RESUMEN
BACKGROUND: To compare the effects of dance and aerobic exercise on cognition and neuropsychiatric symptoms in older people with cognitive impairment. METHODS: Twenty-three older adults (mean age = 78 ± 7 years; males: n = 7, females: n = 16) attending a day care center and diagnosed with cognitive impairment were randomly assigned to a 16-week dance intervention or an aerobic exercise intervention (60 min/week). Cognitive function [Mini-Mental State Examination (MMSE)], neuropsychiatric symptoms [Geriatric Depression Scale-15 (GDS-15), Neuro-Psychiatric Inventory-R (NPI-R)], and physical function [Timed Up and Go (TUG), Activity Daily Living (ADL)] were assessed at baseline and at the end of the intervention. After Borg scale assessment, these two physical activities were performed at similar intensity (60-70% HRR). RESULTS: MMSE score increased significantly after the intervention in the dance group (+ 3.3/+ 14%, p = 0.03), especially memory performance (+1/+220%, p = 0.03), but not in the aerobic exercise group. GDS-15 and NPI-R decreased significantly after the intervention in both groups (p < 0.001). However, no significant effect was found for TUG and ADL. CONCLUSION: Dance is a cost-effective multimodal intervention that could improve cognition. A low-frequency ecological dance intervention (once per week; 60 min) could improve cognition, especially verbal memory. These results should be further investigated for the practice of dance in facilities for older adults.
Asunto(s)
Disfunción Cognitiva , Masculino , Femenino , Humanos , Anciano , Anciano de 80 o más Años , Pruebas Neuropsicológicas , Disfunción Cognitiva/terapia , Ejercicio Físico/psicología , Cognición , Terapia por Ejercicio/métodosRESUMEN
Glioma-derived cell-free DNA (cfDNA) is challenging to detect using liquid biopsy because quantities in body fluids are low. We determined the glioma-derived DNA fraction in cerebrospinal fluid (CSF), plasma, and urine samples from patients using sequencing of personalized capture panels guided by analysis of matched tumor biopsies. By sequencing cfDNA across thousands of mutations, identified individually in each patient's tumor, we detected tumor-derived DNA in the majority of CSF (7/8), plasma (10/12), and urine samples (10/16), with a median tumor fraction of 6.4 × 10-3 , 3.1 × 10-5 , and 4.7 × 10-5 , respectively. We identified a shift in the size distribution of tumor-derived cfDNA fragments in these body fluids. We further analyzed cfDNA fragment sizes using whole-genome sequencing, in urine samples from 35 glioma patients, 27 individuals with non-malignant brain disorders, and 26 healthy individuals. cfDNA in urine of glioma patients was significantly more fragmented compared to urine from patients with non-malignant brain disorders (P = 1.7 × 10-2 ) and healthy individuals (P = 5.2 × 10-9 ). Machine learning models integrating fragment length could differentiate urine samples from glioma patients (AUC = 0.80-0.91) suggesting possibilities for truly non-invasive cancer detection.
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Ácidos Nucleicos Libres de Células , Glioma , Biomarcadores de Tumor , Glioma/genética , Humanos , Biopsia Líquida , Mutación , Plasma , Análisis de Secuencia de ADNRESUMEN
Over the past decade, RNA sequencing (RNA-seq) has become an indispensable tool for transcriptome-wide analysis of differential gene expression and differential splicing of mRNAs. However, as next-generation sequencing technologies have developed, so too has RNA-seq. Now, RNA-seq methods are available for studying many different aspects of RNA biology, including single-cell gene expression, translation (the translatome) and RNA structure (the structurome). Exciting new applications are being explored, such as spatial transcriptomics (spatialomics). Together with new long-read and direct RNA-seq technologies and better computational tools for data analysis, innovations in RNA-seq are contributing to a fuller understanding of RNA biology, from questions such as when and where transcription occurs to the folding and intermolecular interactions that govern RNA function.
