bluuebunny/crossref_metadata_2025_split huggingface dataset:
SpliceMutr enables pan-cancer analysis of splicing-derived neoantigen burden in tumors
Authors: Palmer Theron , Kessler Michael D , Shao Xiaoshan M. , Balan Archana , Yarchoan Mark , Zaidi Neeha , Lopez-Vidal Tamara Y , Saeed Ali , Gore Jessica , Azad Nilofer S , Jaffee Elizabeth M , Favorov Alexander V , Anagnostou Valsamo , Karchin Rachel , Gaykalova Daria A , Danilova Ludmila , Fertig Elana J 
Published: May 2023

AbstractAberrant alternative splicing can generate neoantigens, which can themselves stimulate immune responses and surveillance. Previous methods for quantifying splicing-derived neoantigens are limited by independent references and potential batch effects. Here, we introduce SpliceMutr, a bioinformatics approach and pipeline for identifying splicing derived neoantigens from tumor and normal data. SpliceMutr facilitates the identification of tumor-specific antigenic splice variants, predicts MHC-binding affinity, and estimates splicing antigenicity scores per gene. By applying this tool to genomic data from The Cancer Genome Atlas (TCGA), we generate splicing-derived neoantigens and neoantigenicity scores per sample and across all cancer types and find numerous correlations between splicing antigenicity and well-established biomarkers of anti-tumor immunity. Notably, carriers of mutations within splicing machinery genes have higher splicing antigenicity, which provides support for our approach. Further analysis of splicing antigenicity in cohorts of melanoma patients treated with mono-or combined immune checkpoint inhibition suggest that the abundance of splicing antigens is reduced post-treatment from baseline in patients who progress, likely because of an immunoediting process. We also observe increased splicing antigenicity in responders to immunotherapy, which may relate to an increased capacity to mount an immune response to splicing-derived antigens. We find the splicing antigenicity to be higher in tumor samples when compared to normal, that mutations in the splicing machinery result in increased splicing antigenicity in some cancers, and higher splicing antigenicity is associated with positive response to immune checkpoint inhibitor therapies. Further, this new computational pipeline provides novel analytical capabilities for splicing antigenicity and is openly available for further immuno-oncologic analysis.
Protein-mediated genome folding allosterically enhances site-specific integration of foreign DNA into CRISPRs
Authors: Santiago-Frangos Andrew , Henriques William S. , Wiegand Tanner , Gauvin Colin C. , Buyukyoruk Murat , Graham Ava B. , Wilkinson Royce A. , Triem Lenny , Neselu Kasahun , Eng Edward T. , Lander Gabriel C. , Wiedenheft Blake 
Published: May 2023

AbstractBacteria and archaea acquire resistance to viruses and plasmids by integrating fragments of foreign DNA into the first repeat of a CRISPR array. However, the mechanism of site-specific integration remains poorly understood. Here, we determine a 560 kDa integration complex structure that explains how Cas (Cas1-2/3) and non-Cas proteins (IHF) fold 150 base-pairs of host DNA into a U-shaped bend and a loop that protrude from Cas1-2/3 at right angles. The U-shaped bend traps foreign DNA on one face of the Cas1-2/3 integrase, while the loop places the first CRISPR repeat in the Cas1 active site. Both Cas3s rotate 100-degrees to expose DNA binding sites on either side of the Cas2 homodimer, that each bind an inverted repeat motif in the leader. Leader sequence motifs direct Cas1-2/3-mediated integration to diverse repeat sequences that have a 5’-GT.
The folding-limited nucleation of curli hints at an evolved safety mechanism for functional amyloid production
Authors: Claridge Jolyon K. , Martens Chloe , Pradhan Brajabandhu , Sobott Frank , Sleutel Mike , Remaut Han 
Published: May 2023

