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1.
G3 (Bethesda) ; 14(5)2024 05 07.
Artículo en Inglés | MEDLINE | ID: mdl-38526344

RESUMEN

Whitebark pine (WBP, Pinus albicaulis) is a white pine of subalpine regions in the Western contiguous United States and Canada. WBP has become critically threatened throughout a significant part of its natural range due to mortality from the introduced fungal pathogen white pine blister rust (WPBR, Cronartium ribicola) and additional threats from mountain pine beetle (Dendroctonus ponderosae), wildfire, and maladaptation due to changing climate. Vast acreages of WBP have suffered nearly complete mortality. Genomic technologies can contribute to a faster, more cost-effective approach to the traditional practices of identifying disease-resistant, climate-adapted seed sources for restoration. With deep-coverage Illumina short reads of haploid megagametophyte tissue and Oxford Nanopore long reads of diploid needle tissue, followed by a hybrid, multistep assembly approach, we produced a final assembly containing 27.6 Gb of sequence in 92,740 contigs (N50 537,007 bp) and 34,716 scaffolds (N50 2.0 Gb). Approximately 87.2% (24.0 Gb) of total sequence was placed on the 12 WBP chromosomes. Annotation yielded 25,362 protein-coding genes, and over 77% of the genome was characterized as repeats. WBP has demonstrated the greatest variation in resistance to WPBR among the North American white pines. Candidate genes for quantitative resistance include disease resistance genes known as nucleotide-binding leucine-rich repeat receptors (NLRs). A combination of protein domain alignments and direct genome scanning was employed to fully describe the 3 subclasses of NLRs. Our high-quality reference sequence and annotation provide a marked improvement in NLR identification compared to previous assessments that leveraged de novo-assembled transcriptomes.


Asunto(s)
Genoma de Planta , Anotación de Secuencia Molecular , Pinus , Pinus/genética , Pinus/parasitología , Genómica/métodos , Especies en Peligro de Extinción , Secuenciación de Nucleótidos de Alto Rendimiento
2.
BMC Med Educ ; 24(1): 241, 2024 Mar 06.
Artículo en Inglés | MEDLINE | ID: mdl-38448949

RESUMEN

BACKGROUND: Naloxone is an effective and safe opioid reversal medication now approved by the U.S. Food and Drug Administration (FDA) for use with or without a prescription. Despite this, naloxone dissemination lags at a time when U.S. opioid-related mortality expands. The authors proposed distributing naloxone to all U.S. medical students using established statewide standing prescription orders for naloxone, eliminating the financial burden of over-the-counter costs on students and streamlining workflow for the pharmacy. By focusing naloxone distribution on medical students, we are able to capitalize on a group that is already primed on healthcare intervention, while also working to combat stigma in the emerging physician workforce. METHODS: Beginning August 2022, the authors established a partnership between Harvard Medical School (HMS) and the outpatient pharmacy at Brigham and Women's Hospital (BWH) to facilitate access to naloxone for HMS medical students. BWH developed a HIPAA-secure electronic form to collect individual prescription information. BWH pharmacists processed submissions daily, integrating the naloxone prescription requests into their workflow for in-person pick-up or mail-order delivery. The electronic form was disseminated to medical students through a required longitudinal addiction medicine curriculum, listserv messaging, and an extracurricular harm reduction workshop. RESULTS: Over the 2022-2023 academic year, 63 medical students obtained naloxone kits (two doses per kit) through this collaboration. CONCLUSIONS: We propose that medical schools advocate for a hospital pharmacy-initiated workflow focused on convenience and accessibility to expand naloxone access to medical students as a strategy to strengthen the U.S. emergency response and prevention efforts aimed at reducing opioid-related morbidity and mortality. Expansion of our program to BWH internal medicine residents increased our distribution to over 110 healthcare workers, and efforts to expand the program to other BWH training programs and clinical sites such as the emergency department and outpatient infectious disease clinics are underway. With more than 90,000 medical students in the U.S., we believe that widespread implementation of targeted naloxone training and distribution to this population is an accessible approach to combating the public health crisis of opioid-related overdoses.


