bluuebunny/crossref_metadata_2025_split huggingface dataset:
Low baseline pulmonary levels of cytotoxic lymphocytes as a predisposing risk factor for severe COVID-19
Authors: Duijf Pascal H.G. 
Published: May 2020

AbstractCOVID-19 is caused by the coronavirus SARS-CoV-2 and currently has detrimental human health, community and economic impacts around the world. It is unclear why some SARS-CoV-2-positive individuals remain asymptomatic, while others develop severe symptoms. Baseline pulmonary levels of anti-viral leukocytes, already residing in the lung prior to infection, may orchestrate an effective early immune response and prevent severe symptoms. Using “in silicoflow cytometry”, we deconvoluted the levels of all seven types of anti-viral leukocytes in 1,927 human lung tissues. Baseline levels of CD8+ T cells, resting NK cells and activated NK cells, as well as cytokines that recruit these, are significantly lower in lung tissues with high expression of the SARS-CoV-2 entry receptor ACE2. We observe this in univariate analyses, in multivariate analyses, and in two independent datasets. Relevantly, ACE2 mRNA and protein levels very strongly correlate in human cells and tissues. Above findings also largely apply to the SARS-CoV-2 entry protease TMPRSS2. Both SARS-CoV-2-infected lung cells and COVID-19 lung tissues show upregulation of CD8+ T cell- and NK cell-recruiting cytokines. Moreover, tissue-resident CD8+ T cells and inflammatory NK cells are significantly more abundant in bronchoalveolar lavages from mildly affected COVID-19 patients, compared to severe cases. This suggests that these lymphocytes are important for preventing severe symptoms. Elevated ACE2 expression increases sensitivity to coronavirus infection. Thus, our results suggest that some individuals may be exceedingly susceptible to develop severe COVID-19 due to concomitant high pre-existing ACE2 and TMPRSS expression and low baseline cytotoxic lymphocyte levels in the lung.
Platelet miRNA bio-signature discriminates between dementia with Lewy bodies and Alzheimer disease
Authors: Gámez-Valero Ana , Campdelacreu Jaume , Vilas Dolores , Ispierto Lourdes , Samaniego Daniela , Gascón-Bayarri Jordi , Reñé Ramón , Álvarez Ramiro , Armengol Maria P , Borràs Francesc E. , Beyer Katrin 
Published: May 2020

ABSTRACTDementia with Lewy bodies (DLB) is one of the most common causes of degenerative dementia after Alzheimer’s disease (AD) and presents pathological and clinical overlap with both AD and Parkinson’s disease (PD). Consequently, only one in three DLB cases is diagnosed correctly. Platelets, previously related to neurodegeneration, contain microRNAs (miRNAs) whose analysis may provide disease biomarkers. Here, we profiled the whole platelet miRNA transcriptome from DLB patients and healthy controls. Differentially expressed miRNAs were further validated in three consecutive studies from 2017 to 2019 enrolling 162 individuals, including DLB, AD, and PD patients, and healthy controls. Results comprised a 7-miRNA biosignature, showing the highest diagnostic potential for the differentiation between DLB and AD. Additionally, compared to controls, two miRNAs were down-regulated in DLB, four miRNAs were up-regulated in AD, and two miRNAs were down-regulated in PD. Predictive target analysis identified three disease-specific clusters of pathways as a result of platelet-miRNA deregulation. Our cross-sectional study assesses the identification of a novel, highly specific and sensitive platelet-associated miRNA-based bio-signature, which distinguishes DLB from AD.The paper explainedProblemDementia with Lewy bodies (DLB) presents pathological and clinical overlap with both Alzheimer’s (AD) and Parkinson’s disease (PD), which impairs its correct diagnosis. Although numerous papers report peripheral biomarkers for AD, well-established biomarkers for DLB distinguishing it from AD are still missing. Platelet miRNA transcriptome was analyzed in several works, but their putative role as disease biomarkers for neurological disorders has not been assessed. It would be of paramount importance to establish a blood-based bio-signature as a minimally invasive mean for DLB diagnosis, improving differentiation of DLB patients from controls and AD.ResultsOur study revealed that platelet miRNAs might be promising biomarkers for the correct diagnosis of DLB stratifying patients in comparison with overlapping disorders, especially AD, and may help to highlight possible disease-related processes. In this cross-sectional study, which includes 162 individuals (DLB, AD, PD and healthy controls), platelet-associated miRNA content was disease group-specific. Three different miRNA sets together with their predicted targeted pathways were defined.ImpactThis study suggests that platelet miRNA may serve as DLB biomarker allowing the correct diagnosis and stratification in an easily-applied manner in clinical settings, and may help to highlight possible disease-related processes.
Global Spread of SARS-CoV-2 Subtype with Spike Protein Mutation D614G is Shaped by Human Genomic Variations that Regulate Expression ofTMPRSS2andMX1Genes
Authors: Bhattacharyya Chandrika , Das Chitrarpita , Ghosh Arnab , Singh Animesh K. , Mukherjee Souvik , Majumder Partha P. , Basu Analabha , Biswas Nidhan K. 
Published: May 2020

