bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dissecting signaling regulators driving AXL-mediated bypass resistance and associated phenotypes by phosphosite perturbations
Authors: Creixell Marc , Taylor Scott D. , Gerritsen Jacqueline , Bae Song Yi , Jiang Mingxuan , Augustin Teresa , Loui Michelle , Boixo Carmen , Creixell Pau , White Forest M , Meyer Aaron S 
Published: October 2023

ABSTRACTReceptor tyrosine kinase (RTK)-targeted therapies are often effective but invariably limited by drug resistance. A major mechanism of acquired resistance involves “bypass” switching to alternative pathways driven by non-targeted RTKs that restore proliferation. One such RTK is AXL whose overexpression, frequently observed in bypass resistant tumors, drives both cell survival and associated malignant phenotypes such as epithelial-to-mesenchymal (EMT) transition and migration. However, the signaling molecules and pathways eliciting these responses have remained elusive. To explore these coordinated effects, we generated a panel of mutant lung adenocarcinoma PC9 cell lines in which each AXL intracellular tyrosine residue was mutated to phenylalanine. By integrating measurements of phosphorylation signaling and other phenotypic changes associated with resistance through multivariate modeling, we mapped signaling perturbations to specific resistant phenotypes. Our results suggest that AXL signaling can be summarized into two clusters associated with progressive disease and poor clinical outcomes in lung cancer patients. These clusters displayed favorable Abl1 and SFK motifs and their phosphorylation was consistently decreased by dasatinib. High-throughput kinase specificity profiling showed that AXL likely activates the SFK cluster through FAK1 which is known to complex with Src. Moreover, the SFK cluster overlapped with a previously established focal adhesion kinase (FAK1) signature conferring EMT-mediated erlotinib resistance in lung cancer cells. Finally, we show that downstream of this kinase signaling, AXL and YAP form a positive feedback loop that sustains drug tolerant persister cells. Altogether, this work demonstrates an approach for dissecting signaling regulators by which AXL drives erlotinib resistance-associated phenotypic changes.One-sentence summaryA systems biology approach elucidates the signaling pathways driving AXL-mediated erlotinib resistance in lung cancer.
Low-cost camera-based estrous tracking enables transgenesis inPeromyscus leucopus, the primary reservoir for Lyme disease
Authors: Buchthal Joanna , Chory Emma J. , Hill Zachary , Dennison Christy , Tu Boqiang , Wierenga Rick P. , Çevrim Çağrı , Golas Stefan , Telford Sam R. , McKinley Kara L. , Jaenisch Rudolf , Markoulaki Styliani , Esvelt Kevin M. 
Published: October 2023

CRISPR/Cas9 technology has revolutionized the production of animal models by reducing experimental timelines, slashing costs and streamlining gene editing, leading to a rapid expansion in the number of unique models for the study of human disease and gene function. However, most non-model animals, many of which are important in cancer and aging research, remain recalcitrant to genome engineering due to our limited understanding of their reproductive biology. Many wild rodents that transmit human diseases remain particularly challenging to engineer due to low pregnancy rates, the lack of external copulatory plugs, and susceptibility to premature termination of pregnancy. Here, we present low-cost activity-based estrous tracking for the efficient generation of timed pregnant and pseudopregnant white-footed mice and extend this tracking method to both lab mice and hamsters. Leveraging this technology, we demonstrate the generation of engineeredPeromyscus leucopus, the primary reservoir for Lyme disease-causing bacteria and a putative model organism for studies of aging. These tools have broad implications for biomedical research and ecological engineering.Abstract Figure
Preventing NK cell activation in the damaged liver induced by cabozantinib/PD-1 blockade increases survival in hepatocellular carcinoma models
Authors: Morita Satoru , Kikuchi Hiroto , Birch Grace , Matsui Aya , Morita Atsuyo , Kobayashi Tatsuya , Ruan Zhiping , Huang Peigen , Hernandez Alexei , Coyne Erin M. , Shin Sarah M. , Yarchoan Mark , Mino-Kenudson Mari , Romee Rizwan , Ho Won Jin , Duda Dan G. 
Published: October 2023

