bluuebunny/crossref_metadata_2025_split huggingface dataset:
TMEM106B is increased in Multiple Sclerosis plaques, and deletion causes accumulation of lipid after demyelination
Authors: Shafit-Zagardo Bridget , Sidoli Simone , Goldman James E. , DuBois Juwen C. , Corboy John R. , Strittmatter Stephen M. , Guzik Hillary , Graff Sarah , Nagra Rashed M. 
Published: May 2022

AbstractDuring inflammatory, demyelinating diseases such as multiple sclerosis (MS) axonal damage is prevalent early in the disease course. Axonal damage includes swellings, defects in transport, and failure to clear damaged intracellular proteins, all of which affect recovery and compromise the integrity of neurons and remyelination. Autophagy and the clearance of damaged cell components by the proteasome are important for the maintenance of normal cellular turnover; and the restoration of cellular homeostasis. The gradual accumulation of insoluble proteins in the brain is known to impair recovery from several neurodegenerative diseases. In this study, we used mass spectrometry to identify insoluble proteins within high-speed, mercaptoethanol/sarcosyl-insoluble pellets from purified white matter plaques isolated from the brains of individuals with MS. We determined that insoluble transmembrane protein106B (TMEM106B), expressed in neurons and glia and normally lysosomal-associated, is increased in MS plaques relative to normal-appearing white matter from individuals with Alzheimer’s disease and non-neurologic controls. We found that decreased TMEM106B protein in mice results in significant axonal damage and lipid droplet accumulation in the spinal cord following chronic myelin oligodendrocyte glycoprotein-induced experimental autoimmune encephalomyelitis. When TMEM106Bt/t mice were treated with cuprizone to experimentally induce demyelination, a significant increase in lipid deposition was observed in the corpus callosum of TMEM106Bt/t mice post-cuprizone withdrawal. Our study shows that the brain and spinal cord from challenged TMEM106Bt/t mice accumulate OilRedO+/Perilipin2+ lipid droplets. We postulate that increased insolubility of TMEM106B in MS plaques limits debris clearance by the lysosome which over time contributes to failed remyelination and axonal defects.Abbreviated AbstractTransmembrane protein106B (TMEM106B), a lysosome-associated protein, is significantly less soluble in multiple sclerosis plaques than in white matter controls. Decreased TMEM106B produces significant axonal damage and lipid accumulation in mouse models of demyelinating diseases. TMEM106B insolubility and likely loss of function may limit lysosome transport and contribute to CNS pathology.
Mechanistic target of rapamycin (mTOR) regulates self-sustained quiescence, tumor indolence and late clinical metastasis in a Beclin-1-dependent manner
Authors: Nicco Carole , Thomas Marine , Guillermet Julie , Havard Maryline , Laurent-Tchenio Fanny , Doridot Ludivine , Dautry François , Batteux Frédéric , Tchenio Thierry 
Published: May 2022

AbstractSelf-sustained quiescence (SSQ) has been characterized as a stable but reversible non-proliferative cellular state that limits the cloning of cultured cancer cells. By developing refined clonogenic assays, we showed here that cancer cells in SSQ can be selected with anticancer agents and that culture at low cell density induced SSQ in pancreas and prostate adenocarcinoma cells. Pre-culture of cells in 3D or their pretreatment with pharmacological inhibitors of mechanistic target of rapamycin (mTOR) synergize with low cell density for induction of SSQ in a Beclin-1-dependent manner. Dissociated pancreatic adenocarcinoma (PAAD) cells rendered defective for SSQ by down-regulating Beclin-1 expression exhibit higher tumor growth rate when injected subcutaneously into mice. Conversely, dissociated PAAD cells in SSQ promote the formation of small indolent tumors that eventually transitioned to a rapid growth phase. Ex vivo clonogenic assays showed that up to 40% of clonogenic cancer cells enzymatically dissociated from resected fast-growing tumors could enter SSQ, suggesting that SSQ could significantly impact the proliferation of cancer cells that are naturally dispersed from tumors. Remarkably, the kinetics of clinical metastatic recurrence in 124 patients with pancreatic adenocarcinoma included in the TGCA-PAAD project could be predicted from Beclin-1 and Cyclin-A2 mRNA levels in their primary tumor, Cyclin A2 mRNA being a marker of both cell proliferation and mTOR complex 1 activity. Overall, our data show that SSQ is likely to promote the late development of clinical metastases and suggest that identifying new agents targeting cancer cells in SSQ could help improve patient survival.
Loss of CD24 promotes radiation- and chemo-resistance by inducing stemness properties associated with a hybrid E/M state in breast cancer cells
Authors: Bontemps Isaline , Lallemand Céline , Biard Denis , Dechamps Nathalie , Kortulewski Thierry , Bourneuf Emmanuelle , Siberchicot Capucine , Boussin François , Chevillard Sylvie , Campalans Anna , Lebeau Jérôme 
Published: May 2022

