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1.
Cell ; 185(14): 2478-2494.e28, 2022 07 07.
Artículo en Inglés | MEDLINE | ID: mdl-35662413

RESUMEN

Glucagon-like peptide-1 (GLP-1) is a signal peptide released from enteroendocrine cells of the lower intestine. GLP-1 exerts anorectic and antimotility actions that protect the body against nutrient malabsorption. However, little is known about how intestinal GLP-1 affects distant organs despite rapid enzymatic inactivation. We show that intestinal GLP-1 inhibits gastric emptying and eating via intestinofugal neurons, a subclass of myenteric neurons that project to abdominal sympathetic ganglia. Remarkably, cell-specific ablation of intestinofugal neurons eliminated intestinal GLP-1 effects, and their chemical activation functioned as a GLP-1 mimetic. GLP-1 sensing by intestinofugal neurons then engaged a sympatho-gastro-spinal-reticular-hypothalamic pathway that links abnormal stomach distension to craniofacial programs for food rejection. Within this pathway, cell-specific activation of discrete neuronal populations caused systemic GLP-1-like effects. These molecularly identified, delimited enteric circuits may be targeted to ameliorate the abdominal bloating and loss of appetite typical of gastric motility disorders.


Asunto(s)
Apetito , Péptido 1 Similar al Glucagón/metabolismo , Íleon , Neuronas , Estómago , Abdomen , Animales , Comunicación Celular , Receptor del Péptido 1 Similar al Glucagón/metabolismo , Íleon/inervación , Íleon/metabolismo , Masculino , Ratones , Neuronas/metabolismo , Óxido Nítrico/metabolismo , Transducción de Señal , Estómago/inervación , Estómago/metabolismo
2.
Nat Immunol ; 25(3): 483-495, 2024 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-38177283

RESUMEN

Tumor cells and surrounding immune cells undergo metabolic reprogramming, leading to an acidic tumor microenvironment. However, it is unclear how tumor cells adapt to this acidic stress during tumor progression. Here we show that carnosine, a mobile buffering metabolite that accumulates under hypoxia in tumor cells, regulates intracellular pH homeostasis and drives lysosome-dependent tumor immune evasion. A previously unrecognized isoform of carnosine synthase, CARNS2, promotes carnosine synthesis under hypoxia. Carnosine maintains intracellular pH (pHi) homeostasis by functioning as a mobile proton carrier to accelerate cytosolic H+ mobility and release, which in turn controls lysosomal subcellular distribution, acidification and activity. Furthermore, by maintaining lysosomal activity, carnosine facilitates nuclear transcription factor X-box binding 1 (NFX1) degradation, triggering galectin-9 and T-cell-mediated immune escape and tumorigenesis. These findings indicate an unconventional mechanism for pHi regulation in cancer cells and demonstrate how lysosome contributes to immune evasion, thus providing a basis for development of combined therapeutic strategies against hepatocellular carcinoma that exploit disrupted pHi homeostasis with immune checkpoint blockade.


Asunto(s)
Carcinoma Hepatocelular , Carnosina , Neoplasias Hepáticas , Humanos , Homeostasis , Lisosomas , Hipoxia , Concentración de Iones de Hidrógeno , Microambiente Tumoral
3.
Cell ; 183(7): 1867-1883.e26, 2020 12 23.
Artículo en Inglés | MEDLINE | ID: mdl-33248023

RESUMEN

Biliary atresia (BA) is a severe cholangiopathy that leads to liver failure in infants, but its pathogenesis remains to be fully characterized. By single-cell RNA profiling, we observed macrophage hypo-inflammation, Kupffer cell scavenger function defects, cytotoxic T cell expansion, and deficiency of CX3CR1+effector T and natural killer (NK) cells in infants with BA. More importantly, we discovered that hepatic B cell lymphopoiesis did not cease after birth and that tolerance defects contributed to immunoglobulin G (IgG)-autoantibody accumulation in BA. In a rhesus-rotavirus induced BA model, depleting B cells or blocking antigen presentation ameliorated liver damage. In a pilot clinical study, we demonstrated that rituximab was effective in depleting hepatic B cells and restoring the functions of macrophages, Kupffer cells, and T cells to levels comparable to those of control subjects. In summary, our comprehensive immune profiling in infants with BA had educed that B-cell-modifying therapies may alleviate liver pathology.


Asunto(s)
Atresia Biliar/inmunología , Atresia Biliar/terapia , Hígado/inmunología , Animales , Antígenos CD20/metabolismo , Linfocitos B/inmunología , Atresia Biliar/sangre , Atresia Biliar/tratamiento farmacológico , Biopsia , Receptor 1 de Quimiocinas CX3C/metabolismo , Muerte Celular , Línea Celular , Proliferación Celular , Transdiferenciación Celular , Niño , Preescolar , Estudios de Cohortes , Citotoxicidad Inmunológica , Modelos Animales de Enfermedad , Femenino , Humanos , Inmunoglobulina G/metabolismo , Lactante , Inflamación/patología , Células Asesinas Naturales/inmunología , Macrófagos del Hígado/patología , Hígado/patología , Cirrosis Hepática/sangre , Cirrosis Hepática/complicaciones , Cirrosis Hepática/inmunología , Cirrosis Hepática/patología , Depleción Linfocítica , Linfopoyesis , Masculino , Ratones Endogámicos BALB C , Fagocitosis , ARN/metabolismo , Rituximab/administración & dosificación , Rituximab/farmacología , Rituximab/uso terapéutico , Rotavirus/fisiología , Análisis de la Célula Individual , Células TH1/inmunología , Células Th17/inmunología
4.
Cell ; 176(5): 1098-1112.e18, 2019 02 21.
Artículo en Inglés | MEDLINE | ID: mdl-30794774

