Molecular mechanisms and animal models of spinal muscular atrophy

AbstractSpinal muscular atrophy (SMA), the leading genetic cause of infant mortality, is characterized by the degeneration of spinal motor neurons and muscle atrophy. Although the genetic cause of SMA has been mapped to the Survival Motor Neuron1 (SMN1) gene, mechanisms underlying selective motor neuron degeneration in SMA remain largely unknown. Here we review the latest developments and our current understanding of the molecular mechanisms underlying SMA pathogenesis, focusing on the animal model systems that have been developed, as well as new diagnostic and treatment strategies that have been identified using these model systems. This article is part of a special issue entitled: Neuromuscular Diseases: Pathology and Molecular Pathogenesis

Exploring the Efficacy of the Helen B. Landgarten Art Therapy Clinic’s Transition to Telehealth During COVID-19

This research qualitatively explores the impacts of the Helen B. Landgarten Art therapy Clinic’s transition to art therapy telehealth services during the COVID-19 pandemic. The purpose of this research was to explore the efficacy of interventions and the clinical themes that emerged as a result of telehealth art therapy services delivered to marginalized communities through the Helen B. Landgarten Art Therapy Clinic. Data that was collected includes anonymous surveys from administrators, teachers, and caregivers of those receiving services and facilitators of services, semi-structured interviews with administrators, teachers, and caregivers of those receiving services, as well as a focus group with facilitators of services. Through the analysis of data several findings suggest that art therapy telehealth can provide a safe space for engagement in mental health and be more accessible to marginalized communities. These findings potentially open new doors for further inquiry into art therapy telehealth

3D-cultured blastoids model human embryogenesis from pre-implantation to early gastrulation stages

Naive human pluripotent stem cells have the remarkable ability to self-organize into blastocyst-like structures ( blastoids ) that model lineage segregation in the pre-implantation embryo. However, the extent to which blastoids can recapitulate the defining features of human post-implantation development remains unexplored. Here, we report that blastoids cultured on thick three-dimensional (3D) extracellular matrices capture hallmarks of early post-implantation development, including epiblast lumenogenesis, rapid expansion and diversification of trophoblast lineages, and robust invasion of extravillous trophoblast cells by day 14. Extended blastoid culture results in the localized activation of primitive streak marker TBXT and the emergence of embryonic germ layers by day 21. We also show that the modulation of WNT signaling alters the balance between epiblast and trophoblast fates in post-implantation blastoids. This work demonstrates that 3D-cultured blastoids offer a continuous and integrated in vitro model system of human embryonic and extraembryonic development from pre-implantation to early gastrulation stages

Age and Diet Affect Gene Expression Profile in Canine Skeletal Muscle

We evaluated gene transcription in canine skeletal muscle (biceps femoris) using microarray analysis to identify effects of age and diet on gene expression. Twelve female beagles were used (six 1-year olds and six 12-year olds) and they were fed one of two experimental diets for 12 months. One diet contained primarily plant-based protein sources (PPB), whereas the second diet contained primarily animal-based protein sources (APB). Affymetrix GeneChip Canine Genome Arrays were used to hybridize extracted RNA. Age had the greatest effect on gene transcription (262 differentially expressed genes), whereas the effect of diet was relatively small (22 differentially expressed genes). Effects of age (regardless of diet) were most notable on genes related to metabolism, cell cycle and cell development, and transcription function. All these genes were predominantly down-regulated in geriatric dogs. Age-affected genes that were differentially expressed on only one of two diets were primarily noted in the PPB diet group (144/165 genes). Again, genes related to cell cycle (22/35) and metabolism (15/19) had predominantly decreased transcription in geriatric dogs, but 6/8 genes related to muscle development had increased expression. Effects of diet on muscle gene expression were mostly noted in geriatric dogs, but no consistent patterns in transcription were observed. The insight these data provide into gene expression profiles of canine skeletal muscle as affected by age, could serve as a foundation for future research pertaining to age-related muscle diseases

AI is a viable alternative to high throughput screening: a 318-target study

: High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, high-quality X-ray crystal structures, or manual cherry-picking of compounds. We show that the molecules selected by the AtomNet® model are novel drug-like scaffolds rather than minor modifications to known bioactive compounds. Our empirical results suggest that computational methods can substantially replace HTS as the first step of small-molecule drug discovery

Impact of opioid-free analgesia on pain severity and patient satisfaction after discharge from surgery: multispecialty, prospective cohort study in 25 countries

