bluuebunny/crossref_metadata_2025_split huggingface dataset:
CRISPR-Cas9-mediated genome engineering exaggerates genomic deletion at 10q23.31 including thePTENgene locus mimicking cancer profiles
Authors: Geng Keyi , Merino Lara G. , Veiga Raül G. , Sommerauer Christian , Epperlein Janine , Brinkman Eva K. , Kutter Claudia 
Published: April 2023

ABSTRACTThe CRISPR-Cas9 system is a powerful tool for studying gene functions and has tremendous potential for disease treatment. However, precise genome editing requires thorough assessments to minimize unintended on- and off-target effects. Here, we report an unexpected deletion of a 287 kb region on Chromosome 10 (10q23.31) in chronic myelogenous leukemia HAP1 cells, which are frequently used in CRISPR screens. The deleted region encodes regulatory genes, includingPAPSS2, ATAD1, KLLN, andPTEN. We found that this deletion was not a direct consequence of CRISPR-Cas9 off-targeting but rather occurred frequently by the process of generating CRISPR-Cas9-modifed cells. The deletion was associated with global changes in histone acetylation and gene expression, affecting fundamental cellular processes such as cell cycle and DNA replication. We detected this deletion in cancer patient genomes. As in HAP1 cells, the deletion contributed to similar gene expression patterns among cancer patients despite interindividual differences. Overall, our findings suggest that the unintended deletion of 10q23.31 can confound CRISPR-Cas9 studies, highlights the importance of assessing unintended genomic changes in CRISPR-Cas9-modified cells and may have clinical significance in cancer research.HighlightsCRISPR-Cas9-modified HAP1 cells carry an unexpected large genomic deletion at 10q23.31 encompassing four protein-coding genes frequently expressed across various cell types.The 10q23.31 deletion is accompanied by global changes in histone modification and transcriptomes.The generation of CRISPR-Cas9-modified cells rather than Cas9 activity increases the frequencies of the deletion at 10q23.31.The 10q23.31 deletion identified in HAP1 cells resembles a commonly occurring deletion pattern in cancer patients.
Probing Altered Receptor Specificities of Antigenically Drifting Human H3N2 Viruses by Chemoenzymatic Synthesis, NMR and Modeling
Authors: Unione Luca , Ammerlaan Augustinus N.A. , Bosman Gerlof P , Broszeit Frederik , van der Woude Roosmarijn , Liu Yanyan , Ma Shengzhou , Liu Lin , Diercks Tammo , Ardá Ana , de Vries Robert P. , Boons Geert-Jan 
Published: April 2023

AbstractPrototypic receptors for human influenza viruses are cell surfaceN-glycans carrying α2,6-linked sialosides. Under immune pressure, A/H3N2 influenza viruses have emerged with altered receptor specificities that appear to recognize α2,6-linked sialosides presented on extendedN-acetyl-lactosamine (LacNAc) moieties. Here, molecular recognition features of such drifted hemagglutinin’s (HAs) are examined by chemoenzymatic synthesis of complexN-glycans having13C-labeled monosaccharides at strategic positions. The labeled glycans were employed in 2D STD-1H and13C-HSQC NMR experiments to pinpoint which monosaccharides of the extended LacNAc chain engage with evolutionarily distinct HAs. The NMR data in combination with computational and mutagenesis studies demonstrate that mutations distal to the receptor binding domain of recent HAs have created an extended binding site that can directly interact with the extended LacNAc chain. A fluorine containing sialyl-LacNAc derivative is used as NMR probe to derive relative binding affinities and confirmed the contribution of the extended LacNAc chain for binding.
TREM2 mediates MHCII-associated CD4+T cell response against gliomas
Authors: Zheng Jiaying , Wang Lingxiao , Zhao Shunyi , Zhang Wenjing , Chang Yuzhou , Dheer Aastha , Gao Shan , Xu Shengze , Ayasoufi Katayoun , Al-kharboosh Rawan , Xie Manling , Johnson Aaron J. , Dong Haidong , Quiñones-Hinojosa Alfredo , Wu Long-Jun 
Published: April 2023

