bluuebunny/crossref_metadata_2025 huggingface dataset:
Therapy-induced transdifferentiation promotes glioma growth independent of EGFR signaling
Authors: Oh Hwanhee , Hwang Inah , Wu Lingxiang , Cao Dongqing , Yao Jun , Ying Haoqiang , Li Jian Yi , Yao Yu , Hu Baoli , Wang Qianghu , Zheng Hongwu , Paik Jihye
Published: June 2020

Epidermal growth factor receptor (EGFR) is frequently amplified, mutated and overexpressed in malignant gliomas. Yet the EGFR-targeted therapies have thus far produced only marginal clinical response, and the underlying mechanism remains poorly understood. Through analyses of an inducible oncogenic EGFR-driven glioma mouse model system, our current study reveals a small population of glioma cells that can evade therapy-initiated apoptosis and potentiate relapse development by adopting a mesenchymal-like phenotypic state that no longer depends on oncogenic EGFR signaling. Transcriptome analyses of proximal and distal treatment responses further identify TGFβ/YAP/Slug signaling cascade activation as major regulatory mechanism that promotes therapy-induced glioma mesenchymal lineage transdifferentiation. Following anti-EGFR treatment, the TGFβ secreted from the stressed glioma cells acts to promote YAP nuclear translocation and activation, which subsequently stimulates upregulation of the pro-mesenchymal transcriptional factor Slug and then glioma lineage transdifferentiation towards a stable therapy-refractory state. Blockade of this adaptive response through enforced dominant negative YAP expression significantly delayed anti-EGFR relapse and significantly prolonged animal survival. Together, our findings shed new insight into EGFR-targeted therapy resistance and suggest that combinatorial therapies of targeting both EGFR and mechanisms underlying glioma lineage transdifferentiation could ultimately lead to deeper and more durable responses.

Significance

This study demonstrates that molecular reprogramming and lineage transdifferentiation underlie anti-EGFR therapy resistance and is clinically relevant to the development of new combinatorial targeting strategies against malignant gliomas carrying aberrant EGFR signaling.
Highly multiplexed oligonucleotide probe-ligation testing enables efficient extraction-free SARS-CoV-2 detection and viral genotyping
Authors: Credle Joel J. , Robinson Matthew L , Gunn Jonathan , Monaco Daniel , Sie Brandon , Tchir Alexandra , Hardick Justin , Zheng Xuwen , Shaw-Saliba Kathryn , Rothman Richard E. , Eshleman Susan H. , Pekosz Andrew , Hansen Kasper , Mostafa Heba , Steinegger Martin , Larman H. Benjamin
Published: June 2020

The emergence of SARS-CoV-2 has caused the current COVID-19 pandemic with catastrophic societal impact. Because many individuals shed virus for days before symptom onset, and many show mild or no symptoms, an emergent and unprecedented need exists for development and deployment of sensitive and high throughput molecular diagnostic tests. RNA-mediated oligonucleotide Annealing Selection and Ligation with next generation DNA sequencing (RASL-seq) is a highly multiplexed technology for targeted analysis of polyadenylated mRNA, which incorporates sample barcoding for massively parallel analyses. Here we present a more generalized method, capture RASL-seq (“cRASL-seq”), which enables analysis of any targeted pathogen-(and/or host-) associated RNA molecules. cRASL-seq enables highly sensitive (down to ∼1-100 pfu/ml or cfu/ml) and highly multiplexed (up to ∼10,000 target sequences) detection of pathogens. Importantly, cRASL-seq analysis of COVID-19 patient nasopharyngeal (NP) swab specimens does not involve nucleic acid extraction or reverse transcription, steps that have caused testing bottlenecks associated with other assays. Our simplified workflow additionally enables the direct and efficient genotyping of selected, informative SARS-CoV-2 polymorphisms across the entire genome, which can be used for enhanced characterization of transmission chains at population scale and detection of viral clades with higher or lower virulence. Given its extremely low per-sample cost, simple and automatable protocol and analytics, probe panel modularity, and massive scalability, we propose that cRASL-seq testing is a powerful new surveillance technology with the potential to help mitigate the current pandemic and prevent similar public health crises.
Egr1loss-of-function promotes beige adipocyte differentiation and activation specifically in inguinal subcutaneous white adipose tissue
Authors: Bléher Marianne , Meshko Berbang , Gergondey Rachel , Kovacs Yoann , Duprez Delphine , L’Honoré Aurore , Havis Emmanuelle
Published: June 2020

Exercise, cold exposure and fasting lead to the differentiation of inducible-brown adipocytes, called beige adipocytes, within white adipose tissue and have beneficial effects on fat burning and metabolism, through heat production. This browning process is associated with an increased expression of the key thermogenic mitochondrial uncoupling protein 1, Ucp1. Egr1 transcription factor has been described as a regulator of white and beige differentiation programs, and Egr1 depletion is associated with a spontaneous increase of subcutaneous white adipose tissue browning, in absence of external stimulation. Here, we demonstrate thatEgr1mutant mice exhibit a restrainedUcp1expression specifically increased in subcutaneous fat, resulting in a metabolic shift to a more brown-like, oxidative metabolism, which was not observed in other fat depots. In addition,Egr1is necessary and sufficient to promote white and alter beige adipocyte differentiation of mouse stem cells. These results suggest that modulation ofEgr1expression could represent a promising therapeutic strategy to increase energy expenditure and to restrain obesity-associated metabolic disorders.
ATP dependent DNA transport within cohesin: Scc2 clamps DNA on top of engaged heads while Scc3 promotes entrapment within the SMC-kleisin ring
Authors: Collier James E , Lee Byung-Gil , Roig Maurici B , Yatskevich Stanislav , Petela Naomi J , Metson Jean , Voulgaris Menelaos , Llamazares Andres Gonzalez , Löwe Jan , Nasmyth Kim A
Published: June 2020