AbstractThe addition of anti-VEGF antibody treatment to immune checkpoint blockade (ICB) has increased the efficacy of immunotherapy in advanced hepatocellular carcinoma (HCC). Despite an initial promise, adding multitargeted kinase inhibitors of VEGFR with ICB has failed to increase survival in HCC. To reveal the mechanisms underlying treatment failure, we studied the effects of cabozantinib/ICB using orthotopic murine HCC models with or without liver damage. We monitored tumor growth and liver function, recorded survival outcomes, and performed immune profiling studies for intra-tumoral and surrounding liver. Cabozantinib/ICB treatment led to tumor regression and significantly improved survival in mice with normal livers. However, consistent with the clinical findings, combination therapy failed to show survival benefits despite similar tumor control when tested in the same models but in mice with liver fibrosis. Moreover, preclinical and clinical data converged, showing that activating immune responses by cabozantinib/ICB treatment induced hepatoxicity. Immune profiling revealed that combination therapy effectively reprogrammed the tumor immune microenvironment and increased NK cell infiltration and activation in the damaged liver tissue. Surprisingly, systemic depletion of NK reduced hepatotoxicity elicited by the combination therapy without compromising its anti-cancer effect, and significantly enhanced the survival benefit even in mice with HCC and underlying liver fibrosis. These findings demonstrate that preventing NK activation allowed for maintaining a favorable therapeutic ratio when combining ICB with cabozantinib in advanced HCC models.
Genome wide association study of Arabidopsis seed mucilage layers at a regional scale
Authors: Viudes Sébastien , Zamar Rémy , Burlat Vincent , Roux Fabrice , Dunand Christophe 
Published: October 2023

ABSTRACTThe myxospermous speciesArabidopsis thalianaextrudes a polysaccharidic mucilage from the seed coat epidermis during imbibition. The whole seed mucilage can be divided into a seed-adherent layer and a fully soluble layer, both layers presenting natural genetic variations. The adherent mucilage is variable in size and composition, while the soluble mucilage is variable in composition and physical properties. Studies reporting both the genetic architecture and the putative selective agents acting on this natural genetic variation are scarce. In this study, we set up a Genome Wide Association study (GWAS) based on 424 natural accessions collected from 166 natural populations ofA. thalianalocated south-west of France and previously characterized for a very important number of abiotic and biotic factors. We identified an extensive genetic variation for both mucilage layers. The adherent mucilage was mainly related to precipitation and temperature whereas the non-adherent mucilage was unrelated to any environmental factors. By combining a hierarchical Bayesian model with a local score approach, we identified 55 and 28 candidate genes, corresponding to 26 and 10 QTLs for the adherent and non-adherent mucilages, respectively. Putative or characterized function and expression data available in the literature were used to filter the candidate genes. Only one gene among our set of candidate genes was already described as a seed mucilage actor, leaving a large set of new candidates putatively implicated inseed mucilage synthesis or release. The present study lay out foundation to understand the influence of regional ecological factors acting on seed mucilage inA. thaliana.
Inhibiting the GPI Transamidase Subunit GPAA1 Abolishes CD24 Surface Localization and Enhances Macrophage-Mediated Phagocytosis of Ovarian Cancer Cells
Authors: Mishra Alok K. , Ye Tianyi , Banday Shahid , Thakare Ritesh P. , Su Chinh Tran-To , Pham Ngoc N. H. , Ali Amjad , Kulshreshtha Ankur , Chowdhury Shreya Roy , Simone Tessa M. , Hu Kai , Zhu Lihua Julie , Eisenhaber Birgit , Deibler Sara K. , Simin Karl , Thompson Paul R. , Eisenhaber Frank , Malonia Sunil K. , Green Michael R. 
Published: October 2023

SUMMARYThe CD24-Siglec10 signaling axis is an immune checkpoint pathway that shields ovarian cancer cells from phagocytosis by tumor-associated macrophages (TAMs), making it an appealing immunotherapeutic target. Here, we investigate factors influencing CD24 cell surface expression and assess their suitability as drug targets. Using a CRISPR-based knockout screen, we identify GPAA1 (glycosylphosphatidylinositol anchor attachment-1) as a positive regulator of CD24 cell surface expression. GPAA1 is a crucial component of the multi-subunit GPI transamidase complex, which facilitates the attachment of GPI lipid anchor to the C-terminus of CD24, enabling its surface localization. Reducing the activity of GPAA1 in ovarian cancer cells, either by genetic ablation or targeting with an aminopeptidase inhibitor bestatin, disrupts GPI attachment to CD24. This disruption impairs CD24 cell surface localization, enhances phagocytosis by TAMs, and suppresses tumor growth in mice. Our study highlights the potential of GPAA1 targeting as a therapeutic approach for CD24-positive ovarian cancers.
Multi-Omics Insights into Grapevine Ecodormancy to Budburst Transition: Interplay of Gene Expression, miRNA Regulation, and DNA Methylation
Authors: Shinde Harshraj , Raihan Tajbir , Anand Lakshay , Perry Sharyn E. , Geneve Robert L. , Rodriguez Lopez Carlos M. 
Published: October 2023

