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1.
Immunity ; 57(8): 1923-1938.e7, 2024 Aug 13.
Artículo en Inglés | MEDLINE | ID: mdl-38878769

RESUMEN

Fasting is associated with improved outcomes in cancer. Here, we investigated the impact of fasting on natural killer (NK) cell anti-tumor immunity. Cyclic fasting improved immunity against solid and metastatic tumors in an NK cell-dependent manner. During fasting, NK cells underwent redistribution from peripheral tissues to the bone marrow (BM). In humans, fasting also reduced circulating NK cell numbers. NK cells in the spleen of fasted mice were metabolically rewired by elevated concentrations of fatty acids and glucocorticoids, augmenting fatty acid metabolism via increased expression of the enzyme CPT1A, and Cpt1a deletion impaired NK cell survival and function in this setting. In parallel, redistribution of NK cells to the BM during fasting required the trafficking mediators S1PR5 and CXCR4. These cells were primed by an increased pool of interleukin (IL)-12-expressing BM myeloid cells, which improved IFN-γ production. Our findings identify a link between dietary restriction and optimized innate immune responses, with the potential to enhance immunotherapy strategies.


Asunto(s)
Ayuno , Células Asesinas Naturales , Ratones Endogámicos C57BL , Animales , Células Asesinas Naturales/inmunología , Células Asesinas Naturales/metabolismo , Ratones , Humanos , Neoplasias/inmunología , Médula Ósea/inmunología , Médula Ósea/metabolismo , Ratones Noqueados , Interferón gamma/metabolismo , Interferón gamma/inmunología , Bazo/inmunología , Bazo/metabolismo , Inmunidad Innata/inmunología , Interleucina-12/metabolismo , Interleucina-12/inmunología , Receptores CXCR4/metabolismo
2.
Cell ; 167(5): 1150-1154, 2016 11 17.
Artículo en Inglés | MEDLINE | ID: mdl-27863233

RESUMEN

We review emerging strategies to protect the privacy of research participants in international epigenome research: open consent, genome donation, registered access, automated procedures, and privacy-enhancing technologies.


Asunto(s)
Genómica/ética , Genómica/legislación & jurisprudencia , Difusión de la Información , Privacidad , Secuenciación de Nucleótidos de Alto Rendimiento , Proyecto Genoma Humano/ética , Proyecto Genoma Humano/legislación & jurisprudencia , Humanos , Análisis de Secuencia de ADN
3.
Nat Immunol ; 19(9): 973-985, 2018 09.
Artículo en Inglés | MEDLINE | ID: mdl-30127434

RESUMEN

Human inborn errors of IFN-γ immunity underlie mycobacterial diseases. We describe patients with Mycobacterium bovis (BCG) disease who are homozygous for loss-of-function mutations of SPPL2A. This gene encodes a transmembrane protease that degrades the N-terminal fragment (NTF) of CD74 (HLA invariant chain) in antigen-presenting cells. The CD74 NTF therefore accumulates in the HLA class II+ myeloid and lymphoid cells of SPPL2a-deficient patients. This toxic fragment selectively depletes IL-12- and IL-23-producing CD1c+ conventional dendritic cells (cDC2s) and their circulating progenitors. Moreover, SPPL2a-deficient memory TH1* cells selectively fail to produce IFN-γ when stimulated with mycobacterial antigens in vitro. Finally, Sppl2a-/- mice lack cDC2s, have CD4+ T cells that produce small amounts of IFN-γ after BCG infection, and are highly susceptible to infection with BCG or Mycobacterium tuberculosis. These findings suggest that inherited SPPL2a deficiency in humans underlies mycobacterial disease by decreasing the numbers of cDC2s and impairing IFN-γ production by mycobacterium-specific memory TH1* cells.


Asunto(s)
Ácido Aspártico Endopeptidasas/genética , Ácido Aspártico Endopeptidasas/metabolismo , Células Dendríticas/inmunología , Proteínas de la Membrana/metabolismo , Infecciones por Mycobacterium/inmunología , Mycobacterium bovis/fisiología , Mycobacterium tuberculosis/fisiología , Células TH1/inmunología , Tuberculosis/inmunología , Animales , Antígenos de Diferenciación de Linfocitos B/metabolismo , Células Cultivadas , Antígenos HLA/metabolismo , Antígenos de Histocompatibilidad Clase II/metabolismo , Humanos , Inmunidad , Memoria Inmunológica , Lactante , Interferón gamma/metabolismo , Linfadenopatía , Masculino , Proteínas de la Membrana/genética , Ratones , Ratones Endogámicos C57BL , Ratones Noqueados , Mutación/genética , Infecciones por Mycobacterium/genética , Vacunación
5.
Nature ; 626(8000): 864-873, 2024 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-38326607

