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1.
Cell ; 186(17): 3606-3618.e16, 2023 08 17.
Artigo em Inglês | MEDLINE | ID: mdl-37480850

RESUMO

Injury induces systemic responses, but their functions remain elusive. Mechanisms that can rapidly synchronize wound responses through long distances are also mostly unknown. Using planarian flatworms capable of whole-body regeneration, we report that injury induces extracellular signal-regulated kinase (Erk) activity waves to travel at a speed 10-100 times faster than those in other multicellular tissues. This ultrafast propagation requires longitudinal body-wall muscles, elongated cells forming dense parallel tracks running the length of the organism. The morphological properties of muscles allow them to act as superhighways for propagating and disseminating wound signals. Inhibiting Erk propagation prevents tissues distant to the wound from responding and blocks regeneration, which can be rescued by a second injury to distal tissues shortly after the first injury. Our findings provide a mechanism for long-range signal propagation in large, complex tissues to coordinate responses across cell types and highlight the function of feedback between spatially separated tissues during whole-body regeneration.


Assuntos
Planárias , Regeneração , Animais , Sistema de Sinalização das MAP Quinases , Músculos , Fosforilação , Planárias/fisiologia , Processamento de Proteína Pós-Traducional
2.
Cell ; 181(3): 590-603.e16, 2020 04 30.
Artigo em Inglês | MEDLINE | ID: mdl-32272060

RESUMO

Conversion of glial cells into functional neurons represents a potential therapeutic approach for replenishing neuronal loss associated with neurodegenerative diseases and brain injury. Previous attempts in this area using expression of transcription factors were hindered by the low conversion efficiency and failure of generating desired neuronal types in vivo. Here, we report that downregulation of a single RNA-binding protein, polypyrimidine tract-binding protein 1 (Ptbp1), using in vivo viral delivery of a recently developed RNA-targeting CRISPR system CasRx, resulted in the conversion of Müller glia into retinal ganglion cells (RGCs) with a high efficiency, leading to the alleviation of disease symptoms associated with RGC loss. Furthermore, this approach also induced neurons with dopaminergic features in the striatum and alleviated motor defects in a Parkinson's disease mouse model. Thus, glia-to-neuron conversion by CasRx-mediated Ptbp1 knockdown represents a promising in vivo genetic approach for treating a variety of disorders due to neuronal loss.


Assuntos
Neurogênese/fisiologia , Neuroglia/metabolismo , Células Ganglionares da Retina/metabolismo , Animais , Sistemas CRISPR-Cas/fisiologia , Diferenciação Celular/fisiologia , Células Cultivadas , Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas/genética , Modelos Animais de Doenças , Dopamina/metabolismo , Regulação da Expressão Gênica/genética , Ribonucleoproteínas Nucleares Heterogêneas/genética , Ribonucleoproteínas Nucleares Heterogêneas/metabolismo , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Doenças do Sistema Nervoso/metabolismo , Neurônios/metabolismo , Doença de Parkinson/metabolismo , Proteína de Ligação a Regiões Ricas em Polipirimidinas/genética , Proteína de Ligação a Regiões Ricas em Polipirimidinas/metabolismo , Células Ganglionares da Retina/fisiologia
3.
Cell ; 183(4): 1013-1023.e13, 2020 11 12.
Artigo em Inglês | MEDLINE | ID: mdl-32970990

RESUMO

Understanding how potent neutralizing antibodies (NAbs) inhibit SARS-CoV-2 is critical for effective therapeutic development. We previously described BD-368-2, a SARS-CoV-2 NAb with high potency; however, its neutralization mechanism is largely unknown. Here, we report the 3.5-Å cryo-EM structure of BD-368-2/trimeric-spike complex, revealing that BD-368-2 fully blocks ACE2 recognition by occupying all three receptor-binding domains (RBDs) simultaneously, regardless of their "up" or "down" conformations. Also, BD-368-2 treats infected adult hamsters at low dosages and at various administering windows, in contrast to placebo hamsters that manifested severe interstitial pneumonia. Moreover, BD-368-2's epitope completely avoids the common binding site of VH3-53/VH3-66 recurrent NAbs, evidenced by tripartite co-crystal structures with RBDs. Pairing BD-368-2 with a potent recurrent NAb neutralizes SARS-CoV-2 pseudovirus at pM level and rescues mutation-induced neutralization escapes. Together, our results rationalized a new RBD epitope that leads to high neutralization potency and demonstrated BD-368-2's therapeutic potential in treating COVID-19.