Background: Balancing opioid stewardship and the need for adequate analgesia following discharge after surgery is challenging. This study aimed to compare the outcomes for patients discharged with opioid versus opioid-free analgesia after common surgical procedures.Methods: This international, multicentre, prospective cohort study collected data from patients undergoing common acute and elective general surgical, urological, gynaecological, and orthopaedic procedures. The primary outcomes were patient-reported time in severe pain measured on a numerical analogue scale from 0 to 100% and patient-reported satisfaction with pain relief during the first week following discharge. Data were collected by in-hospital chart review and patient telephone interview 1 week after discharge.Results: The study recruited 4273 patients from 144 centres in 25 countries; 1311 patients (30.7%) were prescribed opioid analgesia at discharge. Patients reported being in severe pain for 10 (i.q.r. 1-30)% of the first week after discharge and rated satisfaction with analgesia as 90 (i.q.r. 80-100) of 100. After adjustment for confounders, opioid analgesia on discharge was independently associated with increased pain severity (risk ratio 1.52, 95% c.i. 1.31 to 1.76; P < 0.001) and re-presentation to healthcare providers owing to side-effects of medication (OR 2.38, 95% c.i. 1.36 to 4.17; P = 0.004), but not with satisfaction with analgesia (beta coefficient 0.92, 95% c.i. -1.52 to 3.36; P = 0.468) compared with opioid-free analgesia. Although opioid prescribing varied greatly between high-income and low- and middle-income countries, patient-reported outcomes did not.Conclusion: Opioid analgesia prescription on surgical discharge is associated with a higher risk of re-presentation owing to side-effects of medication and increased patient-reported pain, but not with changes in patient-reported satisfaction. Opioid-free discharge analgesia should be adopted routinely

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

The Somatic Genomic Landscape of Chromophobe Renal Cell Carcinoma

We describe the landscape of somatic genomic alterations of 66 chromophobe renal cell carcinomas (ChRCCs) based on multidimensional and comprehensive characterization, including mitochondrial DNA (mtDNA) and whole genome sequencing. The result is consistent that ChRCC originates from the distal nephron compared to other kidney cancers with more proximal origins. Combined mtDNA and gene expression analysis implicates changes in mitochondrial function as a component of the disease biology, while suggesting alternative roles for mtDNA mutations in cancers relying on oxidative phosphorylation. Genomic rearrangements lead to recurrent structural breakpoints within TERT promoter region, which correlates with highly elevated TERT expression and manifestation of kataegis, representing a mechanism of TERT up-regulation in cancer distinct from previously-observed amplifications and point mutations

Insights from primary immunodeficiencies: investigating the role of GIMAP6 in the immune system

While molecular, cellular, and animal models play a vital role in immunological research, the study of patients with inborn errors of immunity provides a unique opportunity to elucidate the direct importance of specific genes in the human immune system. In this thesis, I have investigated the disease etiology of four sets of patients believed to have novel primary immunodeficiencies (PIDs) using whole exome sequencing coupled with in vitro and in vivo assays of both patient cells and model systems. In one patient, I confirmed a mutation in DNMT3B, a DNA methyltransferase known to cause a previously identified PID. I next investigated whether a homozygous missense mutation in TICAM2, a toll-like receptor signaling adaptor, might underlie the disease of a patient with recurrent pneumonia. In collaborative project, I then examined the potential role of a newly described PID-associated gene, GTPase of the immunity-associated protein 5 (GIMAP5), in autophagy and metabolism. GIMAP5 is a member of a family of conserved GTPases with a poorly understood role in leukocyte development and survival. Stemming from the work on the GIMAP5 cohort, I identified a patient presenting with splenomegaly and autoimmunity who has a novel homozygous missense mutation in GIMAP6. The majority of this thesis focuses on verification of GIMAP6 as a PID-associated gene and investigation of its molecular function. Using both patient cells and knockout mouse models, I demonstrated an autophagic defect in GIMAP6-deficient T cells, implicating GIMAP6 as a regulator of autophagy. Furthermore, I determined that Gimap6 knockout mice have early mortality due to microangiopathic kidney disease. I demonstrated that this renal disease was not immune-mediated therefore implying that GIMAP6 has a novel role in endothelial cell function. The work presented in this thesis thus highlights both the challenges of studying PIDs and the promise of these diseases to help elucidate the mechanisms of human immunity and therapies for PID patients.</p

Insights from primary immunodeficiencies: investigating the role of GIMAP6 in the immune system

While molecular, cellular, and animal models play a vital role in immunological research, the study of patients with inborn errors of immunity provides a unique opportunity to elucidate the direct importance of specific genes in the human immune system. In this thesis, I have investigated the disease etiology of four sets of patients believed to have novel primary immunodeficiencies (PIDs) using whole exome sequencing coupled with in vitro and in vivo assays of both patient cells and model systems. In one patient, I confirmed a mutation in DNMT3B, a DNA methyltransferase known to cause a previously identified PID. I next investigated whether a homozygous missense mutation in TICAM2, a toll-like receptor signaling adaptor, might underlie the disease of a patient with recurrent pneumonia. In collaborative project, I then examined the potential role of a newly described PID-associated gene, GTPase of the immunity-associated protein 5 (GIMAP5), in autophagy and metabolism. GIMAP5 is a member of a family of conserved GTPases with a poorly understood role in leukocyte development and survival. Stemming from the work on the GIMAP5 cohort, I identified a patient presenting with splenomegaly and autoimmunity who has a novel homozygous missense mutation in GIMAP6. The majority of this thesis focuses on verification of GIMAP6 as a PID-associated gene and investigation of its molecular function. Using both patient cells and knockout mouse models, I demonstrated an autophagic defect in GIMAP6-deficient T cells, implicating GIMAP6 as a regulator of autophagy. Furthermore, I determined that Gimap6 knockout mice have early mortality due to microangiopathic kidney disease. I demonstrated that this renal disease was not immune-mediated therefore implying that GIMAP6 has a novel role in endothelial cell function. The work presented in this thesis thus highlights both the challenges of studying PIDs and the promise of these diseases to help elucidate the mechanisms of human immunity and therapies for PID patients.</p