Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 33
Filtrar
Más filtros

Banco de datos
Tipo del documento
País de afiliación
Intervalo de año de publicación
1.
Am J Physiol Heart Circ Physiol ; 320(1): H323-H337, 2021 01 01.
Artículo en Inglés | MEDLINE | ID: mdl-33164548

RESUMEN

Interleukin-4 receptor α (IL4Rα) signaling plays an important role in cardiac remodeling during myocardial infarction (MI). However, the target cell type(s) of IL4Rα signaling during this remodeling remains unclear. Here, we investigated the contribution of endogenous myeloid-specific IL4Rα signaling in cardiac remodeling post-MI. We established a murine myeloid-specific IL4Rα knockout (MyIL4RαKO) model with LysM promoter-driven Cre recombination. Macrophages from MyIL4RαKO mice showed significant downregulation of alternatively activated macrophage markers but an upregulation of classical activated macrophage markers both in vitro and in vivo, indicating the successful inactivation of IL4Rα signaling in macrophages. To examine the role of myeloid IL4Rα during MI, we subjected MyIL4RαKO and littermate floxed control (FC) mice to MI. We found that cardiac function was significantly impaired as a result of myeloid-specific IL4Rα deficiency. This deficiency resulted in a dysregulated inflammatory response consisting of decreased production of anti-inflammatory cytokines. Myeloid IL4Rα deficiency also led to reduced collagen 1 deposition and an imbalance of matrix metalloproteinases (MMPs)/tissue inhibitors of metalloproteinases (TIMPs), with upregulated MMPs and downregulated TIMPs, which resulted in insufficient fibrotic remodeling. In conclusion, this study identifies that myeloid-specific IL4Rα signaling regulates inflammation and fibrotic remodeling during MI. Therefore, myeloid-specific activation of IL4Rα signaling could offer protective benefits after MI.NEW & NOTEWORTHY This study showed, for the first time, the role of endogenous IL4Rα signaling in myeloid cells during cardiac remodeling and the underlying mechanisms. We identified myeloid cells are the critical target cell types of IL4Rα signaling during cardiac remodeling post-MI. Deficiency of myeloid IL4Rα signaling causes deteriorated cardiac function post-MI, due to dysregulated inflammation and insufficient fibrotic remodeling. This study sheds light on the potential of activating myeloid-specific IL4Rα signaling to modify remodeling post-MI. This brings hope to patients with MI and diminishes side effects by cell type-specific instead of whole body treatment.


Asunto(s)
Citocinas/metabolismo , Mediadores de Inflamación/metabolismo , Macrófagos/metabolismo , Infarto del Miocardio/metabolismo , Miocardio/metabolismo , Receptores de Superficie Celular/metabolismo , Función Ventricular Izquierda , Remodelación Ventricular , Animales , Células Cultivadas , Modelos Animales de Enfermedad , Fibrosis , Activación de Macrófagos , Macrófagos/patología , Masculino , Ratones Endogámicos BALB C , Ratones Endogámicos C57BL , Ratones Noqueados , Infarto del Miocardio/genética , Infarto del Miocardio/patología , Infarto del Miocardio/fisiopatología , Miocardio/patología , Receptores de Superficie Celular/deficiencia , Receptores de Superficie Celular/genética , Transducción de Señal
2.
Proc Natl Acad Sci U S A ; 114(45): 11832-11837, 2017 11 07.
Artículo en Inglés | MEDLINE | ID: mdl-29078370

RESUMEN

The day we understand the time evolution of subcellular events at a level of detail comparable to physical systems governed by Newton's laws of motion seems far away. Even so, quantitative approaches to cellular dynamics add to our understanding of cell biology. With data-guided frameworks we can develop better predictions about, and methods for, control over specific biological processes and system-wide cell behavior. Here we describe an approach for optimizing the use of transcription factors (TFs) in cellular reprogramming, based on a device commonly used in optimal control. We construct an approximate model for the natural evolution of a cell-cycle-synchronized population of human fibroblasts, based on data obtained by sampling the expression of 22,083 genes at several time points during the cell cycle. To arrive at a model of moderate complexity, we cluster gene expression based on division of the genome into topologically associating domains (TADs) and then model the dynamics of TAD expression levels. Based on this dynamical model and additional data, such as known TF binding sites and activity, we develop a methodology for identifying the top TF candidates for a specific cellular reprogramming task. Our data-guided methodology identifies a number of TFs previously validated for reprogramming and/or natural differentiation and predicts some potentially useful combinations of TFs. Our findings highlight the immense potential of dynamical models, mathematics, and data-guided methodologies for improving strategies for control over biological processes.