AbstractCOVID-19 pandemic is a major human tragedy. Worldwide, SARS-CoV-2 has already infected over 3 million and has killed about 230,000 people. SARS-CoV-2 originated in China and, within three months, has evolved to an additional 10 subtypes. One particular subtype with a non-silent (Aspartate to Glycine) mutation at 614thposition of the Spike protein (D614G) rapidly outcompeted other pre-existing subtypes, including the ancestral. We assessed that D614G mutation generates an additional serine protease (Elastase) cleavage site near the S1-S2 junction of the Spike protein. We also identified that a single nucleotide deletion (delC) at a known variant site (rs35074065) in a cis-eQTL ofTMPRSS2, is extremely rare in East Asians but is common in Europeans and North Americans. The delC allele facilitates entry of the 614G subtype into host cells, thus accelerating the spread of 614G subtype in Europe and North America where the delC allele is common. The delC allele at the cis-eQTL locus rs35074065 ofTMPRSS2leads to overexpression of bothTMPRSS2and a nearby geneMX1. The cis-eQTL site, rs35074065 overlaps with a transcription factor binding site of an activator (IRF1) and a repressor (IRF2). IRF1 activator can bind to variant delC allele, but IRF2 repressor fails to bind. Thus, in an individual carrying the delC allele, there is only activation, but no repression. On viral entry,IRF1mediated upregulation ofMX1leads to neutrophil infiltration and processing of 614G mutated Spike protein by neutrophil Elastase. The simultaneous processing of 614G spike protein by TMPRSS2 and Elastase serine proteases facilitates the entry of the 614G subtype into host cells. Thus, SARS-CoV-2, particularly the 614G subtype, has spread more easily and with higher frequency to Europe and North America where the delC allele regulating expression ofTMPRSS2andMX1host proteins is common, but not to East Asia where this allele is rare.
Integrated requirement of non-specific and sequence-specific DNA binding in MYC-driven transcription
Authors: Pellanda Paola , Dalsass Mattia , Filipuzzi Marco , Loffreda Alessia , Verrecchia Alessandro , Cano Virginia Castillo , Doni Mirko , Morelli Marco J. , Beaulieu Marie-Eve , Soucek Laura , Mazza Davide , Mapelli Marina , Kress Theresia , Amati Bruno , Sabò Arianna 
Published: May 2020

AbstractEukaryotic transcription factors recognize specific DNA sequence motifs, but are also endowed with generic, non-specific DNA-binding activity: how these binding modes are integrated to determine select transcriptional outputs remains unresolved. We designed mutants of the MYC transcription factor bearing substitutions in residues that contact either the DNA backbone or specific bases within the consensus binding motif (E-box), and profiled their DNA-binding and gene-regulatory activities in murine cells. Our data reveal that non-specific DNA binding is required for MYC to engage onto active regulatory elements in the genome, preceding sequence recognition; beyond merely stabilizing MYC onto select target loci, sequence-specific binding contributes to its precise positioning and – most unexpectedly – to transcriptional activationper se. In particular, at any given binding intensity, promoters targeted via the cognate DNA motif were more frequently activated by MYC. Hence, seemingly promiscuous chromatin interaction profiles actually encompass diverse DNA-binding modalities, driving defined, sequence-dependent transcriptional responses.
Global genetic patterns reveal host tropism versus cross-taxon transmission of bat Betacoronaviruses
Authors: Bacus Michael G. , Dayap Stephen Adrian H. , Tampon Nikki Vanesa T. , Udarbe Marielle M. , Puentespina Roberto P. , Villanueva Sharon Yvette Angelina M. , de Cadiz Aleyla E. , Achondo Marion John Michael M. , Murao Lyre Anni E. 
Published: May 2020