SUMMARYThere is compelling evidence that cancer stem cells (CSCs) play an essential role in failure of conventional antitumor therapy. In breast cancer, CD24-/low/CD44+ phenotype as well as a high aldehyde dehydrogenase activity (ALDH+) are widely associated with CSC subtypes. Furthermore, CD24-/low/CD44+ pattern is also characteristic of the mesenchymal cells generated by an epithelial-mesenchymal transition (EMT). CD24 is a surface marker expressed in many tumor types, however, its biological functions and role in cancer progression and treatment resistance remain poorly documented. We have previously shown that loss of CD24 expression in breast cancer cells is associated with radiation resistance, in relationship with the control of oxidative stress. Because ROS are known to mediate the effects of anticancer drugs as well as ionizing radiation, we investigated if CD24 could be defined as an actor of both radiation- and chemo-resistance of breast cancer cells. Using the HMLE breast cancer cell model, we observed that loss of CD24 expression induces stemness properties associated with the acquisition of a hybrid E/M phenotype. The CD24-/low cells were intrinsically more resistant than CD24+ cells. The resistance was linked to a lower level of ROS, and CD24 controlled ROS levels through the regulation of mitochondrial functions independently of antioxidant activity. Together, these results suggest a key role of CD24 in de-differentiation process of breast cancer cells, promoting acquisition of therapeutic resistance properties.
Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians
Authors: Gounot Jean-Sebastien , Minghao Chia , Bertrand Denis , Saw Woei-Yuh , Ravikrishnan Aarthi , Low Adrian , Ding Yichen , Qi Amanda Ng Hui , Lin Tan Linda Wei , Yik-Ying Teo , Seedorf Henning , Nagarajan Niranjan 
Published: May 2022

AbstractDespite extensive efforts to address it, the vastness of uncharacterized ‘dark matter’ microbial genetic diversity can impact short-read sequencing based metagenomic studies. Population-specific biases in genomic reference databases can further compound this problem. Leveraging advances in long-read and Hi-C technologies, we deeply characterized 109 gut microbiomes from three ethnicities in Singapore to comprehensively reconstruct 4,497 medium and high-quality metagenome assembled genomes, 1,708 of which were missing in short-read only analysis and with >28× N50 improvement. Species-level clustering identified 70 (>10% of total) novel gut species out of 685, improved reference genomes for 363 species (53% of total), and discovered 3,413 strains that are unique to these populations. Among the top 10 most abundant gut bacteria in our study, one of the species and >80% of all strains were not represented in existing databases. Annotation of biosynthetic gene clusters (BGCs) uncovered more than 27,000 BGCs with a large fraction (36-88%) not represented in current databases, and with several unique clusters predicted to produce bacteriocins that could significantly alter microbiome community structure. These results reveal the significant uncharacterized gut microbial diversity in Southeast Asian populations and highlight the utility of hybrid metagenomic references for bioprospecting and disease-focused studies.
The Ndc80-Cdt1-Ska1 complex constitute a minimal processive kinetochore-microtubule coupling unit
Authors: Rahi Amit , Chakraborty Manas , Agarwal Shivangi , Vosberg Kristen , Agarwal Shivani , Wang Annie Y. , McKenney Richard J. , Varma Dileep 
Published: May 2022

