bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cas9 nickase-mediated contraction of CAG/CTG repeats at multiple disease loci
Authors: Murillo Alvaro , Alpaugh Melanie , Larin Meghan , Randall Emma L. , Heraty Laura , Durairaj Ruban Rex , Aston Alys N. , Taylor Alysha S. , Monteys Alex Mas , Stöberl Nina , Heuchan Aeverie E. R. , Aeschlimann Pascale , Bhattacharyya Soumyasree , Allen Nicholas D. , Puymirat Jack , Davidson Beverly L. , Cicchetti Francesca , Lelos Mariah , Dion Vincent 
Published: February 2024

AbstractExpanded CAG/CTG repeats cause at least 15 different neurodegenerative and neuromuscular diseases that all remain without an effective disease modifying treatment. Because the size of the repeat tract accounts for the majority of the variation in disease severity, contracting them presents an attractive therapeutic avenue. Here, we show that the CRISPR-Cas9 nickase targeting the CAG/CTG repeat itself leads to efficient contractions in Huntington’s disease patient-derived neurons and astrocytes, as well as in myotonic dystrophy type 1 patient-derived neurons. Using single-cell DNA sequencing, PCR-free whole genome sequencing, and targeted long-read sequencing of theHTTlocus, we found no off-target mutations above background in neurons and astrocytes. Furthermore, we delivered the Cas9 nickase and sgRNA stereotactically to a mouse model of Huntington’s disease using adeno-associated viruses, and found contractions accumulating in over half of the infected cells over a period of 5 months. We also found that the Cas9 nickase was prone to silencing, further improving the safety of the approach. Our results provide the proof of concept for using the Cas9 nickase to contract the repeat tract safely in multiple cell types and diseases.
The SUMOylation inhibitor TAK-981 (Subasumstat) triggers IFN-I-dependent activation of Natural Killer cells against Acute Myeloid Leukemias
Authors: Hallal Rawan , De Toledo Marion , Tempé Denis , Zemiti Sara , Coënon Loïs , Gitenay Delphine , George Simon , Bonnet Sarah , Gabellier Ludovic , Cartron Guillaume , Pelegrin Mireia , Villalba Martin , Bossis Guillaume 
Published: February 2024

AbstractNatural Killer (NK) cells play a pivotal role in mounting an anti-cancer immune response. Patients with diminished NK cells number and activity face less favorable prognosis. Promising therapeutic strategies include the adoptive transfer of NK cells or the reactivation of patients’ own NK cells. TAK-981, a first-in-class inhibitor of SUMOylation undergoing phase I/II clinical trials for cancer, is emerging as an immunomodulatory drug. Here, we demonstrate that TAK-981 activates NK cells from healthy donors and patients with Acute Myeloid Leukemia (AML), a cancer with very poor prognosis. TAK-981 heightens their degranulation capacity, secretion of inflammatory cytokines (IFN-γ, TNF-α, FasL), and cytotoxicity against AML cells.In vivo, TAK-981 also enhances the anti-leukemic activity ofex-vivoexpanded human NK cells. At the molecular level, TAK-981 first inducesIFNB1gene in NK cells, leading to the secretion of type I Interferon (IFN-I), which binds to the Interferon receptor IFNAR. This induces Interferon-Stimulated Genes (ISG) and activates NK cellsin vitroandin vivo. Finally, TAK-981 stimulates IFN-I secretion by monocytes, which contributes to the activation of NK cellsin trans. Altogether, targeting SUMOylation could be a promising strategy to reactivate AML patients’ NK cells and enhance the efficiency of NK cells-based therapies.Abstract Figure
A circadian transcriptional sub-network andEARLY FLOWERING 3control timing of senescence and grain nutrition in bread wheat
Authors: Buckley Christopher R. , Boyte Joshua M. , Albiston Robert L. , Hyles Jessica , Beasley Jesse T , Johnson Alexander AT , Trevaskis Ben , Fournier-Level Alexandre , Haydon Michael J. 
Published: February 2024

