RESUMEN
Today's genomics workflows typically require alignment to a reference sequence, which limits discovery. We introduce a unifying paradigm, SPLASH (Statistically Primary aLignment Agnostic Sequence Homing), which directly analyzes raw sequencing data, using a statistical test to detect a signature of regulation: sample-specific sequence variation. SPLASH detects many types of variation and can be efficiently run at scale. We show that SPLASH identifies complex mutation patterns in SARS-CoV-2, discovers regulated RNA isoforms at the single-cell level, detects the vast sequence diversity of adaptive immune receptors, and uncovers biology in non-model organisms undocumented in their reference genomes: geographic and seasonal variation and diatom association in eelgrass, an oceanic plant impacted by climate change, and tissue-specific transcripts in octopus. SPLASH is a unifying approach to genomic analysis that enables expansive discovery without metadata or references.
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Algoritmos , Genómica , Genoma , Análisis de Secuencia de ARN , Humanos , Antígenos HLA/genética , Análisis de la Célula IndividualRESUMEN
Learning has been associated with modifications of synaptic and circuit properties, but the precise changes storing information in mammals have remained largely unclear. We combined genetically targeted voltage imaging with targeted optogenetic activation and silencing of pre- and post-synaptic neurons to study the mechanisms underlying hippocampal behavioral timescale plasticity. In mice navigating a virtual-reality environment, targeted optogenetic activation of individual CA1 cells at specific places induced stable representations of these places in the targeted cells. Optical elicitation, recording, and modulation of synaptic transmission in behaving mice revealed that activity in presynaptic CA2/3 cells was required for the induction of plasticity in CA1 and, furthermore, that during induction of these place fields in single CA1 cells, synaptic input from CA2/3 onto these same cells was potentiated. These results reveal synaptic implementation of hippocampal behavioral timescale plasticity and define a methodology to resolve synaptic plasticity during learning and memory in behaving mammals.
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Región CA1 Hipocampal , Hipocampo , Ratones , Animales , Región CA1 Hipocampal/fisiología , Hipocampo/fisiología , Plasticidad Neuronal/fisiología , Aprendizaje/fisiología , Neuronas , Transmisión Sináptica/fisiología , MamíferosRESUMEN
KCR channelrhodopsins (K+-selective light-gated ion channels) have received attention as potential inhibitory optogenetic tools but more broadly pose a fundamental mystery regarding how their K+ selectivity is achieved. Here, we present 2.5-2.7 Å cryo-electron microscopy structures of HcKCR1 and HcKCR2 and of a structure-guided mutant with enhanced K+ selectivity. Structural, electrophysiological, computational, spectroscopic, and biochemical analyses reveal a distinctive mechanism for K+ selectivity; rather than forming the symmetrical filter of canonical K+ channels achieving both selectivity and dehydration, instead, three extracellular-vestibule residues within each monomer form a flexible asymmetric selectivity gate, while a distinct dehydration pathway extends intracellularly. Structural comparisons reveal a retinal-binding pocket that induces retinal rotation (accounting for HcKCR1/HcKCR2 spectral differences), and design of corresponding KCR variants with increased K+ selectivity (KALI-1/KALI-2) provides key advantages for optogenetic inhibition in vitro and in vivo. Thus, discovery of a mechanism for ion-channel K+ selectivity also provides a framework for next-generation optogenetics.
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Channelrhodopsins , Rhinosporidium , Humanos , Channelrhodopsins/química , Channelrhodopsins/genética , Channelrhodopsins/metabolismo , Channelrhodopsins/ultraestructura , Microscopía por Crioelectrón , Canales Iónicos , Potasio/metabolismo , Rhinosporidium/químicaRESUMEN
ChRmine, a recently discovered pump-like cation-conducting channelrhodopsin, exhibits puzzling properties (large photocurrents, red-shifted spectrum, and extreme light sensitivity) that have created new opportunities in optogenetics. ChRmine and its homologs function as ion channels but, by primary sequence, more closely resemble ion pump rhodopsins; mechanisms for passive channel conduction in this family have remained mysterious. Here, we present the 2.0 Å resolution cryo-EM structure of ChRmine, revealing architectural features atypical for channelrhodopsins: trimeric assembly, a short transmembrane-helix 3, a twisting extracellular-loop 1, large vestibules within the monomer, and an opening at the trimer interface. We applied this structure to design three proteins (rsChRmine and hsChRmine, conferring further red-shifted and high-speed properties, respectively, and frChRmine, combining faster and more red-shifted performance) suitable for fundamental neuroscience opportunities. These results illuminate the conduction and gating of pump-like channelrhodopsins and point the way toward further structure-guided creation of channelrhodopsins for applications across biology.
