bluuebunny/crossref_metadata_2025_split huggingface dataset:
RhoA activation promotes glucose uptake to elevate proliferation in MAPK inhibitor resistant melanoma cells
Authors: Murali Vasanth Siruvallur , Rajendran Divya , Isogai Tadamoto , DeBerardinis Ralph J. , Danuser Gaudenz 
Published: January 2024

AbstractCutaneous melanomas harboring a B-RafV600Emutation are treated with immune check point inhibitors or kinase inhibitor combination therapies relying on MAPK inhibitors (MAPKi) Dabrafenib and Trametinib (Curti and Faries, 2021). However, cells become resistant to treatments over the timespan of a few months. Resistance to MAPKi has been associated with adoption of an aggressive amoeboid phenotype characterized by elevated RhoA signaling, enhanced contractility and thick cortical filamentous actin (F-actin) structures (Kim et al., 2016; Misek et al., 2020). Targeting active RhoA through Rho-kinase (ROCK) inhibitors, either alone or in combination with immunotherapies, reverts MAPKi-resistance (Misek et al., 2020; Orgaz et al., 2020). Yet, the mechanisms for this behavior remain largely unknown. Given our recent findings of cytoskeleton’s role in cancer cell proliferation (Mohan et al., 2019), survival (Weems et al., 2023), and metabolism (Park et al., 2020), we explored possibilities by which RhoA-driven changes in cytoskeleton structure may confer resistance. We confirmed elevated activation of RhoA in a panel of MAPKi-resistant melanoma cell lines, leading to a marked increase in the presence of contractile F-actin bundles. Moreover, these cells had increased glucose uptake and glycolysis, a phenotype disrupted by pharmacological perturbation of ROCK. However, glycolysis was unaffected by disruption of F-actin bundles, indicating that glycolytic stimulation in MAPKi-resistant melanoma is independent of F-actin organization. Instead, our findings highlight a mechanism in which elevated RhoA signaling activates ROCK, leading to the activation of insulin receptor substrate 1 (IRS1) and P85 of the PI3K pathway, which promotes cell surface expression of GLUT1 and elevated glucose uptake. Application of ROCK inhibitor GSK269962A results in reduced glucose uptake and glycolysis, thus impeding cell proliferation. Our study adds a mechanism to the proposed use of ROCK inhibitors for long-term treatments on MAPKi-resistant melanomas.
Functional profiling of the male gametophyte-specific promoter fragment ofArabidopsis PIRL6gene and prediction ofcis-regulatory elements
Authors: Ajith T.G. , Shah Jasmine M. 
Published: January 2024

AbstractGametophyte-specific promoters drive the expression of genes in male and/or female gametophytes. These have applications in breeding experiments, gene function identification, developmental biology-related studies, and off-lately in genome editing also. ThePlant Intracellular Ras-group Leucine-Rich-Repeat6 (PIRL6) gene is known to be necessary for male and female gametogenesis. Using theGUS-based deletion analysis, we have identified thePIRL6promoter length that is essential for exclusive expression in the male gametophyte ofArabidopsis thaliana.We studied the strength of various lengths ofPIRL6promoters in different tissues, by GUS expression quantification. The male-gametophyte-specific promoter segment (PA1) exhibited stronger expression in mature anthers than the younger ones. We identified 50 other genes that co-expressed withPIRL6inArabidopsisusing the Expression Angler tool. Gene ontology (GO) analysis shows that these 51 co-expressing genes were predominantly involved in cell differentiation. By comparing the promoter sequences of these 51 genes, the presence of three over-represented known motifs, POLLEN1LELAT52, ACGTATERD1 and CIACADIANLELHC was identified. We could also predict the presence of three novelcis-regulatory elements in the co-expressing gene network using the MEME suite tool. Additionally, we confirmed the functionality of the ABRE and P-box elements present inPIRL6promoter using the tobacco leaf transient assay. Thus, we cloned and functionally confirmed the promoter region ofPIRL6required for male gametophyte-specific expression, compared this promoter with those of 50 other co-expressed genes and predicted their functions, and analyzed theircisregulatory regions and predicted three novel motifs also.Key messageA pollen-specific promoter fragment ofPIRL6was functionally characterized usingGUS-based deletion analysis. Fifty other co-expressed genes were compared and novelcis-regulatory elements were predicted. Two hormone-responsive elements in thePIRL6promoter were found to influence theGUSexpression. PA1 promoter can be used in experiments that require male gametophyte-specific expression of genes.
The decision of male medaka to mate or fight depends on two complementary androgen signaling pathways
Authors: Nishiike Yuji , Okubo Kataaki 
Published: January 2024