In addition to extruding DNA loops, cohesin entraps within its SMC-kleisin ring (S-K) individual DNAs during G1 and sister DNAs during S-phase. All three activities require related hook-shaped proteins called Scc2 and Scc3. Using thiol-specific crosslinking we provide rigorous proof of entrapment activity in vitro. Scc2 alone promotes entrapment of DNAs in the E-S and E-K compartments, between ATP-bound engaged heads and the SMC hinge and associated kleisin, respectively. This does not require ATP hydrolysis nor is it accompanied by entrapment within S-K rings, which is a slower process requiring Scc3. Cryo-EM reveals that DNAs transported into E-S/E-K compartments are “clamped” in a sub-compartment created by Scc2’s association with engaged heads whose coiled coils are folded around their elbow. We suggest that clamping may be a recurrent feature of cohesin complexes active in loop extrusion and that this conformation precedes the S-K entrapment required for sister chromatid cohesion.
Ozone therapy for patients with COVID-19 pneumonia: a Quasi-Randomized Controlled Trial
Authors: Hernández Alberto , Viñals Montserrat , Pablos Asunción , Vilás Francisco , Papadakos Peter J , Wijeysundera Duminda , Bergese Sergio D. , Vives Marc
Published: June 2020

Background

There is still no specific treatment strategies for COVID-19 other than supportive management. The potential biological benefits of ozonated autohemotherapy include reduced tissue hypoxia, decreased hypercoagulability, modulated immune function with inhibition of inflammatory mediators, improved phagocytic function, and impaired viral replication.

Objective

To determine the impact of the use of ozonated blood on time to clinical improvement in patients with severe COVID-19 pneumonia.

Design

A Quasi-Randomized Controlled Trial determined by admittance to the hospital based on bed availability.

Setting

Internal Medicine ward at Policlinica Ibiza Hospital, Spain.

Participants

Eighteen patients with COVID-19 infection (laboratory confirmed) severe pneumonia admitted to hospital between 20th March and 19th April 2020. The mean age of the cohort was 68 years-old and 72% (n=13) were male.

Intervention

Patients admitted to the hospital during the study period were pre-randomized to different beds based on bed availability. Depending on the bed the patient was admitted, the treatment was ozone autohemotherapy or standard treatment. Patients in the therapy arm received ozonated blood twice daily starting on the day of admission for a median of four days. Each treatment involved administration of 200 mL autologous whole blood enriched with 200 mL of oxygen-ozone mixture with a 40 μg/mL ozone concentration.

Main Outcomes

The primary outcome was time from hospital admission to clinical improvement, which was defined as either hospital discharge or a two-point improvement in clinical status measured on a six-point ordinal scale. Secondary outcomes were clinical improvement measured on the 7th, 14th and 28th day after admission, as well as time to a two-fold reduction in concentrations of C-reactive protein, ferritin, D-dimer and lactate dehydrogenase.

Results

Nine patients (50%) received ozonated autohemotherapy beginning on the day of admission. Ozonated autohemotherapy was associated with shorter time to clinical improvement (median [IQR]), 7 days [6-10] vs 28 days [8-31], p=0.04) and better outcomes at 14-days (88.8% vs 33.3%, p=0.01). In risk-adjusted analyses, ozonated autohemotherapy was associated with a shorter mean time to clinical improvement (−11.3 days, p=0.04, 95% CI −22.25 to −0.42).

Conclusion

Ozonated autohemotherapy was associated with a significantly shorter time to clinical improvement in this quasi-randomized controlled trial. Given the small sample size and study design, these results require evaluation in larger randomized controlled trials.
Vimentin is Required for Tumor Progression and Metastasis in a Mouse Model of Non-Small Cell Lung Cancer
Authors: Berr Alexandra L. , Wiese Kristin , dos Santos Gimena , Davis Jennifer M. , Koch Clarissa M. , Anekalla Kishore R. , Kidd Martha , Cheng Yuan , Hu Yuan-Shih , Ridge Karen M.
Published: June 2020

Vimentin, a type III intermediate filament, is highly expressed in aggressive epithelial cancers and is associated with increased rates of metastasis. We show that vimentin is causally required for lung cancer metastasis using a genetic mouse model of lung adenocarcinoma (LSL-KrasG12D;Tp53fl/fl, termedKPV+/+) crossed with vimentin-null mice (thereby creatingKPV−/−mice). BothKPV+/+andKPV−/−mice developed lung tumors, yetKPV−/−mice had delayed tumorigenesis and prolonged survival.KPV+/+cells implanted in the flank metastasized to the lung whileKPV−/−cells did not, providing additional evidence that vimentin is required for metastasis. Differential expression analysis of RNA-seq data demonstrated thatKPV−/−cells had suppressed expression of genes that drive epithelial-to-mesenchymal transition, migration, and invasion, processes that are critical to the metastatic cascade. Integrative metabolomic and transcriptomic analysis revealed altered glutaminolysis, withKPV−/−cells accumulating glutathione, leading to impaired cell motility in response to oxidative stress. Together, these results show that loss of vimentin impairs epithelial-to-mesenchymal transition and regulation of the oxidative stress response, resulting in decreased metastasis in murine lung adenocarcinoma.
The Arabidopsis NRT1/PTR FAMILY Protein NPF7.3/NRT1.5 is an Indole-3-butyric Acid Transporter Involved in Root Gravitropism
Authors: Watanabe Shunsuke , Takahashi Naoki , Kanno Yuri , Suzuki Hiromi , Aoi Yuki , Takeda-Kamiya Noriko , Toyooka Kiminori , Kasahara Hiroyuki , Hayashi Ken-Ichiro , Umeda Masaaki , Seo Mitsunori
Published: June 2020

