bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human colorectal cancer: upregulation of the adaptor protein Rai in TILs leads to cell dysfunction by sustaining GSK-3 activation and PD-1 expression
Authors: Montecchi Tommaso , Nannini Giulia , Domiziana De Tommaso , Cassioli Chiara , Coppola Federica , Ringressi Maria Novella , Carraro Fabio , Naldini Antonella , Taddei Antonio , Marotta Giuseppe , Amedei Amedeo , Baldari Cosima , Ulivieri Cristina 
Published: June 2023

AbstractBackgroundThe immunosuppressive tumor microenvironment (TME) of colorectal cancer (CRC) is a major hurdle for immune checkpoint inhibitor-based therapies. Hence characterization of the signaling pathways driving T cell exhaustion within TME is a critical need for the discovery of novel therapeutic targets and the development of effective therapies. We previously showed that i) the adaptor protein Rai is a negative regulator of T cell receptor signaling and T helper 1 (Th1)/Th17 cell differentiation; and ii) Rai deficiency is implicated in the hyperactive phenotype of T cells in autoimmune diseases.MethodsThe expression level of Rai was measured by qRT-PCR in paired peripheral blood T cells and T cells infiltrating tumor tissue and the normal adjacent tissue in CRC patients. The impact of HIF-1α on Rai expression was evaluated in T cells exposed to hypoxia and by performing chromatin immunoprecipitation assays and RNA interference assays. The mechanism by which upregulation of Rai in T cells promotes T cell exhaustion were evaluated by flow cytometric, qRT-PCR and western blot analyses.ResultsWe show that Rai is a novel HIF-1α-responsive gene that is upregulated in tumor infiltrating lymphocytes of CRC patients compared to patient-matched circulating T cells. Rai upregulation in T cells promoted PD-1 expression and impaired antigen-dependent degranulation of CD8+T cells by inhibiting phospho-inactivation of glycogen synthase kinase (GSK)-3, a central regulator of PD- 1 expression and T cell-mediated anti-tumor immunity.ConclusionsOur data identify Rai as a hitherto unknown regulator of the TME-induced exhausted phenotype of human T cells.What is already known on this topicTumor hypoxia contributes to establish an immunosuppressive microenvironment that unleashes T cell function and limits the efficacy of immunotherapy in CRC.The molecular mechanisms underlying the impact of hypoxia on the signaling pathways controlling PD-1 expression are unknown.What this study addsA Rai/Akt/GSK-3 axis regulates PD-1 expression following TCR/CD28 co-stimulationThis study uncovers the signaling pathway controlling hypoxia-dependent T cell exhaustion.How this study might affect research, practice or policyRai expression levels in TILs of CRC patients might be explored as a potential new biomarker of T cell exhaustion and a predictive biomarker for anti-PD-1 response.
Divergent iron-regulatory states contribute to heterogeneity in breast cancer aggressiveness
Authors: Leineweber William D. , Rowell Maya Z. , Ranamukhaarachchi Sural , Walker Alyssa , Li Yajuan , Villazon Jorge , Farrera Aida Mestre , Hu Zhimin , Yang Jing , Shi Lingyan , Fraley Stephanie I. 
Published: June 2023

AbstractPrimary tumors with similar mutational profiles can progress to vastly different outcomes where transcriptional state, rather than mutational profile, predicts prognosis. A key challenge is to understand how distinct tumor cell states are induced and maintained. In triple negative breast cancer cells, invasive behaviors and aggressive transcriptional signatures linked to poor patient prognosis can emerge in response to contact with collagen type I. Herein, collagen-induced migration heterogeneity within a TNBC cell line was leveraged to identify transcriptional programs associated with invasive versus non-invasive phenotypes and implicate molecular switches. Phenotype-guided sequencing revealed that invasive cells upregulate iron uptake and utilization machinery, anapleurotic TCA cycle genes, actin polymerization promoters, and a distinct signature of Rho GTPase activity and contractility regulating genes. The non-invasive cell state is characterized by actin and iron sequestration modules along with glycolysis gene expression. These unique tumor cell states are evident in patient tumors and predict divergent outcomes for TNBC patients. Glucose tracing confirmed that non-invasive cells are more glycolytic than invasive cells, and functional studies in cell lines and PDO models demonstrated a causal relationship between phenotype and metabolic state. Mechanistically, the OXPHOS dependent invasive state resulted from transient HO-1 upregulation triggered by contact with dense collagen that reduced heme levels and mitochondrial chelatable iron levels. This induced expression of low cytoplasmic iron response genes regulated by ACO1/IRP1. Knockdown or inhibition of HO-1, ACO1/IRP1, MRCK, or OXPHOS abrogated invasion. These findings support an emerging theory that heme and iron flux serve as important regulators of TNBC aggressiveness.
Hippocampal sharp-wave ripples correlate with naturally occurring self-generated thoughts in humans
Authors: Iwata Takamitsu , Yanagisawa Takufumi , Ikegaya Yuji , Smallwood Jonathan , Fukuma Ryohei , Oshino Satoru , Tani Naoki , Khoo Hui Ming , Kishima Haruhiko 
Published: June 2023

