bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid and automated quantification of TDP-43 and FUS mislocalisation for screening of frontotemporal dementia and amyotrophic lateral sclerosis gene variants
Authors: Oyston Lisa J. , Ubiparipovic Stephanie , Fitzpatrick Lauren , Hallupp Marianne , Boccanfuso Lauren M. , Kwok John B. , Dobson-Stone Carol 
Published: March 2021

AbstractBackgroundIdentified genetic mutations cause 20% of frontotemporal dementia (FTD) and 5-10% of amyotrophic lateral sclerosis (ALS) cases: however, for the remainder of patients the origin of the disease is uncertain. The overlap in genetic, clinical and pathological presentation of FTD and ALS suggests these two diseases are related. Post-mortem, 97% of ALS and ∼50% of FTD patients show redistribution of the nuclear proteins TDP-43 or FUS to the cytoplasm within affected neurons. We exploited this predominant neuropathological feature to develop an automated method for the quantification of cytoplasmic TDP-43 and FUS in human cell lines.ResultsUtilising fluorescently-tagged cDNA constructs to identify cells of interest, the fluorescence intensity of TDP-43 or FUS was measured in the nucleus and cytoplasm of HEK293 and SH-SY5Y cells. Confocal microscope images were input into the freely available software CellProfiler, which was used to isolate and measure the two cellular compartments. Significant increases in the amount of cytoplasmic TDP-43 and FUS were detectable in cells expressing known ALS-causativeTARDBPandFUSgene mutations. Pharmacological intervention with the apoptosis inducer staurosporine also induced measurable cytoplasmic mislocalisation of endogenous FUS. Additionally, this technique was able to detect the subtler effect of mutation in a secondary gene (CYLD) on endogenous TDP-43 localisation.ConclusionsThese findings validate this methodology as a novelin vitrotechnique for the quantification of TDP-43 or FUS mislocalisation that can be used to assess the pathogenicity of predicted FTD- or ALS-causative mutations.
The DMT and Psilocin Treatment Changes CD11b+ Activated Microglia Immunological Phenotype
Authors: Kozłowska Urszula , Klimczak Aleksandra , Wiatr Kalina , Figiel Maciej 
Published: March 2021

AbstractPsychedelics are new, promising candidate molecules for clinical use in psychiatric disorders such as Treatment-Resistant Depression (TRD) and Post Traumatic Stress Disorder (PTSD). They were recently also proposed as molecules supporting neural tissue repair by anti-inflammatory properties. Here we reported that two classic psychedelics, DMT and psilocin, can influence microglial functions by reducing the level of TLR4, p65, CD80 proteins, which are markers of the immune response, and upregulat TREM2 neuroprotective receptor. Psilocin also secured neuronal survival in the neuron-microglia co-culture model by attenuating the phagocytic function of microglia. We conclude that DMT and psilocin regulate the immunomodulatory potential of microglia. Of note, psychedelics were previously reported as a relatively safe treatment approach. The demonstrated regulation of inflammatory molecules and microglia phagocytosis suggests that psychedelics or their analogs are candidates in the therapy of neurological disorders where microglia and inflammation significantly contribute to pathogenic disease mechanisms.
An Investigation into Patient-Specific 3D Printed Titanium Stents and the use of Etching to Overcome Selective Laser Melting Design Constraints
Authors: McGee Orla M. , Geraghty Sam , Hughes Celia , Jamshidi Parastoo , Kenny Damien P. , Attallah Moataz M. , Lally Caitríona 
Published: March 2021

AbstractThere is currently a clear clinical need in the area of stenting for paediatric patients, whereby currently commercially available adult stents are often required to be used off-label for paediatric patients resulting in less than optimal outcomes. The increasingly widespread use of CT and/or MR imaging for pre-surgical assessment, and the emergence of additive manufacturing processes such as 3D printing, could enable bespoke devices to be produced efficiently and cost-effectively. However, 3D printed metallic stents need to be self-supporting leading to limitations in the design of stents available through additive manufacturing. In this study we investigate the use of etching to overcome these design constraints and improve stent surface finish. Furthermore, using a combination of experimental bench testing and finite element methods we investigate how etching influences stent performance and using an inverse finite element approach the material properties of the printed and etched stents were calibrated and compared. Finally, using patient-specific finite element models the stent performance was tested to assess patient outcomes. Within this study, etching is confirmed as a means to create open-cell stent designs whilst conforming to additive manufacturing ‘rules’ and concomitantly improving stent surface finish. Additionally, the feasibility of using an in-vivo imaging to product development pipeline is demonstrated that enables patient-specific stents to be produced for varying anatomies to achieve optimum device performance.Figure 1.Graphical abstract.
Combined MEK and STAT3 inhibition reprograms stromal inflammation to overcome immunotherapy resistance in pancreatic cancer
Authors: Datta Jashodeep , Dai Xizi , Bianchi Anna , De Castro Silva Iago , Mehra Siddharth , Garrido Vanessa , Lamichhane Purushottam , Singh Samara , Zhou Zhiqun , Dosch Austin R. , Messaggio Fanuel , Ban Yuguang , Umland Oliver , Hosein Peter J. , Nagathihalli Nagaraj S. , Merchant Nipun B. 
Published: March 2021