RESUMEN

Macrophage activation is controlled by a balance between activating and inhibitory receptors1-7, which protect normal tissues from excessive damage during infection8,9 but promote tumour growth and metastasis in cancer7,10. Here we report that the Kupffer cell lineage-determining factor ID3 controls this balance and selectively endows Kupffer cells with the ability to phagocytose live tumour cells and orchestrate the recruitment, proliferation and activation of natural killer and CD8 T lymphoid effector cells in the liver to restrict the growth of a variety of tumours. ID3 shifts the macrophage inhibitory/activating receptor balance to promote the phagocytic and lymphoid response, at least in part by buffering the binding of the transcription factors ELK1 and E2A at the SIRPA locus. Furthermore, loss- and gain-of-function experiments demonstrate that ID3 is sufficient to confer this potent anti-tumour activity to mouse bone-marrow-derived macrophages and human induced pluripotent stem-cell-derived macrophages. Expression of ID3 is therefore necessary and sufficient to endow macrophages with the ability to form an efficient anti-tumour niche, which could be harnessed for cell therapy in cancer.


Asunto(s)
Proteínas Inhibidoras de la Diferenciación , Macrófagos del Hígado , Neoplasias , Animales , Humanos , Ratones , Células de la Médula Ósea/citología , Linfocitos T CD8-positivos/citología , Linfocitos T CD8-positivos/inmunología , Linaje de la Célula , Células Madre Pluripotentes Inducidas/citología , Proteínas Inhibidoras de la Diferenciación/deficiencia , Proteínas Inhibidoras de la Diferenciación/genética , Proteínas Inhibidoras de la Diferenciación/metabolismo , Células Asesinas Naturales/citología , Células Asesinas Naturales/inmunología , Macrófagos del Hígado/citología , Macrófagos del Hígado/inmunología , Macrófagos del Hígado/metabolismo , Hígado/inmunología , Hígado/patología , Activación de Macrófagos , Proteínas de Neoplasias , Neoplasias/inmunología , Neoplasias/patología , Neoplasias/terapia , Fagocitosis
6.
Nature ; 630(8017): 752-761, 2024 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-38867045

RESUMEN

Mutations accumulate in the genome of every cell of the body throughout life, causing cancer and other diseases1,2. Most mutations begin as nucleotide mismatches or damage in one of the two strands of the DNA before becoming double-strand mutations if unrepaired or misrepaired3,4. However, current DNA-sequencing technologies cannot accurately resolve these initial single-strand events. Here we develop a single-molecule, long-read sequencing method (Hairpin Duplex Enhanced Fidelity sequencing (HiDEF-seq)) that achieves single-molecule fidelity for base substitutions when present in either one or both DNA strands. HiDEF-seq also detects cytosine deamination-a common type of DNA damage-with single-molecule fidelity. We profiled 134 samples from diverse tissues, including from individuals with cancer predisposition syndromes, and derive from them single-strand mismatch and damage signatures. We find correspondences between these single-strand signatures and known double-strand mutational signatures, which resolves the identity of the initiating lesions. Tumours deficient in both mismatch repair and replicative polymerase proofreading show distinct single-strand mismatch patterns compared to samples that are deficient in only polymerase proofreading. We also define a single-strand damage signature for APOBEC3A. In the mitochondrial genome, our findings support a mutagenic mechanism occurring primarily during replication. As double-strand DNA mutations are only the end point of the mutation process, our approach to detect the initiating single-strand events at single-molecule resolution will enable studies of how mutations arise in a variety of contexts, especially in cancer and ageing.


Asunto(s)
Disparidad de Par Base , Daño del ADN , ADN de Cadena Simple , Análisis de Secuencia de ADN , Imagen Individual de Molécula , Humanos , Envejecimiento/genética , Desaminasas APOBEC/genética , Desaminasas APOBEC/metabolismo , Disparidad de Par Base/genética , Citidina Desaminasa/metabolismo , Citidina Desaminasa/genética , Citosina/metabolismo , Desaminación , Daño del ADN/genética , Reparación de la Incompatibilidad de ADN/genética , Replicación del ADN/genética , ADN de Cadena Simple/genética , Genoma Mitocondrial/genética , Mutación , Neoplasias/genética , Análisis de Secuencia de ADN/métodos , Análisis de Secuencia de ADN/normas , Imagen Individual de Molécula/métodos , Masculino , Femenino
7.
Nature ; 633(8029): 417-425, 2024 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-39198650