AbstractCore features of human cognition, for example, the experience of mind wandering, highlight the importance of the capacity to focus on information separate from the here and now. However, the brain mechanisms that underpin these self-generated states remain unclear. An emerging hypothesis is that self-generated states depend on the process of memory replay, which, in animals, is linked to sharp-wave ripples (SWRs) originating in the hippocampus. SWRs are transient high-frequency oscillations that exhibit circadian fluctuations and, in the laboratory, are important for memory and planning. Local field potentials were recorded from the hippocampus of 11 patients with epilepsy for up to 15 days, and experience sampling was used to describe their association with ongoing thought patterns. SWRs were correlated with patterns of vivid, intrusive ongoing thoughts unrelated to the task being performed, establishing their contribution to the ongoing thoughts that humans experience in daily life.
Cognitive Model Discovery via Disentangled RNNs
Authors: Miller Kevin J. , Eckstein Maria , Botvinick Matthew M. , Kurth-Nelson Zeb 
Published: June 2023

AbstractComputational cognitive models are a fundamental tool in behavioral neuroscience. They instantiate in software precise hypotheses about the cognitive mechanisms underlying a particular behavior. Constructing these models is typically a difficult iterative process that requires both inspiration from the literature and the creativity of an individual researcher. Here, we adopt an alternative approach to learn parsimonious cognitive models directly from data. We fit behavior data using a recurrent neural network that is penalized for carrying information forward in time, leading to sparse, interpretable representations and dynamics. When fitting synthetic behavioral data from known cognitive models, our method recovers the underlying form of those models. When fit to laboratory data from rats performing a reward learning task, our method recovers simple and interpretable models that make testable predictions about neural mechanisms.
Targeting the Microbiome to Improve Gut Health and Breathing Function After Spinal Cord Injury
Authors: Wilson Jessica N. , Kigerl Kristina A. , Sunshine Michael D. , Taylor Chase E. , Speed Sydney L. , Rose Breanna C. , Calulot Chris M. , Dong Brittany E. , Hawkinson Tara R. , Clarke Harrison A. , Bachstetter Adam D. , Waters Christopher M. , Sun Ramon C. , Popovich Phillip G. , Alilain Warren J. 
Published: June 2023

ABSTRACTSpinal cord injury (SCI) is a devastating condition characterized by impaired motor and sensory function, as well as internal organ pathology and dysfunction. This internal organ dysfunction, particularly gastrointestinal (GI) complications, and neurogenic bowel, can reduce the quality of life of individuals with an SCI and potentially hinder their recovery. The gut microbiome impacts various central nervous system functions and has been linked to a number of health and disease states. An imbalance of the gut microbiome, i.e., gut dysbiosis, contributes to neurological disease and may influence recovery and repair processes after SCI. Here we examine the impact of high cervical SCI on the gut microbiome and find that transient gut dysbiosis with persistent gut pathology develops after SCI. Importantly, probiotic treatment improves gut health and respiratory motor function measured through whole-body plethysmography. Concurrent with these improvements was a systemic decrease in the cytokine tumor necrosis factor-alpha and an increase in neurite sprouting and regenerative potential of neurons. Collectively, these data reveal the gut microbiome as an important therapeutic target to improve visceral organ health and respiratory motor recovery after SCI.Research HighlightsCervical spinal cord injury (SCI) causes transient gut dysbiosis and persistent gastrointestinal (GI) pathology.Treatment with probiotics after SCI leads to a healthier GI tract and improved respiratory motor recovery.Probiotic treatment decreases systemic tumor necrosis factor-alpha and increases the potential for sprouting and regeneration of neurons after SCI.The gut microbiome is a valid target to improve motor function and secondary visceral health after SCI.
Liquid-like condensates mediate competition between actin branching and bundling
Authors: Graham Kristin , Chandrasekaran Aravind , Wang Liping , Yang Noel , Lafer Eileen M. , Rangamani Padmini , Stachowiak Jeanne C. 
Published: June 2023

