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1.
N Engl J Med ; 390(16): 1467-1480, 2024 Apr 25.
Artículo en Inglés | MEDLINE | ID: mdl-38657244

RESUMEN

BACKGROUND: Patients with relapsed or refractory hematologic cancers have a poor prognosis. Chimeric antigen receptor (CAR) T-cell therapy as a bridge to allogeneic hematopoietic stem-cell transplantation (HSCT) has the potential for long-term tumor elimination. However, pre-HSCT myeloablation and graft-versus-host disease (GVHD) prophylaxis agents have toxic effects and could eradicate residual CAR T cells and compromise antitumor effects. Whether the integration of CAR T-cell therapy and allogeneic HSCT can preserve CAR T-cell function and improve tumor control is unclear. METHODS: We tested a novel "all-in-one" strategy consisting of sequential CD7 CAR T-cell therapy and haploidentical HSCT in 10 patients with relapsed or refractory CD7-positive leukemia or lymphoma. After CAR T-cell therapy led to complete remission with incomplete hematologic recovery, patients received haploidentical HSCT without pharmacologic myeloablation or GVHD prophylaxis drugs. Toxic effects and efficacy were closely monitored. RESULTS: After CAR T-cell therapy, all 10 patients had complete remission with incomplete hematologic recovery and grade 4 pancytopenia. After haploidentical HSCT, 1 patient died on day 13 of septic shock and encephalitis, 8 patients had full donor chimerism, and 1 patient had autologous hematopoiesis. Three patients had grade 2 HSCT-associated acute GVHD. The median follow-up was 15.1 months (range, 3.1 to 24.0) after CAR T-cell therapy. Six patients remained in minimal residual disease-negative complete remission, 2 had a relapse of CD7-negative leukemia, and 1 died of septic shock at 3.7 months. The estimated 1-year overall survival was 68% (95% confidence interval [CI], 43 to 100), and the estimated 1-year disease-free survival was 54% (95% CI, 29 to 100). CONCLUSIONS: Our findings suggest that sequential CD7 CAR T-cell therapy and haploidentical HSCT is safe and effective, with remission and serious but reversible adverse events. This strategy offers a feasible approach for patients with CD7-positive tumors who are ineligible for conventional allogeneic HSCT. (Funded by the National Natural Science Foundation of China and the Key Project of Science and Technology Department of Zhejiang Province; ClinicalTrials.gov numbers, NCT04599556 and NCT04538599.).


Asunto(s)
Enfermedad Injerto contra Huésped , Trasplante de Células Madre Hematopoyéticas , Inmunoterapia Adoptiva , Leucemia , Linfoma , Receptores Quiméricos de Antígenos , Adolescente , Adulto , Femenino , Humanos , Masculino , Persona de Mediana Edad , Adulto Joven , Antígenos CD7 , Terapia Combinada , Enfermedad Injerto contra Huésped/prevención & control , Trasplante de Células Madre Hematopoyéticas/efectos adversos , Trasplante de Células Madre Hematopoyéticas/métodos , Inmunoterapia Adoptiva/efectos adversos , Inmunoterapia Adoptiva/métodos , Leucemia/terapia , Leucemia/mortalidad , Linfoma/mortalidad , Linfoma/terapia , Receptores Quiméricos de Antígenos/uso terapéutico , Inducción de Remisión , Trasplante Homólogo , Recurrencia , Anciano
2.
Genome Med ; 15(1): 115, 2023 12 18.
Artículo en Inglés | MEDLINE | ID: mdl-38111063

RESUMEN

Identifying expressed somatic mutations from single-cell RNA sequencing data de novo is challenging but highly valuable. We propose RESA - Recurrently Expressed SNV Analysis, a computational framework to identify expressed somatic mutations from scRNA-seq data. RESA achieves an average precision of 0.77 on three in silico spike-in datasets. In extensive benchmarking against existing methods using 19 datasets, RESA consistently outperforms them. Furthermore, we applied RESA to analyze intratumor mutational heterogeneity in a melanoma drug resistance dataset. By enabling high precision detection of expressed somatic mutations, RESA substantially enhances the reliability of mutational analysis in scRNA-seq. RESA is available at https://github.com/ShenLab-Genomics/RESA .