RESUMEN

Severe defects in human IFNγ immunity predispose individuals to both Bacillus Calmette-Guérin disease and tuberculosis, whereas milder defects predispose only to tuberculosis1. Here we report two adults with recurrent pulmonary tuberculosis who are homozygous for a private loss-of-function TNF variant. Neither has any other clinical phenotype and both mount normal clinical and biological inflammatory responses. Their leukocytes, including monocytes and monocyte-derived macrophages (MDMs) do not produce TNF, even after stimulation with IFNγ. Blood leukocyte subset development is normal in these patients. However, an impairment in the respiratory burst was observed in granulocyte-macrophage colony-stimulating factor (GM-CSF)-matured MDMs and alveolar macrophage-like (AML) cells2 from both patients with TNF deficiency, TNF- or TNFR1-deficient induced pluripotent stem (iPS)-cell-derived GM-CSF-matured macrophages, and healthy control MDMs and AML cells differentiated with TNF blockers in vitro, and in lung macrophages treated with TNF blockers ex vivo. The stimulation of TNF-deficient iPS-cell-derived macrophages with TNF rescued the respiratory burst. These findings contrast with those for patients with inherited complete deficiency of the respiratory burst across all phagocytes, who are prone to multiple infections, including both Bacillus Calmette-Guérin disease and tuberculosis3. Human TNF is required for respiratory-burst-dependent immunity to Mycobacterium tuberculosis in macrophages but is surprisingly redundant otherwise, including for inflammation and immunity to weakly virulent mycobacteria and many other infectious agents.


Asunto(s)
Macrófagos , Tuberculosis Pulmonar , Factores de Necrosis Tumoral , Adulto , Femenino , Humanos , Masculino , Factor Estimulante de Colonias de Granulocitos y Macrófagos/metabolismo , Homocigoto , Células Madre Pluripotentes Inducidas/metabolismo , Células Madre Pluripotentes Inducidas/inmunología , Células Madre Pluripotentes Inducidas/citología , Inflamación/inmunología , Interferón gamma/inmunología , Mutación con Pérdida de Función , Pulmón/citología , Pulmón/efectos de los fármacos , Macrófagos/citología , Macrófagos/efectos de los fármacos , Macrófagos/inmunología , Macrófagos/metabolismo , Macrófagos/patología , Macrófagos Alveolares/citología , Macrófagos Alveolares/efectos de los fármacos , Macrófagos Alveolares/inmunología , Macrófagos Alveolares/microbiología , Macrófagos Alveolares/patología , Mycobacterium tuberculosis/inmunología , Fenotipo , Especies Reactivas de Oxígeno/metabolismo , Receptores Tipo I de Factores de Necrosis Tumoral/deficiencia , Receptores Tipo I de Factores de Necrosis Tumoral/genética , Receptores Tipo I de Factores de Necrosis Tumoral/metabolismo , Estallido Respiratorio , Tuberculosis Pulmonar/inmunología , Tuberculosis Pulmonar/microbiología , Tuberculosis Pulmonar/genética , Inhibidores del Factor de Necrosis Tumoral/farmacología , Factores de Necrosis Tumoral/deficiencia , Factores de Necrosis Tumoral/genética , Adolescente , Adulto Joven
8.
Nature ; 618(7966): 698-707, 2023 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-37344646

RESUMEN

Embryo-derived tissue-resident macrophages are the first representatives of the haematopoietic lineage to emerge in metazoans. In mammals, resident macrophages originate from early yolk sac progenitors and are specified into tissue-specific subsets during organogenesis-establishing stable spatial and functional relationships with specialized tissue cells-and persist in adults. Resident macrophages are an integral part of tissues together with specialized cells: for instance, microglia reside with neurons in brain, osteoclasts reside with osteoblasts in bone, and fat-associated macrophages reside with white adipocytes in adipose tissue. This ancillary cell type, which is developmentally and functionally distinct from haematopoietic stem cell and monocyte-derived macrophages, senses and integrates local and systemic information to provide specialized tissue cells with the growth factors, nutrient recycling and waste removal that are critical for tissue growth, homeostasis and repair. Resident macrophages contribute to organogenesis, promote tissue regeneration following damage and contribute to tissue metabolism and defence against infectious disease. A correlate is that genetic or environment-driven resident macrophage dysfunction is a cause of degenerative, metabolic and possibly inflammatory and tumoural diseases. In this Review, we aim to provide a conceptual outline of our current understanding of macrophage physiology and its importance in human diseases, which may inform and serve the design of future studies.