Asunto(s)
Estudiantes de Medicina , Femenino , Estados Unidos , Humanos , Epidemia de Opioides , Analgésicos Opioides/uso terapéutico , Instituciones de Atención Ambulatoria , Curriculum
3.
Cancer Res Commun ; 4(1): 38-54, 2024 01 05.
Artículo en Inglés | MEDLINE | ID: mdl-38059556

RESUMEN

Single-cell transcriptomics studies have begun to identify breast epithelial cell and stromal cell specific transcriptome differences between BRCA1/2 mutation carriers and non-carriers. We generated a single-cell transcriptome atlas of breast tissues from BRCA1, BRCA2 mutation carriers and compared this single-cell atlas of mutation carriers with our previously described single-cell breast atlas of healthy non-carriers. We observed that BRCA1 but not BRCA2 mutations altered the ratio between basal (basal-myoepithelial), luminal progenitor (luminal adaptive secretory precursor, LASP), and mature luminal (luminal hormone sensing) cells in breast tissues. A unique subcluster of cells within LASP cells is underrepresented in case of BRCA1 and BRCA2 mutation carriers compared with non-carriers. Both BRCA1 and BRCA2 mutations specifically altered transcriptomes in epithelial cells which are an integral part of NFκB, LARP1, and MYC signaling. Signaling pathway alterations in epithelial cells unique to BRCA1 mutations included STAT3, BRD4, SMARCA4, HIF2A/EPAS1, and Inhibin A signaling. BRCA2 mutations were associated with upregulation of IL6, PDK1, FOXO3, and TNFSF11 signaling. These signaling pathway alterations are sufficient to alter sensitivity of BRCA1/BRCA2-mutant breast epithelial cells to transformation as epithelial cells from BRCA1 mutation carriers overexpressing hTERT + PIK3CAH1047R generated adenocarcinomas, whereas similarly modified mutant BRCA2 cells generated basal carcinomas in NSG mice. Thus, our studies provide a high-resolution transcriptome atlas of breast epithelial cells of BRCA1 and BRCA2 mutation carriers and reveal their susceptibility to PIK3CA mutation-driven transformation. SIGNIFICANCE: This study provides a single-cell atlas of breast tissues of BRCA1/2 mutation carriers and demonstrates that aberrant signaling due to BRCA1/2 mutations is sufficient to initiate breast cancer by mutant PIK3CA.


Asunto(s)
Proteína BRCA1 , Mutación de Línea Germinal , Animales , Ratones , Proteína BRCA1/genética , Proteína BRCA2/genética , Proteínas Nucleares/genética , Factores de Transcripción/genética , Proteínas Proto-Oncogénicas c-myc/genética , Transducción de Señal/genética , Oncogenes , Carcinogénesis/genética
4.
bioRxiv ; 2023 Nov 17.
Artículo en Inglés | MEDLINE | ID: mdl-38014212

RESUMEN

Whitebark pine (WBP, Pinus albicaulis ) is a white pine of subalpine regions in western contiguous US and Canada. WBP has become critically threatened throughout a significant part of its natural range due to mortality from the introduced fungal pathogen white pine blister rust (WPBR, Cronartium ribicola ) and additional threats from mountain pine beetle ( Dendroctonus ponderosae ), wildfire, and maladaptation due to changing climate. Vast acreages of WBP have suffered nearly complete mortality. Genomic technologies can contribute to a faster, more cost-effective approach to the traditional practices of identifying disease-resistant, climate-adapted seed sources for restoration. With deep-coverage Illumina short-reads of haploid megametophyte tissue and Oxford Nanopore long-reads of diploid needle tissue, followed by a hybrid, multistep assembly approach, we produced a final assembly containing 27.6 Gbp of sequence in 92,740 contigs (N50 537,007 bp) and 34,716 scaffolds (N50 2.0 Gbp). Approximately 87.2% (24.0 Gbp) of total sequence was placed on the twelve WBP chromosomes. Annotation yielded 25,362 protein-coding genes, and over 77% of the genome was characterized as repeats. WBP has demonstrated the greatest variation in resistance to WPBR among the North American white pines. Candidate genes for quantitative resistance include disease resistance genes known as nucleotide-binding leucine-rich-repeat receptors (NLRs). A combination of protein domain alignments and direct genome scanning was employed to fully describe the three subclasses of NLRs (TNL, CNL, RNL). Our high-quality reference sequence and annotation provide a marked improvement in NLR identification compared to previous assessments that leveraged de novo assembled transcriptomes.