Asunto(s)
Algoritmos , Reprogramación Celular/genética , Biología Computacional/métodos , Fibroblastos/citología , Factores de Transcripción/genética , Sitios de Unión/genética , Ciclo Celular/genética , Diferenciación Celular , Células Cultivadas , Reprogramación Celular/fisiología , Perfilación de la Expresión Génica , Genoma Humano/genética , Humanos , Modelos Genéticos
3.
J Biol Chem ; 293(23): 8775-8786, 2018 06 08.
Artículo en Inglés | MEDLINE | ID: mdl-29636416

RESUMEN

Obesity-induced chronic inflammation is associated with metabolic disease. Results from mouse models utilizing a high-fat diet (HFD) have indicated that an increase in activated macrophages, including CD11c+ adipose tissue macrophages (ATMs), contributes to insulin resistance. Obesity primes myeloid cell production from hematopoietic stem cells (HSCs) and Toll-like receptor 4 (TLR4), and the downstream TIR domain-containing adapter protein-inducing interferon-ß (TRIF)- and MyD88-mediated pathways regulate production of similar myeloid cells after lipopolysaccharide stimulation. However, the role of these pathways in HFD-induced myelopoiesis is unknown. We hypothesized that saturated fatty acids and HFD alter myelopoiesis by activating TLR4 pathways in HSCs, differentially producing pro-inflammatory CD11c+ myeloid cells that contribute to obesity-induced metabolic disease. Results from reciprocal bone marrow transplants (BMTs) with Tlr4-/- and WT mice indicated that TLR4 is required for HFD-induced myelopoiesis and production of CD11c+ ATMs. Experiments with homozygous knockouts of Irakm (encoding a suppressor of MyD88 inactivation) and Trif in competitive BMTs revealed that MyD88 is required for HFD expansion of granulocyte macrophage progenitors and that Trif is required for pregranulocyte macrophage progenitor expansion. A comparison of WT, Tlr4-/-, Myd88-/-, and Trif-/- mice on HFD demonstrated that TLR4 plays a role in the production of CD11c+ ATMs, and both Myd88-/- and Trif-/- mice produced fewer ATMs than WT mice. Moreover, HFD-induced TLR4 activation inhibited macrophage proliferation, leading to greater accumulation of recruited CD11c+ ATMs. Our results indicate that HFD potentiates TLR4 and both its MyD88- and TRIF-mediated downstream pathways within progenitors and adipose tissue and leads to macrophage polarization.


Asunto(s)
Proteínas Adaptadoras del Transporte Vesicular/inmunología , Antígeno CD11c/inmunología , Macrófagos/patología , Factor 88 de Diferenciación Mieloide/inmunología , Mielopoyesis , Obesidad/patología , Receptor Toll-Like 4/inmunología , Tejido Adiposo/inmunología , Tejido Adiposo/patología , Animales , Dieta Alta en Grasa/efectos adversos , Inflamación/etiología , Inflamación/inmunología , Inflamación/patología , Macrófagos/inmunología , Masculino , Ratones Endogámicos C57BL , Ratones Obesos , Obesidad/complicaciones , Obesidad/etiología , Obesidad/inmunología
4.
J Immunol ; 197(9): 3650-3661, 2016 11 01.
Artículo en Inglés | MEDLINE | ID: mdl-27683748

RESUMEN

Dynamic changes of adipose tissue leukocytes, including adipose tissue macrophage (ATM) and adipose tissue dendritic cells (ATDCs), contribute to obesity-induced inflammation and metabolic disease. However, clear discrimination between ATDC and ATM in adipose tissue has limited progress in the field of immunometabolism. In this study, we use CD64 to distinguish ATM and ATDC, and investigated the temporal and functional changes in these myeloid populations during obesity. Flow cytometry and immunostaining demonstrated that the definition of ATM as F4/80+CD11b+ cells overlaps with other leukocytes and that CD45+CD64+ is specific for ATM. The expression of core dendritic cell genes was enriched in CD11c+CD64- cells (ATDC), whereas core macrophage genes were enriched in CD45+CD64+ cells (ATM). CD11c+CD64- ATDCs expressed MHC class II and costimulatory receptors, and had similar capacity to stimulate CD4+ T cell proliferation as ATMs. ATDCs were predominantly CD11b+ conventional dendritic cells and made up the bulk of CD11c+ cells in adipose tissue with moderate high-fat diet exposure. Mixed chimeric experiments with Ccr2-/- mice demonstrated that high-fat diet-induced ATM accumulation from monocytes was dependent on CCR2, whereas ATDC accumulation was less CCR2 dependent. ATDC accumulation during obesity was attenuated in Ccr7-/- mice and was associated with decreased adipose tissue inflammation and insulin resistance. CD45+CD64+ ATM and CD45+CD64-CD11c+ ATDCs were identified in human obese adipose tissue and ATDCs were increased in s.c. adipose tissue compared with omental adipose tissue. These results support a revised strategy for unambiguous delineation of ATM and ATDC, and suggest that ATDCs are independent contributors to adipose tissue inflammation during obesity.