Asunto(s)
Enfermedad , Macrófagos , Animales , Humanos , Diferenciación Celular , Linaje de la Célula , Células Madre Hematopoyéticas/citología , Macrófagos/citología , Macrófagos/metabolismo , Macrófagos/patología , Macrófagos/fisiología , Microglía/citología , Monocitos/citología , Especificidad de Órganos
9.
Nature ; 615(7954): 836-840, 2023 03.
Artículo en Inglés | MEDLINE | ID: mdl-36949188

RESUMEN

Photosystems II and I (PSII, PSI) are the reaction centre-containing complexes driving the light reactions of photosynthesis; PSII performs light-driven water oxidation and PSI further photo-energizes harvested electrons. The impressive efficiencies of the photosystems have motivated extensive biological, artificial and biohybrid approaches to 're-wire' photosynthesis for higher biomass-conversion efficiencies and new reaction pathways, such as H2 evolution or CO2 fixation1,2. Previous approaches focused on charge extraction at terminal electron acceptors of the photosystems3. Electron extraction at earlier steps, perhaps immediately from photoexcited reaction centres, would enable greater thermodynamic gains; however, this was believed impossible with reaction centres buried at least 4 nm within the photosystems4,5. Here, we demonstrate, using in vivo ultrafast transient absorption (TA) spectroscopy, extraction of electrons directly from photoexcited PSI and PSII at early points (several picoseconds post-photo-excitation) with live cyanobacterial cells or isolated photosystems, and exogenous electron mediators such as 2,6-dichloro-1,4-benzoquinone (DCBQ) and methyl viologen. We postulate that these mediators oxidize peripheral chlorophyll pigments participating in highly delocalized charge-transfer states after initial photo-excitation. Our results challenge previous models that the photoexcited reaction centres are insulated within the photosystem protein scaffold, opening new avenues to study and re-wire photosynthesis for biotechnologies and semi-artificial photosynthesis.


Asunto(s)
Fotosíntesis , Complejo de Proteína del Fotosistema I , Complejo de Proteína del Fotosistema II , Clorofila/metabolismo , Oxidación-Reducción , Complejo de Proteína del Fotosistema I/metabolismo , Complejo de Proteína del Fotosistema II/metabolismo , Factores de Tiempo , Ciclo del Carbono , Dióxido de Carbono/metabolismo , Hidrógeno/metabolismo , Cianobacterias/metabolismo , Electrones , Termodinámica
10.
Am J Hum Genet ; 111(5): 825-832, 2024 05 02.
Artículo en Inglés | MEDLINE | ID: mdl-38636509

RESUMEN

Next-generation sequencing has revolutionized the speed of rare disease (RD) diagnoses. While clinical exome and genome sequencing represent an effective tool for many RD diagnoses, there is room to further improve the diagnostic odyssey of many RD patients. One recognizable intervention lies in increasing equitable access to genomic testing. Rural communities represent a significant portion of underserved and underrepresented individuals facing additional barriers to diagnosis and treatment. Primary care providers (PCPs) at local clinics, though sometimes suspicious of a potential benefit of genetic testing for their patients, have significant constraints in pursuing it themselves and rely on referrals to specialists. Yet, these referrals are typically followed by long waitlists and significant delays in clinical assessment, insurance clearance, testing, and initiation of diagnosis-informed care management. Not only is this process time intensive, but it also often requires multiple visits to urban medical centers for which distance may be a significant barrier to rural families. Therefore, providing early, "direct-to-provider" (DTP) local access to unrestrictive genomic testing is likely to help speed up diagnostic times and access to care for RD patients in rural communities. In a pilot study with a PCP clinic in rural Kansas, we observed a minimum 5.5 months shortening of time to diagnosis through the DTP exome sequencing program as compared to rural patients receiving genetic testing through the "traditional" PCP-referral-to-specialist scheme. We share our experience to encourage future partnerships beyond our center. Our efforts represent just one step in fostering greater diversity and equity in genomic studies.


Asunto(s)
Pruebas Genéticas , Genómica , Accesibilidad a los Servicios de Salud , Enfermedades Raras , Población Rural , Humanos , Pruebas Genéticas/métodos , Enfermedades Raras/genética , Enfermedades Raras/diagnóstico , Genómica/métodos , Niño , Masculino , Secuenciación de Nucleótidos de Alto Rendimiento , Femenino
11.
Am J Hum Genet ; 111(1): 96-118, 2024 01 04.
Artículo en Inglés | MEDLINE | ID: mdl-38181735

