bluuebunny/crossref_metadata_2025 huggingface dataset:
Spatial transcriptome sequencing of FFPE tissues at cellular level
Authors: Liu Yang , Enninful Archibald , Deng Yanxiang , Fan Rong
Published: October 2020

Formalin-fixed paraffin-embedded (FFPE) tissues are the most abundant archivable specimens in clinical tissue banks, but unfortunately incompatible with single-cell level whole transcriptome sequencing due to RNA degradation in storage and RNA damage in extraction. We developed an in-tissue barcoding approach namely DBiT-seq for spatially revolved whole transcriptome sequencing at cellular level, which required no tissue dissociation or RNA exaction, thus potentially more suited for FFPE samples. Herein, we demonstrated spatial transcriptome sequencing of embryonic and adult mouse FFPE tissue sections at cellular level (25μm pixel size) with high coverage (>1,000 genes per pixel). Spatial transcriptome of an E10.5 mouse embryo identified all major anatomical features in the brain and abdominal region. Integration with singlecell RNA-seq data for cell type identification indicated that most tissue pixels were dominated by single-cell transcriptional phenotype. Spatial mapping of adult mouse aorta, atrium, and ventricle tissues identified the spatial distribution of a variety of cell types. Spatial transcriptome sequencing of FFPE samples at cellular level may provide enormous opportunities in a wide range of biomedical research. It may allow us to exploit the huge resource of clinical tissue specimens to study human disease mechanisms and discover tissue biomarkers or therapeutic targets.
The effect of functionally-guided-connectivity-based rTMS on amygdala activation
Authors: Beynel L. , Campbell E. , Naclerio M. , Galla J.T. , Ghosal A. , Michael A.M , Kimbrel N.A. , Davis S.W. , Appelbaum L.G.
Published: October 2020

Repetitive transcranial magnetic stimulation (rTMS) has fundamentally transformed how we treat psychiatric disorders, but is still in need of innovation to optimally correct dysregulation that occurs throughout the fronto-limbic network. rTMS is often applied over the prefrontal cortex, a central node in this network, but less attention is given to subcortical areas because they lie at depths beyond the electric field penetration of rTMS. Recent studies have demonstrated that the effectiveness of rTMS is dependent on the functional connectivity between deep subcortical areas and superficial targets, indicating that leveraging such connectivity may improve dosing approaches for rTMS interventions. The current preliminary study, therefore, sought to test whether task-related, fMRI-connectivity-based rTMS could be used to modulate amygdala activation through its connectivity with the medial prefrontal cortex (mPFC). For this purpose, fMRI was collected on participants to identify a node in the mPFC that showed the strongest negative connectivity with right amygdala, as defined by psychophysiological interaction analysis. To promote long-lasting Hebbian-like effects, and potentially stronger modulation, 5Hz rTMS was then applied to this target as participants viewed frightening video-clips that engaged the fronto-limbic network. Post-rTMS fMRI results revealed promising increases in both the left mPFC and right amygdala, for active rTMS compared to sham. While these modulatory findings are promising, they differ from the a priori expectation that excitatory 5Hz rTMS over a negatively connected node would reduce amygdala activity. As such, further research is needed to better understand how connectivity influences TMS effects on distal structures, and to leverage this information to improve therapeutic applications.
An attempt to optimize human resources allocation based on spatial diversity of COVID-19 cases in Poland
Authors: Jarynowski Andrzej , Wójta-Kempa Monika , Krzowski Łukasz
Published: October 2020

Our task is to examine the relationship between the SARS-CoV-2 arrival and the number of confirmed COVID-19 cases in the first wave (period from March 4 to May 22, 2020 (unofficial data)), and socio-economic variables at the powiat (county) level (NUTS-4) using simple statistical techniques such as data visualization, correlation analysis, spatial clustering and multiple linear regression. We showed that immigration and the logarithm of general mobility is the best predictor of SARS-CoV-2 arrival times, while emigration, industrialization and air quality explain the most of the size of the epidemic in poviats. On the other hand, infection dynamics is driven to a lesser extent by previously postulated variables such as population size and density, income or the size of the elderly population. Our analyses could support Polish authorities in preparation for the second wave of infections and optimal management of resources as we have provided a proposition of optimal distribution of human resources between poviats.
Sociodemographic and access-related correlates of sanitary pads among college students in Lucknow during Covid19
Authors: Garg Surbhi , Alvi Ruqayya , Gupta Suman , Ahmad Absar
Published: October 2020

Introduction

Sanitary napkin is an essential aspect of the Menstrual management materials for women and adolescent girls between menarche and menopause. Despite being an important issue concerning women and girls in the menstruating age group, access to menstrual hygiene products neglected during the COVID19 pandemic. Further, there is no evidence of the practice of menstrual hygiene products in Indian settings during this period. This paper investigates the prevalence of socio-demographic correlations of access to sanitary napkins among college students in Lucknow.

Methods

An online retrospective cross-sectional survey was conducted in Lucknow in September 2020. In total, 1439 participants took part in the survey. After removing 55 participants, those quit the survey by clicking on the disagree button and 13 were not satisfying inclusion criteria. So the final samples were 1371, which were included in the analysis. Students of UG and PG currently studying in colleges in the Lucknow were eligible to participate. The data collection was anonymous. Responses were analysed using descriptive and bivariate logistic regression.