AbstractThe Ndc80 kinetochore complex is essential for robust kinetochore-microtubule (k-MT) attachments during mitosis. Ndc80 has been shown to recruit the Ska1 complex to kinetochores, where Ska1 is thought to aid in k-MT coupling by Ndc80. Our previous work has shown that Cdt1, a DNA replication licensing factor, is a novel mitotic spindle-associated protein that is also recruited to kinetochores via Ndc80 and is required for stabilizing k-MT attachments. In this study, we developed auxin-induced degron (AID)-tagging to validate the previously demonstrated mitotic role of Cdt1. We demonstrate a direct interaction between Cdt1 and Ska1 that is essential for proper recruitment of Cdt1 to kinetochores and spindle microtubules. We find that Cdk1’dependent phosphorylation of Cdt1 during mitosis is critical for Ska1-binding, consequently regulating the stabilization of metaphase k-MT attachments and normal mitotic progression. Total internal reflection fluorescence microscopy (TIR-FM) experiments reveal that Cdt1 synergizes with the Ndc80 and the Ska1 complexes for microtubule-binding. Further, we show that single Cdt1 molecules form diffusive tripartite complexes with Ndc80 and Ska1 that can processively track the ends of dynamic microtubules in vitro. Taken together our data identifies a minimal molecular unit responsible for bidirectional processive tip tracking of kinetochores.
A microfluidic droplet array demonstrating high-throughput screening in individual lipid-producing microalgae
Authors: Zheng Guoxia , Gu Furong , Cui Yutong , Lu Ling , Hu Xuejun , Wang Lin , Wang Yunhua 
Published: May 2022

AbstractMicroalgae are a group of photoautotrophic microorganisms which could use carbon dioxide for autosynthesis. They have been envisioned as one of the most prospective feedstock for renewable oil. However, great endeavors will still be needed to increase their economic feasibility; the screening of competitive species and suitable culture conditions are such issues. To greatly accelerate these rather laborious steps and also improve their experimental lump-sum-manner, we developed a microfluidic droplet-based 2×103 resolution “identification card”, which allowed high throughput real-time monitoring of individual algae among population. A novel fluid-blocking-based droplet generating and trapping performance were integrated in the platform which made it excellent in operational simplicity, rapidity and stability and full of the potentials in single-cell-isolation/screening. The developed platform was successfully used to screen three unicellular algae, namely, Isochrysis zhanjiangensis, Platymonas subcordiformis and Platymonas helgolandica var. tsingtaoensis. In situ bioassays of the lipid accumulation and cell proliferation at single cell level for interspecies comparison were possible. Nitrogen stress condition can be indentified that induce positive-skewed frequency distribution of lipid content.
Automated systematic evaluation of cryo-EM specimens with SmartScope
Authors: Bouvette Jonathan , Huang Qinwen , Riccio Amanda A. , Copeland William C. , Bartesaghi Alberto , Borgnia Mario J. 
Published: May 2022

AbstractPropelled by improvements in hardware for data collection and processing, single particle cryo-electron microscopy has rapidly gained relevance in structural biology. Yet, finding the conditions to stabilize a macromolecular target for imaging remains the most critical barrier to determining its structure. Attaining the optimal specimen requires the evaluation of multiple grids in a microscope as conditions are varied. While automation has significantly increased the speed of data collection, optimization is still carried out manually. This laborious process which is highly dependent on subjective assessments, inefficient and prone to error, often determines the success of a project. Here, we present SmartScope, the first framework to streamline, standardize, and automate specimen evaluation in cryo-electron microscopy. SmartScope employs deep-learning-based object detection to identify and classify features suitable for imaging, allowing it to perform thorough specimen screening in a fully automated manner. A web interface provides remote control over the automated operation of the microscope in real time and access to images and annotation tools. Manual annotations can be used to re-train the feature recognition models, leading to improvements in performance. Our automated tool for systematic evaluation of specimens streamlines structure determination and lowers the barrier of adoption for cryo-electron microscopy.
Developmental dynamics of the postsynaptic proteome to understand synaptic maturation and dysmaturation
Authors: Kaizuka Takeshi , Suzuki Takehiro , Kishi Noriyuki , Kilimann Manfred W. , Ueyama Takehiko , Watanabe Masahiko , Okano Hideyuki , Dohmae Naoshi , Takumi Toru 
Published: May 2022