Assuntos
Anticorpos Neutralizantes/imunologia , Anticorpos Antivirais/imunologia , Betacoronavirus/imunologia , Infecções por Coronavirus/patologia , Pneumonia Viral/patologia , Animais , Anticorpos Neutralizantes/química , Anticorpos Neutralizantes/uso terapêutico , Anticorpos Antivirais/química , Anticorpos Antivirais/uso terapêutico , Reações Antígeno-Anticorpo , Sítios de Ligação , COVID-19 , Infecções por Coronavirus/tratamento farmacológico , Infecções por Coronavirus/virologia , Cricetinae , Microscopia Crioeletrônica , Modelos Animais de Doenças , Epitopos/química , Epitopos/imunologia , Feminino , Pulmão/patologia , Masculino , Simulação de Dinâmica Molecular , Pandemias , Pneumonia Viral/tratamento farmacológico , Pneumonia Viral/virologia , Estrutura Quaternária de Proteína , SARS-CoV-2 , Glicoproteína da Espícula de Coronavírus/química , Glicoproteína da Espícula de Coronavírus/imunologia
4.
Cell ; 182(1): 245-261.e17, 2020 07 09.
Artigo em Inglês | MEDLINE | ID: mdl-32649877

RESUMO

Genomic studies of lung adenocarcinoma (LUAD) have advanced our understanding of the disease's biology and accelerated targeted therapy. However, the proteomic characteristics of LUAD remain poorly understood. We carried out a comprehensive proteomics analysis of 103 cases of LUAD in Chinese patients. Integrative analysis of proteome, phosphoproteome, transcriptome, and whole-exome sequencing data revealed cancer-associated characteristics, such as tumor-associated protein variants, distinct proteomics features, and clinical outcomes in patients at an early stage or with EGFR and TP53 mutations. Proteome-based stratification of LUAD revealed three subtypes (S-I, S-II, and S-III) related to different clinical and molecular features. Further, we nominated potential drug targets and validated the plasma protein level of HSP 90ß as a potential prognostic biomarker for LUAD in an independent cohort. Our integrative proteomics analysis enables a more comprehensive understanding of the molecular landscape of LUAD and offers an opportunity for more precise diagnosis and treatment.


Assuntos
Adenocarcinoma de Pulmão/metabolismo , Neoplasias Pulmonares/metabolismo , Proteômica , Adenocarcinoma de Pulmão/genética , Povo Asiático/genética , Biomarcadores Tumorais/genética , Biomarcadores Tumorais/metabolismo , Sistemas de Liberação de Medicamentos , Feminino , Perfilação da Expressão Gênica , Regulação Neoplásica da Expressão Gênica , Humanos , Neoplasias Pulmonares/genética , Masculino , Pessoa de Meia-Idade , Mutação/genética , Estadiamento de Neoplasias , Fosfoproteínas/metabolismo , Análise de Componente Principal , Prognóstico , Proteoma/metabolismo , Resultado do Tratamento , Proteína Supressora de Tumor p53/genética
5.
Cell ; 181(7): 1502-1517.e23, 2020 06 25.
Artigo em Inglês | MEDLINE | ID: mdl-32559462

