Somatic cell nuclear transfer and transcription-factor-based reprogramming revert adult cells to an embryonic state, and yield pluripotent stem cells that can generate all tissues. Through different ...mechanisms and kinetics, these two reprogramming methods reset genomic methylation, an epigenetic modification of DNA that influences gene expression, leading us to hypothesize that the resulting pluripotent stem cells might have different properties. Here we observe that low-passage induced pluripotent stem cells (iPSCs) derived by factor-based reprogramming of adult murine tissues harbour residual DNA methylation signatures characteristic of their somatic tissue of origin, which favours their differentiation along lineages related to the donor cell, while restricting alternative cell fates. Such an 'epigenetic memory' of the donor tissue could be reset by differentiation and serial reprogramming, or by treatment of iPSCs with chromatin-modifying drugs. In contrast, the differentiation and methylation of nuclear-transfer-derived pluripotent stem cells were more similar to classical embryonic stem cells than were iPSCs. Our data indicate that nuclear transfer is more effective at establishing the ground state of pluripotency than factor-based reprogramming, which can leave an epigenetic memory of the tissue of origin that may influence efforts at directed differentiation for applications in disease modelling or treatment.
Celotno besedilo
Dostopno za:
DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Gene expression profiling using microarrays has been limited to comparisons of gene expression between small numbers of samples within individual experiments. However, the unknown and variable ...sensitivities of each probeset have rendered the absolute expression of any given gene nearly impossible to estimate. We have overcome this limitation by using a very large number (>10,000) of varied microarray data as a common reference, so that statistical attributes of each probeset, such as the dynamic range and threshold between low and high expression, can be reliably discovered through meta-analysis. This strategy is implemented in a web-based platform named "Gene Expression Commons" (https://gexc.stanford.edu/) which contains data of 39 distinct highly purified mouse hematopoietic stem/progenitor/differentiated cell populations covering almost the entire hematopoietic system. Since the Gene Expression Commons is designed as an open platform, investigators can explore the expression level of any gene, search by expression patterns of interest, submit their own microarray data, and design their own working models representing biological relationship among samples.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Epigenetic modifications must underlie lineage-specific differentiation as terminally differentiated cells express tissue-specific genes, but their DNA sequence is unchanged. Haematopoiesis provides ...a well-defined model to study epigenetic modifications during cell-fate decisions, as multipotent progenitors (MPPs) differentiate into progressively restricted myeloid or lymphoid progenitors. Although DNA methylation is critical for myeloid versus lymphoid differentiation, as demonstrated by the myeloerythroid bias in Dnmt1 hypomorphs, a comprehensive DNA methylation map of haematopoietic progenitors, or of any multipotent/oligopotent lineage, does not exist. Here we examined 4.6 million CpG sites throughout the genome for MPPs, common lymphoid progenitors (CLPs), common myeloid progenitors (CMPs), granulocyte/macrophage progenitors (GMPs), and thymocyte progenitors (DN1, DN2, DN3). Marked epigenetic plasticity accompanied both lymphoid and myeloid restriction. Myeloid commitment involved less global DNA methylation than lymphoid commitment, supported functionally by myeloid skewing of progenitors following treatment with a DNA methyltransferase inhibitor. Differential DNA methylation correlated with gene expression more strongly at CpG island shores than CpG islands. Many examples of genes and pathways not previously known to be involved in choice between lymphoid/myeloid differentiation have been identified, such as Arl4c and Jdp2. Several transcription factors, including Meis1, were methylated and silenced during differentiation, indicating a role in maintaining an undifferentiated state. Additionally, epigenetic modification of modifiers of the epigenome seems to be important in haematopoietic differentiation. Our results directly demonstrate that modulation of DNA methylation occurs during lineage-specific differentiation and defines a comprehensive map of the methylation and transcriptional changes that accompany myeloid versus lymphoid fate decisions.
Celotno besedilo
Dostopno za:
DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
BACKGROUNDPatients hospitalized for COVID-19 exhibit diverse clinical outcomes, with outcomes for some individuals diverging over time even though their initial disease severity appears similar to ...that of other patients. A systematic evaluation of molecular and cellular profiles over the full disease course can link immune programs and their coordination with progression heterogeneity.METHODSWe performed deep immunophenotyping and conducted longitudinal multiomics modeling, integrating 10 assays for 1,152 Immunophenotyping Assessment in a COVID-19 Cohort (IMPACC) study participants and identifying several immune cascades that were significant drivers of differential clinical outcomes.RESULTSIncreasing disease severity was driven by a temporal pattern that began with the early upregulation of immunosuppressive metabolites and then elevated levels of inflammatory cytokines, signatures of coagulation, formation of neutrophil extracellular traps, and T cell functional dysregulation. A second immune cascade, predictive of 28-day mortality among critically ill patients, was characterized by reduced total plasma Igs and B cells and dysregulated IFN responsiveness. We demonstrated that the balance disruption between IFN-stimulated genes and IFN inhibitors is a crucial biomarker of COVID-19 mortality, potentially contributing to failure of viral clearance in patients with fatal illness.CONCLUSIONOur longitudinal multiomics profiling study revealed temporal coordination across diverse omics that potentially explain the disease progression, providing insights that can inform the targeted development of therapies for patients hospitalized with COVID-19, especially those who are critically ill.TRIAL REGISTRATIONClinicalTrials.gov NCT04378777.FUNDINGNIH (5R01AI135803-03, 5U19AI118608-04, 5U19AI128910-04, 4U19AI090023-11, 4U19AI118610-06, R01AI145835-01A1S1, 5U19AI062629-17, 5U19AI057229-17, 5U19AI125357-05, 5U19AI128913-03, 3U19AI077439-13, 5U54AI142766-03, 5R01AI104870-07, 3U19AI089992-09, 3U19AI128913-03, and 5T32DA018926-18); NIAID, NIH (3U19AI1289130, U19AI128913-04S1, and R01AI122220); and National Science Foundation (DMS2310836).