AbstractIt is nearly two decades ago that the ‘thin aggregative fimbriae’ which had been shown to enhance the biofilm formation ofSalmonella enteriditisandEscherichia coliwere identified as amyloid fibers. The realization that natural proteins can develop amyloidogenic traits as part of their functional repertoire instigated a search for similar proteins across all kingdoms of life. That pursuit has since unearthed dozens of candidates which now constitute the family of proteins referred to as functional amyloids (FA). FAs are promising candidates for future synthetic biology applications in that they marry the structural benefits of the amyloid fold (self-assembly and stability) while steering clear of the cytotoxicity issues that are typically linked to amyloid associated human pathologies. Unfortunately, the extreme aggregation propensity of FAs and the associated operational difficulties are restricting their adoption in real-world applications, underscoring the need for additional processes to control the amyloid reaction. Here we untangle the molecular mechanism of amyloid formation of the canonical functional amyloid curli using NMR, native mass spectrometry and cryo-electron microscopy. Our results are consistent with folding-limited one-step amyloid nucleation that has emerged as an evolutionary balance between efficient extracellular polymerization, while steering clear of pre-emptive nucleation in the periplasm. Sequence analysis of the amyloid curlin kernel suggests a finetuning of the rate of monomer folding via modulation of the secondary structure propensity of the pre-amyloid species, opening new potential avenues towards control of the amyloid reaction.
Network Pharmacology and molecular docking approach to unveil the mechanism ofHypericum perforatumin the management of Alzheimer’s disorder
Authors: Dogra Vishali , Choudhary Manjusha , Parashar Arun , Choudhary Nitesh 
Published: May 2023

AbstractThe pathogenesis of Alzheimer’s disease (AD) is not fully understood which limits the availability of safer and more efficient therapeutic strategies for the management of AD. There has been growing interest in recent years in exploring the potential of herbal medicines as a source of safer and alternative therapeutic strategies for the management of AD. This study aims to discover the mechanism ofHypericum perforatumin the management of AD using network pharmacology and molecular docking approach. The results of network pharmacology suggest that 39 bioactive molecules ofH. perforatumtarget 127 genes associated with AD, amongst which ATP-dependent translocase, acetylcholinesterase, amyloid-β precursor protein, β-secretase 1, carbonic anhydrase 2, dipeptidyl peptidase 4, epidermal growth factor receptor, tyrosine-protein phosphatase non-receptor type 1, α-synuclein, and vascular endothelial growth factor A seems to be the prominent target of these molecules. Further, the results of molecular docking predicted amentoflavone, I3,II8-biapigenin, rutin, miquelianin, quercetin, luteolin, and nicotiflorin as a promising modulator of target proteins which were determined from network pharmacology to be associated with AD. Our findings suggest thatH. perforatumcould be a safer and more promising alternative therapeutic strategy for the management of AD by targeting multiple pathways of AD pathogenesis.
Nunchaku: Optimally partitioning data into piece-wise linear segments
Authors: Huo Yu , Li Hongpei , Wang Xiao , Du Xiaochen , Swain Peter S. 
Published: May 2023

AbstractWhen analysing two-dimensional data sets, scientists are often interested in regions where one variable depends linearly on the other. Typically they use anad hocmethod to do so. Here we develop a statistically rigorous, Bayesian approach to infer the optimal partitioning of a data set into contiguous piece-wise linear segments. Ournunchakualgorithm is freely available. Focusing on microbial growth, we usenunchakuto identify the range of optical density where the density is linearly proportional to the number of cells and to automatically find the regions of exponential growth for bothEscherichia coliandSaccharomyces cerevisiae. For budding yeast, we consequently are able to infer the Monod constant for growth on fructose. Our algorithm lends itself to automation and high throughput studies, increases reproducibility, and will facilitate data analysis for a broad range of scientists.
Assessing the role of trypsin in quantitative plasma- and single-cell proteomics towards clinical application
Authors: Woessmann Jakob , Petrosius Valdemaras , Üresin Nil , Kotol David , Aragon-Fernandez Pedro , Hober Andreas , Keller Ulrich auf dem , Edfors Fredrik , Schoof Erwin M. 
Published: May 2023