RESUMO

RNA viruses are a major human health threat. The life cycles of many highly pathogenic RNA viruses like influenza A virus (IAV) and Lassa virus depends on host mRNA, because viral polymerases cleave 5'-m7G-capped host transcripts to prime viral mRNA synthesis ("cap-snatching"). We hypothesized that start codons within cap-snatched host transcripts could generate chimeric human-viral mRNAs with coding potential. We report the existence of this mechanism of gene origination, which we named "start-snatching." Depending on the reading frame, start-snatching allows the translation of host and viral "untranslated regions" (UTRs) to create N-terminally extended viral proteins or entirely novel polypeptides by genetic overprinting. We show that both types of chimeric proteins are made in IAV-infected cells, generate T cell responses, and contribute to virulence. Our results indicate that during infection with IAV, and likely a multitude of other human, animal and plant viruses, a host-dependent mechanism allows the genesis of hybrid genes.


Assuntos
Capuzes de RNA/genética , Infecções por Vírus de RNA/genética , Proteínas Recombinantes de Fusão/genética , Regiões 5' não Traduzidas/genética , Animais , Bovinos , Linhagem Celular , Cricetinae , Cães , Humanos , Vírus da Influenza A/metabolismo , Camundongos , Proteínas Mutantes Quiméricas/genética , Proteínas Mutantes Quiméricas/metabolismo , Fases de Leitura Aberta/genética , Capuzes de RNA/metabolismo , Infecções por Vírus de RNA/metabolismo , Vírus de RNA/genética , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , RNA Viral/metabolismo , RNA Polimerase Dependente de RNA/genética , RNA Polimerase Dependente de RNA/metabolismo , Proteínas Recombinantes de Fusão/metabolismo , Transcrição Gênica/genética , Proteínas Virais/metabolismo , Replicação Viral/genética
6.
Cell ; 177(6): 1600-1618.e17, 2019 05 30.
Artigo em Inglês | MEDLINE | ID: mdl-31150625

RESUMO

Autism spectrum disorder (ASD) manifests as alterations in complex human behaviors including social communication and stereotypies. In addition to genetic risks, the gut microbiome differs between typically developing (TD) and ASD individuals, though it remains unclear whether the microbiome contributes to symptoms. We transplanted gut microbiota from human donors with ASD or TD controls into germ-free mice and reveal that colonization with ASD microbiota is sufficient to induce hallmark autistic behaviors. The brains of mice colonized with ASD microbiota display alternative splicing of ASD-relevant genes. Microbiome and metabolome profiles of mice harboring human microbiota predict that specific bacterial taxa and their metabolites modulate ASD behaviors. Indeed, treatment of an ASD mouse model with candidate microbial metabolites improves behavioral abnormalities and modulates neuronal excitability in the brain. We propose that the gut microbiota regulates behaviors in mice via production of neuroactive metabolites, suggesting that gut-brain connections contribute to the pathophysiology of ASD.


Assuntos
Transtorno do Espectro Autista/microbiologia , Sintomas Comportamentais/microbiologia , Microbioma Gastrointestinal/fisiologia , Animais , Transtorno do Espectro Autista/metabolismo , Transtorno do Espectro Autista/fisiopatologia , Bactérias , Comportamento Animal/fisiologia , Encéfalo/metabolismo , Modelos Animais de Doenças , Humanos , Camundongos , Microbiota , Fatores de Risco
7.
Cell ; 172(1-2): 218-233.e17, 2018 01 11.
Artigo em Inglês | MEDLINE | ID: mdl-29249357

RESUMO

Signaling pathways that promote adipose tissue thermogenesis are well characterized, but the limiters of energy expenditure are largely unknown. Here, we show that ablation of the anti-inflammatory cytokine IL-10 improves insulin sensitivity, protects against diet-induced obesity, and elicits the browning of white adipose tissue. Mechanistic studies define bone marrow cells as the source of the IL-10 signal and adipocytes as the target cell type mediating these effects. IL-10 receptor alpha is highly enriched in mature adipocytes and is induced in response to differentiation, obesity, and aging. Assay for transposase-accessible chromatin sequencing (ATAC-seq), ChIP-seq, and RNA-seq reveal that IL-10 represses the transcription of thermogenic genes in adipocytes by altering chromatin accessibility and inhibiting ATF and C/EBPß recruitment to key enhancer regions. These findings expand our understanding of the relationship between inflammatory signaling pathways and adipose tissue function and provide insight into the physiological control of thermogenesis that could inform future therapy.


