bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pan-cancer analyses of the associations between 109 pre-existing conditions and cancer treatment patterns across 19 adult cancers
Authors: Chang Wai Hoong , Lai Alvina G. 
Published: November 2022

AbstractComorbidities present considerable challenges to cancer treatment and care. However, little is known about the effect of comorbidity on cancer treatment decisions across a wide range of cancer types and treatment modalities. Harnessing a cohort of 280,543 patients spanning 19 site-specific cancers, we explored pan-cancer frequencies of 109 comorbidities. Multinomial regression revealed that patients with comorbidity exhibited lower odds of receiving chemotherapy and multimodality treatment. End-stage renal disease was significantly associated with a decreased odds of receiving chemotherapy and surgery. Patients with prostate cancer who have comorbid non-acute cystitis, obstructive and reflux uropathy, urolithiasis, or hypertension were less likely to receive chemotherapy. Among patients with breast cancer, dementia, left bundle branch block, peripheral arterial disease, epilepsy, Barrett’s oesophagus, ischaemic stroke, unstable angina and asthma were associated with lower odds of receiving multimodal chemotherapy, radiotherapy and surgery. Comorbidity is also consistently associated with the lower odds of receiving chemotherapy when comparing across 10 drug classes. Patients with comorbid dementia, intracerebral haemorrhage, subarachnoid haemorrhage, oesophageal varices, liver fibrosis sclerosis and cirrhosis and secondary pulmonary hypertension were less likely to receive antimetabolites. Comorbidity can influence the effectiveness and tolerability of cancer treatment and ultimately, prognosis. Multi-specialty collaborative care is essential for the management of comorbidity during cancer treatment, including prophylactic measures to manage toxicities.
Single-spore germination analyses reveal that calcium released duringClostridioides difficilegermination functions in a feed-forward loop
Authors: Ribis John W. , Melo Luana , Shrestha Shailab , Giacalone David , Rodriguez Enrique E. , Shen Aimee , Rohlfing Amy 
Published: November 2022

AbstractClostridioides difficileinfections begin when its metabolically dormant spores germinate in response to sensing bile acid germinants alongside amino acid and divalent cation co-germinants in the small intestine. While bile acid germinants are essential forC. difficilespore germination, it is currently unclear whether both co-germinant signals are required. One model proposes that divalent cations, particularly Ca2+, are essential for inducing germination, while another proposes that either co-germinant class can induce germination. The former model is based on the finding that spores defective in releasing large stores of internal Ca2+in the form of calcium dipicolinic acid (CaDPA) cannot germinate when germination is induced with bile acid germinant and amino acid co-germinant alone. However, since the reduced optical density of CaDPA-less spores makes it difficult to accurately measure their germination, we developed a novel automated, time-lapse microscopy-based germination assay to analyze CaDPA mutant germination at the single-spore level. Using this assay, we found that CaDPA mutant spores germinate in the presence of amino acid co-germinant and bile acid germinant. Higher levels of amino acid co-germinants are nevertheless required to induce CaDPA mutant spores to germinate relative to WT spores because CaDPA released by WT spores during germination can function in a feedforward loop to potentiate the germination of other spores within the population. Collectively, these data indicate that Ca2+is not essential for inducingC. difficilespore germination because amino acid and Ca2+co-germinant signals are sensed by parallel signaling pathways.ImportanceClostridioides difficilespore germination is essential for this major nosocomial pathogen to initiate infection.C. difficilespores germinate in response to sensing bile acid germinant signals alongside co-germinant signals. There are two classes of co-germinant signals: Ca2+and amino acids. Prior work suggested that Ca2+is essential forC. difficilespore germination based on bulk population analyses of germinating CaDPA mutant spores. Since these assays rely on optical density to measure spore germination and the optical density of CaDPA mutant spores is reduced relative to WT spores, this bulk assay is limited in its capacity to analyze germination. To overcome this limitation, we developed an automated image analysis pipeline to monitorC. difficilespore germination using time-lapse microscopy. With this analysis pipeline, we demonstrate that, although Ca2+is dispensable for inducingC. difficilespore germination, CaDPA can function in a feedforward loop to potentiate the germination of neighboring spores.
IL-11 disrupts alveolar epithelial progenitor function
Authors: Kortekaas Rosa K. , Geillinger-Kästle Kerstin E. , Borghuis Theo , Belharch Kaoutar , Webster Megan , Timens Wim , Burgess Janette K. , Gosens Reinoud 
Published: November 2022

