bluuebunny/crossref_metadata_2025_split huggingface dataset:
CanLncG4: A database curated for the assessment of G4s in the lncRNAs dysregulated in various human cancers
Authors: Sharma Shubham , Yusuf Muhammad , Barbhuiya Noman Hasif , Ramolia Harshit , Shukla Chinmayee , Singh Deepshikha , Datta Bhaskar 
Published: February 2024

AbstractLong non-coding RNAs (lncRNAs) comprise a substantive part of the human genome and have emerged as crucial participants of cellular processes and disease pathogenesis. Dysregulated expression of lncRNAs in cancer contributes to various hallmarks of the disease, presenting novel opportunities for diagnosis and therapy. G-quadruplexes (G4s) within lncRNAs have gained attention, though their systematic evaluation in cancer biology is yet to be performed. In this work, we have formulated CanLncG4, a comprehensive database integrating experimentally validated associations between lncRNAs and cancer, and detailed predictions of their G4-forming potential. CanLncG4 categorizes predicted G4 motifs into anticipated G4 types and offers insights into the subcellular localization of the corresponding lncRNAs. It provides information on lncRNA-RNA and lncRNA-protein interactions, together with the RNA G4-binding capabilities of these proteins. To ensure the accuracy and validity of the data sourced from various databases, a meticulous examination of the output data was conducted to identify any discrepancies, including incorrect, missing, or duplicate entries. Additionally, scientific literature mining was performed to cross-validate the gathered information. Data from G4-prediction tools was generated using multiple parameter combinations to determine the parameters that yield more relevant and accurate predictions of the G4-forming potential. We validate ourin silicoG4-prediction pipeline throughin vitroexperiments, affirming the presence of G4s within specific cancer-dysregulated lncRNAs, thereby illustrating the predictive capability of CanLncG4. CanLncG4 represents a valuable resource for investigating G4-mediated lncRNA functions in diverse human cancers. It is expected to provide distinctive leads about G4-mediated lncRNA-protein interactions. CanLncG4 comprehensively documents 17,666 entries, establishing correlations between 6,408 human lncRNAs encompassing their transcript variants, and 15 distinct types of human cancers. The database is freely available athttps://canlncg4.com/, offering researchers a valuable tool for exploring lncRNA and G4 biology towards cancer diagnosis and therapeutics.
Regionalized cell and gene signatures govern oesophageal epithelial homeostasis
Authors: Grommisch David , Lund Harald , Eenjes Evelien , Julien Anais , Göritz Christian , Harris Robert A. , Sandberg Rickard , Hagemann-Jensen Michael , Genander Maria 
Published: February 2024

AbstractRegionalized disease prevalence is a common feature of the gastrointestinal tract. Herein, we employed regionally resolved Smart-seq3 single-cell sequencing, generating a comprehensive cell atlas of the adult mouse oesophagus. Characterizing the oesophageal axis, we unveil non-uniform distribution of epithelial basal cells, fibroblasts and immune cells. In addition, we reveal a position-dependent, but cell subpopulation-independent, transcriptional signature, collectively generating a regionalized oesophageal landscape.Combiningin vivomodels with organoid co-cultures, we demonstrate that proximal and distal basal progenitor cell states are functionally distinct. We find that proximal fibroblasts are more permissive for organoid growth compared to distal fibroblasts and that the immune cell profile is regionalized in two dimensions, where proximal-distal and epithelial-stromal gradients impact epithelial maintenance. Finally, we predict and verify how WNT-, BMP-, IGF-and NRG-signalling are differentially engaged along the oesophageal axis.We establish a cellular and transcriptional framework for understanding oesophageal regionalization, providing a functional basis for epithelial disease susceptibility.
Mucin MUC5B levels are reduced in the colonic epithelia of ulcerative colitis patients
Authors: Ding Wei , Koltun Walter A. , Yochum Gregory S. 
Published: February 2024