AbstractAdult male animals typically court and attempt to mate with females, while attacking other males. Emerging evidence from mice indicates that neurons expressing the estrogen receptor ESR1 in behaviorally relevant brain regions play a central role in mediating these mutually exclusive behavioral responses to conspecifics. However, the findings in mice are unlikely to apply to most other vertebrates, where androgens — rather than estrogens — have been implicated in male behaviors. Here we report that male medaka (Oryzias latipes) lacking one of the two androgen receptor subtypes (Ara) are less aggressive toward other males and instead actively court them, while those lacking the other subtype (Arb) are less motivated to mate with females and conversely attack them. These findings indicate that, in male medaka, the Ara- and Arb-mediated androgen signaling pathways facilitate appropriate behavioral responses, while simultaneously suppressing inappropriate responses, to males and females, respectively. Notably, males lacking either receptor retain the ability to discriminate the sex of conspecifics, suggesting a defect in the subsequent decision-making process to mate or fight. We further show that Ara and Arb are expressed in intermingled but largely distinct populations of neurons, and stimulate the expression of different behaviorally relevant genes including galanin and vasotocin, respectively. Collectively, our results demonstrate that male teleosts make adaptive decisions to mate or fight as a result of the activation of one of two complementary androgen signaling pathways, depending on the sex of the conspecific that they encounter.
Internal regulation between constitutively expressed T cell coinhibitory receptors BTLA and CD5 and tolerance in recent thymic emigrants
Authors: Adegoke Adeolu O. , Thangavelu Govindarajan , Chou Ting-Fang , Petersen Marcos , Kakugawa Kiyokazu , May Julia F. , Joannou Kevin , Wang Qingyang , Ellestad Kristofor K. , Boon Louis , Bretscher Peter A. , Cheroutre Hilde , Kronenberg Mitchell , Baldwin Troy A. , Anderson Colin C. 
Published: January 2024

AbstractSeveral coinhibitory receptors are upregulated upon activation, whereas a small number of coinhibitory receptors are expressed constitutively by naive T cells. The relationship between constitutively expressed coinhibitors is unknown. We found an inverse relationship between two constitutively expressed coinhibitors, CD5 and BTLA; BTLA expression was low in the thymus and high in the periphery, corresponding respectively with high and low CD5 expression. Germline or induced deletion ofBtlain somatic cells demonstrated a causal relationship between BTLA expression and CD5 levels in T cells of central and peripheral lymphoid tissues. The effect of BTLA on CD5 expression on thymic and peripheral CD4 T cells was due to BTLA signaling, rather than signaling by its ligand, the herpes virus mediator (HVEM). Regulation was maintained in mice with a non-signaling HVEM mutant but was lost inTnfrsf14−/−(Hvem−/−) mice. Increased CD5 levels have been positively associated with increased recognition of self-peptide MHC complexes. Thus, control of CD5 expression by BTLA signals early in T cell ontogeny suggested that BTLA might be important for establishing self-tolerance in newly generated T cells. Consistent with this concept, we found that BTLA, as well as the inducible coinhibitor PD-1, were needed post thymic selection in recent thymic emigrants (RTE) to establish self-tolerance. RTE lacking BTLA caused a multiorgan autoimmune disease whose development required CD4 T cells and MHC class II. Together, our findings identify a negative regulatory pathway allowing constitutively expressed coinhibitory receptors to calibrate their expression in thymic T cell differentiation. Expression of constitutive and induced coinhibitory receptors is needed to establish tolerance in the periphery for RTE.
Whole-cortex simulation reveals spatiotemporal patterns emerging from the interplay of network connectivity and intracellular dynamics
Authors: Sun Guanhua , Hazelden James , Kim Ruby , Forger Daniel 
Published: January 2024