Assuntos
Adipócitos/metabolismo , Montagem e Desmontagem da Cromatina , Metabolismo Energético , Interleucina-10/metabolismo , Termogênese , Fatores Ativadores da Transcrição/metabolismo , Animais , Proteína beta Intensificadora de Ligação a CCAAT/metabolismo , Linhagem Celular , Células Cultivadas , Interleucina-10/genética , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Transdução de Sinais
8.
Cell ; 169(7): 1291-1302.e14, 2017 Jun 15.
Artigo em Inglês | MEDLINE | ID: mdl-28602353

RESUMO

The emergence of sensory-guided behavior depends on sensorimotor coupling during development. How sensorimotor experience shapes neural processing is unclear. Here, we show that the coupling between motor output and visual feedback is necessary for the functional development of visual processing in layer 2/3 (L2/3) of primary visual cortex (V1) of the mouse. Using a virtual reality system, we reared mice in conditions of normal or random visuomotor coupling. We recorded the activity of identified excitatory and inhibitory L2/3 neurons in response to transient visuomotor mismatches in both groups of mice. Mismatch responses in excitatory neurons were strongly experience dependent and driven by a transient release from inhibition mediated by somatostatin-positive interneurons. These data are consistent with a model in which L2/3 of V1 computes a difference between an inhibitory visual input and an excitatory locomotion-related input, where the balance between these two inputs is finely tuned by visuomotor experience.


Assuntos
Desempenho Psicomotor , Córtex Visual/fisiologia , Animais , Retroalimentação Sensorial , Feminino , Interneurônios/citologia , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Neurônios/citologia , Optogenética , Estimulação Luminosa , Córtex Visual/citologia , Percepção Visual
9.
Immunity ; 55(5): 862-878.e8, 2022 05 10.
Artigo em Inglês | MEDLINE | ID: mdl-35508166

RESUMO

Macrophage colony stimulating factor-1 (CSF-1) plays a critical role in maintaining myeloid lineage cells. However, congenital global deficiency of CSF-1 (Csf1op/op) causes severe musculoskeletal defects that may indirectly affect hematopoiesis. Indeed, we show here that osteolineage-derived Csf1 prevented developmental abnormalities but had no effect on monopoiesis in adulthood. However, ubiquitous deletion of Csf1 conditionally in adulthood decreased monocyte survival, differentiation, and migration, independent of its effects on bone development. Bone histology revealed that monocytes reside near sinusoidal endothelial cells (ECs) and leptin receptor (Lepr)-expressing perivascular mesenchymal stromal cells (MSCs). Targeted deletion of Csf1 from sinusoidal ECs selectively reduced Ly6C- monocytes, whereas combined depletion of Csf1 from ECs and MSCs further decreased Ly6Chi cells. Moreover, EC-derived CSF-1 facilitated recovery of Ly6C- monocytes and protected mice from weight loss following induction of polymicrobial sepsis. Thus, monocytes are supported by distinct cellular sources of CSF-1 within a perivascular BM niche.