Mutations in the Bone Morphogenetic Protein (BMP) pathway are associated with a range of defects in skeletal formation. Genetic analysis of BMP signaling requirements is complicated by the presence ...of three partially redundant BMPs that are required for multiple stages of limb development. We generated an inducible allele of a BMP inhibitor, Gremlin, which reduces BMP signaling. We show that BMPs act in a dose and time dependent manner in which early reduction of BMPs result in digit loss, while inhibiting overall BMP signaling between E10.5 and E11.5 allows polydactylous digit formation. During this period, inhibiting BMPs extends the duration of FGF signaling. Sox9 is initially expressed in normal digit ray domains but at reduced levels that correlate with the reduction in BMP signaling. The persistence of elevated FGF signaling likely promotes cell proliferation and survival, inhibiting the activation of Sox9 and secondarily, inhibiting the differentiation of Sox9-expressing chondrocytes. Our results provide new insights into the timing and clarify the mechanisms underlying BMP signaling during digit morphogenesis.
•We generated an inducible allele Gremlin that results in reduced BMP activity.•Inhibiting mesodermal BMPs between E10.5 and 11.5 results in polydactylous limbs.•Inhibiting mesodermal BMPs results in persistent FGF signaling.•Digit rays are specified normally but have delays in chondrogenic differentiation.
ObjectiveTo estimate exposure-response relationships between respirable dust, respirable quartz and lung function loss in black South African gold miners.Methods520 mineworkers aged >37 years were ...enrolled in a cross-sectional study. Gravimetric dust measurements were used to calculate cumulative respirable dust and quartz exposures. Excess lung function loss was defined as predicted minus observed forced expiratory volume in one second (FEV1) and forced vital capacity (FVC). The association between excess loss and exposure was estimated, adjusting for smoking, tuberculosis and silicosis.ResultsMean service length was 21.8 years, mean respirable dust 0.37 mg/m3 and mean respirable quartz 0.053 mg/m3. After adjustment, 1 mg-yr/m3 increase in cumulative respirable dust exposure was associated with 18.7 ml mean excess loss in FVC 95% confidence interval (CI) 0.3, 37.1 and 16.2 ml in FEV1 (95% CI -0.3, 32.6). Mean excess loss with silicosis was 224.1 ml in FEV1 and 123.6 ml in FVC; with tuberculosis 347.4 ml in FEV1 and 264.3 ml in FVC.ConclusionDespite a healthy worker effect, lung function loss was demonstrable whether due to silicosis, tuberculosis or an independent effect of dust. A miner working at a respirable dust intensity of 0.37 mg/m3 for 30 years would lose on average an additional 208 ml in FVC (95% CI 3, 412) in the absence of other disease, an impact greater than that of silicosis and comparable to that of tuberculosis. Improved dust control on the South African gold mines would reduce the risk of silicosis, tuberculosis and lung function impairment.
Aims: To examine the effect of silica exposure, in the absence of silicosis, on the prevalence of pulmonary tuberculosis (PTB), which is epidemic among South African gold miners. Methods: ...Cross-sectional study of 520 gold miners over 37 years of age. Length of service, and cumulative and average dust and quartz exposure indices were derived for each miner. Chest radiographs were read for PTB by two NIOSH “B” readers. PTB was defined as a self-reported history of PTB or PTB on chest radiograph. Logistic regression was used to adjust for age, smoking, and silicosis. PTB effects of different exposure metrics for silica, scaled on their interquartile range (IQR), were compared. Results: Means (ranges) were: age 46.7 (37.1–59.9) years; length of service 21.8 (6.3–34.5) years; average intensity of respirable quartz 0.053 (0–0.095) mg/m3. PTB prevalence was 19.4% (95% CI 16.0 to 22.8) on history alone, and 35.2% (95% CI 31.1 to 39.3) on history or on chest radiograph. Length of service was poorly predictive of PTB, while all exposure indices which included dust or quartz yielded prevalence odds ratios (PORs) of approximately 1.4 (95% CI ∼1.1 to 1.8) for changes of one interquartile range in exposure. Controlling for silicosis—by adjustment or restriction—did not modify these results. Drillers and winch operators had the highest PTB prevalences and the highest dust and silica exposures. Conclusion: Older in-service gold miners in South Africa have a high prevalence of PTB, which is significantly associated with dust and silica exposure, even in the absence of silicosis. Limitations include a survivor workforce and the use of cumulative exposures based on current exposures. Dust control is an important component in control of the PTB epidemic in South African gold mines.