Asunto(s)
Tejido Adiposo/inmunología , Células Dendríticas/inmunología , Inflamación/inmunología , Macrófagos/inmunología , Obesidad/inmunología , Animales , Células Cultivadas , Dieta Alta en Grasa , Perfilación de la Expresión Génica , Humanos , Inmunofenotipificación , Resistencia a la Insulina , Ratones , Ratones Endogámicos C57BL , Ratones Noqueados , Receptores CCR2/genética , Receptores CCR7/genética , Receptores de IgG/metabolismo
5.
Proc Natl Acad Sci U S A ; 112(26): 8002-7, 2015 Jun 30.
Artículo en Inglés | MEDLINE | ID: mdl-26080430

RESUMEN

The 4D organization of the interphase nucleus, or the 4D Nucleome (4DN), reflects a dynamical interaction between 3D genome structure and function and its relationship to phenotype. We present initial analyses of the human 4DN, capturing genome-wide structure using chromosome conformation capture and 3D imaging, and function using RNA-sequencing. We introduce a quantitative index that measures underlying topological stability of a genomic region. Our results show that structural features of genomic regions correlate with function with surprising persistence over time. Furthermore, constructing genome-wide gene-level contact maps aided in identifying gene pairs with high potential for coregulation and colocalization in a manner consistent with expression via transcription factories. We additionally use 2D phase planes to visualize patterns in 4DN data. Finally, we evaluated gene pairs within a circadian gene module using 3D imaging, and found periodicity in the movement of clock circadian regulator and period circadian clock 2 relative to each other that followed a circadian rhythm and entrained with their expression.


Asunto(s)
Núcleo Celular/metabolismo , Genoma Humano , Interfase , Ritmo Circadiano/genética , Redes Reguladoras de Genes , Humanos
6.
Dev Biol ; 397(1): 31-44, 2015 Jan 01.
Artículo en Inglés | MEDLINE | ID: mdl-25236433

RESUMEN

Extraocular muscles (EOMs) are highly specialized skeletal muscles that originate from the head mesoderm and control eye movements. EOMs are uniquely spared in Duchenne muscular dystrophy and animal models of dystrophin deficiency. Specific traits of myogenic progenitors may be determinants of this preferential sparing, but very little is known about the myogenic cells in this muscle group. While satellite cells (SCs) have long been recognized as the main source of myogenic cells in adult muscle, most of the knowledge about these cells comes from the prototypic limb muscles. In this study, we show that EOMs, regardless of their distinctive Pax3-negative lineage origin, harbor SCs that share a common signature (Pax7(+), Ki67(-), Nestin-GFP(+), Myf5(nLacZ+), MyoD-positive lineage origin) with their limb and diaphragm somite-derived counterparts, but are remarkably endowed with a high proliferative potential as revealed in cell culture assays. Specifically, we demonstrate that in adult as well as in aging mice, EOM SCs possess a superior expansion capacity, contributing significantly more proliferating, differentiating and renewal progeny than their limb and diaphragm counterparts. These robust growth and renewal properties are maintained by EOM SCs isolated from dystrophin-null (mdx) mice, while SCs from muscles affected by dystrophin deficiency (i.e., limb and diaphragm) expand poorly in vitro. EOM SCs also retain higher performance in cell transplantation assays in which donor cells were engrafted into host mdx limb muscle. Collectively, our study provides a comprehensive picture of EOM myogenic progenitors, showing that while these cells share common hallmarks with the prototypic SCs in somite-derived muscles, they distinctively feature robust growth and renewal capacities that warrant the title of high performance myo-engines and promote consideration of their properties for developing new approaches in cell-based therapy to combat skeletal muscle wasting.


