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1.
Cell ; 187(1): 62-78.e20, 2024 01 04.
Artículo en Inglés | MEDLINE | ID: mdl-38096822

RESUMEN

The microbiota influences intestinal health and physiology, yet the contributions of commensal protists to the gut environment have been largely overlooked. Here, we discover human- and rodent-associated parabasalid protists, revealing substantial diversity and prevalence in nonindustrialized human populations. Genomic and metabolomic analyses of murine parabasalids from the genus Tritrichomonas revealed species-level differences in excretion of the metabolite succinate, which results in distinct small intestinal immune responses. Metabolic differences between Tritrichomonas species also determine their ecological niche within the microbiota. By manipulating dietary fibers and developing in vitro protist culture, we show that different Tritrichomonas species prefer dietary polysaccharides or mucus glycans. These polysaccharide preferences drive trans-kingdom competition with specific commensal bacteria, which affects intestinal immunity in a diet-dependent manner. Our findings reveal unappreciated diversity in commensal parabasalids, elucidate differences in commensal protist metabolism, and suggest how dietary interventions could regulate their impact on gut health.


Asunto(s)
Microbioma Gastrointestinal , Parabasalidea , Polisacáridos , Animales , Humanos , Ratones , Fibras de la Dieta , Intestino Delgado/metabolismo , Polisacáridos/metabolismo , Parabasalidea/metabolismo , Carbohidratos de la Dieta/metabolismo , Biodiversidad
2.
Cell ; 186(14): 3111-3124.e13, 2023 07 06.
Artículo en Inglés | MEDLINE | ID: mdl-37348505

RESUMEN

The gut microbiome modulates immune and metabolic health. Human microbiome data are biased toward industrialized populations, limiting our understanding of non-industrialized microbiomes. Here, we performed ultra-deep metagenomic sequencing on 351 fecal samples from the Hadza hunter-gatherers of Tanzania and comparative populations in Nepal and California. We recovered 91,662 genomes of bacteria, archaea, bacteriophages, and eukaryotes, 44% of which are absent from existing unified datasets. We identified 124 gut-resident species vanishing in industrialized populations and highlighted distinct aspects of the Hadza gut microbiome related to in situ replication rates, signatures of selection, and strain sharing. Industrialized gut microbes were found to be enriched in genes associated with oxidative stress, possibly a result of microbiome adaptation to inflammatory processes. This unparalleled view of the Hadza gut microbiome provides a valuable resource, expands our understanding of microbes capable of colonizing the human gut, and clarifies the extensive perturbation induced by the industrialized lifestyle.


Asunto(s)
Microbioma Gastrointestinal , Microbiota , Humanos , Microbioma Gastrointestinal/genética , Metagenoma , Eucariontes , Secuenciación de Nucleótidos de Alto Rendimiento , Metagenómica
3.
Blood ; 143(2): 178-182, 2024 Jan 11.
Artículo en Inglés | MEDLINE | ID: mdl-37963262

RESUMEN

ABSTRACT: Nonmelanoma skin cancers (NMSCs) in ruxolitinib-treated patients with myeloproliferative neoplasms behave aggressively, with adverse features and high recurrence. In our cohort, mortality from metastatic NMSC exceeded that from myelofibrosis. Vigilant skin assessment, counseling on NMSC risks, and prospective ruxolitinib-NMSC studies are crucial.


Asunto(s)
Trastornos Mieloproliferativos , Pirazoles , Pirimidinas , Neoplasias Cutáneas , Humanos , Estudios Prospectivos , Trastornos Mieloproliferativos/tratamiento farmacológico , Nitrilos , Neoplasias Cutáneas/tratamiento farmacológico
4.
Biomacromolecules ; 25(6): 3823-3830, 2024 Jun 10.
Artículo en Inglés | MEDLINE | ID: mdl-38773865

RESUMEN

Sustainability and circularity are key issues facing the global polymer industry. The search for biodegradable and environmentally-friendly polymers that can replace conventional materials is a difficult challenge that has been met with limited success. Alternatives must be cost-effective, scalable, and provide equivalent performance. We report that latexes made by the conventional emulsion polymerization of vinyl acetate and functional vinyl ester monomers are efficient thickeners for consumer products and biodegrade in wastewater. This approach uses readily-available starting materials and polymerization is carried out in water at room temperature, in one pot, and generates negligible waste. Moreover, the knowledge that poly(vinyl ester)s are biodegradable will lead to the design of new green polymer materials.