ABSTRACTTriggering receptor expressed on myeloid cells 2 (TREM2) was recently highlighted as a novel immune suppressive marker in peripheral tumors. The aim of this study was to characterizeTREM2expression in gliomas and investigate its contribution in glioma progression by usingTrem2-/-mouse line. Our results showed that higherTREM2expression was correlated with poor prognosis in glioma patients. Unexpectedly, TREM2 deficiency did not have a beneficial effect in a pre-clinical model of glioma. The increasedTREM2expression in glioma was likely due to increased myeloid cell infiltration, as evidenced by our single-cell analysis showing that almost all microglia and macrophages in gliomas were TREM2+. Furthermore, we found that deficiency of TREM2 impaired tumor-myeloid phagocytosis and MHCII presentation, and significantly reduced CD4+T cells in tumor hemispheres. Our results revealed a previously unrecognized protective role of tumor-myeloid TREM2 in promoting MHCII-associated CD4+T cell response against gliomas.SUMMARYAuthors found that although higherTREM2expression is correlated with poor prognosis in glioma patients, its absence has no beneficial effect in a pre-clinical model of glioma. Deficiency of TREM2 impairs myeloid cell phagocytosis of tumor debris, leading to a reduction in MHCII-dependent CD4+anti-glioma immunity.
Hierarchical TAF1-dependent co-translational assembly of the basal transcription factor TFIID
Authors: Bernardini Andrea , Mukherjee Pooja , Scheer Elisabeth , Kamenova Ivanka , Antonova Simona , Sanchez Paulina Karen Mendoza , Yayli Gizem , Morlet Bastien , Timmers H.T. Marc , Tora László 
Published: April 2023

ABSTRACTLarge heteromeric multiprotein complexes play pivotal roles at every step of gene expression in eukaryotic cells. Among them, the 20-subunit basal transcription factor TFIID nucleates RNA polymerase II preinitiation complex at gene promoters. Here, by combining systematic RNA-immunoprecipitation (RIP) experiments, single-molecule imaging, proteomics and structure-function analyses, we show that TFIID biogenesis occurs co-translationally. We discovered that all protein heterodimerization steps happen during protein synthesis. We identify TAF1 – the largest protein in the complex – as a critical factor for TFIID assembly. TAF1 acts as a flexible scaffold that drives the co-translational recruitment of TFIID submodules preassembled in the cytoplasm. Altogether, our data suggest a multistep hierarchical model for TFIID biogenesis that culminates with the co-translational assembly of the complex onto the nascent TAF1 polypeptide. We envision that this assembly strategy could be shared with other large heteromeric protein complexes.
Structural Plasticity of GABAergic Pallidothalamic Terminals in MPTP-treated Parkinsonian Monkeys: A 3D Electron Microscopic Analysis
Authors: Masilamoni GJ , Kelly H , Swain AJ , Pare JF , Villalba RM , Smith Y 
Published: April 2023

AbstractThe globus pallidus pars interna (GPi) is a major source of GABAergic inhibition upon the motor thalamus. GPi neurons are endowed with properties that allow them to fire at a high rate and maintain a tonic inhibitory influence upon thalamocortical neurons. In parkinsonism, the firing rate of GPi neurons is further increased and their firing pattern switches from a tonic to a bursty mode, two pathophysiological changes associated with increased GABAergic pallidothalamic activity. At the thalamic level, GPi terminals display ultrastructural features (large diameter, multiple synapses, large number of mitochondria) that allow them to maintain tonic synaptic inhibition at high firing rate upon thalamocortical neurons in the parvocellular ventral anterior nucleus (VApc) and the centromedian nucleus (CM), the two main GPi-recipient motor thalamic nuclei in nonhuman primates. To determine if changes of GPi neurons activity are associated with neuroplastic reorganization of GPi terminals and their synapses, we used a Single Block Facing/Scanning Electron Microscopy (SBF/SEM), high resolution 3D electron microscopic approach to compare the morphometry of GPi terminals between 2 control and 2 MPTP-treated parkinsonian monkeys. Our findings demonstrate that pallidothalamic terminals in VApc and CM undergo major ultrastructural changes in parkinsonian monkeys: (1) increased terminal volume in both nuclei, (2) increased surface area of synapses in both nuclei, (3) increased number of synapses/GPi terminals in the CM, but not VApc, (4) increased total volume of mitochondria/terminals in both nuclei but not in the number of mitochondria. In contrast, the ultrastructure of putative GABAergic terminals from the reticular thalamic nucleus was not affected in both the VApc and CM of parkinsonian monkeys. Our findings also show striking morphological differences in terminal volume, number/area of synapses and volume/number of mitochondria between GPi terminals in VApc and CM of control monkeys. In conclusion, results of this study demonstrate that GABAergic pallidothalamic terminals are endowed with a high level of structural plasticity that may contribute to the development and maintenance of the abnormal increase in pallidal GABAergic outflow to the thalamus in the parkinsonian state. Furthermore, the evidence for ultrastructural differences between GPi terminals in VApc and CM suggests that Morphologically distinct pallidothalamic terminals underlie specific physiological properties of pallidal inputs to VApc and CM in normal and diseased states.
Rev-Rev Response Element Activity Selection Bias at the HIV Transmission Bottleneck
Authors: Jackson Patrick E. H. , Holsey Jordan , Turse Lauren , Hammarskjold Marie-Louise , Rekosh David 
Published: April 2023