RESUMEN

PPFIA3 encodes the protein-tyrosine phosphatase, receptor-type, F-polypeptide-interacting-protein-alpha-3 (PPFIA3), which is a member of the LAR-protein-tyrosine phosphatase-interacting-protein (liprin) family involved in synapse formation and function, synaptic vesicle transport, and presynaptic active zone assembly. The protein structure and function are evolutionarily well conserved, but human diseases related to PPFIA3 dysfunction are not yet reported in OMIM. Here, we report 20 individuals with rare PPFIA3 variants (19 heterozygous and 1 compound heterozygous) presenting with developmental delay, intellectual disability, hypotonia, dysmorphisms, microcephaly or macrocephaly, autistic features, and epilepsy with reduced penetrance. Seventeen unique PPFIA3 variants were detected in 18 families. To determine the pathogenicity of PPFIA3 variants in vivo, we generated transgenic fruit flies producing either human wild-type (WT) PPFIA3 or five missense variants using GAL4-UAS targeted gene expression systems. In the fly overexpression assays, we found that the PPFIA3 variants in the region encoding the N-terminal coiled-coil domain exhibited stronger phenotypes compared to those affecting the C-terminal region. In the loss-of-function fly assay, we show that the homozygous loss of fly Liprin-α leads to embryonic lethality. This lethality is partially rescued by the expression of human PPFIA3 WT, suggesting human PPFIA3 function is partially conserved in the fly. However, two of the tested variants failed to rescue the lethality at the larval stage and one variant failed to rescue lethality at the adult stage. Altogether, the human and fruit fly data reveal that the rare PPFIA3 variants are dominant-negative loss-of-function alleles that perturb multiple developmental processes and synapse formation.


Asunto(s)
Proteínas de Drosophila , Discapacidad Intelectual , Trastornos del Neurodesarrollo , Adulto , Animales , Humanos , Alelos , Animales Modificados Genéticamente , Drosophila , Proteínas de Drosophila/genética , Discapacidad Intelectual/genética , Péptidos y Proteínas de Señalización Intracelular , Trastornos del Neurodesarrollo/genética , Proteínas Tirosina Fosfatasas
12.
Genome Res ; 2024 Aug 06.
Artículo en Inglés | MEDLINE | ID: mdl-39107043

RESUMEN

TBC1D3 is a primate-specific gene family that has expanded in the human lineage and has been implicated in neuronal progenitor proliferation and expansion of the frontal cortex. The gene family and its expression have been challenging to investigate because it is embedded in high-identity and highly variable segmental duplications. We sequenced and assembled the gene family using long-read sequencing data from 34 humans and 11 non-human primate species. Our analysis shows that this particular gene family has independently duplicated in at least five primate lineages, and the duplicated loci are enriched at sites of large-scale chromosomal rearrangements on Chromosome 17. We find that all human copy number variation maps to two distinct clusters located at Chromosome 17q12 and that humans are highly structurally variable at this locus, differing by as many as 20 copies and ~1 Mbp in length depending on haplotypes. We also show evidence of positive selection, as well as a significant change in the predicted human TBC1D3 protein sequence. Lastly, we find that, despite multiple duplications, human TBC1D3 expression is limited to a subset of copies and, most notably, from a single paralog group: TBC1D3-CDKL These observations may help explain why a gene potentially important in cortical development can be so variable in the human population.

13.
Proc Natl Acad Sci U S A ; 121(43): e2403808121, 2024 Oct 22.
Artículo en Inglés | MEDLINE | ID: mdl-39401354

RESUMEN

Mumps outbreaks among fully vaccinated young adults have raised questions about potential waning of immunity over time and need for a third dose of the measles, mumps, rubella (MMR) vaccine. However, there are currently limited data on real-life effectiveness of the third-dose MMR vaccine in preventing mumps. Here, we used a deterministic compartmental model to infer the effectiveness of the third-dose MMR vaccine in preventing mumps cases by analyzing the mumps outbreak that occurred at the University of Iowa between August 24, 2015, and May 13, 2016. The modeling approach further allowed us to evaluate the population-level impact of vaccination by different timing in relation to the start of the outbreak and varied coverage levels, and to account for potential sources of bias in estimating vaccine effectiveness. We found large uncertainty in vaccine effectiveness estimates; however, our models showed that early introduction of a third dose of MMR vaccine during a mumps outbreak can be effective in preventing transmission. School holidays, such as the winter break, likely played important roles in preventing mumps transmission.


Asunto(s)
Brotes de Enfermedades , Vacuna contra el Sarampión-Parotiditis-Rubéola , Paperas , Paperas/epidemiología , Paperas/prevención & control , Paperas/inmunología , Humanos , Vacuna contra el Sarampión-Parotiditis-Rubéola/administración & dosificación , Vacuna contra el Sarampión-Parotiditis-Rubéola/inmunología , Brotes de Enfermedades/prevención & control , Iowa/epidemiología , Adolescente , Femenino , Vacunación , Universidades , Masculino , Niño , Adulto Joven , Adulto
14.
Am J Hum Genet ; 110(2): 240-250, 2023 02 02.
Artículo en Inglés | MEDLINE | ID: mdl-36669496

