Understanding complex tissues requires single-cell deconstruction of gene regulation with precision and scale. Here, we assess the performance of a massively parallel droplet-based method for mapping ...transposase-accessible chromatin in single cells using sequencing (scATAC-seq). We apply scATAC-seq to obtain chromatin profiles of more than 200,000 single cells in human blood and basal cell carcinoma. In blood, application of scATAC-seq enables marker-free identification of cell type-specific cis- and trans-regulatory elements, mapping of disease-associated enhancer activity and reconstruction of trajectories of cellular differentiation. In basal cell carcinoma, application of scATAC-seq reveals regulatory networks in malignant, stromal and immune cells in the tumor microenvironment. Analysis of scATAC-seq profiles from serial tumor biopsies before and after programmed cell death protein 1 blockade identifies chromatin regulators of therapy-responsive T cell subsets and reveals a shared regulatory program that governs intratumoral CD8
T cell exhaustion and CD4
T follicular helper cell development. We anticipate that scATAC-seq will enable the unbiased discovery of gene regulatory factors across diverse biological systems.
Parasitic helminths have coevolved with humans over millennia, intricately refining and developing an array of mechanisms to suppress or skew the host's immune system, thereby promoting their ...long-term survival. Some helminths, such as hookworms, cause little to no overt pathology when present in modest numbers and may even confer benefits to their human host. To exploit this evolutionary phenomenon, clinical trials of human helminth infection have been established and assessed for safety and efficacy for a range of immune dysfunction diseases and have yielded mixed outcomes. Studies of live helminth therapy in mice and larger animals have convincingly shown that helminths and their excretory/secretory products possess anti-inflammatory drug-like properties and represent an untapped pharmacopeia. These anti-inflammatory moieties include extracellular vesicles, proteins, glycans, post-translational modifications, and various metabolites. Although the concept of helminth-inspired therapies holds promise, it also presents a challenge to the drug development community, which is generally unfamiliar with foreign biologics that do not behave like antibodies. Identification and characterization of helminth molecules and vesicles and the molecular pathways they target in the host present a unique opportunity to develop tailored drugs inspired by nature that are efficacious, safe, and have minimal immunogenicity. Even so, much work remains to mine and assess this out-of-the-box therapeutic modality. Industry-based organizations need to consider long-haul investments aimed at unraveling and exploiting unique and differentiated mechanisms of action as opposed to toe-dipping entries with an eye on rapid and profitable turnarounds.
Polypharmacy Management in Older Patients Hoel, Robert William; Giddings Connolly, Ryan M; Takahashi, Paul Y
Mayo Clinic proceedings,
01/2021, Volume:
96, Issue:
1
Journal Article
Peer reviewed
Open access
Medications to treat disease and extend life in our patients often amass in quantities, resulting in what has been termed "polypharmacy." This imprecise label usually describes the accumulation of 5, ...and often more, medications. Polypharmacy in advancing age frequently results in drug therapy problems related to interactions, drug toxicity, falls with injury, delirium, and nonadherence. Polypharmacy is associated with resulting increased hospitalizations and higher costs of care for individuals and health care systems. To reduce polypharmacy, we delineate a systematic, consultative approach to identify highest-risk medications and drug-therapy problems. We address strategic reductions (deprescribing) of medications in palliative care, long-term care, and ambulatory older adults. Best practices for reducing opioids, benzodiazepines, and other high-risk medications include education about risk and agreement by patients and their families, advocates, and care teams. Addressing deprescribing should be within the framework of patients' health status as their care and goals transition from longevity to a plan of maintaining alertness, comfort, and satisfaction of quality of life. A team approach to address polypharmacy and avoidance of high-risk therapy is optimal within long-term care. Patients with terminal illnesses or those moving toward a comfort-care emphasis benefit from medication adjustments that are recognized beneficially within each patient's care goals. In caring for older adults, the acknowledgement that complicated regimens and high-risk medications requires a care plan to reduce or prevent medication-related problems and costs that are associated with polypharmacy.