AbstractThe postsynaptic density (PSD) is a protein condensate composed of ∼1,000 proteins beneath the postsynaptic membrane of excitatory synapses. The number, shape, and plasticity of synapses are altered during development. However, the dynamics of synaptic protein composition across development have not been fully understood. Here we show alterations of PSD protein composition in mouse and primate brains during development. Proteins involved in synapse regulation are enriched in the differentially expressed (288 decreased and 267 increased) proteins on mouse PSD after a 2-week-old. We find that the changes in PSD protein abundance in mouse brains correlate with gene expression levels in postnatal mice and perinatal primates. This alteration of PSD composition is likely to be defective in the brains of mouse models or patients with autism spectrum disorder (ASD). Finally, we demonstrate that the brain of the common marmoset (Callithrix jacchus) changes PSD composition after the juvenile period. The alteration of PSD composition after 2-month-old is distinct from that observed in mice. Our results provide a comprehensive architecture of the remodeling of PSD composition across development, which may explain the molecular basics of synapse maturation and the pathology of psychiatric disorders, such as ASD.
Multiple instance learning to predict immune checkpoint blockade efficacy using neoantigen candidates
Authors: Lang Franziska , Sorn Patrick , Schrörs Barbara , Weber David , Kramer Stefan , Sahin Ugur , Löwer Martin 
Published: May 2022

AbstractA successful response to immune checkpoint blockade treatment (ICB) depends on the functional re-invigoration of neoantigen-specific T cells and their anti-tumoral activity. Previous studies showed that the patient’s neoantigen candidate load is an imperfect predictor of the response to ICB. Further studies provided evidence that the overall response to ICB is also affected by the qualitative properties of a few or even single candidates, limiting the predictive power based on candidate quantity alone.To our knowledge, this is the first study to predict the response to ICB therapy based on qualitative neoantigen candidate profiles in the context of the mutation type, using a multiple instance learning approach. Multiple instance learning is a special branch of machine learning which classifies labelled bags that are formed by a set of unlabeled instances. The multiple instance learning approach performed systematically better than random guessing and was independent of the neoantigen candidate load. Qualitative modeling performed better in comparison to the quantitative approach, in particular for modelling low-abundant fusion genes. Our findings suggest that multiple instance learning is an appropriate method to predict immunotherapy efficacy based on qualitative neoantigen candidate profiles without relying on direct T-cell response information and provide a foundation for future developments in the field.
Suppression of tumor/host intrinsic CMTM6 drives anti-tumor cytotoxicity in a PD-L1 independent manner
Authors: Long Yiru , Chen Runqiu , Yu Xiaolu , Tong Yongliang , Peng Xionghua , Li Fanglin , Hu Chao , Sun Jianhua , Gong Likun 
Published: May 2022

AbstractCKLF-like MARVEL transmembrane domain-containing 6 (CMTM6) has been identified as a regulator of membranal programmed death ligand 1 (PD-L1) stability and a factor associated with malignancy progression, but the effects and mechanisms of CMTM6 on tumor growth, as well as its potential for therapy, are still largely unknown. Here, we show that tumor CMTM6 increased with progression in both clinical patients and mice. Ablation of CMTM6 resulted in significant retardation of human and murine tumor growth dependent on T-lymphocyte immunity. Tumor CMTM6 suppression broke resistance to immune checkpoint inhibitors and remodeled the tumor immune microenvironment, as specific antitumor cytotoxicity was enhanced and contributed primarily to tumor inhibition. Further, without the PD-1/PD-L1 axis, CMTM6 suppression still significantly dampened tumor growth dependent on cytotoxic cells. Notably, we identified that CMTM6 was widely expressed on immune cells. T-cell CMTM6 increased with sustained immune activation and intratumoral immune exhaustion and affected the T-cell-intrinsic PD-L1 levels. Host CMTM6 knockout significantly restrained tumor growth dependent on CD8+ T-cells, and similarly, not entirely dependent on PD-L1. Thus, we developed and evaluated the antitumor efficacy of CMTM6-targeting adeno-associated virus (AAV), which effectively mobilized antitumor immunity and could be combined with various antitumor drugs. Our findings reveal that both tumor and host CMTM6 are deeply involved in tumor immunity with or without the PD-1/PD-L1 axis and that gene therapy targeting CMTM6 is a promising strategy for cancer immunotherapy.One Sentence SummaryEven in the absence of the PD-1/PD-L1 axis, tumor or host CMTM6 deficiency can mediate cytotoxicity-dependent anti-tumor immune responses, allowing CMTM6 to be a novel target for scAAV-mediated oncoimmunology gene therapy and combination treatment.
Piezo buffers mechanical stress via modulation of intracellular Ca2+ handling in the Drosophila heart
Authors: Zechini Luigi , Camilleri-Brennan Julian , Walsh Jonathan , Beaven Robin , Moran Oscar , Hartley Paul S. , Diaz Mary , Denholm Barry 
Published: May 2022