Asunto(s)
Emulsiones , Emulsiones/química , Polimerizacion , Polímeros/química , Álcalis/química , Biodegradación Ambiental , Látex/química , Compuestos de Vinilo/química , Aguas Residuales/química
5.
J Immunol ; 209(2): 379-390, 2022 07 15.
Artículo en Inglés | MEDLINE | ID: mdl-35768150

RESUMEN

NK cells are promising cellular therapeutics against hematological and solid malignancies. Immunogenetic studies have identified that various activating killer cell Ig-like receptors (KIRs) are associated with cancer outcomes. Specifically, KIR2DS2 has been associated with reduced incidence of relapse following transplant in hematological malignancies and improved outcomes in solid tumors, but the mechanism remains obscure. Therefore, we investigated how KIR2DS2 expression impacts NK cell function. Using a novel flow cytometry panel, we show that human NK cells with high KIR2DS2 expression have enhanced spontaneous activation against malignant B cell lines, liver cancer cell lines, and primary chronic lymphocytic leukemia cells. Surface expression of CD16 was increased on KIR2DS2high NK cells, and, accordingly, KIR2DS2high NK cells had increased activation against lymphoma cells coated with the clinically relevant anti-CD20 Abs rituximab and obinutuzumab. Bulk RNA sequencing revealed that KIR2DS2high NK cells have upregulation of NK-mediated cytotoxicity, translation, and FCGR gene pathways. We developed a novel single-cell RNA-sequencing technique to identify KIR2DS2+ NK cells, and this confirmed that KIR2DS2 is associated with enhanced NK cell-mediated cytotoxicity. This study provides evidence that KIR2DS2 marks a population of NK cells primed for anticancer activity and indicates that KIR2DS2 is an attractive target for NK-based therapeutic strategies.


Asunto(s)
Células Asesinas Naturales , Receptores KIR , Antígenos CD20/metabolismo , Línea Celular Tumoral , Citometría de Flujo , Humanos , Células Asesinas Naturales/metabolismo , Receptores KIR/genética , Receptores KIR/metabolismo , Rituximab/metabolismo , Rituximab/farmacología , Rituximab/uso terapéutico
6.
Mol Cell ; 63(4): 633-646, 2016 08 18.
Artículo en Inglés | MEDLINE | ID: mdl-27499295

RESUMEN

The repair outcomes at site-specific DNA double-strand breaks (DSBs) generated by the RNA-guided DNA endonuclease Cas9 determine how gene function is altered. Despite the widespread adoption of CRISPR-Cas9 technology to induce DSBs for genome engineering, the resulting repair products have not been examined in depth. Here, the DNA repair profiles of 223 sites in the human genome demonstrate that the pattern of DNA repair following Cas9 cutting at each site is nonrandom and consistent across experimental replicates, cell lines, and reagent delivery methods. Furthermore, the repair outcomes are determined by the protospacer sequence rather than genomic context, indicating that DNA repair profiling in cell lines can be used to anticipate repair outcomes in primary cells. Chemical inhibition of DNA-PK enabled dissection of the DNA repair profiles into contributions from c-NHEJ and MMEJ. Finally, this work elucidates a strategy for using "error-prone" DNA-repair machinery to generate precise edits.


