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Kidney disease is highly heritable; however, the causal genetic variants, the cell types in which these variants function, and the molecular mechanisms underlying kidney disease remain largely unknown. To identify genetic loci affecting kidney function, we performed a GWAS using multiple kidney function biomarkers and identified 462 loci. To begin to investigate how these loci affect kidney function, we generated single-cell chromatin accessibility (scATAC-seq) maps of the human kidney and identified candidate cis-regulatory elements (cCREs) for kidney podocytes, tubule epithelial cells, and kidney endothelial, stromal, and immune cells. Kidney tubule epithelial cCREs explained 58% of kidney function SNP-heritability and kidney podocyte cCREs explained an additional 6.5% of SNP-heritability. In contrast, little kidney function heritability was explained by kidney endothelial, stromal, or immune cell-specific cCREs. Through functionally informed fine-mapping, we identified putative causal kidney function variants and their corresponding cCREs. Using kidney scATAC-seq data, we created a deep learning model (which we named ChromKid) to predict kidney cell type-specific chromatin accessibility from sequence. ChromKid and allele specific kidney scATAC-seq revealed that many fine-mapped kidney function variants locally change chromatin accessibility in tubule epithelial cells. Enhancer assays confirmed that fine-mapped kidney function variants alter tubule epithelial regulatory element function. To map the genes which these regulatory elements control, we used CRISPR interference (CRISPRi) to target these regulatory elements in tubule epithelial cells and assessed changes in gene expression. CRISPRi of enhancers harboring kidney function variants regulated NDRG1 and RBPMS expression. Thus, inherited differences in tubule epithelial NDRG1 and RBPMS expression may predispose to kidney disease in humans. We conclude that genetic variants affecting tubule epithelial regulatory element function account for most SNP-heritability of human kidney function. This work provides an experimental approach to identify the variants, regulatory elements, and genes involved in polygenic disease.
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A key aspect of nutrient absorption is the exquisite division of labour across the length of the small intestine, with individual nutrients taken up at different proximal:distal positions. For millennia, the small intestine was thought to comprise three segments with indefinite borders: the duodenum, jejunum and ileum. By examining the fine-scale longitudinal transcriptional patterns that span the mouse and human small intestine, we instead identified five domains of nutrient absorption that mount distinct responses to dietary changes, and three regional stem cell populations. Molecular domain identity can be detected with machine learning, which provides a systematic method to computationally identify intestinal domains in mice. We generated a predictive model of transcriptional control of domain identity and validated the roles of Ppar-δ and Cdx1 in patterning lipid metabolism-associated genes. These findings represent a foundational framework for the zonation of absorption across the mammalian small intestine.
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Duodeno , Intestino Delgado , Humanos , Ratones , Animales , Intestino Delgado/metabolismo , Duodeno/metabolismo , Intestinos , Yeyuno/metabolismo , Íleon/metabolismo , MamíferosRESUMEN
A key aspect of nutrient absorption is the exquisite division of labor across the length of the small intestine, with individual classes of micronutrients taken up at different positions. For millennia, the small intestine was thought to comprise three segments with indefinite borders: the duodenum, jejunum, and ileum. By examining fine-scale longitudinal segmentation of the mouse and human small intestines, we identified transcriptional signatures and upstream regulatory factors that define five domains of nutrient absorption, distinct from the three traditional sections. Spatially restricted expression programs were most prominent in nutrient-absorbing enterocytes but initially arose in intestinal stem cells residing in three regional populations. While a core signature was maintained across mice and humans with different diets and environments, domain properties were influenced by dietary changes. We established the functions of Ppar-Ạand Cdx1 in patterning lipid metabolism in distal domains and generated a predictive model of additional transcription factors that direct domain identity. Molecular domain identity can be detected with machine learning, representing the first systematic method to computationally identify specific intestinal regions in mice. These findings provide a foundational framework for the identity and control of longitudinal zonation of absorption along the proximal:distal small intestinal axis.