Active membrane transport of plant hormones and their related compounds is an essential process that determines the distribution of the compounds within plant tissues and, hence, regulates various physiological events. Here, we report that the Arabidopsis NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER FAMILY 7.3 (NPF7.3) protein functions as a transporter of indole-3-butyric acid (IBA), a precursor of the major endogenous auxin indole-3-acetic acid (IAA). When expressed in yeast, NPF7.3 mediated cellular IBA uptake. Loss-of-functionnpf7.3mutants showed defective root gravitropism with reduced IBA levels and auxin responses. Nevertheless, the phenotype was restored by exogenous application of IAA but not by IBA treatment.NPF7.3was expressed in pericycle cells and the root tip region including root cap cells of primary roots where the IBA-to-IAA conversion occurs. Our findings indicate that NPF7.3-mediated IBA uptake into specific cells is required for the generation of appropriate auxin gradients within root tissues.
Aster repulsion drives local ordering in an active system
Authors: de-Carvalho Jorge , Tlili Sham , Hufnagel Lars , Saunders Timothy E. , Telley Ivo A.
Published: June 2020

Biological systems are a form of active matter, which often undergo rapid changes in their material state,e.g. liquid to solid transitions. Yet, such systems often also display remarkably ordered structures. It remains an open question as to how local ordering occurs within active systems. Here, we utilise the rapid early development ofDrosophila melanogasterembryos to uncover the mechanisms driving short-ranged order. During syncytial stage, nuclei synchronously divide (within a single cell defined by the ellipsoidal eggshell) for nine cycles after which most of the nuclei reach the cell cortex. Despite the rapid nuclear division and repositioning, the spatial pattern of nuclei at the cortex is highly regular. Such precision is important for subsequent cellularisation and morphological transformations. We utiliseex vivoexplants and mutant embryos to reveal that microtubule asters ensure the regular distribution and maintenance of nuclear positions in the embryo. For large networks of nuclei, such as in the embryo, we predict – and experimentally verify – the formation of force chains. Theex vivoextracts enabled us to deduce the force potential between single asters. We use this to predict how the nuclear division axis orientation in smallex vivosystems depend on aster number. Finally, we demonstrate that, upon nucleus removal from the cortex, microtubule force potentials can reorient subsequent nuclear divisions to minimise the size of pattern defects. Overall, we show that short-ranged microtubule-mediated repulsive interactions between asters can drive ordering within an active system.
Structural basis of GIRK2 channel modulation by cholesterol and PIP2
Authors: Mathiharan Yamuna Kalyani , Glaaser Ian W. , Zhao Yulin , Robertson Michael J. , Skiniotis Georgios , Slesinger Paul A.
Published: June 2020

G protein-gated inwardly rectifying potassium (GIRK) channels play important roles in controlling cellular excitability in the heart and brain. While structural data begin to unravel the molecular basis for G protein and alcohol dependent activation of GIRK channels, little is known about the modulation by cholesterol. Here, we present cryo-electron microscopy (cryoEM) structures of GIRK2 in the presence and absence of the cholesterol analog cholesteryl hemisuccinate (CHS), and PIP2. The structures and their comparison reveal that CHS binds near PIP2in lipid-facing hydrophobic pockets of the transmembrane domain (TMD). CHS potentiates the effects of PIP2, which stabilizes the inter-domain region and promotes the engagement of the cytoplasmic domain (CTD) onto the transmembrane region. The results suggest that CHS acts as a positive allosteric modulator and identify novel therapeutic sites for modulating GIRK channels in the brain.
Adipose Tissue is a Critical Regulator of Osteoarthritis
Authors: Collins Kelsey H. , Lenz Kristin L. , Pollitt Eleanor N. , Ferguson Daniel , Hutson Irina , Springer Luke E. , Oestreich Arin K. , Tang Ruhang , Choi Yun-Rak , Meyer Gretchen A. , Teitelbaum Steven L. , Pham Christine T.N. , Harris Charles A. , Guilak Farshid
Published: June 2020

Osteoarthritis (OA), the leading cause of pain and disability worldwide, disproportionally affects obese individuals. The mechanisms by which adipose tissue leads to the onset and progression of OA are unclear due to the complex interactions between the metabolic, biomechanical, and inflammatory factors that accompany obesity. We used a murine model of lipodystrophy (LD) to examine the direct contribution of adipose tissue to OA. Knee joints of LD mice were protected from spontaneous or post-traumatic OA, on either a chow and high fat diet, despite similar body weight and the presence of systemic inflammation. These findings indicate that adipose tissue itself plays a critical role in the pathophysiology of OA. Susceptibility to post-traumatic OA was reintroduced into LD mice using implantation of adipose tissue derived from wildtype animals or mouse embryonic fibroblasts that undergo spontaneous adipogenesis, implicating paracrine signaling from fat, rather than body weight, as a critical mediator of joint degeneration.
Akt is required for artery formation during embryonic vascular development
Authors: Zhou Wenping , Ristori Emma , He Liqun , Ghersi Joey J , Mehta Sameet , Zhang Rong , Betsholtz Christer , Nicoli Stefania , Sessa William C.
Published: June 2020