Asunto(s)
Distrofina/fisiología , Regulación del Desarrollo de la Expresión Génica , Músculo Esquelético/embriología , Regeneración/fisiología , Células Satélite del Músculo Esquelético/citología , Células Madre/citología , Animales , Linaje de la Célula , Proliferación Celular , Separación Celular , Trasplante de Células , Modelos Animales de Enfermedad , Distrofina/deficiencia , Extremidades/embriología , Femenino , Citometría de Flujo , Masculino , Ratones , Ratones Endogámicos C57BL , Ratones Endogámicos mdx , Ratones Transgénicos , Distrofia Muscular de Duchenne/genética
7.
J Biol Chem ; 290(21): 13250-62, 2015 May 22.
Artículo en Inglés | MEDLINE | ID: mdl-25869128

RESUMEN

Women of reproductive age are protected from metabolic disease relative to postmenopausal women and men. Most preclinical rodent studies are skewed toward the use of male mice to study obesity-induced metabolic dysfunction because of a similar protection observed in female mice. How sex differences in obesity-induced inflammatory responses contribute to these observations is unknown. We have compared and contrasted the effects of high fat diet-induced obesity on glucose metabolism and leukocyte activation in multiple depots in male and female C57Bl/6 mice. With both short term and long term high fat diet, male mice demonstrated increased weight gain and CD11c(+) adipose tissue macrophage content compared with female mice despite similar degrees of adipocyte hypertrophy. Competitive bone marrow transplant studies demonstrated that obesity induced a preferential contribution of male hematopoietic cells to circulating leukocytes and adipose tissue macrophages compared with female cells independent of the sex of the recipient. Sex differences in macrophage and hematopoietic cell in vitro activation in response to obesogenic cues were observed to explain these results. In summary, this report demonstrates that male and female leukocytes and hematopoietic stem cells have cell-autonomous differences in their response to obesity that contribute to an amplified response in males compared with females.


Asunto(s)
Glucemia/metabolismo , Dieta Alta en Grasa/efectos adversos , Células Madre Hematopoyéticas/citología , Inflamación/inmunología , Obesidad/etiología , Tejido Adiposo/citología , Tejido Adiposo/inmunología , Tejido Adiposo/metabolismo , Animales , Biomarcadores/análisis , Células Cultivadas , Ensayo de Unidades Formadoras de Colonias , Femenino , Citometría de Flujo , Prueba de Tolerancia a la Glucosa , Células Madre Hematopoyéticas/metabolismo , Inmunohistoquímica , Inflamación/complicaciones , Inflamación/patología , Lípidos/análisis , Masculino , Ratones , Ratones Endogámicos C57BL , Mielopoyesis/fisiología , Obesidad/metabolismo , Obesidad/patología , Factores Sexuales , Aumento de Peso
8.
ArXiv ; 2024 May 20.
Artículo en Inglés | MEDLINE | ID: mdl-38827457

RESUMEN

Biomarkers enable objective monitoring of a given cell or state in a biological system and are widely used in research, biomanufacturing, and clinical practice. However, identifying appropriate biomarkers that are both robustly measurable and capture a state accurately remains challenging. We present a framework for biomarker identification based upon observability guided sensor selection. Our methods, Dynamic Sensor Selection (DSS) and Structure-Guided Sensor Selection (SGSS), utilize temporal models and experimental data, offering a template for applying observability theory to unconventional data obtained from biological systems. Unlike conventional methods that assume well-known, fixed dynamics, DSS adaptively select biomarkers or sensors that maximize observability while accounting for the time-varying nature of biological systems. Additionally, SGSS incorporates structural information and diverse data to identify sensors which are resilient against inaccuracies in our model of the underlying system. We validate our approaches by performing estimation on high dimensional systems derived from temporal gene expression data from partial observations.

9.
Sci Rep ; 13(1): 2651, 2023 02 14.
Artículo en Inglés | MEDLINE | ID: mdl-36788340

RESUMEN

Obesity induces a chronic inflammatory state associated with changes in adipose tissue macrophages (ATMs). Macrophage scavenger receptor 1 (MSR1) has been implicated in the regulation of adipose tissue inflammation and diabetes pathogenesis; however, reports have been mixed on the contribution of MSR1 in obesity and glucose intolerance. We observed increased MSR1 expression in VAT of obese diabetic individuals compared to non-diabetic and single nuclear RNA sequencing identified macrophage-specific expression of MSR1 in human adipose tissue. We examined male Msr1-/- (Msr1KO) and WT controls and observed protection from obesity and AT inflammation in non-littermate Msr1KO mice. We then evaluated obese littermate Msr1+/- (Msr1HET) and Msr1KO mice. Both Msr1KO mice and Msr1HET mice became obese and insulin resistant when compared to their normal chow diet counterparts, but there was no Msr1-dependent difference in body weight, glucose metabolism, or insulin resistance. Flow cytometry revealed no significant differences between genotypes in ATM subtypes or proliferation in male and female mice. We observed increased frequency of proliferating ATMs in obese female compared to male mice. Overall, we conclude that while MSR1 is a biomarker of diabetes status in human adipose tissue, in mice Msr1 is not required for obesity-associated insulin resistance or ATM accumulation.