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Channelrhodopsins/química , Channelrhodopsins/metabolismo , Activación del Canal Iónico , Animales , Channelrhodopsins/ultraestructura , Microscopía por Crioelectrón , Femenino , Células HEK293 , Humanos , Masculino , Ratones Endogámicos C57BL , Modelos Moleculares , Optogenética , Filogenia , Ratas Sprague-Dawley , Bases de Schiff/química , Células Sf9 , Relación Estructura-ActividadRESUMEN
Mammals have evolved neurophysiologic reflexes, such as coughing and scratching, to expel invading pathogens and noxious environmental stimuli. It is well established that these responses are also associated with chronic inflammatory diseases, including asthma and atopic dermatitis. However, the mechanisms by which inflammatory pathways promote sensations such as itch remain poorly understood. Here, we show that type 2 cytokines directly activate sensory neurons in both mice and humans. Further, we demonstrate that chronic itch is dependent on neuronal IL-4Rα and JAK1 signaling. We also observe that patients with recalcitrant chronic itch that failed other immunosuppressive therapies markedly improve when treated with JAK inhibitors. Thus, signaling mechanisms previously ascribed to the immune system may represent novel therapeutic targets within the nervous system. Collectively, this study reveals an evolutionarily conserved paradigm in which the sensory nervous system employs classical immune signaling pathways to influence mammalian behavior.
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Prurito/inmunología , Células Receptoras Sensoriales/inmunología , Células Receptoras Sensoriales/metabolismo , Transducción de Señal , Enfermedades de la Piel/inmunología , Animales , Ganglios Espinales , Humanos , Interleucina-13/inmunología , Interleucina-4/inmunología , Janus Quinasa 1/metabolismo , Ratones , Ratones Endogámicos C57BL , Prurito/metabolismo , Enfermedades de la Piel/patologíaRESUMEN
The RNA-induced silencing complex (RISC), which powers RNA interference (RNAi), consists of a guide RNA and an Argonaute protein that slices target RNAs complementary to the guide. We find that, for different guide-RNA sequences, slicing rates of perfectly complementary bound targets can be surprisingly different (>250-fold range), and that faster slicing confers better knockdown in cells. Nucleotide sequence identities at guide-RNA positions 7, 10, and 17 underlie much of this variation in slicing rates. Analysis of one of these determinants implicates a structural distortion at guide nucleotides 6-7 in promoting slicing. Moreover, slicing directed by different guide sequences has an unanticipated, 600-fold range in 3'-mismatch tolerance, attributable to guides with weak (AU-rich) central pairing requiring extensive 3' complementarity (pairing beyond position 16) to more fully populate the slicing-competent conformation. Together, our analyses identify sequence determinants of RISC activity and provide biochemical and conformational rationale for their action.