5.
Genes (Basel) ; 14(10)2023 09 26.
Artículo en Inglés | MEDLINE | ID: mdl-37895219

RESUMEN

Mesenchymal stem cells (MSC) are multipotent stem cells that can differentiate into multiple cell types, including osteoblasts, chondrocytes, and adipocytes. Osteoblast differentiation is reduced during osteoporosis development, resulting in reduced bone formation. Further, MSC isolated from different donors possess distinct osteogenic capacity. In this study, we used single-cell multiomic analysis to profile the transcriptome and epigenome of MSC from four healthy donors. Data were obtained from ~1300 to 1600 cells for each donor. These cells were clustered into four groups, indicating that MSC from different donors have distinct chromatin accessible regulatory elements for regulating gene expression. To investigate the mechanism by which MSC undergo osteogenic differentiation, we used the chromatin accessibility data from the single-cell multiome data to identify individual-specific enhancer-promoter pairs and evaluated the expression levels and activities of the transcriptional regulators. The MSC from four donors showed distinct differentiation potential into osteoblasts. MSC of donor 1 showed the largest average motif activities, indicating that MSC from donor 1 was most likely to differentiate into osteoblasts. The results of our validation experiments were consistent with the bioinformatics prediction. We also tested the enrichment of genome-wide association study (GWAS) signals of several musculoskeletal disease traits in the patient-specific chromatin accessible regions identified in the single-cell multiome data, including osteoporosis, osteopenia, and osteoarthritis. We found that osteoarthritis-associated variants were only enriched in the regions identified from donor 4. In contrast, osteoporosis and osteopenia variants were enriched in regions from donor 1 and least enriched in donor 4. Since osteoporosis and osteopenia are related to the density of bone cells, the enrichment of variants from these traits should be correlated with the osteogenic potential of MSC. In summary, this study provides large-scale data to link regulatory elements with their target genes to study the regulatory relationships during the differentiation of mesenchymal stem cells and provide a deeper insight into the gene regulatory mechanism.


Asunto(s)
Enfermedades Óseas Metabólicas , Células Madre Mesenquimatosas , Osteoartritis , Osteoporosis , Humanos , Osteogénesis/genética , Multiómica , Estudio de Asociación del Genoma Completo , Diferenciación Celular/genética , Células Madre Mesenquimatosas/metabolismo , Osteoporosis/genética , Enfermedades Óseas Metabólicas/metabolismo , Osteoartritis/metabolismo , Cromatina/metabolismo
6.
Nature ; 615(7954): 848-853, 2023 03.
Artículo en Inglés | MEDLINE | ID: mdl-36813960

RESUMEN

Global net land carbon uptake or net biome production (NBP) has increased during recent decades1. Whether its temporal variability and autocorrelation have changed during this period, however, remains elusive, even though an increase in both could indicate an increased potential for a destabilized carbon sink2,3. Here, we investigate the trends and controls of net terrestrial carbon uptake and its temporal variability and autocorrelation from 1981 to 2018 using two atmospheric-inversion models, the amplitude of the seasonal cycle of atmospheric CO2 concentration derived from nine monitoring stations distributed across the Pacific Ocean and dynamic global vegetation models. We find that annual NBP and its interdecadal variability increased globally whereas temporal autocorrelation decreased. We observe a separation of regions characterized by increasingly variable NBP, associated with warm regions and increasingly variable temperatures, lower and weaker positive trends in NBP and regions where NBP became stronger and less variable. Plant species richness presented a concave-down parabolic spatial relationship with NBP and its variability at the global scale whereas nitrogen deposition generally increased NBP. Increasing temperature and its increasing variability appear as the most important drivers of declining and increasingly variable NBP. Our results show increasing variability of NBP regionally that can be mostly attributed to climate change and that may point to destabilization of the coupled carbon-climate system.


