Single-cell multi-omics of human clonal hematopoiesis reveals that DNMT3A R882 mutations perturb early progenitor states through selective hypomethylation

Somatic mutations in cancer genes have been ubiquitously detected in clonal expansions across healthy human tissue, including in clonal hematopoiesis. However, mutated and wildtype cells are morphologically and phenotypically similar, limiting the ability to link genotypes with cellular phenotypes. To overcome this limitation, we leveraged multi-modality single-cell sequencing, capturing the mutation with transcriptomes and methylomes in stem and progenitors from individuals with DNMT3A R882 mutated clonal hematopoiesis. DNMT3A mutations resulted in myeloid over lymphoid bias, and in expansion of immature myeloid progenitors primed toward megakaryocytic-erythroid fate. We observed dysregulated expression of lineage and leukemia stem cell markers. DNMT3A R882 led to preferential hypomethylation of polycomb repressive complex 2 targets and a specific sequence motif. Notably, the hypomethylation motif is enriched in binding motifs of key hematopoietic transcription factors, serving as a potential mechanistic link between DNMT3A R882 mutations and aberrant transcriptional phenotypes. Thus, single-cell multi-omics pave the road to defining the downstream consequences of mutations that drive human clonal mosaicism.

Transcranial alternating current stimulation does not modulate corticospinal activity in humans

Transcranial alternating current stimulation (TACS) is commonly used to synchronise the output of a cortical area to other parts of the nervous system, but evidence for this based on brain recordings in humans is challenging. The brain transmits beta oscillations (~21Hz) to tonically contracted limb muscles linearly and through the fastest corticospinal pathways. Therefore, muscle activity may be used as a proxy measure for the level of beta entrainment in the corticospinal tract due to TACS over motor cortex. Here, we assessed if TACS is able to modulate the neural inputs to muscles, which would provide an indirect evidence for TACS-driven neural entrainment. In the first part of this study, we ran a series of simulations of motor neuron (MN) pools receiving inputs from corticospinal neurons with different levels of beta entrainment. Results indicated that MNs should be highly sensitive to changes in corticospinal beta activity. Then, we ran experiments on healthy human subjects (N=10) in which TACS (at 1mA) was delivered over the motor cortex at 21Hz (beta stimulation), or at 7Hz or 40Hz (control conditions) while the abductor digiti minimi (ADM) or the tibialis anterior muscle (TA) were tonically contracted. Muscle activity was measured using high-density electromyography, which allowed us to decompose the spiking activity of pools of motor units innervating the studied muscles. By analysing motor unit pool activity, we observed that none of the tested TACS conditions could consistently alter the spectral characteristics of the common neural inputs received by the muscles. These results suggest that 1mA-TACS over motor cortex given at frequencies in the beta band does not affect corticospinal beta entrainment.

Cellular and Molecular Targets for Non-Invasive, Non-Pharmacological Therapeutic/Rehabilitative Interventions in Acute Ischemic Stroke

BACKGROUND: Cerebral circulation delivers the blood flow to the brain through a dedicated network of sanguine vessels. A healthy human brain can regulate cerebral blood flow (CBF) according to any physiological or pathological challenges. The brain is protected by its self-regulatory mechanisms, which are dependent on neuronal and support cellular populations, including endothelial ones, as well as metabolic, and even myogenic factors. OBJECTIVES: Accumulating data suggest that “non-pharmacological” approaches might provide new opportunities for stroke therapy, such as electro-/acupuncture, hyperbaric oxygen therapy, hypothermia/cooling, photobiomodulation, therapeutic gases, transcranial direct current stimulations, or transcranial magnetic stimulations. We reviewed the recent data on the mechanisms and clinical implications of these non-pharmaceutical treatments. METHODS: To present the state-of-the-art for currently available non-invasive, non-pharmacological-related interventions in acute ischemic stroke, we accomplished this synthetic and systematic literature review based on the Preferred Reporting Items for Systematic Principles Reviews and Meta-Analyses (PRISMA). RESULTS: The initial number of obtained articles was 313. After fulfilling the five steps in the filtering/selection methodology, 54 fully eligible papers were selected for synthetic review. We enhanced our documentation with other bibliographic resources connected to our subject, identified in the literature within a non-standardized search, to fill the knowledge gaps. Fifteen clinical trials were also identified. DISCUSSION: Non-invasive, non-pharmacological therapeutic/rehabilitative interventions for acute ischemic stroke are mainly holistic therapies. Therefore, most of them are not yet routinely used in clinical practice, despite some possible beneficial effects, which have yet to be supplementarily proven in more related studies. Moreover, few of the identified clinical trials are already completed and most do not have final results. CONCLUSIONS: This review synthesizes the current findings on acute ischemic stroke therapeutic/rehabilitative interventions, described as non-invasive and non-pharmacological.