Asunto(s)
Melanoma , Análisis de la Célula Individual , Humanos , Reproducibilidad de los Resultados , Análisis de Secuencia de ARN/métodos , Análisis de la Célula Individual/métodos , Mutación , Melanoma/genética , Perfilación de la Expresión Génica/métodos , Análisis por Conglomerados , Programas Informáticos
3.
Cell ; 186(13): 2765-2782.e28, 2023 06 22.
Artículo en Inglés | MEDLINE | ID: mdl-37327786

RESUMEN

Cancer is characterized by hypomethylation-associated silencing of large chromatin domains, whose contribution to tumorigenesis is uncertain. Through high-resolution genome-wide single-cell DNA methylation sequencing, we identify 40 core domains that are uniformly hypomethylated from the earliest detectable stages of prostate malignancy through metastatic circulating tumor cells (CTCs). Nested among these repressive domains are smaller loci with preserved methylation that escape silencing and are enriched for cell proliferation genes. Transcriptionally silenced genes within the core hypomethylated domains are enriched for immune-related genes; prominent among these is a single gene cluster harboring all five CD1 genes that present lipid antigens to NKT cells and four IFI16-related interferon-inducible genes implicated in innate immunity. The re-expression of CD1 or IFI16 murine orthologs in immuno-competent mice abrogates tumorigenesis, accompanied by the activation of anti-tumor immunity. Thus, early epigenetic changes may shape tumorigenesis, targeting co-located genes within defined chromosomal loci. Hypomethylation domains are detectable in blood specimens enriched for CTCs.


Asunto(s)
Metilación de ADN , Neoplasias de la Próstata , Animales , Humanos , Masculino , Ratones , Carcinogénesis/genética , ADN , Epigénesis Genética , Neoplasias de la Próstata/genética , Células Neoplásicas Circulantes
4.
NPJ Precis Oncol ; 7(1): 25, 2023 Mar 02.
Artículo en Inglés | MEDLINE | ID: mdl-36864091

RESUMEN

Immune checkpoint blockade (ICB) has demonstrated efficacy in patients with melanoma, but many exhibit poor responses. Using single cell RNA sequencing of melanoma patient-derived circulating tumor cells (CTCs) and functional characterization using mouse melanoma models, we show that the KEAP1/NRF2 pathway modulates sensitivity to ICB, independently of tumorigenesis. The NRF2 negative regulator, KEAP1, shows intrinsic variation in expression, leading to tumor heterogeneity and subclonal resistance.

5.
Cell Rep ; 42(3): 112129, 2023 03 28.
Artículo en Inglés | MEDLINE | ID: mdl-36821441

RESUMEN

TGF-ß induces senescence in embryonic tissues. Whether TGF-ß in the hypoxic tumor microenvironment (TME) induces senescence in cancer and how the ensuing senescence-associated secretory phenotype (SASP) remodels the cellular TME to influence immune checkpoint inhibitor (ICI) responses are unknown. We show that TGF-ß induces a deeper senescent state under hypoxia than under normoxia; deep senescence correlates with the degree of E2F suppression and is marked by multinucleation, reduced reentry into proliferation, and a distinct 14-gene SASP. Suppressing TGF-ß signaling in tumors in an immunocompetent mouse lung cancer model abrogates endogenous senescent cells and suppresses the 14-gene SASP and immune infiltration. Untreated human lung cancers with a high 14-gene SASP display immunosuppressive immune infiltration. In a lung cancer clinical trial of ICIs, elevated 14-gene SASP is associated with increased senescence, TGF-ß and hypoxia signaling, and poor progression-free survival. Thus, TME-induced senescence may represent a naturally occurring state in cancer, contributing to an immune-suppressive phenotype associated with immune therapy resistance.


Asunto(s)
Neoplasias Pulmonares , Factor de Crecimiento Transformador beta , Ratones , Animales , Humanos , Fenotipo , Modelos Animales de Enfermedad , Microambiente Celular , Microambiente Tumoral , Senescencia Celular/fisiología
6.
ACS Appl Mater Interfaces ; 14(17): 19388-19396, 2022 May 04.
Artículo en Inglés | MEDLINE | ID: mdl-35442619

