bluuebunny/crossref_metadata_2025_split huggingface dataset:
Noninvasive Diagnosis of Acute Rejection in Renal Transplant Patients Using Mass Spectrometric Analysis of Urine Samples: A Multicenter Diagnostic Phase III Trial
Authors: Gwinner Wilfried , Karch Annika , Braesen Jan H. , Khalifa Abedalrazag A. , Metzger Jochen , Naesens Maarten , Van Loon Elisabet , Anglicheau Dany , Marquet Pierre , Budde Klemens , Matz Mareen , Arns Wolfgang , Fischereder Michael , Habicht Antje , Eisenberger Ute , Mühlfeld Anja , Busch Martin , Wiesener Michael , Scheffner Irina , Koch Armin 
Published: April 2022

Background.
Timely recognition and treatment of acute kidney graft rejection is important to prevent premature graft failure. A predefined urinary marker set for acute T cell–mediated rejection (TCMR) containing 14 peptides was tested for this purpose in a multicenter in-place validation study.

Methods.
Three hundred twenty-nine prospectively collected and 306 archived urine samples from 11 transplant centers in Germany, France, and Belgium were examined. Samples were taken immediately before a biopsy, performed for graft dysfunction within the first transplant year. Primary outcomes were sensitivity and specificity of the marker set for the diagnosis of biopsy-proven acute TCMR, with prespecified thresholds of 83% for sensitivity and 70% for specificity.

Results.
Eighty-two patients (13%) had acute TCMR grade I–III. In relation to the biopsy diagnosis of TCMR, the sensitivity of the urine test was 0.66 (95% confidence interval, 0.56-0.76) and the specificity 0.47 (95% confidence interval, 0.43-0.51), with an area under the curve (AUC) of 0.60. The different TCMR grades I–III were not reflected by the marker set, and borderline TCMR was not specifically detected. Secondary independent masked assessment of biopsies consented by 2 pathologists revealed an interobserver kappa value of 0.49 for diagnosing TCMR, compared with the local center’s diagnosis. Using this consensus diagnosis, the AUC of the urine test was 0.63 (sensitivity 0.73, specificity 0.45). Post hoc optimization of the marker set improved the diagnostic performance in the study cohort (AUC 0.67) and in an independent patient cohort (AUC 0.69).

Conclusions.
This study illustrates the difficulty of proteomics-based diagnosis of TCMR and highlights the need for rigorous independent in-place validation and optimization of diagnostic biomarkers.
Candidate genes associated with neurological manifestations of COVID-19: Meta-analysis using multiple computational approaches
Authors: Hazra Suvojit , Chaudhuri Alok Ghosh , Tiwary Basant K. , Chakrabarti Nilkanta 
Published: April 2022

ABSTRACTCOVID-19 develops certain neurological symptoms, the molecular pathophysiology of which is obscure. In the present study, two networks were constructed and their hub-bottleneck and driver nodes were evaluated to consider them as ‘target genes’ followed by identifying ‘candidate genes’ and their associations with neurological phenotypes of COVID-19. A tripartite network was first constructed using literature-based neurological symptoms of COVID-19 as input. The target genes evaluated therefrom were then used as query genes to identify the co-expressed genes from the RNA-sequence data of the frontal cortex of COVID-19 patients using pair-wise mutual information to genes. A ‘combined gene network’ (CGN) was constructed with 189 genes selected from TN and 225 genes co-expressed in COVID-19. Total 44 ‘target genes’ evaluated from both networks and their connecting genes in respective networks were analyzed functionally by measuring pair-wise ‘semantic similarity scores’ (SSS) and finding Enrichr annotation terms against a set of genes. A new integrated ‘weighted harmonic mean score’ was formulated using SSS and STRING-based ‘combined score’ to select 21 gene-pairs among ‘target genes’ that provided 21 ‘candidate genes’ with their properties as ‘indispensable driver nodes’ of CGN. Finally, six pairs providing seven prevalent candidate genes (ADAM10, ADAM17, AKT1, CTNNB1, ESR1, PIK3CA, FGFR1) exhibited direct linkage with the neurological phenotypes under tumour/cancer, cellular signalling, neurodegeneration and neurodevelopmental diseases. The other phenotypes under behaviour/cognitive and motor dysfunctions showed indirect associations with the former genes through other candidate genes. The pathophysiology of ‘prevalent candidate genes’ has been discussed for better interpretation of neurological manifestation in COVID-19.
A discovery pipeline for identification and in vivo validation of drugs that alter T cell/ dendritic cell interaction
Authors: Scales Hannah E. , Keijzer Chantal , Evertsson Emma , Garside Paul , Delaney Stephen , Brewer James M. 
Published: April 2022