Assuntos
Fator Estimulador de Colônias de Macrófagos , Células-Tronco Mesenquimais , Animais , Medula Óssea , Células da Medula Óssea , Células Endoteliais , Fator Estimulador de Colônias de Macrófagos/farmacologia , Camundongos , Monócitos
10.
Mol Cell ; 83(17): 3171-3187.e7, 2023 09 07.
Artigo em Inglês | MEDLINE | ID: mdl-37597514

RESUMO

Hydroxycarboxylic acid receptor 2 (HCAR2), modulated by endogenous ketone body ß-hydroxybutyrate and exogenous niacin, is a promising therapeutic target for inflammation-related diseases. HCAR2 mediates distinct pathophysiological events by activating Gi/o protein or ß-arrestin effectors. Here, we characterize compound 9n as a Gi-biased allosteric modulator (BAM) of HCAR2 and exhibit anti-inflammatory efficacy in RAW264.7 macrophages via a specific HCAR2-Gi pathway. Furthermore, four structures of HCAR2-Gi complex bound to orthosteric agonists (niacin or monomethyl fumarate), compound 9n, and niacin together with compound 9n simultaneously reveal a common orthosteric site and a unique allosteric site. Combined with functional studies, we decipher the action framework of biased allosteric modulation of compound 9n on the orthosteric site. Moreover, co-administration of compound 9n with orthosteric agonists could enhance anti-inflammatory effects in the mouse model of colitis. Together, our study provides insight to understand the molecular pharmacology of the BAM and facilitates exploring the therapeutic potential of the BAM with orthosteric drugs.


Assuntos
Colite , Receptores Acoplados a Proteínas G , Animais , Camundongos , Regulação Alostérica , Colite/induzido quimicamente , Colite/tratamento farmacológico , Colite/metabolismo , Subunidades alfa Gi-Go de Proteínas de Ligação ao GTP , Inflamação/tratamento farmacológico , Corpos Cetônicos , Niacina/farmacologia , Receptores Acoplados a Proteínas G/agonistas , Receptores Acoplados a Proteínas G/metabolismo
11.
Trends Biochem Sci ; 49(6): 494-505, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38565496

RESUMO

Autophagy - a highly regulated intracellular degradation process - is pivotal in maintaining cellular homeostasis. Liquid-liquid phase separation (LLPS) is a fundamental mechanism regulating the formation and function of membrane-less compartments. Recent research has unveiled connections between LLPS and autophagy, suggesting that phase separation events may orchestrate the spatiotemporal organization of autophagic machinery and cargo sequestration. The Unc-51-like kinase (ULK)/autophagy-related 1 (Atg1) family of proteins is best known for its regulatory role in initiating autophagy, but there is growing evidence that the functional spectrum of ULK/Atg1 extends beyond autophagy regulation. In this review, we explore the spatial and temporal regulation of the ULK/Atg1 family of kinases, focusing on their recruitment to LLPS-driven compartments, and highlighting their multifaceted functions beyond their traditional role.


Assuntos
Proteína Homóloga à Proteína-1 Relacionada à Autofagia , Autofagia , Humanos , Proteína Homóloga à Proteína-1 Relacionada à Autofagia/metabolismo , Animais , Proteínas Serina-Treonina Quinases/metabolismo , Proteínas Serina-Treonina Quinases/química
12.
Nature ; 609(7925): 197-203, 2022 09.
Artigo em Inglês | MEDLINE | ID: mdl-35882349

RESUMO

Archaea synthesize isoprenoid-based ether-linked membrane lipids, which enable them to withstand extreme environmental conditions, such as high temperatures, high salinity, and low or high pH values1-5. In some archaea, such as Methanocaldococcus jannaschii, these lipids are further modified by forming carbon-carbon bonds between the termini of two lipid tails within one glycerophospholipid to generate the macrocyclic archaeol or forming two carbon-carbon bonds between the termini of two lipid tails from two glycerophospholipids to generate the macrocycle glycerol dibiphytanyl glycerol tetraether (GDGT)1,2. GDGT contains two 40-carbon lipid chains (biphytanyl chains) that span both leaflets of the membrane, providing enhanced stability to extreme conditions. How these specialized lipids are formed has puzzled scientists for decades. The reaction necessitates the coupling of two completely inert sp3-hybridized carbon centres, which, to our knowledge, has not been observed in nature. Here we show that the gene product of mj0619 from M. jannaschii, which encodes a radical S-adenosylmethionine enzyme, is responsible for biphytanyl chain formation during synthesis of both the macrocyclic archaeol and GDGT membrane lipids6. Structures of the enzyme show the presence of four metallocofactors: three [Fe4S4] clusters and one mononuclear rubredoxin-like iron ion. In vitro mechanistic studies show that Csp3-Csp3 bond formation takes place on fully saturated archaeal lipid substrates and involves an intermediate bond between the substrate carbon and a sulfur of one of the [Fe4S4] clusters. Our results not only establish the biosynthetic route for tetraether formation but also improve the use of GDGT in GDGT-based paleoclimatology indices7-10.


