bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mathematically mapping the network of cells in the tumor microenvironment
Authors: van Santvoort Mike , Lapuente-Santana Óscar , Finotello Francesca , van der Hoorn Pim , Eduati Federica 
Published: February 2023

AbstractCell-cell interaction networks are pivotal in cancer development and treatment response. These networks can be inferred from data; however, this process often combines data from multiple patients, and/or creates networks on a cell-types level. It creates a good average overview of cell-cell interaction networks but fails to capture patient heterogeneity and/or masks potentially relevant local network structures. We propose a mathematical model based on random graphs (called RaCInG) to alleviate these issues using prior knowledge on potential cellular interactions and patient’s bulk RNA-seq data. We have applied RaCInG to extract 444 network features related to the tumor microenvironment, unveiled associations with immune response and subtypes, and identified cancer-type specific differences in inter-cellular signaling. Additionally, we have used RaCInG to explain how immune phenotypes regulated by context-specific intercellular communication affect immunotherapy response. RaCInG is a modular pipeline, and we envision its application for cell-cell interaction reconstruction in different contexts.
Genome sequencing, assembly and annotation of the carob tree, Ceratonia siliqua(Eudicots:Fabaceae)
Authors: Bibi Androniki C. , Ioannidis Panagiotis , Bazakos Christos , Kalantidis Kriton 
Published: February 2023

AbstractThe carob tree,Ceratonia siliqua, is an evergreen tree that belongs to the family of Fabaceae. It has been cultivated for thousands of years in Mediterranean countries and thus, has a considerable impact on the nutrition of humans as well as other animals of this region. Despite its importance, genomic resources are still scarce for this plant species. To fill this gap, we undertook the sequencing, assembly and annotation of the carob tree genome, which resulted in the first, nearly chromosome-level assembly for this plant species. The total assembly size is 492 Mbp which is close to the previously estimated genome size. The assembly N50 is 34.99 Mbp, thus showing a high contiguity, which is also evident from the fact that >98% of the assembly is contained in as few as 17 very large contigs. Moreover, both the genome sequence as well as the predicted gene set contain more than 96% of conserved, full-length BUSCOs. Finally, a comparative orthology analysis with 10 other plant species showed that the vast majority of the predicted carob tree genes have orthologs in the other plants and only a small fraction of them appears to be species-specific. Additional analyses are in progress for a more detailed study of the agronomic traits of this important legume.
Theta and alpha EEG oscillations reflect sleep need — except during the wake maintenance zone
Authors: Snipes Sophia , Meier Elias , Meissner Sarah , Landolt Hans-Peter , Huber Reto 
Published: February 2023

ABSTRACTIncreasing time spent awake results in accumulated sleep need, a process known as sleep homeostasis. Sleep homeostasis combines with a 24 h circadian rhythm to determine when and for how long we sleep. Both sleep homeostasis and the circadian rhythm substantially affect spectral power of the wake electroencephalogram (EEG), but not in ways predicted by current models. Specifically, these models hypothesize that time spent awake increases neuronal synaptic strength, which increases synchronization and should therefore increase oscillatory activity. However, the dominant wake EEG oscillations, measured as theta (4-8 Hz) and alpha power (8-12 Hz), do not follow the predicted buildup in homeostatic sleep pressure with time awake. This is due to a limitation of spectral power analysis, which does not distinguish between changes in the amplitude of oscillations from changes in the quantity of oscillations present in the signal. We wished to determine whether the amplitudes of EEG oscillations would specifically reflect homeostatic sleep pressure, independently from changes in quantity. We collected data from 18 young healthy adults during a 4-h sleep / 24-h extended wake paradigm. We indeed found that theta and alpha oscillation amplitudes reflect homeostatic sleep pressure, increasing along a saturating exponential function with time awake. Instead, theta quantities increased linearly with time awake, and alpha quantities decreased. Notably, theta and alpha amplitudes temporarily decreased during the wake maintenance zone (WMZ), a 3-4 h time window just before bedtime when it is difficult to fall asleep. Using pupillometry, we also found that mean pupil diameter increased during this window, while variance decreased. These results suggest that the WMZ is dependent on an alerting signal from the ascending arousal system. The WMZ therefore counteracts the observed build-up in homeostatic sleep pressure reflected in EEG amplitudes by temporarily desynchronizing cortical activity.
The fitness effects of codon composition of the horizontally transferred antibiotic resistance genes intensify at sub-lethal antibiotic levels
Authors: Shaferman Michael , Gensel Melis , Alon Noga , Alasad Khawla , Rotblat Barak , Serohijos Adrian W.R. , Alfonta Lital , Bershtein Shimon 
Published: February 2023