ABSTRACTThe interaction between T cells and dendritic cells (DC) is central to determining whether or not an adaptive immune response develops. Autoimmune diseases like rheumatoid arthritis result from inappropriate activation of self-antigen specific T cells, therefore targeting the interaction between T cells and DCs is of considerable therapeutic interest. Here, we describe the development and validation of a drug development platform that includes a high-throughput image-based screening assay and a complementary in vivo model. The in vitro assay directly measures the ability of compounds to influence the interaction of T cells with DC, both negatively and positively. While the in vivo model allows the validation of hit molecules directly in the lymph nodes of intact animals. Using this pipeline, we identify a new function for the protein kinase inhibitor AS703569 by inhibiting T cell/ DC interactions in vitro and in vivo.
UBC9 and EME1 sumoylation foster ribosomal DNA damage repair in CPT response
Authors: Nagamalleswari Easa , Bakshi Karishma , Breucker Jan , Gschweitl Michaela , González-Prieto Román , Eisenhardt Nathalie , Fatouros Chronis , Chaugule Viduth K , Vertegaal Alfred C.O. , Pichler Andrea 
Published: April 2022

AbstractUBC9 sumoylation (S*UBC9) in mammals contributes to SUMO target discrimination, biochemically1. Here, we present biological insights by characterizing a sumoylation mimetic UBC9-fusion (mCS~UBC9) in comparison to its wild-type (mCUBC9). We observe that sumoylation promotes UBC9’s stability, nuclear localization and is beneficial for cell survival. We identified EME1, the regulatory subunit of the structure-specific endonuclease EME1-MUS81, as S*UBC9 substrate and demonstrate EME1 and UBC9 sumoylation being advantageous for survival upon Camptothecin (CPT) exposure. Moreover, mCS~UBC9 expression enhances double-strand breaks (DSBs) and replication upon CPT treatment, features assigned to the EME1-MUS81 complex2. EME1 and mCS~UBC9 co-localize in nucleolar repair-condensates, that enlarge and round when exposed to the drug. Together, these findings imply that S*UBC9-induced EME1 sumoylation improves ribosomal rDNA repair, which might prevent dangerous second template switches in highly repetitive ribosomal chromatin and allow the converging replication fork to complete DNA replication. Finally, we discuss implications of these findings for anti-cancer therapy.
Influence of RNA circularity on Target RNA-Directed MicroRNA Degradation
Authors: Wightman Federico Fuchs , Lukin Jerónimo , Giusti Sebastián , Soutschek Michael , Bragado Laureano , Pozzi Berta , González Paula , Fededa Juan P. , Schratt Gerhard , Fujiwara Rina , Wilusz Jeremy E. , Refojo Damián , de la Mata Manuel 
Published: April 2022

AbstractA subset of circular RNAs (circRNAs) and linear RNAs have been proposed to “sponge” or block microRNA activity. Additionally, certain RNAs induce microRNA destruction through the process of Target RNA-Directed MicroRNA Degradation (TDMD), but whether both linear and circular transcripts are equivalent in driving TDMD is unknown. Here we study whether circular/linear topology of endogenous and artificial RNA targets affects TDMD. Consistent with previous knowledge thatCdr1as (ciRS-7)circular RNA protects miR-7 from Cyrano-mediated TDMD, we demonstrate that depletion ofCdr1asreduces miR-7 abundance. In contrast, overexpression of an artificial linear version ofCdr1asdrives miR-7 degradation. Using plasmids that express a circRNA with minimal co-expressed cognate linear RNA, we show differential effects on TDMD that cannot be attributed to the nucleotide sequence, as the TDMD properties of a sequence often differ between its circular and linear forms. By analysing RNA sequencing data of a neuron differentiation system, we further detect potential effects of circRNAs on microRNA stability. Our results support the view that RNA circularity influences TDMD, either enhancing or inhibiting it on specific microRNAs.
The specific roles of renal macrophages in monitoring and clearing off intratubular particles
Authors: He Jian , Cao Yangyang , Zhu Qian , Wang Xinge , Cheng Guo , Wang Qiang , Han Fei , Shi Peng , Shen Xiao Z 
Published: April 2022