RESUMEN

Ethylene (C2H4) is an important product in carbon dioxide electroreduction (CO2RR) because of the essential role it plays in chemical industry. While several strategies have been proposed to tune the selectivity of Cu-based catalysts in order to achieve high C2H4 faradaic efficiency, maintaining high selectivity toward C2H4 in CO2RR remains an unresolved problem hampering the deployment of CO2 conversion technology due to the lack of stable electrocatalysts. Here, we develop a facile method to deposit a layer of Cu2O on Cu foil by an electrochemical pulsed potential treatment. This method is capable to easily scale up and synthesize multiple electrodes in one step. After the synthesis, the pulsed copper foil, denoted as P-Cu, exhibits good C2H4 faradaic efficiency of ∼50% in CO2RR at a potential around -1.0 V vs. RHE. The C2H4 selectivity is also found to be quantitatively correlated with the roughness factor (RF) of Cu-based catalysts. More importantly, for the first time, we demonstrate that the P-Cu electrode is quite durable in CO2RR to produce C2H4 for more than 6 months.

7.
Chemosphere ; 295: 133929, 2022 May.
Artículo en Inglés | MEDLINE | ID: mdl-35149017

RESUMEN

It still remains a hotspot and great challenge to efficiently remove the nitrate nitrogen from high salt wastewater. Herein, a novel three dimensional porous bimetallic copper-nickel alloy electrode was fabricated with Ni foam (NiF) as substrate. The physicochemical and electrochemical characterization results showed Cu-Ni/NiF electrode possessed the smaller particle size (0.3-1.0 µm) and electrode film resistance comparing with Ni/NiF and Cu/NiF electrodes. Besides, higher double layer capacitance (Cdl) for Cu-Ni/NiF electrode indicated more electrochemical active sites could be used in the electrochemical nitrate nitrogen (NO3--N) removal. The electrochemical experiments showed the Cu-Ni/NiF electrode had the optimal NO3--N reduction ability and almost 100% NO3--N removal could be achieved with 30 min. All NO3--N removal processes were in accord with the pseudo-first-order reaction kinetics completely. The gaseous nitrogen selectivity for Cu-Ni/NiF electrode could reach 80.9% within 300 min. Stability assessment experiments indicated the Cu-Ni/NiF electrode all kept an excellent stability with Na2SO4 or NaCl electrolyte and the Cl- addition could significantly improve the gaseous nitrogen selectivity. Finally, a possible removal mechanism of NO3--N was proposed. This work offered a direction for designing non-noble bimetallic electrodes for nitrate removal.


Asunto(s)
Nitratos , Nitrógeno , Electrodos , Nitratos/química , Óxidos de Nitrógeno
8.
Mol Cell ; 81(19): 4041-4058.e15, 2021 10 07.
Artículo en Inglés | MEDLINE | ID: mdl-34624217

RESUMEN

Deregulation of oncogenic signals in cancer triggers replication stress. Immediate early genes (IEGs) are rapidly and transiently expressed following stressful signals, contributing to an integrated response. Here, we find that the orphan nuclear receptor NR4A1 localizes across the gene body and 3' UTR of IEGs, where it inhibits transcriptional elongation by RNA Pol II, generating R-loops and accessible chromatin domains. Acute replication stress causes immediate dissociation of NR4A1 and a burst of transcriptionally poised IEG expression. Ectopic expression of NR4A1 enhances tumorigenesis by breast cancer cells, while its deletion leads to massive chromosomal instability and proliferative failure, driven by deregulated expression of its IEG target, FOS. Approximately half of breast and other primary cancers exhibit accessible chromatin domains at IEG gene bodies, consistent with this stress-regulatory pathway. Cancers that have retained this mechanism in adapting to oncogenic replication stress may be dependent on NR4A1 for their proliferation.


Asunto(s)
Neoplasias de la Mama/metabolismo , Proliferación Celular , Proteínas Inmediatas-Precoces/metabolismo , Mitosis , Células Neoplásicas Circulantes/metabolismo , Miembro 1 del Grupo A de la Subfamilia 4 de Receptores Nucleares/metabolismo , Regiones no Traducidas 3' , Animales , Antineoplásicos/farmacología , Sitios de Unión , Neoplasias de la Mama/tratamiento farmacológico , Neoplasias de la Mama/genética , Neoplasias de la Mama/patología , Proliferación Celular/efectos de los fármacos , Ensamble y Desensamble de Cromatina , Femenino , Regulación Neoplásica de la Expresión Génica , Inestabilidad Genómica , Células HEK293 , Humanos , Proteínas Inmediatas-Precoces/genética , Indoles/farmacología , Células MCF-7 , Ratones Endogámicos NOD , Ratones SCID , Mitosis/efectos de los fármacos , Células Neoplásicas Circulantes/efectos de los fármacos , Células Neoplásicas Circulantes/patología , Miembro 1 del Grupo A de la Subfamilia 4 de Receptores Nucleares/antagonistas & inhibidores , Miembro 1 del Grupo A de la Subfamilia 4 de Receptores Nucleares/genética , Fenilacetatos/farmacología , Proteínas Proto-Oncogénicas c-fos/genética , Proteínas Proto-Oncogénicas c-fos/metabolismo , Estructuras R-Loop , ARN Polimerasa II/genética , ARN Polimerasa II/metabolismo , Transducción de Señal , Elongación de la Transcripción Genética , Células Tumorales Cultivadas , Ensayos Antitumor por Modelo de Xenoinjerto
9.
Nature ; 594(7862): 283-288, 2021 06.
Artículo en Inglés | MEDLINE | ID: mdl-33981036