One of the first events in the development of the cardiovascular system is morphogenesis of the main embryonic artery, the dorsal aorta (DA). The DA forms via a conserved genetic process mediated by the migration, specification, and organization of endothelial progenitor cells into a distinct arterial lineage and vessel type. Several angiogenic factors activate different signaling pathways to control DA formation, however the physiological relevance of distinct kinases in this complex process remains unclear. Here, we identify the role of Akt during early vascular development by generating mutant zebrafish lines that lack expression ofaktisoforms. Live cell imaging coupled with single cell RNA sequencing ofaktmutants reveal that Akt is required for proper development of the DA by sustaining arterial cell progenitor specification and segregation. Mechanistically, inhibition of active FOXO inaktmutants rescues impaired arterial development but not the expression of arterial markers, whereas Notch activation rescues arterial marker expression. Our work suggests that Akt activity is critical for early artery development, in part via FOXO and Notch-mediated regulation.
Multiple competing RNA structures dynamically control alternative splicing in human ATE1 gene
Authors: Kalinina Marina , Skvortsov Dmitry , Kalmykova Svetlana , Ivanov Timofei , Dontsova Olga , Pervouchine Dmitri D.
Published: June 2020

The mammalianAte1gene encodes an arginyl transferase enzyme, which is essential for embryogenesis, male meiosis, and regulation of the cytoskeleton. Reduced levels ofAte1are associated with malignant transformations and serve as a prognostic indicator of prostate cancer metastasis. The tumor suppressor function ofAte1depends on the inclusion of one of the two mutually exclusive exons (MXE), exons 7a and 7b. Here, we report that the molecular mechanism underlying MXE splicing in Ate1 involves five conserved regulatory intronic elements R1–R5, of which R1 and R4 compete for base pairing with R3, while R2 and R5 form an ultra-long-range RNA structure spanning 30 Kb. In minigenes, single and double mutations that disrupt base pairings in R1R3 and R3R4 lead to the loss of MXE splicing, while compensatory triple mutations that restore the RNA structure also revert splicing to that of the wild type. Blocking the competing base pairings by locked nucleic acid (LNA)/DNA mixmers complementary to R3 leads to the loss of MXE splicing, while the disruption of the ultra-long-range R2R5 interaction changes the ratio of mutually exclusive isoforms in the endogenousAte1pre-mRNA. The upstream exon 7a becomes more included than the downstream exon 7b in response to RNA Pol II slowdown, however it fails to do so when the ultra-long-range R2R5 interaction is disrupted. In sum, we demonstrated that mutually exclusive splicing inAte1is controlled by two independent, dynamically interacting and functionally distinct RNA structure modules. The molecular mechanism proposed here opens new horizons for the development of therapeutic solutions, including antisense correction of splicing.
Per-sample standardization and asymmetric winsorization lead to accurate clustering of RNA-seq expression profiles
Authors: Risso Davide , Pagnotta Stefano M.
Published: June 2020

Motivation

Data transformations are an important step in the analysis of RNA-seq data. Nonetheless, the impact of transformations on the outcome of unsupervised clustering procedures is still unclear.

Results

Here, we present an Asymmetric Winsorization per Sample Transformation (AWST), which is robust to data perturbations and removes the need for selecting the most informative genes prior to sample clustering. Our procedure leads to robust and biologically meaningful clusters both in bulk and in single-cell applications.

Availability

The AWST method is available athttps://github.com/drisso/awst. The code to reproduce the analyses is available athttps://github.com/drisso/awst_analysis.
Drebrin mediates scar formation and astrocyte reactivity during brain injury by inducing RAB8 tubular endosomes
Authors: Schiweck Juliane , Murk Kai , Ledderose Julia , Münster-Wandowski Agnieszka , Vida Imre , Eickholt Britta J.
Published: June 2020

The brain of mammals lacks a significant ability to regenerate neurons and is thus particularly vulnerable. To protect the brain from injury and disease, damage control by astrocytes through astrogliosis and scar formation is vital. Here, we show that brain injury triggers anad hocupregulation of the actin-binding protein Drebrin (DBN) in astrocytes, which is essential for the formation and maintenance of glial scarsin vivo. In turn, DBN loss leads to defective glial scar formation and excessive neurodegeneration following mild brain injuries. At the cellular level, DBN switches actin homeostasis from ARP2/3-dependent arrays to microtubule-compatible scaffolds and facilitates the formation of RAB8-positive membrane tubules. This injury-specific RAB8 membrane compartment serves as hub for the trafficking of surface proteins involved in astrogliosis and adhesive responses, such as β1-integrin. Our work identifies DBN as pathology-specific actin regulator, and establishes DBN-dependent membrane trafficking as crucial mechanism in protecting the brain from escalating damage following traumatic injuries.
Synchronization, stochasticity and phase waves in neuronal networks with spatially-structured connectivity
Authors: Kulkarni Anirudh , Ranft Jonas , Hakim Vincent
Published: June 2020