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Proteínas Argonautas , Conformación de Ácido Nucleico , ARN Guía de Sistemas CRISPR-Cas , Complejo Silenciador Inducido por ARN , Proteínas Argonautas/metabolismo , Proteínas Argonautas/genética , Proteínas Argonautas/química , Humanos , Complejo Silenciador Inducido por ARN/metabolismo , Complejo Silenciador Inducido por ARN/genética , Complejo Silenciador Inducido por ARN/química , Cinética , ARN Guía de Sistemas CRISPR-Cas/genética , ARN Guía de Sistemas CRISPR-Cas/metabolismo , Interferencia de ARN , Secuencia de Bases , Células HEK293RESUMEN
Lymphangitis and the formation of tertiary lymphoid organs (TLOs) in the mesentery are features of Crohn's disease. Here, we examined the genesis of these TLOs and their impact on disease progression. Whole-mount and intravital imaging of the ileum and ileum-draining collecting lymphatic vessels (CLVs) draining to mesenteric lymph nodes from TNFΔARE mice, a model of ileitis, revealed TLO formation at valves of CLVs. TLOs obstructed cellular and molecular outflow from the gut and were sites of lymph leakage and backflow. Tumor necrosis factor (TNF) neutralization begun at early stages of TLO formation restored lymph transport. However, robustly developed, chronic TLOs resisted regression and restoration of flow after TNF neutralization. TNF stimulation of cultured lymphatic endothelial cells reprogrammed responses to oscillatory shear stress, preventing the induction of valve-associated genes. Disrupted transport of immune cells, driven by loss of valve integrity and TLO formation, may contribute to the pathology of Crohn's disease.
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Enfermedad de Crohn/inmunología , Células Endoteliales/inmunología , Íleon/inmunología , Linfa/metabolismo , Vasos Linfáticos/inmunología , Mesenterio/inmunología , Estructuras Linfoides Terciarias/inmunología , Factor de Necrosis Tumoral alfa/metabolismo , Animales , Movimiento Celular , Células Cultivadas , Modelos Animales de Enfermedad , Humanos , Ileítis , Linfangitis , Ratones , Ratones Noqueados , Estrés MecánicoRESUMEN
A wealth of evidence has emerged that there is an association between aging, senescence and tumorigenesis. Senescence, a biological process by which cells cease to divide and enter a status of permanent cell cycle arrest, contributes to aging and aging-related diseases, including cancer. Aging populations have the higher incidence of cancer due to a lifetime of exposure to cancer-causing agents, reduction of repairing DNA damage, accumulated genetic mutations, and decreased immune system efficiency. Cancer patients undergoing cytotoxic therapies, such as chemotherapy and radiotherapy, accelerate aging. There is growing evidence that p53/MDM2 (murine double minute 2) axis is critically involved in regulation of aging, senescence and oncogenesis. Therefore, in this review, we describe the functions and mechanisms of p53/MDM2-mediated senescence, aging and carcinogenesis. Moreover, we highlight the small molecular inhibitors, natural compounds and PROTACs (proteolysis targeting chimeras) that target p53/MDM2 pathway to influence aging and cancer. Modification of p53/MDM2 could be a potential strategy for treatment of aging, senescence and tumorigenesis.
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Envejecimiento , Carcinogénesis , Senescencia Celular , Neoplasias , Proteínas Proto-Oncogénicas c-mdm2 , Transducción de Señal , Proteína p53 Supresora de Tumor , Humanos , Proteínas Proto-Oncogénicas c-mdm2/metabolismo , Proteína p53 Supresora de Tumor/metabolismo , Envejecimiento/metabolismo , Animales , Neoplasias/metabolismo , Neoplasias/etiología , Neoplasias/patología , Neoplasias/tratamiento farmacológico , Carcinogénesis/metabolismo , Transformación Celular Neoplásica/metabolismo , Transformación Celular Neoplásica/genéticaRESUMEN
Limiting CD4+ T cell responses is important to prevent solid organ transplant rejection. In a mouse model of costimulation blockade-dependent cardiac allograft tolerance, we previously reported that alloreactive CD4+ conventional T cells (Tconvs) develop dysfunction, losing proliferative capacity. In parallel, induction of transplantation tolerance is dependent on the presence of regulatory T cells (Tregs). Whether susceptibility of CD4+ Tconvs to Treg suppression is modulated during tolerance induction is unknown. We found that alloreactive Tconvs from transplant tolerant mice had augmented sensitivity to Treg suppression when compared with memory T cells from rejector mice and expressed a transcriptional profile distinct from these memory T cells, including down-regulated expression of the transcription factor Special AT-rich sequence-binding protein 1 (Satb1). Mechanistically, Satb1 deficiency in CD4+ T cells limited their expression of CD25 and IL-2, and addition of Tregs, which express higher levels of CD25 than Satb1-deficient Tconvs and successfully competed for IL-2, resulted in greater suppression of Satb1-deficient than wild-type Tconvs in vitro. In vivo, Satb1-deficient Tconvs were more susceptible to Treg suppression, resulting in significantly prolonged skin allograft survival. Overall, our study reveals that transplantation tolerance is associated with Tconvs' susceptibility to Treg suppression, via modulated expression of Tconv-intrinsic Satb1. Targeting Satb1 in the context of Treg-sparing immunosuppressive therapies might be exploited to improve transplant outcomes.