AbstractHIV is not efficiently transmitted between hosts, and selection of viral variants occurs during the process of sexual transmission. The factors that confer selective advantage at the transmission bottleneck remain incompletely understood. We explored whether differences in the Rev-Rev Response Element (RRE) regulatory axis of HIV affect transmission fitness, since functional variation in the Rev-RRE axis in different viral isolates has been shown to affect replication kinetics and relative expression of many HIV proteins. Single genome HIV sequences were identified from nine linked subject pairs near the time of female-to-male transmission. Using a rapid flow-cytometric assay, we found that the functional Rev-RRE activity varied significantly between isolates. Moreover, it was generally lower in recipients’ viruses compared to the corresponding donor viruses. In six of nine transmission events, recipient virus Rev-RRE activity clustered at the extreme low end of the range of donor virus activity. Rev-RRE pair activity was an unpredictable product of component Rev and RRE activity variation. These data indicate selection pressure on the Rev-RRE axis during female-to-male sexual transmission. Variation in the activity of the Rev-RRE axis may permit viral adaptation to different fitness landscapes and could play an important role in HIV pathogenesis.
Predation and competition drive trait diversity across space and time
Authors: Neale Zoey , Rudolf Volker H. W. 
Published: April 2023

AbstractCompetition should play a key role in shaping community assembly and thereby local and regional biodiversity patterns. However, identifying its relative importance and effects in natural communities is challenging because theory suggests that competition can lead to different and even opposing patterns depending on the underlying mechanisms. Here, we’ve taken a different approach: rather than attempting to indirectly infer competition from diversity patterns, we compared trait diversity patterns in odonate (dragonfly and damselfly) communities across different spatial and temporal scales along a natural competition-predation gradient. At the local scale (within a community), we found that trait diversity increased with the size of top predators (from invertebrates to fish). This relationship is consistent with differences in taxonomic diversity, suggesting that competition reduces local trait diversity through competitive exclusion. Spatial (across communities) and temporal (within communities over time) trait variation peaked in communities with intermediated predators indicating that both high levels of competition or predation select for trait-convergence of communities. This indicates that competition acts as a deterministic force that reduces trait diversity at the local, regional, and temporal scales, which contrasts with patterns at the taxonomic level. Overall, results from this natural experiment reveal how competition and predation interact to shape biodiversity patterns in natural communities across spatial and temporal scales and provide new insights into the underlying mechanisms.Open Research statementData and/or code are provided as private-for-peer review via the following link: [Link to external storage location] and will be made publicly available with publication
Ancient Fish Lineages Illuminate Toll-Like Receptor Diversification in Early Vertebrate Evolution
Authors: Carlson Kara B. , Nguyen Cameron , Wcisel Dustin J. , Yoder Jeffrey A. , Dornburg Alex 
Published: April 2023