ABSTRACTCellular remodeling of actin networks underlies cell motility during key morphological events, from embryogenesis to metastasis. In these transformations there is an inherent competition between actin branching and bundling, because steric clashes among branches create a mechanical barrier to bundling. Recently, liquid-like condensates consisting purely of proteins involved in either branching or bundling of the cytoskeleton have been found to catalyze their respective functions. Yet in the cell, proteins that drive branching and bundling are present simultaneously. In this complex environment, which factors determine whether a condensate drives filaments to branch versus becoming bundled? To answer this question, we added the branched actin nucleator, Arp2/3, to condensates composed of VASP, an actin bundling protein. At low actin to VASP ratios, branching activity, mediated by Arp2/3, robustly inhibited VASP-mediated bundling of filaments, in agreement with agent-based simulations. In contrast, as the actin to VASP ratio increased, addition of Arp2/3 led to formation of aster-shaped structures, in which bundled filaments emerged from a branched actin core, analogous to filopodia emerging from a branched lamellipodial network. These results demonstrate that multi-component, liquid-like condensates can modulate the inherent competition between bundled and branched actin morphologies, leading to organized, higher-order structures, similar to those found in motile cells.SIGNIFICANCE STATEMENTReorganization of actin filaments allows cells to migrate, which is required for embryonic development, wound healing, and cancer metastasis. During migration, the leading-edge of the cell consists of needle-like protrusions of bundled actin, which emanate from a sheet of branched actin. Given that the proteins responsible for both architectures are present simultaneously, what determines whether actin filaments will be branched or bundled? Here we show that liquid-like condensates, composed of both branching and bundling proteins, can mediate the inherent competition between these fundamentally different ways of organizing actin networks. This work demonstrates that by tuning the composition of condensates, we can recapitulate the transition from branched to bundled networks, a key step in cell migration.
The presence of a G-quadruplex prone sequence upstream of a minimal promoter increases transcriptional activity in the yeastS. cerevisiae
Authors: Kratochvilová Libuše , Vojsovič Matúš , Valková Natália , Šislerová Lucie , El Rashed Zeinab , Inga Alberto , Monti Paola , Brázda Václav 
Published: June 2023

AbstractNon-canonical secondary structures in DNA are increasingly being revealed as critical players in DNA metabolism, including modulating the accessibility and activity of promoters. These structures comprise the so-called G-quadruplexes (G4s) that are formed from sequences rich in guanine bases. Using a well-defined transcriptional reporter system, we sought to systematically investigate the impact of the presence of G4 structures on transcription in yeastS. cerevisiae. To this aim, different G4 prone sequences were modeled to vary the chance of intramolecular G4 formation, analyzedin vitroby Thioflavin T binding test and circular dichroism and then placed at the yeastADE2locus on chromosome XV, downstream and adjacent to a P53 response element (RE) and upstream from a minimalCYC1promoter and Luciferase 1 (LUC1) reporter gene in isogenic strains. While the minimalCYC1promoter provides for basal reporter activity, the P53 RE enablesLUC1transactivation under the control of the human P53 family proteins expressed under the inducibleGAL1promoter. Thus, the impact of the different G4 prone sequences on both basal and P53 family proteins dependent expression was measured after shifting the yeast cells onto galactose containing medium. The results showed that the presence of G4 prone sequences upstream of a yeast minimal promoter can increase its basal activity proportionally to their potential to form intramolecular G4 structures; consequently, this improved accessibility, when present near the target binding site of P53 family transcription factors can be exploited in order to regulate the transcriptional activity of P53, P63 and P73 proteins.
Connexin 43 and Cell Culture Substrate Differentially Regulate OCY454 Osteocytic Differentiation and Signaling to Primary Bone Cells
Authors: Hoppock Gabriel A. , Buettmann Evan G. , Denisco Joseph A. , Goldscheitter Galen M , Condyles Sebastian N. , Juhl Otto J. , Friedman Michael A. , Zhang Yue , Donahue Henry J. 
Published: June 2023