ABSTRACTBackground & AimsUlcerative colitis (UC) is an inflammatory bowel disease (IBD) where a defect in the colonic epithelial barrier elicits a chronic and unresolved inflammatory response against luminal microbiota. Mucins are heavily glycosylated proteins secreted by goblet cells that form gelatinous layers to protect the colonic epithelium. Whereas the role of the major colonic mucin, MUC2, is established in UC, few reports have analyzed MUC5B in this disease. In this study, we investigated MUC5B expression in colonic tissues and organoid cultures from UC patients and non-IBD controls.MethodsMUC5Btranscripts were analyzed in colonic regions from UC patients and controls using RT-qPCR. MUC5B protein levels in colonic tissues were analyzed and quantified by immunohistochemistry. Patient-derived epithelial organoids were stained for MUC5B, E-cadherin and F-actin. Organoids were treated with interleukin 1 beta (IL-1β) andMUC5Btranscripts were analyzed by RT-qPCR. MUC5B proteins were assessed in IL-1β-treated organoids by immunofluorescent microscopy.ResultsMUC5Btranscripts and proteins were expressed in the healthy colon and their levels were decreased in UC tissues. MUC5B proteins were reduced in organoids derived from UC tissues. IL-1β treatment of control organoids stimulated expression of acidic mucins,MUC5Btranscripts and MUC5B proteins.MUC5Btranscripts were not induced by IL-1β in UC-derived organoids.ConclusionsMUC5B levels are reduced in UC colons and its expression is induced by the IL-1β pro-inflammatory cytokine. These results suggest that MUC5B contributes to the protective colonic mucin layer and that this function is likely compromised in UC.
diaPASEF Enables High-throughput Proteomic Analysis of Host Cell Proteins for Biopharmaceutical Process Development
Authors: Tsukidate Taku , Stiving Alyssa Q. , Rivera Shannon , Sahoo Ansuman , Madabhushi Sri , Li Xuanwen 
Published: February 2024

ABSTRACTMonitoring and quantifying host cell proteins (HCPs) in biotherapeutics production processes is crucial to ensure product quality, stability, and safety. Liquid chromatography–mass spectrometry (LC–MS) analysis has emerged as an important tool for identifying and quantifying individual HCPs. However, LC-MS–based approaches face challenges due to the wide dynamic range between HCPs and the therapeutic protein, as well as laborious sample preparation and long instrument time. To address these limitations, we evaluated the application of parallel accumulation–serial fragmentation combined with data-independent acquisition (diaPASEF), to HCP analysis for biopharmaceutical process development applications. We evaluated different library generation strategies and LC methods, demonstrating the suitability of these workflows for various HCP analysis needs such as in-depth characterization and high-throughput analysis of process intermediates. Remarkably, the diaPASEF approach enabled the quantification of hundreds of HCPs that were undetectable by a standard data-dependent acquisition mode while considerably improving sample requirement, throughput, coverage, quantitative precision, and data completeness.
The wide spectrum anti-inflammatory activity of andrographolide in comparison to NSAIDs: a promising therapeutic compound against the cytokine storm
Authors: Low Mitchell , Suresh Harsha , Zhou Xian , Bhuyan Deep Jyoti , Alsherbiny Muhammad A. , Khoo Cheang , Münch Gerald , Li Chun Guang 
Published: February 2024

AbstractThe challenges of the COVID-19 pandemic have highlighted an increasing clinical demand for safe and effective treatment options against an overzealous immune defence response, also known as the “cytokine storm”. Andrographolide is a naturally derived bioactive compound with promising anti-inflammatory activity in many clinical studies. However, its cytokine-inhibiting activity, in direct comparison to commonly used nonsteroidal anti-inflammatory drugs (NSAIDs), has not been extensively investigated in existing literature. The anti-inflammatory activities of andrographolide and common NSAIDs, such as diclofenac, aspirin, paracetamol and ibuprofen were measured on lipopolysaccharide (LPS) and interferon-γ induced RAW264.7 cells. The levels of PGE2, nitric oxide (NO), TNF-α & LPS-induced release of pro-inflammatory cytokines on differentiated human macrophage THP-1 cells were measured against increasing concentrations of andrographolide and aforementioned NSAIDs. The associated mechanistic pathway was examined on NFκB using flow cytometry on the human endothelial-leukocyte adhesion molecule (ELAM9) (E-selectin) transfected RAW264.7 cells with green fluorescent protein (GFP). Andrographolide exhibited broad and potent anti-inflammatory and cytokine-inhibiting activity in both cell lines by inhibiting the release of IL-6, TNF-α and IFN-γ, which are known to play a key role in the etiology of cytokine storm and the pathogenesis of inflammation. In comparison, the tested NSAIDs demonstrated weak or no activity against proinflammatory mediators except for PGE2, where the activity of andrographolide (IC50= 8.8 µM, 95% CI= 7.4 to 10.4 µM) was comparable to that of paracetamol (IC50= 7.73 µM, 95% CI = 6.14 to 9.73 µM). The anti-inflammatory action of andrographolide was associated with its potent downregulation of NFκB. The wide-spectrum anti-inflammatory activity of andrographolide demonstrates its therapeutic potential against cytokine storms as an alternative to NSAIDs.
Metabolicshift to serine pathway induced by lipids confers oncogenic properties in non-transformed breast cells
Authors: Eduardo Mariana Bustamante , Cottone Gannon , McCloskey Curtis W. , Liu Shiyu , Zappia Maria Paula , Benevolenskaya Elizaveta V. , Islam A.B.M.M.K. , Frolov Maxim V. , Palma Flavio R. , Gao Peng , Setya Joel , Gao Hongyu , Xuei Xiaoling , Khokha Rama , Locasale Jason , Bonini Marcelo G. , Chandel Navdeep S. , Khan Seema A. , Clare Susan E. 
Published: February 2024