RESUMEN

Spinal muscular atrophy, a leading cause of early infant death, is caused by bi-allelic mutations of SMN1. Sequence analysis of SMN1 is challenging due to high sequence similarity with its paralog SMN2. Both genes have variable copy numbers across populations. Furthermore, without pedigree information, it is currently not possible to identify silent carriers (2+0) with two copies of SMN1 on one chromosome and zero copies on the other. We developed Paraphase, an informatics method that identifies full-length SMN1 and SMN2 haplotypes, determines the gene copy numbers, and calls phased variants using long-read PacBio HiFi data. The SMN1 and SMN2 copy-number calls by Paraphase are highly concordant with orthogonal methods (99.2% for SMN1 and 100% for SMN2). We applied Paraphase to 438 samples across 5 ethnic populations to conduct a population-wide haplotype analysis of these highly homologous genes. We identified major SMN1 and SMN2 haplogroups and characterized their co-segregation through pedigree-based analyses. We identified two SMN1 haplotypes that form a common two-copy SMN1 allele in African populations. Testing positive for these two haplotypes in an individual with two copies of SMN1 gives a silent carrier risk of 88.5%, which is significantly higher than the currently used marker (1.7%-3.0%). Extending beyond simple copy-number testing, Paraphase can detect pathogenic variants and enable potential haplotype-based screening of silent carriers through statistical phasing of haplotypes into alleles. Future analysis of larger population data will allow identification of more diverse haplotypes and genetic markers for silent carriers.


Asunto(s)
Atrofia Muscular Espinal , Lactante , Humanos , Atrofia Muscular Espinal/genética , Atrofia Muscular Espinal/diagnóstico , Mutación , Dosificación de Gen , Linaje , Análisis de Secuencia , Proteína 1 para la Supervivencia de la Neurona Motora/genética , Proteína 2 para la Supervivencia de la Neurona Motora/genética
15.
Am J Hum Genet ; 110(8): 1394-1413, 2023 08 03.
Artículo en Inglés | MEDLINE | ID: mdl-37467750

RESUMEN

DExD/H-box RNA helicases (DDX/DHX) are encoded by a large paralogous gene family; in a subset of these human helicase genes, pathogenic variation causes neurodevelopmental disorder (NDD) traits and cancer. DHX9 encodes a BRCA1-interacting nuclear helicase regulating transcription, R-loops, and homologous recombination and exhibits the highest mutational constraint of all DDX/DHX paralogs but remains unassociated with disease traits in OMIM. Using exome sequencing and family-based rare-variant analyses, we identified 20 individuals with de novo, ultra-rare, heterozygous missense or loss-of-function (LoF) DHX9 variant alleles. Phenotypes ranged from NDDs to the distal symmetric polyneuropathy axonal Charcot-Marie-Tooth disease (CMT2). Quantitative Human Phenotype Ontology (HPO) analysis demonstrated genotype-phenotype correlations with LoF variants causing mild NDD phenotypes and nuclear localization signal (NLS) missense variants causing severe NDD. We investigated DHX9 variant-associated cellular phenotypes in human cell lines. Whereas wild-type DHX9 was restricted to the nucleus, NLS missense variants abnormally accumulated in the cytoplasm. Fibroblasts from an individual with an NLS variant also showed abnormal cytoplasmic DHX9 accumulation. CMT2-associated missense variants caused aberrant nucleolar DHX9 accumulation, a phenomenon previously associated with cellular stress. Two NDD-associated variants, p.Gly411Glu and p.Arg761Gln, altered DHX9 ATPase activity. The severe NDD-associated variant p.Arg141Gln did not affect DHX9 localization but instead increased R-loop levels and double-stranded DNA breaks. Dhx9-/- mice exhibited hypoactivity in novel environments, tremor, and sensorineural hearing loss. All together, these results establish DHX9 as a critical regulator of mammalian neurodevelopment and neuronal homeostasis.


Asunto(s)
Enfermedad de Charcot-Marie-Tooth , Trastornos del Neurodesarrollo , Animales , Humanos , Ratones , Línea Celular , Enfermedad de Charcot-Marie-Tooth/genética , ARN Helicasas DEAD-box/genética , Diclorodifenil Dicloroetileno , ADN Helicasas , Mamíferos , Proteínas de Neoplasias/genética
16.
Proc Natl Acad Sci U S A ; 120(10): e2214357120, 2023 Mar 07.
Artículo en Inglés | MEDLINE | ID: mdl-36848560

RESUMEN

Improving Coulombic efficiency (CE) is key to the adoption of high energy density lithium metal batteries. Liquid electrolyte engineering has emerged as a promising strategy for improving the CE of lithium metal batteries, but its complexity renders the performance prediction and design of electrolytes challenging. Here, we develop machine learning (ML) models that assist and accelerate the design of high-performance electrolytes. Using the elemental composition of electrolytes as the features of our models, we apply linear regression, random forest, and bagging models to identify the critical features for predicting CE. Our models reveal that a reduction in the solvent oxygen content is critical for superior CE. We use the ML models to design electrolyte formulations with fluorine-free solvents that achieve a high CE of 99.70%. This work highlights the promise of data-driven approaches that can accelerate the design of high-performance electrolytes for lithium metal batteries.