Asunto(s)
Proteínas Bacterianas/metabolismo , Sistemas CRISPR-Cas , Roturas del ADN de Doble Cadena , Reparación del ADN por Unión de Extremidades , Endonucleasas/metabolismo , Edición Génica , Perfilación de la Expresión Génica/métodos , Proteínas Bacterianas/genética , Proteína 9 Asociada a CRISPR , Endonucleasas/genética , Células HCT116 , Células HEK293 , Humanos , Células K562 , Interferencia de ARN , ARN Guía de Kinetoplastida/genética , ARN Guía de Kinetoplastida/metabolismo , Factores de Tiempo , Transfección
7.
J Ren Nutr ; 34(2): 170-176, 2024 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-37839591

RESUMEN

OBJECTIVE: The American Medical Association recommends health information to be written at a 6th grade level reading level. Our aim was to determine whether Artificial Intelligence can outperform the existing health information on kidney stone prevention and treatment. METHODS: The top 50 search results for "Kidney Stone Prevention" and "Kidney Stone Treatment" on Google, Bing, and Yahoo were selected. Duplicate webpages, advertisements, pages intended for health professionals such as science articles, links to videos, paid subscription pages, and links nonrelated to kidney stone prevention and/or treatment were excluded. Included pages were categorized into academic, hospital-affiliated, commercial, nonprofit foundations, and other. Quality and readability of webpages were evaluated using validated tools, and the reading level was descriptively compared with ChatGPT generated health information on kidney stone prevention and treatment. RESULTS: 50 webpages on kidney stone prevention and 49 on stone treatment were included in this study. The reading level was determined to equate to that of a 10th to 12th grade student. Quality was measured as "fair" with no pages scoring "excellent" and only 20% receiving a "good" quality. There was no significant difference between pages from academic, hospital-affiliated, commercial, and nonprofit foundation publications. The text generated by ChatGPT was considerably easier to understand with readability levels measured as low as 5th grade. CONCLUSIONS: The language used in existing information on kidney stone disease is of subpar quality and too complex to understand. Machine learning tools could aid in generating information that is comprehensible by the public.


Asunto(s)
Inteligencia Artificial , Cálculos Renales , Estados Unidos , Humanos , Comprensión , Cálculos Renales/prevención & control , Internet
8.
Infect Immun ; 91(2): e0057022, 2023 02 16.
Artículo en Inglés | MEDLINE | ID: mdl-36692308

RESUMEN

A disrupted "dysbiotic" gut microbiome engenders susceptibility to the diarrheal pathogen Clostridioides difficile by impacting the metabolic milieu of the gut. Diet, in particular the microbiota-accessible carbohydrates (MACs) found in dietary fiber, is one of the most powerful ways to affect the composition and metabolic output of the gut microbiome. As such, diet is a powerful tool for understanding the biology of C. difficile and for developing alternative approaches for coping with this pathogen. One prominent class of metabolites produced by the gut microbiome is short-chain fatty acids (SCFAs), the major metabolic end products of MAC metabolism. SCFAs are known to decrease the fitness of C. difficile in vitro, and high intestinal SCFA concentrations are associated with reduced fitness of C. difficile in animal models of C. difficile infection (CDI). Here, we use controlled dietary conditions (8 diets that differ only by MAC composition) to show that C. difficile fitness is most consistently impacted by butyrate, rather than the other two prominent SCFAs (acetate and propionate), during murine model CDI. We similarly show that butyrate concentrations are lower in fecal samples from humans with CDI than in those from healthy controls. Finally, we demonstrate that butyrate impacts growth in diverse C. difficile isolates. These findings provide a foundation for future work which will dissect how butyrate directly impacts C. difficile fitness and will lead to the development of diverse approaches distinct from antibiotics or fecal transplant, such as dietary interventions, for mitigating CDI in at-risk human populations. IMPORTANCE Clostridioides difficile is a leading cause of infectious diarrhea in humans, and it imposes a tremendous burden on the health care system. Current treatments for C. difficile infection (CDI) include antibiotics and fecal microbiota transplant, which contribute to recurrent CDIs and face major regulatory hurdles, respectively. Therefore, there is an ongoing need to develop new ways to cope with CDI. Notably, a disrupted "dysbiotic" gut microbiota is the primary risk factor for CDI, but we incompletely understand how a healthy microbiota resists CDI. Here, we show that a specific molecule produced by the gut microbiota, butyrate, is negatively associated with C. difficile burdens in humans and in a mouse model of CDI and that butyrate impedes the growth of diverse C. difficile strains in pure culture. These findings help to build a foundation for designing alternative, possibly diet-based, strategies for mitigating CDI in humans.