Oscillations in the beta/low gamma range (10-45 Hz) are recorded in diverse neural structures. They have successfully been modeled as sparsely synchronized oscillations arising from reciprocal interactions between randomly connected excitatory (E) pyramidal cells and local interneurons (I). The synchronization of spatially distant oscillatory spiking E-I modules has been well studied in the rate model framework but less so for modules of spiking neurons. Here, we first show that previously proposed modifications of rate models provide a quantitative description of spiking E-I modules of Exponential Integrate-and-Fire (EIF) neurons. This allows us to analyze the dynamical regimes of sparsely synchronized oscillatory E-I modules connected by long-range excitatory interactions, for two modules, as well as for a chain of such modules. For modules with a large number of neurons (> 105), we obtain results similar to previously obtained ones based on the classic deterministic Wilson-Cowan rate model, with the added bonus that the results quantitatively describe simulations of spiking EIF neurons. However, for modules with a moderate (~ 104) number of neurons, stochastic variations in the spike emission of neurons are important and need to be taken into account. On the one hand, they modify the oscillations in a way that tends to promote synchronization between different modules. On the other hand, independent fluctuations on different modules tend to disrupt synchronization. The correlations between distant oscillatory modules can be described by stochastic equations for the oscillator phases that have been intensely studied in other contexts. On shorter distances, we develop a description that also takes into account amplitude modes and that quantitatively accounts for our simulation data. Stochastic dephasing of neighboring modules produces transient phase gradients and the transient appearance of phase waves. We propose that these stochastically-induced phase waves provide an explanative framework for the observations of traveling waves in the cortex during beta oscillations.
A Deep Dive into DNA Base Pairing Interactions Under Water
Authors: Li Rongpeng , Mak Chi H.
Published: June 2020

Base pairing plays a pivotal role in DNA functions and replication fidelity. But while the complementarity between Watson-Crick matched bases is generally believed to arise from the different number of hydrogen bonds in G|C pairs versus A|T, the energetics of these interactions are heavily renormalized by the aqueous solvent. Employing large-scale Monte Carlo simulations, we have extracted the solvent contribution to the free energy for canonical and some noncanonical and stacked base pairs. For all of them, the solvent’s contribution to the base pairing free energy is exclusively destabilizing. While the direct hydrogen bonding interactions in the G|C pair is much stronger than A|T, the thermodynamic resistance produced by the solvent also pushes back much stronger against G|C compared to A|T, generating an only ~1 kcal/mol free energy difference between them. We have profiled the density of water molecules in the solvent adjacent to the bases and observed a “freezing” behavior where waters are recruited into the gap between the bases to compensate for the unsatisfied hydrogen bonds between them. A very small number of water molecules that are associated with the Watson-Crick donor/acceptor atoms turn out to be responsible for the majority of solvent’s thermodynamic resistance to base pairing. The absence or presence of these near-field waters can be used to enhance fidelity during DNA replication.

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An OpenData portal to share COVID-19 drug repurposing data in real time
Authors: Brimacombe Kyle R. , Zhao Tongan , Eastman Richard T. , Hu Xin , Wang Ke , Backus Mark , Baljinnyam Bolormaa , Chen Catherine Z. , Chen Lu , Eicher Tara , Ferrer Marc , Fu Ying , Gorshkov Kirill , Guo Hui , Hanson Quinlin M. , Itkin Zina , Kales Stephen C. , Klumpp-Thomas Carleen , Lee Emily M. , Michael Sam , Mierzwa Tim , Patt Andrew , Pradhan Manisha , Renn Alex , Shinn Paul , Shrimp Jonathan H. , Viraktamath Amit , Wilson Kelli M. , Xu Miao , Zakharov Alexey V. , Zhu Wei , Zheng Wei , Simeonov Anton , Mathé Ewy A. , Lo Donald C. , Hall Matthew D. , Shen Min
Published: June 2020

The National Center for Advancing Translational Sciences (NCATS) has developed an online open science data portal for its COVID-19 drug repurposing campaign – named OpenData – with the goal of making data across a range of SARS-CoV-2 related assays available in real-time. The assays developed cover a wide spectrum of the SARS-CoV-2 life cycle, including both viral and human (host) targets. In total, over 10,000 compounds are being tested in full concentration-response ranges from across multiple annotated small molecule libraries, including approved drug, repurposing candidates and experimental therapeutics designed to modulate a wide range of cellular targets. The goal is to support research scientists, clinical investigators and public health officials through open data sharing and analysis tools to expedite the development of SARS-CoV-2 interventions, and to prioritize promising compounds and repurposed drugs for further development in treating COVID-19.
C11orf95-RELA Reprograms 3D Epigenome in Supratentorial Ependymoma
Authors: Zhu Jacqueline Jufen , Jillette Nathaniel , Li Xiao-Nan , Cheng Albert Wu , Lau Ching C
Published: June 2020

Supratentorial ependymoma (ST-EPN) is a type of malignant brain tumor mainly seen in children. Since 2014, it has been known that an intrachromosomal fusionC11orf95-RELAis an oncogenic driver in ST-EPN1but the molecular mechanisms of oncogenesis are unclear. Here we show that the C11orf95 component of the fusion protein dictates DNA binding activity while the RELA component is required for driving the expression of ependymoma-associated genes. Epigenomic characterizations using ChIP-seq and HiChIP approaches reveal that C11orf95-RELA modulates chromatin states and mediates chromatin interactions, leading to transcriptional reprogramming in ependymoma cells. Our findings provide important characterization of the molecular underpinning ofC11orf95-RELAfusion and shed light on potential therapeutic targets forC11orf95-RELAsubtype ependymoma.
PIVOTAL: Prioritizing variants of uncertain significance with spatial genomic patterns in the 3D proteome
Authors: Liang Siqi , Mort Matthew , Stenson Peter D. , Cooper David N. , Yu Haiyuan
Published: June 2020

