Dissociation protocols used for sarcoma tissues bias the transcriptome observed in single-cell and single-nucleus RNA sequencing.

BACKGROUND: Single-cell RNA-seq has emerged as an innovative technology used to study complex tissues and characterize cell types, states, and lineages at a single-cell level. Classification of bulk tumors by their individual cellular constituents has also created new opportunities to generate single-cell atlases for many organs, cancers, and developmental models. Despite the tremendous promise of this technology, recent evidence studying epithelial tissues and diverse carcinomas suggests the methods used for tissue processing, cell disaggregation, and preservation can significantly bias gene expression and alter the observed cell types. To determine whether sarcomas - tumors of mesenchymal origin - are subject to the same technical artifacts, we profiled patient-derived tumor explants (PDXs) propagated from three aggressive subtypes: osteosarcoma (OS), Ewing sarcoma (ES), desmoplastic small round cell tumor (DSRCT). Given the rarity of these sarcoma subtypes, we explored whether single-nuclei RNA-seq from more widely available archival frozen specimens could accurately be identified by gene expression signatures linked to tissue phenotype or pathognomonic fusion proteins. RESULTS: We systematically assessed dissociation methods across different sarcoma subtypes. We compared gene expression from single-cell and single-nucleus RNA-sequencing of 125,831 whole-cells and nuclei from ES, DSRCT, and OS PDXs. We detected warm dissociation artifacts in single-cell samples and gene length bias in single-nucleus samples. Classic sarcoma gene signatures were observed regardless of the dissociation method. In addition, we showed that dissociation method biases could be computationally corrected. CONCLUSIONS: We highlighted transcriptional biases, including warm dissociation and gene-length biases, introduced by the dissociation method for various sarcoma subtypes. This work is the first to characterize how the dissociation methods used for sc/snRNA-seq may affect the interpretation of the molecular features in sarcoma PDXs.

Bioactivity-guided isolation of trypanocidal coumarins and dihydro-pyranochromones from selected Apiaceae plant species.

Bioactivity-guided isolation of natural products from plant matrices is widely used in drug discovery. Here, this strategy was applied to identify trypanocidal coumarins effective against the parasite Trypanosoma cruzi, the etiologic agent of Chagas disease (American trypanosomiasis). Previously, phylogenetic relationships of trypanocidal activity revealed a coumarin-associated antichagasic hotspot in the Apiaceae. In continuation, a total of 35 ethyl acetate extracts of different Apiaceae species were profiled for selective cytotoxicity against T. cruzi epimastigotes over host CHO-K1 and RAW264.7 cells at 10 µg/mL. A flow cytometry-based T. cruzi trypomastigote cellular infection assay was employed to measure toxicity against the intracellular amastigote stage. Among the tested extracts, Seseli andronakii aerial parts, Portenschlagiella ramosissima and Angelica archangelica subsp. litoralis roots exhibited selective trypanocidal activity and were subjected to bioactivity-guided fractionation and isolation by countercurrent chromatography. The khellactone ester isosamidin isolated from the aerial parts of S. andronakii emerged as a selective trypanocidal molecule (selectivity index ∼9) and inhibited amastigote replication in CHO-K1 cells, though it was significantly less potent than benznidazole. The khellactone ester praeruptorin B and the linear dihydropyranochromones 3'-O-acetylhamaudol and ledebouriellol isolated from the roots of P. ramosissima were more potent and efficiently inhibited the intracellular amastigote replication at < 10 µM. The furanocoumarins imperatorin, isoimperatorin and phellopterin from A. archangelica inhibited T. cruzi replication in host cells only in combination, indicative of superadditive effects, while alloimperatorin was more active in fractions. Our study reports preliminary structure-activity relationships of trypanocidal coumarins and shows that pyranocoumarins and dihydropyranochromones are potential chemical scaffolds for antichagasic drug discovery.

Guides to Advance Teaching Evaluation (GATEs): A Resource for STEM Departments Planning Robust and Equitable Evaluation Practices.