AbstractCircadian clocks control daily and seasonal timing of physiology and development. Because of their influence on photoperiodic flowering, variants in circadian clock genes have been selected for phenology during domestication of cereal crops. To explore the potential impact of this genetic variation on circadian-regulated traits, we investigated the relationship of the circadian clock and leaf senescence in hexaploid bread wheat. Phenotyping of a collection of elite wheat cultivars identified significant variation in circadian rhythms which was associated with timing of senescence and nutrient mobilisation efficiency. RNA sequencing revealed substantial reorganisation of the circadian-regulated transcriptome during senescence and a transcriptional sub-network representing a link between the circadian oscillator and regulators of leaf senescence. We used genotypes of multiple circadian clock genes to assign cultivars to ‘chronotypes’, which could be used to predict circadian-regulated phenotypes. This identified a deletion variant ofEARLY FLOWERING 3-D1 (ELF3-D1)attributed to a phenology locus,Earliness per se (Eps-D1),and we used near-isogenic lines (NILs) to show that it affects timing of senescence and grain protein content (GPC). Thus, there are potential consequences of circadian clock genes selected for phenology on other valuable crop traits.
Molecular dynamics simulations reveal molecular mechanisms for the gain and loss of function effects of fourSCN2Avariants
Authors: Bhattarai Nisha , Montanucci Ludovica , Brünger Tobias , Pérez-Palma Eduardo , Martin William , Smith Iris Nira , Eng Charis , Cheng Feixiong , Helbig Ingo , Møller Rikke S , Brunklaus Andreas , Schorge Stephanie , Lal Dennis 
Published: February 2024

ABSTRACTSCN2Agene disorders cover a wide range of medical conditions, from epileptic encephalopathies to neurodevelopmental disorders. The variants of these disorders, studied through electrophysiology, show complex behaviors that go beyond simple classification as either gain or loss of function. In our study, we simulated the biophysical effects of variants (R937C,V208E,S1336Y, andR853Q) to understand their impact. Our findings reveal that all these variants negatively affect the structural stability of the gene, withR937Cbeing the most unstable. Specifically,R937Cdisrupts important charged interactions affecting sodium ion flow, whileS1336Yintroduces a new interaction that impacts the channel’s inactivation gate. Conversely, the variantsV208EandR853Q, which are located in the voltage-sensing domains, have opposite effects:R853Qincreases compactness and interaction, whereasV208Eshows a decrease. Our computer-based method offers a scalable way to gain crucial insights into how genetic variants influence channel dysfunction and contribute to neurodevelopmental disorders.AUTHOR SUMMARYDespite numerous advancements in computational methods for predicting variant pathogenicity in theSCN2Agene, understanding the precise biophysical molecular mechanisms associated with each variant at the atomic level remains a challenge. Presently, variants are predominantly categorized as either gain or loss of function, often overlooking critical structural details associated with these variants. This study focuses on elucidating the molecular mechanisms linked to the four most commonSCN2Avariants using all-atom molecular dynamics simulations, employing three replicas for each system. Our findings offer insights into the potential mechanisms underlying these four variants, thereby providing explanations for the observed electrophysiological outcomes. This investigation significantly contributes to enhancing our comprehension of howSCN2Avariants manifest in various diseases. It underscores the importance of unraveling the biophysical properties underlying potential disease mechanisms, which could potentially enhance diagnostic and therapeutic strategies for patients afflicted withSCN2A-related disorders.
Functional avidity of anti-B7H3 CAR-T constructs predicts antigen density thresholds for triggering effector function
Authors: Barisa Marta , Zappa Elisa , Muller Henrike , Shah Rivani , Buhl Juliane , Draper Benjamin , Himsworth Courtney , Bowers Chantelle , Munnings-Tomes Sophie , Nicolaidou Marilena , Morlando Sonia , Birley Katie , Leboreiro-Babe Clara , Vitali Alice , Privitera Laura , O’Sullivan Kyle , Greppi Ailsa , Buschhaus Magdalena , Román Mario Barrera , de Blank Sam , van den Ham Femke , van ‘t Veld Brenna R. , Ferry Gabrielle , Donovan Laura K. , Chesler Louis , Molenaar Jan , Drost Jarno , Rios Anne , Chester Kerry , Wienke Judith , Anderson John 
Published: February 2024