AbstractIL-11 is linked to the pathogenesis of idiopathic pulmonary fibrosis (IPF), since IL-11 induces myofibroblast differentiation and stimulates their excessive collagen deposition in the lung. The alveolar architecture is disrupted in IPF, yet the effect of IL-11 on dysregulated alveolar repair associated with IPF remains to be elucidated.We hypothesized that epithelial-fibroblast communication associated with lung repair is disrupted by IL-11. Thus, we studied whether IL-11 affects the repair responses of alveolar lung epithelium using mouse lung organoids and precision cut lung slices (PCLS). Additionally, we assessed the anatomical distribution of IL-11 and IL-11 receptor in human control and IPF lungs using immunohistochemistry.IL-11 protein was observed in human control lungs in airway epithelium, macrophages and in IPF lungs, in areas of AT2 cell hyperplasia. IL-11R staining was predominantly present in smooth muscle and macrophages. In mouse organoid co-cultures of epithelial cells with lung fibroblasts, IL-11 decreased organoid number and reduced the fraction of pro-SPC expressing organoids, indicating dysfunctional regeneration initiated by epithelial progenitors. In mouse PCLS alveolar marker gene expression declined, whereas airway markers were increased. The response of primary human fibroblasts to IL-11 on gene expression level was minimal, though bulk RNA-sequencing revealed IL-11 modulated a number of processes which may play a role in IPF, including unfolded protein response, glycolysis and Notch signaling.In conclusion, IL-11 disrupts alveolar epithelial regeneration by inhibiting progenitor activation and suppressing the formation of mature alveolar epithelial cells. The contribution of dysregulated fibroblast – epithelial communication to this process appears to be limited.
A mitochondrial SCF-FBXL4 ubiquitin E3 ligase complex restrains excessive mitophagy to prevent mitochondrial disease
Authors: Cao Yu , Zheng Jing , Wan Huayun , Sun Yuqiu , Fu Song , Liu Shanshan , He Baiyu , Cai Gaihong , Cao Yang , Huang Huanwei , Li Qi , Ma Yan , Chen She , Wang Fengchao , Jiang Hui 
Published: November 2022

SUMMARYMitophagy is a fundamental quality control mechanism of mitochondria. Its regulatory mechanisms and pathological implications remain poorly understood. Here via a mitochondria-targeted screen, we found that knockout (KO) of FBXL4, a mitochondrial disease gene, hyperactivates mitophagy at basal conditions. Subsequent counter screen revealed that FBXL4-KO hyperactivates mitophagy via two mitophagy receptors BNIP3 and NIX. We determined that FBXL4 functions as an integral outer-membrane protein that forms an SCF-FBXL4 ubiquitin E3 ligase complex. SCF-FBXL4 ubiquitinates BNIP3 and NIX to target them for degradation. Pathogenic FBXL4 mutations disrupt SCF-FBXL4 assembly and impair substrate degradation.Fbxl4−/−mice exhibit elevated BNIP3 and NIX proteins, hyperactive mitophagy, and perinatal lethality. Importantly, knockout of eitherBnip3orNixrescues metabolic derangements and viability of theFbxl4−/−mice. Together, beyond identifying SCF-FBXL4 as a novel mitochondrial ubiquitin E3 ligase restraining basal mitophagy, our results reveal hyperactivated mitophagy as a cause of mitochondrial disease and suggest therapeutic strategies.
Silc1 long noncoding RNA is an immediate-early gene promoting efficient memory formation
Authors: Perry Rotem Ben-Tov , Tsoory Michael , Tolmasov Michael , Ulitsky Igor 
Published: November 2022

AbstractLong noncoding RNAs (lncRNAs) are expressed in many brain circuits and neuronal types, but their significance to normal brain functions has remained largely unknown. Here, we study the functions in the central nervous system ofSilc1, a lncRNA we previously showed to be important for neuroregeneration in the peripheral nervous system. We found thatSilc1is rapidly and strongly induced upon stimulation in the hippocampus and is required for efficient spatial learning.Silc1production is important for the induction ofSox11(its cis-regulated target gene) throughout the CA1-CA3 regions and the proper expression of keySox11target genes. Consistent with its newly found role in neuronal plasticity, we find that during aging and in models of Alzheimer’s diseaseSilc1levels decline. Overall, we uncover a novel plasticity pathway, in whichSilc1acts as an immediate-early gene to activateSox11to induce a neuronal growth-associated transcriptional program important for memory formation.
A broad-spectrum macrocyclic peptide inhibitor of the SARS-CoV-2 spike protein
Authors: Thijssen Vito , Hurdiss Daniel L. , Debski-Antoniak Oliver J. , Spence Matthew A. , Franck Charlotte , Norman Alexander , Aggarwal Anupriya , Mokiem Nadia J. , van Dongen David A. A. , Vermeir Stein W. , Liu Minglong , Li Wentao , Chatziandreou Marianthi , Donselaar Tim , Du Wenjuan , Drulyte Ieva , Bosch Berend-Jan , Snijder Joost , Turville Stuart , Payne Richard J. , Jackson Colin J. , van Kuppeveld Frank J. M. , Jongkees Seino A. K. 
Published: November 2022