Draft Genome Sequence of Bifidobacterium adolescentis 4-2, Isolated from Healthy Human Feces

Bifidobacterium adolescentis 4-2 was isolated from healthy human feces. Here, we report a draft genome sequence of this bacterium, which may clarify the functionality of gut microbiota-brain communication. The draft genome comprises 2.39 Mb, with an average G+C content of 59.2% and 2,028 coding DNA sequences. An operon for GABA biosynthesis was observed in the draft genome.

The effect of observational learning on the development of central sensitization

Watching other people in pain may affect one’s own experience of pain. It is unknown whether it can also modulate secondary mechanical hypersensitivity. We have addressed this question in two experiments in healthy human volunteers. In experiment 1 we tested, on a large sample (N=83), five videos of a model demonstrating high or low pain during high frequency stimulation (HFS) of the skin, a procedure known to induce secondary mechanical hypersensitivity. The aim was to select the two videos rated with the highest and lowest expected pain and fear (high pain and low pain videos). Morevoer, we have explored the correlation between empathy and fear scores. In experiment 2 (N=44), two groups of participants were randomly allocated to watching either the low or the high pain video, and subsequently underwent HFS. The high pain video group reported increased pain during HFS. The two groups differed in the magnitude of secondary mechanical hypersensitivity after HFS, but the unpleasantness scores for mechanical stimulation after HFS, as well as spread of hyperalgesia were not statistically different. Empathy scores correlated positively with fear reports in experiment 1 but not experiment 2. Unexpectedly, we found higher scores of fear of pain for the high pain video only in experiment 1. In summary, observational learning of a model demonstrating high pain seems to have a stastistically significant but small effect on pinprick hypersensitivity. Its operating mechanisms remain partially elusive.

Control Framework for Sloped Walking With a Powered Transfemoral Prosthesis

User customization of a lower-limb powered Prosthesis controller remains a challenge to this date. Controllers adopting impedance control strategies mandate tedious tuning for every joint, terrain condition, and user. Moreover, no relationship is known to exist between the joint control parameters and the slope condition. We present a control framework composed of impedance control and trajectory tracking, with the transitioning between the two strategies facilitated by Bezier curves. The impedance (stiffness and damping) functions vary as polynomials during the stance phase for both the knee and ankle. These functions were derived through least squares optimization with healthy human sloped walking data. The functions derived for each slope condition were simplified using principal component analysis. The weights of the resulting basis functions were found to obey monotonic trends within upslope and downslope walking, proving the existence of a relationship between the joint parameter functions and the slope angle. Using these trends, one can now design a controller for any given slope angle. Amputee and able-bodied walking trials with a powered transfemoral prosthesis revealed the controller to generate a healthy human gait. The observed kinematic and kinetic trends with the slope angle were similar to those found in healthy walking.