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Supervivencia de Injerto , Proteínas de Unión a la Región de Fijación a la Matriz , Linfocitos T Reguladores , Factores de Transcripción , Tolerancia al Trasplante , Animales , Supervivencia de Injerto/genética , Supervivencia de Injerto/inmunología , Memoria Inmunológica/genética , Interleucina-2/metabolismo , Proteínas de Unión a la Región de Fijación a la Matriz/genética , Proteínas de Unión a la Región de Fijación a la Matriz/metabolismo , Ratones , Ratones Endogámicos C57BL , Linfocitos T Reguladores/inmunología , Factores de Transcripción/genética , Factores de Transcripción/metabolismo , Tolerancia al Trasplante/genética , Tolerancia al Trasplante/inmunologíaRESUMEN
In current clinical practice, radiotherapy (RT) is prescribed as a pre-determined total dose divided over daily doses (fractions) given over several weeks. The treatment response is typically assessed months after the end of RT. However, the conventional one-dose-fits-all strategy may not achieve the desired outcome, owing to patient and tumor heterogeneity. Therefore, a treatment strategy that allows for RT dose personalization based on each individual response is preferred. Multiple strategies have been adopted to address this challenge. As an alternative to current known strategies, artificial intelligence (AI)-derived mechanism-independent small data phenotypic medicine (PM) platforms may be utilized for N-of-1 RT personalization. Unlike existing big data approaches, PM does not engage in model refining, training, and validation, and guides treatment by utilizing prospectively collected patient's own small datasets. With PM, clinicians may guide patients' RT dose recommendations using their responses in real-time and potentially avoid over-treatment in good responders and under-treatment in poor responders. In this paper, we discuss the potential of engaging PM to guide clinicians on upfront dose selections and ongoing adaptations during RT, as well as considerations and limitations for implementation. For practicing oncologists, clinical trialists, and researchers, PM can either be implemented as a standalone strategy or in complement with other existing RT personalizations. In addition, PM can either be used for monotherapeutic RT personalization, or in combination with other therapeutics (e.g. chemotherapy, targeted therapy). The potential of N-of-1 RT personalization with drugs will also be presented.
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Neoplasias , Medicina de Precisión , Humanos , Medicina de Precisión/métodos , Neoplasias/radioterapia , Inteligencia Artificial , Fenotipo , Dosificación RadioterapéuticaRESUMEN
Following solid organ transplantation, small precursor populations of polyclonal CD8+ T cells specific for any graft-expressed antigen preferentially expand their high-affinity clones. This phenomenon, termed "avidity maturation," results in a larger population of CD8+ T cells with increased sensitivity to alloantigen, posing a greater risk for graft rejection. Using a mouse model of minor-mismatched skin transplantation, coupled with the tracking of 2 skin graft-reactive CD8+ T cell receptor-transgenic tracer populations with high and low affinity for the same peptide-major histocompatibility complex, we explored the conventional paradigm that CD8+ T cell avidity maturation occurs through T cell receptor affinity-based competition for cognate antigen. Our data revealed "interclonal CD8-CD8 help," whereby lower/intermediate affinity clones help drive the preferential expansion of their higher affinity counterparts in an interleukin-2/CD25-dependent manner. Consequently, the CD8-helped high-affinity clones exhibit greater expansion and develop augmented effector functions in the presence of their low-affinity counterparts, correlating with more severe graft damage. Finally, interclonal CD8-CD8 help was suppressed by costimulation blockade treatment. Thus, high-affinity CD8+ T cells can leverage help from low-affinity CD8+ T cells of identical specificity to promote graft rejection. Suppressing provision of interclonal CD8-CD8 help may be important to improve transplant outcomes.