ABSTRACTPancreatic ductal adenocarcinoma (PDAC) is characterized by immune exclusion, pro-inflammatory polarization of cancer-associated fibroblasts (CAF), and resistance to immune checkpoint inhibition (ICI). We have previously demonstrated that reciprocally activated RAS/MEK/ERK and JAK/STAT3 pathways mediate therapeutic resistance, while combined MEK and STAT3 inhibition (MEKi+STAT3i) overcomes such resistance in preclinical models. We now show that combined MEKi+STAT3i not only alters stromal architecture but also uncovers stromal plasticity by revealing a substantial attenuation ofIl6/Cxcl1-expressing secretory andLrrc15-expressing myofibroblastic CAF phenotypes with a concomitant enrichment ofLy6a/Cd34-expressing CAF phenotypes exhibiting mesenchymal progenitor-like properties via single-cell RNA sequencing inPtf1acre/+;LSL-KrasG12D/+;Tgfbr2flox/flox(PKT) mice. This remodeling of CAF heterogeneity is associated with reprogramming of immunosuppressive myeloid populations and enhanced trafficking of CD8+T-cells which exhibit a distinct effector transcriptional program. These MEKi+STAT3i-mediated repercussions are in part CAF-dependent, since CRISPR/Cas9 genetic silencing of CAF-restrictedMek1/Stat3mitigates inflammatory CAF polarization and myeloid infiltrationin vivo. Addition of MEKi+STAT3i to PD-1 blockade overcomes ICI resistance by significantly augmenting anti-tumor responses and dramatically improving survival in PKT mice compared with anti-PD-1 monotherapy. The addition of MEKi+STAT3i to PD-1 blockade not only augments the recruitment of activated and memory T-cell populations, but also improves their degranulating capacity and functional cytotoxicity compared to PD-1 blockade alone. Importantly, treatment of a patient with chemotherapy-refractory metastatic PDAC with MEKi (Trametinib), STAT3i (Ruxolitinib), and PD-1 inhibitor (Nivolumab) was well-tolerated and yielded clinical benefit. These data uncover a novel paradigm in which combined MEKi+STAT3i reprograms stromal inflammation and immune tolerance to overcome immunotherapy resistance in PDAC.
Neuronal cultures show bidirectional axonal conduction with antidromic action potentials depolarizing the soma
Authors: Mateus JC , Lopes CDF , Aroso M , Costa AR , Gerós A , Meneses J , Faria P , Neto E , Lamghari M , Sousa MM , Aguiar P 
Published: March 2021

ABSTRACTRecent technological advances are revealing the complex physiology of the axon and challenging long-standing assumptions. Namely, while most action potential (AP) initiation occurs at the axon initial segment in central nervous system neurons, initiation in distal parts of the axon has been shown to occur in both physiological and pathological conditions. However, such ectopic action potential (EAP) activity has not been reported yet in studies using neuronal cultures and its functional role, if exists, is still not clear. Here, we show the spontaneous occurrence of EAPs and effective antidromic conduction in hippocampal neuronal cultures. We also observe a significant fraction of bidirectional axonal conduction in dorsal root ganglia neuronal cultures. We investigate and characterize this antidromic propagation via a combination of microfluidics, microelectrode arrays, advanced data analysis andin silicostudies. We show that EAPs and antidromic conduction can occur spontaneously, and after distal axotomy or physiological changes in the axon biochemical environment. Conduction velocity is asymmetrical, with antidromic conduction being slower than orthodromic. Importantly, EAPs may carry information and can have a functional impact on the neuron, as they consistently depolarize the soma. Thus, plasticity or gene transduction mechanisms triggered by soma depolarization can also be affected by these antidromic APs. Altogether these findings have important implications for the study of neuronal functionin vitro, reshaping our understanding on how information flows in neuronal cultures.
Hypothalamic perineuronal nets are regulated by sex and dietary interventions
Authors: Zhang Nan , Yan Zili , Liu Hailan , Yu Meng , He Yang , Liu Hesong , Liang Chen , Tu Longlong , Wang Lina , Yin Na , Han Junying , Scarcelli Nikolas , Yang Yongjie , Wang Chunmei , Zeng Tianshu , Chen Lu-Lu , Xu Yong 
Published: March 2021