AbstractConnexin 43 (Cx43), the predominate gap junction protein in bone, is essential for intercellular communication and skeletal homeostasis. Previous work suggests osteocyte-specific deletion of Cx43 leads to increased bone formation and resorption, however the cell-autonomous role of osteocytic Cx43 in promoting increased bone remodeling is unknown. Recent studies using 3D culture substrates in OCY454 cells suggest 3D cultures may offer increased bone remodeling factor expression and secretion, such as sclerostin and RANKL. In this study, we compared culturing OCY454 osteocytes on 3D Alvetex scaffolds to traditional 2D tissue culture, both with (WT) and without Cx43 (Cx43 KO). Conditioned media from OCY454 cell cultures was used to determine soluble signaling to differentiate primary bone marrow stromal cells into osteoblasts and osteoclasts. OCY454 cells cultured on 3D portrayed a mature osteocytic phenotype, relative to cells on 2D, shown by increased osteocytic gene expression and reduced cell proliferation. In contrast, OCY454 differentiation based on these same markers was not affected by Cx43 deficiency in 3D. Interestingly, increased sclerostin secretion was found in 3D cultured WT cells compared to Cx43 KO cells. Conditioned media from Cx43 KO cells promoted increased osteoblastogenesis and increased osteoclastogenesis, with maximal effects from 3D cultured Cx43 KO cells. These results suggest Cx43 deficiency promotes increased bone remodeling in a cell autonomous manner with minimal changes in osteocyte differentiation. Finally, 3D cultures appear better suited to study mechanisms from Cx43-deficient OCY454 osteocytesin vitrodue to their ability to promote osteocyte differentiation, limit proliferation, and increase bone remodeling factor secretion.New and Noteworthy3D cell culture of OCY454 cells promoted increased differentiation compared to traditional 2D culture. While Cx43 deficiency did not affect OCY454 differentiation, it resulted in increased signaling, promoting osteoblastogenesis and osteoclastogenesis. Our results suggest Cx43 deficiency promotes increased bone remodeling in a cell autonomous manner with minimal changes in osteocyte differentiation. Also, 3D cultures appear better suited to study mechanisms in Cx43-deficient OCY454 osteocytes.
Specific prostaglandins are produced in the migratory cells and the surrounding substrate to promoteDrosophilaborder cell migration
Authors: Mellentine Samuel Q. , Ramsey Anna S. , Li Jie , Brown Hunter N. , Tootle Tina L. 
Published: June 2023

AbstractA key regulator of collective cell migration is prostaglandin (PG) signaling. However, it remains largely unclear whether PGs act within the migratory cells or their microenvironment to promote migration. Here we useDrosophilaborder cell migration as a model to uncover the cell-specific roles of two PGs in collective migration. Prior work shows PG signaling is required for on-time migration and cluster cohesion. We find that the PGE2synthase cPGES is required in the substrate, while the PGF2αsynthase Akr1B is required in the border cells for on-time migration. Akr1B acts in both the border cells and their substrate to regulate cluster cohesion. One means by which Akr1B regulates border cell migration is by promoting integrin-based adhesions. Additionally, Akr1B limits myosin activity, and thereby cellular stiffness, in the border cells, whereas cPGES limits myosin activity in both the border cells and their substrate. Together these data reveal that two PGs, PGE2and PGF2α, produced in different locations, play key roles in promoting border cell migration. These PGs likely have similar migratory versus microenvironment roles in other collective cell migrations.
The haplolethal genewupAof Drosophila exhibits potential as a target for an X-poisoning gene drive
Authors: Lawler Clancy D. , Parra Nuñez Ana Karla , Hernandes Natalia , Bhide Soumitra , Lohrey Isabelle , Baxter Simon , Robin Charles 
Published: June 2023