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Empalme Alternativo , Perfilación de la Expresión Génica/historia , Secuenciación de Nucleótidos de Alto Rendimiento/historia , ARN Mensajero/biosíntesis , ARN Mensajero/genética , Análisis de Secuencia de ARN/historia , Historia del Siglo XXI , Humanos , ARN Mensajero/historiaRESUMEN
Circulating tumour DNA (ctDNA) detection and monitoring have enormous potential clinical utility in oncology. We describe here a fast, flexible and cost-effective method to profile multiple genes simultaneously in low input cell-free DNA (cfDNA): Next Generation-Targeted Amplicon Sequencing (NG-TAS). We designed a panel of 377 amplicons spanning 20 cancer genes and tested the NG-TAS pipeline using cell-free DNA from two HapMap lymphoblastoid cell lines. NG-TAS consistently detected mutations in cfDNA when mutation allele fraction was > 1%. We applied NG-TAS to a clinical cohort of metastatic breast cancer patients, demonstrating its potential in monitoring the disease. The computational pipeline is available at https://github.com/cclab-brca/NGTAS_pipeline .
Asunto(s)
Biomarcadores de Tumor/genética , ADN Tumoral Circulante/genética , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Análisis de Secuencia de ADN/métodos , Programas Informáticos , Biomarcadores de Tumor/sangre , Línea Celular Tumoral , ADN Tumoral Circulante/sangre , Costos y Análisis de Costo , Femenino , Secuenciación de Nucleótidos de Alto Rendimiento/economía , Humanos , Mutación , Análisis de Secuencia de ADN/economíaRESUMEN
Maintenance of genome stability is a key issue for cell fate that could be compromised by chromosome deletions and translocations caused by DNA double-strand breaks (DSBs). Thus development of precise and sensitive tools for DSBs labeling is of great importance for understanding mechanisms of DSB formation, their sensing and repair. Until now there has been no high resolution and specific DSB detection technique that would be applicable to any cells regardless of their size. Here, we present i-BLESS, a universal method for direct genome-wide DNA double-strand break labeling in cells immobilized in agarose beads. i-BLESS has three key advantages: it is the only unbiased method applicable to yeast, achieves a sensitivity of one break at a given position in 100,000 cells, and eliminates background noise while still allowing for fixation of samples. The method allows detection of ultra-rare breaks such as those forming spontaneously at G-quadruplexes.
RESUMEN
BACKGROUND: Approximately 90% of colorectal cancer (CRC) deaths are caused by tumors ability to migrate into the adjacent tissues and metastase into distant organs. More than 40 genes have been causally linked to the development of CRC but no mutations have been associated with metastasis yet. To identify molecular basis of CRC metastasis we performed whole-exome and genome-scale transcriptome sequencing of 7 liver metastases along with their matched primary tumours and normal tissue. Multiple, spatially separated fragments of primary tumours were analyzed in each case. Uniformly malignant tissue specimen were selected with macrodissection, for three samples followed with laser microdissection. RESULTS: > 100 sequencing coverage allowed for detection of genetic alterations in subpopulation of tumour cells. Mutations in KRAS, APC, POLE, and PTPRT, previously associated with CRC development, were detected in most patients. Several new associations were identified, including PLXND1, CELSR3, BAHD1 and PNPLA6. CONCLUSIONS: We confirm the essential role of inflammation in CRC progression but question the mechanism of matrix metalloproteinases activation described in other work. Comprehensive sequencing data made it possible to associate genome-scale mutation distribution with gene expression patterns. To our knowledge, this is the first work to report such link in CRC metastasis context.