Variants of uncertain significance (VUS) have posed an increasingly prominent challenge to clinicians due to their growing numbers and difficulties in making clinical responses to them. Currently there are no existing methods that leverage the spatial relationship of known disease mutations and genomic properties for prioritizing variants of uncertain significance. More importantly, disease genes often associate with multiple clinically distinct diseases, but none of the existing variant prioritization methods provide clues as to the specific type of disease potentially associated with a given variant. We present PIVOTAL, a spatial neighborhood-based method using three-dimensional structural models of proteins, that significantly improves current variant prioritization tools and identifies potential disease etiology of candidate variants on a proteome scale. Using PIVOTAL, we made pathogenicity predictions for over 140,000 VUS and deployed a web application (http://pivotal.yulab.org) that enables users both to explore these data and to perform custom calculations.
Distinct Roles of Tumor-Associated Mutations in Collective Cell Migration
Authors: Lee Rachel M. , Vitolo Michele I. , Losert Wolfgang , Martin Stuart S.
Published: June 2020

Recent evidence suggests that groups of cells are more likely to form clinically dangerous metastatic tumors, emphasizing the importance of understanding mechanisms underlying collective behavior. The emergent collective behavior of migrating cell sheetsin vitrohas been shown to be disrupted in tumorigenic cells but the connection between this behavior andin vivotumorigenicity is unclear. Here we use particle image velocimetry to measure a multi-dimensional collective migration phenotype for genetically defined cell lines that range in theirin vivobehavior from non-tumorigenic to aggressively metastatic. By using cells with controlled mutations, we show that PTEN deletion enhances collective migration, while Ras activation suppresses it, even when combined with PTEN deletion. These opposing effects on collective migration phenotype of two mutations that are frequently found in patient tumors could be exploited in clinical assessments of metastatic potential or in the development of novel treatments for metastatic disease.
In vivofluorescence imaging with a flat, lensless microscope
Authors: Adams Jesse K. , Boominathan Vivek , Gao Sibo , Rodriguez Alex V. , Yan Dong , Kemere Caleb , Veeraraghavan Ashok , Robinson Jacob T.
Published: June 2020

Fluorescence imaging over large areas of the brain in freely behaving animals would allow researchers to better understand the relationship between brain activity and behavior; however, traditional microscopes capable of high spatial resolution and large fields of view (FOVs) require large and heavy lenses that restrict animal movement. While lensless imaging has the potential to achieve both high spatial resolution and large FOV with a thin lightweight device, lensless imaging has yet to be achievedin vivodue to two principal challenges: (a) biological tissue typically has lower contrast than resolution targets, and (b) illumination and filtering must be integrated into this non-traditional device architecture. Here, we show thatin vivofluorescence imaging is possible with a thin lensless microscope by optimizing the phase mask and computational reconstruction algorithms, and integrating fiber optic illumination and thin-film color filters. The result is a flat, lensless imager that achieves better than 10 μm spatial resolution and a FOV that is 30× larger than other cellular resolution miniature microscopes.
Mucosal vaccine adjuvant cyclic di-GMP differentiates lung moDCs into Bcl6+and Bcl6−mature moDCs to induce lung memory CD4+THcells and lung TFHcells respectively
Authors: Mansouri Samira , Katikaneni Divya S , Gogoi Himanshu , Jin Lei
Published: June 2020

Induction of lung T-cell responses, including memory CD4+THand TFHcells, are highly desirable for vaccines against respiratory infections. We recently showed that the non-migratory monocytes-derived DCs (moDCs) induced lung TFHcells. However, the DCs subset inducing lung CD4+memory THcells is unknown. Here, using conditional knockout mice and adoptive cell transfer, we first established that moDCs are essential for lung mucosal, but are dispensable for systemic, vaccine responses. Next, we showed that intranasal administration of adjuvant cyclic di-GMP differentiated lung moDCs into Bcl6+and Bcl6-moDCs promoting lung memory THcells and lung TFHcells, respectively. Mechanistically, soluble TNF from lung TNFR2+cDC2 subpopulation mediates the induction of lung Bcl6+moDCs. Last, we designed fusion proteins targeting soluble or transmembrane TNF to lung moDCs and generated Bcl6+, Bcl6-lung moDCs respectively. Together, our study revealed lung mature moDCs heterogeneity and showed a moDCs-targeting strategy to enhance lung mucosal vaccine responses.
Single-cell analysis reveals diverse stromal subsets associated with immune evasion in triple-negative breast cancer
Authors: Wu Sunny Z. , Roden Daniel L. , Wang Chenfei , Holliday Holly , Harvey Kate , Cazet Aurélie S. , Murphy Kendelle J. , Pereira Brooke , Al-Eryani Ghamdan , Bartonicek Nenad , Hou Rui , Torpy James R. , Junankar Simon , Chan Chia-Ling , Lam Eric , Hui Mun N. , Gluch Laurence , Beith Jane , Parker Andrew , Robbins Elizabeth , Segara Davendra , Mak Cindy , Cooper Caroline , Warrier Sanjay , Forrest Alistair , Powell Joseph , O’Toole Sandra , Cox Thomas R. , Timpson Paul , Lim Elgene , Liu X. Shirley , Swarbrick Alexander
Published: June 2020