Asunto(s)
Resistencia a la Insulina , Obesidad , Receptores Depuradores de Clase A , Animales , Femenino , Masculino , Ratones , Tejido Adiposo/metabolismo , Inflamación/metabolismo , Insulina/metabolismo , Resistencia a la Insulina/genética , Ratones Endogámicos C57BL , Obesidad/complicaciones , Obesidad/genética , Obesidad/metabolismo , Receptores Depuradores de Clase A/metabolismo
10.
JCI Insight ; 8(19)2023 Oct 09.
Artículo en Inglés | MEDLINE | ID: mdl-37651193

RESUMEN

Adipose tissue macrophage (ATM) infiltration is associated with adipose tissue dysfunction and insulin resistance in mice and humans. Recent single-cell data highlight increased ATM heterogeneity in obesity but do not provide a spatial context for ATM phenotype dynamics. We integrated single-cell RNA-Seq, spatial transcriptomics, and imaging of murine adipose tissue in a time course study of diet-induced obesity. Overall, proinflammatory immune cells were predominant in early obesity, whereas nonresident antiinflammatory ATMs predominated in chronic obesity. A subset of these antiinflammatory ATMs were transcriptomically intermediate between monocytes and mature lipid-associated macrophages (LAMs) and were consistent with a LAM precursor (pre-LAM). Pre-LAMs were spatially associated with early obesity crown-like structures (CLSs), which indicate adipose tissue dysfunction. Spatial data showed colocalization of ligand-receptor transcripts related to lipid signaling among monocytes, pre-LAMs, and LAMs, including Apoe, Lrp1, Lpl, and App. Pre-LAM expression of these ligands in early obesity suggested signaling to LAMs in the CLS microenvironment. Our results refine understanding of ATM diversity and provide insight into the dynamics of the LAM lineage during development of metabolic disease.


Asunto(s)
Tejido Adiposo , Obesidad , Humanos , Ratones , Animales , Tejido Adiposo/metabolismo , Obesidad/metabolismo , Macrófagos/metabolismo , Dieta , Lípidos
11.
Mol Metab ; 66: 101642, 2022 12.
Artículo en Inglés | MEDLINE | ID: mdl-36402403

RESUMEN

BACKGROUND: Adipose tissue macrophages (ATMs) are a well characterized regulator of adipose tissue inflammatory tone. Previously defined by the M1 vs M2 classification, we now have a better understanding of ATM diversity that departs from the old paradigm and reports a spectrum of ATM function and phenotypes in both brown and white adipose tissue. SCOPE OF REVIEW: This review provides an updated overview of ATM activation and function, ATM diversity in humans and rodents, and novel ATM functions that contribute to metabolic homeostasis and disease. MAJOR CONCLUSIONS: While the paradigm that resident ATMs predominate in the lean state and obesity leads to the accumulation of lipid-associated and inflammatory ATMs still broadly remains rigorously supported, the details of this model continue to be refined and single cell data provide new insight into ATM subtypes and states.


Asunto(s)
Tejido Adiposo , Inflamación , Humanos , Inflamación/metabolismo , Tejido Adiposo/metabolismo , Macrófagos/metabolismo , Obesidad/metabolismo , Tejido Adiposo Blanco/metabolismo
12.
JCI Insight ; 7(3)2022 02 08.
Artículo en Inglés | MEDLINE | ID: mdl-34990410

RESUMEN

Increased adipose tissue macrophages (ATMs) correlate with metabolic dysfunction in humans and are causal in development of insulin resistance in mice. Recent bulk and single-cell transcriptomics studies reveal a wide spectrum of gene expression signatures possible for macrophages that depends on context, but the signatures of human ATM subtypes are not well defined in obesity and diabetes. We profiled 3 prominent ATM subtypes from human adipose tissue in obesity and determined their relationship to type 2 diabetes. Visceral adipose tissue (VAT) and s.c. adipose tissue (SAT) samples were collected from diabetic and nondiabetic obese participants to evaluate cellular content and gene expression. VAT CD206+CD11c- ATMs were increased in diabetic participants, were scavenger receptor-rich with low intracellular lipids, secreted proinflammatory cytokines, and diverged significantly from 2 CD11c+ ATM subtypes, which were lipid-laden, were lipid antigen presenting, and overlapped with monocyte signatures. Furthermore, diabetic VAT was enriched for CD206+CD11c- ATM and inflammatory signatures, scavenger receptors, and MHC II antigen presentation genes. VAT immunostaining found CD206+CD11c- ATMs concentrated in vascularized lymphoid clusters adjacent to CD206-CD11c+ ATMs, while CD206+CD11c+ were distributed between adipocytes. Our results show ATM subtype-specific profiles that uniquely contribute to the phenotypic variation in obesity.