Results

In this study, 1371 students were included, making a response rate of 96.2 percent. Nearly 12.5 percent of students reported about difficulty encountered during the lockdown. Muslims, Father education illiterate or upto12th, father occupation as farmer, monthly salary less than 25 thousand, residence as rural, and history of reusable clothes were more likely to face problems to access sanitary pads during the lockdown in Lucknow (P < .05).

Conclusions

During COVID-19 lockdown, about 12.5 % of girls were dependent on either locally available resources as absorbents during menstruation or paid more to access in Lucknow. Because of the lockdown, many people have lost their livelihood. More than ever, economically low-income families are reluctant to spend on sanitary pads, which is why few college girls were going back to their previous handling periods by using rags.

Highlights

The prevalence of menstrual management products during Covid19 were unknown

Women and Adolescents in India suffer the shortages of Sanitary napkin during lockdown

Prevalence of access to sanitary pads should emphasis different focal points
Innate immune cytokine profiling and biomarker identification for outcome in dengue patients
Authors: Pradeep Sai Pallavi , Venkatesh Pooja Hoovina , Manchala Nageswar R. , Veedu Arjun Vayal , Basavaraju Rajani K. , Selvasundari Leela , Ramakrishna Manikanta , Chandrakiran Yogitha , Krishnamurthy Vishwanath , Holigi Shivaranjani , Thomas Tinku , Ross Cecil R. , Dias Mary , Satchidanandam Vijaya
Published: October 2020

Biomarkers of progression to severe dengue are urgently required for effective patient management. Innate immune cells have been implicated in the enhancement of infection and “cytokine storm” associated with dengue severity. Using intracellular cytokine staining and flow cytometry, we observed significantly higher proportions of innate immune cells secreting inflammatory cytokines dominated by IFN-γ and TNF-α at admission associated with good prognosis. Secondary dengue predisposed to severe outcomes. In patients with severe dengue and those with liver impairment, early activation as well as efficient down-regulation of innate responses were compromised. IFN-γ+CD56+CD3+NKT cells and IL-6+granulocytes served as novel biomarkers of progression to severity (composite AUC=0.85-0.9). Strong correlations among multiple cytokine-secreting innate cell subsets pointed to coordinated activation of the entire innate immune system by DENV.

One Sentence Summary

Activation and efficient attenuation of innate immunity are both compromised in severe dengue.
Long-Term Exposure to Fine Particulate Matter, Lung Function and Cognitive Performance: A Prospective Dutch Cohort Study on the Underlying Routes
Authors: Aretz Benjamin , Janssen Fanny , Vonk Judith M. , Heneka Michael T. , Boezen H. Marike , Doblhammer Gabriele
Published: October 2020

Background

Exposure to fine particulate matter and black carbon is related to cognitive impairment and poor lung function, but less is known about the routes taken by different types of air pollutants to affect cognition.

Objectives

We tested two possible routes of fine particulate matter (PM2.5) and black carbon (BC) in impairing cognition, and evaluated their importance: a direct route over the olfactory nerve or the blood stream, and an indirect route over the lung.

Methods

We used longitudinal observational data for 31232 people aged 18+ from 2006 to 2015 from the Dutch Lifelines cohort study. By linking current and past home addresses to air pollution exposure data from ELAPSE, long-term average exposure (≥ ten years) to PM2.5 and BC was calculated. Lung function was assessed by spirometry and Global Initiative (GLI) z-scores of forced expiratory volume in 1s (FEV1) and forced vital capacity (FVC) were calculated. Cognitive performance was measured by cognitive processing time (CPT) assessed by the Cogstate Brief Battery. Linear structural equation modeling was performed to test the direct/indirect associations.

Results

Higher exposure to PM2.5 but not BC was directly related to higher CPT and thus slower cognitive processing speed [18.33 (×10−3) SD above the mean (95% CI: 6.84, 29.81)]. The direct association of PM2.5 constituted more than 97% of the total effect. Mediation by lung function was low for PM2.5 with a mediated proportion of 1.78% (FEV1) and 2.62% (FVC), but higher for BC (28.49% and 46.22% respectively).

Discussion

Our results emphasize the importance of the lung acting as a mediator in the relationship between both exposure to PM2.5 and BC, and cognitive performance. However, higher exposure to PM2.5 was mainly directly associated with worse cognitive performance, which emphasizes the health-relevance of fine particles due to their ability to reach vital organs directly.
Physical Activity Decreases the Prevalence of COVID-19-associated Hospitalization: Brazil EXTRA Study
Authors: de Souza Francis Ribeiro , Motta-Santos Daisy , Santos Soares Douglas dos , de Lima Juliana Beust , Cardozo Gustavo Gonçalves , Pinto Guimarães Luciano Santos , Negrão Carlos Eduardo , dos Santos Marcelo Rodrigues
Published: October 2020

Objectives

We compared physical activity levels before the outbreak and quarantine measures with COVID-19-associated hospitalization prevalence in surviving patients infected with SARS-CoV-2. Additionally, we investigated the association of physical activity levels with symptoms of the disease, length of hospital stay, and mechanical ventilation.