RESUMEN

Homologous recombination (HR) repairs DNA double-strand breaks (DSBs) in the S and G2 phases of the cell cycle1-3. Several HR proteins are preferentially recruited to DSBs at transcriptionally active loci4-10, but how transcription promotes HR is poorly understood. Here we develop an assay to assess the effect of local transcription on HR. Using this assay, we find that transcription stimulates HR to a substantial extent. Tethering RNA transcripts to the vicinity of DSBs recapitulates the effects of local transcription, which suggests that transcription enhances HR through RNA transcripts. Tethered RNA transcripts stimulate HR in a sequence- and orientation-dependent manner, indicating that they function by forming DNA-RNA hybrids. In contrast to most HR proteins, RAD51-associated protein 1 (RAD51AP1) only promotes HR when local transcription is active. RAD51AP1 drives the formation of R-loops in vitro and is required for tethered RNAs to stimulate HR in cells. Notably, RAD51AP1 is necessary for the DSB-induced formation of DNA-RNA hybrids in donor DNA, linking R-loops to D-loops. In vitro, RAD51AP1-generated R-loops enhance the RAD51-mediated formation of D-loops locally and give rise to intermediates that we term 'DR-loops', which contain both DNA-DNA and DNA-RNA hybrids and favour RAD51 function. Thus, at DSBs in transcribed regions, RAD51AP1 promotes the invasion of RNA transcripts into donor DNA, and stimulates HR through the formation of DR-loops.


Asunto(s)
ADN/genética , ADN/metabolismo , Recombinación Homóloga/genética , Estructuras R-Loop/genética , ARN Mensajero/genética , ARN Mensajero/metabolismo , Transcripción Genética , Factores de Transcripción con Motivo Hélice-Asa-Hélice Básico/genética , Línea Celular , ADN/química , Roturas del ADN de Doble Cadena , Reparación del ADN , Proteínas de Unión al ADN/metabolismo , Genes/genética , Genes Reporteros/genética , Proteínas Fluorescentes Verdes/genética , Humanos , Técnicas In Vitro , ARN Mensajero/química , Proteínas de Unión al ARN/metabolismo , Recombinasa Rad51/metabolismo
10.
Hum Reprod ; 36(2): 318-330, 2021 01 25.
Artículo en Inglés | MEDLINE | ID: mdl-33313772