AbstractSince its initial discovery over 50 years ago, understanding the evolution of the vertebrate adaptive immune response has been a major area of research focus for comparative geneticists. However, how the evolutionary novelty of an adaptive immune response impacted the diversity of receptors associated with the innate immune response has received considerably less attention until recently. Here we investigate the diversification of vertebrate Toll-like receptors (TLRs), one of the most ancient and well conserved innate immune receptor families found across the Tree of Life, integrating genomic data that represent all major vertebrate lineages with new transcriptomic data from Polypteriformes, the earliest diverging ray-finned fish lineage. Our analyses reveal TLR sequences that reflect the 6 major TLR subfamilies, TLR1, TLR3, TLR4, TLR5, TLR7, and TLR11, and also currently unnamed, yet phylogenetically distinct TLR clades. We additionally recover evidence for a pulse of gene gain coincident with the rise of the adaptive immune response in jawed vertebrates, followed by a period of rapid gene loss during the Cretaceous. These gene losses are primarily concentrated in marine teleost fish and synchronous with the mid Cretaceous anoxic event, a period of rapid extinction for marine species. Finally, we reveal a mismatch between phylogenetic placement and gene nomenclature for up to 50% of TLRs found in clades such as ray-finned fishes, cyclostomes, amphibians, and elasmobranchs. Collectively these results provide an unparalleled perspective of TLR diversity, and offer a ready framework for testing gene annotations in non-model species.
A single amino acid substitution in MdLAZY1A dominantly impairs shoot gravitropism inMalus
Authors: Dougherty Laura , Borejsza-Wysocka Ewa , Miaule Alexandre , Wang Ping , Zheng Desen , Jansen Michael , Brown Susan , Piñeros Miguel , Dardick Christopher , Xu Kenong 
Published: April 2023

AbstractPlant architecture is one of the most important factors that determines crop yield potential and productivity. In apple (Malus), genetic improvement of tree architecture has been challenging due to a long juvenile phase and their growth as complex trees composed of a distinct scion and a rootstock. To better understand the genetic control of apple tree architecture, the dominant weeping growth phenotype was investigated. We report the identification ofMdLAZY1A(MD13G1122400) as the genetic determinant underpinning theWeeping(W)locus that largely controls weeping growth inMalus.MdLAZY1Ais one of the four paralogs in apple that are most closely related toAtLAZY1involved in gravitropism inArabidopsis. The weeping allele (MdLAZY1A-W) contains a single nucleotide mutation c.584T>C that leads to a leucine to proline (L195P) substitution within a predicted transmembrane domain that co-localizes with Region III, one of the five conserved regions in LAZY1-like proteins. Subcellular localization revealed that MdLAZY1A localizes to the plasma membrane and nucleus in plant cells. Over-expressing the weeping allele in apple cultivar Royal Gala (RG) with standard growth habit impaired its gravitropic response and altered the growth to weeping-like. Suppressing the standard allele (MdLAZY1A-S) by RNA interference (RNAi) in RG similarly changed the branch growth direction to downward. Overall, the L195P mutation in MdLAZY1A is genetically causal for weeping growth, underscoring not only the crucial roles of residue L195 and Region III in MdLAZY1A-mediated gravitropic response, but also a potential DNA base editing target for tree architecture improvement inMalusand other crops.
Oncogenic Ras, Yki and Notch signals converge to confer clone competitiveness through Upd2
Authors: Wang Ying , He Jingjing , Deng Mingxi , Yan Yan 
Published: April 2023

AbstractIt has long been proposed that cell competition functions to remove precancerous clones. A classical model is the removal of polarity-deficient clones such as thescribble(scrib) mutant clones inDrosophilaimaginal discs. The activation of Ras, Yki or Notch signaling robustly reverses thescribmutant clonal fate from elimination to tumorous growth. Using single-cell transcriptomics techniques to profile wing imaginal discs harboring thescribmutant clones in combination with different signals, we found that a critical converging point downstream of Ras, Yki and Notch signals is the upregulation of Upd2, which is necessary to promote tumorous growth. Unexpectedly, while Upd2 is not required for cell survivalper se, Upd2-deficient clones are efficiently wiped out from epithelia, indicating that Upd2 is a previously unrecognized cell competition factor.
Mrs4 loss of function in fungi during adaptation to the cystic fibrosis lung
Authors: Murante Daniel , Demers Elora G. , Kurbessoian Tania , Ruzic Marina , Ashare Alix , Stajich Jason E. , Hogan Deborah A. 
Published: April 2023