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Linfocitos T CD8-positivos , Rechazo de Injerto , Ratones Endogámicos C57BL , Trasplante de Piel , Animales , Linfocitos T CD8-positivos/inmunología , Ratones , Rechazo de Injerto/inmunología , Isoantígenos/inmunología , Ratones Transgénicos , Ratones Endogámicos BALB C , Supervivencia de Injerto/inmunología , Receptores de Antígenos de Linfocitos T/inmunología , Receptores de Antígenos de Linfocitos T/metabolismo , Receptores de Antígenos de Linfocitos T/genéticaRESUMEN
Electric pacing of human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM) has been increasingly used to simulate cardiac arrhythmias in vitro and to enhance cardiomyocyte maturity. However, the impact of electric pacing on cellular electrophysiology and Ca2+ handling in differentiated hiPSC-CM is less characterized. Here we studied the effects of electric pacing for 24 h or 7 days at a physiological rate of 60 beats/min on cellular electrophysiology and Ca2+ cycling in late-stage, differentiated hiPSC-CM (>90% troponin+, >60 days postdifferentiation). Electric culture pacing for 7 days did not influence cardiomyocyte cell size, apoptosis, or generation of reactive oxygen species in differentiated hiPSC-CM compared with 24-h pacing. However, epifluorescence measurements revealed that electric pacing for 7 days improved systolic Ca2+ transient amplitude and Ca2+ transient upstroke, which could be explained by elevated sarcoplasmic reticulum Ca2+ load and SERCA activity. Diastolic Ca2+ leak was not changed in line-scanning confocal microscopy, suggesting that the improvement in systolic Ca2+ release was not associated with a higher open probability of ryanodine receptor (RyR)2 during diastole. Whereas bulk cytosolic Na+ concentration and Na+/Ca2+ exchanger (NCX) activity were not changed, patch-clamp studies revealed that chronic pacing caused a slight abbreviation of the action potential duration (APD) in hiPSC-CM. We found in whole cell voltage-clamp measurements that chronic pacing for 7 days led to a decrease in late Na+ current, which might explain the changes in APD. In conclusion, our results show that chronic pacing improves systolic Ca2+ handling and modulates the electrophysiology of late-stage, differentiated hiPSC-CM. This study might help to understand the effects of electric pacing and its numerous applications in stem cell research including arrhythmia simulation.NEW & NOTEWORTHY Electric pacing is increasingly used in research with human induced pluripotent stem cell cardiomyocytes (hiPSC-CM), for example to simulate arrhythmias but also to enhance maturity. Therefore, it is mandatory to understand the effects of pacing itself on cellular electrophysiology in late-stage, matured hiPSC-CM. This study provides an electrophysiological characterization of the effects of chronic electric pacing at a physiological rate on differentiated hiPSC-CM.
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Señalización del Calcio , Calcio , Diferenciación Celular , Células Madre Pluripotentes Inducidas , Miocitos Cardíacos , Canal Liberador de Calcio Receptor de Rianodina , Humanos , Miocitos Cardíacos/metabolismo , Células Madre Pluripotentes Inducidas/metabolismo , Calcio/metabolismo , Canal Liberador de Calcio Receptor de Rianodina/metabolismo , Potenciales de Acción , ATPasas Transportadoras de Calcio del Retículo Sarcoplásmico/metabolismo , Retículo Sarcoplasmático/metabolismo , Intercambiador de Sodio-Calcio/metabolismo , Estimulación Cardíaca Artificial , Especies Reactivas de Oxígeno/metabolismo , Factores de Tiempo , Células CultivadasRESUMEN
The nervous system plays important roles in homeostasis and inflammatory responses in tissues. However, the regulation of lymph nodes (LN) by nerves remains largely unknown. Huang et al. demonstrate that LNs are innervated by unique peptidergic nociceptors that signal to various endothelial, stromal, and immune cell types in LNs.