The challenge of linking intergenic mutations to target genes has limited molecular understanding of human diseases. Here we show that H3K27ac HiChIP generates high-resolution contact maps of active ...enhancers and target genes in rare primary human T cell subtypes and coronary artery smooth muscle cells. Differentiation of naive T cells into T helper 17 cells or regulatory T cells creates subtype-specific enhancer-promoter interactions, specifically at regions of shared DNA accessibility. These data provide a principled means of assigning molecular functions to autoimmune and cardiovascular disease risk variants, linking hundreds of noncoding variants to putative gene targets. Target genes identified with HiChIP are further supported by CRISPR interference and activation at linked enhancers, by the presence of expression quantitative trait loci, and by allele-specific enhancer loops in patient-derived primary cells. The majority of disease-associated enhancers contact genes beyond the nearest gene in the linear genome, leading to a fourfold increase in the number of potential target genes for autoimmune and cardiovascular diseases.
Gut microbiota, obesity and diabetes Patterson, Elaine; Ryan, Paul M; Cryan, John F ...
Postgraduate medical journal,
05/2016, Volume:
92, Issue:
1087
Journal Article
Peer reviewed
Open access
The central role of the intestinal microbiota in the progression and, equally, prevention of metabolic dysfunction is becoming abundantly apparent. The symbiotic relationship between intestinal ...microbiota and host ensures appropriate development of the metabolic system in humans. However, disturbances in composition and, in turn, functionality of the intestinal microbiota can disrupt gut barrier function, a trip switch for metabolic endotoxemia. This low-grade chronic inflammation, brought about by the influx of inflammatory bacterial fragments into circulation through a malfunctioning gut barrier, has considerable knock-on effects for host adiposity and insulin resistance. Conversely, recent evidence suggests that there are certain bacterial species that may interact with host metabolism through metabolite-mediated stimulation of enteric hormones and other systems outside of the gastrointestinal tract, such as the endocannabinoid system. When the abundance of these keystone species begins to decline, we see a collapse of the symbiosis, reflected in a deterioration of host metabolic health. This review will investigate the intricate axis between the microbiota and host metabolism, while also addressing the promising and novel field of probiotics as metabolic therapies.
•3D random pore model for graphite oxidation includes closed pores, sample size, and shape.•Model agrees well with 30 experimental datasets covering 10 different graphite grades.•Oxidation is faster ...for finer pores, smaller samples, lower density, and/or higher reactivity.•Modeled reactivity ratios demonstrate reasonable activation energy for kinetic regime.•Current kinetic control formulation can be extended to include diffusion control.
Thermal oxidation mass loss of synthetic graphite can be life-limiting for high-temperature applications. The complex microstructure of synthetic graphite has made it difficult to predict oxidation-induced changes.Specifically, there are no accepted models for predicting oxidation pore growth, which affects properties and performance.
This paper presents the application of a three-dimensional microstructure-based model for synthetic graphite oxidation in the kinetic regime. Pore structure is described with randomly-placed spheres, whose growth rate is dependent on the penetration depth of oxidant. Pore structure, intrinsic reactivity, sample size, geometry, and initially closed porosity are included in the model. Oxidation mass loss occurs faster for finer pore size, lower bulk density, higher reactivity, and/or smaller samples.
For model validation, 30 datasets representing ten (mostly nuclear) high-purity graphite grades were selected, covering air oxidation temperatures from 450 to 750 °C and sample masses spanning four orders of magnitude. Agreements between model and experiment were judged reasonable, particularly the effects of microstructure and sample mass. For the temperature effect, aggregated reactivity ratios showed an activation energy of 187 kJ/mol, within expected kinetic range. To the author's knowledge, this model is the first three-dimensional microstructure-based approach for graphite air oxidation in the kinetic regime.
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Vulnerability to relapse during periods of attempted abstinence from cocaine use is hypothesized to result from the rewiring of brain reward circuitries, particularly ventral tegmental area (VTA) ...dopamine neurons. How cocaine exposures act on midbrain dopamine neurons to precipitate addiction-relevant changes in gene expression is unclear. We found that histone H3 glutamine 5 dopaminylation (H3Q5dop) plays a critical role in cocaine-induced transcriptional plasticity in the midbrain. Rats undergoing withdrawal from cocaine showed an accumulation of H3Q5dop in the VTA. By reducing H3Q5dop in the VTA during withdrawal, we reversed cocaine-mediated gene expression changes, attenuated dopamine release in the nucleus accumbens, and reduced cocaine-seeking behavior. These findings establish a neurotransmission-independent role for nuclear dopamine in relapse-related transcriptional plasticity in the VTA.