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Mutations in the gene encoding the zinc-finger transcription factor Ikaros (IKZF1) are found in patients with immunodeficiency, leukemia, and autoimmunity. Although Ikaros has a well-established function in modulating gene expression programs important for hematopoietic development, its role in other cell types is less well defined. Here, we uncover functions for Ikaros in thymic epithelial lineage development in mice and show that Ikzf1 expression in medullary thymic epithelial cells (mTECs) is required for both autoimmune regulator-positive (Aire+) mTEC development and tissue-specific antigen (TSA) gene expression. Accordingly, TEC-specific deletion of Ikzf1 in mice results in a profound decrease in Aire+ mTECs, a global loss of TSA gene expression, and the development of autoimmunity. Moreover, Ikaros shapes thymic mimetic cell diversity, and its deletion results in a marked expansion of thymic tuft cells and muscle-like mTECs and a loss of other Aire-dependent mimetic populations. Single-cell analysis reveals that Ikaros modulates core transcriptional programs in TECs that correlate with the observed cellular changes. Our findings highlight a previously undescribed role for Ikaros in regulating epithelial lineage development and function and suggest that failed thymic central tolerance could contribute to the autoimmunity seen in humans with IKZF1 mutations.
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Tolerancia Central , Timo , Humanos , Ratones , Animales , Diferenciación Celular , Factores de Transcripción , Regulación de la Expresión GénicaRESUMEN
The gastrointestinal tract relies on the production, maturation, and transit of mucin to protect against pathogens and to lubricate the epithelial lining. Although the molecular and cellular mechanisms that regulate mucin production and movement are beginning to be understood, the upstream epithelial signals that contribute to mucin regulation remain unclear. Here, we report that the inflammatory cytokine tumor necrosis factor (TNF), generated by the epithelium, contributes to mucin homeostasis by regulating both cell differentiation and cystic fibrosis transmembrane conductance regulator (CFTR) activity. We used genetic mouse models and noninflamed samples from patients with inflammatory bowel disease (IBD) undergoing anti-TNF therapy to assess the effect of in vivo perturbation of TNF. We found that inhibition of epithelial TNF promotes the differentiation of secretory progenitor cells into mucus-producing goblet cells. Furthermore, TNF treatment and CFTR inhibition in intestinal organoids demonstrated that TNF promotes ion transport and luminal flow via CFTR. The absence of TNF led to slower gut transit times, which we propose results from increased mucus accumulation coupled with decreased luminal fluid pumping. These findings point to a TNF/CFTR signaling axis in the adult intestine and identify epithelial cell-derived TNF as an upstream regulator of mucin homeostasis.
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Regulador de Conductancia de Transmembrana de Fibrosis Quística , Mucinas , Humanos , Animales , Ratones , Mucinas/genética , Mucinas/metabolismo , Regulador de Conductancia de Transmembrana de Fibrosis Quística/genética , Inhibidores del Factor de Necrosis Tumoral , Células Epiteliales/metabolismo , Diferenciación Celular , Factores de Necrosis Tumoral , HomeostasisRESUMEN
Background: Donation after circulatory death (DCD) liver allografts are associated with higher rates of primary non-function (PNF) and ischemic cholangiopathy (IC). Advanced recovery techniques, including thoracoabdominal normothermic regional perfusion (TA-NRP), may improve organ utilization and patient and allograft outcomes. Given the increasing US experience with TA-NRP DCD recovery, we evaluated outcomes of DCD liver allografts transplanted after TA-NRP. Methods: Liver allografts transplanted from DCD donors after TA-NRP were identified from 5/1/2021 to 1/31/2022 across 8 centers. Donor data included demographics, functional warm ischemic time (fWIT), total warm ischemia time (tWIT) and total time on TA-NRP. Recipient data included demographics, model of end stage liver disease (MELD) score, etiology of liver disease, PNF, cold ischemic time (CIT), liver function tests, intensive care unit (ICU) and hospital length of stay (LOS), post-operative transplant related complications. Results: The donors' median age was 32 years old and median BMI was 27.4. Median fWIT was 20.5â min; fWIT exceeded 30â min in two donors. Median time to initiation of TA-NRP was 4â min and median time on bypass was 66â min. The median recipient listed MELD and MELD at transplant were 22 and 21, respectively. Median allograft CIT was 292â min. The median length of follow up was 257 days. Median ICU and hospital LOS were 2 and 7 days, respectively. Three recipients required management of anastomotic biliary strictures. No patients demonstrated IC, PNF or required re-transplantation. Conclusion: Liver allografts from TA-NRP DCD donors demonstrated good early allograft and recipient outcomes.