ABSTRACTDuring the filtrate of the glomerulus flows though the renal tubular system, a variety of microscopic sediment particles, including mineral crystals resulting from urine concentration, are generated. Dislodging these particles in the intratubular compartment is critical to ensure free flow of filtrate and the final formation of urine. However, the underlying mechanism for the clearance is unclear. Here, using high-resolution microscopy, we uncovered that the juxtatubular macrophages in the medulla constitutively formed transepithelial protrusions and were “sampling” urine contents. These behaviors were strengthened in the development of nephrolithiasis. In particular, the juxtatubular macrophages were efficient in sequestering and phagocytosing intraluminal sediment particles, and occasionally making transmigration to the tubule lumen to escort the excretion of urine particles. Specific depletion of renal macrophages precipitated kidney stone formation and aggravated the accompanied inflammation upon hyperoxaluria challenge. Thus, renal macrophages undertake a specific role in maintaining the tubular system unobstructed.
Preclinical evaluation of CDK4 phosphorylation predicts high sensitivity of malignant pleural mesotheliomas to CDK4/6 inhibition
Authors: Paternot Sabine , Raspé Eric , Meiller Clément , Tarabichi Maxime , Assié Jean-Baptiste , Libert Frederick , Remmelink Myriam , Bisteau Xavier , Pauwels Patrick , Blum Yuna , Le Stang Nolwenn , Tabone-Eglinger Séverine , Galateau-Sallé Françoise , Blanquart Christophe , Van Meerbeeck Jan P. , Berghmans Thierry , Jean Didier , Roger Pierre P. 
Published: April 2022

AbstractMalignant pleural mesothelioma (MPM) is an aggressive cancer with limited therapeutic options. In this study, we evaluated the impact of CDK4/6 inhibition by palbociclib in a panel of 28 MPM cell lines, including 19 patient-derived cell lines, using a variety of approaches including RNA-sequencing. Palbociclib used alone sufficed to strongly and durably inhibit the proliferation of 23 MPM cell lines, indicating a unique sensitivity of MPM to CDK4/6 inhibition. Importantly, insensitivity to palbociclib was mostly explained by the lack of active T172-phosphorylated CDK4. This was associated with the high p16INK4A (CDKN2A) levels that accompany RB1 defects or inactivation, and also (unexpectedly) cyclin E1 over-expression in the presence of wild-type RB1. Prolonged treatment with palbociclib irreversibly inhibited proliferation despite re-induction of cell cycle genes upon drug washout. A senescence-associated secretory phenotype including various potentially immunogenic components was also irreversibly induced. Phosphorylated CDK4 was detected in 80% of 47 MPM tumors indicating their intrinsic sensitivity to CDK4/6 inhibitors. The absence of this phosphorylation in some highly proliferative MPM tumors was linked to partial deletions of RB1, leading to very high p16 (CDKN2A) expression. Our study strongly supports the clinical evaluation of CDK4/6 inhibitory drugs for MPM treatment, in monotherapy or combination therapy.
Fatty sweet symphony: Decoding distinct ganglioside patterns of native and differentiated mesenchymal stem cells by a novel glycolipidomics profiling strategy
Authors: Hohenwallner Katharina , Troppmair Nina , Panzenboeck Lisa , Kasper Cornelia , El Abiead Yasin , Koellensperger Gunda , Lamp Leonida M. , Hartler Jürgen , Egger Dominik , Rampler Evelyn 
Published: April 2022