ABSTRACTThroughout its lifetime the heart is buffeted continuously by dynamic mechanical forces resulting from contraction of the heart muscle itself and fluctuations in haemodynamic load and pressure. These forces are in flux on a beat-by-beat basis, resulting from changes in posture, physical activity or emotional state, and over longer timescales due to altered physiology (e.g. pregnancy) or as a consequence of ageing or disease (e.g. hypertension). It has been known for over a century of the heart’s ability to sense differences in haemodynamic load and adjust contractile force accordingly1-4. These adaptive behaviours are important for cardiovascular homeostasis, but the mechanism(s) underpinning them are incompletely understood. Here we present evidence that the mechanically-activated ion channel, Piezo, is an important component of the Drosophila heart’s ability to adapt to mechanical force. We find Piezo is a sarcoplasmic reticulum (SR)-resident channel and is part of a mechanism that regulates Ca2+ handling in cardiomyocytes in response to mechanical stress. Our data support a simple model in which Drosophila Piezo transduces mechanical force such as stretch into a Ca2+ signal, originating from the SR, that modulates cardiomyocyte contraction. We show that Piezo mutant hearts fail to buffer mechanical stress, have altered Ca2+ handling, become prone to arrhythmias and undergo pathological remodelling.
Understanding the role of c-di-AMP signaling in determining antibiotic tolerance in Mycobacterium smegmatis: generation of resistant mutants and regrowth of persisters
Authors: Pal Aditya Kumar , Ghosh Anirban 
Published: May 2022

AbstractIn this study, we probe the role of secondary messenger c-di-AMP in drug tolerance, which includes both persister and resistant mutant characterization of Mycobacterium smegmatis. Specifically, with the use of c-di-AMP null and overproducing mutants, we showed how c-di-AMP plays a significant role in resistance mutagenesis against antibiotics with different mechanisms of action. We elucidated the specific molecular mechanism linking the elevated intracellular c-di-AMP level and high mutant generation and highlighted the significance of non-homology-based DNA repair. Further investigation enabled us to identify the unique mutational landscape of target and non-target mutation categories linked to intracellular c-di-AMP levels. Overall fitness cost of unique target mutations was estimated in different strain backgrounds, and then we showed the critical role of c-di-AMP in driving epistatic interactions between resistance genes, resulting in the evolution of multi-drug tolerance. Finally, we identified the role of c-di-AMP in persister cells regrowth and mutant enrichment upon cessation of antibiotic treatment.
Insulin Receptor Loss Impairs Mammary Tumorigenesis in Mice
Authors: Podmore Lauren , Poloz Yekaterina , Iorio Catherine , Mouaaz Samar , Nixon Kevin , Smirnov Petr , McDonnell Brianna , Lam Sonya , Zhang Bowen , Tharmapalan Pirashaanthy , Sarkar Soumili , Vyas Foram , Ennis Marguerite , Dowling Ryan , Stambolic Vuk 
Published: May 2022

SummaryBreast cancer (BC) prognosis and outcome are adversely affected by obesity. Hyperinsulinemia, common in obese state, is associated with higher risk of death and recurrence in BC. Up to 80% of breast cancers overexpress the insulin receptor (INSR), which correlates with worse prognosis. INSR role in mammary tumorigenesis was tested by generating MMTV-driven polyoma middle T (PyMT) and ErbB2/Her2 BC mouse models, respectively, with coordinate mammary epithelium-restricted deletion ofINSR. In both models, deletion of either one or both copies ofINSRled to a marked delay in tumor onset and burden. Longitudinal phenotypic characterization of mouse tumours and cells revealed that INSR deletion impacted tumour initiation, not progression and metastasis. INSR upheld a bioenergetic phenotype in non-transformed mammary epithelial cells, independent of its kinase activity. Similarity of phenotypes elicited by deletion of one or both copies ofINSRsuggest a dose-dependent threshold for INSR impact on mammary tumorigenesis.