Asunto(s)
Secuestro de Carbono , Carbono , Cambio Climático , Ecosistema , Mapeo Geográfico , Plantas , Carbono/análisis , Carbono/metabolismo , Dióxido de Carbono/análisis , Dióxido de Carbono/metabolismo , Secuestro de Carbono/fisiología , Estaciones del Año , Atmósfera/química , Océano Pacífico , Temperatura , Nitrógeno/metabolismo , Plantas/clasificación , Plantas/metabolismo , Medición de Riesgo
7.
Nat Commun ; 13(1): 5650, 2022 09 26.
Artículo en Inglés | MEDLINE | ID: mdl-36163192

RESUMEN

Most biological rates depend on the rate of respiration. Temperature variation is typically considered the main driver of daily plant respiration rates, assuming a constant daily respiration rate at a set temperature. Here, we show empirical data from 31 species from temperate and tropical biomes to demonstrate that the rate of plant respiration at a constant temperature decreases monotonically with time through the night, on average by 25% after 8 h of darkness. Temperature controls less than half of the total nocturnal variation in respiration. A new universal formulation is developed to model and understand nocturnal plant respiration, combining the nocturnal decrease in the rate of plant respiration at constant temperature with the decrease in plant respiration according to the temperature sensitivity. Application of the new formulation shows a global reduction of 4.5 -6 % in plant respiration and an increase of 7-10% in net primary production for the present-day.


Asunto(s)
Hojas de la Planta , Plantas , Dióxido de Carbono , Ecosistema , Respiración , Temperatura , Árboles
8.
Nat Commun ; 13(1): 4781, 2022 08 15.
Artículo en Inglés | MEDLINE | ID: mdl-35970991

RESUMEN

The observed global net land carbon sink is captured by current land models. All models agree that atmospheric CO2 and nitrogen deposition driven gains in carbon stocks are partially offset by climate and land-use and land-cover change (LULCC) losses. However, there is a lack of consensus in the partitioning of the sink between vegetation and soil, where models do not even agree on the direction of change in carbon stocks over the past 60 years. This uncertainty is driven by plant productivity, allocation, and turnover response to atmospheric CO2 (and to a smaller extent to LULCC), and the response of soil to LULCC (and to a lesser extent climate). Overall, differences in turnover explain ~70% of model spread in both vegetation and soil carbon changes. Further analysis of internal plant and soil (individual pools) cycling is needed to reduce uncertainty in the controlling processes behind the global land carbon sink.


Asunto(s)
Dióxido de Carbono , Secuestro de Carbono , Carbono , Dióxido de Carbono/análisis , Ecosistema , Plantas , Suelo , Incertidumbre
9.
Pathog Immun ; 7(1): 1-18, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-35178490

RESUMEN

BACKGROUND: Uropathogenic Escherichia coli (UPEC) infections are common and when they disseminate can be of high morbidity. METHODS: We studied the effects of UPEC infection using single cell RNA sequencing (scRNAseq) in zebrafish. Bulk RNA sequencing has historically been used to evaluate gene expression patterns, but scRNAseq allows gene expression to be evaluated at the single cell level and is optimal for evaluating heterogeneity within cell types and rare cell types. Zebrafish cohorts were injected with either saline or UPEC, and scRNAseq and canonical pathway analyses were performed. RESULTS: Canonical pathway analysis of scRNAseq data provided key information regarding innate immune pathways in the cells determined to be thymus cells, ionocytes, macrophages/monocytes, and pronephros cells. Pathways activated in thymus cells included interleukin 6 (IL-6) signaling and production of reactive oxygen species. Fc receptor-mediated phagocytosis was a leading canonical pathway in the pronephros and macrophages. Genes that were downregulated in UPEC vs saline exposed embryos involved the cellular response to the Gram-negative endotoxin lipopolysaccharide (LPS) and included Forkhead Box O1a (Foxo1a), Tribbles Pseudokinase 3 (Trib3), Arginase 2 (Arg2) and Polo Like Kinase 3 (Plk3). CONCLUSIONS: Because 4-day post fertilization zebrafish embryos only have innate immune systems, the scRNAseq provides insights into pathways and genes that cell types utilize in the bacterial response. Based on our analysis, we have identified genes and pathways that might serve as genetic targets for treatment and further investigation in UPEC infections at the single cell level.

