bluuebunny/crossref_metadata_2025_split huggingface dataset:
EWS-FLI1 Expression in Human Embryonic MSCs Leads to Transcriptional Reprograming, Defective DNA Damage Repair and Ewing Sarcoma
Authors: Hernández-Muñoz Inmaculada , Cuervas Irene , Prada Estela , Pulecio Julian , Gimeno Ramón , Andrades Evelyn , Gómez-González Soledad , Berenguer-Molins Pau , Acedo-Terrades Ariadna , Perera-Bel Júlia , Bódalo Marta , Nonell Lara , Pérez Elena , Grases Daniela , Mata Caterina , Yélamos José , Richaud Yvonne , Vidal Enrique , Cuartero Yasmina , Le Dily François , Suñol Mariona , Manzanares Alejandro , Raya Angel , Mora Jaume 
Published: January 2025

ABSTRACTEwing sarcoma (ES) is an aggressive bone and soft tissue neoplasm characterized byEWSR1/ETSrearrangements and whose cellular origin remains unclear. EWS-FLI1 expression in human pediatric mesenchymal stem cells (hpMSCs) induces a quantitatively and qualitatively different transcriptional response than its expression in human adult MSCs (haMSCs), but fails to form tumorsin vivo. ES cells have early developmental lineage signatures distinct from postnatal MSCs. Here, we have generated MSCs from experimental teratomas out of human embryonic stem cells (heSCs). Transduction of these human embryonic mesenchymal stem cells (heMSCs) with EWS-FLI1 results in the acquisition of an ES transcriptome, although the oncogene does not preferentially bind to promoters, but to intronic and intergenic microsatellites with >10 CA dinucleotides and GGAA repeats, respectively. In heMSCs, EWS-FLI1 directly regulates BRCA1 expression, although EWS-FLI1-expressing cells show defects in DNA damage repair. Xenografting of EWS-FLI1-transduced heMSCs resulted in the formation of tumors expressing characteristic ES markers. In summary, EWS-FLI1 enforces an aberrant transcriptome and endowsin vivotransforming capacity when expressed in an undifferentiated early heMSC. Our approach represents an innovative experimental method for understanding critical aspects of the biology of developmental tumors, from leukemia to sarcomas, in which few (even single) genetic alterations are able to transform a fetal stem cell.
Reactivation of developmentally silenced globin genes through genomic deletions reveals that enhancer distance matters
Authors: Felder Anna-Karina , Tjalsma Sjoerd J.D. , Verhagen Han J.M.P. , Majied Rezin , Verstegen Marjon J.A.M. , Verheul Thijs C.J. , Mohnani Rebecca , Gremmen Richard , Krijger Peter H.L. , Philipsen Sjaak , van den Akker Emile , de Laat Wouter 
Published: January 2025

AbstractThe human genome contains regulatory DNA elements, enhancers, that can activate gene transcription over long chromosomal distances. Here, we show that enhancer distance can be critical for gene silencing. We demonstrate that linear recruitment of the normally distalHBBsuper-enhancer to developmentally silencedHBGpromoters, through deletion or inversion of intervening DNA sequences, results in strongly reactivatedHBGexpression in adult erythroid cells andex vivodifferentiated hematopoietic stem and progenitor cells. A similar observation is made in theHBAlocus, where deletion-to-recruit of the distal enhancer strongly reactivates embryonicHBZexpression. Overall, our work assigns function to seemingly non-regulatory genomic segments: by providing linear separation they may support genes to autonomously control their transcriptional response to distal enhancers.
Cortical Response to Acute Implantation of the Utah Optrode Array in Macaque Cortex
Authors: Villamarin-Ortiz Adrián , Reiche Christopher F. , Federer Frederick , Clark Andrew M. , Rolston John D. , Soto-Sánchez Cristina , Fernandez Eduardo , Blair Steve , Angelucci Alessandra 
Published: January 2025