ABSTRACTPerineuronal nets (PNNs) are widely present in the hypothalamus, and are thought to provide physical protection and ion buffering for neurons, and regulate their synaptic plasticity and intracellular signaling. Recent evidence indicates that PNNs in the mediobasal hypothalamus plays an important role in the regulation of glucose homeostasis. However, whether and how hypothalamic PNNs are regulated are not fully understood. In the present study, we examined whether PNNs in various hypothalamic regions in mice can be regulated by sex, gonadal hormones, dietary interventions, or their interactions. We demonstrated that gonadal hormones are required to maintain normal PNNs in the arcuate nucleus of hypothalamus in both male and female mice. In addition, PNNs in the terete hypothalamic nucleus display a sexual dimorphism with females higher than males, and high-fat diet feeding increases terete PNNs only in female mice but not in male mice. On the other hand, PNNs in other hypothalamic regions are not influenced by sex, gonadal hormones or dietary interventions. In summary, we demonstrated that hypothalamic PNNs are regulated in a region-specific manner and these results provide a framework to further investigate the potential functions of PNNs in regulating energy/glucose homeostasis at the interplay of sex, gonadal hormones and diets.
Impaired Cx43 gap junction endocytosis causes cardiovascular defects in zebrafish
Authors: Hyland Caitlin , Mfarej Michael , Hiotis Giorgos , Lancaster Sabrina , Novak Noelle , Kathryn Iovine M. , Falk Matthias M. 
Published: March 2021

AbstractGap junction proteins, termed connexins (Cx), mediate direct cell-to-cell communication by forming channels that physically couple cells, thereby linking their cytoplasm, permitting exchange of molecules, ions, and electrical impulses. The most ubiquitously expressed gap junction protein, connexin43 (Cx43) has been implicated in cardiovascular diseases including arrhythmias, cardiomyopathies, hypertension and diabetes. The Cx43 C-terminal (CT) domain serves as the regulatory hub of the protein affecting all aspects of gap junction function. Here, deletion within the Cx43 CT (amino acids 256-289), a region known to encode key residues regulating gap junction turnover is employed to examine the effects of dysregulated Cx43 gap junction endocytosis using cultured cells (Cx43Δ256-289) and zebrafish model (cx43lh10). We report that this CT deletion causes defective gap junction endocytosis as well as increased gap junction intercellular communication (GJIC). Increased Cx43 protein content in cx43lh10zebrafish, specifically in the cardiac tissue, larger gap junction plaques and longer Cx43 protein half-lives coincide with severely impaired cardiovascular development. These findings suggest that normal, unimpaired Cx43 gap junction endocytosis and turnover is an essential aspect of gap junction function as demonstrated here for cardiovascular development that when impaired can give rise to arrhythmias, heart malformations and aberrant vasculature structure and function.
Habitual Coffee Consumption Increases Risks for Metabolic Diseases: Genome-wide Association Studies and a Phenotype-wide Two Sample Mendelian Randomization Analysis
Authors: Li Jiuling , Choudhury Tasnim , Zhang Miaoran , Chen Lanlan , Wen Jianping , Liu Wanqing , Chen Peng 
Published: March 2021