RESUMEN

Increased levels of intestinal bile acids (BAs) are a risk factor for colorectal cancer (CRC). Here, we show that the convergence of dietary factors (high-fat diet) and dysregulated WNT signaling (APC mutation) alters BA profiles to drive malignant transformations in Lgr5-expressing (Lgr5+) cancer stem cells and promote an adenoma-to-adenocarcinoma progression. Mechanistically, we show that BAs that antagonize intestinal farnesoid X receptor (FXR) function, including tauro-ß-muricholic acid (T-ßMCA) and deoxycholic acid (DCA), induce proliferation and DNA damage in Lgr5+ cells. Conversely, selective activation of intestinal FXR can restrict abnormal Lgr5+ cell growth and curtail CRC progression. This unexpected role for FXR in coordinating intestinal self-renewal with BA levels implicates FXR as a potential therapeutic target for CRC.


Asunto(s)
Neoplasias Intestinales/metabolismo , Células Madre Neoplásicas/metabolismo , Receptores Citoplasmáticos y Nucleares/metabolismo , Animales , Ácidos y Sales Biliares/metabolismo , Línea Celular , Proliferación Celular/genética , Neoplasias Colorrectales/metabolismo , Ácido Desoxicólico/metabolismo , Regulación Neoplásica de la Expresión Génica/genética , Humanos , Neoplasias Intestinales/genética , Intestinos , Hígado , Ratones , Ratones Endogámicos C57BL , Células Madre Neoplásicas/fisiología , Organoides/metabolismo , Receptores Citoplasmáticos y Nucleares/genética , Factores de Riesgo , Transducción de Señal , Ácido Taurocólico/análogos & derivados , Ácido Taurocólico/metabolismo , Vía de Señalización Wnt/genética , Vía de Señalización Wnt/fisiología
5.
Immunity ; 54(7): 1611-1621.e5, 2021 07 13.
Artículo en Inglés | MEDLINE | ID: mdl-34166623

RESUMEN

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants continue to emerge during the global pandemic and may facilitate escape from current antibody therapies and vaccine protection. Here we showed that the South African variant B.1.351 was the most resistant to current monoclonal antibodies and convalescent plasma from coronavirus disease 2019 (COVID-19)-infected individuals, followed by the Brazilian variant P.1 and the United Kingdom variant B.1.1.7. This resistance hierarchy corresponded with Y144del and 242-244del mutations in the N-terminal domain and K417N/T, E484K, and N501Y mutations in the receptor-binding domain (RBD) of SARS-CoV-2. Crystal structure analysis of the B.1.351 triple mutant (417N-484K-501Y) RBD complexed with the monoclonal antibody P2C-1F11 revealed the molecular basis for antibody neutralization and escape. B.1.351 and P.1 also acquired the ability to use mouse and mink ACE2 receptors for entry. Our results demonstrate major antigenic shifts and potential broadening of the host range for B.1.351 and P.1 variants, which poses serious challenges to current antibody therapies and vaccine protection.


Asunto(s)
Enzima Convertidora de Angiotensina 2/metabolismo , Anticuerpos Neutralizantes/inmunología , Evasión Inmune , SARS-CoV-2/inmunología , Animales , Anticuerpos Monoclonales/química , Anticuerpos Monoclonales/inmunología , Anticuerpos Neutralizantes/química , Variación Antigénica/genética , COVID-19/inmunología , COVID-19/virología , Especificidad del Huésped , Humanos , Evasión Inmune/genética , Ratones , Visón , Mutación , Unión Proteica , SARS-CoV-2/genética , SARS-CoV-2/fisiología , Glicoproteína de la Espiga del Coronavirus/química , Glicoproteína de la Espiga del Coronavirus/genética , Glicoproteína de la Espiga del Coronavirus/inmunología , Glicoproteína de la Espiga del Coronavirus/metabolismo , Internalización del Virus
6.
Mol Cell ; 81(23): 4942-4953.e8, 2021 12 02.
Artículo en Inglés | MEDLINE | ID: mdl-34655516

RESUMEN

The distribution, dynamics, and function of RNA structures in human development are under-explored. Here, we systematically assayed RNA structural dynamics and their relationship with gene expression, translation, and decay during human neurogenesis. We observed that the human ESC transcriptome is globally more structurally accessible than differentiated cells and undergoes extensive RNA structure changes, particularly in the 3' UTR. Additionally, RNA structure changes during differentiation are associated with translation and decay. We observed that RBP and miRNA binding is associated with RNA structural changes during early neuronal differentiation, and splicing is associated during later neuronal differentiation. Furthermore, our analysis suggests that RBPs are major factors in structure remodeling and co-regulate additional RBPs and miRNAs through structure. We demonstrated an example of this by showing that PUM2-induced structure changes on LIN28A enable miR-30 binding. This study deepens our understanding of the widespread and complex role of RNA-based gene regulation during human development.