The tumour stroma regulates nearly all stages of carcinogenesis. Stromal heterogeneity in human triple-negative breast cancers (TNBCs) remains poorly understood, limiting the development of stromal-targeted therapies. Single cell RNA-sequencing of five TNBCs revealed two cancer-associated fibroblast (CAF) and two perivascular-like (PVL) subpopulations. CAFs clustered into two states, the first with features of myofibroblasts and the second characterised by high expression of growth factors and immunomodulatory molecules. PVL cells clustered into two states consistent with a differentiated and immature phenotype. We showed that these stromal states have distinct morphologies, spatial relationships and functional properties in regulating the extracellular matrix. Using cell-signalling predictions, we provide evidence that stromal-immune crosstalk actsviaa diverse array of immunoregulatory molecules. Importantly, the investigation of gene signatures from inflammatory-CAFs and differentiated-PVL cells in independent TNBC patient cohorts revealed strong associations with cytotoxic T-cell dysfunction and exclusion, respectively. Such insights present promising candidates to further investigate for new therapeutic strategies in the treatment of TNBCs.
Compensatory hippocampal neurogenesis in the absence of cognitive impairment following experimental hippocampectomy in adult rats
Authors: Cardoso Giuliana T. M. , Gomes-Leal Walace , Franco Edna C. S. , Gama Jessica S. , Gomes Francinaldo L. , Brino Ana Leda F. , Pereira Antonio , Lima. Silene M. A.
Published: June 2020

Temporal lobe epilepsy (TLE) is the commonest type of focal epilepsy in adult humans. In refractory TLE, patients are indicated for unilateral resection of the affected hippocampus (hippocampectomy), which generally does not cause any cognitive impairment. Once adult hippocampus is a region of endogenous neurogenesis, we have hypothesized that a compensatory increase in hippocampal neurogenesis might occur in the remaining hippocampus after unilateral hippocampectomy. To test this hypothesis, we performed unilateral hippocampectomy in adult Wistar rats (n=12). Sham animals were not hippocampectomized (n=6). Animals were deeply anesthetized and adjacent cortex and hippocampus of the left hemisphere were completely removed. They were perfused at 15 (G15, n=6) or 30 (G30, n=6) days post-surgery. Behavioral tests were performed to address possible cognitive impairments. We did not find any cognitive impairment in the hippocampectomized animals. Histopathology was performed using thionine staining and mature neurons and migratory neuroblasts were immunolabeled using anti-NeuN and anti-doublecortin (DCX) antibodies, respectively. The remaining hippocampus presented higher numbers of DCX positive cells compared to control (p<0.001) at both G15 and G30. The results suggest increased compensatory adult neurogenesis following experimental unilateral hippocampectomy in adult rats, which may contribute to absence of cognitive impairments.
Post-weaning social isolation increases ΔFosB/FosB protein expression in the prefrontal cortex and hippocampus in mice
Authors: Noback Michael , Zhang Gongliang , White Noelle , Barrow James C. , Carr Gregory V.
Published: June 2020

Social isolation is a growing public health concern across the lifespan. Specifically, isolation early in life, during critical periods of brain development, increases the risk of psychiatric disorders later in life. Previous studies of isolation models in mice have shown distinct neurological abnormalities in various regions of the brain, but the mechanism linking the experience of isolation to these phenotypes is unclear. In this study, we show that ΔFosB, a long-lived transcription factor associated with chronic stress responses and drug-induced neuroplasticity, is upregulated in the medial prefrontal cortex and hippocampus of adult C57BL/6J mice isolated for two weeks post-weaning. Additionally, a related transcription factor, FosB, is also increased in the medial prefrontal cortex in socially isolated females. These results show that short-term isolation during the critical post-weaning period has long-lasting and sex-dependent effects on gene expression in brain.
Scaling of gene transcriptional gradients with brain size across mouse development
Authors: Gladys Lau Hoi Yan , Fornito Alex , Fulcher Ben D.
Published: June 2020

The structure of the adult brain is the result of complex physical mechanisms acting through development. These physical processes, acting in threedimensional space, mean that the brain’s spatial embedding plays a key role in its organization, including the gradient-like patterning of gene expression that encodes the molecular underpinning of functional specialization. However, we do not yet understand how the dramatic changes in brain shape and size that occur in early development influence the brain’s transcriptional architecture. Here we investigate the spatial embedding of transcriptional patterns of over 1800 genes across seven time points through mousebrain development using data from the Allen Developing Mouse Brain Atlas. We find that transcriptional similarity decreases exponentially with separation distance across all developmental time points, with a correlation length scale that follows a powerlaw scaling relationship with a linear dimension of brain size. This scaling suggests that the mouse brain achieves a characteristic balance between local molecular similarity (homogeneous gene expression within a specialized brain area) and longer-range diversity (between functionally specialized brain areas) throughout its development. Extrapolating this mouse developmental scaling relationship to the human cortex yields a prediction consistent with the value measured from microarray data. We introduce a simple model of brain growth as spatially autocorrelated gene-expression gradients that expand through development, which captures key features of the mouse developmental data. Complementing the well-known exponential distance rule for structural connectivity, our findings characterize an analogous exponential distance rule for transcriptional gradients that scales across mouse brain development, providing new understanding of spatial constraints on the brain’s molecular patterning.
Comparative study of four SARS-CoV-2 Nucleic Acid Amplification Test (NAAT) platforms demonstrates that ID NOW performance is impaired substantially by patient and specimen type
Authors: Lephart Paul R. , Bachman Michael , LeBar William , McClellan Scott , Barron Karen , Schroeder Lee , Newton Duane W.
Published: June 2020