Most science, technology, engineering, and mathematics (STEM) departments inadequately evaluate teaching, which means they are not equipped to recognize or reward effective teaching. As part of a project at one institution, we observed that departmental chairs needed help recognizing the decisions they would need to make to improve teaching evaluation practices. To meet this need, we developed the Guides to Advance Teaching Evaluation (GATEs), using an iterative development process. The GATEs are designed to be a planning tool that outlines concrete goals to guide reform in teaching evaluation practices in STEM departments at research-intensive institutions. The GATEs are grounded in the available scholarly literature and guided by existing reform efforts and have been vetted with STEM departmental chairs. The GATEs steer departments to draw on three voices to evaluate teaching: trained peers, students, and the instructor. This research-based resource includes three components for each voice: 1) a list of departmental target practices to serve as goals; 2) a characterization of common starting places to prompt reflection; and 3) ideas for getting started. We provide anecdotal examples of potential uses of the GATEs for reform efforts in STEM departments and as a research tool to document departmental practices at different time points.

Correlation of nuclear pIGF-1R/IGF-1R and YAP/TAZ in a tissue microarray with outcomes in osteosarcoma patients.

Osteosarcoma (OS) is a genetically diverse bone cancer that lacks a consistent targetable mutation. Recent studies suggest the IGF/PI3K/mTOR pathway and YAP/TAZ paralogs regulate cell fate and proliferation in response to biomechanical cues within the tumor microenvironment. How this occurs and their implication upon osteosarcoma survival, remains poorly understood. Here, we show that IGF-1R can translocate into the nucleus, where it may act as part of a transcription factor complex. To explore the relationship between YAP/TAZ and total and nuclear phosphorylated IGF-1R (pIGF-1R), we evaluated sequential tumor sections from a 37-patient tissue microarray by confocal microscopy. Next, we examined the relationship between stained markers, clinical disease characteristics, and patient outcomes. The nuclear to cytoplasmic ratios (N:C ratio) of YAP and TAZ strongly correlated with nuclear pIGF-1R (r = 0.522, p = 0.001 for each pair). Kaplan-Meier analyses indicated that nuclear pIGF-1R predicted poor overall survival, a finding confirmed in the Cox proportional hazards model. Though additional investigation in a larger prospective study will be required to validate the prognostic accuracy of these markers, our results may have broad implications for the new class of YAP, TAZ, AXL, or TEAD inhibitors that have reached early phase clinical trials this year.

Multi-site desmoplastic small round cell tumors are genetically related and immune-cold.

Desmoplastic small round cell tumor (DSRCT) is a highly aggressive soft tissue sarcoma that is characterized by the EWSR1-WT1 fusion protein. Patients present with hundreds of tumor implants in their abdominal cavity at various sites. To determine the genetic relatedness among these sites, exome and RNA sequencing were performed on 22 DSRCT specimens from 14 patients, four of whom had specimens from various tissue sites. Multi-site tumors from individual DSRCT patients had a shared origin and were highly related. Other than the EWSR1-WT1 fusion, very few secondary cancer gene mutations were shared among the sites. Among these, ARID1A, was recurrently mutated, which corroborates findings by others in DSRCT patients. Knocking out ARID1A in JN-DSRCT cells using CRISPR/CAS9 resulted in significantly lower cell proliferation and increased drug sensitivity. The transcriptome data were integrated using network analysis and drug target database information to identify potential therapeutic opportunities in EWSR1-WT1-associated pathways, such as PI3K and mTOR pathways. Treatment of JN-DSRCT cells with the PI3K inhibitor alpelisib and mTOR inhibitor temsirolimus reduced cell proliferation. In addition, the low mutation burden was associated with an immune-cold state in DSRCT. Together, these data reveal multiple genomic and immune features of DSRCT and suggest therapeutic opportunities in patients.

The androgen receptor is a therapeutic target in desmoplastic small round cell sarcoma.