Asunto(s)
Clostridioides difficile , Infecciones por Clostridium , Humanos , Animales , Ratones , Butiratos , Tolerancia , Antibacterianos/farmacología , Antibacterianos/uso terapéutico , Ácidos Grasos Volátiles
9.
Diabetes Obes Metab ; 25(5): 1203-1212, 2023 05.
Artículo en Inglés | MEDLINE | ID: mdl-36594522

RESUMEN

AIMS: To investigate a prebiotic fibre-enriched nutritional formula on health-related quality of life and metabolic control in type 2 diabetes. MATERIALS AND METHODS: This was a 12-week, double-blind, placebo-controlled study with an unblinded dietary advice only comparator arm. Participants were randomized 2:1:1 to a prebiotic fibre-enriched nutritional formula (Active), a placebo fibre-absent nutritional formula (Placebo), or non-blinded dietary advice alone (Diet). Primary endpoint was change in core Type 2 Diabetes Distress Assessment System (cT2-DDAS) at week 12. Glycated haemoglobin (HbA1c) change was a key secondary endpoint. RESULTS: In total, 192 participants were randomized. Mean age was 54.3 years, HbA1c 7.8%, and body mass index 35.9 kg/m2 . At week 12, cT2-DDAS reduced significantly in Active versus Placebo (-0.4, p = .03), and HbA1c was reduced significantly in Active vs Placebo (-0.64%, p = .01). Gut microbiome sequencing revealed that the relative abundance of two species of butyrate-producing bacteria (Roseburia faecis and Anaerostipes hadrus) increased significantly in Active vs. Placebo. CONCLUSIONS: A microbiome-targeting nutritional formula significantly improved cT2-DDAS and HbA1c, suggesting the potential for prebiotic fibre as a complement to lifestyle and/or pharmaceutical interventions for managing type 2 diabetes.


Asunto(s)
Diabetes Mellitus Tipo 2 , Microbioma Gastrointestinal , Humanos , Persona de Mediana Edad , Diabetes Mellitus Tipo 2/tratamiento farmacológico , Hemoglobina Glucada , Calidad de Vida , Prebióticos , Método Doble Ciego , Hipoglucemiantes/uso terapéutico
10.
Knee Surg Sports Traumatol Arthrosc ; 31(3): 793-802, 2023 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-34981161

RESUMEN

PURPOSE: UKA has higher revision risk, particularly for lower volume surgeons. While robotic-arm assisted systems allow for increased accuracy, introduction of new systems has been associated with learning curves. The aim of this study was to determine the learning curve of a UKA robotic-arm assisted system. The hypothesis was that this may affect operative times, patient outcomes, limb alignment, and component placement. METHODS: Between 2017 and 2021, five surgeons performed 152 consecutive robotic-arm assisted primary medial UKA, and measurements of interest were recorded. Patient outcomes were measured with Oxford Knee Score, EuroQol-5D, and Forgotten Joint Score at 6 weeks, 1 year, and 2 years. Surgeons were grouped into 'low' and 'high' usage groups based on total UKA (manual and robotic) performed per year. RESULTS: A learning curve of 11 cases was found with operative time (p < 0.01), femoral rotation (p = 0.02), and insert sizing (p = 0.03), which highlighted areas that require care during the learning phase. Despite decreased 6-week EQ-5D-5L VAS in the proficiency group (77 cf. 85, p < 0.01), no difference was found with implant survival (98.2%) between phases (p = 0.15), or between 'high' and 'low' usage surgeons (p = 0.23) at 36 months. This suggested that the learning curve did not lead to early adverse effects in this patient cohort. CONCLUSION: Introduction of a UKA robotic-arm assisted system showed learning curves for operative times and insert sizing but not for implant survival at early follow-up. The short learning curve regardless of UKA usage indicated that robotic-arm assisted UKA may be particularly useful for low-usage surgeons. LEVEL OF EVIDENCE: Level III, Retrospective cohort study.