AbstractIn grapevine, the transition from a dormant bud to budburst is a critical developmental process related to vegetative and reproductive growth. We generated a time series analysis (five sampling time points) and used transcriptome, small RNA, and whole-genome bisulfite sequencing to characterize this transition. Ecodormant buds took an average of 17 days to budburst. Transcriptome analysis identified a total of 7002 differentially expressed genes across all sampling times and revealed that the brassinosteroid metabolism and the linoleic acid metabolism pathways are upregulated and downregulated respectively across all time points. Gene expression cluster analysis identified the activation of the photosynthesis pathway and photosynthesis related genes during this transition. miRNA expression analysis identified a steady increase in expression of two miRNAs, miR159a and miR159b during the transition from dormancy to budburst. Our analysis suggests that these two miRNAs promote budburst by repressing the expression of auxin responsive genes. Finally, a continued increase in CG methylation levels was observed during the dormancy to budburst transition. Differential methylation analysis, considering dormant buds as the control stage, yielded 6354 differentially methylated regions across the genome. Two glucosidase genes exhibited increases in promoter methylation and a corresponding decrease in gene expression in our analysis. This study provides a multi-omics view of grapevine bud transition from dormancy to bud burst and unveils the interacting genetic and epigenetic networks regulating this process.
Endovascular Thrombectomy versus Intravenous Alteplase for Distal Vessel Occlusions: A Propensity Score-Matched Analysis
Authors: Yoshie Tomohide , Ueda Toshihiro , Hasegawa Yasuhiro , Takeuchi Masataka , Morimoto Masafumi , Tsuboi Yoshifumi , Yamamoto Ryoo , Kaku Shogo , Junichi Ayabe , Akiyama Takekazu , Yamamoto Daisuke , Mori Kentaro , Kagami Hiroshi , Ito Hidemichi , Onodera Hidetaka , Kaga Yasuyuki , Ohtsubo Haruki , Tatsuno Kentaro , Usuki Noriko , Takaishi Satoshi , Yamano Yoshihisa 
Published: October 2023

AbstractsBackgroundThe benefits of endovascular thrombectomy (EVT) for distal medium vessel occlusions (DMVOs) are not well established. This study aimed to evaluate whether EVT is superior to intravenous tissue plasminogen activator (IV tPA) alone in DMVOs.MethodsThis study analyzed data from the K-NET Registry, a prospective, multicenter, observational registry of acute ischemic stroke patients treated with EVT or IV tPA. The study evaluated patients with acute DMVOs who were treated with EVT and/or IV tPA. DMVOs was defined as occlusions in M2-M3 segment of the middle cerebral artery, anterior cerebral artery, or posterior cerebral artery. The analysis included primary DMVOs and excluded secondary DMVOs, such as distal embolism after recanalization of proximal vessel occlusion. Propensity score-matched analysis was conducted to compare the outcomes between EVT and IV tPA alone. A good outcome was defined as a modified Rankin Scale score of 0-2 or no worsening at 90 days. An excellent outcome was defined as an mRS score of 0-1.ResultsThe study included 1148 patients with DMVOs, of whom 816 were treated with EVT and 332 were IV tPA alone. Before propensity score matching, the incidence of good and excellent outcomes was significantly lower in EVT group (good outcomes: EVT 50.3% vs. IV tPA 68.0%, p<0.01; excellent outcomes: 39.8% vs. 59.8%, p<0.001). After propensity score matching, there were no significant differences between EVT and IV tPA groups in good outcomes (EVT 57.8% vs. IV tPA 61.3%, p=0.51), excellent outcomes (46.6% vs. 55.0%, p=0.17), all cerebral hemorrhage (11.6% vs. 12.7%, p=0.74), and symptomatic hemorrhage (2.9% vs. 0.6%, p=0.13). Subarachnoid hemorrhage was more frequent in EVT group (14.5% vs. IV tPA 0%).ConclusionsThe benefits of EVT for acute DMVOs were similar to IV-tPA alone. Randomized multicenter trials are warranted to establish the superiority of EVT over IV-tPA alone for DMVOs.
New avenues for human blood plasma biomarker discovery via improved in-depth analysis of the low-abundantN-glycoproteome
Authors: Zuniga-Banuelos Frania J. , Hoffmann Marcus , Reichl Udo , Rapp Erdmann 
Published: October 2023