The advent of the COVID-19 pandemic in the United States created a unique situation where multiple molecular diagnostic assays with various indications for use in the detection of SARS-CoV-2 rapidly received Emergency Use Authorization by the FDA, were validated by laboratories and utilized clinically, all within a period of a few weeks. We compared the performance of four of these assays that were being evaluated for use at our institution: Abbott RealTime m2000 SARS-CoV-2 Assay, DiaSorin Simplexa COVID-19 Direct, Cepheid Xpert Xpress SARS-CoV-2 and Abbott ID NOW COVID-19. Nasopharyngeal and nasal specimens were collected from 88 ED and hospital-admitted patients and tested by the four methods in parallel to compare performance. ID NOW performance stood out as significantly worse than the other three assays despite demonstrating comparable analytic sensitivity. Further study determined that the use of a foam nasal swab compared to a nylon flocked nasopharyngeal swab, as well as use in a population chronically vs. acutely positive for SARS-CoV-2, were significant factors in the poor comparable performance.
Effect of gamma sterilization on filtering efficiency of various respiratory facemasks
Authors: Kumar Amit , Sangeetha D.N. , Yuvaraj Ramani , Menaka M. , Subramanian V. , Venkatraman B.
Published: June 2020

Three types of respiratory masks viz N95, nonwoven fabric and double layer cotton cloth are being used as an essential inhalation protective measure against COVID-19 by suppressing the entry of respiratory droplets. The filtering efficiency of these masks were tested before and after sterilisation using gamma radiation for the two flow rate conditions corresponding normal breath rate (20lpm) and during sneezing/coughing (90lpm).Sterilisation is carried out using a gamma irradiator containing Co-60 source for the two dose exposures viz. 15kGy and 25kGy.The filtering efficiency for surgical (nonwoven fabric) and double layer cotton cloth mask is found to vary from 18% to 22% for the cumulative particle of size ≥ 0.3µm in both un-irradiated and irradiated condition. The filtration efficiency of N95 mask is found to be reduced to 70% for the most penetrating particle size (0.3 µm) with the flow rate of 20lpm and further reduced for particles in the range of 0.1 and 0.2µm with flow rate of 90 lpm. The reduction in efficiency after gamma sterilization is associated with reduction of electrostatic interaction of filter medium with particles laden in the air stream. Even with reduced filtering efficiency due to gamma sterilisation, the N95 masks are much superior than the surgical and cloth masks. Instead of disposing N95 mask after single use, they can be reused a few times as N70 mask during this pandemic crisis after sterilisation using gamma radiation.
Anemia and iron metabolism in COVID-19: A systematic review and meta-analysis
Authors: Taneri Petek Eylul , Alejandro Gómez-Ochoa Sergio , Llanaj Erand , Francis Raguindin Peter , Rojas Lyda Z. , Wyssmann Beatrice Minder , Kopp-Heim Doris , Hautz Wolf E. , Eisenga Michele F. , Franco Oscar H. , Glisic Marija , Muka Taulant
Published: June 2020

Iron metabolism and anemia may play an important role in multiple organ dysfunction syndrome in Coronavirus disease 2019 (COVID-19). If confirmed, this has important implications for the more than 1.62 billion people estimated to have anemia globally. We conducted a systematic review and meta-analysis to evaluate biomarkers of anemia and iron metabolism (hemoglobin, ferritin, transferrin, soluble transferrin receptor, hepcidin, haptoglobin, unsaturated iron-binding capacity, erythropoietin, free erythrocyte protoporphyrine, and prevalence of anemia) in patients diagnosed with COVID-19, and explore their prognostic value. Six bibliographic databases were searched up to May 5th2020. We included 56 unique studies, with data from 14,044 COVID-19 patients (59 years median age). Pooled mean hemoglobin and ferritin levels in COVID-19 patients across all ages were 130.41 g/L (95% Confidence Interval (CI), 128.42; 132.39) and 673.91 ng/mL (95% CI, 420.98; 926.84), respectively. Hemoglobin levels decreased with advancing age and increasing percentage of comorbid and critically ill patients, while levels of ferritin increased with increasing male proportion and mean hemoglobin levels. Compared to moderate cases, severe cases had lower pooled mean hemoglobin [weighted mean difference (WMD), –4.21 (95% CI –6.63; –1.78)] and higher ferritin [WMD, –730.55 ng/mL (95% CI 413.24; 1047.85)]. A significant difference in mean ferritin level of 1027.23 ng/mL (95% CI 819.53; 1234.94) was found between survivors and non-survivors, but not in hemoglobin levels. No studies provided information on anemia or other biomarkers of interest. Future studies should explore the impact of iron metabolism and anemia and in the pathophysiology, prognosis, and treatment of COVID-19.
Are antibodies tests accurate? Understanding predictive values and uncertainty of serology tests for the novel coronavirus
Authors: Brownstein Naomi C , Chen Yian Ann
Published: June 2020

Antibodies testing in the coronavirus era is frequently promoted, but the underlying statistics behind their validation has come under more scrutiny in recent weeks. We provide calculations, interpretations, and plots of positive and negative predictive values under a variety of scenarios. Prevalence, sensitivity, and specificity are estimated within ranges of values from researchers and antibodies manufacturers. Illustrative examples are highlighted, and interactive plots are provided in the Supplementary Material. Implications are discussed for society overall and across diverse locations with different levels of disease burden. Specifically, the proportion of positive serology tests that are false can differ drastically from up to 3% to 88% for people from different places with different proportions of infected people in the populations while the false negative rate is typically under 10%.