AbstractChimeric Antigen receptor T cell (CAR-T) treatments for solid cancers have been compromised by limited expansion and survival in the tumor microenvironment following interaction with antigen-expressing target cells. Using B7H3 as a model antigen with broad clinical applicability, we evaluated the relationship between the antibody/antigen affinity of three clinical candidate binders and the three following functional characteristics: functional avidity, prolonged cytotoxicity in tumoroid re-stimulation assays, andin vivoanti-tumoral responses. BEHAV3D video-microscopy assessed distinct CAR-T cell behaviors at single cell resolution. T cell exhaustion did not dictate effector function. Rather, we demonstrated a threshold avidity of CAR-T / tumor cell interaction, characterized by longer cumulative CD8+CAR-T / tumor target interaction times, and required for adequate CAR-T cell expansion to result in sustained tumor control upon re-challenge. These results provide new insights into design of CAR-T cells for antigen-dim cell targeting, and avoidance of antigen-dim tumor relapse.
Importance of environmental signals for proper cardiac morphological development in Atlantic salmon
Authors: Vindas Marco A. , Engdal Vilde Arntzen , Kavaliauskiene Simona , Folkedal Ole , Höglund Erik , Moyano Marta , Øverli Øyvind , Frisk Michael , Johansen Ida B. 
Published: February 2024

AbstractThe hearts of salmonids display remarkable plasticity, adapting to various environmental factors that influence cardiac function and demand. For instance, in response to cold temperature, the salmonid heart undergoes growth and remodeling to counterbalance the reduced contractile function associated with dropping temperatures. Alongside heart size, the distinct pyramidal shape of the wild salmonid heart is essential for optimal cardiac performance, yet the environmental drivers behind this optimal cardiac morphology remain to be fully understood. Intriguingly, farmed salmonids often have rounded, asymmetrical ventricles and misaligned bulbi from an early age. These deformities are noteworthy given that farmed salmon are often not exposed to natural cues, such as a gradual temperature increase and changing day lengths, during critical developmental stages. In this study, we investigated whether natural environmental conditions during early life stages are pivotal for proper cardiac morphology. Atlantic salmon were raised under simulated natural conditions (low temperature with a natural photoperiod; SIMNAT) and compared with those reared under simulated farming conditions (SIMFARM). Our findings reveal that the ventricle shape and bulbus alignment in SIMNAT fish closely resemble those of wild salmon, while functional analyses indicate significant differences between SIMNAT and SIMFARM hearts, suggesting diastolic dysfunction and higher cardiac workload in SIMFARM hearts. These findings highlight the profound influence of environmental factors such as water temperature and photoperiod on the structural development of the salmonid heart, underscoring the importance of early environmental conditions for cardiac health.
The DC1 domain protein Vacuoleless Gametophytes regulates stamen development in Arabidopsis
Authors: Amigo Natalia L. , Arias Leonardo A. , Marchetti Fernanda , D’Ippólito Sebastián , Cascallares Milagros , Lorenzani Salvador , Frik Jesica , Lombardo María Cristina , Terrile María Cecilia , Casalongue Claudia A. , Pagnussat Gabriela C. , Fiol Diego F. 
Published: February 2024