Methods

Between June 2020 and August 2020, we invited Brazilian survivors and fully recovered patients infected with SARS-CoV-2 to respond to an online questionnaire. We shared the electronic link to the questionnaire on the internet. In this cross-sectional study, we collected data about clinical outcomes (symptoms, medications, hospitalization, and length of hospital stay) and cofactors, such as age, sex, ethnicity, preexisting diseases, socioeconomic and educational, and physical activity levels using the International Physical Activity Questionnaire (IPAQ short version).

Results

Out of 938 patients, 91 (9.7%) were hospitalized due to COVID-19. In a univariate analysis, sex, age, and BMI were all associated with hospitalizations due to COVID-19. Men had a higher prevalence of hospitalization (66.6%, P=0.013). Patients older than 65 years, obese, and with preexisting disease had a higher prevalence of COVID-19-related hospitalizations. In a multivariate regression model, performance of at least 150 min/wk (moderate) and/or 75 min/wk (vigorous) physical activity was associated with a lower prevalence of hospitalizations after adjustment for age, sex, BMI, and preexisting diseases (PR=0.657; P=0.046).

Conclusions

Sufficient physical activity levels are associated with a lower prevalence of COVID-19-related hospitalizations. Performing at least 150 minutes a week of moderate-intensity, or 75 minutes a week of vigorous-intensity physical activity reduces this prevalence by 34.3%.

(EXTRA SARS-CoV-2 Study, ClinicalTrials.gov number, NCT04396353)
Characteristics and Factors Associated with COVID-19 Infection, Hospitalization, and Mortality Across Race and Ethnicity
Authors: Dai Chengzhen L. , Kornilov Sergey A. , Roper Ryan T. , Cohen-Cline Hannah , Jade Kathleen , Smith Brett , Heath James R. , Diaz George , Goldman Jason D. , Magis Andrew T. , Hadlock Jennifer J.
Published: October 2020

Background

Data on the characteristics of COVID-19 patients disaggregated by race/ethnicity remain limited. We evaluated the sociodemographic and clinical characteristics of patients across racial/ethnic groups and assessed their associations with COVID-19 outcomes.

Methods

This retrospective cohort study examined 629,953 patients tested for SARS-CoV-2 in a large health system spanning California, Oregon, and Washington between March 1 and December 31, 2020. Sociodemographic and clinical characteristics were obtained from electronic health records. Odds of SARS-CoV-2 infection, COVID-19 hospitalization, and in-hospital death were assessed with multivariate logistic regression.

Results

570,298 patients with known race/ethnicity were tested for SARS-CoV-2, of whom 27.8% were non-White minorities. 54,645 individuals tested positive, with minorities representing 50.1%. Hispanics represented 34.3% of infections but only 13.4% of tests. While generally younger than White patients, Hispanics had higher rates of diabetes but fewer other comorbidities. 8,536 patients were hospitalized and 1,246 died, of whom 56.1% and 54.4% were non-White, respectively. Racial/ethnic distributions of outcomes across the health system tracked with state-level statistics. Increased odds of testing positive and hospitalization were associated with all minority races/ethnicities. Hispanic patients also exhibited increased morbidity, and Hispanic race/ethnicity was associated with in-hospital mortality (OR: 1.39 [95% CI: 1.14-1.70]).

Conclusion

Major healthcare disparities were evident, especially among Hispanics who tested positive at a higher rate, required excess hospitalization and mechanical ventilation, and had higher odds of in-hospital mortality despite younger age. Targeted, culturally-responsive interventions and equitable vaccine development and distribution are needed to address the increased risk of poorer COVID-19 outcomes among minority populations.

Key points

Racial/ethnic disparities are evident in the disaggregated characteristics of COVID-19 patients. Minority patients experience increased odds of SARS-CoV-2 infection and COVID-19 hospitalization. Hospitalized Hispanic patients presented with more severe illness, experienced increased morbidity, and faced increased mortality.
Direct cleavage of human NLRP1 by enteroviral 3C protease triggers inflammasome activation in airway epithelium
Authors: Robinson Kim S. , Sen Tan Kai , Thiam Teo Daniel Eng , Hui Ong Hsiao , Au Bijin , Lim Chrissie , Sheng Lew Tian , Jang Hann Justin Chu , Kwong Chow Vincent Tak , De Yun Wang , Zhong Franklin L. , Reversade Bruno
Published: October 2020

Viruses pose a constant threat to human health. As a result our innate immune system has evolved multiple strategies to detect the presence of intracellular viral ‘pathogen-associated molecular patterns’ (PAMPs) (1). The full repertoire of human immune sensors and their PAMP ligands are not completely understood. Here we report that human NLRP1 senses and is activated by 3C proteases (3Cpros) of enteroviruses. Mechanistically, 3Cpros cleave human NLRP1 at a single site immediately after its primate-specific PYRIN domain, leading to oligomerization of its C-terminal fragment. Expression of 3Cpros in primary human cells cause NLRP1-dependent ASC oligomerization, pyroptotic cell death and IL-1 secretion. Consistent with our observation that NLRP1 is the predominant endogenous inflammasome sensor in human airway epithelium, we find that its genetic deletion, or that of ASC, abrogates IL-18 secretion from rhinovirus (HRV)-infected primary human bronchial epithelial cells. Our findings identify the first cognate PAMP ligand for human NLRP1 and assign a new function for the NLRP1 inflammasome in human antiviral immunity and airway inflammation. These results challenge the widely held notion that viral proteases largely serve to disable host immune sensing, and suggest that the human NLRP1 inflammasome may be a therapeutic target to treat inflammatory airway diseases including asthma.