AbstractThe ongoing COVID-19 pandemic has had great societal and health consequences. Despite the availability of vaccines, infection rates remain high due to immune evasive Omicron sublineages. Broad-spectrum antivirals are needed to safeguard against emerging variants and future pandemics. We used mRNA display under a reprogrammed genetic code to find a spike-targeting macrocyclic peptide that inhibits SARS-CoV-2 Wuhan strain infection and pseudoviruses containing spike proteins of SARS-CoV-2 variants or related sarbecoviruses. Structural and bioinformatic analyses reveal a conserved binding pocket between the receptor binding domain, N-terminal domain and S2 region, distal to the ACE2 receptor-interaction site. Our data reveal a hitherto unexplored site of vulnerability in sarbecoviruses that peptides and potentially other drug-like molecules can target.Significance statementThis study reports on the discovery of a macrocyclic peptide that is able to inhibit SARS-CoV-2 infection by exploiting a new vulnerable site in the spike glycoprotein. This region is highly conserved across SARS-CoV-2 variants and the subgenus sarbecovirus. Due to the inaccessability and mutational contraint of this site, it is anticipated to be resistant to the development of resistance through antibody selective pressure. In addition to the discovery of a new molecule for development of potential new peptide or biomolecule therapeutics, the discovery of this broadly active conserved site can also stimulate a new direction of drug development, which together may prevent future outbreaks of related viruses.
The circular RNA Ataxia-telangiectasia mutated (cATM) regulates oxidative stress in smooth muscle cells in expanding abdominal aortic aneurysms
Authors: Fasolo F. , Winski G. , Li Z. , Wu Z. , Winter H. , Glukha N. , Roy J. , Hultgren R. , Pauli J. , Busch A. , Sachs N. , Knappich C. , Eckstein H.H. , Boon R.A. , Paloschi V. , Maegdefessel L. 
Published: November 2022

ABSTRACTAn abdominal aortic aneurysm (AAA) is a pathological widening of the aortic wall characterized by loss of smooth muscle cells (SMCs), extracellular matrix degradation, and local inflammation. This condition is often asymptomatic until rupture occurs, leading to high morbidity and mortality rates. Diagnosis is often accidental, and for now, the only available treatment option remains surgical intervention. Circular RNAs (circRNAs) are RNA loops that originated from backsplicing, which have received increasing attention as a novel class of functional non-coding RNAs contributing to cardiovascular physiology and disease. Their high structural stability, combined with a remarkable enrichment in body fluids, make circRNAs promising disease biomarkers. We aimed to investigate the contribution of circRNAs to AAA pathogenesis and their potential application as biomarkers for AAA diagnosis. Combined circRNA array and quantitative real-time PCR analysis revealed the presence of differentially expressed circular transcripts stemming from AAA-relevant geneloci. Among these, the circRNA to the Ataxia-telangiectasia mutated gene (cATM) was upregulated in human AAA tissue specimens, in AAA patient-derived SMCs, and serum samples collected from aneurysm patients. In control primary aortic SMCs, cATMincreased upon angiotensin II stimulation, while its silencing triggered apoptosis. Furthermore, doxorubicin could induce cATM expression, supporting a link with acute stress response in SMCs. Constitutively higher cATMexpressing AAA patient-derived SMCs were less vulnerable to oxidative stress-induced cell death and survival pathways enriched when compared to control SMCs. Taken together, this data supports the role ofcATMin adapting SMCs to oxidative stress in the vascular AAA micromilieu. This molecular signature provides an additional parameter to be included in procedures for AAA screening in combination with already established practices.
Defining transcription factor nucleosome binding with Pioneer-seq
Authors: Tsompana Maria , Wilson Patrick D. , Murugaiyan Vijaya , Handelmann Christopher R. , Buck Michael J. 
Published: November 2022