ABSTRACTVacuoleless Gametophytes (VLG) is a DC1 domain protein that was initially characterized as essential for early female and male gametophytes development in Arabidopsis. However, VLG expression was also detected in stamens, pistils and other sporophytic tissues, implying a broader role for this protein. As homozygous insertional VLG lines resulted unviable, we generated Arabidopsis amiRNAVLGknock-down plants to study the role of VLG in sporophyte development. The phenotypic characterization ofVLGknock-down plants showed reduced seed set and indehiscent anthers with shorter filaments and stigma exsertion. Moreover, amiRNAVLGknock-down plants displayed unbroken stomia and septa, markedly reduced endothecium lignification, diminished ROS accumulation, and lower transcript levels of genes involved in jasmonic acid and lignin biosynthesis. The indehiscent phenotype was rescued by exogenous application of either jasmonic acid or H2O2. Altogether, our results suggest that VLG is involved in lignin and jasmonic acid biosynthesis pathways, and that proper levels of VLG are required in the process that leads to stomium breakage and anther dehiscence. Our findings shed light on the mechanisms underlying stamen development and provide new insights into the roles of a DC1 domain protein in plant reproduction.Key MessageVacuoleless Gametophytes participates in anther dehiscence through a process that involves JA, ROS and lignin accumulation.
Transcriptional profiling sheds light on the fibrotic aspects of idiopathic subglottic tracheal stenosis
Authors: Direder Martin , Laggner Maria , Copic Dragan , Klas Katharina , Bormann Daniel , Schweiger Thomas , Hoetzenecker Konrad , Aigner Clemens , Ankersmit Hendrik Jan , Mildner Michael 
Published: February 2024

1AbstractIdiopathic subglottic stenosis (ISGS) is a rare fibrotic disease of the upper trachea with an unknown pathomechanism. It typically affects adult Caucasian female patients, leading to severe airway constrictions caused by progressive scar formation and inflammation with clinical symptoms of dyspnoea, stridor and potential changes to the voice. Endoscopic treatment frequently leads to recurrence, whereas surgical resection and reconstruction provides excellent long-term functional outcome. This study aimed to identify so far unrecognized pathologic aspects of ISGS using single cell RNA sequencing. Our scRNAseq analysis uncovered the cellular composition of the subglottic scar tissue, including the presence of a pathologic, profibrotic fibroblast subtype and the presence of Schwann cells in a profibrotic state. In addition, a pathology-associated increase of plasma cells was identified. Using extended bioinformatics analyses, we decoded pathology-associated changes of factors of the extracellular matrix. Our data identified ongoing fibrotic processes in ISGS and provide novel insights on the contribution of fibroblasts, Schwann cells and plasma cells to the pathogenesis of ISGS. This knowledge could impact the development of novel approaches for diagnosis and therapy of ISGS.
Epigenetic histone modifications H3K36me3 and H4K5/8/12/16ac induce open polynucleosome conformations via different mechanisms
Authors: Lin Yi-Yun , Müller Peter , Karagianni Evdoxia , Vanderlinden Willem , Lipfert Jan 
Published: February 2024

AbstractNucleosomes are the basic compaction unit of chromatin and nucleosome structure, and their higher-order assemblies regulate genome accessibility. Many post-translational modifications alter nucleosome dynamics, nucleosome-nucleosome interactions, and ultimately chromatin structure and gene expression. Here, we investigate the role of two post-translational modifications associated with actively transcribed regions, H3K36me3 and H4K5/8/12/16ac, in the contexts of tri-nucleosome arrays that provide a tractable model system for quantitative single-molecule analysis, while enabling us to probe nucleosome-nucleosome interactions. Direct visualization by AFM imaging reveals that H3K36me3 and H4K5/8/12/16ac nucleosomes adopt much more open and loose conformations than unmodified nucleosomes. Similarly, magnetic tweezers force spectroscopy shows a reduction in DNA outer turn wrapping and nucleosome-nucleosome interactions for the modified nucleosomes. The results suggest that for H3K36me3 the increased breathing and outer DNA turn unwrapping seen in mononucleosomes propagates to more open conformations in nucleosome arrays. In contrast, the even more open structures of H4K5/8/12/16ac nucleosome arrays do not appear to derive from the dynamics of the constituent mononucleosomes, but are driven by reduced nucleosome-nucleosome interactions, suggesting that stacking interaction can overrule DNA breathing of individual nucleosomes. We anticipate that our methodology will be broadly applicable to reveal the influence of other post-translational modifications and action of nucleosome remodelers.
Free radical production induced by visible light in live fruit flies
Authors: Daplan Ekin , Turin Luca 
Published: February 2024