Asunto(s)
Tejido Adiposo/metabolismo , Diabetes Mellitus Tipo 2/genética , Regulación de la Expresión Génica , Resistencia a la Insulina/genética , Macrófagos/metabolismo , Glicoproteínas de Membrana/genética , Obesidad/genética , Receptores Inmunológicos/genética , Adipocitos/metabolismo , Tejido Adiposo/patología , Adulto , Anciano , Anciano de 80 o más Años , ADN/genética , Diabetes Mellitus Tipo 2/metabolismo , Diabetes Mellitus Tipo 2/patología , Femenino , Estudios de Seguimiento , Humanos , Macrófagos/patología , Masculino , Glicoproteínas de Membrana/biosíntesis , Persona de Mediana Edad , Obesidad/metabolismo , Obesidad/patología , Receptores Inmunológicos/biosíntesis , Factores de Tiempo , Adulto Joven
13.
iScience ; 25(9): 104846, 2022 Sep 16.
Artículo en Inglés | MEDLINE | ID: mdl-36043052

RESUMEN

WAPL, cohesin's DNA release factor, regulates three-dimensional (3D) chromatin architecture. The 3D chromatin structure and its relevance to mature T cell functions is not well understood. We show that in vivo lymphopenic expansion, and alloantigen-driven proliferation, alters the 3D structure and function of the genome in mature T cells. Conditional deletion of WAPL, cohesin's DNA release factor, in T cells reduced long-range genomic interactions and altered chromatin A/B compartments and interactions within topologically associating domains (TADs) of the chromatin in T cells at baseline. WAPL deficiency in T cells reduced loop extensions, changed expression of cell cycling genes and reduced proliferation following in vitro and in vivo stimulation, and reduced severity of graft-versus-host disease (GVHD) following experimental allogeneic hematopoietic stem cell transplantation. These data collectively characterize 3D genomic architecture of T cells in vivo and demonstrate biological and clinical implications for its disruption by cohesin release factor WAPL.

14.
Nat Commun ; 13(1): 5498, 2022 09 20.
Artículo en Inglés | MEDLINE | ID: mdl-36127324

RESUMEN

Chromatin architecture, a key regulator of gene expression, can be inferred using chromatin contact data from chromosome conformation capture, or Hi-C. However, classical Hi-C does not preserve multi-way contacts. Here we use long sequencing reads to map genome-wide multi-way contacts and investigate higher order chromatin organization in the human genome. We use hypergraph theory for data representation and analysis, and quantify higher order structures in neonatal fibroblasts, biopsied adult fibroblasts, and B lymphocytes. By integrating multi-way contacts with chromatin accessibility, gene expression, and transcription factor binding, we introduce a data-driven method to identify cell type-specific transcription clusters. We provide transcription factor-mediated functional building blocks for cell identity that serve as a global signature for cell types.


Asunto(s)
Cromatina , Genoma Humano , Adulto , Cromatina/genética , Cromosomas , Genoma Humano/genética , Humanos , Recién Nacido , Conformación Molecular , Factores de Transcripción/genética
15.
iScience ; 24(12): 103452, 2021 Dec 17.
Artículo en Inglés | MEDLINE | ID: mdl-34877507

RESUMEN

Every human somatic cell inherits a maternal and a paternal genome, which work together to give rise to cellular phenotypes. However, the allele-specific relationship between gene expression and genome structure through the cell cycle is largely unknown. By integrating haplotype-resolved genome-wide chromosome conformation capture, mature and nascent mRNA, and protein binding data from a B lymphoblastoid cell line, we investigate this relationship both globally and locally. We introduce the maternal and paternal 4D Nucleome, enabling detailed analysis of the mechanisms and dynamics of genome structure and gene function for diploid organisms. Our analyses find significant coordination between allelic expression biases and local genome conformation, and notably absent expression bias in universally essential cell cycle and glycolysis genes. We propose a model in which coordinated biallelic expression reflects prioritized preservation of essential gene sets.

16.
Artículo en Inglés | MEDLINE | ID: mdl-33289324

RESUMEN

Generating needed cell types using cellular reprogramming is a promising strategy for restoring tissue function in injury or disease. A common method for reprogramming is addition of one or more transcription factors that confer a new function or identity. Advancements in transcription factor selection and delivery have culminated in successful grafting of autologous reprogrammed cells, an early demonstration of their clinical utility. Though cellular reprogramming has been successful in a number of settings, identification of appropriate transcription factors for a particular transformation has been challenging. Computational methods enable more sophisticated prediction of relevant transcription factors for reprogramming by leveraging gene expression data of initial and target cell types, and are built on mathematical frameworks ranging from information theory to control theory. This review highlights the utility and impact of these mathematical frameworks in the field of cellular reprogramming. This article is categorized under: Reproductive System Diseases > Reproductive System Diseases>Genetics/Genomics/Epigenetics Reproductive System Diseases > Reproductive System Diseases>Stem Cells and Development Reproductive System Diseases > Reproductive System Diseases>Computational Models.