10.
G3 (Bethesda) ; 12(1)2022 01 04.
Artículo en Inglés | MEDLINE | ID: mdl-35100403

RESUMEN

Sequencing, assembly, and annotation of the 26.5 Gbp hexaploid genome of coast redwood (Sequoia sempervirens) was completed leading toward discovery of genes related to climate adaptation and investigation of the origin of the hexaploid genome. Deep-coverage short-read Illumina sequencing data from haploid tissue from a single seed were combined with long-read Oxford Nanopore Technologies sequencing data from diploid needle tissue to create an initial assembly, which was then scaffolded using proximity ligation data to produce a highly contiguous final assembly, SESE 2.1, with a scaffold N50 size of 44.9 Mbp. The assembly included several scaffolds that span entire chromosome arms, confirmed by the presence of telomere and centromere sequences on the ends of the scaffolds. The structural annotation produced 118,906 genes with 113 containing introns that exceed 500 Kbp in length and one reaching 2 Mb. Nearly 19 Gbp of the genome represented repetitive content with the vast majority characterized as long terminal repeats, with a 2.9:1 ratio of Copia to Gypsy elements that may aid in gene expression control. Comparison of coast redwood to other conifers revealed species-specific expansions for a plethora of abiotic and biotic stress response genes, including those involved in fungal disease resistance, detoxification, and physical injury/structural remodeling and others supporting flavonoid biosynthesis. Analysis of multiple genes that exist in triplicate in coast redwood but only once in its diploid relative, giant sequoia, supports a previous hypothesis that the hexaploidy is the result of autopolyploidy rather than any hybridizations with separate but closely related conifer species.


Asunto(s)
Sequoia , Evolución Biológica , Cromosomas , Genoma , Secuenciación de Nucleótidos de Alto Rendimiento , Sequoia/genética
11.
G3 (Bethesda) ; 11(12)2021 12 08.
Artículo en Inglés | MEDLINE | ID: mdl-34515796

RESUMEN

Aegilops tauschii is the donor of the D subgenome of hexaploid wheat and an important genetic resource. The reference-quality genome sequence Aet v4.0 for Ae. tauschii acc. AL8/78 was therefore an important milestone for wheat biology and breeding. Further advances in sequencing acc. AL8/78 and release of the Aet v5.0 sequence assembly are reported here. Two new optical maps were constructed and used in the revision of pseudomolecules. Gaps were closed with Pacific Biosciences long-read contigs, decreasing the gap number by 38,899. Transposable elements and protein-coding genes were reannotated. The number of annotated high-confidence genes was reduced from 39,635 in Aet v4.0 to 32,885 in Aet v5.0. A total of 2245 biologically important genes, including those affecting plant phenology, grain quality, and tolerance of abiotic stresses in wheat, was manually annotated and disease-resistance genes were annotated by a dedicated pipeline. Disease-resistance genes encoding nucleotide-binding site domains, receptor-like protein kinases, and receptor-like proteins were preferentially located in distal chromosome regions, whereas those encoding transmembrane coiled-coil proteins were dispersed more evenly along the chromosomes. Discovery, annotation, and expression analyses of microRNA (miRNA) precursors, mature miRNAs, and phasiRNAs are reported, including miRNA target genes. Other small RNAs, such as hc-siRNAs and tRFs, were characterized. These advances enhance the utility of the Ae. tauschii genome sequence for wheat genetics, biotechnology, and breeding.


