bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multi-Omics Analysis Reveals the Attenuation of the Interferon Pathway as a Driver of Chemo-Refractory Ovarian Cancer
Authors: Afenteva Daria , Yu Rong , Rajavuori Anna , Salvadores Marina , Launonen Inga-Maria , Lavikka Kari , Zhang Kaiyang , Marchi Giovanni , Jamalzadeh Sanaz , Isoviita Veli-Matti , Li Yilin , Micoli Giulia , Erkan Erdogan Pekcan , Falco Matias M. , Ungureanu Daniela , Lahtinen Alexandra , Oikkonen Jaana , Hietanen Sakari , Vähärautio Anna , Sur Inderpreet , Virtanen Anni , Färkkilä Anniina , Hynninen Johanna , Muranen Taru A. , Taipale Jussi , Hautaniemi Sampsa 
Published: March 2024

AbstractOvarian high-grade serous carcinoma (HGSC) represents the deadliest gynecological malignancy, with 10-15% of patients exhibiting primary resistance to first-line chemotherapy. These primarily chemo-refractory patients have particularly poor survival outcomes, emphasizing the urgent need for developing predictive biomarkers and novel therapeutic approaches. Here, we show that interferon type I (IFN-I) pathway activity in cancer cells is a crucial determinant of chemotherapy response in HGSC. Through a comprehensive multi-omics analysis within the DECIDER observational trial (ClinicalTrials.govidentifierNCT04846933) cohort, we identified that chemo-refractory HGSC is characterized by diminished IFN-I and enhanced hypoxia pathway activities. Importantly, IFN-I pathway activity was independently prognostic for patient survival, highlighting its potential as a biomarker. Our results elucidate the heterogeneity of treatment response at the molecular level and suggest that augmentation of IFN-I response could enhance chemosensitivity in refractory cases. This study underscores the potential of the IFN-I pathway as a therapeutic target and advocates for the initiation of clinical trials testing external modulators of the IFN-I response, promising a significant stride forward in the treatment of refractory HGSC.
Transcriptomic Changes in Oligodendrocyte Lineage Cells During the Juvenile to Adult Transition in the Mouse Corpus Callosum
Authors: Hoshino Tomonori , Takase Hajime , Hamanaka Gen , Kimura Shintaro , Fukuda Norito , Mandeville Emiri T , Lok Josephine , Lo Eng H , Arai Ken 
Published: March 2024

AbstractThe corpus callosum, a major white matter tract in the brain, undergoes age-related functional changes. To extend our investigation of age-related gene expression dynamics in the mouse corpus callosum, we compared RNA-seq data from 2-week-old and 12-week-old wild-type C57BL/6J mice and identified the differentially expressed genes (e.g.,Serpinb1a, Ndrg1, Dnmt3a, etc.) between these ages. Interestingly, we found that genes highly expressed in myelinating oligodendrocytes were upregulated in 12-week-old mice compared to 2-week-old mice, while genes highly expressed in oligodendrocyte precursor cells (OPCs) and newly formed oligodendrocytes were downregulated. Furthermore, by comparing these genes with the datasets from 20-week-old and 96-week-old mice, we identified novel sets of genes with age-dependent variations in the corpus callosum. These gene expression changes potentially affect key biological pathways and may be closely linked to age-related neurological disorders, including dementia and stroke. Therefore, our results provide an additional dataset to explore age-dependent gene expression dynamics of oligodendrocyte lineage cells in the corpus callosum.
Elucidating the link between binding statistics and Shannon information in biological cooperative networks
Authors: Banerjee Kinshuk , Das Biswajit 
Published: March 2024

AbstractCooperative response is ubiquitous and vital for regulatory control and ultra-sensitivity in various cellular biophysical processes. Ligands, acting as signaling molecules, carry information which is transmitted through the elements of the biochemical network during binding processes. In this work, we address a fundamental issue regarding the link between the information content of the various states of the binding network and the observable binding statistics. Two seminal models of cooperativity,viz., the Koshland-Nemethy-Filmer (KNF) network and the Monod-Wyman-Changeux (MWC) network are considered for this purpsoe which are solved using the chemical master equation approach. Our results establish that the variation of Shannon information associated with the network states has a generic form related to the average binding number. Further, the logarithmic sensitivity of the slope of Shannon information is shown to be related to the Hill slope in terms of the variance of the binding number distributions.1
Remodeling Ca2+dynamics by targeting a promising E-box containing G-quadruplex atORAI1promoter in triple-negative breast cancer
Authors: Chatterjee Oishika , Jana Jagannath , Panda Suman , Dutta Anindya , Sharma Akshay , Saurav Suman , Motiani Rajender K. , Weisz Klaus , Chatterjee Subhrangsu 
Published: March 2024