Asunto(s)
Redes Reguladoras de Genes , Estudio de Asociación del Genoma Completo , Neurogénesis , Neuronas/metabolismo , Transcripción Genética , Regiones no Traducidas 3' , Diferenciación Celular , Análisis por Conglomerados , Técnicas Genéticas , Células HEK293 , Humanos , MicroARNs/metabolismo , Modelos Estadísticos , Neuronas/fisiología , Conformación de Ácido Nucleico , ARN/análisis , Empalme del ARN , Proteínas de Unión al ARN/metabolismo , Especificidad por Sustrato , Biología de Sistemas , Transcriptoma
7.
Mol Cell ; 81(11): 2290-2302.e7, 2021 06 03.
Artículo en Inglés | MEDLINE | ID: mdl-33831358

RESUMEN

Cancer cells adapt their metabolism to support elevated energetic and anabolic demands of proliferation. Folate-dependent one-carbon metabolism is a critical metabolic process underpinning cellular proliferation supplying carbons for the synthesis of nucleotides incorporated into DNA and RNA. Recent research has focused on the nutrients that supply one-carbons to the folate cycle, particularly serine. Tryptophan is a theoretical source of one-carbon units through metabolism by IDO1, an enzyme intensively investigated in the context of tumor immune evasion. Using in vitro and in vivo pancreatic cancer models, we show that IDO1 expression is highly context dependent, influenced by attachment-independent growth and the canonical activator IFNγ. In IDO1-expressing cancer cells, tryptophan is a bona fide one-carbon donor for purine nucleotide synthesis in vitro and in vivo. Furthermore, we show that cancer cells release tryptophan-derived formate, which can be used by pancreatic stellate cells to support purine nucleotide synthesis.


Asunto(s)
Carcinoma Ductal Pancreático/genética , Indolamina-Pirrol 2,3,-Dioxigenasa/genética , Neoplasias Pancreáticas/genética , Células Estrelladas Pancreáticas/metabolismo , Escape del Tumor/efectos de los fármacos , Aloinjertos , Animales , Antineoplásicos/farmacología , Carbono/inmunología , Carbono/metabolismo , Carcinoma Ductal Pancreático/tratamiento farmacológico , Carcinoma Ductal Pancreático/inmunología , Carcinoma Ductal Pancreático/mortalidad , Línea Celular Tumoral , Formiatos/inmunología , Formiatos/metabolismo , Regulación Neoplásica de la Expresión Génica , Humanos , Indolamina-Pirrol 2,3,-Dioxigenasa/inmunología , Interferón gamma/genética , Interferón gamma/inmunología , Redes y Vías Metabólicas/efectos de los fármacos , Redes y Vías Metabólicas/genética , Ratones , Ratones Endogámicos C57BL , Ratones Desnudos , Oximas/farmacología , Neoplasias Pancreáticas/tratamiento farmacológico , Neoplasias Pancreáticas/inmunología , Neoplasias Pancreáticas/mortalidad , Células Estrelladas Pancreáticas/efectos de los fármacos , Células Estrelladas Pancreáticas/inmunología , Proteínas Proto-Oncogénicas p21(ras)/genética , Proteínas Proto-Oncogénicas p21(ras)/inmunología , Serina/inmunología , Serina/metabolismo , Serina/farmacología , Transducción de Señal , Sulfonamidas/farmacología , Triptófano/inmunología , Triptófano/metabolismo , Triptófano/farmacología , Proteína p53 Supresora de Tumor/genética , Proteína p53 Supresora de Tumor/inmunología
8.
Nature ; 612(7938): 132-140, 2022 12.
Artículo en Inglés | MEDLINE | ID: mdl-36385533

RESUMEN

Bacteria have evolved diverse immunity mechanisms to protect themselves against the constant onslaught of bacteriophages1-3. Similar to how eukaryotic innate immune systems sense foreign invaders through pathogen-associated molecular patterns4 (PAMPs), many bacterial immune systems that respond to bacteriophage infection require phage-specific triggers to be activated. However, the identities of such triggers and the sensing mechanisms remain largely unknown. Here we identify and investigate the anti-phage function of CapRelSJ46, a fused toxin-antitoxin system that protects Escherichia coli against diverse phages. Using genetic, biochemical and structural analyses, we demonstrate that the C-terminal domain of CapRelSJ46 regulates the toxic N-terminal region, serving as both antitoxin and phage infection sensor. Following infection by certain phages, newly synthesized major capsid protein binds directly to the C-terminal domain of CapRelSJ46 to relieve autoinhibition, enabling the toxin domain to pyrophosphorylate tRNAs, which blocks translation to restrict viral infection. Collectively, our results reveal the molecular mechanism by which a bacterial immune system directly senses a conserved, essential component of phages, suggesting a PAMP-like sensing model for toxin-antitoxin-mediated innate immunity in bacteria. We provide evidence that CapRels and their phage-encoded triggers are engaged in a 'Red Queen conflict'5, revealing a new front in the intense coevolutionary battle between phages and bacteria. Given that capsid proteins of some eukaryotic viruses are known to stimulate innate immune signalling in mammalian hosts6-10, our results reveal a deeply conserved facet of immunity.