Systematic identification of ACE2 expression modulators reveals cardiomyopathy as a risk factor for mortality in COVID-19 patients

Background Angiotensin-converting enzyme 2 (ACE2) is the cell-entry receptor for SARS-CoV-2. It plays critical roles in both the transmission and the pathogenesis of COVID-19. Comprehensive profiling of ACE2 expression patterns could reveal risk factors of severe COVID-19 illness. While the expression of ACE2 in healthy human tissues has been well characterized, it is not known which diseases and drugs might be associated with ACE2 expression. Results We develop GENEVA (GENe Expression Variance Analysis), a semi-automated framework for exploring massive amounts of RNA-seq datasets. We apply GENEVA to 286,650 publicly available RNA-seq samples to identify any previously studied experimental conditions that could be directly or indirectly associated with ACE2 expression. We identify multiple drugs, genetic perturbations, and diseases that are associated with the expression of ACE2, including cardiomyopathy, HNF1A overexpression, and drug treatments with RAD140 and itraconazole. Our joint analysis of seven datasets confirms ACE2 upregulation in all cardiomyopathy categories. Using electronic health records data from 3936 COVID-19 patients, we demonstrate that patients with pre-existing cardiomyopathy have an increased mortality risk than age-matched patients with other cardiovascular conditions. GENEVA is applicable to any genes of interest and is freely accessible at http://genevatool.org. Conclusions This study identifies multiple diseases and drugs that are associated with the expression of ACE2. The effect of these conditions should be carefully studied in COVID-19 patients. In particular, our analysis identifies cardiomyopathy patients as a high-risk group, with increased ACE2 expression in the heart and increased mortality after SARS-COV-2 infection.

Tandem Substitutions in Somatic Hypermutation

Upon antigen recognition, activation-induced cytosine deaminase initiates affinity maturation of the B-cell receptor by somatic hypermutation (SHM) through error-prone DNA repair pathways. SHM typically creates single nucleotide substitutions, but tandem substitutions may also occur. We investigated incidence and sequence context of tandem substitutions by massive parallel sequencing of V(D)J repertoires in healthy human donors. Mutation patterns were congruent with SHM-derived single nucleotide mutations, delineating initiation of the tandem substitution by AID. Tandem substitutions comprised 5,7% of AID-induced mutations. The majority of tandem substitutions represents single nucleotide juxtalocations of directly adjacent sequences. These observations were confirmed in an independent cohort of healthy donors. We propose a model where tandem substitutions are predominantly generated by translesion synthesis across an apyramidinic site that is typically created by UNG. During replication, apyrimidinic sites transiently adapt an extruded configuration, causing skipping of the extruded base. Consequent strand decontraction leads to the juxtalocation, after which exonucleases repair the apyramidinic site and any directly adjacent mismatched base pairs. The mismatch repair pathway appears to account for the remainder of tandem substitutions. Tandem substitutions may enhance affinity maturation and expedite the adaptive immune response by overcoming amino acid codon degeneracies or mutating two adjacent amino acid residues simultaneously.

Different Fruit-Specific Promoters Drive AtMYB12 Expression to Improve Phenylpropanoid Accumulation in Tomato

Tomato is an economically crucial vegetable/fruit crop globally. Tomato is rich in nutrition and plays an essential role in a healthy human diet. Phenylpropanoid, a critical compound in tomatoes, reduces common degenerative and chronic diseases risk caused by oxidative stress. As an MYB transcription factor, ATMYB12 can increase phenylpropanoid content by activating phenylpropanoid synthesis related genes, such as PAL, C4H, 4CL, CHS. However, the heterologous expression of AtMYB12 in tomatoes can be altered through transgenic technologies, such as unstable expression vectors and promoters with different efficiency. In the current study, the efficiency of other fruit-specific promoters, namely E8S, 2A12, E4, and PG, were compared and screened, and we determined that the expression efficiency of AtMYB12 was driven by the E8S promoter was the highest. As a result, the expression of phenylpropanoid synthesis related genes was regulated by AtMYB12, and the phenylpropanoid accumulation in transgenic tomato fruits increased 16 times. Additionally, the total antioxidant capacity of fruits was measured through Trolox equivalent antioxidant capacity (TEAC) assay, which was increased by 2.4 times in E8S transgenic lines. TEAC was positively correlated with phenylpropanoid content. Since phenylpropanoid plays a crucial role in the human diet, expressing AtMYB12 with stable and effective fruit-specific promoter E8S could improve tomato’s phenylpropanoid and nutrition content and quality. Our results can provide genetic resources for the subsequent improvement of tomato varieties and quality, which is significant for human health.