One Sentence Summary

Human NLRP1 is activated by enteroviral 3C proteases
High Throughput Volume Flow Cytometry (parallel-iLIFE) Resolves Mitochondrial Network On the Go
Authors: Kumar Prashant , Joshi Prakash , Basumatary Jigmi , Mondal Partha Pratim
Published: October 2020

Cell screening and viability studies are paramount to access cell morphology and intracellular molecular variations within large heterogeneous populations of cells. This forms the basis for diagnosis of infections, evaluating immunohistochemistry and routine histopathology. The proposed volume flow cytometry (also termed as, parallel Integrated Light-sheet imaging and flow-based enquiry (parallel-iLIFE)) is a powerful method that adds new capabilities (3D volume visualization, organelle-level resolution and multi-organelle screening) powered by light sheet based illumination. Unlike state-of-the-art point-illumination based imaging cytometry techniques, light sheet based parallel-iLIFE technique is capable of screening species with high throughput and near diffraction-limited resolution. The flow system was realized on a multichannel (Y-type) microfluidic chip that enables visualization of mitochondrial network of several cells in-parallel at a relatively high flow-rate of 2000nl/min. The calibration of system requires study of point emitters (fluorescent beads) at physiologically relevant flow-rates (50−2000nl/min) for determining flow-induced optical aberration in the system point spread function (PSF). Subsequently, recorded raw images and volumes were deconvolved with flow-variant PSF to reconstruct cellular mitochondrial network. High throughput investigation of HeLa cells were carried out at sub-cellular resolution in real-time and critical parameters (mitochondria count and size distribution, morphology and cell strain statistics) are determined on-the-go. These parameters determine the physiological state of cells and the changes in mitochondrial distribution over-time that may have consequences in disease diagnosis. The development of volume flow cytometry system (parallel-iLIFE) and its suitability to study sub-cellular components at high-throughput high-content capacity with organelle-level resolution may enable disease diagnosis on a single microfluidic chip.
DEBKS: A Tool to Detect Differentially Expressed Circular RNA
Authors: Liu Zelin , Ding Huiru , She Jianqi , Chen Chunhua , Zhang Weiguang , Yang Ence
Published: October 2020

Circular RNAs (circRNAs) are involved in various biological processes and in disease pathogenesis. However, only a small number of functional circRNAs have been identified among hundreds of thousands of circRNA species, partly because most current methods are based on circular junction counts and overlook the fact that circRNA is formed from the host gene by back-splicing (BS). To distinguish between expression originating from BS and that from the host gene, we present DEBKS, a software program to streamline the discovery of differential BS between two rRNA-depleted RNA sequencing (RNA-seq) sample groups. By applying real and simulated data and employing RT-qPCR for validation, we demonstrate that DEBKS is efficient and accurate in detecting circRNAs with differential BS events between paired and unpaired sample groups. DEBKS is available athttps://github.com/yangence/DEBKSas open-source software.
RNA regulates Glycolysis and Embryonic Stem Cell Differentiation via Enolase 1
Authors: Huppertz Ina , Perez-Perri Joel I. , Mantas Panagiotis , Sekaran Thileepan , Schwarzl Thomas , Dimitrova-Paternoga Lyudmila , Hennig Janosch , Neveu Pierre A. , Hentze Matthias W.
Published: October 2020

Cells must coordinate their metabolism and fate trajectories (1, 2), but the underlying mechanisms are only beginning to be discovered. To understand why the glycolytic enzyme enolase 1 (ENO1) binds RNA (3–6), we studied this phenomenon in vitro, in human cells, and during mouse embryonic stem cell differentiation. We find specific cellular RNA ligands that inhibit ENO1’s enzymatic activity in vitro. Increasing the concentration of these ligands in cultured cells inhibits glycolysis. We demonstrate that pluripotent stem cells expressing an ENO1 mutant that is hyper-inhibited by RNA are severely impaired in their glycolytic capacity and in endodermal differentiation, whereas cells with an RNA binding-deficient ENO1 mutant display disproportionately high endodermal marker expression. Our findings uncover ENO1 riboregulation as a novel form of metabolic control. They also describe an unprecedented mechanism involved in the regulation of stem cell differentiation.