AbstractThe rampant variability in codon bias existing between bacterial genomes is expected to interfere with horizontal gene transfer (HGT), a phenomenon that drives bacterial adaptation. However, delineating the constraints imposed by codon bias on functional integration of the transferred genes is complicated by multiple genomic and functional barriers controlling HGT, and by the dependence of the evolutionary outcomes of HGT on the host’s environment. Here, we designed an experimental system in which codon composition of the transferred genes is the only variable triggering fitness change of the host. We replacedE. coli’s chromosomalfolAgene encoding dihydrofolate reductase, an essential enzyme that constitutes a target for trimethoprim, with combinatorial libraries of synonymous codons offolAgenes from trimethoprim-sensitiveListeria grayiand trimethoprim-resistantNeisseria sicca.The resulting populations underwent selection at a range of trimethoprim concentrations, and the ensuing changes in variant frequencies were used to infer the fitness effects of the individual combinations of codons. We found that when HGT causes overstabilization of the 5’-end mRNA, the fitness contribution of mRNA folding stability dominates over that of codon optimality. The 5’-end overstabilization can also lead to mRNA accumulation outside of the polysome, thus preventing the decay of the foreign transcripts despite the codon composition-driven reduction in translation efficiency. Importantly, the fitness effects of mRNA stability or codon optimality become apparent only at sub-lethal levels of trimethoprim individually tailored for each library, emphasizing the central role of the host’s environment in shaping the codon bias compatibility of horizontally transferred genes.
Deformed wingsis an Atg8a-interacting protein that negatively regulates autophagy
Authors: Kołodziej Marta , Tsapras Panagiotis , Konstantinou Aristi , Cameron Alexander D. , Promponas Vasilis , Nezis Ioannis P. 
Published: February 2023

AbstractLC3 (microtubule-associated protein 1 light chain 3, called Atg8 in yeast andDrosophila), is one of the most well-studied autophagy-related proteins. LC3 controls selectivity of autophagic degradation by interacting with LIR (LC3-interacting region) motifs also known as AIM (Atg8-interacting motifs) on selective autophagy receptors that carry cargo for degradation. Non-degradative roles of LIR motif-dependent interactions of LC3 are poorly understood. Here, we used yeast-two hybrid screening and Alpha Fold structural predictions, and we identified transcription factor Dwg (Deformed wings) as an Atg8a-interacting protein inDrosophila. Dwg-Atg8a interaction is LIR-motif dependent. We further show that Dwg is a negative regulator of autophagy. Our results provide novel insights on non-degradative roles of LIR motif dependent interactions of Atg8a and the transcriptional regulation of autophagy inDrosophila.
Chemo-sEVs release in cisplatin-resistance ovarian cancer cells are regulated by the lysosomal function
Authors: Cerda-Troncoso Cristóbal , Grünenwald Felipe , Arias-Muñoz Eloísa , Cavieres Viviana A. , Caceres-Verschae Albano , Hernández Sergio , Gaete-Ramírez Belén , Álvarez-Astudillo Francisca , Acuña Rodrigo A , Ostrowski Matias , Burgos Patricia V. , Varas-Godoy Manuel 
Published: February 2023