AbstractEmerging infectious diseases due to coronavirus (CoV) infections have received significant global attention in the past decade and have been linked to bats as the original source. The diversity, distribution, and host associations of bat CoVs were investigated to assess their potential for zoonotic transmission. Phylogenetic, network, and principal coordinate analysis confirmed the classification of betacoronaviruses (BetaCoVs) into five groups (2A to 2E) and a potentially novel group, with further division of 2D into five subgroups. The genetic co-clustering of BetaCoVs among closely related bats reflects host taxon-specificity with each bat family as the host for a specific BetaCoV group, potentially a natural barrier against random transmission. The divergent pathway of BetaCoV and host evolution suggests that the viruses were introduced just prior to bat dispersal and speciation. As such, deviant patterns were observed such as for 2D-IV, wherein cross-taxon transmission due to overlap in bat habitats and geographic range among genetically divergent African bat hosts could have played a strong role on their shared CoV lineages. In fact, a few bat taxa especially the subfamily Pteropodinae were shown to host diverse groups of BetaCoVs. Therefore, ecological imbalances that disturb bat distribution may lead to loss of host specificity through cross-taxon transmission and multi-CoV infection. Hence, initiatives that minimize the destruction of wildlife habitats and limit wildlife-livestock-human interfaces are encouraged to help maintain the natural state of bat BetaCoVs in the wild.ImportanceBat Betacoronaviruses (BetaCoVs) pose a significant threat to global public health and have been implicated in several epidemics such as the recent pandemic by severe acute respiratory syndrome coronavirus 2. Here, we show that bat BetaCoVs are predominantly host-specific, which could be a natural barrier against infection of other host types. However, a strong overlap in bat habitat and geographic range may facilitate viral transmission to unrelated hosts, and a few bat families have already been shown to host multi-CoV variants. We predict that continued disturbances on the ecological balance may eventually lead to loss of host specificity. When combined with enhanced wildlife-livestock-human interfaces, spillover to humans may be further facilitated. We should therefore start to define the ecological mechanisms surrounding zoonotic events. Global surveillance should be expanded and strengthened to assess the complete picture of bat coronavirus diversity and distribution and their potential to cause spillover infections.
Pooling RT-PCR test of SARS-CoV-2 for large cohort of “healthy” and infection-suspected patients: A prospective and consecutive study on 1,000 individuals
Authors: Hirotsu Yosuke , Maejima Makoto , Shibusawa Masahiro , Nagakubo Yuki , Hosaka Kazuhiro , Amemiya Kenji , Sueki Hitomi , Hayakawa Miyoko , Mochizuki Hitoshi , Omata Masao 
Published: May 2020

AbstractBackgroundSARS-CoV-2 testing reagents are expected to become in short supply worldwide. However, little is unknown whether the pooling strategy detects SARS-CoV-2 with accuracy.MethodTo validate the feasibility of pooling samples, serial dilution analysis and spike-in experiment were conducted using synthetic DNA and nucleic acids extracted from SARS-CoV-2 positive and negative patients. Furthermore, we studied a total of 1,000 individuals, who were 667 “healthy” (195 healthcare workers and 472 hospitalized patients with other disorders than COVID-19 infection) individuals and 333 infection-suspected patients with cough and fever, were tested.ResultsSerial dilution analysis showed the limit of detection of around 10-100 copies according to National Institute of Infectious Diseases, Japan. Spike-in experiment demonstrated RT-qPCR detect positive signal in pooling samples of SARS-CoV-2 negative and positive patient at the 5-, 10-, 20-fold dilution. By screening with pooling strategy by the end of April, 2020, there are 12 COVID-19 patients in 333 infection suspected patients (3.6%) and zero in 667 “healthy”. We obtained these results with total running 538 times (instead of 1,000 times) by pooling strategy.ConclusionPooling samples is feasible for saving test reagents and detecting SARS-CoV-2 in clinical setting to prevent the spread of the virus and nosocomial transmission.
Deciphering the temporal heterogeneity of cancer-associated fibroblast subpopulations in breast cancer
Authors: Venning Freja Albjerg , Zornhagen Kamilla Westarp , Wullkopf Lena , Hajkarim Morteza Chalabi , Won Kyoung Jae , Madsen Chris Denis , Erler Janine Tera 
Published: May 2020