AbstractBackground and aimsCoffee is one of the most widely consumed beverages in the world and has received considerable concerns regarding its impact on human health. Mendelian randomization (MR) could be valuable to explore the potential health effects of coffee via instrumental variables. In this study, we aim to identify novel genetic loci associated with habitual coffee consumption using genome-wide meta-analysis (GWMA) and to evaluate the broad impact of coffee consumption on human health and disease risk via a large-scale, phenotype-wide, two sample Mendelian randomization (TSMR) analysis.MethodsWe conducted a genome-wide association study (GWAS) among 283,926 coffee consumers of European ancestry in the UK Biobank (UKBB) to identify single nucleotide polymorphisms (SNPs) associated with the amount of coffee consumption (cups/day, GWAS 1), caffeine intake (GWAS 2) as well as the intake of non-caffeine substance in coffee (GWAS 3). The GWAS 1 results were further combined with the published results from the Coffee and Caffeine Genetics Consortium (CCGC) for a GWMA. TSMR were performed to evaluate the causal-relationship between coffee/caffeine/non-caffeine substance consumption and 1,101 diseases and health traits.ResultsThe GWMA identified 50 lead SNPs among 19 genomic regions for habitual coffee consumption. Nine out of the 19 loci were novel, including ADAMTSL4-AS1, CACNA2D2, LINC02123-ADCY2, UBD-SNORD32B, SEMA4D-GADD45G, LOC101929457-LINGO1, RAI1, HCN2,and BRWD1. The GWAS 2 and 3 identified 2 (SORCS2 and SLC39A8) and 5 (LINC02060-LINC00461, AGR3-AHR, PRR4-TAS2R14, CYP1A1-CYP1A2, and FTO) genomic regions, respectively. TSMR analysis indicated that coffee consumption increased the risk of high blood lipids, obesity, and diabetes. Meanwhile, intake of caffeine and non-caffeine coffee components decreased and increased some of the blood lipids levels, respectively.ConclusionsOur study provided evidence that habitual coffee consumption could increase the risk of metabolic perturbations. The bioactive components in coffee, other than caffeine, may be more harmful to human health. Our findings have significant implications for global public health given the increasing burden of metabolic diseases.
Drug development of an affinity enhanced, broadly neutralizing heavy chain-only antibody that restricts SARS-CoV-2 in rodents
Authors: Schepens Bert , van Schie Loes , Nerinckx Wim , Roose Kenny , Van Breedam Wander , Fijalkowska Daria , Devos Simon , Weyts Wannes , De Cae Sieglinde , Vanmarcke Sandrine , Lonigro Chiara , Eeckhaut Hannah , Van Herpe Dries , Borloo Jimmy , Oliveira Ana Filipa , Catani Joao Paulo , Creytens Sarah , De Vlieger Dorien , Michielsen Gitte , Zavala Marchan Jackeline Cecilia , Moschonas George D. , Rossey Iebe , Sedeyn Koen , Van Hecke Annelies , Zhang Xin , Langendries Lana , Jacobs Sofie , ter Horst Sebastiaan , Seldeslachts Laura , Liesenborghs Laurens , Boudewijns Robbert , Thibaut Hendrik Jan , Dallmeier Kai , Velde Greetje Vande , Weynand Birgit , Beer Julius , Schnepf Daniel , Ohnemus Annette , Remory Isabel , Foo Caroline S. , Abdelnabi Rana , Maes Piet , Kaptein Suzanne J. F. , Rocha-Pereira Joana , Jochmans Dirk , Delang Leen , Peelman Frank , Staeheli Peter , Schwemmle Martin , Devoogdt Nick , Tersago Dominique , Germani Massimiliano , Heads James , Henry Alistair , Popplewell Andrew , Ellis Mark , Brady Kevin , Turner Alison , Dombrecht Bruno , Stortelers Catelijne , Neyts Johan , Callewaert Nico , Saelens Xavier 
Published: March 2021

AbstractWe have identified camelid single-domain antibodies (VHHs) that cross-neutralize SARS-CoV-1 and −2, such as VHH72, which binds to a unique highly conserved epitope in the viral receptor-binding domain (RBD) that is difficult to access for human antibodies. Here, we establish a protein engineering path for how a stable, long-acting drug candidate can be generated out of such a VHH building block. When fused to human IgG1-Fc, the prototype VHH72 molecule prophylactically protects hamsters from SARS-CoV-2. In addition, we demonstrate that both systemic and intranasal application protects hACE-2-transgenic mice from SARS-CoV-2 induced lethal disease progression. To boost potency of the lead, we used structure-guided molecular modeling combined with rapid yeast-based Fc-fusion prototyping, resulting in the affinity-matured VHH72_S56A-Fc, with subnanomolar SARS-CoV-1 and −2 neutralizing potency. Upon humanization, VHH72_S56A was fused to a human IgG1 Fc with optimized manufacturing homogeneity and silenced effector functions for enhanced safety, and its stability as well as lack of off-target binding was extensively characterized. Therapeutic systemic administration of a low dose of VHH72_S56A-Fc antibodies strongly restricted replication of both original and D614G mutant variants of SARS-CoV-2 virus in hamsters, and minimized the development of lung damage. This work led to the selection of XVR011 for clinical development, a highly stable anti-COVID-19 biologic with excellent manufacturability. Additionally, we show that XVR011 is unaffected in its neutralizing capacity of currently rapidly spreading SARS-CoV-2 variants, and demonstrate its unique, wide scope of binding across the Sarbecovirus clades.
Atrxdeletion impairs cGAS-STING signaling and increases response to radiation and oncolytic herpesvirus in sarcoma
Authors: Floyd Warren , Pierpoint Matthew , Su Chang , Luo Lixia , Deland Katherine , Wisdom Amy J. , Zhu Daniel , Ma Yan , DeWitt Suzanne Bartholf , Williams Nerissa T. , Somarelli Jason A. , Corcoran David L. , Eward William C. , Cardona Diana M. , Kirsch David G. 
Published: March 2021