17.
Mol Metab ; 39: 100983, 2020 09.
Artículo en Inglés | MEDLINE | ID: mdl-32229247

RESUMEN

OBJECTIVE: Expansion of visceral adipose tissue (VAT) and metabolic inflammation are consequences of obesity and associated with type 2 diabetes (T2DM). Metabolically activated adipose tissue macrophages (ATMs) undergo qualitative and quantitative changes that influence their inflammatory responses. How these cells contribute to insulin resistance (IR) in humans is not well understood. Cholesterol 25-Hydroxylase (CH25H) converts cholesterol into 25-Hydroxycholesterol (25-HC), an oxysterol that modulates immune responses. Using human and murine models, we investigated the role of CH25H in metabolic inflammation. METHODS: We performed transcriptomic (RNASeq) analysis on the human whole AT biopsies and sorted ATMs from obese non-diabetic (NDM) and obese diabetic (DM) subjects to inquire if CH25H was increased in DM. We challenged mice lacking Ch25h with a high-fat diet (HFD) to characterize their metabolic and immunologic profiling. Ch25h KO mice and human adipose tissue biopsies from NDM and DM subjects were analyzed. LC-MS was conducted to measure 25-HC level in AT. In vitro analysis permitted us to investigate the effect of 25-HC on cytokine expression. RESULTS: In our RNASeq analysis of human visceral and subcutaneous biopsies, gene pathways related to inflammation were increased in obese DM vs. non-DM subjects that included CH25H. CH25H was enriched in the stromal vascular fraction of human adipose tissue and highly expressed in CD206+ human ATMs by flow cytometry analysis. We measured the levels of the oxysterols, 25-HC and 7α25diHC, in human visceral adipose tissue samples and showed a correlation between BMI and 25-HC. Using mouse models of diet-induced obesity (DIO), we found that HFD-induced Ch25h expression in eWAT and increased levels of 25-HC in AT. On HFD, Ch25h KO mice became obese but exhibited reduced plasma insulin levels, improved insulin action, and decreased ectopic lipid deposit. Improved insulin sensitivity in Ch25h KO mice was due to attenuation of CD11c+ adipose tissue macrophage infiltration in eWAT. Finally, by testing AT explants, bone marrow-derived macrophages (BMDMs) and SVF cells from Ch25h deficient mice, we observed that 25-HC is required for the expression of pro-inflammatory genes. 25-HC was also able to induce inflammatory genes in preadipocytes. CONCLUSIONS: Our data suggest a critical role for CH25H/25-HC in the progression of meta-inflammation and insulin resistance in obese humans and mouse models of obesity. In response to obesogenic stimuli, CH25H/25-HC could exert a pro-inflammatory role.


Asunto(s)
Tejido Adiposo/metabolismo , Diabetes Mellitus Tipo 2/complicaciones , Diabetes Mellitus Tipo 2/metabolismo , Obesidad/complicaciones , Obesidad/metabolismo , Paniculitis/etiología , Esteroide Hidroxilasas/metabolismo , Células 3T3-L1 , Adulto , Animales , Biomarcadores , Citocinas/metabolismo , Diabetes Mellitus Tipo 2/diagnóstico , Modelos Animales de Enfermedad , Susceptibilidad a Enfermedades , Femenino , Perfilación de la Expresión Génica , Regulación de la Expresión Génica , Humanos , Resistencia a la Insulina/genética , Macrófagos/inmunología , Macrófagos/metabolismo , Masculino , Metaboloma , Ratones , Ratones Noqueados , Persona de Mediana Edad , Obesidad/diagnóstico , Paniculitis/metabolismo , Paniculitis/patología , Análisis de Secuencia de ARN , Transducción de Señal , Esteroide Hidroxilasas/genética
18.
Front Physiol ; 11: 903, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32848853