Assuntos
Proteínas Arqueais , Éteres de Glicerila , Lipídeos de Membrana , Methanocaldococcus , Proteínas Arqueais/química , Proteínas Arqueais/isolamento & purificação , Proteínas Arqueais/metabolismo , Carbono/química , Carbono/metabolismo , Glicerol/química , Glicerol/metabolismo , Éteres de Glicerila/química , Éteres de Glicerila/metabolismo , Lipídeos de Membrana/biossíntese , Lipídeos de Membrana/química , Lipídeos de Membrana/metabolismo , Methanocaldococcus/química , Methanocaldococcus/enzimologia , Methanocaldococcus/metabolismo , S-Adenosilmetionina/metabolismo , Terpenos/química , Terpenos/metabolismo
13.
Nature ; 604(7907): 723-731, 2022 04.
Artigo em Inglês | MEDLINE | ID: mdl-35418686

RESUMO

Studying tissue composition and function in non-human primates (NHPs) is crucial to understand the nature of our own species. Here we present a large-scale cell transcriptomic atlas that encompasses over 1 million cells from 45 tissues of the adult NHP Macaca fascicularis. This dataset provides a vast annotated resource to study a species phylogenetically close to humans. To demonstrate the utility of the atlas, we have reconstructed the cell-cell interaction networks that drive Wnt signalling across the body, mapped the distribution of receptors and co-receptors for viruses causing human infectious diseases, and intersected our data with human genetic disease orthologues to establish potential clinical associations. Our M. fascicularis cell atlas constitutes an essential reference for future studies in humans and NHPs.


Assuntos
Macaca fascicularis , Transcriptoma , Animais , Comunicação Celular , Macaca fascicularis/genética , Receptores Virais/genética , Transcriptoma/genética , Via de Sinalização Wnt
14.
Nature ; 607(7917): 97-103, 2022 07.
Artigo em Inglês | MEDLINE | ID: mdl-35255492

RESUMO

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2-4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes-including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)-in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease.


Assuntos
COVID-19 , Estado Terminal , Genoma Humano , Interações Hospedeiro-Patógeno , Sequenciamento Completo do Genoma , Transportadores de Cassetes de Ligação de ATP , COVID-19/genética , COVID-19/mortalidade , COVID-19/patologia , COVID-19/virologia , Moléculas de Adesão Celular , Cuidados Críticos , Estado Terminal/mortalidade , Selectina E , Fator VIII , Fucosiltransferases , Genoma Humano/genética , Estudo de Associação Genômica Ampla , Interações Hospedeiro-Patógeno/genética , Humanos , Subunidade beta de Receptor de Interleucina-10 , Lectinas Tipo C , Mucina-1 , Proteínas do Tecido Nervoso , Proteínas de Transferência de Fosfolipídeos , Receptores de Superfície Celular , Proteínas Repressoras , SARS-CoV-2/patogenicidade , Galactosídeo 2-alfa-L-Fucosiltransferase
15.
Development ; 151(20)2024 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-38477640