AbstractGangliosides are an indispensable glycolipid class concentrated on cell surfaces with a critical role in stem cell differentiation. Nonetheless, owing to the lack of suitable methods for scalable analysis covering the full scope of ganglioside molecular diversity, their mechanistic properties in signaling and differentiation remain undiscovered to a large extent. This work introduces a sensitive and comprehensive ganglioside assay based on liquid chromatography, high-resolution mass spectrometry, and multistage fragmentation. Complemented by an open-source data evaluation workflow, we provide automated in-depth lipid species-level and molecular species-level annotation based on decision rule sets for all major ganglioside classes. Compared to conventional state-of-the-art methods, the presented ganglioside assay offers (1) increased sensitivity, (2) superior structural elucidation, and (3) the possibility to detect novel ganglioside species. A major reason for the highly improved sensitivity is the optimized spectral readout based on the unique capability of two parallelizable mass analyzers for multistage fragmentation. In addition to the significant technological advance, we identified 263 ganglioside species including cell-state-specific markers and previously unreported gangliosides in native and differentiated human mesenchymal stem cells. A general increase of the ganglioside numbers upon differentiation was observed as well as cell-state-specific clustering based on the ganglioside species patterns. By proving the predictive power of gangliosides as ubiquitous cell state-specific markers, we demonstrated the high throughput universal capability of our novel analytical strategy, which comes with new insights on the biological role of gangliosides in stem cell differentiation. Our analytical workflow will pave the way for new ganglioside- and glycolipid-based clusters of differentiation markers to determine stem cell phenotypes.
Every individual makes a difference: A trinity derived from linking individual brain morphometry, connectivity and mentalising ability
Authors: Li Zhaoning , Dong Qunxi , Hu Bin , Wu Haiyan 
Published: April 2022

AbstractMentalising ability, indexed as the ability to understand others’ beliefs, feelings, intentions, thoughts and traits, is a pivotal and fundamental component of human social cognition. However, considering the multifaceted nature of mentalising ability, little research has focused on characterising individual differences in different mentalising components. And even less research has been devoted to investigating how the variance in the structural and functional patterns of the amygdala and hippocampus, two vital subcortical regions of the ‘social brain’, are related to inter-individual variability in mentalising ability. Here, as a first step toward filling these gaps, we exploited inter-subject representational similarity analysis (IS-RSA) to assess relationships between amygdala and hippocampal morphometry (surface-based multivariate morphometry statistics, MMS), connectivity (resting-state functional connectivity, rs-FC) and mentalising ability (interactive mentalisation questionnaire (IMQ) scores) across the participants (N= 24). In IS-RSA, we proposed a novel pipeline, i.e., computing patching and pooling operations-based surface distance (CPP-SD), to obtain a decent representation for high-dimensional MMS data. On this basis, we found significant correlations (i.e., secondorder isomorphisms) between these three distinct modalities, indicating that a trinity existed in idiosyncratic patterns of brain morphometry, connectivity and mentalising ability. Notably, a region-related mentalising specificity emerged from these associations: self-self and self-other mentalisation are more related to the hippocampus, while other-self mentalisation shows a closer link with the amygdala. Furthermore, by utilising the dyadic regression analysis, we observed significant interactions such that subject pairs with similar morphometry had even greater mentalising similarity if they were also similar in rs-FC. Altogether, we demonstrated the feasibility and illustrated the promise of using IS-RSA to study individual differences, deepening our understanding of how individual brains give rise to their mentalising abilities.
Tomographic-encoded multiphoton (TEMP) microscopy
Authors: He Hongsen , Dong Xin , Ren Yu-Xuan , Lai Cora S. W. , Tsia Kevin K. , Wong Kenneth K. Y. 
Published: April 2022

ABSTRACTAxial scanning in multiphoton microscopy (MPM) is typically realized by mechanically shifting either the objective or the sample. However, the scan speed is usually hindered by the mechanical inertia of the bulky mass. Although the extended depth of field provided by the non-diffracting beam allows fast volumetric imaging, it abandons the axial resolution. Here, we demonstrate a novel and powerful tomographic technique using the Bessel droplet in MPM, termed Tomographic-Encoded MultiPhoton (TEMP) microscopy. We show that benefiting from the high-order nonlinear excitation in MPM, the side-lobes cancellation and smaller beam focus of the Bessel droplet realize better image quality. The TEMP microscopy allows fast axial scanning, less risks of photodamage and photobleaching, and high-resolution and high-contrast imaging. Furthermore, fewer raw images are required for the 3D image reconstruction. To demonstrate its usability and advantages for scattering tissues and biomedical applications, we showcase the TEMP microscopy with highly scattering fluorescence microspheres and mouse brain slice. More details can be visualized by the Bessel droplet compared with the conventional Gaussian and Bessel beam. More importantly, the TEMP technique is an easy-plug-in method for the current microscopy system. The TEMP microscopy is promising for fast volumetric multiphoton imaging, especially for highly scattering tissues.
Protein engineering approach to enhance activity assays of mono-ADP-ribosyltransferases through proximity
Authors: Galera-Prat Albert , Alaviuhkola Juho , Alanen Heli I. , Lehtiö Lari 
Published: April 2022

