associated genes, most of which harbor bivalent histone marks at their promoters. In FBXO11-/- erythroblasts, these gene promoters bind BAHD1 and fail to recruit the erythroid transcription factor GATA1. The BAHD1 complex interacts physically with PRC2, and depletion of either component restores FBXO11-deficient erythroid gene expression. Our studies identify BAHD1 as a novel effector of PRC2-mediated repression and reveal how a single E3 ubiquitin ligase eliminates PRC2 repression at many developmentally poised bivalent genes during erythropoiesis.


Subject(s)
Chromosomal Proteins, Non-Histone/metabolism , Erythropoiesis/physiology , F-Box Proteins/metabolism , Gene Expression Regulation/physiology , Polycomb Repressive Complex 2/metabolism , Protein-Arginine N-Methyltransferases/metabolism , Cell Line , Erythroblasts/metabolism , Humans , Proteolysis
20.
J Immunol ; 207(10): 2411-2416, 2021 11 15.
Article in English | MEDLINE | ID: mdl-34663620

ABSTRACT

Programmed cell death (PCD) is essential for the innate immune response, which serves as the first line of defense against pathogens. Caspases regulate PCD, immune responses, and homeostasis. Caspase-8 specifically plays multifaceted roles in PCD pathways including pyroptosis, apoptosis, and necroptosis. However, because caspase-8-deficient mice are embryonically lethal, little is known about how caspase-8 coordinates different PCD pathways under physiological conditions. Here, we report an anti-inflammatory role of caspase-8 during influenza A virus infection. We generated viable mice carrying an uncleavable version of caspase-8 (Casp8 DA/DA). We demonstrated that caspase-8 autoprocessing was responsible for activating caspase-3, thereby suppressing gasdermin D-mediated pyroptosis and inflammatory cytokine release. We also found that apoptotic and pyroptotic pathways were activated at the same time during influenza A virus infection, which enabled the cell-intrinsic anti-inflammatory function of the caspase-8-caspase-3 axis. Our findings provide new insight into the immunological consequences of caspase-8-coordinated PCD cross-talk under physiological conditions.


Subject(s)
Caspase 3/immunology , Caspase 8/immunology , Intracellular Signaling Peptides and Proteins/immunology , Orthomyxoviridae Infections/immunology , Phosphate-Binding Proteins/immunology , Animals , Caspase 3/metabolism , Caspase 8/metabolism , Cell Death , Cytokines , Influenza A virus/immunology , Influenza A virus/metabolism , Mice , Orthomyxoviridae Infections/metabolism
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