AbstractTo understand implications of protein glycosylation for clinical diagnostic and biopharmaceuticals, innovative glycoproteomic technologies are required. Recently, significant advances were made, particularly toward structure-focusedN-glyco-proteomic analyses. The mass spectrometric analysis of intactN-glycopeptides using stepped collision fragmentation along with glycan oxonium ion profiling now enables to reliably discriminate between differentN-glycan structures. Still, there are weaknesses that currentN-glycoproteomic approaches must overcome: 1) handling of incorrect identifications, 2) identification of rare and modifiedN-glycans, and 3) insufficient glycoproteomic coverage, especially in complex samples. To address these shortcomings, we have developed an innovativeN-glycoproteomic workflow that aims at providing comprehensive site-specific and structuralN-glycoproteomic data on human blood plasma glycoproteins. The workflow features protein depletion plus various fractionation strategies and the use of high-resolution mass spectrometry with stepped collision fragmentation. Furthermore, by including a decision tree procedure established for data validation, we could significantly improve the description of theN-glycan micro-heterogeneity. Our data analysis workflow allows the reliable differentiation of ambiguousN-glycan structures like antenna-versus core-fucosylation plus the modified and rareN-glycans such as sulfated and glucuronidated ones. With this workflow, we were able to advance in the analysis of human blood plasma glycoproteins to concentrations as low as 10 pg/mL. A total of 1,929N-glycopeptides and 942N-glycosites derived from 805 human middle-to low-abundant glycoproteins were identified. Overall, the presented workflow holds great potential to improve our understanding of protein glycosylation and to foster the discovery of blood plasma biomarkers.Abstract Figure
Unique Binding and Stabilization Mechanisms Employed By and Engineered Into Nanobodies
Authors: Ketaren Natalia E. , Fridy Peter C. , Malashkevich Vladimir , Sanyal Tanmoy , Brillantes Marc , Thompson Mary K. , Oren Deena A. , Bonanno Jeffrey B. , Šali Andrej , Almo Steven C. , Chait Brian T. , Rout Michael P. 
Published: October 2023

AbstractNanobodies are single domain antibody variants that bind an antigen with the precision and affinity of a conventional antibody at only a fraction of their size. In solving the crystal structures of our nanobody-GFP complexes and compared with other available structures, we uncover mechanism that enable nanobodies to function so efficiently and effectively as single-domain antibodies. We show that unlike conventional antibodies, a nanobody repertoire maximizes sampling of their antigen surface by binding a single antigen in at least three different orientations which can be predicted by their paratope composition. We also structurally reengineering these nanobodies to improve their antigen affinity, their stability, or both – results which also revealed the strong connection between nanobody stability and affinity. We achieved this by either directly modifying the paratope, or by altering a particular region within their third framework, which is a highly conserved area that we determined plays a role in controlling nanobody stability. Our study suggests that these unique characteristics of nanobodies allow them to interact with antigens as effectively as conventional antibodies, despite their smaller size. This understanding provides methods to facilitate optimizing, humanizing and functionalizing nanobodies, thus paving the way for their utilization in diverse areas such as research, diagnostics, and therapeutic development.Significance StatementNanobodies are a unique type of antibody fragment found in select animals, containing all its antigen binding ability reduced to a single ∼15 kDa protein. There is increasing development of nanobodies for research, diagnostics, and therapeutics, yet how nanobodies function so effectively as single domain antigen binders with the precision and affinity of conventional antibodies is unclear. In this study, we present key observations to help answer this question, where one key finding is the strong relationship between nanobody stability and antigen affinity aided by the identification of a highly conserved region in nanobodies essential for maintaining nanobody stability. This region may have been retained in nanobodies in lieu of stabilizing mechanisms induced by dimerization as seen in conventional antibodies.
Modulating Mesenchymal Stromal Cell Microenvironment Alters Exosome RNA Content and Ligament Healing Capacity
Authors: Chamberlain Connie S. , Prabahar Archana , Kink John A , Mueller Erika , Li Yiyao , Yopp Stephanie , Capitini Christian M. , Hematti Peiman , Murphy William L. , Vanderby Ray , Jiang Peng 
Published: October 2023