RESUMEN

STUDY QUESTION: Is it possible to evaluate the methylome of individual oocytes to investigate the DNA methylome alterations in metaphase II (MII) oocytes with reduced embryo developmental potential? SUMMARY ANSWER: The DNA methylome of each human first polar body (PB1) closely mirrored that of its sibling MII oocyte; hypermethylated long interspersed nuclear element (LINE) and long terminal repeats (LTRs) and methylation aberrations in PB1 promoter regions may indicate poor embryo development. WHAT IS KNOWN ALREADY: The developmental potential of an embryo is determined by the oocyte's developmental competence, and the PB1 is a good substitute to examine the chromosomal status of the corresponding oocyte. However, DNA methylation, a key epigenetic modification, also regulates gene expression and embryo development. STUDY DESIGN, SIZE, DURATION: Twelve pairs of PB1s and sibling MII oocytes were biopsied and sequenced to compare their methylomes. To further investigate the methylome of PB1s and the potential epigenetic factors that may affect oocyte quality, MII oocytes (n = 74) were fertilized through ICSI, while PB1s were biopsied and profiled to measure DNA methylation. The corresponding embryos were further cultured to track their development potential. The oocytes and sperm samples used in this study were donated by healthy volunteers with signed informed consent. PARTICIPANTS/MATERIALS, SETTING, METHODS: Single-cell methylome sequencing was applied to obtain the DNA methylation profiles of PB1s and oocytes. The DNA methylome of PB1s was compared between the respective group of oocytes that progressed to blastocysts and the group of oocytes that failed to develop. DNA methylation levels of corresponding regions and differentially methylated regions were calculated using customized Perl and R scripts. RNA-seq data were downloaded from a previously published paper and reanalysed. MAIN RESULTS AND THE ROLE OF CHANCE: The results from PB1-MII oocyte pair validated that PB1 contains nearly the same methylome (average Pearson correlation is 0.92) with sibling MII oocyte. LINE and LTR expression increased markedly after fertilization. Moreover, the DNA methylation levels in LINE (including LINE1 and LINE2) and LTR were significantly higher in the PB1s of embryos that could not reach the blastocyst stage (Wilcoxon-Matt-Whitney test, P < 0.05). DNA methylation in PB1 promoters correlated negatively with gene expression of MII oocyte. Regarding the methylation status of the promoter regions, 66 genes were hypermethylated in the developmental arrested group, with their related functions (significantly enriched in several Gene Ontology terms) including transcription, positive regulation of adenylate cyclase activity, mitogen-activated protein kinase (MAPK) cascade and intracellular oestrogen receptor signalling pathway. LARGE SCALE DATA: N/A. LIMITATIONS, REASONS FOR CAUTION: Data analysis performed in this study focused on the competence of human oocytes and compared them with maternal genetic and epigenetic profiles. Therefore, data regarding the potential regulatory roles of paternal genomes in embryo development are lacking. WIDER IMPLICATIONS OF THE FINDINGS: The results from PB1-oocyte pairs demonstrated that PB1s shared similar methylomes with their sibling oocytes. The selection of the good embryos for transfer should not only rely on morphology but also consider the DNA methylation of the corresponding PB1 and therefore MII oocyte. The application of early-stage analysis of PB1 offers an option for high-quality oocyte and embryo selection, which provides an additional tool for elective single embryo transfer in assisted reproduction. STUDY FUNDING/COMPETING INTEREST(S): This study was supported by the National Key Research and Development Program of China (2018YFC1004003, 2017YFA0103801), the National Natural Science Foundation of China (81730038, 3187144, 81521002) and the Strategic Priority Research Program of the Chinese Academy of Sciences (XDA16020703). The authors have no conflicts of interest to declare.


Asunto(s)
Epigenoma , Cuerpos Polares , China , Desarrollo Embrionario/genética , Humanos , Masculino , Oocitos
11.
Cancer Discov ; 11(3): 678-695, 2021 03.
Artículo en Inglés | MEDLINE | ID: mdl-33203734

RESUMEN

Circulating tumor cells (CTC) are shed by cancer into the bloodstream, where a viable subset overcomes oxidative stress to initiate metastasis. We show that single CTCs from patients with melanoma coordinately upregulate lipogenesis and iron homeostasis pathways. These are correlated with both intrinsic and acquired resistance to BRAF inhibitors across clonal cultures of BRAF-mutant CTCs. The lipogenesis regulator SREBP2 directly induces transcription of the iron carrier Transferrin (TF), reducing intracellular iron pools, reactive oxygen species, and lipid peroxidation, thereby conferring resistance to inducers of ferroptosis. Knockdown of endogenous TF impairs tumor formation by melanoma CTCs, and their tumorigenic defects are partially rescued by the lipophilic antioxidants ferrostatin-1 and vitamin E. In a prospective melanoma cohort, presence of CTCs with high lipogenic and iron metabolic RNA signatures is correlated with adverse clinical outcome, irrespective of treatment regimen. Thus, SREBP2-driven iron homeostatic pathways contribute to cancer progression, drug resistance, and metastasis. SIGNIFICANCE: Through single-cell analysis of primary and cultured melanoma CTCs, we have uncovered intrinsic cancer cell heterogeneity within lipogenic and iron homeostatic pathways that modulates resistance to BRAF inhibitors and to ferroptosis inducers. Activation of these pathways within CTCs is correlated with adverse clinical outcome, pointing to therapeutic opportunities.This article is highlighted in the In This Issue feature, p. 521.