Asunto(s)
Aegilops , Genoma de Planta , Fitomejoramiento , Poaceae/genética , Triticum/genética
12.
Plant J ; 108(4): 960-976, 2021 11.
Artículo en Inglés | MEDLINE | ID: mdl-34218494

RESUMEN

The continuous increase in global population prompts increased wheat production. Future wheat (Triticum aestivum L.) breeding will heavily rely on dissecting molecular and genetic bases of wheat yield and related traits which is possible through the discovery of quantitative trait loci (QTLs) in constructed populations, such as recombinant inbred lines (RILs). Here, we present an evaluation of 92 RILs in a bi-parental RIL mapping population (the International Triticeae Mapping Initiative Mapping Population [ITMI/MP]) using newly generated phenotypic data in 3-year experiments (2015), older phenotypic data (1997-2009), and newly created single nucleotide polymorphism (SNP) marker data based on 92 of the original RILs to search for novel and stable QTLs. Our analyses of more than 15 unique traits observed in multiple experiments included analyses of 46 traits in three environments in the USA, 69 traits in eight environments in Germany, 149 traits in 10 environments in Russia, and 28 traits in four environments in India (292 traits in 25 environments) with 7584 SNPs (292 × 7584 = 2 214 528 data points). A total of 874 QTLs were detected with limit of detection (LOD) scores of 2.01-3.0 and 432 QTLs were detected with LOD > 3.0. Moreover, 769 QTLs could be assigned to 183 clusters based on the common markers and relative proximity of related QTLs, indicating gene-rich regions throughout the A, B, and D genomes of common wheat. This upgraded genotype-phenotype information of ITMI/MP can assist breeders and geneticists who can make crosses with suitable RILs to improve or investigate traits of interest.


Asunto(s)
Marcadores Genéticos/genética , Genoma de Planta/genética , Polimorfismo de Nucleótido Simple/genética , Sitios de Carácter Cuantitativo/genética , Triticum/genética , Mapeo Cromosómico , Productos Agrícolas , Cruzamientos Genéticos , Grano Comestible/genética , Genotipo , Endogamia , Familia de Multigenes , Fenotipo
13.
Front Genet ; 12: 663487, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33968139

RESUMEN

Single-cell RNA sequencing reveals gene expression differences between individual cells and also identifies different cell populations that are present in the bulk starting material. To obtain an accurate assessment of patient samples, single-cell suspensions need to be generated as soon as possible once the tissue or sample has been collected. However, this requirement poses logistical challenges for experimental designs involving multiple samples from the same subject since these samples would ideally be processed at the same time to minimize technical variation in data analysis. Although cryopreservation has been shown to largely preserve the transcriptome, it is unclear whether the freeze-thaw process might alter gene expression profiles in a cell-type specific manner or whether changes in cell-type proportions might also occur. To address these questions in the context of multiple myeloma clinical studies, we performed single-cell RNA sequencing (scRNA-seq) to compare fresh and frozen cells isolated from bone marrow aspirates of six multiple myeloma patients, analyzing both myeloma cells (CD138+) and cells constituting the microenvironment (CD138-). We found that cryopreservation using 90% fetal calf serum and 10% dimethyl sulfoxide resulted in highly consistent gene expression profiles when comparing fresh and frozen samples from the same patient for both CD138+ myeloma cells (R ≥ 0.96) and for CD138- cells (R ≥ 0.9). We also demonstrate that CD138- cell-type proportions showed minimal alterations, which were mainly related to small differences in immune cell subtype sensitivity to the freeze-thaw procedures. Therefore, when processing fresh multiple myeloma samples is not feasible, cryopreservation is a useful option in single-cell profiling studies.