Asunto(s)
Artroplastia de Reemplazo de Rodilla , Prótesis de la Rodilla , Osteoartritis de la Rodilla , Procedimientos Quirúrgicos Robotizados , Humanos , Artroplastia de Reemplazo de Rodilla/efectos adversos , Curva de Aprendizaje , Estudios Retrospectivos , Osteoartritis de la Rodilla/cirugía , Estudios Prospectivos , Resultado del Tratamiento , Articulación de la Rodilla/cirugía
11.
J Arthroplasty ; 38(6S): S238-S245, 2023 06.
Artículo en Inglés | MEDLINE | ID: mdl-36933677

RESUMEN

BACKGROUND: Ideal goals for alignment and balance in total knee arthroplasty (TKA) remain controversial. We aimed to compare initial alignment and balance using mechanical alignment (MA) and kinematic alignment (KA) techniques and to analyze the percentage of knees that could achieve balance using limited adjustments to component position. METHODS: Prospective data on 331 primary robotic TKAs (115 MAs and 216 KAs) were analyzed. Medial and lateral virtual gaps were recorded in both flexion and extension. A computer algorithm was used to calculate potential (theoretical) implant alignment solutions to achieve balance within 1 millimeter (mm) without soft tissue release given an alignment philosophy (MA or KA), angular boundaries (±1, ±2, or ±3°), and gap targets (equal gaps or lateral laxity allowed). The percentage of knees that could theoretically achieve balance was compared. RESULTS: Less than 5% of TKAs were initially balanced. Limited adjustments to component position increased the percentage of TKAs that could be balanced in a graduated manner, with no difference between MA and KA start points: adjustments of ±1 (10% versus 6%, P = .17), ±2 (42% versus 39%, P = .61), or of ±3 (54% versus 51%, P = .66). A higher percentage of TKAs could be balanced when a greater range for lateral gap laxity was allowed. Balancing from KA resulted in increased joint line obliquity in the final implant alignment. CONCLUSION: A high percentage of TKAs can be balanced without soft tissue release using minor adjustments to component position. Surgeons should consider the relationship between alignment and balance goals when optimizing component positioning in TKA.


Asunto(s)
Artroplastia de Reemplazo de Rodilla , Prótesis de la Rodilla , Osteoartritis de la Rodilla , Procedimientos Quirúrgicos Robotizados , Humanos , Artroplastia de Reemplazo de Rodilla/métodos , Articulación de la Rodilla/cirugía , Estudios Prospectivos , Rodilla/cirugía , Osteoartritis de la Rodilla/cirugía , Rango del Movimiento Articular , Fenómenos Biomecánicos
12.
Folia Phoniatr Logop ; 75(2): 81-89, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-36103862

RESUMEN

INTRODUCTION: Students and professionals in communication sciences and disorders (CSD) need to exhibit good critical thinking (CT) skills when engaged in clinical tasks. CSD clinicians must make decisions that are free from biases and support their claim with facts. Thus, CSD clinicians need to be trained to question their clinical practices and to skeptically evaluate new practices that develop. A content-specific CT test can help determine if students are developing these skills. However, to date, no such content-specific CT assessment exists for CSD. The purpose of this study was to determine the reliability of the current version of a specific content CT assessment, the Critical Thinking in Communication Sciences and Disorders (CTCSD). METHODS: A sample of 150 CSD graduate students enrolled in three programs participated. They completed an online Qualtrics survey that consisted of the CTCSD. They completed the Qualtrics survey twice, once at the beginning of a semester and once at the end. The participant responses were independently scored by two research associates. The data were analyzed for reliability in three ways. Intra-subject reliability was assessed by comparing scores across the two testing sessions. Internal consistency of the items to measure a common construct was assessed using Cronbach's alpha and Guttman's Lambda 6. Inter-rater reliability was assessed using Cohen's Kappa coefficient. In addition, the time used to complete the survey was analyzed. RESULTS: The students from the three programs scored similarly on the CTCSD. High reliability ratings occurred for the intra-subject, internal consistency, and inter-rater measures. DISCUSSION/CONCLUSION: The results indicate the reliability of the CTCSD. In combination with previous results indicating the face, construct, and criterion validity of the CTCSD, it appears to have psychometric strength. The CTCSD may help academic and clinical faculty select learning activities and focus feedback to their graduate students in order to reinforce skills the students exhibit and to develop other skills.