Asunto(s)
Ferroptosis/genética , Lipogénesis/genética , Melanoma/genética , Melanoma/metabolismo , Células Neoplásicas Circulantes/metabolismo , Proteína 2 de Unión a Elementos Reguladores de Esteroles/genética , Transferrina/metabolismo , Biomarcadores de Tumor , Células Cultivadas , Susceptibilidad a Enfermedades , Regulación Neoplásica de la Expresión Génica , Técnicas de Silenciamiento del Gen , Humanos , Melanoma/patología , Mutación , Células Neoplásicas Circulantes/patología , Transducción de Señal , Análisis de la Célula Individual , Proteína 2 de Unión a Elementos Reguladores de Esteroles/metabolismo
12.
Data Brief ; 30: 105192, 2020 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-32300612

RESUMEN

To better understand the extent of how the air temperature and mean radiant temperature may vary both spatially and temporally in a radiantly heated space, we conducted a seven-day experiment in the architectural laboratory at School of Architecture, Princeton University. The primary intent of this paper was to decouple the measurement of the air temperature and mean radiant temperature. We collected a large dataset that shows temporal and spatial variations. To do so, we used non-contact infrared thermometer to measure the surface temperatures of the surrounding surfaces inside the laboratory. The geometry of the laboratory is simplified into a box, the corresponding view factor from every point within the box can be calculated towards each internal surface. These view factors are then combined with the measured surface temperatures to produce mean radiant temperatures. This spatial mean radiant temperature distribution was then compared with the air temperature distribution measured by the air temperature sensors suspended from the ceiling of the laboratory. We believe making these data available will help future researchers working on similar problems to develop protocols than the state-of-the-art measurement techniques observed among different thermal comfort or radiant heat transfer research.

13.
Sci Rep ; 10(1): 2652, 2020 Feb 14.
Artículo en Inglés | MEDLINE | ID: mdl-32060327

RESUMEN

For thermal comfort research, globe thermometers have become the de facto tool for mean radiant temperature, tr, measurement. They provide a quick means to survey the radiant environment in a space with nearly a century of trials to reassure researchers. However, as more complexity is introduced to built environments, we must reassess the accuracy of globe measurements. In particular, corrections for globe readings taking wind into account rely on a forced convection heat transfer coefficient. In this study, we investigate potential errors introduced by buoyancy driven flow, or free convection, induced by radiant forcing of a black globe's surface to a temperature different from the air. We discovered this error in an experimental radiant cooling system with high separation of air to radiant temperature. Empirical simulations and the data collected in a radiant cooling setup together demonstrate the influence of free convection on the instrument's readings. Initial simulation and data show that tr measurements neglecting free convection when calculating tr from air temperatures of 2 K above tr could introduce a mechanism for globe readings to incorrectly track air temperatures. The experimental data constructed to test this hypothesis showed the standard correction readings are 1.94 ± 0.90 °C higher than the ground truth readings for all measurements taken in the experiment. The proposed mixed convection correction is 0.51 ± 1.07 °C higher than the ground truth, and is most accurate at low air speeds, within 0.25 ± 0.60 °C. This implies a potential systematic error in millions of measurements over the past 30 years of thermal comfort research. Future work will be carried out to experimentally validate this framework in a controlled climate chamber environment, examining the tradeoffs between accuracy and precision with globe thermometer measurements.

14.
Proc Natl Acad Sci U S A ; 116(52): 26835-26845, 2019 Dec 26.
Artículo en Inglés | MEDLINE | ID: mdl-31843922

RESUMEN

Transcriptional profiling has defined pancreatic ductal adenocarcinoma (PDAC) into distinct subtypes with the majority being classical epithelial (E) or quasi-mesenchymal (QM). Despite clear differences in clinical behavior, growing evidence indicates these subtypes exist on a continuum with features of both subtypes present and suggestive of interconverting cell states. Here, we investigated the impact of different therapies being evaluated in PDAC on the phenotypic spectrum of the E/QM state. We demonstrate using RNA-sequencing and RNA-in situ hybridization (RNA-ISH) that FOLFIRINOX combination chemotherapy induces a common shift of both E and QM PDAC toward a more QM state in cell lines and patient tumors. In contrast, Vitamin D, another drug under clinical investigation in PDAC, induces distinct transcriptional responses in each PDAC subtype, with augmentation of the baseline E and QM state. Importantly, this translates to functional changes that increase metastatic propensity in QM PDAC, but decrease dissemination in E PDAC in vivo models. These data exemplify the importance of both the initial E/QM subtype and the plasticity of E/QM states in PDAC in influencing response to therapy, which highlights their relevance in guiding clinical trials.