14.
Nat Commun ; 12(1): 2405, 2021 04 23.
Artículo en Inglés | MEDLINE | ID: mdl-33893305

RESUMEN

Kidney intercalated cells are involved in acid-base homeostasis via vacuolar ATPase expression. Here we report six human intercalated cell subtypes, including hybrid principal-intercalated cells identified from single cell transcriptomics. Phagosome maturation is a biological process that increases in biological pathway analysis rank following exposure to uropathogenic Escherichia coli in two of the intercalated cell subtypes. Real time confocal microscopy visualization of murine renal tubules perfused with green fluorescent protein expressing Escherichia coli or pHrodo Green E. coli BioParticles demonstrates that intercalated cells actively phagocytose bacteria then acidify phagolysosomes. Additionally, intercalated cells have increased vacuolar ATPase expression following in vivo experimental UTI. Taken together, intercalated cells exhibit a transcriptional response conducive to the kidney's defense, engulf bacteria and acidify the internalized bacteria. Intercalated cells represent an epithelial cell with characteristics of professional phagocytes like macrophages.


Asunto(s)
Células Epiteliales/inmunología , Riñón/inmunología , Fagocitos/inmunología , Escherichia coli Uropatógena/inmunología , Ácidos/química , Animales , Células Cultivadas , Células Epiteliales/citología , Células Epiteliales/metabolismo , Perfilación de la Expresión Génica/métodos , Humanos , Riñón/citología , Riñón/metabolismo , Túbulos Renales Colectores/citología , Ratones Endogámicos C57BL , Ratones Transgénicos , Microscopía Confocal , Fagocitos/citología , Análisis de la Célula Individual/métodos , ATPasas de Translocación de Protón Vacuolares/metabolismo
15.
Cell Rep Med ; 2(3): 100219, 2021 03 16.
Artículo en Inglés | MEDLINE | ID: mdl-33763657

RESUMEN

Single-cell RNA sequencing (scRNA-seq) is an evolving technology used to elucidate the cellular architecture of adult organs. Previous scRNA-seq on breast tissue utilized reduction mammoplasty samples, which are often histologically abnormal. We report a rapid tissue collection/processing protocol to perform scRNA-seq of breast biopsies of healthy women and identify 23 breast epithelial cell clusters. Putative cell-of-origin signatures derived from these clusters are applied to analyze transcriptomes of ~3,000 breast cancers. Gene signatures derived from mature luminal cell clusters are enriched in ~68% of breast cancers, whereas a signature from a luminal progenitor cluster is enriched in ~20% of breast cancers. Overexpression of luminal progenitor cluster-derived signatures in HER2+, but not in other subtypes, is associated with unfavorable outcome. We identify TBX3 and PDK4 as genes co-expressed with estrogen receptor (ER) in the normal breasts, and their expression analyses in >550 breast cancers enable prognostically relevant subclassification of ER+ breast cancers.


Asunto(s)
Neoplasias de la Mama/genética , Linaje de la Célula/genética , Células Epiteliales/metabolismo , Receptor alfa de Estrógeno/genética , Piruvato Deshidrogenasa Quinasa Acetil-Transferidora/genética , Receptor ErbB-2/genética , Proteínas de Dominio T Box/genética , Adulto , Atlas como Asunto , Neoplasias de la Mama/metabolismo , Neoplasias de la Mama/mortalidad , Neoplasias de la Mama/patología , Células Epiteliales/clasificación , Células Epiteliales/citología , Receptor alfa de Estrógeno/metabolismo , Femenino , Perfilación de la Expresión Génica , Regulación Neoplásica de la Expresión Génica , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Glándulas Mamarias Humanas/citología , Glándulas Mamarias Humanas/metabolismo , Pronóstico , Piruvato Deshidrogenasa Quinasa Acetil-Transferidora/metabolismo , Receptor ErbB-2/metabolismo , Transducción de Señal , Análisis de la Célula Individual/métodos , Células Madre/citología , Células Madre/metabolismo , Análisis de Supervivencia , Proteínas de Dominio T Box/metabolismo , Transcriptoma
17.
Theor Appl Genet ; 133(9): 2545-2554, 2020 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-32494869