Asunto(s)
Bacteriófagos , Proteínas de la Cápside , Escherichia coli , Inmunidad Innata , Animales , Antitoxinas/inmunología , Bacteriófagos/inmunología , Proteínas de la Cápside/inmunología , Escherichia coli/inmunología , Escherichia coli/virología , Eucariontes/inmunología , Moléculas de Patrón Molecular Asociado a Patógenos/inmunología
9.
Genome Res ; 34(1): 134-144, 2024 02 07.
Artículo en Inglés | MEDLINE | ID: mdl-38191205

RESUMEN

Large-scale genetic mutant libraries are powerful approaches to interrogating genotype-phenotype correlations and identifying genes responsible for certain environmental stimuli, both of which are the central goal of life science study. We produced the first large-scale CRISPR-Cas9-induced library in a nonmodel multicellular organism, Bombyx mori We developed a piggyBac-delivered binary genome editing strategy, which can simultaneously meet the requirements of mixed microinjection, efficient multipurpose genetic operation, and preservation of growth-defect lines. We constructed a single-guide RNA (sgRNA) plasmid library containing 92,917 sgRNAs targeting promoters and exons of 14,645 protein-coding genes, established 1726 transgenic sgRNA lines following microinjection of 66,650 embryos, and generated 300 mutant lines with diverse phenotypic changes. Phenomic characterization of mutant lines identified a large set of genes responsible for visual phenotypic or economically valuable trait changes. Next, we performed pooled context-specific positive screens for tolerance to environmental pollutant cadmium exposure, and identified KWMTBOMO12902 as a strong candidate gene for breeding applications in sericulture industry. Collectively, our results provide a novel and versatile approach for functional B. mori genomics, as well as a powerful resource for identifying the potential of key candidate genes for improving various economic traits. This study also shows the effectiveness, practicality, and convenience of large-scale mutant libraries in other nonmodel organisms.


Asunto(s)
Bombyx , Animales , Bombyx/genética , ARN Guía de Sistemas CRISPR-Cas , Mutagénesis , Edición Génica/métodos , Animales Modificados Genéticamente/genética , Sistemas CRISPR-Cas
10.
Nat Methods ; 21(3): 411-422, 2024 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-38177506

RESUMEN

RNA structure is critical for multiple steps in gene regulation. However, how the structures of transcripts differ both within and between individual cells is unknown. Here we develop a SHAPE-inspired method called single-cell structure probing of RNA transcripts that enables simultaneous determination of transcript secondary structure and abundance at single-cell resolution. We apply single-cell structure probing of RNA transcripts to human embryonic stem cells and differentiating neurons. Remarkably, RNA structure is more homogeneous in human embryonic stem cells compared with neurons, with the greatest homogeneity found in coding regions. More extensive heterogeneity is found within 3' untranslated regions and is determined by specific RNA-binding proteins. Overall RNA structure profiles better discriminate cell type identity and differentiation stage than gene expression profiles alone. We further discover a cell-type variable region of 18S ribosomal RNA that is associated with cell cycle and translation control. Our method opens the door to the systematic characterization of RNA structure-function relationships at single-cell resolution.


Asunto(s)
ARN , Humanos , ARN/genética , ARN/química , ARN Mensajero/genética , Secuencia de Bases , Conformación de Ácido Nucleico , Diferenciación Celular
11.
J Neurosci ; 44(13)2024 Mar 27.
Artículo en Inglés | MEDLINE | ID: mdl-38302441

RESUMEN

Ocular position drifts during gaze fixation are significantly less well understood than microsaccades. We recently identified a short-latency ocular position drift response, of ∼1 min arc amplitude, that is triggered within <100 ms by visual onsets. This systematic eye movement response is feature-tuned and seems to be coordinated with a simultaneous resetting of the saccadic system by visual stimuli. However, much remains to be learned about the drift response, especially for designing better-informed neurophysiological experiments unraveling its mechanistic substrates. Here we systematically tested multiple new feature tuning properties of drift responses. Using highly precise eye tracking in three male rhesus macaque monkeys, we found that drift responses still occur for tiny foveal visual stimuli. Moreover, the responses exhibit size tuning, scaling their amplitude (both up and down) as a function of stimulus size, and they also possess a monotonically increasing contrast sensitivity curve. Importantly, short-latency drift responses still occur for small peripheral visual targets, which additionally introduce spatially directed modulations in drift trajectories toward the appearing peripheral stimuli. Drift responses also remain predominantly upward even for stimuli exclusively located in the lower visual field and even when starting gaze position is upward. When we checked the timing of drift responses, we found it was better synchronized to stimulus-induced saccadic inhibition than to stimulus onset. These results, along with a suppression of drift response amplitudes by peristimulus saccades, suggest that drift responses reflect the rapid impacts of short-latency and feature-tuned visual neural activity on final oculomotor control circuitry in the brain.