ABSTRACTOptogenetics has transformed the study of neural circuit function, but limitations in its application to species with large brains, such as non-human primates (NHPs), remain. A major challenge in NHP optogenetics is delivering light to sufficiently large volumes of deep neural tissue with high spatiotemporal precision, without simultaneously affecting superficial tissue. To overcome these limitations, we recently developed and testedin vivoin NHP cortex, the Utah Optrode Array (UOA). This is a 10×10 array of penetrating glass shanks, tiling a 4×4mm2area, bonded to interleaved needle-aligned and interstitial µLED arrays, which allows for independent photostimulation of deep and superficial brain tissue. Here, we investigate the acute biological response to UOA implantation in NHP cortex, with the goal of optimizing device design for reduced insertion trauma and subsequent chronic response. To this goal, we systematically vary UOA shank diameter, surface texture, tip geometry, and insertion pressure, and assess their effects on astrocytes, microglia, and neuronal viability, following acute implantation. We find that UOAs with shanks of smaller diameter, smooth surface texture and round tips cause the least damage. Higher insertion pressures have limited effects on the inflammatory response, but lead to greater tissue compression. Our results highlight the importance of balancing shank diameter, tip geometry, and insertion pressure in UOA design for preserving tissue integrity and improving long-term UOA performance and biocompatibility.
Conservation of symmetry breaking at the level of chromatin accessibility between fly species with unrelated anterior determinants
Authors: Amiri Ezra E. , Tenger-Trolander Ayse , Li Muzi , Julian Alexander Thomas , Kasan Koray , Sanders Sheri A. , Blythe Shelby , Schmidt-Ott Urs 
Published: January 2025

AbstractEstablishing the anterior-posterior body axis is a fundamental process during embryogenesis, and the fruit fly,Drosophila melanogaster, provides one of the best-known case studies of this process. In Drosophila, localized mRNA ofbicoidserves as anterior determinant (AD). Bicoid engages in a concentration-dependent competition with nucleosomes and initiates symmetry-breaking along the AP axis by promoting chromatin accessibility at the loci of transcription factor (TF) genes that are expressed in the anterior of the embryo. However, ADs of other fly species are unrelated and structurally distinct, and little is known about how they function. We addressed this question in the moth fly,Clogmia albipunctata, in which a maternally expressed transcript isoform of the pair-rule segmentation geneodd-pairedis localized in the anterior egg and has been co-opted as AD. We provide ade novoassembly and annotation of the Clogmia genome and describe how knockdown ofzeldaand maternalodd-pairedtranscript affect chromatin accessibility and expression of TF-encoding loci. The results of these experiments suggest direct roles of Cal-Zld in opening and closing chromatin during nuclear cleavage cycles and show that Clogmia’s maternalodd-pairedactivity promotes chromatin accessibility and anterior expression during the early phase of zygotic genome activation at Clogmia’shomeobrainandsloppy-pairedloci. We conclude that unrelated dipteran ADs initiate anterior-posterior axis-specification at the level of enhancer accessibility and thathomeobrainandsloppy-pairedhomologs may serve a more widely conserved role in the initiation of anterior pattern formation given their early anterior expression and function in head development in other insects.
ECM Signatures Reveal Quiescent Stem Cell Diversity in the Colonic Niche
Authors: Hickey Séamus E. , Andreatta Massimo , Enright Christina , Boucrot Emmanuel , Kiely Patrick , Cashman Siobhán B. , Carmona Saintiago J. , McGourty Kieran 
Published: January 2025

ABSTRACTColonic stem cells have a key role in the continuous regeneration of a healthy intestinal epithelium. Despite considerable advances in single-cell omics technologies, the transcriptional heterogeneity of rare cell types such as colonic stem cells, as well as their functional states and niche-specific behaviors, remain poorly characterised. In this study, we leverage a meta-analysis of scRNA-seq and spatial transcriptomic datasets to comprehensively map the heterogeneity of colonic stem cells. We identify multiple, previously underappreciated stem cell states, including distinct quiescent subtypes marked byCDKN1A(P21),CDKN1B(P27), andCDKN1C(P57), proliferative populations defined byMKI67(Ki67) andLRIG1, and a lineage-committed intermediate subpopulation expressingMUC2. Strikingly, we find that these states can be robustly identified solely by their extracellular matrix (ECM) gene expression signatures, revealing ECM composition as a critical determinant of stem cell identity. Notably, LAMA1 expression is highly specific to the P57+ quiescent population, linking laminin-mediated microenvironments to the active maintenance of deep quiescence, consistent with our recent findings associating LAMA1 with quiescent cell survival. By applying these ECM gene signatures, we delineate discrete “micro-niches” of quiescent stem cells in healthy tissue and provide evidence that analogous states persist in the colorectal cancer (CRC) environment. Extending our approach to an unrelated tissue, the pancreas, we detect parallel quiescent cell subtypes, illustrating the broader applicability of ECM-based signatures. Taken together, our findings redefine the concept of stem cell heterogeneity in the colon, establish ECM-driven gene signatures as a powerful tool for characterizing stem cell states, and offer new perspectives on the niche-dependent regulation of both healthy and cancerous stem cell populations.
EPSD 2.0: An Updated Database of Protein Phosphorylation Sites across Eukaryotic Species
Authors: Chen Miaomiao , Gou Yujie , Lei Ming , Xiao Leming , Zhao Miaoying , Huang Xinhe , Liu Dan , Feng Zihao , Peng Di , Xue Yu 
Published: January 2025