RESUMEN

KEY MESSAGE: A locus for perennial growth was mapped on Lophopyrum elongatum chromosome arm 4ES and introgressed into the wheat genome. Evidence was obtained that in addition to chromosome 4E, other L. elongatum chromosomes control perennial growth. Monocarpy versus polycarpy is one of the fundamental developmental dichotomies in flowering plants. Advances in the understanding of the genetic basis of this dichotomy are important for basic biological reasons and practically for genetic manipulation of growth development in economically important plants. Nine wheat introgression lines (ILs) harboring germplasm of the Lophopyrum elongatum genome present in the octoploid amphiploid Triticum aestivum cv. Chinese Spring (subgenomes AABBDD) × L. elongatum (genomes EE) were selected from a population of ILs developed earlier. These ILs were employed here in genomic analyses of post-sexual cycle regrowth (PSCR), which is a component of polycarpy in caespitose L. elongatum. Analyses of disomic substitution (DS) lines confirmed that L. elongatum chromosome 4E confers PSCR on wheat. The gene was mapped into a short distal region of L. elongatum arm 4ES and was tentatively named Pscr1. ILs harboring recombined chromosomes with 4ES segments, including Pscr1, incorporated into the distal part of the 4DS chromosome arm were identified. Based on the location, Pscr1 is not orthologous with the rice rhizome-development gene Rhz2 located on rice chromosome Os3, which is homoeologous with chromosome 4E, but it may correspond to the Teosinte branched1 (TB1) gene, which is located in the introgressed region in the L. elongatum and Ae. tauschii genomes. A hexaploid IL harboring a large portion of the E-genome but devoid of chromosome 4E also expressed PSCR, which provided evidence that perennial growth is controlled by genes on other L. elongatum chromosomes in addition to 4E.


Asunto(s)
Genes de Plantas , Fitomejoramiento , Poaceae/crecimiento & desarrollo , Triticum/genética , Mapeo Cromosómico , Cromosomas de las Plantas , Genotipo , Poaceae/genética , Polimorfismo de Nucleótido Simple , Poliploidía
19.
Theor Appl Genet ; 133(4): 1227-1241, 2020 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-31980837

RESUMEN

KEY MESSAGE: We introgressed wheatgrass germplasm from the octoploid amphiploid Triticum aestivum× Lophopyrum elongatum into wheat by manipulating the wheat Ph1 gene and discovered and characterized 130 introgression lines harboring single or, in various combinations, complete and recombined L. elongatum chromosomes. Diploid wheatgrass Lophopyrum elongatum (genomes EE) possesses valuable traits for wheat genetics and breeding. We evaluated several strategies for introgression of this germplasm into wheat. To detect it, we developed and validated multiplexed sets of Sequenom MassARRAY single nucleotide polymorphism (SNP) markers, which differentiated disomic and monosomic L. elongatum chromosomes from wheat chromosomes. We identified 130 introgression lines (ILs), which harbored 108 complete and 89 recombined L. elongatum chromosomes. Of the latter, 59 chromosomes were recombined by one or more crossovers and 30 were involved in centromeric (Robertsonian) translocations or were telocentric. To identify wheat chromosomes substituted for or recombined with L. elongatum chromosomes, we genotyped the ILs with the wheat 90-K Infinium SNP array. We found that most of the wheat 90-K probes correctly detected their targets in the L. elongatum genome and showed that some wheat SNPs are ancient and had originated prior to the divergence of the wheat and L. elongatum lineages. Of the 130 ILs, 52% were homozygous for Ph1 deletion and thus are staged to be recombined further. We failed to detect in the L. elongatum genome the 4/5 reciprocal translocation that has been reported in Thinopyrum bessarabicum and several other Triticeae genomes.


Asunto(s)
Cruzamientos Genéticos , Genoma de Planta , Endogamia , Ploidias , Poaceae/genética , Triticum/genética , Pan , Cromosomas de las Plantas/genética , Marcadores Genéticos , Polimorfismo de Nucleótido Simple/genética
20.
Theor Appl Genet ; 132(12): 3449, 2019 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-31578615

RESUMEN

Unfortunately, the 9th author name was incorrectly published in the original publication. The complete correct name is given below.

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