AbstractMass spectrometry-based bottom-up proteomics is rapidly evolving and routinely applied in large biomedical studies. Proteases are a central component of every bottom-up proteomics experiment, digesting proteins into peptides. Trypsin has been the most widely applied protease in proteomics, due to its characteristics. With ever-larger cohort sizes and possible future clinical application of mass spectrometry-based proteomics, the technical impact of trypsin becomes increasingly relevant. To assess possible biases introduced by trypsin digestion, we evaluated the impact of eight commercially available trypsins in a variety of bottom-up proteomics experiments, and across a range of protease concentrations and storage times. To investigate the universal impact of these technical attributes, we included bulk HeLa-cell lysate, human plasma and single HEK293 cells, which were analyzed over a range of Selected Reaction Monitoring (SRM), Data-Independent Acquisition (DIA), and Data-Dependent Acquisition (DDA) instrument methods on three LC-MS instruments. Quantification methods employed encompassed both label-free approaches and absolute quantification utilizing spike-in heavy-labeled recombinant protein fragment standards. Based on this extensive dataset, we report variations between commercial trypsins, their source, as well as their concentration. Furthermore, we provide suggestions on the handling of trypsin in large scale studies.
Trypanosoma bruceibloodstream form mitochondrion is capable of ATP production by substrate phoshorylation
Authors: Gergana Taleva , Michaela Husova , Brian Panicucci , Carolina Hierro-Yap , Erika Pineda , Biran Marc , Moos Martin , Šimek Petr , Frederic Bringaud , Alena Zíková 
Published: May 2023

AbstractThe bloodstream formTrypanosoma bruceimaintains essential mitochondrial membrane potential (ΔΨm) through the reverse activity of FoF1-ATP synthase. The ATP that drives this activity is thought to be generated by glycolysis and imported from the cytosol via an ATP/ADP carrier (AAC). We have shown that this carrier is the only carrier that can import ATP into the mitochondrial matrix to power the FoF1-ATPase. Contrary to expectations, its deletion has no effect on parasite growth, virulence and levels of ΔΨm, suggesting that ATP is produced intramitochondrially by substrate phosphorylation pathways. Therefore, we knocked out the succinyl-CoA synthetase (SCoAS) gene, a key enzyme that produces ATP through substrate phosphorylation. Its absence resulted in changes in the metabolic landscape of the parasite, lower virulence, and reduced mitochondrial ATP content. This minimal mitochondrial ATP pool was maintained by AAC activity as evidenced by the 25- fold increase in sensitivity of the mutant parasites to AAC inhibitor carboxyatractyloside. Under nutrient-limited conditions, suppression of SCoAS expression by RNA interference negatively affected cell growth and levels of ΔΨm. We concluded that the bloodstream mitochondrion is capable of generating ATP via substrate phosphorylation pathways, the importance of which depends on environmental conditions.
A cytological and functional framework of the meiotic spindle assembly checkpoint inArabidopsis thaliana
Authors: Lampou Konstantinos , Böwer Franziska , Komaki Shinichiro , Köhler Maren , Schnittger Arp 
Published: May 2023

AbstractThe spindle assembly checkpoint (SAC) is a surveillance mechanism active during metaphase to prevent aneuploidy. The SAC is especially important during meiosis to maintain genome stability over generations and sustain fertility. However, despite its crucial role for reproduction and breeding, little is known about the plant meiotic SAC. Here, we present a cytological and functional framework of the SAC in male meiocytes ofArabidopsis thaliana. Using live-cell imaging, we have dissected the temporal association of SAC components with the kinetochore and have identified the three conserved kinases BMF1, MPS1 and AURORA as crucial regulators of the loading of BMF3 to kinetochores. Functionally characterizing core SAC components, we found that BUB3.3 has a predominant and previously not recognized role in chromosome congression. We suggest that BUB3.3 is involved in efficient kinetochore-microtubule interactions. Furthermore, the meiotic SAC is only active for a limited time under severe microtubule destabilizing conditions leading to the hypothesis that the relaxed nature of the meiotic SAC is a gateway to polyploidization and hence might contribute to genome evolution in plants.
Thioredoxin regulates the redox state and the activity of the human tRNA ligase complex
Authors: Jaksch Dhaarsini , Irnstorfer Johanna , Kalman Petra-Franziska , Martinez Javier 
Published: May 2023