15.
Nat Commun ; 10(1): 2854, 2019 06 28.
Artículo en Inglés | MEDLINE | ID: mdl-31253781

RESUMEN

SETD1A, a Set1/COMPASS family member maintaining histone-H3-lysine-4 (H3K4) methylation on transcriptionally active promoters, is overexpressed in breast cancer. Here, we show that SETD1A supports mitotic processes and consequentially, its knockdown induces senescence. SETD1A, through promoter H3K4 methylation, regulates several genes orchestrating mitosis and DNA-damage responses, and its depletion causes chromosome misalignment and segregation defects. Cell cycle arrest in SETD1A knockdown senescent cells is independent of mutations in p53, RB and p16, known senescence mediators; instead, it is sustained through transcriptional suppression of SKP2, which degrades p27 and p21. Rare cells escaping senescence by restoring SKP2 expression display genomic instability. In > 200 cancer cell lines and in primary circulating tumor cells, SETD1A expression correlates with genes promoting mitosis and cell cycle suggesting a broad role in suppressing senescence induced by aberrant mitosis. Thus, SETD1A is essential to maintain mitosis and proliferation and its suppression unleashes the tumor suppressive effects of senescence.


Asunto(s)
Senescencia Celular/fisiología , Regulación de la Expresión Génica/fisiología , N-Metiltransferasa de Histona-Lisina/metabolismo , Mitosis/fisiología , Línea Celular Tumoral , N-Metiltransferasa de Histona-Lisina/genética , Histonas , Humanos , Metilación , Proteínas Supresoras de Tumor/genética , Proteínas Supresoras de Tumor/metabolismo
16.
Science ; 362(6418): 1060-1063, 2018 11 30.
Artículo en Inglés | MEDLINE | ID: mdl-30498128

RESUMEN

Although genomic instability, epigenetic abnormality, and gene expression dysregulation are hallmarks of colorectal cancer, these features have not been simultaneously analyzed at single-cell resolution. Using optimized single-cell multiomics sequencing together with multiregional sampling of the primary tumor and lymphatic and distant metastases, we developed insights beyond intratumoral heterogeneity. Genome-wide DNA methylation levels were relatively consistent within a single genetic sublineage. The genome-wide DNA demethylation patterns of cancer cells were consistent in all 10 patients whose DNA we sequenced. The cancer cells' DNA demethylation degrees clearly correlated with the densities of the heterochromatin-associated histone modification H3K9me3 of normal tissue and those of repetitive element long interspersed nuclear element 1. Our work demonstrates the feasibility of reconstructing genetic lineages and tracing their epigenomic and transcriptomic dynamics with single-cell multiomics sequencing.


Asunto(s)
Neoplasias Colorrectales/genética , Epigenómica/métodos , Análisis de la Célula Individual/métodos , Metilación de ADN , Femenino , Estudio de Asociación del Genoma Completo , Histonas , Humanos , Masculino , Análisis de Secuencia de ADN
17.
J Am Chem Soc ; 140(41): 13190-13194, 2018 10 17.
Artículo en Inglés | MEDLINE | ID: mdl-30278133

RESUMEN

High-resolution detection of genome-wide 5-hydroxymethylcytosine (5hmC) sites of small-scale samples remains challenging. Here, we present hmC-CATCH, a bisulfite-free, base-resolution method for the genome-wide detection of 5hmC. hmC-CATCH is based on selective 5hmC oxidation, chemical labeling and subsequent C-to-T transition during PCR. Requiring only nanoscale input genomic DNA samples, hmC-CATCH enabled us to detect genome-wide hydroxymethylome of human embryonic stem cells in a cost-effective manner. Further application of hmC-CATCH to cell-free DNA (cfDNA) of healthy donors and cancer patients revealed base-resolution hydroxymethylome in the human cfDNA for the first time. We anticipate that our chemical biology approach will find broad applications in hydroxymethylome analysis of limited biological and clinical samples.