AbstractRecent advances in Graphics Processing Unit (GPU) computing have allowed for computational models of whole-brain activity at unprecedented scales. In this work, we use desktop computers to build and simulate a whole-cortex mouse brain model using Hodgkin-Huxley type models for all the most active neurons in the mouse cortex. We compare the model dynamics over different types of connectivity, ranging from uniform random to realistic connectivity derived from experimental data on cell positions and the Allen Brain Atlas. By changing the external drive and coupling strength of neurons in the network, we can produce a wide range of oscillations in the gamma through delta bands. While the global mean-field behaviors of different connectivities share some similarities, an experimentally determined hierarchical connectivity allows for complex, heterogeneous behaviors typically seen in EEG recordings that are not observed in networks with nearest neighbors or uniform coupling. Moreover, our simulations reveal a wide range of spatiotemporal patterns, such as rotational or planar traveling waves, that are observed in experiments. Different traveling waves are observed with different connectivity and coupling strengths on the same connectivity. Our simulations show that many cortical behaviors emerge at scale with the full complexity of the network structure and ionic dynamics. We also provide a computational framework to explore these cortex- wide behaviors further.
Deubiquitinating enzyme mutagenesis screens identify a USP43 driven HIF-1 transcriptional response
Authors: Pauzaite Tekle , Wit Niek , Seear Rachel V , Nathan James A 
Published: January 2024

AbstractThe ubiquitination and proteasome-mediated degradation of Hypoxia Inducible Factors (HIFs) is central to metazoan oxygen-sensing, but the involvement of deubiquitinating enzymes (DUBs) in HIF signalling is less clear. Here, using a bespoke DUBs sgRNA library we conduct CRISPR/Cas9 mutagenesis screens to determine how DUBs are involved in HIF signalling. Alongside defining DUBs involved in HIF activation or suppression, we identify USP43 as a DUB required for efficient activation of a HIF response. USP43 is hypoxia regulated and selectively associates with the HIF-1α isoform, and while USP43 does not alter HIF-1α stability, it facilitates HIF-1 nuclear accumulation and binding to its target genes. Mechanistically, USP43 associates with 14-3-3 proteins in a hypoxia and phosphorylation dependent manner to increase the nuclear pool of HIF-1. Together, our results unveil the DUB landscape in HIF signalling, and highlight the multifunctionality of DUBs, illustrating that they can provide important signalling functions alongside their catalytic roles.
Flap endonuclease Substrate Interactions studied using Dynamic Single-Molecule Atomic Force Microscopy
Authors: Verma Vinny , Brudenell Emma L. , Cussons Sophie , Phipps Janine , Kong Su Chii , Sayers Jon R. , Hobbs Jamie K. 
Published: January 2024

AbstractFlap endonucleases (FENs) recognise and cleave DNA substrates containing a 5’-single-strand (ss) of nucleic acid branching off a double-stranded (ds) DNA to yield a nicked duplex during DNA replication. Dynamic Atomic Force Microscopy of an inactive FEN mutant complexed with branched DNA revealed mobilisation of immobilised DNA, indicating that protein interaction affected substrate conformation and disrupted the forces that anchored it to the poly-L-ornithine -treated mica surface. Enzymatically-active FEN was seen intermittently binding DNA, altering its conformation and cleaving the ssDNA branch. We developed a method using motion tracking for quantifying the movement of DNA sections, by visually segmenting DNA and tracking each segment to recognise the DNA sections most affected by the protein. It was found that whilst bound, FEN caused localised DNA bending, and changes in DNA shape were witnessed in the short time span of the protein’s appearance close to the nucleic acid, followed by protein adsorption on the mica surface. The results provide the first dynamic observations of FEN-DNA interaction. FEN initially binds to the dsDNA, slides to find the ds/ssDNA junction, and the 5’ ssDNA likely threads through a hole in the enzyme which leads to enzymatic hydrolysis of the branched substrate.
Iron deficiency in people with obesity drives defective Natural Killer cell mitochondrial fitness and function
Authors: De Barra Conor , Ryan Eimear , Sugrue Michelle , Ryan Odhran , Lynn Evelyn , Heneghan Helen M. , McCarthy Cormac , Moynagh Paul N. , Sinclair Linda V. , Jones Nicholas , Hogan Andrew E. , O’Shea Donal 
Published: January 2024