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Mammalian carotid body arterial chemoreceptors function as an early warning system for hypoxia, triggering acute life-saving arousal and cardiorespiratory reflexes. To serve this role, carotid body glomus cells are highly sensitive to decreases in oxygen availability. While the mitochondria and plasma membrane signaling proteins have been implicated in oxygen sensing by glomus cells, the mechanism underlying their mitochondrial sensitivity to hypoxia compared to other cells is unknown. Here, we identify HIGD1C, a novel hypoxia-inducible gene domain factor isoform, as an electron transport chain complex IV-interacting protein that is almost exclusively expressed in the carotid body and is therefore not generally necessary for mitochondrial function. Importantly, HIGD1C is required for carotid body oxygen sensing and enhances complex IV sensitivity to hypoxia. Thus, we propose that HIGD1C promotes exquisite oxygen sensing by the carotid body, illustrating how specialized mitochondria can be used as sentinels of metabolic stress to elicit essential adaptive behaviors.
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Cuerpo Carotídeo , Animales , Oxígeno/metabolismo , Células Quimiorreceptoras/metabolismo , Mitocondrias/metabolismo , Hipoxia/metabolismo , Mamíferos/metabolismoRESUMEN
The autoimmune regulator (Aire), a well-defined transcriptional regulator in the thymus, is also found in extrathymic Aire-expressing cells (eTACs) in the secondary lymphoid organs. eTACs are hematopoietic antigen-presenting cells and inducers of immune tolerance, but their precise identity has remained unclear. Here, we use single-cell multiomics, transgenic murine models, and functional approaches to define eTACs at the transcriptional, genomic, and proteomic level. We find that eTACs consist of two similar cell types: CCR7+ Aire-expressing migratory dendritic cells (AmDCs) and an Airehi population coexpressing Aire and retinoic acid receptorrelated orphan receptor γt (RORγt) that we term Janus cells (JCs). Both JCs and AmDCs have the highest transcriptional and genomic homology to CCR7+ migratory dendritic cells. eTACs, particularly JCs, have highly accessible chromatin and broad gene expression, including a range of tissue-specific antigens, as well as remarkable homology to medullary thymic epithelium and RANK-dependent Aire expression. Transgenic self-antigen expression by eTACs is sufficient to induce negative selection and prevent autoimmune diabetes. This transcriptional, genomic, and functional symmetry between eTACs (both JCs and AmDCs) and medullary thymic epitheliumthe other principal Aire-expressing population and a key regulator of central toleranceidentifies a core program that may influence self-representation and tolerance across the spectrum of immune development.
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Epitelio/inmunología , Análisis de la Célula Individual , Timo/inmunología , Factores de Transcripción/inmunología , Animales , Tolerancia Inmunológica/inmunología , Ratones , Ratones Endogámicos C57BL , Ratones Endogámicos NOD , Ratones Transgénicos , Timo/citología , Proteína AIRERESUMEN
There remains a critical need for improved staging of non-small-cell lung cancer, as recurrence and mortality due to undetectable metastases at the time of surgery remain high even after complete resection of tumors currently categorized as 'early stage.' A 14-gene quantitative PCR-based expression profile has been extensively validated to better identify patients at high-risk of 5-year mortality after surgical resection than conventional staging - mortality that almost always results from previously undetectable metastases. Furthermore, prospective studies now suggest a predictive benefit in disease-free survival when the assay is used to guide adjuvant chemotherapy decisions in early-stage non-small-cell lung cancer patients.
Lay abstract There is a need for improvement in the way early-stage non-small-cell lung cancers are staged and treated because many patients with 'early-stage' disease suffer high rates of cancer recurrence after surgery. In recent years, a specialized test has been developed to allow better characterization of a tumor's risk of recurrence based on the genes being expressed by tumor cells. Use of this test, in conjunction with standard staging methods, is better able to identify patients at high risk of cancer recurrence after surgery. Evidence suggests that giving chemotherapy to patients at high risk of recurrence after surgery reduces recurrence rates and improves long-term patient survival.