Knowledge of oncogenic mutations can inspire therapeutic strategies that are synthetically lethal, affecting cancer cells while sparing normal cells. Lenalidomide is an active agent in the activated ...B cell-like (ABC) subtype of diffuse large B cell lymphoma (DLBCL), but its mechanism of action is unknown. Lenalidomide kills ABC DLBCL cells by augmenting interferon β (IFNβ) production, owing to the oncogenic MYD88 mutations in these lymphomas. In a cereblon-dependent fashion, lenalidomide downregulates IRF4 and SPIB, transcription factors that together prevent IFNβ production by repressing IRF7 and amplify prosurvival NF-κB signaling by transactivating CARD11. Blockade of B cell receptor signaling using the BTK inhibitor ibrutinib also downregulates IRF4 and consequently synergizes with lenalidomide in killing ABC DLBCLs, suggesting attractive therapeutic strategies.
► Lenalidomide kills ABC DLBCLs by decreasing expression of IRF4 and SPIB ► IRF4 and SPIB maintain ABC DLBCL viability ► IRF4 and SPIB block toxic IFNβ production while enhancing prosurvival NF-κB activity ► Lenalidomide and BCR pathway drugs synergize to inhibit IRF4 and kill ABC DLBCLs
Background:
This study is a retrospective review of prospectively gathered data determining the postoperative outcomes of patients who underwent operative treatment to address chronic syndesmotic ...instability.
Methods:
The cohort is composed of 19 individuals who elected to undergo operative treatment of chronic syndesmotic instability. The operative repair consisted of arthroscopic debridement in all cases with reduction and suture button fixation of those patients who had greater than 4 mm of syndesmotic diastasis on arthroscopic evaluation. All patients had a minimum of 24 months follow-up. This study retrospectively examined the prospectively gathered preoperative and postoperative outcome scores to include a Visual Analog Scale (VAS) pain score and an American Orthopaedic Foot & Ankle Society (AOFAS) ankle-hindfoot score. In addition, patients were questioned on their ability to return to their preinjury level of activity and their ability to continue running sports. Fourteen patients returned their postoperative surveys.
Results:
Mean AOFAS scores improved significantly from 48 to 82.7 (P = .014). Mean VAS scores improved from 6.1 to 1.0 (P = .002). Overall, 86% (12/14) of patients were able to return to running and 79% (11/14) of patients were able to return to their preinjury level of sport. Preoperative and postoperative weight-bearing ankle radiographs were reviewed to evaluate the tibiofibular clear space and overlap. The clear space measured on anteroposterior (AP) radiographs decreased from 5.4 mm to 4.6 mm (P = .005), the clear space evaluated on the mortise radiograph decreased from 4.5 mm to 3.6 mm (P = .006), and the overlap measured on the AP radiograph increased from 5.7 mm to 6.9 mm (P = .019). All radiographs were measured by a board-certified musculoskeletal radiologist.
Conclusion:
This study presents a treatment method that can be instituted at the time of diagnosis for syndesmotic injuries with greater than 4 mm of diastasis that were treated with debridement and stabilization. The results of this treatment technique are promising, with significant improvements in subjective outcome scores and a high rate of return to running sports.
Level of Evidence:
Level IV, retrospective case series.
We present Omni-ATAC, an improved ATAC-seq protocol for chromatin accessibility profiling that works across multiple applications with substantial improvement of signal-to-background ratio and ...information content. The Omni-ATAC protocol generates chromatin accessibility profiles from archival frozen tissue samples and 50-μm sections, revealing the activities of disease-associated DNA elements in distinct human brain structures. The Omni-ATAC protocol enables the interrogation of personal regulomes in tissue context and translational studies.
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