Asunto(s)
Estudiantes , Pensamiento , Humanos , Reproducibilidad de los Resultados , Psicometría , Encuestas y Cuestionarios , Comunicación
13.
Macromol Rapid Commun ; 43(13): e2100773, 2022 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-35271740

RESUMEN

Poly(acrylic acid) (PAA) is produced on an industrial scale and widely-used in applications such as personal care products and cleaning formulations that end up "down-the-drain." Relatively high molecular weight PAA is considered poorly biodegradable, but little is known about the biodegradability of low molecular weight PAA at the wastewater treatment plant according to current regulatory and industrial Organization for Economic Co-operation and Development (OECD) standards. The synthesis, separation, and characterization of a series of ultralow dispersity PAA oligomers (i.e., D < 1.10) in the molecular weight range Mn ≈ 350-1200 Da and the results of biodegradability testing are reported. Miniaturized, high-throughput screening studies in a parallel respirometer reveals a strong trend toward lower biodegradation at higher molecular weight; these results are confirmed and expanded using standardized method OECD 301F. Biodegradability reaches ≈40% at Mn = 380 Da, ≈26% at Mn = 770 Da, and ≈17% at Mn = 1190 Da for discrete polyacid oligomers. These data not only shed light on potential biodegradation mechanisms for linear PAA, but also may inspire the future design of biodegradable PAA-containing macromolecules.


Asunto(s)
Resinas Acrílicas , Biodegradación Ambiental , Peso Molecular
15.
PLoS Biol ; 16(5): e2006188, 2018 05.
Artículo en Inglés | MEDLINE | ID: mdl-29734335

RESUMEN

When core body temperature increases, appetite and food consumption decline. A higher core body temperature can occur during exercise, during exposure to warm environmental temperatures, or during a fever, yet the mechanisms that link relatively warm temperatures to appetite suppression are unknown. A recent study in PLOS Biology demonstrates that neurons in the mouse hypothalamus that express pro-opiomelanocortin (POMC), a neural population well known to suppress food intake, also express a temperature-sensitive ion channel, transient receptor potential vanilloid 1 (TRPV1). Slight increases in body temperature cause a TRPV1-dependent increase in activity in POMC neurons, which suppresses feeding in mice. Taken together, this study suggests a novel mechanism linking body temperature and food-seeking behavior.


Asunto(s)
Regulación del Apetito/fisiología , Calor , Neuronas/metabolismo , Proopiomelanocortina/metabolismo , Animales , Temperatura Corporal , Humanos , Canales Catiónicos TRPV/metabolismo
16.
Cytopathology ; 32(5): 621-630, 2021 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-34033159

RESUMEN

OBJECTIVE: Rearranged ROS1, present in 1%-2% of non-small cell lung cancer (NSCLC) patients, usually young, never or light smokers, is assessed by fluorescence in situ hybridization (FISH) to determine eligibility for tyrosine kinase inhibitors (TKI). Immunohistochemistry (IHC) for the protein product of ROS1 rearrangement, a cost-effective alternative, is validated on cytology and small biopsy samples. METHODS: From 1 March to 31 December 2019, cytology cell blocks and small biopsy samples from a selected cohort of NSCLC patients were concurrently tested for ROS1 gene rearrangement by Vysis 6q22 Break Apart FISH probe and IHC using Cell Signalling D4D6 antibody. Mismatch cases were tested by an RNA fusion next generation sequencing (NGS) panel. RESULTS: In a prospective population of 95 cases, 91 were negative and two were positive by both FISH and IHC. Both dual positive cases were female never smokers and benefited from TKI treatment. Another two cases were positive by FISH but negative by IHC and repeat by NGS showed one to be negative but one failed. Turnaround time for IHC was 0 to 8 days from request to authorisation, whilst that of FISH was 9 to 42 days at a cost of £51 and £159 respectively. CONCLUSION: IHC to assess for the protein product of ROS1 gene rearrangement on cytology cell blocks and small biopsy samples in a routine setting is a promising screening method to assess eligibility for TKI treatment with positive and indeterminate cases confirmed by FISH or NGS as it has good negative predictive value, faster turnaround time and is cost effective, with proven technical and clinical validation.