AbstractNatural killer (NK) cells are a population of innate effector lymphocytes, involved in host-defences against viral infections and cancer. Upon activation, NK cells can produce a milieu of cytotoxic molecules and cytokines, which can directly target infected and transformed cells, but also amplify an immune response. Metabolic rewiring underpins NK cell effector functionality, providing the required signals, energy and biointermediates to support their immune responses. Obesity is associated with significant defects in the functionality of human NK cells, especially in the periphery. Dysregulated cellular metabolism has been demonstrated to be a major mechanistic driver of the reported defects. However, how obesity links to defective NK cell metabolism and functionality remains unclear. Iron deficiency is a common co-morbidity in people living with obesity (PWO). Recent studies have highlighted the importance for iron in host immunity, with murine models of iron deficiency resulting in defective cellular metabolism and function. We hypothesized that obesity-driven iron deficiency might underpin the reported defects in NK cells. Our data demonstrates that in response to cytokine stimulation, healthy human NK cells utilize iron to support their metabolic activity and cytokine responses. In a cohort of PWO, we demonstrate alterations in NK cell metabolism, mitochondrial fitness and cytokine production. Furthermore, upon stratification into PWO with normal iron status versus low iron status, we show the observed obesity-related defects in NK cell metabolism, mitochondrial fitness and cytokine production are concentrated in the PWO with low-iron status. Collectively, our data highlights the importance of iron for human NK cell responses and provides evidence that obesity-driven defects in NK cell metabolism and function are linked in part to altered iron availability.
Evidence for compensatory evolution within pleiotropic regulatory elements
Authors: Kliesmete Zane , Orchard Peter , Lee Victor Yan Kin , Geuder Johanna , Krauß Simon M. , Ohnuki Mari , Jocher Jessica , Vieth Beate , Enard Wolfgang , Hellmann Ines 
Published: January 2024

AbstractPleiotropy, measured as expression breadth across tissues, is one of the best predictors for protein sequence and expression conservation. In this study, we investigated its effect on the evolution of cis-regulatory elements (CREs). To this end, we carefully reanalyzed the Epigenomics Roadmap data for nine fetal tissues, assigning a measure of pleiotropic degree to nearly half a million CREs. To assess the functional conservation of CREs, we generated ATAC-seq and RNA-seq data from humans and macaques. We found that more pleiotropic CREs exhibit greater conservation in accessibility, and the mRNA expression levels of the associated genes are more conserved. This trend of higher conservation for higher degrees of pleiotropy persists when analyzing the transcription factor binding repertoire. In contrast, simple DNA sequence conservation of orthologous sites between species tends to be even lower for pleiotropic CREs than for species-specific CREs. Combining various lines of evidence, we suggest that the lack of sequence conservation for functionally conserved pleiotropic elements is due to compensatory evolution within these large pleiotropic CREs. Furthermore, for less pleiotropic CREs, we find an indication of compensation across CREs. This suggests that pleiotropy is also a good predictor for the functional conservation of CREs, but this is not reflected in the sequence conservation for pleiotropic CREs.
Pangenome reconstruction in rats enhances genotype-phenotype mapping and novel variant discovery
Authors: Villani Flavia , Guarracino Andrea , Ward Rachel R , Green Tomomi , Emms Madeleine , Pravenec Michal , Prins Pjotr , Garrison Erik , Williams Robert W. , Chen Hao , Colonna Vincenza 
Published: January 2024

SummaryThe HXB/BXH family of recombinant inbred rat strains is a unique genetic resource that has been extensively phenotyped over 25 years, resulting in a vast dataset of quantitative molecular and physiological phenotypes. We built a pangenome graph from 10x Genomics Linked-Read data for 31 recombinant inbred rats to study genetic variation and association mapping. The pangenome includes 0.2Gb of sequence that is not present the reference mRatBN7.2, confirming the capture of substantial additional variation. We validated variants in challenging regions, including complex structural variants resolving into multiple haplotypes. Phenome-wide association analysis of validated SNPs uncovered variants associated with glucose/insulin levels and hippocampal gene expression. We propose an interaction betweenPirl1l1, chromogranin expression,TNF-αlevels, and insulin regulation. This study demonstrates the utility of linked-read pangenomes for comprehensive variant detection and mapping phenotypic diversity in a widely used rat genetic reference panel.
Generation of Systemic Chimeras via Rabbit Induced Pluripotent Stem Cells Reprogrammed with KLF2, ERAS, and PRMT6
Authors: Perold Florence , Pham Hong-Thu , Pijoff Yannicke , Doerflinger Nathalie , Rival-Gervier Sylvie , Moulin Anaïs , Jouneau Luc , Pain Bertrand , Joly Thierry , Duranthon Véronique , Afanassieff Marielle , Savatier Pierre , Beaujean Nathalie 
Published: January 2024