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Biomarcadores de Tumor/genética , Carcinoma de Pulmón de Células no Pequeñas/mortalidad , Neoplasias Pulmonares/mortalidad , Técnicas de Diagnóstico Molecular/métodos , Recurrencia Local de Neoplasia/epidemiología , Carcinogénesis/genética , Carcinoma de Pulmón de Células no Pequeñas/diagnóstico , Carcinoma de Pulmón de Células no Pequeñas/genética , Carcinoma de Pulmón de Células no Pequeñas/terapia , Quimioterapia Adyuvante/estadística & datos numéricos , Toma de Decisiones Clínicas , Conjuntos de Datos como Asunto , Supervivencia sin Enfermedad , Perfilación de la Expresión Génica , Regulación Neoplásica de la Expresión Génica , Humanos , Neoplasias Pulmonares/diagnóstico , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/terapia , Técnicas de Diagnóstico Molecular/estadística & datos numéricos , Recurrencia Local de Neoplasia/genética , Recurrencia Local de Neoplasia/prevención & control , Estadificación de Neoplasias/métodos , Neumonectomía/estadística & datos numéricos , Estudios Prospectivos , Reacción en Cadena en Tiempo Real de la Polimerasa , Medición de Riesgo/métodosRESUMEN
Naturally occurring cases of monogenic type 1 diabetes (T1D) help establish direct mechanisms driving this complex autoimmune disease. A recently identified de novo germline gain-of-function (GOF) mutation in the transcriptional regulator STAT3 was found to cause neonatal T1D. We engineered a novel knock-in mouse incorporating this highly diabetogenic human STAT3 mutation (K392R) and found that these mice recapitulated the human autoimmune diabetes phenotype. Paired single-cell TCR and RNA sequencing revealed that STAT3-GOF drives proliferation and clonal expansion of effector CD8+ cells that resist terminal exhaustion. Single-cell ATAC-seq showed that these effector T cells are epigenetically distinct and have differential chromatin architecture induced by STAT3-GOF. Analysis of islet TCR clonotypes revealed a CD8+ cell reacting against known antigen IGRP, and STAT3-GOF in an IGRP-reactive TCR transgenic model demonstrated that STAT3-GOF intrinsic to CD8+ cells is sufficient to accelerate diabetes onset. Altogether, these findings reveal a diabetogenic CD8+ T cell response that is restrained in the presence of normal STAT3 activity and drives diabetes pathogenesis.
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Linfocitos T CD8-positivos/inmunología , Diabetes Mellitus Tipo 1/genética , Diabetes Mellitus Tipo 1/inmunología , Tolerancia Inmunológica/genética , Mutación/genética , Factor de Transcripción STAT3/genética , Animales , Autoinmunidad , Proliferación Celular , Quimiotaxis/genética , Reactividad Cruzada/inmunología , Citotoxicidad Inmunológica/genética , Modelos Animales de Enfermedad , Epigénesis Genética , Mutación con Ganancia de Función , Heterocigoto , Humanos , Ratones , Fenotipo , Regulación hacia ArribaRESUMEN
Accurately representing the Indian Ocean Dipole (IOD) is crucial for reliable climate predictions and future projections. However, El Niño-Southern Oscillation (ENSO) and IOD interact, making it necessary to evaluate ENSO and IOD simultaneously. Using the historical simulation from 32 fifth phase of Coupled Model Intercomparison Project (CMIP5) models and 34 CMIP6 models, here we find that there are some modest changes in the basic characteristics of the IOD and ENSO from CMIP5 to CMIP6. Firstly, there is a slight shift in the seasonality of IOD toward an earlier peak in September in CMIP6, from November in CMIP5. Secondly, inter-model spread in the frequency of ENSO and the IOD has reduced in CMIP6 relative to CMIP5. ENSO asymmetry is still underestimated in CMIP6, based on the skewness of the Niño3 index, while the IOD skewness has degraded from CMIP5. Finally, mean state SST biases impact on the strength of the IOD; the Pacific cold tongue mean state is important in CMIP5, but in CMIP6 the Pacific warm pool mean state is more important.