AbstractHuman mono-ADP-ribosylating PARP enzymes have been linked to several clinically relevant processes and many of these PARPs have been suggested as potential drug targets. Despite recent advances in the field, efforts to discover such compounds have been hindered by the lack of tools to rapidly screen for high potency compounds and profile them against the different PARP enzymes of the ARTD family. We here expanded the methods and engineered mono-ART catalytic fragments to be incorporated into a cellulosome-based octavalent scaffold. Compared to the free enzymes, the scaffold-based system results in an improved activity for the tested PARPs due to improved solubility, stability and the proximity of the catalytic domains, altogether boosting their activity beyond 10-fold in the case of PARP12. This allows us to measure their enhanced activity using a simple and easily accessible homogeneous NAD+ conversion assay, facilitating its automation to reduce the assay volume and lowering the assay costs. The approach will enable the discovery of more potent compounds due to increased assay sensitivity and it can be applied to compound screening campaigns as well as inhibitor profiling.
The conserved centrosomal motif, γTuNA, forms a dimer that directly activates microtubule nucleation by the γ-tubulin ring complex (γTuRC)
Authors: Rale Michael , Romer Brianna , Mahon Brian P. , Travis Sophie M. , Petry Sabine 
Published: April 2022

1.SummaryTo establish the microtubule cytoskeleton, the cell must tightly regulate when and where microtubules are nucleated. This regulation involves controlling the initial nucleation template, the γ-tubulin ring complex (γTuRC). Although γTuRC is present throughout the cytoplasm, its activity is restricted to specific sites including the centrosome and Golgi. The well-conserved γ-tubulin nucleation activator (γTuNA) domain has been reported to increase the number of microtubules generated by γTuRCs. Here we utilize Xenopus egg extract and in vitro single molecule imaging assays to show that γTuNA activates microtubule nucleation in extract and directly activates γTuRC in vitro. Via mutation analysis, we find that γTuNA is an obligate dimer. Moreover, efficient dimerization as well as γTuNA’s L70, F75, and L77 residues are required for binding to and activation of γTuRC. Finally, we find that γTuNA’s activating effect opposes inhibitory regulation by stathmin. In sum, our study illuminates how γTuRC is controlled in space and time in order to build specific cytoskeletal structures.
Ribosome stalling during selenoprotein translation exposes a ferroptosis vulnerability in cancer
Authors: Li Zhipeng , Ferguson Lucas , Deol Kirandeep K. , Roberts Melissa A. , Magtanong Leslie , Bassik Michael C. , Dixon Scott J. , Ingolia Nicholas T. , Olzmann James A. 
Published: April 2022

ABSTRACTFerroptosis is a regulated, iron-dependent form of necrosis that is triggered by the accumulation of oxidatively damaged phospholipids1–3. Glutathione peroxidase 4 (GPX4) prevents ferroptosis by converting phospholipid hydroperoxides into non-toxic lipid alcohols4, 5. Ferroptosis has been implicated in the pathology of several degenerative conditions and inhibiting GPX4 activity has emerged as a therapeutic strategy to induce cancer cell death1, 2. However, many cancer cell lines are resistant to GPX4 inhibition6, and the mechanisms that regulate GPX4 activity and ferroptosis resistance remain incompletely understood. Here, employing a synthetic lethal CRISPR-Cas9 screen in a triple negative breast cancer (TNBC) cell line, we identify LRP8 (also known as ApoER2) as a ferroptosis resistance factor. LRP8 is upregulated in cancer, and we find that it promotes ferroptosis resistance in cancer cells in both 2-dimensional (2-D) cell culture and 3-dimensional (3-D) spheroid models. Mechanistically, loss of LRP8 decreases cellular selenium levels, resulting in the reduced expression of a subset of selenoproteins, including GPX4. Remarkably, the reduction in GPX4 is not due to the classic hierarchical selenoprotein regulatory program7, 8. Instead, our findings demonstrate that the translation of GPX4 is severely impaired in the selenium-deficient LRP8 knockout (KO) cells due to extensive ribosome stalling at the inefficiently decoded GPX4 selenocysteine (SEC) UGA codon, which results in ribosome collisions and early translation termination. Thus, our findings reveal ribosome stalling and collisions during GPX4 translation as targetable ferroptosis vulnerabilities in cancer cells.