AbstractORAI1 is an intrinsic component of store-operated calcium entry (SOCE) that strictly regulates Ca2+influx in most non-excitable cells. ORAI1 has been extensively studied to have been overexpressed in various cancer phenotypes, and its signal transduction has been associated with oncotherapy resistance. There is extensive proteomic interaction of ORAI1 with other channels and effectors, resulting in various altered phenotypes. However, the transcription regulation of this gene is not well understood. We have found a putative G-quadruplex (G4) motif,ORAI1-Pu, in the upstream promoter region of the gene, having regulatory functions. High-resolution 3-D NMR structure elucidation suggests thatORAI1-Puis a stable parallel-stranded G4, having an unusual 8-nt loop imparting dynamics without affecting the structural stability. The protruded loop further houses an E-box motif that provides a docking site for transcription factors like Zeb1. The G4 structure was also endogenously observed using Chromatin Immunoprecipitation (ChIP) with anti-G4 antibody (BG4) in the MDA-MB-231 cell line overexpressingORAI1. Ligand-mediated stabilization suggested that the stabilized G4 represses transcription in cancer cell line MDA-MB-231. Downregulation of transcription further cascaded down to a decrease in Ca2+entry by the SOCE pathway, as observed by Fura-2 confocal Ca2+imaging.
Non-invasive and painless mid-infrared modulation increases collagen in human and mouse skin
Authors: Wang Zeyu , Zhu Jiahui , Wang Yuting , Chen Shuai , Xu Senlin , Li Yaoying , Hu Tianxing , Li Yang , Wang Xuanyue , Ji Renyue , Li Sunny C. , Yang Yan , Jia Hongbo , Chen Xiaowei , Fan Xing , Ge Lan , Zhang Jianxiong 
Published: March 2024

AbstractStimulating collagen production in skin helps to enhance vitality while decelerating aging- associated processes in skin tissue. However, current approaches to enhancing collagen production are commonly limited by accompanying pain and trauma. Here, we report that mid-infrared modulation (MIMO) at an intensity of 70 mW/cm2promotes collagen production in human or mouse skin in vivo without generating excessive heat. We found that protein levels of the collagen- degrading endopeptidase, MMP-1, were decreased in the skin of mice following MIMO treatment, whereas the collagen synthesis-related factors, TGF-β, HSP47, and HSP70, were all increased. In addition, MIMO stimulated collagen secretion in human dermal fibroblasts in vitro. This work demonstrates that MIMO is an effective, non-invasive, and painless intervention for in vivo enhancement of collagen production in the skin.One Sentence SummaryMid-infrared modulation promotes collagen production
Cell viscosity influences hematogenous dissemination and metastatic extravasation of tumor cells
Authors: Gensbittel Valentin , Follain Gautier , Bochler Louis , Uhlmann Klemens , Lefèbvre Olivier , Larnicol Annabel , Harlepp Sébastien , Goswami Ruchi , Girardo Salvatore , Hyenne Vincent , Mittelheisser Vincent , Kräter Martin , Balzani Daniel , Guck Jochen , Osmani Naël , Goetz Jacky G. 
Published: March 2024

AbstractMetastases arise from a multi-step process during which tumor cells change their mechanics in response to microenvironmental cues. While such mechanical adaptability could influence metastatic success, how tumor cell mechanics directly impacts intravascular behavior of circulating tumor cells (CTCs) remains poorly understood. In the present study, we demonstrate how the deformability of CTCs affects hematogenous dissemination and identify the mechanical profiles that favor metastatic extravasation. Combining intravital microscopy with CTC-mimicking elastic beads and mechanically-tuned tumor cells, we demonstrate that the inherent properties of circulating objects dictate their ability to enter constraining vessels. We identify cellular viscosity as the key property that governs CTC circulation and arrest patterns. We further demonstrate that cellular viscosity is required for efficient extravasation and find that properties that favor extravasation and subsequent metastatic outgrowth can be opposite. Altogether, we identify CTC viscosity as a key biomechanical parameter that shapes several steps of metastasis.
Defining the function of disease variants with CRISPR editing and multimodal single cell sequencing
Authors: Baglaenko Yuriy , Curtis Michelle , Suqri Majd Al , Agnew Ryan , Nathan Aparna , Mire Hafsa M , Mah-Som Annelise Yoo , Liu David R. , Newby Gregory A. , Raychaudhuri Soumya 
Published: March 2024