AbstractATRXis one of the most frequently altered genes in solid tumors, and mutation is especially frequent in soft tissue sarcomas. However, the role ofATRXin tumor development and response to cancer therapies remains poorly understood. Here, we developed a primary mouse model of soft tissue sarcoma and showed thatAtrxdeleted tumors are more sensitive to radiation therapy. In the absence ofAtrx, irradiated sarcomas have increased persistent DNA damage, telomere dysfunction, and mitotic catastrophe. We find thatAtrxdeleted sarcomas have a reduced adaptive immune response, impaired cGAS-STING signaling, and increased sensitivity to an oncolytic herpesvirus therapy. Translation of these results to patients withATRXmutant cancers could enable genomically-guided cancer therapeutic approaches that improve patient outcomes.
The chromatin factor ROW cooperates with BEAF-32 in regulating long-range inducible genes
Authors: Herman Neta , Kadener Sebastian , Shifman Sagiv 
Published: March 2021

AbstractInsulator proteins located at the boundaries of topological associated domains (TAD) are involved in regulating chromatin loops. Yet, how chromatin loops contribute to transcription regulation is still not clear. Here we show that Relative-of-WOC (ROW) is essential for the long-range transcription regulation mediated by the Boundary Element-Associated Factor of 32kD (BEAF-32). We found that ROW physically interacts with heterochromatin proteins (HP1b and HP1c) and the insulator protein BEAF-32. The co-localization happens at TAD boundaries where ROW, through its AT-hooks motifs, binds AT-rich sequences flanked by BEAF-32 binding sites and motifs. Knockdown ofrowresulted in downregulation of genes that are long-range targets of BEAF-32 and bound indirectly by ROW (without binding motif). Analysis of high- throughput chromosome conformation capture (Hi-C) data revealed long-range interactions between promoters of housekeeping genes bound directly by ROW and promoters of developmental genes bound indirectly by ROW. Thus, our results show cooperation between BEAF-32 and the ROW complex, which includes HP1 proteins, to regulate the transcription of developmental and inducible genes by chromatin loops.
Pediatric nasal epithelial cells are less permissive to SARS-CoV-2 replication compared to adult cells
Authors: Zhu Yanshan , Chew Keng Yih , Wu Melanie , Karawita Anjana C. , McCallum Georgina , Steele Lauren E , Yamamoto Ayaho , Labzin Larisa L. , Yarlagadda Tejasri , Khromykh Alexander A. , Wang Xiaohui , Sng Julian , Stocks Claudia J. , Xia Yao , Kollmann Tobias R. , Martino David , Joensuu Merja , Meunier Frédéric A. , Balistreri Giuseppe , Bielefeldt-Ohmann Helle , Bowen Asha C. , Kicic Anthony , Sly Peter D. , Spann Kirsten M. , Short Kirsty R. 
Published: March 2021

AbstractChildren typically experience more mild symptoms of COVID-19 when compared to adults. There is a strong body of evidence that children are also less susceptible to SARS-CoV-2 infection with the ancestral viral isolate. However, the emergence of SARS-CoV-2 variants of concern (VOCs) has been associated with an increased number of pediatric infections. Whether this is the result of widespread adult vaccination or fundamental changes in the biology of SARS-CoV-2 remains to be determined. Here, we use primary nasal epithelial cells from children and adults, differentiated at an air-liquid interface to show that the ancestral SARS-CoV-2 replicates to significantly lower titers in the nasal epithelial cells of children compared to those of adults. This was associated with a heightened antiviral response to SARS-CoV-2 in the nasal epithelial cells of children. Importantly, the Delta variant also replicated to significantly lower titres in the nasal epithelial cells of children. This trend was markedly less pronounced in the case of Omicron. It is also striking to note that, at least in terms of viral RNA, Omicron replicated better in pediatric NECs compared to both Delta and the ancestral virus. Taken together, these data show that the nasal epithelium of children supports lower infection and replication of ancestral SARS-CoV-2, although this may be changing as the virus evolves.