ABSTRACTOvarian cancer (OvCa) is an aggressive disease usually treated with cisplatin (CDDP)-based therapy. However, among the different types of cancers treated with CDDP, OvCa commonly develops chemoresistance to this treatment. The small extracellular vesicles (sEVs) play a central role in chemoresistance. In response to chemotherapy, resistant cells secrete sEVs named chemo-sEVs characterized by specific cargo landscape content involved in the transfer of chemoresistance to recipient cells. sEVs encompass a variety of vesicle types, including exosomes, and are formed as intraluminal vesicles (ILVs) within multivesicular endosomes (MVEs). MVEs follow at least two trafficking pathways regulated by RAB GTPase family members; 1) a secretory pathway where MVEs fuse with the plasma membrane (PM) for sEVs secretion, where RAB27A is the most studied; 2) a degradative pathway where MVEs fuse with lysosomes, an event controlled by RAB7. There is growing evidence suggesting that a loss of lysosomal function can increase sEVs secretion; however, whether sEVs secretion and the transfer of CDDP chemoresistance in OvCa is the result of a fine regulation between these two MVEs trafficking pathways is unknown. In this work, we study the status of these two pathways, between CDDP-sensitive (A2780) and CDDP-resistant (A2780cis) OvCa cells. We found A2780cis cells have an increased number of MVEs and ILVs structures, together with higher levels of ESCRTs machinery components and RAB27A, compared to A2780 cells. Moreover, CDDP promotes the secretion of chemo-sEVs in A2780cis cells. Interestingly, chemo-sEVs contain a high number of proteins related to DNA damage response. In addition, we determine A2780cis cells have a poor lysosomal function with reduced levels of RAB7. Surprisingly, silencing of RAB27A in A2780cis cells was found to be sufficient to restore lysosomal function and levels of RAB7 in A2780cis cells, switching into an A2780-like cellular phenotype. Next, we found rapamycin, a potent enhancer of lysosomal function, reduced the secretion of chemo-sEVs. Taken together, these results indicate that the secretion of chemo-sEVs in OvCa cells is determined by the balance between secretory MVEs and MVEs that are destined for lysosomal degradation. Thus, our results suggest that adjusting this balance between these two MVEs trafficking pathways could be a promising strategy for overcoming CDDP chemoresistance in OvCa.Graphical Abstract
A Soluble Platelet-Derived Growth Factor Receptor-β Originates via Pre-mRNA Splicing in the Healthy Brain and is Differentially Regulated during Hypoxia and Aging
Authors: Payne Laura Beth , Abdelazim Hanaa , Hoque Maruf , Barnes Audra , Mironovova Zuzana , Willi Caroline E. , Darden Jordan , Jenkins-Houk Clifton , Sedovy Meghan W. , Johnstone Scott R. , Chappell John C. 
Published: February 2023

ABSTRACT/SUMMARYThe platelet-derived growth factor-BB (PDGF-BB) pathway provides critical regulation of cerebrovascular pericytes, orchestrating their investment and retention within the brain microcirculation. Dysregulated PDGF Receptor-beta (PDGFRβ) signaling can lead to pericyte defects that compromise blood-brain barrier (BBB) integrity and cerebral perfusion, impairing neuronal activity and viability, which fuels cognitive and memory deficits. Receptor tyrosine kinases (RTKs) like PDGF-BB and vascular endothelial growth factor-A (VEGF-A) are often modulated by soluble isoforms of cognate receptors that establish signaling activity within a physiological range. Soluble PDGFRβ (sPDGFRβ) isoforms have been reported to form by enzymatic cleavage from cerebrovascular mural cells, and pericytes in particular, largely under pathological conditions. However, pre-mRNA alternative splicing has not been widely explored as a possible mechanism for generating sPDGFRβ variants, and specifically during tissue homeostasis. Here, we found sPDGFRβ protein in the murine brain and other tissues under normal, physiological conditions. Utilizing brain samples for follow-on analysis, we identified mRNA sequences corresponding to sPDGFRβ isoforms, which facilitated construction of predicted protein structures and related amino acid sequences. Human cell lines yielded comparable sequences and protein model predictions. Retention of ligand binding capacity was confirmed for sPDGFRβ by co-immunoprecipitation. Visualizing fluorescently labeled sPDGFRβ transcripts revealed a spatial distribution corresponding to murine brain pericytes alongside cerebrovascular endothelium. Soluble PDGFRβ protein was detected throughout the brain parenchyma in distinct regions such as along the lateral ventricles, with signals also found more broadly adjacent to cerebral microvessels consistent with pericyte labeling. To better understand how sPDGFRβ variants might be regulated, we found elevated transcript and protein levels in the murine brain with age, and acute hypoxia increased sPDGFRβ variant transcripts in a cell-based model of intact vessels. Our findings indicate that soluble isoforms of PDGFRβ likely arise from pre-mRNA alternative splicing, in addition to enzymatic cleavage mechanisms, and these variants exist under normal physiological conditions. Follow-on studies will be needed to establish potential roles for sPDGFRβ in regulating PDGF-BB signaling to maintain pericyte quiescence, BBB integrity, and cerebral perfusion – critical processes underlying neuronal health and function, and in turn memory and cognition.
Structural basis for inhibition of mycobacterial ATP synthase by squaramides and second generation diarylquinolines
Authors: Courbon Gautier M. , Palme Paul R. , Mann Lea , Richter Adrian , Imming Peter , Rubinstein John L. 
Published: February 2023