AbstractAlthough mesenchymal stromal cell (MSC) based therapies hold promise in regenerative medicine, their applications in clinical settings remain challenging due to issues such as immunocompatibility and cell stability. MSC-derived exosomes, small vesicles carrying various bioactive molecules, are a promising cell-free therapy to promote tissue regeneration. However, it remains unknown mainly regarding the ability to customize the content of MSC-derived exosomes, how alterations in the MSC microenvironment influence exosome content, and the effects of such modifications on healing efficiency and mechanical properties in tissue regeneration. In this study, we used anin vitrosystem of human MSC-derived exosomes and anin vivorat ligament injury model to address these questions. We found a context-dependent correlation between exosomal and parent cell RNA content. Under native conditions, the correlation was moderate but heightened with microenvironmental changes.In vivorat ligament injury model showed that MSC-derived exosomes increased ligament max load and stiffness. We also found that changes in the MSCs’ microenvironment significantly influence the mechanical properties driven by exosome treatment. Additionally, a link was identified between altered exosomal microRNA levels and expression changes in microRNA targets in ligaments. These findings elucidate the nuanced interplay between MSCs, their exosomes, and tissue regeneration.Graphic Abstract
Exploring global and specific pathogenic mechanisms in Chronic Chagas Cardiomyopathy through multi-omics integration
Authors: Brochet Pauline , Kalil Jorge , Procaccio Vincent , Cunha-Neto Edecio , Spinelli Lionel , Chevillard Christophe 
Published: October 2023

AbstractChagas disease is a neglected disease from South America caused by a parasite,Trypanosoma cruzi. While most of infected people remains asymptomatic, around 30% develop Chronic Chagas Cardiomyopathy (CCC), a very lethal cardiomyopathy characterized by an exacerbate inflammatory response. The last few years, our team has set up multiple omics analysis. Briefly, we have pointed the over-expression of many genes involved in the Th1 lymphocyte response, as well as some epigenetic features potentially involved in their regulation, including miRNA, lncRNA and methylation site. Moreover, some mitochondria mutation seems to predispose to the development of CCC. In order to understand and characterize the impact of genetic and epigenetic elements on the pathogenic process associated to CCC, we have performed here a multi-omics integration, combining transcriptomic, methylomic, miRNomic and mitochondria sequencing. We have identified two distinct pathogenic pathways that vary among patients with chronic Chagas cardiomyopathy (CCC). One pathway is primarily influenced by IRF4, a transcription factor known for its involvement in the development of both B and T cells, while the other is driven by TLR signaling. Notably, genes related to B cells play a role in both of these processes. Additionally, we have detected certain similarities in the B cell receptors of all CCC patients, which may potentially contribute to autoimmunity. While further analysis is necessary to validate these findings, they collectively enhance our understanding of the pathogenic mechanisms associated with CCC.
Cruise Control Study: Simplification of IVF Monitoring in a Mixed Protocol Using a Novel Dosing Regimen
Authors: Benguigui Jonas , Kadoch Eva , Bannan Amro , Phillips Simon , Hemmings Robert , Bissonnette François , Kadoch Isaac-Jacques 
Published: October 2023

ABSTRACTObjectiveTo identify the subset of the in vitro fertilization (IVF) population suitable for minimal monitoring by implementing a novel dosing regimen.MethodsA retrospective study conducted between April 2021 and August 2022. Eligible participants were aged 18 or older, had undergone IVF stimulation using an antagonist protocol, and were prescribed a combination of follitropin delta and human menopausal gonadotropin. The dosage was either based on a patient-specific dosing regimen developed by the ovo clinic utilizing weight and AMH levels (Group 1, n=356) or determined through clinical evaluation by the physician (Group 2, n=358). On day 6, ultrasound and serum hormone analyses were performed, with adjustments made solely to the menotropin dosage in necessary.ResultsThe study enrolled a total of 714 patients. In Group 1, 80,3% of patients were stimulated at maximal doses compared to 14,5% in Group 2. No cases of moderate or severe cases of ovarian hyperstimulation syndrome (OHSS) were recorded. The frequency of dose adjustments before day 10 was minimal. Patients treated with non-maximal doses according to the dosing regimen showed significantly fewer adjustments on day 6 compared to those treated according to physician’s assessment (24.6% versus 46.9%, p<0.001). Among this subgroup, OHSS risk was observed in 30.4% of cases.ConclusionOur innovative dosing regimen suggests that initial monitoring on day 10 would suffice for IVF patients with low ovarian reserve undergoing maximal stimulation.