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A series of crystalline nickel(II) complexes (1-3) based on inexpensive bis(thiosemicarbazone) ligands diacetylbis(4-methyl-3-thiosemicarbazone) (H2ATSM), diacetylbis(4,4-dimethyl-3-thiosemicarbazone) (H2ATSDM), and diacetylbis[4-(2,2,2-trifluoroethyl)-3-thiosemicarbazone] (H2ATSM-F6) were synthesized and characterized by single-crystal X-ray diffraction and NMR, UV-visible, and Fourier transform infrared spectroscopies. Modified electrodes GC-1-GC-3 were prepared with films of 1-3 deposited on glassy carbon and evaluated as potential hydrogen evolution reaction (HER) catalysts. HER studies in 0.5 M aqueous H2SO4 (10 mA cm-2) revealed dramatic shifts in the overpotential from 0.740 to 0.450 V after extended cycling for 1 and 2. The charge-transfer resistances for GC-1-GC-3 were determined to be 270, 160, and 630 Ω, respectively. Characterization of the modified surfaces for GC-1 and GC-2 by scanning electron microscopy and Raman spectroscopy revealed similar crystalline coatings before HER that changed to surface-modified crystallites after conditioning. The surface of GC-3 had an initial glasslike appearance before HER that delaminated after HER. The differences in the surface morphology and the effect of conditioning are correlated with crystal-packing effects. Complexes 1 and 2 pack as columns of interacting complexes in the crystallographic a direction with short interplanar spacings between 3.37 and 3.54 Å. Complex 3 packs as columns of isolated molecules in the crystallographic b direction with long-range interplanar spacings of 9.40 Å.
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Marine heatwaves (MHWs) can cause devastating impacts to marine life. Despite the serious consequences of MHWs, our understanding of their drivers is largely based on isolated case studies rather than any systematic unifying assessment. Here we provide the first global assessment under a consistent framework by combining a confidence assessment of the historical refereed literature from 1950 to February 2016, together with the analysis of MHWs determined from daily satellite sea surface temperatures from 1982-2016, to identify the important local processes, large-scale climate modes and teleconnections that are associated with MHWs regionally. Clear patterns emerge, including coherent relationships between enhanced or suppressed MHW occurrences with the dominant climate modes across most regions of the globe - an important exception being western boundary current regions where reports of MHW events are few and ocean-climate relationships are complex. These results provide a global baseline for future MHW process and prediction studies.
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We have demonstrated a simple and scalable fabrication process for defect-rich MoS2 directly from ammonium tetrathiomolybdate precursor using intense pulse light treatment in milliseconds durations. The formation of MoS2 from the precursor film after intense pulsed light exposure was confirmed with XPS, XRD, electron microscopy and Raman spectroscopy. The resulting material exhibited high activity for the hydrogen evolution reaction (HER) in acidic media, requiring merely 200 mV overpotential to reach a current density of 10 mA cm-2. Additionally, the catalyst remained highly active for HER over extended durability testing with the overpotential increasing by 28 mV following 1000 cycles. The roll-to-roll amenable fabrication of this highly-active material could be adapted for mass production of electrodes comprised of earth-abundant materials for water splitting applications.
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BACKGROUND: Lateral abdominal wall defects are a significant contributor to patient morbidity and mortality in the United States. Reconstruction involving flank hernias and bulges is relatively scarce in the literature despite its serious consequences. The authors aim to identify an objective approach for the evaluation and successful repair of defects of the lateral abdominal wall. METHODS: A retrospective analysis was carried out on patients presenting for open repair of a lateral wall defect performed by a single surgeon. Over a 5-year period, there were 29 consecutive patients with a mean follow-up period of 21.2 months. Patient demographics including body mass index, number of hernia defects, number of previous repairs/abdominal operations, defect size, operative time, blood loss, and complications (e.g., recurrence/bulge, seroma, hematoma, wound infection, persistent pain, skin breakdown, and fascial dehiscence) were collected. RESULTS: Patients who underwent flank hernia repairs using an inlay/underlay nonbridged technique with the use of acellular dermal matrix had low recurrence and overall complication rates. Only one patient (3.4 percent) had a recurrence at follow-up, and another patient (3.4 percent) had developed a bulge. CONCLUSIONS: The authors' data indicate successful results when their technique is applied. Proper patient selection is essential, along with a thorough understanding of anatomy and techniques for successful reconstruction. The authors recommend using an inlay (preferred) or underlay repair with acellular dermal matrix to reinforce the surrounding musculofascial closure. This technique, in conjunction with the authors' holistic abdominal wall reconstruction protocol, has optimized outcomes and identified a successful multidisciplinary strategy for the reconstruction of lateral wall defects. CLINICAL QUESTION/LEVEL OF EVIDENCE: Therapeutic, IV.