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Inmunidad , Ganglios Linfáticos , Homeostasis , Células Receptoras Sensoriales , Células del EstromaRESUMEN
Immune checkpoint blockade is limited by resistance to treatment, with many patients not achieving durable antitumor responses. Self-renewing (T cell factor 1+ [TCF1+]) CD8+ T cells have recently been implicated in efficacy of anti-programmed cell death protein 1 (anti-PD-1). Mice challenged with syngeneic tumors were treated with anti-PD-1 and/or a reversible inhibitor of PI3K δ, designed to promote T cell self-renewal. Growth of tumors in untreated mice was characterized by waning proportions of TCF1+ T cells, suggesting self-renewing T cells become limiting for successful immunotherapy. Higher proportions of TCF1+ T cells in tumor and blood correlated with better control of tumor growth. Combining anti-PD-1 and inhibitor of PI3K δ conferred superior protection compared with either monotherapy and was associated with higher frequency of TCF1+ T cells in tumor and blood compared with anti-PD-1 alone. These findings reveal predictive importance of self-renewing T cells in anti-tumor immunity and suggest that resistance-directed strategies to enhance T cell self-renewal could potentiate the efficacy of PD-1 blockade.
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Linfocitos T CD8-positivos , Neoplasias , Animales , Muerte Celular , Inmunoterapia , Ratones , Fosfatidilinositol 3-Quinasas , Factor 1 de Transcripción de Linfocitos TRESUMEN
The human cerebral cortex is distinguished by its large size and abundant gyrification, or folding. However, the evolutionary mechanisms that drive cortical size and structure are unknown. Although genes that are essential for cortical developmental expansion have been identified from the genetics of human primary microcephaly (a disorder associated with reduced brain size and intellectual disability) 1 , studies of these genes in mice, which have a smooth cortex that is one thousand times smaller than the cortex of humans, have provided limited insight. Mutations in abnormal spindle-like microcephaly-associated (ASPM), the most common recessive microcephaly gene, reduce cortical volume by at least 50% in humans2-4, but have little effect on the brains of mice5-9; this probably reflects evolutionarily divergent functions of ASPM10,11. Here we used genome editing to create a germline knockout of Aspm in the ferret (Mustela putorius furo), a species with a larger, gyrified cortex and greater neural progenitor cell diversity12-14 than mice, and closer protein sequence homology to the human ASPM protein. Aspm knockout ferrets exhibit severe microcephaly (25-40% decreases in brain weight), reflecting reduced cortical surface area without significant change in cortical thickness, as has been found in human patients3,4, suggesting that loss of 'cortical units' has occurred. The cortex of fetal Aspm knockout ferrets displays a very large premature displacement of ventricular radial glial cells to the outer subventricular zone, where many resemble outer radial glia, a subtype of neural progenitor cells that are essentially absent in mice and have been implicated in cerebral cortical expansion in primates12-16. These data suggest an evolutionary mechanism by which ASPM regulates cortical expansion by controlling the affinity of ventricular radial glial cells for the ventricular surface, thus modulating the ratio of ventricular radial glial cells, the most undifferentiated cell type, to outer radial glia, a more differentiated progenitor.