AbstractA lipid metabolism gene signature is associated with the risk of estrogen negative breast cancer (ER-BC). In vitro, lipid exposure alters histone methylation affecting gene expression and increasing flux through various metabolic reactions; but little is known about the mechanism(s) linking lipids and epigenetic reprogramming with the genesis of ER-BC. Here we show that the metabolism of the medium-chain fatty acid Octanoic Acid (OA) in preference to glucose and glutamine results in a metabolic shift toward the serine pathway increasing the production of SAM, glutathione, and 2-HG, with implications for oncogenesis: SAM production results in epigenetic fostered plasticity leading to reprogramming/selecting cells that express Neural, EMT and BC related genes. 2-HG exposure results in appearance of DNA breaks, potentially consequent to the inhibition of essential demethylases for HR repair. ROS increases shortly after OA exposure and is mitigated by antioxidant defenses, which favors/enables the survival of specific cell subtypes.
Identification and characterization of a skin microbiome onCaenorhabditis eleganssuggests environmental microbes confer cuticle protection
Authors: Haghani Nadia , Lampe Robert H. , Samuel Buck , Chalasani Sreekanth H. , Matty Molly A. 
Published: February 2024

AbstractIn the wild,C. elegansare emersed in environments teeming with a veritable menagerie of microorganisms. TheC. eleganscuticular surface serves as a barrier and first point of contact with this microbial milieux. Here, we identify microbes fromC. elegansnatural habitats that associate with its cuticle, constituting a simple ‘skin microbiome’. We rear our animals on a modified CeMbio, mCeMbio, a consortium of ecologically relevant microbes. We first combine standard microbiological methods with an adapted micro skin-swabbing tool to describe the skin-resident bacteria on theC. eleganssurface. Further, we conduct 16S rRNA gene sequencing studies to identify relative shifts in the proportion of mCeMbio bacteria upon surface-sterilization, implying distinct skin-and gut-microbiomes. We find that some strains of bacteria, includingEnterobacter sp.JUb101, are primarily found on the nematode skin, while others likeStenotrophomonas indicatrixJUb19 andOchrobactrum vermisMYb71 are predominantly in the animal’s gut. Finally, we show that this skin microbiome promotes host cuticle integrity in harsh environments. Together, we identify a skin microbiome for the well-studied nematode model and propose its value in conferring host fitness advantages in naturalized contexts.ImportanceThe genetic model organismC. eleganshas recently emerged as a tool for understanding host-microbiome interactions. Nearly all of these studies either focus on pathogenic or gut-resident microbes. Little is known about the existence of native, non-pathogenic skin microbes or their function. We show that members of a modifiedC. elegansmodel microbiome, mCeMbio, can adhere to the animal’s cuticle and confer protection from noxious environments. We combine a novel micro-swab tool, the first 16S microbial sequencing data from relatively unperturbedC. elegans, and physiological assays to demonstrate microbially mediated protection of the skin. This work serves as a foundation to explore wildC. elegansskin microbiomes and useC. elegansas a model for skin research.
Antagonistic Roles of Tau and MAP6 in Regulating Neuronal Development
Authors: Sun Xiaohuan , Yu Wenqian , Baas Peter W. , Toyooka Kazuhito , Qiang Liang 
Published: February 2024