AbstractThe mammalian tRNA ligase complex (tRNA-LC) catalyzes the splicing of intron-containing pre-tRNAs in the nucleus and the splicing ofXBP1mRNA during the unfolded protein response (UPR) in the cytoplasm. We recently reported that the tRNA-LC co-evolved with PYROXD1, an essential oxidoreductase that protects the catalytic cysteine of RTCB, the catalytic subunit of the tRNA-LC, against aerobic oxidation. In this study we show that the oxidoreductase Thioredoxin (TRX) preserves the enzymatic activity of RTCB under otherwise inhibiting concentrations of oxidants. TRX physically interacts with oxidized RTCB, and reduces and re-activates RTCB through the action of its redox-active cysteine pair. We further show that TRX interacts with RTCB at late stages of UPR. Since the interaction requires oxidative conditions, our findings suggest that prolonged UPR generates reactive oxygen species. Thus, our results support a functional role for TRX in securing and repairing the active site of the tRNA-LC, thereby allowing pre-tRNA splicing and UPR to occur when cells encounter mild, but still inhibitory levels of reactive oxygen species.
SOX7: Novel Autistic Gene Identified by Analysis of Multi-Omics Data
Authors: Gonzales Samantha , Zhao Jane Zizhen , Choi Na Young , Acharya Prabha , Jeong Sehoon , Lee Moo-Yeal 
Published: May 2023

ABSTRACTBackgroundGenome-wide association studies and next generation sequencing data analyses based on DNA information have identified thousands of mutations associated with autism spectrum disorder (ASD). However, more than 99% of identified mutations are non-coding. Thus, it is unclear which of these mutations might be functional and thus potentially causal variants. Transcriptomic profiling using total RNA-sequencing has been one of the most utilized approaches to link protein levels to genetic information at the molecular level. The transcriptome captures molecular genomic complexity that the DNA sequence solely does not. Some mutations alter a gene’s DNA sequence but do not necessarily change expression and/or protein function. To date, few common variants reliably associated with the diagnosis status of ASD despite consistently high estimates of heritability. In addition, reliable biomarkers used to diagnose ASD or molecular mechanisms to define the severity of ASD do not exist.ObjectivesIt is necessary to integrate DNA and RNA testing together to identify true causal genes and propose useful biomarkers for ASD.MethodsWe performed gene-based association studies with adaptive test using genome-wide association studies (GWAS) summary statistics with two large GWAS datasets (ASD 2019 data: 18,382 ASD cases and 27,969 controls [discovery data]; ASD 2017 data: 6,197 ASD cases and 7,377 controls [replication data]) which were obtained from the Psychiatric Genomics Consortium (PGC). In addition, we investigated differential expression for genes identified in gene-based GWAS with a RNA-seq dataset (GSE30573: 3 cases and 3 controls) using the DESeq2 package.ResultsWe identified 5 genes significantly associated with ASD in ASD 2019 data (KIZ-AS1, p=8.67×10−10; KIZ, p=1.16×10−9; XRN2, p=7.73×10−9; SOX7, p=2.22×10−7; PINX1-DT, p=2.14×10−6). Among these 5 genes, gene SOX7 (p=0.00087), LOC101929229 (p=0.009), and KIZ-AS1 (p=0.059) were replicated in ASD 2017 data. KIZ (p=0.06) was close to the boundary of replication in ASD 2017 data. Genes SOX7 (p=0.0017, adjusted p=0.0085), LOC101929229 (also known as PINX1-DT, p=5.83×10−7, adjusted p=1.18×10−5), and KIZ (p=0.00099, adjusted p=0.0055) indicated significant expression differences between cases and controls in the RNA-seq data. SOX7 encodes a member of the SOX (SRY-related HMG-box) family of transcription factors pivotally contributing to determining of the cell fate and identity in many lineages. The encoded protein may act as a transcriptional regulator after forming a protein complex with other proteins leading to autism.ConclusionGene SOX7 in the transcription factor family could be associated with ASD. This finding may provide new diagnostic and therapeutic strategies for ASD.
SIX4 Controls STING Expression Enhancing anti-PD-1 Efficacy
Authors: Liang Beiyuan , Zhang Evan H. , Ye Zhen , Storts Hayden , Zheng Xinru , Zaleski Olivia , Jin Wei , Xing Xuanxuan , Wang Jing J. 
Published: May 2023