SummaryLittle is known about the molecular underpinnings of pluripotent stem cells’ (PSCs) ability to colonize the epiblast of preimplantation embryos and generate chimeras. In our study, using rabbit PSCs as a model system, we conducted unbiased screening of a cDNA library that encodes a panel of 36 pluripotency factors. From this screening, we identified KLF2, ERAS and PRMT6, whose overexpression confers the ability for self-renewal in a KOSR/FGF2-free culture medium supplemented with LIF, activin A, PKC and WNT inhibitors. The reprogrammed cells acquired transcriptomic and epigenetic features of naive pluripotency, including the reactivation of the 2ndX-chromosome. Leveraging these PSC lines, we determined the transcriptomic signature of embryonic colonization-competence, demonstrating transcriptional repression of genes involved in MAPK, WNT, HIPPO, and EPH signaling pathways, alongside the activation of genes involved in amino-acid metabolism, NF-kB signaling, and p53 pathway. Remarkably, a subset of reprogrammed cells, expressing CD75 at a high level, gained the ability to produce chimeric fetuses with a high contribution from PSCs in all lineages.
Cross-Domain Text Mining of Pathophysiological Processes Associated with Diabetic Kidney Disease
Authors: Patidar Krutika , Deng Jennifer H. , Mitchell Cassie S. , Ford Versypt Ashlee N. 
Published: January 2024

AbstractDiabetic kidney disease (DKD) remains a significant burden on the healthcare system and is the leading cause of end-stage renal disease worldwide. The pathophysiology of DKD is multifactorial and characterized by various early signs of metabolic impairment, inflammatory biomarkers, and complex pathways that lead to progressive kidney damage. New treatment prospects rely on a comprehensive understanding of disease pathology. The study aimed to identify signaling drivers and pathways that modulate glomerular endothelial dysfunction in DKD via cross-domain text mining with SemNet 2.0. The open-source literature-based discovery approach, SemNet 2.0, leverages the power of text mining 33+ million PubMed articles to provide integrative insight into multiscalar and multifactorial pathophysiology. A set of identified relevant genes and proteins that regulate different pathological events associated with DKD were analyzed and ranked using normalized mean HeteSim scores. High-ranking genes and proteins intersecting three domains—DKD, immune response, and glomerular endothelial cells—were analyzed. The top 10% of ranked concepts mapped to the following biological functions: angiotensin, apoptosis, cell-cell function, cell adhesion, chemotaxis, growth factor signaling, vascular permeability, nitric oxide response, oxidative stress, cytokine response, macrophage signaling, NFκB factor activity, TLR signaling, glucose metabolism, inflammatory response, ERK/MAPK signaling, JAK/STAT signaling, T-cell mediated response, WNT signaling, renin angiotensin system, and NADPH response. High-ranking genes and proteins were used to generate a protein-protein interaction network. This comprehensive analysis identified testable hypotheses for interactions or molecules involved with dysregulated signaling in DKD, which can be further studied through biochemical network models.
Acanthella acutaMitochondrial DNA: Linear Architecture and Other Unique Features
Authors: Ahmed Momin , Kayal Ehsan , Lavrov Dennis V. 
Published: January 2024

AbstractWhileAcanthella acuta(Schmidt 1862), a common demosponge found in the Mediterranean Sea and Atlantic Ocean, is — morphologically — little distinguishable from other sponges, its mitochondrial DNA (mtDNA) is unique within the class. In contrast to all other studied demosponges,A. acutamtDNA appears to be linear and displays several unusual features: inverted terminal repeats, group II introns in three mt-genes, and two unique ORFs. One of the ORFs (ORF1535) combines a DNA-polymerase domain with a DNA-directed RNA-polymerase domain, while the second bears no discernable similarity to any reported sequences. The group II intron within thecox2gene is the first such intron reported in an animal. Our phylogenetic analyses indicate that thecox1intron is related to similar introns found in other demosponges, while thecox2intron is likely not of animal origin. The two domains found withinORF1535do not share a common origin and, along with thecox2intron, were likely acquired by horizontal transfer. The findings of this paper open new avenues of exploration in the understanding of mtDNA linearization within Metazoa.SignificanceThe transition from circular to linear mtDNA architecture is a rare and poorly understood phenomenon in animals. In addition, the few lineages that made this transition (Medusozoa, Calcarea, and Isopoda), adopted linear mt-DNA architecture early in their history, making it difficult to reconstruct the underlying events. The identification of linear mtDNA inAcanthella acutanot only provides an independent example of the origin of linear mtDNA architectures in animals but also an opportunity to investigate its evolution at a much shorter evolutionary time. In particular, the conservation of circular mtDNA in other studied species within the family Dictyonellidae highlights the need to investigate other species in the genusAcanthella, to better understand mtDNA linearization inA. acuta.