17.
Bioinformatics ; 40(3)2024 03 04.
Artículo en Inglés | MEDLINE | ID: mdl-38449289

RESUMEN

MOTIVATION: Human epigenomic data has been generated by large consortia for thousands of cell types to be used as a reference map of normal and disease chromatin states. Since epigenetic data contains potentially identifiable information, similarly to genetic data, most raw files generated by these consortia are stored in controlled-access databases. It is important to protect identifiable information, but this should not hinder secure sharing of these valuable datasets. RESULTS: Guided by the Framework for responsible sharing of genomic and health-related data from the Global Alliance for Genomics and Health (GA4GH), we have developed an approach and a tool to facilitate the exploration of epigenomics datasets' aggregate results, while filtering out identifiable information. Specifically, the EpiVar Browser allows a user to navigate an epigenetic dataset from a cohort of individuals and enables direct exploration of genotype-chromatin phenotype relationships. Because individual genotypes and epigenetic signal tracks are not directly accessible, and rather aggregated in the portal output, no identifiable data is released, yet the interface allows for dynamic genotype-epigenome interrogation. This approach has the potential to accelerate analyses that would otherwise require a lengthy multi-step approval process and provides a generalizable strategy to facilitate responsible access to sensitive epigenomics data. AVAILABILITY AND IMPLEMENTATION: Online portal: https://computationalgenomics.ca/tools/epivar; EpiVar Browser source code: https://github.com/c3g/epivar-browser; bw-merge-window tool source code: https://github.com/c3g/bw-merge-window.


Asunto(s)
Epigenómica , Programas Informáticos , Humanos , Epigenómica/métodos , Genoma , Genómica , Cromatina/genética
18.
Ann Neurol ; 96(2): 262-275, 2024 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-38767012

RESUMEN

OBJECTIVE: This study was undertaken to investigate the effects of dietary caffeine intake on striatal dopamine function and clinical symptoms in Parkinson disease in a cross-sectional and longitudinal setting. METHODS: One hundred sixty-three early Parkinson disease patients and 40 healthy controls were investigated with [123I]FP-CIT single photon emission computed tomography, and striatal dopamine transporter binding was evaluated in association with the level of daily coffee consumption and clinical measures. After a median interval of 6.1 years, 44 patients with various caffeine consumption levels underwent clinical and imaging reexamination including blood caffeine metabolite profiling. RESULTS: Unmedicated early Parkinson disease patients with high coffee consumption had 8.3 to 15.4% lower dopamine transporter binding in all studied striatal regions than low consumers, after accounting for age, sex, and motor symptom severity. Higher caffeine consumption was further associated with a progressive decline in striatal binding over time. No significant effects of caffeine on motor function were observed. Blood analyses demonstrated a positive correlation between caffeine metabolites after recent caffeine intake and dopamine transporter binding in the ipsilateral putamen. INTERPRETATION: Chronic caffeine intake prompts compensatory and cumulative dopamine transporter downregulation, consistent with caffeine's reported risk reduction in Parkinson disease. However, this decline does not manifest in symptom changes. Transiently increased dopamine transporter binding after recent caffeine intake has implications for dopaminergic imaging guidelines. ANN NEUROL 2024;96:262-275.


Asunto(s)
Cafeína , Proteínas de Transporte de Dopamina a través de la Membrana Plasmática , Enfermedad de Parkinson , Humanos , Cafeína/administración & dosificación , Masculino , Femenino , Enfermedad de Parkinson/metabolismo , Enfermedad de Parkinson/diagnóstico por imagen , Persona de Mediana Edad , Anciano , Proteínas de Transporte de Dopamina a través de la Membrana Plasmática/metabolismo , Estudios Transversales , Dopamina/metabolismo , Tomografía Computarizada de Emisión de Fotón Único , Estudios Longitudinales , Café , Cuerpo Estriado/metabolismo , Cuerpo Estriado/diagnóstico por imagen , Cuerpo Estriado/efectos de los fármacos , Tropanos
19.
FASEB J ; 38(17): e70034, 2024 Sep 15.
Artículo en Inglés | MEDLINE | ID: mdl-39248019