AbstractAs one of the most crucial post-translational modifications (PTMs), protein phosphorylation regulates a broad range of biological processes in eukaryotes. Biocuration, integration and annotation of reported phosphorylation events will deliver a valuable resource for the community. Here, we present an updated database, the eukaryotic phosphorylation site database 2.0 (EPSD 2.0), which includes 2,769,163 experimentally identified phosphorylation sites (p-sites) in 362,707 phosphoproteins from 223 eukaryotes. From the literature, 873,718 new p-sites identified through high-throughput phosphoproteomic research were first collected, and 1,078,888 original phosphopeptides together with primary references were reserved. Then, this dataset was merged into EPSD 1.0, comprising 1,616,804 p-sites within 209,326 proteins across 68 eukaryotic organisms [1]. We also integrated 362,190 additional known p-sites from 10 public databases. After redundancy clearance, we manually re-checked each p-site and annotated 88,074 functional events for 32,762 p-sites, covering 58 types of downstream effects on phosphoproteins, and regulatory impacts on 107 biological processes. In addition, phosphoproteins and p-sites in 8 model organisms were meticulously annotated utilizing information supplied by 100 external platforms encompassing 15 areas. These areas included kinase/phosphatase, transcription regulators, three-dimensional structures, physicochemical characteristics, genomic variations, functional descriptions, protein domains, molecular interactions, drug-target associations, disease-related data, orthologs, transcript expression levels, proteomics, subcellular localization, and regulatory pathways. We expect that EPSD 2.0 will become a useful database supporting comprehensive studies on phosphorylation in eukaryotes. The EPSD 2.0 database is freely accessible online athttps://epsd.biocuckoo.cn/.
Challenges and facilitators in pathways to cancer diagnosis in Southern Africa: A qualitative study
Authors: Day S. , Arendse KD. , Scott SE. , Moyo M. , Mzeche S. , Guzha BT. , Tegama N. , Sills VA. , Ras T. , Walter FM. , Moodley J. 
Published: January 2025