AbstractMycobacteria, such asMycobacterium tuberculosis, depend on the activity of adenosine triphosphate (ATP) synthase for growth. The diarylquinoline bedaquiline (BDQ), a mycobacterial ATP synthase inhibitor, is an important medication for treatment of drug-resistant tuberculosis but suffers from off-target effects and is susceptible to resistance mutations. Consequently, both new and improved mycobacterial ATP synthase inhibitors are needed. We used electron cryomicroscopy and biochemical assays to study the interaction ofMycobacterium smegmatisATP synthase with the second generation diarylquinoline TBAJ-876 and the squaramide inhibitor SQ31f. The aryl groups of TBAJ-876 improve binding compared to BDQ, while SQ31f, which blocks ATP synthesis ~10 times more potently than ATP hydrolysis, binds a previously unknown site in the enzyme’s proton-conducting channel. Remarkably, BDQ, TBAJ-876, and SQ31f all induce similar conformational changes in ATP synthase, suggesting the resulting conformation is particularly suited for drug binding. Further, high concentrations of the diarylquinolines uncouple the transmembrane proton motive force while for SQ31f they do not, which may explain why high concentrations of diarylquinolines have been reported to kill mycobacteria while SQ31f has not.
Using single-cell RNA sequencing to generate cell-type-specific split-GAL4 reagents throughout development
Authors: Chen Yu-Chieh David , Chen Yen-Chung , Rajesh Raghuvanshi , Shoji Nathalie , Jacy Maisha , Lacin Haluk , Erclik Ted , Desplan Claude 
Published: February 2023

Cell-type-specific tools facilitate the identification and functional characterization of distinct cell types, which underly the complexity of neuronal circuits. A large collection of existing genetic tools in Drosophila relies on enhancer activity to label different subsets of cells. These enhancer-based GAL4 lines often fail to show a predicable expression pattern to reflect the expression of nearby gene(s), partly due to an incomplete capture of the full gene regulatory elements. While genetic intersectional technique such as the split-GAL4 system further improve cell-type-specificity, it requires significant time and resource to generate and screen through combinations of enhancer expression patterns. In addition, since existing enhancer-based split-GAL4 lines that show cell-type-specific labeling in adult are not necessarily active nor specific in early development, there is a relative lack of tools for the study of neural development. Here, we use an existing single-cell RNA sequencing (scRNAseq) dataset to select gene pairs and provide an efficient pipeline to generate cell-type-specific split-GAL4 lines based on the native genetic regulatory elements. These gene-specific split-GAL4 lines can be generated from a large collection of coding intronic MiMIC/CRIMIC lines either by embryo injection orin vivocassette swapping crosses and/or CRISPR knock-in at the N or C terminal of the gene. We use the developing Drosophila visual system as a model to demonstrate the high prediction power of scRNAseq-guided gene specific split-GAL4 lines in targeting known cell types. The toolkit allows efficient cluster annotation in scRNAseq datasets but also the identification of novel cell types. Lastly, the gene-specific split-GAL4 lines are broadly applicable to Drosophila tissues. Our work opens new avenues for generating cell-type-specific tools for the targeted manipulation of distinct cell types throughout development and represents a valuable resource to the fly research community.Significance StatementUnderstanding the functional role of individual cell types in the nervous systems has remained a major challenge for neuroscience researchers, partly due to incomplete identification and characterization of underlying cell types. To study the development of individual cell types and their functional roles in health and disease, experimental access to a specific cell type is often a prerequisite. Here, we establish an experimental pipeline to generate gene-specific split-GAL4 guided by single-cell RNA sequencing datasets. These lines show high accuracy for labeling targeted cell types from early developmental stages to adulthood and can be applied to any tissues in Drosophila. The collection of gene-speicifc-split-GAL4 will provide a valuable resource to the entire fly research community.
Role of the small protein Mco6 in the mitochondrial sorting and assembly machinery
Authors: Busto Jon V. , Mathar Hannah , Steiert Conny , Schneider Eva F. , Straub Sebastian P. , Ellenrieder Lars , Song Jiyao , Stiller Sebastian B. , Lübbert Philipp , Guiard Bernard , den Brave Fabian , Schulte Uwe , Fakler Bernd , Becker Thomas , Wiedemann Nils 
Published: February 2023