ABSTRACTGene expression requires the targeting of transcription factors (TFs) to regulatory sequences often occluded within nucleosomes. To comprehensively examine TF nucleosome binding, we developed Pioneer-Seq. In Pioneer-seq a library of nucleosomes containing thousands of DNA sequences with TF binding sites in all possible nucleosome orientations is bound to a TF and the protein-nucleosome complex is isolated and quantified. To demonstrate Pioneer-seq we examined nucleosome binding by OCT4, SOX2, KLF4, and c-MYC. Our results demonstrate that KLF4 and SOX2 can bind close to the nucleosome dyad with nucleosome sequence being the major factor regulating TF binding across all studied TFs.
Terminal differentiation of villus-tip enterocytes is governed by distinct members of Tgfβ superfamily
Authors: Berková Linda , Fazilaty Hassan , Yang Qiutan , Kubovčiak Jan , Stastna Monika , Hrckulak Dusan , Vojtechova Martina , Brügger Michael David , Hausmann George , Liberali Prisca , Korinek Vladimir , Basler Konrad , Valenta Tomas 
Published: November 2022

AbstractThe protective and absorptive functions of the intestinal epithelium rely on differentiated enterocytes in the villi. The differentiation of enterocytes is orchestrated by sub-epithelial mesenchymal cells producing distinct ligands along the villus axis, in particular Bmps and Tgfβ. Here we show that individual Bmp ligands and Tgfβ drive distinct enterocytic programs specific to villus zonation. Bmp4 is expressed mainly from the center to the upper part of the villus, and it activates preferentially genes connected to lipid uptake and metabolism. In contrast, Bmp2 is produced by villus-tip mesenchymal cells, and it influences the adhesive properties of villus-tip epithelial cells and the expression of immunomodulators. Hence, Bmp2 promotes the terminal enterocytic differentiation at the villus-tip. Additionally, Tgfβ induces epithelial gene expression programs similar to that triggered by Bmp2. The inhibition of Bmp receptor type Iin vivoand using intestinal organoids lacking Smad4 revealed that Bmp2-driven villus-tip program is activated by a canonical Smad-dependent mechanism. Finally, we established an organoid cultivation system that enriches for villus-tip enterocytes and thereby better mimics the cellular composition of the intestinal epithelium. Altogether our data suggest that not only Bmp gradient, but also the activity of individual Bmp drives specific enterocytic programs.
Dynamic Reassociation of the Nuclear Lamina with Newly Replicated DNA
Authors: Lovejoy Callie M. , Nagarajan Prabakaran , Parthun Mark R. 
Published: November 2022

ABSTRACTThe physical association of specific regions of chromatin with components of the nuclear lamina provides the framework for the 3-dimensionl architecture of the genome. The regulation of these interactions plays a critical role in the maintenance of gene expression patterns and cell identity. The breakdown and reassembly of the nuclear membrane as cells transit mitosis plays a central role in the regulation of the interactions between the genome and the nuclear lamina. However, other nuclear processes, such as transcription, have emerged as regulators of the association of DNA with the nuclear lamina. To determine whether DNA replication also has the potential to regulate DNA-nuclear lamina interactions, we adapted proximity ligation-based chromatin assembly assays to analyze the dynamics of nuclear lamina association with newly replicated DNA. We observe that lamin A/C and lamin B, as well as inner nuclear membrane proteins LBR and emerin, are found in proximity to newly replicated DNA. While core histones rapidly reassociate with DNA following passage of the replication fork, the complete reassociation of nuclear lamina components with newly replicated DNA occurs over a period of approximately 30 minutes. We propose models to describe the disassembly and reassembly of nascent chromatin with the nuclear lamina.
Tautomer-specific deacylation and Ω-loop flexibility explain carbapenem-hydrolyzing, broad-spectrum activity of the KPC-2 β-lactamase
Authors: Tooke Catherine L. , Hinchliffe Philip , Beer Michael , Zinovjev Kirill , Colenso Charlotte K. , Schofield Christopher J. , Mulholland Adrian J. , Spencer James 
Published: November 2022