Asunto(s)
5-Metilcitosina/análogos & derivados , Ácidos Nucleicos Libres de Células/química , Genómica/métodos , 5-Metilcitosina/análisis , 5-Metilcitosina/química , Ácidos Nucleicos Libres de Células/genética , Células Madre Embrionarias/química , Genoma , Humanos , Técnicas de Amplificación de Ácido Nucleico , Oxidación-Reducción , Análisis de Secuencia de ADN
18.
Nat Cell Biol ; 20(10): 1227, 2018 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-30038257

RESUMEN

In the PDF version of this Resource originally published, on the author list the superscript number 9 to indicate Rui Wang was an equally contributing author was missing owing to a technical error. This has now been amended. In addition, the authors wish to replace Supplementary Table 2, as in the original version Group 1 immune cells were mis-classified into Group 46 immune cells, resulting in three groups of immune cells where there should have been four. Supplementary Table 2 has now been replaced.

19.
Nat Cell Biol ; 20(6): 721-734, 2018 06.
Artículo en Inglés | MEDLINE | ID: mdl-29802404

RESUMEN

The development of the digestive tract is critical for proper food digestion and nutrient absorption. Here, we analyse the main organs of the digestive tract, including the oesophagus, stomach, small intestine and large intestine, from human embryos between 6 and 25 weeks of gestation as well as the large intestine from adults using single-cell RNA-seq analyses. In total, 5,227 individual cells are analysed and 40 cell types clearly identified. Their crucial biological features, including developmental processes, signalling pathways, cell cycle, nutrient digestion and absorption metabolism, and transcription factor networks, are systematically revealed. Moreover, the differentiation and maturation processes of the large intestine are thoroughly investigated by comparing the corresponding transcriptome profiles between embryonic and adult stages. Our work offers a rich resource for investigating the gene regulation networks of the human fetal digestive tract and adult large intestine at single-cell resolution.


Asunto(s)
Células Epiteliales/fisiología , Tracto Gastrointestinal/fisiología , Perfilación de la Expresión Génica/métodos , Regulación del Desarrollo de la Expresión Génica , Análisis de Secuencia de ARN/métodos , Análisis de la Célula Individual/métodos , Transcriptoma , Adulto , Factores de Edad , Diferenciación Celular/genética , Proliferación Celular/genética , Células Epiteliales/metabolismo , Tracto Gastrointestinal/embriología , Tracto Gastrointestinal/metabolismo , Marcadores Genéticos , Genotipo , Edad Gestacional , Humanos , Morfogénesis , Fenotipo , Factores de Tiempo
20.
Biol Reprod ; 99(2): 319-325, 2018 08 01.
Artículo en Inglés | MEDLINE | ID: mdl-29579157

RESUMEN

Prion protein (PrP) is encoded by a single copy gene Prnp in many cell and tissue types. PrP is very famous for its infectious conformers (PrPSC) resulting in transmissible spongiform encephalopathies. At present, physiological functions of its cellular isoform (PrPC) remain ambiguous. Although PrPC expression has been found in uterus, whether it functions in maternal-fetal dialogue during early pregnant is unknown. In this study, we examined PrPC mRNA and protein in the uterus of peri-implantation mice, and found that they were expressed with a spatiotemporal dynamic pattern. Interestingly, PrPC was significantly increased in the decidual zones around the implanting embryos at the implantation window stage. To further demonstrate that PrPC is involved in the decidualization of mouse uterus during embryo implantation, we constructed the artificial decidualization models and the delayed implantation models. Once the pseudopregnant mice were artificially induced to decidualization, the PrPC expression then increased significantly in the decidua zone. And also, if the delayed implantation embryos were allowed to implant, PrPC protein was also simultaneously improved in stromal cells surrounding the implanting embryos. Moreover, PrPC expression can be inhibited by progesterone but upregulated by estrogen in mouse uterus. These results suggest that PrPC may play an important role in embryo implantation and decidualization.


Asunto(s)
Implantación del Embrión/fisiología , Proteínas Priónicas/metabolismo , Útero/metabolismo , Animales , Decidua/efectos de los fármacos , Decidua/metabolismo , Implantación del Embrión/efectos de los fármacos , Implantación Tardía del Embrión/efectos de los fármacos , Implantación Tardía del Embrión/fisiología , Estradiol/farmacología , Femenino , Ratones , Progesterona/farmacología , Seudoembarazo/metabolismo , Células del Estroma/efectos de los fármacos , Células del Estroma/metabolismo , Útero/efectos de los fármacos
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