AbstractAssociation of tau with microtubules causes them to be labile while association of MAP6 with microtubules causes them to be stable. As axons differentiate and grow long, tau and MAP6 segregate from one another on individual microtubules, resulting in the formation of stable and labile domains. The functional significance of the yin/yang relationship between tau and MAP6 remained speculative in those studies, with one idea being that such a relationship assists in balancing morphological stability with plasticity. Here, using primary rodent neuronal cultures, we show that depletion of tau has opposite effects compared to depletion of MAP6 on the rate of neuronal development, the efficiency of growth cone turning, and the number of processes and axonal branches. Opposite effects to those of tau depletion were also observed on the rate of neuronal migration, in anin vivoassay, when we depleted MAP6. When tau and MAP6 were depleted together in the cell culture assays, the morphological phenotypes negated one another. Tau and MAP6 are multifunctional proteins, but the present results suggest that the observed effects of their depletion on neuronal development are likely due to their opposite roles in regulating microtubule dynamics.SummaryTau and MAP6 play antagonistic roles in regulating multiple aspects of neuronal development, presumably via their antagonistic effects on microtubule dynamics.
CYpHER: Catalytic extracellular targeted protein degradation with high potency and durable effect
Authors: Crook Zachary R. , Sevilla Gregory P. , Young Pamela , Girard Emily J. , Phi Tinh-Doan , Howard Monique , Price Jason , Olson James M. , Nairn Natalie W. 
Published: February 2024

AbstractMany disease-causing proteins have multiple pathogenic mechanisms, and conventional inhibitors struggle to reliably disrupt more than one. Targeted protein degradation (TPD) can eliminate the protein, and thus all its functions, by directing a cell’s protein turnover machinery towards it. Two established strategies either engage catalytic E3 ligases or drive uptake towards the endolysosomal pathway. Here we describe CYpHER (CatalYticpH-dependentEndolysosomal delivery withRecycling) technology with potency and durability from a novel catalytic mechanism that shares the specificity and straightforward modular design of endolysosomal uptake. By bestowing pH-dependent release on the target engager and using the rapid-cycling transferrin receptor as the uptake receptor, CYpHER induces endolysosomal target delivery while re-using drug, potentially yielding increased potency and reduced off-target tissue exposure risks. The TfR-based approach allows targeting to tumors that overexpress this receptor and offers the potential for transport to the CNS. CYpHER function was demonstratedin vitrowith EGFR and PD-L1, andin vivowith EGFR in a model of EGFR-driven non-small cell lung cancer.
Repolarisation-relaxation dyscoupling and TRPA1 activation permit systolic mechano-arrhythmogenesis
Authors: Cameron Breanne A. , Stoyek Matthew R. , Greiner Joachim , Peyronnet Rémi , Kohl Peter , Quinn T Alexander 
Published: February 2024

ABSTRACTBackgroundThe heart’s mechanical state feeds back to its electrical activity, potentially contributing to arrhythmias (mechano-arrhythmogenesis, MAR). MAR has been mechanistically explained during electrical diastole, when cardiomyocytes are at their resting membrane potential. Conversely, during electrical systole, cardiomyocytes appear to be protected from MAR, even as membrane potential and cytosolic calcium concentration ([Ca2+]i) are simultaneously restored to resting levels during repolarisation (repolarisation-relaxation coupling, RRC). Yet, systolic MAR has been reported in ischaemic myocardium, with unclear underlying mechanisms.MethodsRabbit left ventricular cardiomyocytes were electrically paced and exposed to a simulated ischaemia solution (including hyperkalaemia, acidosis, and block of oxidative phosphorylation) or pinacidil (to simulate ischaemia-induced opening of ATP-sensitive potassium [KATP] channels), with or without glibenclamide (to block KATPchannels). RRC was assessed by simultaneous measurement of membrane voltage and [Ca2+]idynamics with fluorescence imaging. Acute stretch at increasing magnitudes was applied using carbon fibres, with stretch timed to diastole or late systole. Stretch mechanics and the incidence of MAR was assessed by video-based measurement of sarcomere length. Mechanisms contributing to MAR were assessed by buffering [Ca2+]i(BAPTA-AM), stabilising ryanodine receptors (dantrolene), non-specifically blocking mechano-sensitive channels (streptomycin), activating (AITC) or blocking (HC-030031) transient receptor potential kinase ankyrin 1 channels (TRPA1), or chelating (NAC) or blocking production of (DPI) reactive oxygen species (ROS).ResultsIt was reconfirmed that MAR during physiological RRC is rare, while ischaemia- or pharmacologically-induced RRC dyscoupling generates a vulnerable period for systolic MAR. This systolic MAR depends on TRPA1, [Ca2+]i, and ROS, which contribute to stretch-induced excitation and arrhythmia sustenance. An increase in systolic MAR can be prevented by mitigating RRC dyscoupling with KATPchannel block, or by blocking TRPA1, buffering [Ca2+]i, or reducing ROS.ConclusionRRC dyscoupling may be arrhythmogenic in ischaemia and other pathologies associated with systolic MAR, and TRPA1 may be a novel anti-arrhythmic target.
Macropinocytosis mediates resistance to loss of glutamine transport in triple-negative breast cancer
Authors: Wahi Kanu , Freidman Natasha , Wang Qian , Devadason Michelle , Quek Lake-Ee , Pang Angel , Lloyd Larissa , Larance Mark , Zanini Fabio , Harvey Kate , O’Toole Sandra , Guan Yi Fang , Holst Jeff 
Published: February 2024