Asunto(s)
Fijación Ocular , Visión Ocular , Animales , Masculino , Macaca mulatta , Movimientos Oculares , Movimientos Sacádicos , Percepción Visual/fisiología
12.
Circulation ; 149(9): 684-706, 2024 02 27.
Artículo en Inglés | MEDLINE | ID: mdl-37994595

RESUMEN

BACKGROUND: The majority of people with diabetes are susceptible to cardiac dysfunction and heart failure, and conventional drug therapy cannot correct diabetic cardiomyopathy progression. Herein, we assessed the potential role and therapeutic value of USP28 (ubiquitin-specific protease 28) on the metabolic vulnerability of diabetic cardiomyopathy. METHODS: The type 2 diabetes mouse model was established using db/db leptin receptor-deficient mice and high-fat diet/streptozotocin-induced mice. Cardiac-specific knockout of USP28 in the db/db background mice was generated by crossbreeding db/m and Myh6-Cre+/USP28fl/fl mice. Recombinant adeno-associated virus serotype 9 carrying USP28 under cardiac troponin T promoter was injected into db/db mice. High glucose plus palmitic acid-incubated neonatal rat ventricular myocytes and human induced pluripotent stem cell-derived cardiomyocytes were used to imitate diabetic cardiomyopathy in vitro. The molecular mechanism was explored through RNA sequencing, immunoprecipitation and mass spectrometry analysis, protein pull-down, chromatin immunoprecipitation sequencing, and chromatin immunoprecipitation assay. RESULTS: Microarray profiling of the UPS (ubiquitin-proteasome system) on the basis of db/db mouse hearts and diabetic patients' hearts demonstrated that the diabetic ventricle presented a significant reduction in USP28 expression. Diabetic Myh6-Cre+/USP28fl/fl mice exhibited more severe progressive cardiac dysfunction, lipid accumulation, and mitochondrial disarrangement, compared with their controls. On the other hand, USP28 overexpression improved systolic and diastolic dysfunction and ameliorated cardiac hypertrophy and fibrosis in the diabetic heart. Adeno-associated virus serotype 9-USP28 diabetic mice also exhibited less lipid storage, reduced reactive oxygen species formation, and mitochondrial impairment in heart tissues than adeno-associated virus serotype 9-null diabetic mice. As a result, USP28 overexpression attenuated cardiac remodeling and dysfunction, lipid accumulation, and mitochondrial impairment in high-fat diet/streptozotocin-induced type 2 diabetes mice. These results were also confirmed in neonatal rat ventricular myocytes and human induced pluripotent stem cell-derived cardiomyocytes. RNA sequencing, immunoprecipitation and mass spectrometry analysis, chromatin immunoprecipitation assays, chromatin immunoprecipitation sequencing, and protein pull-down assay mechanistically revealed that USP28 directly interacted with PPARα (peroxisome proliferator-activated receptor α), deubiquitinating and stabilizing PPARα (Lys152) to promote Mfn2 (mitofusin 2) transcription, thereby impeding mitochondrial morphofunctional defects. However, such cardioprotective benefits of USP28 were largely abrogated in db/db mice with PPARα deletion and conditional loss-of-function of Mfn2. CONCLUSIONS: Our findings provide a USP28-modulated mitochondria homeostasis mechanism that involves the PPARα-Mfn2 axis in diabetic hearts, suggesting that USP28 activation or adeno-associated virus therapy targeting USP28 represents a potential therapeutic strategy for diabetic cardiomyopathy.


Asunto(s)
Diabetes Mellitus Experimental , Diabetes Mellitus Tipo 2 , Cardiomiopatías Diabéticas , Células Madre Pluripotentes Inducidas , Ubiquitina Tiolesterasa , Animales , Humanos , Ratones , Ratas , Diabetes Mellitus Experimental/complicaciones , Diabetes Mellitus Experimental/genética , Diabetes Mellitus Experimental/metabolismo , Diabetes Mellitus Tipo 2/complicaciones , Diabetes Mellitus Tipo 2/genética , Diabetes Mellitus Tipo 2/metabolismo , Cardiomiopatías Diabéticas/metabolismo , Células Madre Pluripotentes Inducidas/metabolismo , Lípidos , Ratones Noqueados , Miocitos Cardíacos/metabolismo , PPAR alfa/metabolismo , Estreptozocina/metabolismo , Estreptozocina/uso terapéutico , Ubiquitina Tiolesterasa/análisis , Ubiquitina Tiolesterasa/metabolismo
13.
Brief Bioinform ; 24(3)2023 05 19.
Artículo en Inglés | MEDLINE | ID: mdl-37055234