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Neoplasias Colorrectales/genética , Neoplasias Hepáticas/genética , Mutación , Metástasis de la Neoplasia/genética , Neoplasias Colorrectales/patología , Análisis Mutacional de ADN , Exoma , Perfilación de la Expresión Génica , Humanos , Neoplasias Hepáticas/secundario , Análisis de Secuencia de ARNRESUMEN
Pathology archives with linked clinical data are an invaluable resource for translational research, with the limitation that most cancer samples are formalin-fixed paraffin-embedded (FFPE) tissues. Therefore, FFPE tissues are an important resource for genomic profiling studies but are under-utilised due to the low amount and quality of extracted nucleic acids. We profiled the copy number landscape of 356 breast cancer patients using DNA extracted FFPE tissues by shallow whole genome sequencing. We generated a total of 491 sequencing libraries from 2 kits and obtained data from 98.4% of libraries with 86.4% being of good quality. We generated libraries from as low as 3.8â¯ng of input DNA and found that the success was independent of input DNA amount and quality, processing site and age of the fixed tissues. Since copy number alterations (CNA) play a major role in breast cancer, it is imperative that we are able to use FFPE archives and we have shown in this study that sWGS is a robust method to do such profiling.
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Neoplasias de la Mama/genética , Variaciones en el Número de Copia de ADN , ADN/análisis , Formaldehído/química , Adhesión en Parafina/métodos , Fijación del Tejido/métodos , Secuenciación Completa del Genoma/métodos , Biomarcadores de Tumor/genética , Neoplasias de la Mama/patología , Estudios de Casos y Controles , ADN/genética , Femenino , Perfilación de la Expresión Génica , Genómica , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Humanos , Invasividad Neoplásica , Análisis de Secuencia de ADNRESUMEN
Characterising the hierarchy of mammary epithelial cells (MECs) and how they are regulated during adult development is important for understanding how breast cancer arises. Here we report the use of single-cell RNA sequencing to determine the gene expression profile of MECs across four developmental stages; nulliparous, mid gestation, lactation and post involution. Our analysis of 23,184 cells identifies 15 clusters, few of which could be fully characterised by a single marker gene. We argue instead that the epithelial cells-especially in the luminal compartment-should rather be conceptualised as being part of a continuous spectrum of differentiation. Furthermore, our data support the existence of a common luminal progenitor cell giving rise to intermediate, restricted alveolar and hormone-sensing progenitors. This luminal progenitor compartment undergoes transcriptional changes in response to a full pregnancy, lactation and involution. In summary, our results provide a global, unbiased view of adult mammary gland development.
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Diferenciación Celular/genética , Células Epiteliales/metabolismo , Glándulas Mamarias Animales/metabolismo , Análisis de Secuencia de ARN/métodos , Análisis de la Célula Individual/métodos , Transcriptoma , Animales , Células Cultivadas , Femenino , Ontología de Genes , Glándulas Mamarias Animales/citología , Ratones Endogámicos C57BL , Células Madre/citología , Células Madre/metabolismoRESUMEN
Hematopoietic stem and progenitor cells (HSPCs) are vulnerable to endogenous damage and defects in DNA repair can limit their function. The 2 single-stranded DNA (ssDNA) binding proteins SSB1 and SSB2 are crucial regulators of the DNA damage response; however, their overlapping roles during normal physiology are incompletely understood. We generated mice in which both Ssb1 and Ssb2 were constitutively or conditionally deleted. Constitutive Ssb1/Ssb2 double knockout (DKO) caused early embryonic lethality, whereas conditional Ssb1/Ssb2 double knockout (cDKO) in adult mice resulted in acute lethality due to bone marrow failure and intestinal atrophy featuring stem and progenitor cell depletion, a phenotype unexpected from the previously reported single knockout models of Ssb1 or Ssb2 Mechanistically, cDKO HSPCs showed altered replication fork dynamics, massive accumulation of DNA damage, genome-wide double-strand breaks enriched at Ssb-binding regions and CpG islands, together with the accumulation of R-loops and cytosolic ssDNA. Transcriptional profiling of cDKO HSPCs revealed the activation of p53 and interferon (IFN) pathways, which enforced cell cycling in quiescent HSPCs, resulting in their apoptotic death. The rapid cell death phenotype was reproducible in in vitro cultured cDKO-hematopoietic stem cells, which were significantly rescued by nucleotide supplementation or after depletion of p53. Collectively, Ssb1 and Ssb2 control crucial aspects of HSPC function, including proliferation and survival in vivo by resolving replicative stress to maintain genomic stability.