RESUMEN

The function of hydroxysteroid dehydrogenase 12 (HSD17B12) in lipid metabolism is poorly understood. To study this further, we created mice with hepatocyte-specific knockout of HSD17B12 (LiB12cKO). From 2 months on, these mice showed significant fat accumulation in their liver. As they aged, they also had a reduced whole-body fat percentage. Interestingly, the liver fat accumulation did not result in the typical formation of large lipid droplets (LD); instead, small droplets were more prevalent. Thus, LiB12KO liver did not show increased macrovesicular steatosis with the increasing fat content, while microvesicular steatosis was the predominant feature in the liver. This indicates a failure in the LD expansion. This was associated with liver damage, presumably due to lipotoxicity. Notably, the lipidomics data did not support an essential role of HSD17B12 in fatty acid (FA) elongation. However, we did observe a decrease in the quantity of specific lipid species that contain FAs with carbon chain lengths of 18 and 20 atoms, including oleic acid. Of these, phosphatidylcholine and phosphatidylethanolamine have been shown to play a key role in LD formation, and a limited amount of these lipids could be part of the mechanism leading to the dysfunction in LD expansion. The increase in the Cidec expression further supported the deficiency in LD expansion in the LiB12cKO liver. This protein is crucial for the fusion and growth of LDs, along with the downregulation of several members of the major urinary protein family of proteins, which have recently been shown to be altered during endoplasmic reticulum stress.


Asunto(s)
Hígado Graso , Hepatocitos , Gotas Lipídicas , Ratones Noqueados , Animales , Ratones , Gotas Lipídicas/metabolismo , Hepatocitos/metabolismo , Hígado Graso/metabolismo , Hígado Graso/patología , Hígado Graso/genética , 17-Hidroxiesteroide Deshidrogenasas/metabolismo , 17-Hidroxiesteroide Deshidrogenasas/genética , Metabolismo de los Lípidos , Peso Corporal , Hígado/metabolismo , Hígado/patología , Masculino , Ratones Endogámicos C57BL , Ácidos Grasos/metabolismo
20.
Circ Res ; 132(11): e188-e205, 2023 05 26.
Artículo en Inglés | MEDLINE | ID: mdl-37139790

RESUMEN

BACKGROUND: Transverse tubules (t-tubules) form gradually in the developing heart, critically enabling maturation of cardiomyocyte Ca2+ homeostasis. The membrane bending and scaffolding protein BIN1 (bridging integrator 1) has been implicated in this process. However, it is unclear which of the various reported BIN1 isoforms are involved, and whether BIN1 function is regulated by its putative binding partners MTM1 (myotubularin), a phosphoinositide 3'-phosphatase, and DNM2 (dynamin-2), a GTPase believed to mediate membrane fission. METHODS: We investigated the roles of BIN1, MTM1, and DNM2 in t-tubule formation in developing mouse cardiomyocytes, and in gene-modified HL-1 and human-induced pluripotent stem cell-derived cardiomyocytes. T-tubules and proteins of interest were imaged by confocal and Airyscan microscopy, and expression patterns were examined by RT-qPCR and Western blotting. Ca2+ release was recorded using Fluo-4. RESULTS: We observed that in the postnatal mouse heart, BIN1 localizes along Z-lines from early developmental stages, consistent with roles in initial budding and scaffolding of t-tubules. T-tubule proliferation and organization were linked to a progressive and parallel increase in 4 detected BIN1 isoforms. All isoforms were observed to induce tubulation in cardiomyocytes but produced t-tubules with differing geometries. BIN1-induced tubulations contained the L-type Ca2+ channel, were colocalized with caveolin-3 and the ryanodine receptor, and effectively triggered Ca2+ release. BIN1 upregulation during development was paralleled by increasing expression of MTM1. Despite no direct binding between MTM1 and murine cardiac BIN1 isoforms, which lack exon 11, high MTM1 levels were necessary for BIN1-induced tubulation, indicating a central role of phosphoinositide homeostasis. In contrast, the developing heart exhibited declining levels of DNM2. Indeed, we observed that high levels of DNM2 are inhibitory for t-tubule formation, although this protein colocalizes with BIN1 along Z-lines, and binds all 4 isoforms. CONCLUSIONS: These findings indicate that BIN1, MTM1, and DNM2 have balanced and collaborative roles in controlling t-tubule growth in cardiomyocytes.


Asunto(s)
Dinamina II , Miocitos Cardíacos , Animales , Humanos , Ratones , Proteínas Adaptadoras Transductoras de Señales/genética , Proteínas Adaptadoras Transductoras de Señales/metabolismo , Dinamina II/genética , Dinamina II/metabolismo , Miocitos Cardíacos/metabolismo , Proteínas del Tejido Nervioso/metabolismo , Proteínas Nucleares/metabolismo , Isoformas de Proteínas/metabolismo , Proteínas Tirosina Fosfatasas no Receptoras/genética , Proteínas Tirosina Fosfatasas no Receptoras/metabolismo , Proteínas Supresoras de Tumor/metabolismo
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