Abstract / Summary ParagraphGenetic studies have identified thousands of individual disease-associated non-coding alleles, but identification of the causal alleles and their functions remain critical bottlenecks. Even though CRISPR-Cas editing has enabled targeted modification of DNA, inefficient editing leads to heterogeneous outcomes across individual cells, limiting the ability to detect functional consequences of disease alleles. To overcome these challenges, we present a multi-omic single cell sequencing approach that directly identifies genomic DNA edits, assays the transcriptome, and measures cell surface protein expression. We apply this approach to investigate the effects of gene disruption, deletions in regulatory regions, and non-coding single nucleotide polymorphisms. We identify the specific effects of individual SNPs, including the state-specific effects of anIL2RAautoimmune variant in primary human T cells. Multimodal functional genomic single cell assays including DNA sequencing bridge a crucial gap in our understanding of complex human diseases by directly identifying causal variation in primary human cells.
Srs2 binding to PCNA and its sumoylation contribute to RPA antagonism during the DNA damage response
Authors: Fan Jiayi , Dhingra Nalini , Yang Tammy , Yang Vicki , Zhao Xiaolan 
Published: March 2024

AbstractActivation of the DNA damage checkpoint upon genotoxin treatment induces a multitude of cellular changes, such as cell cycle arrest or delay, to cope with genome stress. After prolonged genotoxin treatment, the checkpoint can be downregulated to allow cell cycle and growth resumption. In yeast, downregulation of the DNA damage checkpoint requires the Srs2 DNA helicase, which removes the ssDNA binding complex RPA and the associated Mec1 checkpoint kinase from DNA, thus dampening Mec1-mediated checkpoint. However, it is unclear whether the ‘anti-checkpoint’ role of Srs2 is temporally and spatially regulated to both allow timely checkpoint termination and to prevent superfluous RPA removal. Here we address this question by examining regulatory elements of Srs2, such as its phosphorylation, sumoylation, and protein-interaction sites. Our genetic analyses and checkpoint level assessment suggest that the RPA countering role of Srs2 is promoted by Srs2 binding to PCNA, which recruits Srs2 to a subset of ssDNA regions. RPA antagonism is further fostered by Srs2 sumoylation, which we found depends on the Srs2-PCNA interaction. Srs2 sumoylation is additionally reliant on Mec1 and peaks after Mec1 activity reaches maximal levels. Based on these data, we propose a two- step model of checkpoint downregulation wherein Srs2 recruitment to PCNA proximal ssDNA- RPA filaments and subsequent sumoylation stimulated upon Mec1 hyperactivation facilitate checkpoint recovery. This model suggests that Srs2 removal of RPA is minimized at ssDNA regions with no proximal PCNA to permit RPA-mediated DNA protection at these sites.
Arginine methylation of the p30 C/EBPα oncoprotein regulates progenitor proliferation and myeloid differentiation
Authors: Nguyen Linh T. , Zimmermann Karin , Kowenz-Leutz Elisabeth , Dörr Dorothea , Schütz Anja , Schönheit Jörg , Mildner Alexander , Leutz Achim 
Published: March 2024

ABSTRACTThe transcription factor CCAAT enhancer binding protein alpha (C/EBPα) is a master regulator of myelopoiesis.CEBPAencodes a long (p42) and a truncated (p30) protein isoform from a single mRNA. Mutations that abnormally enhance expression of p30 are associated with acute myelogenous leukemia (AML). We show by mutational analysis that three highly conserved arginine residues (R140,147,154) located at the p30 C/EBPα N-terminus, previously found to be methylated, are involved in myeloid lineage commitment, progenitor proliferation, and differentiation. Replacement with lysine that retains the amino acid side chain charge enhanced progenitor proliferation, while uncharged side chains (alanine or leucine) impaired proliferation and enhanced granulopoietic differentiation. Analysis of protein-protein interactions (PPI) suggested that arginine methylation of p30 C/EBPα differentially determines its capacity to interact with SWI/SNF and MLL complexes. Pharmacological targeting of p30 C/EBPα arginine methylation may have clinical relevance in myeloproliferative and inflammatory diseases, in neutropenia, and in leukemic stem cells.
Broad-Spectrum Coronavirus Inhibitors Discovered by Modeling Viral Fusion Dynamics
Authors: Reilly Charles B. , Moore Joel , Lightbown Shanda , Paul Austin , Bernier Sylvie G. , Carlson Kenneth E. , Ingber Donald E. 
Published: March 2024