AbstractTriple-negative breast cancer (TNBC) relies on glutamine uptake by the transporter ASCT2 to sustain their unique glutamine metabolism and growth. Despite previous data showing cell growth inhibition after ASCT2 knockdown, ASCT2 CRISPR knockout was well-tolerated by breast cancer cell lines. Despite the loss of a glutamine transporter and low rate of glutamine uptake, intracellular glutamine steady state levels were higher in ASCT2 knockout compared to control TNBC cells. Proteomics data revealed upregulation of macropinocytosis, reduction in glutamine efflux and glutamine synthesis in ASCT2 knockout cells. Loss of ASCT2 in TNBC cell line HCC1806 induced a 5-10-fold increase in macropinocytosis across 5 separate ASCT2 knockout clones, compared to a modest 2-fold increase in the shRNA ASCT2 knockdown. By comparison, ASCT2 knockout impaired cell proliferation in a non-macropinocytic breast cancer cell line, HCC1569. These data suggest that macropinocytosis provides a novel resistance mechanism to strategies targeting glutamine uptake alone. Despite this adaptation, TNBC cells continue to rely on glutamine metabolism for their growth, which suggests therapeutic targeting may need to focus on downstream glutamine metabolism pathways.
A highly scalable approach to topic modelling in single-cell data by approximate pseudobulk projection
Authors: Subedi Sishir , Sumida Tomokazu S , Park Yongjin P 
Published: February 2024

AbstractProbabilistic topic modelling has become essential in many types of single-cell data analysis. Based on probabilistic topic assignments in each cell, we identify the latent representation of cellular states, and topic-specific gene frequency vectors provide interpretable bases to be compared with known cell-type-specific marker genes. However, fitting a topic model on a large number of cells would require heavy computational resources–specialized computing units, computing time and memory. Here, we present a scalable approximation method customized for single-cell RNA-seq data analysis, termed ASAP, short for Annotating Single-cell data by Approximate Pseudobulk estimation. Our approach is more accurate than existing methods but requires orders of magnitude less computing time, leaving much lower memory consumption. We also show that our approach is widely applicable for atlas-scale data analysis; our method seamlessly integrates single-cell and bulk data in joint analysis, not requiring additional preprocessing or feature selection steps.
Spiral ganglion neuron degeneration in deafened rats involves innate and adaptive immune responses not requiring complement
Authors: Gansemer Benjamin M. , Rahman Muhammad T. , Zhang Zhenshen , Green Steven H. 
Published: February 2024

AbstractSpiral ganglion neurons (SGNs) transmit auditory information from cochlear hair cells to the brain. SGNs are thus not only important for normal hearing, but also for effective functioning of cochlear implants, which stimulate SGNs when hair cells are missing. SGNs slowly degenerate following aminoglycoside-induced hair cell loss, a process thought to involve an immune response. However, the specific immune response pathways involved remain unknown. We used RNAseq to gain a deeper understanding immune-related and other transcriptomic changes that occur in the rat spiral ganglion after kanamycin-induced deafening. Among the immune and inflammatory genes that were selectively upregulated in deafened spiral ganglia, the complement cascade genes were prominent. We then assessed SGN survival, as well as immune cell infiltration and activation, in the spiral ganglia of rats with a CRISPR-Cas9-mediated knockout of complement component 3 (C3). Similar to previous findings in our lab and other deafened rodent models, we observed infiltration of macrophages and increased expression of CD68, a marker of phagocytic activity and cell activation, in the deafened ganglia. Moreover, we found that the immune response also includes MHCII+ macrophages and CD45+ and lymphocytes, indicative of an adaptive response. However, C3 knockout did affect SGN survival or macrophage infiltration/activation, indicating that complement activation does not play a role in SGN death after deafening. Together, these data suggest that both innate and adaptive immune responses are activated in the deafened spiral ganglion, with the adaptive response directly contributing to cochlear neurodegeneration.