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Evolución Biológica , Corteza Cerebral/anatomía & histología , Corteza Cerebral/metabolismo , Hurones , Eliminación de Gen , Microcefalia/genética , Microcefalia/patología , Proteínas del Tejido Nervioso/deficiencia , Secuencia de Aminoácidos , Animales , Proteínas de Unión a Calmodulina/deficiencia , Proteínas de Unión a Calmodulina/metabolismo , Centrosoma/metabolismo , Corteza Cerebral/patología , Modelos Animales de Enfermedad , Femenino , Hurones/anatomía & histología , Hurones/genética , Edición Génica , Regulación del Desarrollo de la Expresión Génica , Técnicas de Inactivación de Genes , Mutación de Línea Germinal , Humanos , Masculino , Ratones , Proteínas del Tejido Nervioso/química , Proteínas del Tejido Nervioso/genética , Proteínas del Tejido Nervioso/metabolismo , Células-Madre Neurales/metabolismo , Células-Madre Neurales/patología , Tamaño de los Órganos , Transcripción GenéticaRESUMEN
Introduction: Transition from multidisciplinary paediatric to adult care results in a significant change in the intensity of care provided to patients with spina bifida (SB). Objective: To compare planned and unplanned health care utilization and costs of care of transitioning SB patients. Study Design: Through a retrospective population-based cohort study, patients with SB born in Ontario between 1988 and 1999 were studied using routinely collected data analysed at ICES. Patients were followed longitudinally from age 16 to 22 years with comparisons made between the paediatric baseline year (age 16) to the first 3 years of adulthood (ages 19 to 21). A composite primary outcome of unplanned emergency room (ER) visits, hospitalizations and emergency surgical procedures, was compared before and after transition. Secondary outcomes included these variables individually and estimated health care costs. Results: In the 299 patients, no significant differences were identified in the composite primary outcome between periods (P = 0.09). Unplanned ER visits (P = 0.004) and emergency surgical procedures (P = 0.02) increased after transition. Despite this, the estimated individual total cost of care declined after transition (P = 0.03). Further, multivariable analysis identified rural residence (RR 1.78, confidence interval [CI] 1.30 to 2.44) and previous urologic surgery (RR 1.91, CI 1.41 to 2.57) as significant predictors of increased need for emergent care and health care costs, respectively. Conclusion: Patients with SB in Ontario have higher rates of ER usage and unplanned surgery after the transition to adult care. While this does not drive an increase in health care costs, improvements in the care of transitioned SB patients, particularly rural patients and those with prior urologic surgery, may decrease the requirement for acute care.
RESUMEN
Evidence has revealed that transcription factors play essential roles in regulation of multiple cellular processes, including cell proliferation, metastasis, EMT, cancer stem cells and chemoresistance. Dysregulated expression levels of transcription factors contribute to tumorigenesis and malignant progression. The expression of transcription factors is tightly governed by several signaling pathways, noncoding RNAs and E3 ubiquitin ligases. Cancer stem cells (CSCs) have been validated in regulation of tumor metastasis, reoccurrence and chemoresistance in human cancer. Transcription factors have been verified to participate in regulation of CSC formation, including Oct4, SOX2, KLF4, c-Myc, Nanog, GATA, SALL4, Bmi-1, OLIG2, POU3F2 and FOX proteins. In this review article, we will describe the critical role of CSC-related transcription factors. We will further discuss which E3 ligases regulate the degradation of these CSC-related transcription factors and their underlying mechanisms. We also mentioned the functions and mechanisms of EMT-associated transcription factors such as ZEB1, ZEB2, Snail, Slug, Twist1 and Twist2. Furthermore, we highlight the therapeutic potential via targeting E3 ubiquitin ligases for modulation of these transcription factors.
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Neoplasias , Factores de Transcripción , Humanos , Factores de Transcripción/genética , Factores de Transcripción/metabolismo , Ubiquitina-Proteína Ligasas/genética , Ubiquitina-Proteína Ligasas/metabolismo , Transición Epitelial-Mesenquimal/genética , Células Madre Neoplásicas/metabolismo , Neoplasias/tratamiento farmacológico , Neoplasias/genética , Neoplasias/metabolismo , Ubiquitinas/metabolismo , Línea Celular TumoralRESUMEN
The tumor microenvironment (TME) plays an important role in neoplastic development. Matrix metalloproteinases (MMPs) are critically involved in tumorigenesis by modulation of the TME and degradation of the extracellular matrix (ECM) in a large variety of malignancies. Evidence has revealed that dysregulated MMPs can lead to ECM damage, the promotion of cell migration and tumor metastasis. The expression and activities of MMPs can be tightly regulated by TIMPs, multiple signaling pathways and noncoding RNAs. MMPs are also finely controlled by E3 ubiquitin ligases. The current review focuses on the molecular mechanism by which MMPs are governed by E3 ubiquitin ligases in carcinogenesis. Due to the essential role of MMPs in oncogenesis, they have been considered the attractive targets for antitumor treatment. Several strategies that target MMPs have been discovered, including the use of small-molecule inhibitors, peptides, inhibitory antibodies, natural compounds with anti-MMP activity, and RNAi therapeutics. However, these molecules have multiple disadvantages, such as poor solubility, severe side-effects and low oral bioavailability. Therefore, it is necessary to discover the novel inhibitors that suppress MMPs for cancer therapy. Here, we discuss the therapeutic potential of targeting E3 ubiquitin ligases to inhibit MMPs. We hope this review will stimulate the discovery of novel therapeutics for the MMP-targeted treatment of a variety of human cancers.