AbstractKPC-2 (Klebsiella pneumoniaecarbapenemase-2) is a globally disseminated serine-β-lactamase (SBL) responsible for extensive β-lactam antibiotic resistance in Gram-negative pathogens. SBLs inactivate β-lactams via a mechanism involving a hydrolytically labile covalent acyl-enzyme intermediate. Carbapenems, the most potent β-lactams, evade activity of many SBLs by forming long-lived inhibitory acyl-enzymes; however, carbapenemases such as KPC-2 efficiently catalyze deacylation of carbapenem-derived acyl-enzymes. We present high-resolution (1.25-1.4 Å) crystal structures of KPC-2 acyl-enzymes with representative penicillins (ampicillin), cephalosporins (cefalothin) and carbapenems (imipenem, meropenem and ertapenem), obtained utilizing an isosteric deacylation-deficient mutant (E166Q). Mobility of the Ω-loop (residues 165–170) negatively correlates with antibiotic turnover rates (kcat), highlighting the role of this region in positioning catalytic residues for efficient hydrolysis of different β-lactams. Carbapenem-derived acyl-enzyme structures reveal predominance of the Δ1-(2R) imine tautomer, except for the imipenem acyl-enzyme, which is present in dual occupancy in both Δ1-(2R) and (2S) configurations. Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations of deacylation of the KPC-2:meropenem acyl-enzyme, using an adaptive string method (ASM), show that the Δ1-(2R) isomer has a 7 kcal/mol higher barrier for the (rate-determining) formation of the tetrahedral deacylation intermediate than the Δ2 tautomer. The simulations identify tautomer-specific differences in hydrogen bonding networks involving the carbapenem C-3 carboxylate and the deacylating water, that, together with stabilization by protonated N-4 of accumulating negative charge during oxyanion formation, accelerate deacylation of the Δ2-enamine acyl-enzyme compared to the Δ1-imine. Taken together, our data show how the flexible Ω-loop helps confer broad spectrum activity upon KPC-2, while carbapenemase activity stems from efficient deacylation of the Δ2-enamine acyl-enzyme tautomer. Differentiation of the barriers associated with deacylation of these subtly different β-lactam isomers further identifies ASM as a sensitive method for calculation of reaction energetics that can accurately model turnover and, potentially, predict the impact of substrate modifications or point mutations upon activity.
Parallel Activation of Src and Hif1α Increases Localized Glycolytic ATP Generation for Re-assembly of Endothelial Adherens Junctions
Authors: Wang Li , Gajwani Priyanka , Chaturvedi Pallavi , Hong Zhigang , Ye Zijing , Schwarz Gregory J. , Pohl-Avila Nicole M. , Ray Anne-Marie , Krantz Sarah , Toth Peter T , Leckband Deborah E. , Karginov Andrei , Rehman Jalees 
Published: November 2022

AbstractEndothelial adherens junctions (AJs) are critical for the regulation of vascular barrier integrity and undergo dis-assembly during inflammatory injury, thus causing vascular leakiness. AJ re-assembly is thus necessary for restoration of the endothelial barrier following the initial injury. Here we examine the metabolic underpinnings that drive restoration of vascular integrity. In response to inflammatory stimuli, the glycolysis regulatory enzyme PFKFB3 is activated, resulting in a rapid and sustained increase of intracellular glycolytic ATP, especially in the proximity of AJs at the plasma membrane. We engineered a novel chemo-genetic construct (RapT) which allowed for precise temporal control of PFKFB3 recruitment to the plasma membrane. Activation of RapT by rapamycin during the barrier restoration phase increased regional ATP and accelerated AJ re-assembly. Mechanistically, we observed that PFKFB3 is activated through two modes. Src-mediated post-translational phosphorylation rapidly increases PFKFB3 activity. Using another chemo-genetic approach to temporally control Src activity, we found that Src activates PFKFB3 by binding to and phosphorylating it at residues Y175, Y334, and Y363. Tyrosine-phospho-deficient mutants of PFKFB3 at these residues block the glycolytic activation upon inflammatory stimuli. In parallel, elevated reactive oxygen species generated during inflammatory stimulation create pockets of regional hypoxia and allow for increased Hif1α-mediated transcription of PFKFB3, leading to sustained glycolytic activation. Moreover, inhibition of PFKFB3 delays AJ reassembly and restoration of vascular integrity both in vitro and in vivo. In conclusion, we show that while inflammatory activation acutely compromises the endothelial barrier, inflammatory signaling also concomitantly generates a metabolic milieu in anticipation of the subsequent re-assembly of AJs and restoration of the vascular barrier.
High-throughput tagging of endogenous loci for rapid characterization of protein function
Authors: Kim Joonwon , Kratz Alexander F. , Chen Shiye , Sheng Jenny , Zhang Liudeng , Singh Brijesh Kumar , Chavez Alejandro 
Published: November 2022

AbstractTo facilitate the interrogation of protein function at scale, we have developed High-throughput Insertion of Tags Across the Genome (HITAG). HITAG enables users to rapidly produce libraries of cells, each with a different protein of interest C-terminally tagged is based on a modified strategy for performing Cas9-based targeted insertions, coupled with an improved approach for selecting properly tagged lines. Analysis of the resulting clones generated by HITAG reveals high tagging specificity with the majority of tagging events being indel free. Using HITAG, we fuse mCherry to a set of 167 stress granule-associated proteins and elucidate the features which drive a subset of proteins to strongly accumulate within these transient RNA-protein granules.