RESUMEN

Identifying cancer driver genes plays a curial role in the development of precision oncology and cancer therapeutics. Although a plethora of methods have been developed to tackle this problem, the complex cancer mechanisms and intricate interactions between genes still make the identification of cancer driver genes challenging. In this work, we propose a novel machine learning method of heterophilic graph diffusion convolutional networks (called HGDCs) to boost cancer-driver gene identification. Specifically, HGDC first introduces graph diffusion to generate an auxiliary network for capturing the structurally similar nodes in a biomolecular network. Then, HGDC designs an improved message aggregation and propagation scheme to adapt to the heterophilic setting of biomolecular networks, alleviating the problem of driver gene features being smoothed by its neighboring dissimilar genes. Finally, HGDC uses a layer-wise attention classifier to predict the probability of one gene being a cancer driver gene. In the comparison experiments with other existing state-of-the-art methods, our HGDC achieves outstanding performance in identifying cancer driver genes. The experimental results demonstrate that HGDC not only effectively identifies well-known driver genes on different networks but also novel candidate cancer genes. Moreover, HGDC can effectively prioritize cancer driver genes for individual patients. Particularly, HGDC can identify patient-specific additional driver genes, which work together with the well-known driver genes to cooperatively promote tumorigenesis.


Asunto(s)
Neoplasias , Humanos , Neoplasias/genética , Redes Reguladoras de Genes , Medicina de Precisión , Oncogenes , Transformación Celular Neoplásica/genética
14.
Brief Bioinform ; 24(5)2023 09 20.
Artículo en Inglés | MEDLINE | ID: mdl-37738403

RESUMEN

Identifying personalized cancer driver genes and further revealing their oncogenic mechanisms is critical for understanding the mechanisms of cell transformation and aiding clinical diagnosis. Almost all existing methods primarily focus on identifying driver genes at the cohort or individual level but fail to further uncover their underlying oncogenic mechanisms. To fill this gap, we present an interpretable framework, PhenoDriver, to identify personalized cancer driver genes, elucidate their roles in cancer development and uncover the association between driver genes and clinical phenotypic alterations. By analyzing 988 breast cancer patients, we demonstrate the outstanding performance of PhenoDriver in identifying breast cancer driver genes at the cohort level compared to other state-of-the-art methods. Otherwise, our PhenoDriver can also effectively identify driver genes with both recurrent and rare mutations in individual patients. We further explore and reveal the oncogenic mechanisms of some known and unknown breast cancer driver genes (e.g. TP53, MAP3K1, HTT, etc.) identified by PhenoDriver, and construct their subnetworks for regulating clinical abnormal phenotypes. Notably, most of our findings are consistent with existing biological knowledge. Based on the personalized driver profiles, we discover two existing and one unreported breast cancer subtypes and uncover their molecular mechanisms. These results intensify our understanding for breast cancer mechanisms, guide therapeutic decisions and assist in the development of targeted anticancer therapies.


Asunto(s)
Neoplasias de la Mama , Humanos , Femenino , Neoplasias de la Mama/genética , Oncogenes , Mutación , Fenotipo , Investigación
15.
Ann Neurol ; 96(2): 306-320, 2024 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-38752697

RESUMEN

OBJECTIVE: Although accumulating evidence implicating altered gut microbiota in human immunodeficiency virus (HIV) infection and neurodegenerative disorders; however, the association between dysbiosis of the gut microbiota and metabolites in the pathogenesis of HIV-associated neurocognitive disorder (HAND) remains unclear. METHODS: Fecal and plasma samples were obtained from 3 cohorts (HAND, HIV-non-HAND, and healthy controls), metagenomic analysis and metabolomic profiling were performed to investigate alterations in the gut microbial composition and circulating metabolites in HAND. RESULTS: The gut microbiota of people living with HIV (PLWH) had an increased relative abundance of Prevotella and a decreased relative abundance of Bacteroides. In contrast, Prevotella and Megamonas were substantially decreased, and Bacteroides and Phocaeicola were increased in HAND patients. Moreover, untargeted metabolomics identified several neurotransmitters and certain amino acids associated with neuromodulation, and the differential metabolic pathways of amino acids associated with neurocognition were depleted in HAND patients. Notably, most neuromodulatory metabolites are associated with an altered abundance of specific gut bacteria. INTERPRETATION: Our findings provide new insights into the intricate interplay between the gut and microbiome-brain axis in the pathogenesis of HAND, highlighting the potential for developing novel therapeutic strategies that specifically target the gut microbiota. ANN NEUROL 2024;96:306-320.


Asunto(s)
Aminoácidos , Microbioma Gastrointestinal , Metabolómica , Metagenómica , Humanos , Microbioma Gastrointestinal/fisiología , Masculino , Persona de Mediana Edad , Femenino , Metabolómica/métodos , Aminoácidos/metabolismo , Aminoácidos/sangre , Adulto , Infecciones por VIH/complicaciones , Complejo SIDA Demencia/metabolismo , Complejo SIDA Demencia/microbiología , Heces/microbiología , Disbiosis
16.
Nat Chem Biol ; 19(12): 1492-1503, 2023 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-37500770