AbstractBroad-spectrum therapeutics capable of inhibiting SARS-CoV-2, its variants, and related coronaviruses hold promise in curbing the spread of COVID-19 and averting future pandemics. Here, we employed a multidisciplinary approach that included molecular dynamics simulation (MDS) and artificial intelligence (AI)-based docking predictions to identify potent inhibitors that target a conserved region within the SARS-CoV-2 spike protein that mediates membrane fusion by undergoing large-scale mechanical rearrangements.In silicobinding screens honed in on this region, leading to the discovery of FDA-approved drugs and novel molecules predicted to disrupt spike protein conformational changes. These compounds significantly inhibited SARS-CoV-2 infection and blocked the entry of spike protein-bearing pseudotyped α, β, γ, δ variants as well as SARS-CoV and MERS-CoV in cultured human ACE2-expressing cells. The optimized lead compound significantly inhibited SARS-CoV2 infection in mice when administered orally.
Wrapping of single-stranded DNA by Replication Protein A and modulation through phosphorylation
Authors: Chadda Rahul , Kaushik Vikas , Ahmad Iram Munir , Deveryshetty Jaigeeth , Holehouse Alex , Sigurdsson Snorri Th.d , Bothner Brian , Dastvan Reza , Origanti Sofia , Antony Edwin 
Published: March 2024

ABSTRACTSingle-stranded DNA (ssDNA) intermediates, which emerge during DNA metabolic processes are shielded by Replication Protein A (RPA). RPA binds to ssDNA and acts as a gatekeeper, directing the ssDNA towards downstream DNA metabolic pathways with exceptional specificity. Understanding the mechanistic basis for such RPA-dependent specificity requires a comprehensive understanding of the structural conformation of ssDNA when bound to RPA. Previous studies suggested a stretching of ssDNA by RPA. However, structural investigations uncovered a partial wrapping of ssDNA around RPA. Therefore, to reconcile the models, in this study, we measured the end-to-end distances of free ssDNA and RPA-ssDNA complexes using single-molecule FRET and Double Electron-Electron Resonance (DEER) spectroscopy and found only a small systematic increase in the end-to-end distance of ssDNA upon RPA binding. This change does not align with a linear stretching model but rather supports partial wrapping of ssDNA around the contour of DNA binding domains of RPA. Furthermore, we reveal how phosphorylation at the key Ser-384 site in the RPA70 subunit provides access to the wrapped ssDNA by remodeling the DNA-binding domains. These findings establish a precise structural model for RPA-bound ssDNA, providing valuable insights into how RPA facilitates the remodeling of ssDNA for subsequent downstream processes.
A palette of bright and photostable monomeric fluorescent proteins for bacterial time-lapse imaging
Authors: Fraikin Nathan , Couturier Agathe , Lesterlin Christian 
Published: March 2024

SummaryFluorescent proteins (FPs) are pivotal for examining protein production, localization, and dynamics in live bacterial cells. However, the use of FPs in time-lapse imaging is frequently constrained by issues such as oligomerization or limited photostability. Here, we report the engineering of four new fluorescent proteins: mChartreuse (green), mJuniper (cyan), mLemon (yellow), and mLychee (red), using site-directed mutagenesis. These fluorophores outperform current standards for photostability and aggregation properties while retaining high levels of brightness in livingE. colibacteria. Starting with superfolder GFP (sfGFP), we developed mChartreuse, which shows significantly enhanced brightness, stability, and monomericity compared to other GFP variants. From mChartreuse, we derived mJuniper, a cyan fluorescent protein with rapid maturation and high photostability, and mLemon, a yellow fluorescent protein with improved photostability and brightness. We also identified a mutation that eliminates residual oligomerization in red fluorescent proteins derived fromDiscosomaspecies, such as mCherry and mApple. Incorporating this mutation into mApple, along with other substitutions, resulted in mLychee, a bright and photostable monomeric red fluorescent protein. These novel fluorescent proteins advance fluorescence time-lapse analysis in bacteria and their spectral properties match current imaging standards, ensuring seamless integration into existing research workflows.
Enhanced mucosal B- and T-cell responses against SARS-CoV-2 after heterologous intramuscular mRNA prime/intranasal protein boost vaccination with a combination adjuvant
Authors: Laghlali Gabriel , Wiest Matthew J. , Karadag Dilara , Warang Prajakta , O’Konek Jessica J. , Chang Lauren A. , Park Seokchan , Farazuddin Mohammad , Landers Jeffrey J. , Janczak Katarzyna W. , García-Sastre Adolfo , Baker James R. , Wong Pamela T. , Schotsaert Michael 
Published: March 2024