Desmoplastic small round cell tumor (DSRCT) is an aggressive, usually incurable sarcoma subtype that predominantly occurs in post-pubertal young males. Recent evidence suggests that the androgen receptor (AR) can promote tumor progression in DSRCTs. However, the mechanism of AR-induced oncogenic stimulation remains undetermined. Herein, we demonstrate that enzalutamide and AR-directed antisense oligonucleotides (AR-ASO) block 5α-dihydrotestosterone (DHT)-induced DSRCT cell proliferation and reduce xenograft tumor burden. Gene expression analysis and chromatin immunoprecipitation sequencing (ChIP-seq) were performed to elucidate how AR signaling regulates cellular epigenetic programs. Remarkably, ChIP-seq revealed novel DSRCT-specific AR DNA binding sites adjacent to key oncogenic regulators, including WT1 (the C-terminal partner of the pathognomonic fusion protein) and FOXF1. Additionally, AR occupied enhancer sites that regulate the Wnt pathway, neural differentiation, and embryonic organ development, implicating AR in dysfunctional cell lineage commitment. Our findings have direct clinical implications given the widespread availability of FDA-approved androgen-targeted agents used for prostate cancer.

Cardiac spinal deafferentation reduces the susceptibility to sustained ventricular tachycardia in conscious rats.

The response to myocardial ischemia is complex and involves the cardio-cardiac sympathetic reflex. Specifically, cardiac spinal (sympathetic) afferents are excited by ischemic metabolites and elicit an excitatory sympathetic reflex, which plays a major role in the genesis of ventricular arrhythmias. For example, brief myocardial ischemia leads to ATP release, which activates cardiac spinal afferents through stimulation of P2 receptors. Clinical work with patients and preclinical work with animals document that disruption of this reflex protects against ischemia-induced ventricular arrhythmias. However, the role of afferent signals in the initiation of sustained ventricular tachycardia has not been investigated. Therefore, we tested the hypothesis that cardiac spinal deafferentation reduces the susceptibility to sustained ventricular tachycardia in adult (12-15 wk of age), conscious, male Sprague-Dawley rats. To test this hypothesis, the susceptibility to ventricular tachyarrhythmias produced by occlusion of the left main coronary artery was determined in two groups of conscious rats: 1) deafferentation (bilateral excision of the T1-T5 dorsal root ganglia) and 2) control (sham deafferentation). The ventricular arrhythmia threshold (VAT) was defined as the time from coronary occlusion to sustained ventricular tachycardia resulting in a reduction in arterial pressure. Results document a significantly higher VAT in the deafferentation group (7.0 ± 0.7 min) relative to control (4.3 ± 0.3 min) rats. The decreased susceptibility to tachyarrhythmias with deafferentation was associated with a reduced cardiac metabolic demand (lower rate-pressure product and ST segment elevation) during ischemia.

Phylobioactive hotspots in plant resources used to treat Chagas disease.

Globally, more than six million people are infected with Trypanosoma cruzi, the causative protozoan parasite of the vector-borne Chagas disease (CD). We conducted a cross-sectional ethnopharmacological field study in Bolivia among different ethnic groups where CD is hyperendemic. A total of 775 extracts of botanical drugs used in Bolivia in the context of CD and botanical drugs from unrelated indications from the Mediterranean De Materia Medica compiled by Dioscorides two thousand years ago were profiled in a multidimensional assay uncovering different antichagasic natural product classes. Intriguingly, the phylobioactive anthraquinone hotspot matched the antichagasic activity of Senna chloroclada, the taxon with the strongest ethnomedical consensus for treating CD among the Izoceño-Guaraní. Testing common 9,10-anthracenedione derivatives in T. cruzi cellular infection assays demarcates hydroxyanthraquinone as a potential antichagasic lead scaffold. Our study systematically uncovers in vitro antichagasic phylogenetic hotspots in the plant kingdom as a potential resource for drug discovery based on ethnopharmacological hypotheses.

Transcriptional activators YAP/TAZ and AXL orchestrate dedifferentiation, cell fate, and metastasis in human osteosarcoma.