AbstractCancer-associated fibroblasts (CAFs) comprise a heterogeneous population of stromal cells within the tumour microenvironment. CAFs exhibit both tumour-promoting and tumour-suppressing functions, making them exciting targets for improving cancer treatments. A careful identification and characterisation of the CAF heterogeneity is thus necessary before implementing CAF-targeted strategies in cancer. With that in mind, we developed a flow cytometry strategy based on exclusion of non-CAF cells and successfully employed it to explore the temporal heterogeneity of CAFs in two models of triple-negative breast cancer (4T1 and 4T07). Analysing 128 murine tumours we identified 5-6 main CAF subpopulations and numerous minor ones based on the analysis of alpha smooth muscle actin, fibroblast activation protein alpha, platelet derived growth factor receptor alpha and beta, CD26/DPP4 and podoplanin. All markers showed temporal changes, and CD26+ CAFs emerged as a large novel subpopulation. These results form the foundation needed for the future elucidation of tumour-promoting CAF subpopulations.
Limited time window for retinal gene therapy in a preclinical model of ciliopathy
Authors: Datta Poppy , Ruffcorn Avri , Seo Seongjin 
Published: May 2020

ABSTRACTRetinal degeneration is a common clinical feature of ciliopathies, a group of genetic diseases linked to ciliary dysfunction, and gene therapy is an attractive treatment option to prevent vision loss. Although the efficacy of retinal gene therapy is well established by multiple proof-of-concept preclinical studies, its long-term effect, particularly when treatments are given at advanced disease stages, is controversial. Incomplete treatment and intrinsic variability of gene delivery methods may contribute to the variable outcomes. Here, we used a genetic rescue approach to “optimally” treat retinal degeneration at various disease stages and examined the long-term efficacy of gene therapy in a mouse model of ciliopathy. We used a Bardet-Biedl syndrome type 17 (BBS17) mouse model, in which the gene-trap that suppresses Bbs17 (also known as Lztfl1) expression can be removed by tamoxifen administration, restoring normal gene expression systemically. Our data indicate that therapeutic effects of retinal gene therapy decrease gradually as treatments are given at later stages. These results suggest the presence of limited time window for successful gene therapy in certain retinal degenerations. Our study also implies that the long-term efficacy of retinal gene therapy may depend on not only the timing of treatment but also other factors such as the function of mutated genes and residual activities of mutant alleles.
The relationship between fasting-induced torpor, sleep and wakefulness in the laboratory mouse
Authors: Huang Yi G. , Flaherty Sarah J. , Pothecary Carina A. , Foster Russell G. , Peirson Stuart N. , Vyazovskiy Vladyslav V. 
Published: May 2020

AbstractTorpor is a regulated reversible state of metabolic suppression used by many mammalian species to conserve energy. Although torpor has been studied extensively in terms of general physiology, metabolism and neuroendocrinology, the effects of hypometabolism and associated hypothermia on brain activity and states of vigilance have received little attention. Here we performed continuous monitoring of electroencephalogram (EEG), electromyogram (EMG) and peripheral body temperature in adult, male C57BL/6 mice over consecutive days of scheduled restricted feeding. All animals showed prominent bouts of hypothermia that became progressively deeper and longer as fasting progressed. EEG and EMG were markedly affected by hypothermia, although the typical electrophysiological signatures of NREM sleep, REM sleep and wakefulness allowed us to perform vigilance-state classification in all cases. Invariably, hypothermia bouts were initiated from a state indistinguishable from NREM sleep, with EEG power decreasing gradually in parallel with decreasing body temperature. Furthermore, during deep hypothermia REM sleep was largely abolished, but we observed brief and intense bursts of muscle activity, which resembled the regular motor discharges seen during early ontogeny associated with immature sleep patterns. We conclude that torpor and sleep are electrophysiologically on a continuum, and that, in order for torpor to occur, mice need to first transition through euthermic sleep.
Convergent organization of aberrant MYB complex controls oncogenic gene expression in acute myeloid leukemia
Authors: Takao Sumiko , Forbes Lauren , Uni Masahiro , Cheng Shuyuan , Pineda Jose Mario Bello , Tarumoto Yusuke , Cifani Paolo , Minuesa Gerard , Chen Celine , Kharas Michael G. , Bradley Robert K. , Vakoc Christopher R. , Koche Richard P. , Kentsis Alex 
Published: May 2020