RESUMO

Teleost testis development during the annual cycle involves dramatic changes in cellular compositions and molecular events. In this study, the testicular cells derived from adult black rockfish at distinct stages - regressed, regenerating and differentiating - were meticulously dissected via single-cell transcriptome sequencing. A continuous developmental trajectory of spermatogenic cells, from spermatogonia to spermatids, was delineated, elucidating the molecular events involved in spermatogenesis. Subsequently, the dynamic regulation of gene expression associated with spermatogonia proliferation and differentiation was observed across spermatogonia subgroups and developmental stages. A bioenergetic transition from glycolysis to mitochondrial respiration of spermatogonia during the annual developmental cycle was demonstrated, and a deeper level of heterogeneity and molecular characteristics was revealed by re-clustering analysis. Additionally, the developmental trajectory of Sertoli cells was delineated, alongside the divergence of Leydig cells and macrophages. Moreover, the interaction network between testicular micro-environment somatic cells and spermatogenic cells was established. Overall, our study provides detailed information on both germ and somatic cells within teleost testes during the annual reproductive cycle, which lays the foundation for spermatogenesis regulation and germplasm preservation of endangered species.


Assuntos
Espermatogônias , Testículo , Adulto , Masculino , Humanos , Células Intersticiais do Testículo , Células de Sertoli , Espermatogênese
16.
Nat Methods ; 21(8): 1470-1480, 2024 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-38409223

RESUMO

Generative pretrained models have achieved remarkable success in various domains such as language and computer vision. Specifically, the combination of large-scale diverse datasets and pretrained transformers has emerged as a promising approach for developing foundation models. Drawing parallels between language and cellular biology (in which texts comprise words; similarly, cells are defined by genes), our study probes the applicability of foundation models to advance cellular biology and genetic research. Using burgeoning single-cell sequencing data, we have constructed a foundation model for single-cell biology, scGPT, based on a generative pretrained transformer across a repository of over 33 million cells. Our findings illustrate that scGPT effectively distills critical biological insights concerning genes and cells. Through further adaptation of transfer learning, scGPT can be optimized to achieve superior performance across diverse downstream applications. This includes tasks such as cell type annotation, multi-batch integration, multi-omic integration, perturbation response prediction and gene network inference.


Assuntos
Análise de Célula Única , Análise de Célula Única/métodos , Humanos , Biologia Computacional/métodos , Inteligência Artificial , Redes Reguladoras de Genes , Algoritmos , Multiômica
17.
Nat Methods ; 21(8): 1430-1443, 2024 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-39122952

RESUMO

Recent efforts to construct reference maps of cellular phenotypes have expanded the volume and diversity of single-cell omics data, providing an unprecedented resource for studying cell properties. Despite the availability of rich datasets and their continued growth, current single-cell models are unable to fully capitalize on the information they contain. Transformers have become the architecture of choice for foundation models in other domains owing to their ability to generalize to heterogeneous, large-scale datasets. Thus, the question arises of whether transformers could set off a similar shift in the field of single-cell modeling. Here we first describe the transformer architecture and its single-cell adaptations and then present a comprehensive review of the existing applications of transformers in single-cell analysis and critically discuss their future potential for single-cell biology. By studying limitations and technical challenges, we aim to provide a structured outlook for future research directions at the intersection of machine learning and single-cell biology.


Assuntos
Análise de Célula Única , Análise de Célula Única/métodos , Humanos , Aprendizado de Máquina , Animais , Biologia Computacional/métodos , Genômica/métodos
18.
Nat Methods ; 21(6): 1103-1113, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38532015

RESUMO

Cell segmentation is a critical step for quantitative single-cell analysis in microscopy images. Existing cell segmentation methods are often tailored to specific modalities or require manual interventions to specify hyper-parameters in different experimental settings. Here, we present a multimodality cell segmentation benchmark, comprising more than 1,500 labeled images derived from more than 50 diverse biological experiments. The top participants developed a Transformer-based deep-learning algorithm that not only exceeds existing methods but can also be applied to diverse microscopy images across imaging platforms and tissue types without manual parameter adjustments. This benchmark and the improved algorithm offer promising avenues for more accurate and versatile cell analysis in microscopy imaging.