AbstractObjectivesTo explore healthcare workers (HCW) experiences, barriers and facilitators in managing patients with symptoms of possible breast, cervical or colorectal cancer.DesignA qualitative in-depth interview study with HCWs managing patients with breast, cervical and colorectal cancer symptoms. We also conducted workshops with a group of HCWs to check the credibility of the interview findings.SettingThe study was conducted with staff working in primary, secondary and tertiary health facilities in the Eastern and Western Cape in South Africa (SA) and Harare and Bulawayo and their referral provinces in Zimbabwe.ParticipantsHCWs with experience in managing patients with symptoms of possible breast, cervical or colorectal cancer were recruited for the study. Participants were purposively sampled, according to region, healthcare level, and job role. A total of 56 participants (26 in SA and 30 in Zimbabwe) participated in the in-depth interviews. Twenty-six (12 in SA and 14 in Zimbabwe) participated in four clinical advisory group workshops across both countries.ResultsDrawing on the Model of Pathways to Treatment, HCW perceptions of patient-level factors influencing the diagnostic interval included financial limitations, and patients’ absence and delays in attendance. Healthcare provider and system factors included: challenges with referral and feedback systems; training needs; low awareness of protocols and guidelines; inappropriate and suboptimal clinical assessments; and broader socio-economic factors and resource limitations.ConclusionImproving the timely diagnosis of breast, cervical, and colorectal cancer in Southern Africa necessitates targeted strategies that address both patient-related, provider and health-system delays.Strengths and LimitationsTo our knowledge, this is the first study in SA and Zimbabwe that explores healthcare workers across all levels of care perceptions of the challenges and facilitators in the pathways to breast, cervical and colorectal cancer diagnosis.The qualitative nature of the inquiry and strong theoretical underpinning with the Model of Pathways to Treatment enabled in-depth exploration of the research question.The study setting included both urban and rural settings that represent differences in access to cancer care and health systems.We note that the discussion of patient level facilitators and barriers to early diagnosis are the perceptions of HCWs and not the views of the patients themselves.By examining cancer care in two distinct countries, the study provides valuable insights into how different levels of human development index impact healthcare systems and identify unique challenges and best practices. A comparative analysis reveals important differences in health outcomes and resource allocation, which can inform targeted interventions.
Cell heterogeneity and fate bistability drive tissue patterning during intestinal regeneration
Authors: Schwayer C. , Barbiero S. , Brückner D. B. , Baader C. , Repina N. A. , Diaz O. E. , Meylan L. Challet , Kalck V. , Suppinger S. , Yang Q. , Schnabl J. , Kilik U. , Camp J. G. , Stockinger B. , Bühler M. , Stadler M. B. , Hannezo E. , Liberali P. 
Published: January 2025

AbstractTissue regeneration relies on the ability of cells to undergode novopatterning. While tissue patterning has been viewed as the transition from initially identical un-patterned cells to an arrangement of different cell types, recent evidence suggests that initial heterogeneities between cells modulate tissue-scale pattern formation. Yet, how such heterogeneities arise and, thereafter, regulate cell type emergence in a population of cells is poorly understood. Usingin vivoandin vitromouse regenerative systems, we identify a critical tissue density that is required to induce heterogeneous inactivation of the mechanosensor YAP1. Experimental and biophysical approaches demonstrate that YAP1 cell-to-cell heterogeneity pre-patterns the first cell fate decision, via both chromatin remodelling and a supracellular feedback between FOXA1 and Delta-Notch signalling. This feedback motif induces cell fate bistability endowing memory to the system and the maintenance of patterns during homeostasis. These findings reveal a generalisable framework in which transient cell-to-cell heterogeneity, regulated by tissue-scale properties, serves as a critical control parameter for the emergence of cell fate and stable patterning during regeneration.
High resolution multi-scale profiling of embryonic germ cell-like cells derivation reveals pluripotent state transitions in humans
Authors: Stucchi Sarah , Sepulveda-Rincon Lessly P. , Dion Camille , Matassa Gaja , Valenti Alessia , Cheroni Cristina , Vitriolo Alessandro , Prazzoli Filippo , Young George , Rigoli Marco Tullio , Ciprietti Martina , Muda Benedetta , Heckhausen Zoe , Hajkova Petra , Caporale Nicolò , Testa Giuseppe , Leitch Harry G. 
Published: January 2025

AbstractPrimordial germ cells (PGCs) are the embryonic precursors of the gametes. In mice and rats, PGCs can readily acquire pluripotency in vitro by forming embryonic germ cells (EGCs). To date, a comparable in vitro system has not been established in humans, despite the fact that human PGCs (hPGCs) readily undergo pluripotent conversion in the context of germ cell tumorigenesis. Here we report that hPGC-like cells (hPGCLCs) undergo conversion to human embryonic germ-like cells (hEGCLCs) upon exposure to the same inductive signals previously used to derive mouse EGCs. This defined, feeder-free culture system allows efficient derivation of human EGCLCs which can be expanded and maintained in standard human pluripotent stem cell medium. hEGCLCs are transcriptionally similar to human pluripotent stem cells (hPSCs) and can differentiate into all three germ layers, as well as giving rise to PGCLCs once more - demonstrating the interconvertibility of pluripotent states. This is also evident at the epigenetic level, as the initial DNA demethylation that occurs in hPGCLCs is largely reversed in hEGCLCs, restoring DNA methylation to the level observed in hPSCs. This new in vitro model captures the transition from the pluripotent stem cell state to a germ cell identity and back again, and therefore represents a highly tractable system to study pluripotent and epigenetic transitions, including those which occur during human germ cell tumorigenesis.Graphical abstractIn briefWe report the first fully defined system to efficiently convert hPGCLCs to a pluripotent stem cell (PSC) state. We tracked pluripotent state transitions by multi-omic analysis and provided a high-resolution map of the transcriptional and epigenomic transitions upon entry to and exit from the human germline.HighlightsEfficient derivation of hEGCLC in fully defined feeder-free conditionsSingle-cell transcriptomic profiling of transitions from the hPSC state to hPGCLCs and back.Longitudinal DNA methylation profiling highlights the overall reversibility of epigenetic statesMulti-omic gene regulatory network analysis identifies key regulators of pluripotent transitions
A highly stable engineered disulfide bond in the dimer interface ofE. coliorotate phosphoribosyl transferase
Authors: Kurauskas Vilius , Johansson Kristoffer E. , Willemoës Martin , Winther Jakob R. 
Published: January 2025