SUMMARYThe majority of mitochondrial precursor proteins are imported through the Tom40 β-barrel channel of the translocase of the outer membrane (TOM). The sorting and assembly machinery (SAM) is essential for β-barrel membrane protein insertion into the outer membrane and thus required for the assembly of the TOM complex. Here we demonstrate that the a-helical outer membrane protein Mco6 forms a complex with the mitochondrial distribution and morphology protein Mdm10 as part of the SAM machinery. Moreover, Mco6 also interacts with the subunit Mim1 of the mitochondrial import complex (MIM), which is itself required for the biogenesis of a-helical outer membrane proteins.MCO6andMDM10display a negative genetic interaction and aMCO6-MDM10yeast double mutant contains reduced levels of TOM complex. Cells lacking Mco6 affect the levels of Mdm10 and MIM-subunits associated with assembly defects of the TOM complex. Thus, this work reveals a role of the SAMMco6complex for the biogenesis of the mitochondrial outer membrane.
Archaic Introgression Shaped Human Circadian Traits
Authors: Velazquez-Arcelay Keila , Colbran Laura L. , McArthur Evonne , Brand Colin , Rinker David , Siemann Justin , McMahon Douglas , Capra John A. 
Published: February 2023

ABSTRACTIntroductionWhen the ancestors of modern Eurasians migrated out of Africa and interbred with Eurasian archaic hominins, namely Neanderthals and Denisovans, DNA of archaic ancestry integrated into the genomes of anatomically modern humans. This process potentially accelerated adaptation to Eurasian environmental factors, including reduced ultra-violet radiation and increased variation in seasonal dynamics. However, whether these groups differed substantially in circadian biology, and whether archaic introgression adaptively contributed to human chronotypes remains unknown.ResultsHere we traced the evolution of chronotype based on genomes from archaic hominins and present-day humans. First, we inferred differences in circadian gene sequences, splicing, and regulation between archaic hominins and modern humans. We identified 28 circadian genes containing variants with potential to alter splicing in archaics (e.g.,CLOCK,PER2,RORB,RORC), and 16 circadian genes likely divergently regulated between present-day humans and archaic hominins, includingRORA. These differences suggest the potential for introgression to modify circadian gene expression. Testing this hypothesis, we found that introgressed variants are enriched among eQTLs for circadian genes. Supporting the functional relevance of these regulatory effects, we found that many introgressed alleles have associations with chronotype. Strikingly, the strongest introgressed effects on chronotype increase morningness, consistent with adaptations to high latitude in other species. Finally, we identified several circadian loci with evidence of adaptive introgression or latitudinal clines in allele frequency.ConclusionsThese findings identify differences in circadian gene regulation between modern humans and archaic hominins and support the contribution of introgression via coordinated effects on variation in human chronotype.SIGNIFICANCE STATEMENTInterbreeding between humans and Neanderthals created the potential for adaptive introgression as humans moved into environments that had been populated by Neanderthals for hundreds of thousands of years. Here we discover lineage-specific genetic differences in circadian genes and their regulatory elements between humans and Neanderthals. We show that introgressed alleles are enriched for effects on circadian gene regulation, consistently increase propensity for morningness in Europeans, and show evidence of adaptive introgression or associations between latitude and frequency. These results expand our understanding of how the genomes of humans and our closest relatives responded to environments with different light/dark cycles, and demonstrate a coordinated contribution of admixture to human chronotype in a direction that is consistent with adaptation to higher latitudes.