One Sentence Summary

RNA directly regulates enzyme activity to control metabolism and stem cell fate
Mechanisms of scaffold-mediated microcompartment assembly and size-control
Authors: Mohajerani Farzaneh , Sayer Evan , Neil Christopher , Inlow Koe , Hagan Michael F.
Published: October 2020

This article describes a theoretical and computational study of the dynamical assembly of a protein shell around a complex consisting of many cargo molecules and long flexible scaffold molecules. Our study is motivated by bacterial microcompartments, which are proteinaceous organelles that assemble around a condensed droplet of enzymes and reactants. As in many examples of cytoplasmic liquid-liquid phase separation, condensation of the microcompartment interior cargo is driven by long flexible scaffold proteins that have weak multivalent interactions with the cargo. We describe a minimal model for the thermodynamics and dynamics of assembly of a protein shell around cargo and scaffold molecules, with scaffold-mediated cargo coalescence and encapsulation. Our results predict that the shell size, amount of encapsulated cargo, and assembly pathways depend sensitively on properties of the scaffold, including its length and valency of scaffold-cargo interactions. Moreover, the ability of self-assembling protein shells to change their size to accommodate scaffold molecules of different lengths depends crucially on whether the spontaneous curvature radius of the protein shell is smaller or larger than a characteristic elastic length scale of the shell. Beyond natural microcompartments, these results have important implications for synthetic biology efforts to target new molecules for encapsulation by microcompartments or viral shells. More broadly, the results elucidate how cells exploit coupling between self-assembly and liquid-liquid phase separation to organize their interiors.
Methyltransferase-like 3 modulates severe acute respiratory syndrome coronavirus-2 RNA N6-methyladenosine modification and replication
Authors: Zhang Xueyan , Hao Haojie , Ma Li , Zhang Yecheng , Hu Xiao , Chen Zhen , Liu Di , Yuan Jianhui , Hu Zhangli , Guan Wuxiang
Published: October 2020

The coronavirus disease 2019 pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is an ongoing global public crisis. Although viral RNA modification has been reported based on the transcriptome architecture, the types and functions of RNA modification are still unknown. In this study, we evaluated the roles of RNA N6-methyladenosine (m6A) modification in SARS-CoV-2. Our methylated RNA immunoprecipitation sequencing (MeRIP-Seq) analysis showed that SARS-CoV-2 RNA contained m6A modification. Moreover, SARS-CoV-2 infection not only increased the expression of methyltransferase-like 3 (METTL3) but also altered its distribution. Modification of METTL3 expression by short hairpin RNA or plasmid transfection for knockdown or overexpression, respectively, affected viral replication. Furthermore, the viral key protein RdRp interacted with METTL3, and METTL3 was distributed in both the nucleus and cytoplasm in the presence of RdRp. RdRp appeared to modulate the sumoylation and ubiquitination of METTL3 via an unknown mechanism. Taken together, our findings demonstrated that the host m6A modification complex interacted with viral proteins to modulate SARS-CoV-2 replication.
Phylogenetic Permulations: a statistically rigorous approach to measure confidence in associations between phenotypes and genetic elements in a phylogenetic context
Authors: Saputra Elysia , Kowalczyk Amanda , Cusick Luisa , Clark Nathan , Chikina Maria
Published: October 2020

The wealth of high-quality genomes for numerous species has motivated many investigations into the genetic underpinnings of phenotypes. Comparative genomics methods approach this task by identifying convergent shifts at the genetic level that are associated with traits evolving convergently across independent lineages. However, these methods have complex statistical behaviors that are influenced by non-trivial and oftentimes unknown confounding factors. Consequently, using standard statistical analyses in interpreting the outputs of these methods leads to potentially inaccurate conclusions. Here, we introduce phylogenetic permulations, a novel statistical strategy that combines phylogenetic simulations and permutations to calculate accurate, unbiased p-values from phylogenetic methods. Permulations construct the null expectation for p-values from a given phylogenetic method by empirically generating null phenotypes. Subsequently, empirical p-values that capture the true statistical confidence given the correlation structure in the data are directly calculated based on the empirical null expectation. We examine the performance of permulation methods by analyzing both binary and continuous phenotypes, including marine, subterranean, and long-lived large-bodied mammal phenotypes. Our results reveal that permulations improve the statistical power of phylogenetic analyses and correctly calibrate statements of confidence in rejecting complex null distributions while maintaining or improving the enrichment of known functions related to the phenotype. We also find that permulations refine pathway enrichment analyses by correcting for non-independence in gene ranks. Our results demonstrate that permulations are a powerful tool for improving statistical confidence in the conclusions of phylogenetic analysis when the parametric null is unknown.
RNA-binding protein Elavl1/HuR is required for maintenance of cranial neural crest specification
Authors: Hutchins Erica J. , Gandhi Shashank , Chacon Jose , Piacentino Michael L. , Bronner Marianne E.
Published: October 2020

While neural crest development is known to be transcriptionally controlled via sequential activation of gene regulatory networks (GRNs), recent evidence increasingly implicates a role for post-transcriptional regulation in modulating the output of these regulatory circuits. Using available single cell RNA-sequencing datasets from avian embryos to identify potential post-transcriptional regulators, we found thatElavl1, which encodes for an RNA-binding protein with roles in transcript stability, was enriched in the premigratory cranial neural crest. Perturbation of Elavl1 resulted in premature neural crest delamination from the neural tube as well as significant reduction in transcripts associated with the neural crest specification GRN, phenotypes that are also observed with downregulation of the canonical Wnt inhibitorDraxin. ThatDraxinis the primary target for stabilization by Elavl1 during cranial neural crest specification was shown by RNA-sequencing, RNA-immunoprecipitation, RNA decay measurement and proximity ligation assays, further supporting the idea that the downregulation of neural crest specifier expression upon Elavl1 knockdown was largely due to loss ofDraxin. Importantly, exogenous Draxin rescued cranial neural crest specification defects observed with Elavl1 knockdown. Thus, Elavl1 plays a critical a role in the maintenance of cranial neural crest specification viaDraxinmRNA stabilization. Together, these data highlight an important intersection of post-transcriptional regulation with modulation of the neural crest specification GRN.
Climbing up and down binding landscapes: a high-throughput study of mutational effects in homologous protein-protein complexes
Authors: Heyne Michael , Shirian Jason , Cohen Itay , Peleg Yoav , Radisky Evette S. , Papo Niv , Shifman Julia M.
Published: October 2020