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Neoplasias , Microambiente Tumoral , Humanos , Ubiquitina-Proteína Ligasas/genética , Ubiquitina-Proteína Ligasas/metabolismo , Neoplasias/tratamiento farmacológico , Neoplasias/genética , Carcinogénesis , Transformación Celular Neoplásica , Metaloproteinasas de la Matriz , Ubiquitinas/uso terapéuticoRESUMEN
BACKGROUND: One strategy for identifying targets of a regulatory factor is to perturb the factor and use high-throughput RNA sequencing to examine the consequences. However, distinguishing direct targets from secondary effects and experimental noise can be challenging when confounding signal is present in the background at varying levels. RESULTS: Here, we present a statistical modeling strategy to identify microRNAs that are primary substrates of target-directed miRNA degradation (TDMD) mediated by ZSWIM8. This method uses a bi-beta-uniform mixture (BBUM) model to separate primary from background signal components, leveraging the expectation that primary signal is restricted to upregulation and not downregulation upon loss of ZSWIM8. The BBUM model strategy retained the apparent sensitivity and specificity of the previous ad hoc approach but was more robust against outliers, achieved a more consistent stringency, and could be performed using a single cutoff of false discovery rate (FDR). CONCLUSIONS: We developed the BBUM model, a robust statistical modeling strategy to account for background secondary signal in differential expression data. It performed well for identifying primary substrates of TDMD and should be useful for other applications in which the primary regulatory targets are only upregulated or only downregulated. The BBUM model, FDR-correction algorithm, and significance-testing methods are available as an R package at https://github.com/wyppeter/bbum .
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MicroARNs , MicroARNs/genética , Algoritmos , Secuencia de Bases , Modelos Estadísticos , Análisis de Secuencia de ARN/métodos , Secuenciación de Nucleótidos de Alto Rendimiento/métodosRESUMEN
Obesity is associated with dysbiosis and a state of chronic inflammation that contributes to the pathogenesis of metabolic diseases, including diabetes. We have previously shown that obese mice develop glucose intolerance, increased alloreactivity, and accelerated transplant rejection. In the present study, we investigated the influence of the microbiota on diet-induced obesity (DIO)-associated transplant rejection and hyperglycemia. Antibiotic treatment prolonged graft survival and reduced fasting glycemia in high-fat diet (HFD)-fed specific-pathogen-free (SPF) mice, supporting a role for the microbiota in promoting accelerated graft rejection and hyperglycemia induced by DIO. Further supporting a microbiota-dependent effect, fecal microbiota transfer from DIO SPF mice into germ-free mice also accelerated graft rejection when compared with lean mice-fecal microbiota transfer. Notably, HFD could be also detrimental to the graft independently from microbiota, obesity, and hyperglycemia. Thus, whereas HFD-associated hyperglycemia was exclusively microbiota-dependent, HFD affected transplant outcomes via both microbiota-dependent and -independent mechanisms. Importantly, hyperglycemia in DIO SPF mice could be reduced by the addition of the gut commensal Alistipes onderdonkii, which alleviated both HFD-induced inflammation and glucose intolerance. Thus, microbial dysbiosis can be manipulated via antibiotics or select probiotics to counter some of the pathogenic effects of obesity in transplantation.