Asunto(s)
Biopsia/métodos , Citodiagnóstico/métodos , Inmunohistoquímica/métodos , Hibridación Fluorescente in Situ/métodos , Proteínas Tirosina Quinasas/metabolismo , Proteínas Proto-Oncogénicas/metabolismo , Adulto , Anciano , Anciano de 80 o más Años , Carcinoma de Pulmón de Células no Pequeñas/diagnóstico , Carcinoma de Pulmón de Células no Pequeñas/metabolismo , Femenino , Hospitales de Enseñanza/métodos , Humanos , Neoplasias Pulmonares/diagnóstico , Neoplasias Pulmonares/metabolismo , Masculino , Persona de Mediana Edad , Estudios Prospectivos
17.
Nat Methods ; 14(6): 600-606, 2017 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-28459459

RESUMEN

RNA-guided CRISPR-Cas9 endonucleases are widely used for genome engineering, but our understanding of Cas9 specificity remains incomplete. Here, we developed a biochemical method (SITE-Seq), using Cas9 programmed with single-guide RNAs (sgRNAs), to identify the sequence of cut sites within genomic DNA. Cells edited with the same Cas9-sgRNA complexes are then assayed for mutations at each cut site using amplicon sequencing. We used SITE-Seq to examine Cas9 specificity with sgRNAs targeting the human genome. The number of sites identified depended on sgRNA sequence and nuclease concentration. Sites identified at lower concentrations showed a higher propensity for off-target mutations in cells. The list of off-target sites showing activity in cells was influenced by sgRNP delivery, cell type and duration of exposure to the nuclease. Collectively, our results underscore the utility of combining comprehensive biochemical identification of off-target sites with independent cell-based measurements of activity at those sites when assessing nuclease activity and specificity.


Asunto(s)
Sistemas CRISPR-Cas/genética , Mapeo Cromosómico/métodos , Repeticiones Palindrómicas Cortas Agrupadas y Regularmente Espaciadas/genética , Genoma/genética , Secuenciación de Nucleótidos de Alto Rendimiento , Análisis de Secuencia de ADN
18.
Langmuir ; 36(28): 8240-8252, 2020 07 21.
Artículo en Inglés | MEDLINE | ID: mdl-32649210

RESUMEN

We report the aqueous lyotropic mesophase behaviors of protonated amine-based "lipidoids," a class of synthetic lipid-like molecules that mirrors essential structural features of the multitail bacterial amphiphile lipid A. Small-angle X-ray scattering (SAXS) studies demonstrate that the protonation of the tetra(amine) headgroups of six-tail lipidoids in aqueous HCl, HNO3, H2SO4, and H3PO4 solutions variably drives their self-assembly into lamellar (Lα) and inverse micellar (III) lyotropic liquid crystals (LLCs), depending on acid identity and concentration, amphiphile tail length, and temperature. Lipidoid assemblies formed in H2SO4(aq) exhibit rare inverse body-centered cubic (BCC) and inverse face-centered cubic (FCC) micellar morphologies, the latter of which unexpectedly coexists with zero mean curvature Lα phases. Complementary atomistic molecular dynamics (MD) simulations furnish detailed insights into this unusual self-assembly behavior. The unique aqueous lyotropic mesophase behaviors of ammonium lipidoids originate in their dichotomous ability to adopt both inverse conical and chain-extended molecular conformations depending on the number of counterions and their identity, which lead to coexisting supramolecular assemblies with remarkably different mean interfacial curvatures.