Each protein-protein interaction (PPI) has evolved to possess binding affinity that is compatible with its cellular function. As such, cognate enzyme/inhibitor interactions frequently exhibit very high binding affinities, while structurally similar non-cognate PPIs possess substantially weaker binding affinities. To understand how slight differences in sequence and structure could lead to drastic changes in PPI binding free energy (ΔΔGbind), we study three homologous PPIs that span nine orders of magnitude in binding affinity and involve a serine protease interacting with an inhibitor BPTI. Using state-of-the-art methodology that combines protein randomization and affinity sorting coupled to next-generation sequencing and data normalization, we report quantitative binding landscapes consisting of ΔΔGbindvalues for the three PPIs, gleaned from tens of thousands of single and double mutations in the BPTI binding interface. We demonstrate that the three homologous PPIs possess drastically different binding landscapes and lie at different points in respect to the landscape maximum. Furthermore, the three PPIs demonstrate distinct patterns of coupling energies between two simultaneous mutations that depend not only on positions involved but also on the nature of the mutation. Interestingly, we find that in all three PPIs positive epistasis is frequently observed at hot-spot positions where mutations lead to loss of high affinity, while conversely negative epistasis is observed at cold-spot positions, where mutations lead to affinity enhancement. The new insights on PPI evolution revealed in this study will be invaluable in understanding evolution of other biological complexes and can greatly facilitate design of novel high-affinity protein inhibitors.

Significance

Protein-protein interactions (PPIs) have evolved to display binding affinities that can support their function. As such, cognate and non-cognate PPIs could be highly similar structurally but exhibit huge differences in binding affinities. To understand this phenomenon, we studied the effect of tens of thousands of single and double mutations on binding affinity of three homologous protease-inhibitor complexes. We show that binding landscapes of the three complexes are strikingly different and depend on the PPI evolutionary optimality. We observe different patterns of couplings between mutations for the three PPIs with negative and positive epistasis appearing most frequently at hot-spot and cold-spot positions, respectively. The evolutionary trends observed here are likely to be universal to all biological complexes in the cell.
Expression analysis of colon adenocarcinoma in the South Indian population reveals novel signals of pathogenesis
Authors: Ariyannur Prasanth S. , Joy Reenu Anne , Menon Veena , Paulose Roopa Rachael , Pavithran Keechilat , Vasudevan Damodaran M.
Published: October 2020

High throughput somatic expression analyses of colon adenocarcinoma conducted so far were mostly in the western population, and no major studies are currently available in the Indian population. We have performed Nanostring PanCancer pathway panel assay in Stage II colon cancer (n = 11) and compared against normal colon tissues (n = 4). Differentially expressed (DE) genes were identified and superimposed on the Cancer Genome Atlas (TCGA) data, from the Genome Expression Profiling Interactive Analysis (GEPIA) and Tumor Immune Estimation Resource (TIMER).83 out of 730 genes were significantly different (p-value < 0.01), 19 of which had a fold-change |FC(log2)| ≥ 2. A comparison of these signals on TCGA COAD data revealed four common (MET, MCM2, ETV4, and MMP7) and15 uncommon genes. On group comparison, ETV4 expression was significantly higher in microsatellite stable (MSS). Significant DE genes, unique in the study, were INHBA, COL1A1, COL11A1, COMP, SFRP4, and SPP1, which were clustered in STRING.db network analysis and correlated with tumor-infiltrating immune cells in TIMER.MMR functions of colon cancer pathogenesis in India may be differentiated by validating the somatic expression of most common genes identified in the study.
How do neuroglial cells respond to ultrasound induced cavitation?
Authors: Wrede Alex H. , Luo Jie , Montazami Reza , Kanthasamy Anumantha , Hashemi Nicole N.
Published: October 2020

Reactive astrocytes are known to play a vital role in the overall response of the brain during a traumatic brain injury (TBI). Modern studies have speculated the existence of cavitation in the skull during a TBI, which has alarming potential to cause detrimental damages. Previous studies have confirmed the upregulation of various harmful genes in neurodegenerative diseases. Studying the longitudinal presence of these harmful genes in response to cavitation allows for optimized understanding and treatment methods in cavitation exposure. We seek to characterize the longitudinal genetic expression levels that astrocytes exhibit after exposure to cavitation and further elucidate the startling presence of cranial cavitation. Astrocytic expression levels of various common genes that have been documented in TBI research are our target of interest, like, TNFα, IL-1β, and NOS1. Results summarize specific gene trends from 1-48 hours after cavitation. Our data concludes that maximum expression is not consistently exhibited immediately after cavitation exposure, and most genes have individualized genetic trends. IL-1β shows a decreasing expression over 48 hours, and TNFα shows upregulation until the 6 hour time point but then begins to decrease in expression. The upregulation of NOS1 has been documented in neurodegenerative diseases, like Alzheimer’s and Parkinson’s disease. This study has shown a consistent upregulation in NOS1 expression from 0-48 hours. These results postulate a possible linkage between cavitation damage and neurodegenerative diseases. This analysis also provides novelty in optimizing treatments for astrocytic function post-TBI and legitimizing the concern of cranial cavitation existence. These results add motivation for future studies of cavitation elimination or minimization via advanced helmet and airbag engineering.
Chemotherapy response prediction with diffuser elapser network
Authors: Koyuncu Batuhan , Melek Ahmet , Yilmaz Defne , Tuzer Mert , Unlu Mehmet Burcin
Published: October 2020