Osteosarcoma (OS) is a molecularly heterogeneous, aggressive, poorly differentiated pediatric bone cancer that frequently spreads to the lung. Relatively little is known about phenotypic and epigenetic changes that promote lung metastases. To identify key drivers of metastasis, we studied human CCH-OS-D OS cells within a previously described rat acellular lung (ACL) model that preserves the native lung architecture, extracellular matrix, and capillary network. This system identified a subset of cells-termed derived circulating tumor cells (dCTCs)-that can migrate, intravasate, and spread within a bioreactor-perfused capillary network. Remarkably, dCTCs highly expressed epithelial-to-mesenchymal transition (EMT)-associated transcription factors (EMT-TFs), such as ZEB1, TWIST, and SOX9, which suggests that they undergo cellular reprogramming toward a less differentiated state by coopting the same epigenetic machinery used by carcinomas. Since YAP/TAZ and AXL tightly regulate the fate and plasticity of normal mesenchymal cells in response to microenvironmental cues, we explored whether these proteins contributed to OS metastatic potential using an isogenic pair of human OS cell lines that differ in AXL expression. We show that AXL inhibition significantly reduced the number of MG63.2 pulmonary metastases in murine models. Collectively, we present a laboratory-based method to detect and characterize a pure population of dCTCs, which provides a unique opportunity to study how OS cell fate and differentiation contributes to metastatic potential. Though the important step of clinical validation remains, our identification of AXL, ZEB1, and TWIST upregulation raises the tantalizing prospect that EMT-TF-directed therapies might expand the arsenal of therapies used to combat advanced-stage OS.

Oximetry-detected pulsus paradoxus predicts for severity in paediatric asthma.

OBJECTIVE: To evaluate if qualitative visual detection of pulsus paradoxus (PP) on the pulse oximeter plethysmograph can predict outcomes for children with moderate to severe respiratory distress in a paediatric emergency department (ED). DESIGN: Prospective cohort study. SETTING: Paediatric ED of a tertiary paediatrics hospital in Singapore. PATIENTS: Children managed for moderate to severe wheezing in the resuscitation bay of the ED. INTERVENTIONS: Patients were assessed for the presence of PP based on visual detection of oximeter plethysmograph before and after initial inhaled bronchodilator therapy. MAIN OUTCOME MEASURES: These include the need for adjunct medications such as aminophylline or magnesium sulfate, the need for supplementary ventilation and the need for admission to the high dependency unit (HDU) or intensive care unit (ICU). RESULTS: There were 285 patients included in the study, of whom 78 (27.4%) had PP at ED presentation. There were 40 (14.0%) who had PP after initial management. Children who had PP after initial management had significantly relative risks (RR) of requiring adjunct medications (RR 12.5, 95% CI 4.0 to 38.6), need for supplementary ventilation (RR 5.6, 95% CI 1.2 to 26.5) and admission to the HDU/ICU (RR 5.6, 95% CI 3.0 to 10.4). CONCLUSION: Qualitative detection of PP on pulse oximetry can be used as a potential point-of-care tool to help in the assessment of response to initial treatment in paediatric patients with acute moderate to severe asthma exacerbations. Future studies are needed to assess and validate its role in guiding ED management of acute paediatric asthma.

Local Activation of the Alternative Pathway of Complement System in Mycotic Keratitis Patient Tear.

Aspergillus flavus and Fusarium solani are the predominant causative agents of mycotic keratitis in the tropical part of the world. Tear proteins play a major role in the innate immune response against these fungal infections as has been shown by the presence of complement proteins and neutrophil extracellular trap proteins in keratitis patients tear. In this study, we established the presence of the components of the alternate pathway of complement system and their functional state in the tear film of mycotic keratitis patients. The complement proteins namely, C3 and CFH were found only in the open-eye tear of patients but not in control individuals. In vitro analysis showed binding of purified C3b and CFH to fungal spores, which confirmed that the spores can provide a foreign surface for forming the complement complex. Analysis of spore bound tear proteins by mass spectrometry exhibited the presence of known proteins of the alternate pathway complement cascade in keratitis patient tear. Hemolytic assay using rabbit RBC confirmed the presence of a functional alternate pathway of complement cascade in the tear proteome of the patients. The presence of negative regulators, CFH and CFI, in the patient tear indicate that the complement activity is tightly regulated during fungal infection. Mass spectrometry data show vitronectin and clusterin, two known inhibitors of the membrane attack complex only in the patient tear. These data demonstrate the activation of the alternate pathway of complement cascade during the early stages of infection. Interestingly, the production of multiple negative regulators of complement cascade implies the pathogen can effectively evade the host complement system during infection.

Toward assessing traumatic events and stress symptoms in preschool children from low-income families.