ABSTRACTCurrent COVID-19 mRNA vaccines delivered intramuscularly (IM) induce effective systemic immunity, but with suboptimal immunity at mucosal sites, limiting their ability to impart sterilizing immunity. There is strong interest in rerouting immune responses induced in the periphery by parenteral vaccination to the portal entry site of respiratory viruses, such as SARS-CoV-2, by mucosal vaccination. We previously demonstrated the combination adjuvant, NE/IVT, consisting of a nanoemulsion (NE) and an RNA-based RIG-I agonist (IVT) induces potent systemic and mucosal immune responses in protein-based SARS-CoV-2 vaccines administered intranasally (IN). Herein, we demonstrate priming IM with mRNA followed by heterologous IN boosting with NE/IVT adjuvanted recombinant antigen induces strong mucosal and systemic antibody responses and enhances antigen-specific T cell responses in mucosa-draining lymph nodes compared to IM/IM and IN/IN prime/boost regimens. While all regimens induced cross-neutralizing antibodies against divergent variants and sterilizing immunity in the lungs of challenged mice, mucosal vaccination, either as homologous prime/boost or heterologous IN boost after IM mRNA prime was required to impart sterilizing immunity in the upper respiratory tract. Our data demonstrate the benefit of hybrid regimens whereby strong immune responses primed via IM vaccination are rerouted by IN vaccination to mucosal sites to provide optimal protection to SARS-CoV-2.
Uncovering nick DNA binding by LIG1 at the single-molecule level
Authors: Chatterjee Surajit , Chaubet Loïc , van den Berg Aafke , Mukhortava Ann , Gulkis Mitch , Çağlayan Melike 
Published: March 2024

AbstractDNA ligases repair the strand breaks are made continually and naturally throughout the genome, if left unrepaired and allowed to persist, they can lead to genome instability in the forms of lethal double-strand (ds) breaks, deletions, and duplications. DNA ligase 1 (LIG1) joins Okazaki fragments during the replication machinery and seals nicks at the end of most DNA repair pathways. Yet, how LIG1 recognizes its target substrate is entirely missing. Here, we uncover the dynamics of nick DNA binding by LIG1 at the single-molecule level. Our findings reveal that LIG1 binds to dsDNA both specifically and non-specifically and exhibits diffusive behavior to form a stable complex at the nick. Furthermore, by comparing with the LIG1 C-terminal protein, we demonstrate that the N-terminal non-catalytic region promotes binding enriched at nick sites and facilitates an efficient nick search process by promoting 1D diffusion along the DNA. Our findings provide a novel single-molecule insight into the nick binding by LIG1, which is critical to repair broken phosphodiester bonds in the DNA backbone to maintain genome integrity.
Assessing Target of Rapamycin (TOR) activity in the diatomPhaeodactylum tricornutumusing commercially available materials
Authors: Tsuji Yoshinori , Ishikawa Takumi 
Published: March 2024

AbstractTarget of rapamycin (TOR) is a conserved protein kinase that regulates the balance between catabolic and anabolic processes in response to nutrient availability. Although the central role of TOR kinase in nutrient stress responses is well-recognized, little is known about the molecular basis of TOR signaling in ecologically important secondary algae with plastids of red algal origin, such as diatoms, as assessingin vivoTOR kinase activity is a difficult task. To assess TOR kinase activity, the phosphorylation status of downstream components, such as ribosomal protein S6 (RPS6), must be measured. Unlike for model organisms, an antibody that detects phosphorylated (P-) RPS6 in diatoms is not commercially available. Therefore, we developed a convenient method in which P-RPS6 and non-P-RPS6 were detected via Phos-tag affinity electrophoresis and immunoblotting with a commercial antibody that cross-reacts with RPS6 (both P- and non-P-RPS6) in the diatom,Phaeodactylum tricornutum. Using this Phos-tag-based method, we observed a dose-dependent decrease in the P-RPS6/total RPS6 ratio inP. tricornutumcells treated with the TOR kinase inhibitor, AZD-8055. We also observed a reduction in the P-RPS6/total RPS6 ratio during the nitrogen-deficient culture ofP. tricornutum, which indicated the inactivation of TOR kinase in response to nitrogen deficiency. Finally, we demonstrated the potential application of the Phos-tag-based method to other ecologically, evolutionarily, and industrially important secondary algae, such asNannochloropsis oceanica(Stramenopiles), the haptophyteTisochrysis lutea, andEuglena gracilis(Euglenid). As all experimental materials are commercially available, the Phos-tag-based method can be used to promote studies on TOR in diverse algae in different contexts.