AbstractThe genetic disease cystic fibrosis (CF) frequently leads to chronic lung infections by bacteria and fungi. We identified three individuals with CF with persistent lung infections dominated byClavispora(Candida)lusitaniae. Whole genome sequencing analysis of multiple isolates from each infection found evidence for selection for mutants in the geneMRS4in all three distinct lung-associated populations. In each population, we found one or two unfixed, non-synonymous mutations inMRS4relative to the reference allele found in multiple environmental and clinical isolates including the type strain. Genetic and phenotypic analyses found that all evolved alleles led to loss of function of Mrs4, a mitochondrial iron transporter. RNA Seq analyses found that Mrs4 variants with decreased activity led to increased expression of genes involved in iron acquisition mechanisms in both low iron and replete iron conditions. Furthermore, surface iron reductase activity and intracellular iron was much higher in strains with Mrs4 loss of function variants. Parallel studies found that a subpopulation of a CF-associatedExophiala dermatiditisinfection also had a non-synonymous loss of function mutation inMRS4.Together, these data suggest thatMRS4mutations may be beneficial during chronic CF lung infections in diverse fungi perhaps for the purposes of adaptation to an iron restricted environment with chronic infections.
Triggering receptor expressed on myeloid cells 2 (TREM2) regulates phagocytosis in glioblastoma
Authors: Peshoff Mekenzie M. , Gupta Pravesh , Trivedi Rakesh , Oberai Shivangi , Chakrapani Prashanth , Dang Minghao , Milam Nancy , Maynard Mark E. , Vaillant Brian D. , Huse Jason T. , Wang Linghua , Clise-Dwyer Karen , Bhat Krishna P. 
Published: April 2023

AbstractGlioblastomas (GBMs) are tumors of the central nervous system that remain recalcitrant to both standard of care chemo-radiation and immunotherapies. Emerging approaches to treat GBMs include depletion or re-education of innate immune cells including microglia (MG) and macrophages (MACs). Here we show myeloid cell restricted expression of triggering receptor expressed on myeloid cells 2 (TREM2) across low- and high-grade human gliomas. TREM2 expression did not correlate with immunosuppressive pathways, but rather showed strong positive association with phagocytosis markers such as lysozyme (LYZ) and CD163 in gliomas. In line with these observations in patient tumors,Trem2-/-mice did not exhibit improved survival compared to wildtype (WT) mice when implanted with mouse glioma cell lines, unlike observations previously seen in peripheral tumor models. Gene expression profiling revealed pathways related to inflammation, adaptive immunity, and autophagy that were significantly downregulated in tumors fromTrem2-/-mice compared to WT tumors. Using ZsGreen-expressing CT-2A orthotopic implants, we found higher tumor antigen engulfment in Trem2+MACs, MG, and dendritic cells. Our data uncover TREM2 as an important immunomodulator in gliomas and inducing TREM2 mediated phagocytosis can be a potential immunotherapeutic strategy for brain tumors.Key pointsTREM2 is not associated with immunosuppressive molecules in GBMTREM2 is associated with phagocytosis in both human and mouse gliomasDeletion of Trem2 in mice does not improve survival in glioma modelsImportance of the studyTriggering receptor expressed on myeloid cells 2 (TREM2) has been implicated as a major immunoregulator in both neurodegenerative diseases and systemic cancers, yet its functional role in gliomas remains unclear. This study reveals that unlike in other cancers, TREM2 is not associated with immunosuppression in the glioma microenvironment. In fact, TREM2 expression is associated with phagocytosis in both human and mouse gliomas, similar to its role in Alzheimer’s disease. These findings indicate that TREM2 blockade will not be a viable treatment strategy for gliomas. Instead, TREM2 induction may boost the potential of myeloid cells in the tumor microenvironment to engulf cancer cells.
The third symbiotic partner of the volcano lichenCladonia vulcaniSavicz drove adaptation to an extreme environment
Authors: Kono Mieko , Terai Yohey 
Published: April 2023

AbstractChemosynthetic symbioses between sulfur-oxidizing bacteria and aquatic eukaryotes have been discovered globally in sulfide-rich environments, notably deep-sea hydrothermal vents, cold seeps, and sulfidic cave systems. However, to the best of our knowledge, such chemosymbiotic lifestyles have not been reported from terrestrial eukaryotes. Here we report that the volcano lichenCladonia vulcaniSavicz ubiquitously associates with a single bacterial species that could potentially use hydrogen sulfide as a source of energy. We identified sequences of the bacterium in all 27 samples collected from five geothermal areas across Japan with cellular abundance comparable to the fungal partner. The assembled bacterial genome contained genes involved in sulfur oxidation. The stable association with a potential sulfur-oxidizer is likely to represent an obligate tripartite symbiotic system consisting of fungal, algal, and bacterial partners that has enabled adaptation to the extreme environment.