AbstractStructural disulfides are very rarely found in cytoplasmic proteins of mesophilic organisms. Nevertheless, disulfides can form in the cytosol if these are stabilized sufficiently by the supporting protein structure. To investigate the redox properties of structural disulfide bonds, we introduced disulfide bonds into the cytosolic enzyme fromE. coli, orotate phosphoribosyl transferase (OPRT). Because OPRT is a homodimer the introduction of opposing cysteine residues (R44C and D92C) into separate monomers of the enzyme meant that disulfide bond formation could easily be followed by non-reducing SDS-PAGE. Redox titration experiments in DTT buffers revealed that the designed disulfide bond was exceedingly stable with a redox potential of −314 mV, close to that of dithiothreitol (DTT). This interchain disulfide bond improved global thermostability by 5.9°C relative to wild type protein and 21.4°C above its reduced form. The catalytic activity of the enzyme in either its thiol or disulfide state was not substantially affected, indicating structural integrity. Combining an inactive subunit with the asymmetric nature of disulfide bond allowed determination of rates of subunit rearrangement and disulfide formation. The R44C/D92C double mutant resulted in the formation of a symmetric homodimer with two interchain disulfides. The redox potential of this dimer variant was further decreased to −321 mV. However, the global stability of the two-disulfide dimer was not substantially increased relative to the dimer with the single disulfide bond, suggesting that the stabilizing effect was gained by preventing dimer dissociation. Finally, disulfide bond exchange is possible by thioredoxin. With a redox potential similar to that of the eukaryotic cytosol, these mutant variants may provide a new tool for cytosolic redox sensingin vivo, possibly targeting the thioredoxin system.
Perdurant TTC21B protein in the early mouse embryo is required for proper forebrain neural progenitor proliferation
Authors: Niewoehner Rebekah , Paulding David , Leal Jesus , Stottmann Rolf W. 
Published: January 2025

ABSTRACTPrimary cilia play a pivotal role in cellular signaling and development and disruptions in ciliary form and/or function leads to human ciliopathies. Here, we examine the role ofTtc21b, a key component of the intraflagellar transport-A complex, in mouse forebrain development using aTtc21baliennull allele. Our findings reveal significant microcephaly in homozygous mutants is caused by disrupted neural progenitor proliferation and differentiation. Histological and immunohistochemical analyses show an enlarged ventricular zone and reduced cortical plate thickness, accompanied by altered mitotic spindle angles, suggesting defects in symmetric versus asymmetric cell divisions. Despite lowTtc21bexpression in the forebrain epithelium, early embryonic expression patterns imply that perdurant TTC21B protein may underlie these phenotypes. Progenitor proliferation kinetics were disrupted, with fewer cells re-entering the cell cycle, correlating with reduced TBR2-positive intermediate progenitors and altered neurogenesis dynamics. Neuronal processes in the cortical plate were significantly shortened, suggesting cytoskeletal defects specific to terminal differentiation stages. Our findings support a model where earlyTtc21bexpression in precursors destined for the forebrain is critical for sustaining later neural progenitor proliferation and differentiation. These results advance our understanding of primary cilia in cortical development and provide a framework for exploring cytoskeletal contributions to ciliopathies.