19.
J Immunol ; 200(7): 2304-2312, 2018 04 01.
Artículo en Inglés | MEDLINE | ID: mdl-29453281

RESUMEN

Idelalisib is a highly selective oral inhibitor of PI3Kδ indicated for the treatment of patients with relapsed chronic lymphocytic leukemia in combination with rituximab. Despite additive clinical effects, previous studies have paradoxically demonstrated that targeted therapies potentially negatively affect anti-CD20 mAb effector mechanisms. To address these potential effects, we investigated the impact of PI3Kδ inhibition by idelalisib on the effector mechanisms of rituximab and obinutuzumab. At clinically relevant concentrations, idelalisib minimally influenced rituximab- and obinutuzumab-mediated Ab-dependent cellular cytotoxicity and phagocytosis on human lymphoma cell lines, while maintaining the superiority of obinutuzumab-mediated Ab-dependent cellular cytotoxicity. Consistent with this, idelalisib did not influence obinutuzumab-mediated B cell depletion in whole-blood B cell-depletion assays. Further, idelalisib significantly enhanced obinutuzumab-mediated direct cell death of chronic lymphocytic leukemia cells. In murine systems, in vivo inhibition of PI3Kδ minimally interfered with maximal rituximab- or obinutuzumab-mediated depletion of leukemic targets. In addition, the duration of rituximab- and obinutuzumab-mediated depletion of leukemia cells was extended by combination with PI3Kδ inhibition. Collectively, these data demonstrate that PI3Kδ inhibition does not significantly affect the effector mechanisms induced by rituximab or obinutuzumab and provides an effective in vivo therapeutic combination. Therefore, combinations of obinutuzumab and idelalisib are currently being assessed in clinical studies.


Asunto(s)
Anticuerpos Monoclonales Humanizados/farmacología , Citotoxicidad Celular Dependiente de Anticuerpos/efectos de los fármacos , Antineoplásicos/farmacología , Fosfatidilinositol 3-Quinasa Clase I/antagonistas & inhibidores , Inhibidores Enzimáticos/farmacología , Fagocitosis/efectos de los fármacos , Purinas/farmacología , Quinazolinonas/farmacología , Rituximab/farmacología , Animales , Línea Celular Tumoral , Interacciones Farmacológicas , Humanos , Leucemia Linfocítica Crónica de Células B/tratamiento farmacológico , Linfoma/tratamiento farmacológico , Ratones , Ratones Endogámicos C57BL , Ratones SCID , Ratones Transgénicos
20.
Mol Cell Proteomics ; 17(4): 776-791, 2018 04.
Artículo en Inglés | MEDLINE | ID: mdl-29367434

RESUMEN

Chronic lymphocytic leukemia (CLL) is a heterogeneous B-cell cancer exhibiting a wide spectrum of disease courses and treatment responses. Molecular characterization of RNA and DNA from CLL cases has led to the identification of important driver mutations and disease subtypes, but the precise mechanisms of disease progression remain elusive. To further our understanding of CLL biology we performed isobaric labeling and mass spectrometry proteomics on 14 CLL samples, comparing them with B-cells from healthy donors (HDB). Of 8694 identified proteins, ∼6000 were relatively quantitated between all samples (q<0.01). A clear CLL signature, independent of subtype, of 544 significantly overexpressed proteins relative to HDB was identified, highlighting established hallmarks of CLL (e.g. CD5, BCL2, ROR1 and CD23 overexpression). Previously unrecognized surface markers demonstrated overexpression (e.g. CKAP4, PIGR, TMCC3 and CD75) and three of these (LAX1, CLEC17A and ATP2B4) were implicated in B-cell receptor signaling, which plays an important role in CLL pathogenesis. Several other proteins (e.g. Wee1, HMOX1/2, HDAC7 and INPP5F) were identified with significant overexpression that also represent potential targets. Western blotting confirmed overexpression of a selection of these proteins in an independent cohort. mRNA processing machinery were broadly upregulated across the CLL samples. Spliceosome components demonstrated consistent overexpression (p = 1.3 × 10-21) suggesting dysregulation in CLL, independent of SF3B1 mutations. This study highlights the potential of proteomics in the identification of putative CLL therapeutic targets and reveals a subtype-independent protein expression signature in CLL.


Asunto(s)
Linfocitos B/metabolismo , Leucemia Linfocítica Crónica de Células B/metabolismo , Proteínas de Neoplasias/metabolismo , Humanos , Proteómica , Empalmosomas
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