AbstractThe cGAS/STING cytosolic DNA sensing pathway plays a central role in anti-tumor immunity. Expression of STING is tightly regulated and commonly reduced or defective in many types of cancer. We have identified SIX4 as a significant regulator of STING expression in colon cancer cells. We showed that knockout of SIX4 decreased STING expression at the mRNA and protein levels while ectopic expression of SIX4 increased STING expression. Depletion of SIX4 led to attenuated STING activation and downstream signaling. Re-expression of SIX4 or ectopic expression of STING in SIX4 knockout cells reversed the effect. Ectopic expression of SIX4 enhanced DMXAA and cGAMP-induced STING activation and downstream signaling. Importantly, decrease of SIX4 expression substantially decreased tumor infiltration of CD8+T-cells and reduced the efficacy of PD-1 antibodies to diminish tumor growth in immune competent micein vivo. Finally, analysis of TCGA colon cancer dataset indicated that tumors with high SIX4 expression were significantly enriched in the Inflammatory Response pathway. SIX4 expression also correlated with expression of multiple IFN-stimulated genes, inflammatory cytokines and CD8A. Taken together, our results implicate that SIX4 is a principal regulator of STING expression in colon cancer cells, providing an additional mechanism and genetic marker to predict effective immune checkpoint blockade therapy responses.
Integrated Analysis of Cross-Links and Dead-End Peptides for Enhanced Interpretation of Quantitative XL-MS
Authors: Keller Andrew , Tang Xiaoting , Bruce James E. 
Published: May 2023

AbstractXL-MS provides low-resolution structural information of proteins in cells and tissues. Combined with quantitation, it can identify changes in the interactome between samples, for example, control and drug-treated cells, or young and old mice. A difference can originate from protein conformational changes altering the solvent-accessible distance separating the cross-linked residues. Alternatively, a difference can result from conformational changes localized to the cross-linked residues, for example, altering the solvent exposure or reactivity of those residues or post-translational modifications on the cross-linked peptides. In this manner, cross-linking is sensitive to a variety of protein conformational features. Dead-end peptides are cross-links attached only at one end to a protein, the other terminus being hydrolyzed. As a result, changes in their abundance reflect only conformational changes localized to the attached residue. For this reason, analyzing both quantified cross-links and their corresponding dead-end peptides can help elucidate the likely conformational changes giving rise to observed differences of cross-link abundance. We describe analysis of dead-end peptides in the XLinkDB public cross-link database and, with quantified mitochondrial data isolated from failing heart versus healthy mice, show how a comparison of abundance ratios between cross-links and their corresponding dead-end peptides can be leveraged to reveal possible conformational explanations.
Kinetic trapping organizes actin filaments within liquid-like protein droplets
Authors: Chandrasekaran Aravind , Graham Kristin , Stachowiak Jeanne C. , Rangamani Padmini 
Published: May 2023

AbstractActin is essential for various cellular functions such as growth, migration, and endocytosis. Recent evidence suggests that several actin-binding proteins phase separate to form condensates and that actin networks have different architectures in these droplets. In this study, we use computational modeling to investigate the conditions under which actin forms different network organizations in VASP droplets. Our simulations reveal that the binding and unbinding rates of actin and VASP determine the probability of formation of shells and rings, with shells being more probable than rings. The different actin networks are highly dependent on the kinetics of VASP-actin interactions, suggesting that they arise from kinetic trapping. Specifically, we showed that reducing the residence time of VASP on actin filaments promotes assembly of shells rather than rings, where rings require a greater degree of actin bundling. These predictions were tested experimentally using a mutant of VASP, which has decreased bundling capability. Experiments reveal an increase in the abundance of shells in VASP droplets, consistent with our predictions. Finally, we investigated the arrangements of filaments within deformed droplets and found that the filament length largely determines whether a droplet will straighten into a bundle or remain kinetically trapped in a ring-like architecture. The sphere-to-ellipsoid transition is favored under a wide range of conditions while the ellipse-to-rod transition is only permitted when filaments have a specific range of lengths. Our findings have implications for understanding how the interactions between phase-separated actin binding proteins and actin filaments can give rise to different actin network architectures.