Assuntos
Algoritmos , Aprendizado Profundo , Processamento de Imagem Assistida por Computador , Análise de Célula Única , Análise de Célula Única/métodos , Processamento de Imagem Assistida por Computador/métodos , Humanos , Microscopia/métodos , Animais
19.
Nature ; 597(7877): 566-570, 2021 09.
Artigo em Inglês | MEDLINE | ID: mdl-34526715

RESUMO

Numerous post-transcriptional modifications of transfer RNAs have vital roles in translation. The 2-methylthio-N6-isopentenyladenosine (ms2i6A) modification occurs at position 37 (A37) in transfer RNAs that contain adenine in position 36 of the anticodon, and serves to promote efficient A:U codon-anticodon base-pairing and to prevent unintended base pairing by near cognates, thus enhancing translational fidelity1-4. The ms2i6A modification is installed onto isopentenyladenosine (i6A) by MiaB, a radical S-adenosylmethionine (SAM) methylthiotransferase. As a radical SAM protein, MiaB contains one [Fe4S4]RS cluster used in the reductive cleavage of SAM to form a 5'-deoxyadenosyl 5'-radical, which is responsible for removing the C2 hydrogen of the substrate5. MiaB also contains an auxiliary [Fe4S4]aux cluster, which has been implicated6-9 in sulfur transfer to C2 of i6A37. How this transfer takes place is largely unknown. Here we present several structures of MiaB from Bacteroides uniformis. These structures are consistent with a two-step mechanism, in which one molecule of SAM is first used to methylate a bridging µ-sulfido ion of the auxiliary cluster. In the second step, a second SAM molecule is cleaved to a 5'-deoxyadenosyl 5'-radical, which abstracts the C2 hydrogen of the substrate but only after C2 has undergone rehybridization from sp2 to sp3. This work advances our understanding of how enzymes functionalize inert C-H bonds with sulfur.


Assuntos
Bacteroides/enzimologia , Metiltransferases/química , RNA de Transferência/química , RNA de Transferência/metabolismo , S-Adenosilmetionina/metabolismo , Compostos de Sulfidrila/metabolismo , Sulfurtransferases/química , Adenosina/análogos & derivados , Adenosina/metabolismo , Sítios de Ligação , Biocatálise , Isopenteniladenosina/metabolismo , Metiltransferases/metabolismo , Modelos Moleculares , Domínios Proteicos , RNA/metabolismo , Proteínas de Ligação a RNA/química , Proteínas de Ligação a RNA/metabolismo , Especificidade por Substrato , Sulfurtransferases/metabolismo
20.
Nature ; 591(7848): 92-98, 2021 03.
Artigo em Inglês | MEDLINE | ID: mdl-33307546

RESUMO

Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079, P = 1.65 × 10-8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1, OAS2 and OAS3); on chromosome 19p13.2 (rs74956615, P = 2.3 × 10-8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069, P = 3.98 ×  10-12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757, P = 4.99 × 10-8) in the interferon receptor gene IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of IFNAR2, or high expression of TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte-macrophage chemotactic receptor CCR2 is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice.


Assuntos
COVID-19/genética , COVID-19/fisiopatologia , Estado Terminal , 2',5'-Oligoadenilato Sintetase/genética , COVID-19/patologia , Cromossomos Humanos Par 12/genética , Cromossomos Humanos Par 19/genética , Cromossomos Humanos Par 21/genética , Cuidados Críticos , Dipeptidil Peptidases e Tripeptidil Peptidases/genética , Reposicionamento de Medicamentos , Feminino , Estudo de Associação Genômica Ampla , Humanos , Inflamação/genética , Inflamação/patologia , Inflamação/fisiopatologia , Pulmão/patologia , Pulmão/fisiopatologia , Pulmão/virologia , Masculino , Família Multigênica/genética , Receptor de Interferon alfa e beta/genética , Receptores CCR2/genética , TYK2 Quinase/genética , Reino Unido
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