RESUMEN

Enolase 1 (ENO1) is a glycolytic enzyme that plays essential roles in various pathological activities including cancer development. However, the mechanisms underlying ENO1-contributed tumorigenesis are not well explained. Here, we uncover that ENO1, as an RNA-binding protein, binds to the cytosine-uracil-guanine-rich elements of YAP1 messenger RNA to promote its translation. ENO1 and YAP1 positively regulate alternative arachidonic acid (AA) metabolism by inverse regulation of PLCB1 and HPGD (15-hydroxyprostaglandin dehydrogenase). The YAP1/PLCB1/HPGD axis-mediated activation of AA metabolism and subsequent accumulation of prostaglandin E2 (PGE2) are responsible for ENO1-mediated cancer progression, which can be retarded by aspirin. Finally, aberrant activation of ENO1/YAP1/PLCB1 and decreased HPGD expression in clinical hepatocellular carcinoma samples indicate a potential correlation between ENO1-regulated AA metabolism and cancer development. These findings underline a new function of ENO1 in regulating AA metabolism and tumorigenesis, suggesting a therapeutic potential for aspirin in patients with liver cancer with aberrant expression of ENO1 or YAP1.


Asunto(s)
Carcinogénesis , Neoplasias Hepáticas , Humanos , Ácido Araquidónico , Línea Celular Tumoral , Proliferación Celular , Carcinogénesis/genética , Transformación Celular Neoplásica , Fosfopiruvato Hidratasa/genética , Fosfopiruvato Hidratasa/metabolismo , Neoplasias Hepáticas/genética , Aspirina/farmacología , Proteínas de Unión al ADN/genética , Biomarcadores de Tumor , Proteínas Supresoras de Tumor/genética
17.
Nucleic Acids Res ; 51(3): 1050-1066, 2023 02 22.
Artículo en Inglés | MEDLINE | ID: mdl-36660824

RESUMEN

While linear ubiquitin plays critical roles in multiple cell signaling pathways, few substrates have been identified. Global profiling of linear ubiquitin substrates represents a significant challenge because of the low endogenous level of linear ubiquitination and the background interference arising from highly abundant ubiquitin linkages (e.g. K48- and K63-) and from the non-specific attachment of interfering proteins to the linear polyubiquitin chain. We developed a bio-orthogonal linear ubiquitin probe by site-specific encoding of a norbornene amino acid on ubiquitin (NAEK-Ub). This probe facilitates covalent labeling of linear ubiquitin substrates in live cells and enables selective enrichment and identification of linear ubiquitin-modified proteins. Given the fact that the frequent overexpression of the linear linkage-specific deubiquitinase OTULIN correlates with poor prognosis in glioblastoma, we demonstrated the feasibility of the NAEK-Ub strategy by identifying and validating substrates of linear ubiquitination in patient-derived glioblastoma stem-like cells (GSCs). We identified STAT3 as a bona fide substrate of linear ubiquitin, and showed that linear ubiquitination negatively regulates STAT3 activity by recruitment of the phosphatase TC-PTP to STAT3. Furthermore, we demonstrated that preferential expression of OTULIN in GSCs restricts linear ubiquitination on STAT3 and drives persistent STAT3 signaling, and thereby maintains the stemness and self-renewal of GSCs.


Asunto(s)
Glioblastoma , Factor de Transcripción STAT3 , Ubiquitina , Humanos , Poliubiquitina/genética , Transducción de Señal , Factor de Transcripción STAT3/metabolismo , Ubiquitina/metabolismo , Ubiquitinación
18.
Proc Natl Acad Sci U S A ; 119(49): e2211429119, 2022 12 06.
Artículo en Inglés | MEDLINE | ID: mdl-36442087

RESUMEN

The current classification of acute myeloid leukemia (AML) relies largely on genomic alterations. Robust identification of clinically and biologically relevant molecular subtypes from nongenomic high-throughput sequencing data remains challenging. We established the largest multicenter AML cohort (n = 655) in China, with all patients subjected to RNA sequencing (RNA-Seq) and 619 (94.5%) to targeted or whole-exome sequencing (TES/WES). Based on an enhanced consensus clustering, eight stable gene expression subgroups (G1-G8) with unique clinical and biological significance were identified, including two unreported (G5 and G8) and three redefined ones (G4, G6, and G7). Apart from four well-known low-risk subgroups including PML::RARA (G1), CBFB::MYH11 (G2), RUNX1::RUNX1T1 (G3), biallelic CEBPA mutations or -like (G4), four meta-subgroups with poor outcomes were recognized. The G5 (myelodysplasia-related/-like) subgroup enriched clinical, cytogenetic and genetic features mimicking secondary AML, and hotspot mutations of IKZF1 (p.N159S) (n = 7). In contrast, most NPM1 mutations and KMT2A and NUP98 fusions clustered into G6-G8, showing high expression of HOXA/B genes and diverse differentiation stages, from hematopoietic stem/progenitor cell down to monocyte, namely HOX-primitive (G7), HOX-mixed (G8), and HOX-committed (G6). Through constructing prediction models, the eight gene expression subgroups could be reproduced in the Cancer Genome Atlas (TCGA) and Beat AML cohorts. Each subgroup was associated with distinct prognosis and drug sensitivities, supporting the clinical applicability of this transcriptome-based classification of AML. These molecular subgroups illuminate the complex molecular network of AML, which may promote systematic studies of disease pathogenesis and foster the screening of targeted agents based on omics.