Traumatic events can seriously disrupt the development of preschool children. Yet few studies capture developmentally specific examples of traumas and the expression of distress for this age group. Mothers and teachers of 138 preschoolers from low-income families were interviewed about traumatic events and completed a new measure assessing their child's traumatic stress symptoms. They reported traumatic events as the death of a person, death of a pet, family violence, high conflict divorce, sudden family loss, accident or injury, and viewing the World Trade Center attack. Factor analysis of 17 trauma symptoms revealed three internally consistent and valid scales: Intrusions, Emotional Reactivity, and Fears, plus a Total omnibus score. Traumatic stress symptoms varied by the type of event. Scores were higher for traumatic events involving close family members than for distal events.

Intimate partner violence, social support, and employment in the post-welfare reform era.

This prospective study used 3 years of longitudinal data to explore relationships among intimate partner violence (IPV), perceived emotional and material social support, employment stability, and job turnover among current and former female welfare recipients in the immediate post-welfare reform era. Higher levels of current IPV and lower levels of current social support predicted less stable future employment; however, current employment stability did not predict either future IPV or future social support. Current social support did not predict future IPV, and perceived social support did not mediate the relationship between IPV and employment stability during a 3-year period.

The impact of culture and minority status on women's experience of domestic violence.

The influence of culture and ethnic background on women's experience of domestic violence has been explored in research only recently. Here the authors review research about the impact of culture and minority status in the United States on women's experience of domestic violence, considering family structure,immigration, acculturation, oppression, and community response. The authors encourage researchers and service providers to acknowledge the effects on women of sociopolitical dynamics, including racism, and to identify specific aspects of culture that are relevant to intimate partner abuse.

A prospective study of GnRH long agonist versus flexible GnRH antagonist protocol in PCOS: Indian experience.

BACKGROUND: Polycystic ovarian syndrome is a common endocrine disorder of reproductive age women. Many controlled ovarian stimulation (COS) strategies have been offered for the treatment of patients with PCOS undergoing in vitro fertilization, but the optimal protocol is still a controversy. There is no compelling evidence for the advantage of one stimulation protocol over the other. MATERIALS AND METHODS: This is a single-center prospective controlled study comparing long agonist and antagonist protocol in PCOS women. RESULTS: There was no significant difference in live birth rate and clinical pregnancy rate. Rate of ovarian hyperstimulation syndrome was significantly higher in the agonist group. Number of oocytes retrieved, number of follicles and peak estradiol levels were significantly more in the agonist group. CONCLUSION: The GnRH antagonist protocol is an equally effective but safer protocol in PCOS patients compared with the long agonist protocol.

Effect of Pre-ovulatory Single Dose GnRH agonist Therapy on IVF Outcome in GnRH Antagonist Cycles; A Prospective Study.

BACKGROUND: The purpose of present study was to evaluate the role of pre-ovulatory GnRH agonist therapy on IVF outcomes in GnRH antagonist cycles. METHODS: In this prospective study we recruited 100 infertile women undergoing IVF cycles with GnRH antagonists. The patients were assigned to two groups: Group A (the study group, n = 42) were assigned for receiving hCG + triptorelin for the final oocyte maturation and group B (the control group, n = 58) were assigned for only hCG. The t-test, chi-square (χ(2)), and Fisher's exact test were used for data analysis. A p < 0.05 was taken as statistically significant. The results are presented by mean± SD, and in percents (%). RESULTS: LH levels significantly (p < 0.001) increased in the study group on the day of oocyte retrieval. All embryological parameters including the number of mature oocytes, fertilization and cleavage rates, number of high quality embryos and number of cases whose embryos were frozen were non-significantly higher in the study group. There were small but non-significant improvements in the clinical pregnancy, ongoing pregnancy, live birth and implantation rates in the study group. CONCLUSION: Administering a single dose of GnRH agonist before oocyte retrieval in antagonist cycles may be helpful in improving the pregnancy rate but the results need to be verified in a larger trials.

Ovarian torsion in infertility management - Missing the diagnosis means losing the ovary: A high price to pay.

Ovarian torsion is a rare entity and the diagnosis is commonly missed. Here we present a series of two cases of ovarian torsion. First case followed the in vitro fertilization treatment, along with ovarian hyperstimulation syndrome, where even with timely intervention and laparoscopy, we had to compromise one ovary. Second case followed the ovulation induction and intrauterine insemination - where timely intervention helped us to save the ovary.