AbstractVisible light triggers free radical production in alive and intactDrosophila melanogaster. We exposed fruit flies to red (613-631 nm), green (515-535 nm), and blue (455-475 nm) light while we monitored changes in unpaired electron content with an electron spin resonance spectrometer (ESR/EPR). The immediate response to light is a rapid increase in spin content lasting approximately 10 seconds followed by a slower, linear increase for approximately 170 seconds. When the light is turned off, the spin population promptly decays with a similar time course, though never fully returning to baseline. The magnitude and time course of the spin production depends on the wavelength of the light. Initially, we surmised that eumelanin might be responsible for the spin change because of its documented ability for visible light absorption and its highly stable free radical content. To explore this, we utilized different fruit fly strains with varying eumelanin content and clarified the relation of melanin types with the spin response. Our findings revealed that flies with darker cuticle have at least three-fold more unpaired electrons than flies with yellow cuticle. However, to our surprise, the increase in unpaired electron population by light was not drastically different amongst the genotypes. This suggests that light-induced free radical production may not exclusively rely on the presence of black melanin, but may instead be dependent on light effects on quinone-based cuticular polymers.
TIRR regulates mRNA export and association with P bodies in response to DNA damage
Authors: Glossop Michelle S , Chelysheva Irina , Ketley Ruth F , Alagia Adele , Gullerova Monika 
Published: February 2024

AbstractTo ensure the integrity of our genetic code, a coordinated network of signalling and repair proteins known as the DNA damage response (DDR) detects and repairs DNA insults, the most toxic being double-stranded breaks (DSBs). Tudor interacting repair regulator (TIRR) is a key factor in DSB repair, acting through its interaction with p53 binding protein 1 (53BP1). TIRR is also an RNA-binding protein, yet its role in RNA regulation during the DNA damage response remains elusive. Here we show that TIRR selectively binds to a subset of mRNAs in response to DNA damage with preference for transcripts encoding transcription factors and RNA polymerase II (RNAPII) transcription regulators. Upon DNA damage, TIRR interacts with the nuclear export protein Exportin-1 (XPO1), through its nuclear export sequence (NES). Furthermore, TIRR plays a crucial role in modulation of RNA processing bodies (P bodies/PBs). TIRR itself and TIRR-bound RNA co-localises with PBs, and TIRR depletion results in nuclear RNA retention and impaired PB formation. Finally, the role of TIRR in RNA export contributes to efficient DNA damage response. This work reveals intricate involvement of TIRR in orchestrating mRNA nuclear export and storage within PBs, emphasizing its significance in the regulation of RNA-mediated DNA damage response.
Developmental synchrony and extraordinary multiplication rates in pathogenic organisms
Authors: Greischar Megan A. , Childs Lauren M. 
Published: February 2024

AbstractThe multiplication rates of pathogenic organisms influence disease progression, efficacy of immunity and therapeutics, and potential for within-host evolution. Thus, accurate estimates of multiplication rates are essential for biological understanding. We recently showed that common methods for inferring multiplication rates from malaria infection data substantially overestimate true values (i.e., under simulated scenarios), providing context for extraordinarily large estimates in human malaria parasites. A key unknown is whether this bias arises specifically from malaria parasite biology or represents a broader concern. Here we identify the potential for biased multiplication rate estimates across pathogenic organisms with different developmental biology by generalizing a within-host malaria model. We find that diverse patterns of developmental sampling bias—the change in detectability over developmental age—reliably generate overestimates of the fold change in abundance, obscuring not just true growth rates but potentially even whether populations are expanding or declining. This pattern emerges whenever synchrony, the degree to which development is synchronized across the population of pathogenic organisms comprising an infection, decays with time. Only with simulated increases in synchrony do we find noticeable underestimates of multiplication rates. Obtaining robust estimates of multiplication rates may require accounting for diverse patterns of synchrony in pathogenic organisms.Subjectscomputational biology, theoretical biology, ecology, developmental biology