Asunto(s)
Leucemia Mieloide Aguda , Síndromes Mielodisplásicos , Humanos , Transcriptoma , Leucemia Mieloide Aguda/genética , Diferenciación Celular/genética , Células Madre Hematopoyéticas
19.
J Mol Cell Cardiol ; 186: 81-93, 2024 01.
Artículo en Inglés | MEDLINE | ID: mdl-37995517

RESUMEN

AIM: Doxorubicin-induced cardiotoxicity (DIC) is an increasing problem, occurring in many cancer patients receiving anthracycline chemotherapy, ultimately leading to heart failure (HF). Unfortunately, DIC remains difficult to manage due to an ignorance regarding pathophysiological mechanisms. Our work aimed to evaluate the role of HSP47 in doxorubicin-induced HF, and to explore the molecular mechanisms. METHODS AND RESULTS: Mice were exposed to multi-intraperitoneal injection of doxorubicin (DOX, 4mg/kg/week, for 6 weeks continuously) to produce DIC. HSP47 expression was significantly upregulated in serum and in heart tissue in DOX-treated mice and in isolated cardiomyocytes. Mice with cardiac-specific HSP47 overexpression and knockdown were generated using recombinant adeno-associated virus (rAVV9) injection. Importantly, cardiac-specific HSP47 overexpression exacerbated cardiac dysfunction in DIC, while HSP47 knockdown prevented DOX-induced cardiac dysfunction, cardiac atrophy and fibrosis in vivo and in vitro. Mechanistically, we identified that HSP47 directly interacted with IRE1α in cardiomyocytes. Furthermore, we provided powerful evidence that HSP47-IRE1α complex promoted TXNIP/NLRP3 inflammasome and reinforced USP1-mediated NLRP3 ubiquitination. Moreover, NLRP3 deficiency in vivo conspicuously abolished HSP47-mediated cardiac atrophy and fibrogenesis under DOX condition. CONCLUSION: HSP47 was highly expressed in serum and cardiac tissue after doxorubicin administration. HSP47 contributed to long-term anthracycline chemotherapy-associated cardiac dysfunction in an NLRP3-dependent manner. HSP47 therefore represents a plausible target for future therapy of doxorubicin-induced HF.


Asunto(s)
Inflamasomas , Proteína con Dominio Pirina 3 de la Familia NLR , Ratones , Humanos , Animales , Inflamasomas/metabolismo , Proteína con Dominio Pirina 3 de la Familia NLR/genética , Proteína con Dominio Pirina 3 de la Familia NLR/metabolismo , Proteínas del Choque Térmico HSP47/metabolismo , Cardiotoxicidad/metabolismo , Doxorrubicina/farmacología , Endorribonucleasas/metabolismo , Proteínas Serina-Treonina Quinasas/metabolismo , Miocitos Cardíacos/metabolismo , Antibióticos Antineoplásicos/efectos adversos , Atrofia/inducido químicamente , Atrofia/metabolismo , Atrofia/patología , Apoptosis , Estrés Oxidativo
20.
Clin Infect Dis ; 2024 Jan 17.
Artículo en Inglés | MEDLINE | ID: mdl-38236137

RESUMEN

BACKGROUND: Most international treatment guidelines recommend rapid initiation of antiretroviral therapy (ART) for people newly diagnosed with HIV-1 infection, but experiences with rapid ART initiation remain limited in China. We aimed to evaluate the efficacy and safety of efavirenz (400-mg) plus lamivudine and tenofovir disoproxil fumarate (EFV + 3TC + TDF) versus coformulated bictegravir, emtricitabine, tenofovir alafenamide (BIC/FTC/TAF) in rapid ART initiation among HIV-positive men who have sex with men (MSM). METHODS: This multicenter, open-label, randomized clinical trial enrolled MSM aged ≥18 years to start ART within 14 days of confirmed HIV diagnosis. The participants were randomly assigned in a 1:1 ratio to receive EFV(400-mg) + 3TC + TDF or BIC/FTC/TAF. The primary end point was viral suppression (<50 copies/ml) at 48 weeks per FDA Snapshot analysis. RESULTS: Between March 2021 and July 2022, 300 participants were enrolled; 154 were assigned to receive EFV + 3TC + TDF (EFV group) and 146 BIC/FTC/TAF (BIC group). At week 48, 118 (79.2%) and 140 (95.9%) participants in the EFV and BIC group, respectively, were retained in care with viral suppression; and 24 (16.1%) and 1 (0.7%) participant in the EFV and BIC group (p < 0.001), respectively, discontinued treatment due to adverse effects, death, or loss to follow-up. The median increase of CD4 count was 181 and 223 cells/µL (p = 0.020), respectively, for the EFV and BIC group, at week 48. The overall incidence of adverse effects was significantly higher for the EFV group (65.8% vs 37.7%, P < 0.001). CONCLUSION: BIC/FTC/TAF was more efficacious and safer than EFV(400-mg) + 3TC + TDF for rapid ART initiation among HIV-positive MSM in China.

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