Immune checkpoint inhibitors (ICI) targeting CTLA4 or PD-1/PD-L1 have transformed cancer therapy but are associated with immune-related adverse events, including myocarditis. Here, we report a robust ...preclinical mouse model of ICI-associated myocarditis in which monoallelic loss of
in the context of complete genetic absence of
leads to premature death in approximately half of mice. Premature death results from myocardial infiltration by T cells and macrophages and severe ECG abnormalities, closely recapitulating the clinical and pathologic hallmarks of ICI-associated myocarditis observed in patients. Using this model, we show that
and
functionally interact in a gene dosage-dependent manner, providing a mechanism by which myocarditis arises with increased frequency in the setting of combination ICI therapy. We demonstrate that intervention with CTLA4-Ig (abatacept) is sufficient to ameliorate disease progression and additionally provide a case series of patients in which abatacept mitigates the fulminant course of ICI myocarditis. SIGNIFICANCE: We provide a preclinical model of ICI-associated myocarditis which recapitulates this clinical syndrome. Using this model, we demonstrate that CTLA4 and PD-1 (ICI targets) functionally interact for myocarditis development and that intervention with CTLA4-Ig (abatacept) attenuates myocarditis, providing mechanistic rationale and preclinical support for therapeutic clinical studies.
.
.
Ongoing thymopoiesis requires continual seeding from progenitors that reside within the bone marrow (BM), but the identity of the most proximate prethymocytes has remained controversial. Here we take ...a comprehensive approach to prospectively identify the major source of thymocyte progenitors that reside within the BM and blood, and find that all thymocyte progenitor activity resides within a rare Flk2+CD27+ population. The BM Flk2+CD27+ subset is predominantly composed of common lymphoid progenitors (CLPs) and multipotent progenitors. Of these 2 populations, only CLPs reconstitute thymopoiesis rapidly after intravenous injection. In contrast, multipotent progenitor-derived cells reconstitute the thymus with delayed kinetics only after they have reseeded the BM, self-renewed, and generated CLPs. These results identify CLPs as the major source of thymocyte progenitors within the BM.
•In this nationally representative study, caregivers of older adults who reported vision impairment spent 36% more hours providing care and reported that 61% more of their valued activities were ...affected per month.•They also had 46% greater odds of experiencing substantial emotional difficulty, per month, than caregivers of adults without vision impairment.•No differences between caregivers of older adults with and without vision impairment were noted in terms of experiencing substantial physical or financial difficulty.•Caring for older adults with vision impairment requires greater time commitments and has a greater impact on participation in valued activities and emotional well-being than does caring for adults without vision impairment.
The purpose of this study was to examine caregiving relationships for older adults with vision impairment (VI).
Cross-sectional study with a nationally representative sample.
Setting: the National Health and Aging Trends Study linked to the National Study of Caregiving, Year 2011. Study population: 1,776 family or unpaid caregivers to community-dwelling Medicare beneficiaries age ≥65 years old. Outcome measurement: in the preceding month, 1) the number of hours of care provided; 2) the valued activities affected by caregiving; and 3) the odds of experiencing substantial emotional, financial, and physical difficulty related to providing care. Exposure: VI was defined as a report of blindness or difficulty with distance or near vision.
Among 1,776 caregivers, 428 caregivers spent an average ± standard error (SE) of 111 ± 9.1 hours per month assisting older adults with VI, whereas 1,348 spent an average of 72 ± 3.3 hours assisting older adults without VI. In fully adjusted negative binomial regression analyses, caregivers of older adults with VI spent 36% more hours (incident rate ratio IRR: 1.36; 95% confidence interval CI: 1.15-1.60) providing care and reported having 61% more valued activities affected (IRR: 1.61; 95% CI: 1.23-2.10) than caregivers of older adults without VI. In fully adjusted logistic regression analyses, caregivers of older adults with VI had greater odds of emotional (odds ratio OR: 1.46; 95% CI: 1.04-2.03) but not financial (OR: 1.33; 95% CI: 0.87-2.03) or physical (OR: 1.13; 95% CI: 0.74-1.74) difficulty related to providing care than caregivers of older adults without VI.
These results suggest that caring for older adults with VI places different demands on time and emotional wellbeing than caring for older adults without VI, but no differences in financial or physical difficulties.
PDF