ABSTRACTDysregulated gene expression contributes to most prevalent features in human cancers. Here, we show that most subtypes of acute myeloid leukemia (AML) depend on the aberrant assembly of MYB transcriptional co-activator complex. By rapid and selective peptidomimetic interference with the binding of CBP/P300 to MYB, but not CREB or MLL1, we find that the leukemic functions of MYB are mediated by CBP/P300 co-activation of a distinct set of transcription factor complexes. These MYB complexes assemble aberrantly with LYL1, E2A, C/EBP family members, LMO2 and SATB1. They are organized convergently in genetically diverse subtypes of AML, and are at least in part associated with inappropriate transcription factor co-expression. Peptidomimetic remodeling of oncogenic MYB complexes is accompanied by specific proteolysis and dynamic redistribution of CBP/P300 with alternative transcription factors such as RUNX1 to induce myeloid differentiation and apoptosis. Thus, aberrant assembly and sequestration of MYB:CBP/P300 complexes provide a unifying mechanism of oncogenic gene expression in AML. This work establishes a compelling strategy for their pharmacologic reprogramming and therapeutic targeting for diverse leukemias and possibly other human cancers caused by dysregulated gene control.
Transient coupling between subplate and subgranular layers to L1 neurons before and during the critical period
Authors: Meng Xiangying , Xu Yanqing , Kao Joseph P. Y. , Kanold Patrick O. 
Published: May 2020

AbstractCortical layer 1 (L1) contains a diverse population of interneurons which can modulate processing in superficial cortical layers but the intracortical sources of synaptic input to these neurons and how these inputs change over development is unknown. We here investigated the changing intracortical connectivity to L1 in primary auditory cortex (A1) in slices of mouse A1 across development using laser-scanning photostimulation. Before P10 L1 cells receive most excitatory input from within L1, L2/3, L4 and L5/6 as well as the subplate. Excitatory inputs from all layers increase and peak during P10-P16, the peak of the critical period. Inhibitory inputs followed a similar pattern. Functional circuit diversity in L1 emerges after P16. In adult, L1 neurons receive ascending inputs from superficial L2/3 and subgranular L5/6, but only few inputs from L4. A subtype of L1 neurons, NDNF+ neurons, follow a similar pattern, suggesting that transient hyperconnectivity is a universal feature of developing cortical circuits. Our results demonstrate that deep excitatory and superficial inhibitory circuits are tightly linked in early development and might provide a functional scaffold for the layers in between. These results suggest that early thalamic driven spontaneous and sensory activity in subplate can be relayed to L1 from the earliest ages on, that the critical period is characterized by high transient columnar hyperconnectivity, and that in particular circuits originating in L5/6 and subplate might play a key role.
Cyrius: accurateCYP2D6genotyping using whole genome sequencing data
Authors: Chen Xiao , Shen Fei , Gonzaludo Nina , Malhotra Alka , Rogert Cande , Taft Ryan J , Bentley David R , Eberle Michael A 
Published: May 2020

AbstractResponsible for the metabolism of 25% of clinically used drugs,CYP2D6is a critical component of personalized medicine initiatives. GenotypingCYP2D6is challenging due to sequence similarity with its pseudogene paralogCYP2D7and a high number and variety of common structural variants (SVs). Here we describe a novel bioinformatics method, Cyrius, that accurately genotypesCYP2D6using whole-genome sequencing (WGS) data. We show that Cyrius has superior performance (96.5% concordance with truth genotypes) compared to existing methods (84-86.8%). After implementing the improvements identified from the comparison against the truth data, Cyrius’s accuracy has since been improved to 99.3%. Using Cyrius, we built a haplotype frequency database from 2504 ethnically diverse samples and estimate that SV-containing star alleles are more frequent than previously reported. Cyrius will be an important tool to incorporate pharmacogenomics in WGS-based precision medicine initiatives.
Application of aptamers improves CRISPR-based live imaging of plant telomeres
Authors: Khosravi Solmaz , Schindele Patrick , Gladilin Evgeny , Dunemann Frank , Rutten Twan , Puchta Holger , Houben Andreas 
Published: May 2020

AbstractDevelopment of live imaging techniques for providing information how chromatin is organized in living cells is pivotal to decipher the regulation of biological processes. Here, we demonstrate the improvement of a live imaging technique based on CRISPR/Cas9. In this approach, the sgRNA scaffold is fused to RNA aptamers including MS2 and PP7. When the dead Cas9 (dCas9) is co-expressed with chimeric sgRNA, the aptamer-binding proteins fused to fluorescent protein (MCP-FP and PCP-FP) are recruited to the targeted sequence. Compared to previous work with dCas9:GFP, we show that the quality of telomere labelling was improved in transiently transformedNicotiana benthamianausing aptamer-based CRISPR-imaging constructs. Labelling is influenced by the copy number of aptamers and less by the promoter types. The same constructs were not applicable for labelling of repeats in stably transformed plants and roots. The constant interaction of the RNP complex with its target DNA might interfere with cellular processes.HighlightAptamer-based CRISPR imaging: an opportunity for improving live-cell imaging in plants