In solid tumors, elevated fluid pressure and inadequate blood perfusion resulting from unbalanced angiogenesis are the prominent reasons for the ineffective drug delivery inside tumors. To normalize the heterogeneous and tortuous tumor vessel structure, antiangiogenic treatment is an effective approach. Additionally, the combined therapy of antiangiogenic agents and chemotherapy drugs has shown promising effects on enhanced drug delivery. However, the need to find the appropriate scheduling and dosages of the combination therapy is one of the main problems in anticancer therapy. Our study aims to generate a realistic response to the treatment schedule, making it possible for future works to use these patient-specific responses to decide on the optimal starting time and dosages of cytotoxic drug treatment. Our dataset is based on our previous in-silico model with a framework for the tumor microenvironment, consisting of a tumor layer, vasculature network, interstitial fluid pressure, and drug diffusion maps. In this regard, the chemotherapy response prediction problem is discussed in the study, putting forth a proof-of-concept for deep learning models to capture the tumor growth and drug response behaviors simultaneously. The proposed model utilizes multiple convolutional neural network submodels to predict future tumor microenvironment maps considering the effects of ongoing treatment. Since the model has the task of predicting future tumor microenvironment maps, we use two image quality evaluation metrics, which are structural similarity and peak signal-to-noise ratio, to evaluate model performance. We track tumor cell density values of ground truth and predicted tumor microenvironments. The model predicts tumor microenvironment maps seven days ahead with the average structural similarity score of 0.973 and the average peak signal ratio of 35.41 in the test set. It also predicts tumor cell density at the end day of 7 with the mean absolute percentage error of 2.292 ± 1.820.

Author summary

The disorganized structure and leakiness of tumor vessels induce the inadequate blood supply and high fluid pressure within tumors. These features of the tumor microenvironment, identified as delivery barriers, lead to an insufficient amount of drugs to reach the interior parts of tumors. It is observed that the use of anti-vascular drugs makes the structure and function of the tumor vascular system more normal. Moreover, the combination of these drugs with cytotoxic agents provides favorable results with increased treatment response. But, it is also important to adjust the treatment schedule properly. In this regard, we build a deep learning model, designed to examine the tumor response with the ongoing treatment schedule. Our study suggests that deep learning models can be used to predict tumor growth and drug response in the scheduling of cytotoxic drugs.
Characterisation of growth plate dynamics in murine models of osteoarthritis
Authors: Samvelyan Hasmik J. , Madi Kamel , Törnqvist Anna E. , Javaheri Behzad , Staines Katherine A.
Published: October 2020

Background

The purpose of this study was to investigate growth plate dynamics in surgical and loading murine models of osteoarthritis, to understand whether abnormalities in these dynamics predict osteoarthritis vulnerability.

Methods

8-week-old C57BL/6 male mice underwent destabilisation of medial meniscus (DMM) (n =8) surgery in right knee joints. Contralateral left knee joints had no intervention (controls). In 16-week-old C57BL/6 male mice (n= 6), osteoarthritis was induced using non-invasive mechanical loading of right knee joints with peak force of 11N. Non-loaded left knee joints were internal controls. Chondrocyte transiency in tibial articular cartilage and growth plate was confirmed by histology and immunohistochemistry. Tibial subchondral bone parameters were measured using microCT and correlated to 3D GP bridging analysis.

Results

Higher expression of chondrocyte hypertrophy markers; Col10a1 and MMP13 were observed in tibial articular cartilage chondrocytes of DMM and loaded mice. In tibial growth plate, Col10a1 and MMP13 expressions were widely dispersed in a significantly enlarged zones of proliferative and hypertrophic chondrocytes in DMM (p=0.002 andp<0.0001, respectively) and loaded (bothp<0.0001) tibiae of mice compared to their controls. 3D quantification revealed enriched growth plate bridging and higher bridge densities in medial compared to lateral tibiae of DMM and loaded knee joints of the mice. Growth plate dynamics were associated with higher subchondral bone volume fraction (BV/TV; %) in medial tibiae of DMM and loaded knee joints and epiphyseal trabecular bone volume fraction in medial tibiae of loaded knee joints.