RESUMEN

Adipose tissue pathology in obese patients often features impaired adipogenesis, angiogenesis, and chronic low-grade inflammation, all of which are regulated in large part by adipose tissue stromal vascular cells [SVC; i.e., non-adipocyte cells within adipose tissue including preadipocytes, endothelial cells (ECs), and immune cells]. Exercise is known to increase subcutaneous adipose tissue lipolysis, but the impact of exercise on SVCs in adipose tissue has not been explored. The purpose of this study was to assess the effects of a session of exercise on preadipocyte, EC, macrophage, and T cell content in human subcutaneous adipose tissue. We collected abdominal subcutaneous adipose tissue samples from 10 obese adults (BMI 33 ± 3 kg/m2, body fat 41 ± 7%) 12 h after a 60 min acute session of endurance exercise (80 ± 3%HRpeak) vs. no acute exercise session. SVCs were isolated by collagenase digestion and stained for flow cytometry. We found that acute exercise reduced preadipocyte content (38 ± 7 vs. 30 ± 13%SVC; p = 0.04). The reduction was driven by a decrease in CD34hi preadipocytes (18 ± 5 vs. 13 ± 6%SVC; p = 0.002), a subset of preadipocytes that generates high lipolytic rate adipocytes ex vivo. Acute exercise did not alter EC content. Acute exercise also did not change total immune cell, macrophage, or T cell content, and future work should assess the effects of exercise on subpopulations of these cells. We conclude that exercise may rapidly regulate the subcutaneous adipose tissue preadipocyte pool in ways that may help attenuate the high lipolytic rates that are commonly found in obesity.

19.
Obesity (Silver Spring) ; 28(6): 1086-1097, 2020 06.
Artículo en Inglés | MEDLINE | ID: mdl-32281747

RESUMEN

OBJECTIVE: Weight regain after weight loss is common, and there is evidence to suggest negative effects on health because of weight cycling. This study sought to investigate the impact of weight regain in formerly obese mice on adipose tissue architecture and stromal cell function. METHODS: A diet-switch model was employed for obesity induction, weight loss, and weight regain in mice. Flow cytometry quantified adipose tissue leukocytes in adipose tissue. Liver and adipose tissue depots were compared to determine tissue-specific effects of weight cycling. RESULTS: Epididymal white adipose tissue of formerly obese mice failed to expand in response to repeat exposure to high-fat diet and retained elevated numbers of macrophages and T cells. Weight regain was associated with disproportionally elevated liver mass, hepatic triglyceride content, serum insulin concentration, and serum transaminase concentration. These effects occurred despite an extended 6-month weight loss cycle and they demonstrate that formerly obese mice maintain durable alterations in their physiological response to weight regain. Conditioned media from epididymal adipose tissue of formerly obese mice inhibited adipogenesis of 3T3-L1 preadipocytes, suggesting a potential mechanism to explain failed epididymal adipose tissue expansion during weight regain. CONCLUSIONS: Metabolic abnormalities related to defects in adipose tissue expansion and ongoing dysfunction manifest in formerly obese mice during weight regain.


Asunto(s)
Tejido Adiposo/metabolismo , Hígado Graso/metabolismo , Obesidad/metabolismo , Aumento de Peso/fisiología , Animales , Dieta Alta en Grasa , Expresión Génica , Masculino , Ratones , Ratones Endogámicos C57BL , Ratones Obesos
20.
Expert Rev Mol Med ; 11: e18, 2009 Jun 25.
Artículo en Inglés | MEDLINE | ID: mdl-19555515

RESUMEN

The muscular dystrophies are a heterogeneous group of over 40 disorders that are characterised by muscle weakness and wasting. The most common are Duchenne muscular dystrophy and Becker muscular dystrophy, which result from mutations within the gene encoding dystrophin; myotonic dystrophy type 1, which results from an expanded trinucleotide repeat in the myotonic dystrophy protein kinase gene; and facioscapulohumeral dystrophy, which is associated with contractions in the subtelomeric region of human chromosome 1. Currently the only treatments involve clinical management of symptoms, although several promising experimental strategies are emerging. These include gene therapy using adeno-associated viral, lentiviral and adenoviral vectors and nonviral vectors, such as plasmid DNA. Exon-skipping and cell-based therapies have also shown promise in the effective treatment and regeneration of dystrophic muscle. The availability of numerous animal models for Duchenne muscular dystrophy has enabled extensive testing of a wide range of therapeutic approaches for this type of disorder. Consequently, we focus here on the therapeutic developments for Duchenne muscular dystrophy as a model of the types of approaches being considered for various types of dystrophy. We discuss the advantages and limitations of each therapeutic strategy, as well as prospects and recent successes in the context of future clinical applications.


Asunto(s)
Tratamiento Basado en Trasplante de Células y Tejidos/métodos , Terapia Genética/métodos , Distrofias Musculares/terapia , Humanos , Modelos Biológicos
SELECCIÓN DE REFERENCIAS
DETALLE DE LA BÚSQUEDA