AbstractA synthetic gene drive that targets haplolethal genes on the X-chromosome can skew the sex ratio towards males. Like an ‘X-shredder’ it does not involve ‘homing’ and that has advantages including the reduction of gene drive resistance allele formation. We examine this ‘X-poisoning’ strategy by targeting four of the 11 known X-linked haplolethal/haplosterile genes ofDrosophila melanogasterwith CRISPR/Cas9. We find that targeting thewupAgene during spermatogenesis skews the sex ratio so fewer than 14% of progeny are daughters. That is unless we cross the mutagenic males to X^XY female flies that bear attached-X chromosomes, which reverses the inheritance of the poisoned X chromosome so that sons inherit it from their father; in which case only 2% of the progeny are sons. These sex ratio biases suggests that most of the CRISPR/Cas9 mutants we induced in thewupAgene are haplolethal but some are recessive lethal. The males generatingwupAmutants do not suffer from reduced fertility rather the haplolethal mutants arrest development in the late stages of embryogenesis well after fertilized eggs have been laid. This provides a distinct advantage over genetic manipulation strategies involving sterility which can be countered by the remating of females. We also find thatwupAmutants that destroy the nuclear localization signal of shorter isoforms are not haplolethal as long as the open reading frame remains intact. LikeD. melanogaster wupAorthologs ofD. suzukiiandAnophelesmosquitos are found on X chromosomes makingwupAa viable X-poisoning target in multiple species.
Converging on consistent functional connectomics
Authors: Luppi Andrea I. , Gellersen Helena M. , Liu Zhen-Qi , Peattie Alexander R. D. , Manktelow Anne E. , Adapa Ram , Owen Adrian M. , Naci Lorina , Menon David K. , Dimitriadis Stavros I. , Stamatakis Emmanuel A. 
Published: June 2023

AbstractFunctional interactions between brain regions can be viewed as a network, empowering neuroscientists to leverage network science to investigate distributed brain function. However, obtaining a brain network from functional neuroimaging data involves multiple steps of data manipulation, which can drastically affect the organisation and validity of the estimated brain network and its properties. Here, we provide a systematic evaluation of 576 unique data-processing pipelines for functional connectomics from resting-state functional MRI, obtained from all possible recombinations of popular choices for brain atlas type and size, connectivity definition and selection, and global signal regression. We use the portrait divergence, an information-theoretic measure of differences in network topology across scales, to quantify the influence of analytic choices on the overall organisation of the derived functional connectome. We evaluate each pipeline across an entire battery of criteria, seeking pipelines that (i) minimise spurious test-retest discrepancies of network topology, while simultaneously (ii) mitigating motion confounds, and being sensitive to both (iii) inter-subject differences and (iv) experimental effects of interest, as demonstrated by propofol-induced general anaesthesia. Our findings reveal vast and systematic variability across pipelines’ suitability for functional connectomics. Choice of the wrong data-processing pipeline can lead to results that are not only misleading, but systematically so, distorting the functional connectome more drastically than the passage of several months. We also found that the majority of pipelines failed to meet at least one of our criteria. However, we identified 8 candidates satisfying all criteria across each of four independent datasets spanning minutes, weeks, and months, ensuring the generalisability of our recommendations. Our results also generalise to alternative acquisition parameters and preprocessing and denoising choices. By providing the community with a full breakdown of each pipeline’s performance across this multi-dataset, multi-criteria, multi-scale and multi-step approach, we establish a comprehensive set of benchmarks to inform future best practices in functional connectomics.
New genetic tools for mushroom body output neurons in Drosophila
Authors: Rubin Gerald M. , Aso Yoshinori 
Published: June 2023

AbstractHow memories of past events influence behavior is a key question in neuroscience. The major associative learning center in Drosophila, the Mushroom Body (MB), communicates to the rest of the brain through Mushroom Body Output Neurons (MBONs). While 21 MBON cell types have their dendrites confined to small compartments of the MB lobes, analysis of EM connectomes revealed the presence of an additional 14 MBON cell types that are atypical in having dendritic input both within the MB lobes and in adjacent brain regions. Genetic reagents for manipulating atypical MBONs and experimental data on their functions has been lacking. In this report we describe new cell-type-specific GAL4 drivers for many MBONs, including the majority of atypical MBONs. Using these genetic reagents, we conducted optogenetic activation screening to examine their ability to drive behaviors and learning. These reagents provide important new tools for the study of complex behaviors in Drosophila.