Conclusions

The results confirm articular cartilage chondrocyte transiency in a surgical and loaded murine model of osteoarthritis. Herein, we reveal for the first time spatial variation of growth plate bridging in surgical and loaded osteoarthritis models and how these may contribute to anatomical variation in vulnerability of osteoarthritis development.
Ancient DNA from Guam and the Peopling of the Pacific
Authors: Pugach Irina , Hübner Alexander , Hung Hsiao-chun , Meyer Matthias , Carson Mike T. , Stoneking Mark
Published: October 2020

Humans reached the Mariana Islands in the western Pacific by ~3500 years ago, contemporaneous with or even earlier than the initial peopling of Polynesia. They crossed more than 2000 km of open ocean to get there, whereas voyages of similar length did not occur anywhere else until more than 2000 years later. Yet, the settlement of Polynesia has received far more attention than the settlement of the Marianas. There is uncertainty over both the origin of the first colonizers of the Marianas (with different lines of evidence suggesting variously the Philippines, Indonesia, New Guinea, or the Bismarck Archipelago) as well as what, if any, relationship they might have had with the first colonizers of Polynesia. To address these questions, we obtained ancient DNA data from two skeletons from the Ritidian Beach Cave site in northern Guam, dating to ~2200 years ago. Analyses of complete mtDNA genome sequences and genome-wide SNP data strongly support ancestry from the Philippines, in agreement with some interpretations of the linguistic and archaeological evidence, but in contradiction to results based on computer simulations of sea voyaging. We also find a close link between the ancient Guam skeletons and early Lapita individuals from Vanuatu and Tonga, suggesting that the Marianas and Polynesia were colonized from the same source population, and raising the possibility that the Marianas played a role in the eventual settlement of Polynesia.

Significance Statement

We know far more about the settlement of Polynesia than we do about the settlement of the Mariana Islands in the western Pacific. There is debate over where people came from to get to the Marianas, with various lines of evidence pointing to the Philippines, Indonesia, New Guinea, or the Bismarck Archipelago, as well as uncertainty over how the ancestors of the present Mariana Islanders, the Chamorro, might be related to Polynesians. We analyzed ancient DNA from Guam, from two skeletons dating to ~2200 years ago, and found that their ancestry is linked to the Philippines. Moreover, they are closely-related to ancient Polynesians from Vanuatu and Tonga, suggesting that the early Mariana Islanders may have been involved in the colonization of Polynesia.
Structural characterization of HIV-1 matrix mutants implicated in envelope incorporation
Authors: Eastep Gunnar N. , Ghanam Ruba H. , Green Todd J. , Saad Jamil S.
Published: October 2020

During the late phase of HIV-1 infection, viral Gag polyproteins are targeted to the plasma membrane (PM) for assembly. Gag localization at the PM is a prerequisite for the incorporation of the envelope protein (Env) into budding particles. Gag assembly and Env incorporation are mediated by the N-terminal myristoylated matrix (MA) domain of Gag. Nonconservative mutations in the trimer interface of MA (A45E, T70R, and L75G) were found to impair Env incorporation and infectivity, leading to the hypothesis that MA trimerization is an obligatory step for Env incorporation. Conversely, Env incorporation can be rescued by a compensatory mutation in the MA trimer interface (Q63R). The impact of these MA mutations on the structure and trimerization properties of MA is not known. In this study, we employed NMR spectroscopy, x-ray crystallography, and sedimentation techniques to characterize the structure and trimerization properties of HIV-1 MA A45E, Q63R, T70R, and L75G mutant proteins. NMR data revealed that these point mutations did not alter the overall structure and folding of MA but caused minor structural perturbations in the trimer interface. Analytical ultracentrifugation data indicated that mutations had a minimal effect on the MA monomer–trimer equilibrium. The high-resolution x-ray structure of the unmyristoylated MA Q63R protein revealed hydrogen bonding between the side chains of Arg-63 and Ser-67 located in the center of the trimer interface, providing the first structural evidence for a stabilization of the trimer form. These findings advance our knowledge of the interplay of MA trimerization and Env incorporation into HIV-1 particles.
The oncogenic function of PLAGL2 is mediated via specific target genes through a Wnt-independent mechanism in colorectal cancer
Authors: Fischer Anthony D. , Veronese Paniagua Daniel A. , Swaminathan Shriya , Kashima Hajime , Rubin Deborah C. , Madison Blair B.
Published: October 2020

Colorectal cancer (CRC) tumorigenesis and progression are linked to common oncogenic mutations, especially in the tumor suppressorAPC, whose loss triggers the deregulation of TCF4/β-Catenin activity. CRC tumorigenesis is also driven by multiple epi-mutational modifiers, such as transcriptional regulators. We describe the common (and near-universal) activation of the zinc finger transcription factor and Let-7 target PLAGL2 in CRC and find that it is a key driver of intestinal epithelial transformation. PLAGL2 drives proliferation, cell cycle progression, and anchorage-independent growth in CRC cell lines and non-transformed intestinal cells. Investigating effects of PLAGL2 on downstream pathways revealed very modest effects on canonical Wnt signaling. Alternatively, we find pronounced effects on the direct PLAGL2 target genesIGF2,a fetal growth factor, andASCL2, an intestinal stem cell-specific bHLH transcription factor. Inactivation of PLAGL2 in CRC cell lines has pronounced effects on ASCL2 reporter activity. Furthermore, ASCL2 expression can partially rescue deficits of proliferation and cell cycle progression caused by depletion of PLAGL2 in CRC cell lines. Thus, the oncogenic effects of PLAGL2 appear to be mediated via core stem cell and onco-fetal pathways, with minimal effects on downstream Wnt signaling.