bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association of genetic variation inCOL11A1with adolescent idiopathic scoliosis
Authors: Yu Hao , Khanshour Anas M. , Ushiki Aki , Otomo Nao , Koike Yoshinao , Einarsdottir Elisabet , Fan Yanhui , Antunes Lilian , Kidane Yared H. , Cornelia Reuel , Sheng Rory , Zhang Yichi , Pei Jimin , Grishin Nick V. , Evers Bret M. , Cheung Jason Pui Yin , Herring John A. , Terao Chikashi , Song You-Qiang , Gurnett Christina A. , Gerdhem Paul , Ikegawa Shiro , Rios Jonathan J. , Ahituv Nadav , Wise Carol A. 
Published: May 2023

AbstractAdolescent idiopathic scoliosis (AIS) is a common and progressive spinal deformity in children that exhibits striking sexual dimorphism, with girls at more than five-fold greater risk of severe disease compared to boys. Despite its medical impact, the molecular mechanisms that drive AIS are largely unknown. We previously defined a female-specific AIS genetic risk locus in an enhancer near thePAX1gene. Here we sought to define the roles ofPAX1and newly-identified AIS-associated genes in the developmental mechanism of AIS. In a genetic study of 10,519 individuals with AIS and 93,238 unaffected controls, significant association was identified with a variant inCOL11A1encoding collagen (α1) XI (rs3753841; NM_080629.2_c.4004C>T; p.(Pro1335Leu); P=7.07e-11, OR=1.118). Using CRISPR mutagenesis we generatedPax1knockout mice (Pax1-/-). In postnatal spines we found that PAX1 and collagen (α1) XI protein both localize within the intervertebral disc (IVD)-vertebral junction region encompassing the growth plate, with less collagen (α1) XI detected inPax1-/-spines compared to wildtype. By genetic targeting we found that wildtypeCol11a1expression in costal chondrocytes suppresses expression ofPax1and ofMmp3, encoding the matrix metalloproteinase 3 enzyme implicated in matrix remodeling. However, this suppression was abrogated in the presence of the AIS-associatedCOL11A1P1335Lmutant. Further, we found that either knockdown of the estrogen receptor geneEsr2, or tamoxifen treatment, significantly alteredCol11a1andMmp3expression in chondrocytes. We propose a new molecular model of AIS pathogenesis wherein genetic variation and estrogen signaling increase disease susceptibility by altering aPax1-Col11a1-Mmp3signaling axis in spinal chondrocytes.
Wnt4a is indispensable for genital duct elongation but not for gonadal sex differentiation in the medakaOryzias latipes
Authors: Kanamori Akira , Kitani Ryota , Oota Atsuko , Hirano Koudai , Myosho Taijun , Kobayashi Tohru , Kawamura Kouichi , Kato Naoyuki , Ansai Satoshi , Kinoshita Masato 
Published: May 2023

ABSTRACTIn most vertebrates, oviducts are derived from Mullerian ducts and sperm ducts from Wolffian ducts. In teleosts, however, Mullerian ducts are absent. Wolffian ducts function as nephric ducts in both sexes, and genital ducts are formed by posterior extension of either ovaries or testes. Whether genital ducts of teleosts are newly evolved organs or are a variant of the Mullerian ducts is an important question for evolutionary mechanisms of morphogenesis. One of the genes essential for Mullerian duct formation in mice,wnt4, is expressed in the mesenchyme and induces invagination of the coelomic epithelium and its posterior elongation. Here, we approached to the above question by examining genital duct development in mutants of two Wnt4 genes in medaka (wnt4ais orthologous to mousewnt4andwnt4bparalogous). Thewnt4bmutants had short body but were fertile with normal genital ducts. In contrast, both male and femalewnt4amutants had posterior elongation of the gonads stopped within or just outside the coelom, depending on the mutated alleles. Genetic females of thesclmutants (unable to synthesize testosterone or estrogens) have gonads containing both previtellogenic oocytes and spermatogenic cysts. Their gonads do not have ovarian cavities or sperm duct primordia and are lacking genital ducts completely. The results suggest Wnt4a target organs are posterior parts of the ovarian cavities or the sperm duct primordia. Medakawnt4awas expressed in the mesenchyme ventral to the genital ducts in both sexes. Thus, the aborted elongation of genital ducts in thewnt4amutants, the ortholog of mousewnt4, suggests strongly that mouse Mullerian ducts and teleost genital ducts share homologous developmental processes. To further demonstrate this possible homology, mechanisms of genital duct formation and possible roles of Wnt4 should be compared before and after the appearance of Mullerian ducts in vertebrate phylogeny, namely jawless fish and cartilaginous fish. Additionally,wnt4aandwnt4bsingle mutants or double mutants did not show sex-reversal, suggesting both genes are dispensable for gonadal sex differentiation in medaka. This is in contrast to indispensable function of Wnt4 in mammalian ovarian differentiation.
Plant PAXX has an XLF-like function and stimulates DNA end-joining by the Ku-DNA ligase IV-XRCC4 complex
Authors: Khan Hira , Ochi Takashi 
Published: May 2023

AbstractNon-homologous end joining (NHEJ) plays a major role in repairing DNA double-strand breaks (DSBs) and is key to genome stability and editing. The minimal core NHEJ proteins, namely Ku70, Ku80, DNA ligase IV and XRCC4, are conserved, but other factors vary in different eukaryotes groups. In plants, known NHEJ proteins are the core factors only, and the molecular mechanism of plant NHEJ remains unclear. Here, we report a previously unidentified plant ortholog of PAXX, the crystal structure of which showed a similar fold to human PAXX. However, plant PAXX has similar molecular functions to human XLF, by directly interacting with Ku70/80 and XRCC4. This suggests that plant PAXX combines the roles of mammalian PAXX and XLF and that these functions merged into a single protein during evolution. This is consistent with a redundant function of PAXX and XLF in mammals.
The effect of host admixture on wild house mouse gut microbiota is weak when accounting for spatial autocorrelation
Authors: Čížková Dagmar , Schmiedová Lucie , Kváč Martin , Sak Bohumil , Macholán Miloš , Piálek Jaroslav , Kreisinger Jakub 
Published: May 2023

AbstractThe question of how interactions between the gut microbiome and vertebrate hosts contribute to host adaptation and speciation is one of the major problems in current evolutionary research. Using bacteriome and mycobiome metabarcoding, we examined how these two components of the gut microbiota vary with the degree of host admixture in secondary contact between two house mouse subspecies (Mus musculus musculusandM. m. domesticus). We used a large dataset collected at two replicates of the hybrid zone and model-based statistical analyses to ensure the robustness of our results. Assuming that the microbiota of wild hosts suffers from spatial autocorrelation, we directly compared the results of statistical models that were spatially naive with those that accounted for spatial autocorrelation. We showed that neglecting spatial autocorrelation can drastically affect the results and lead to misleading conclusions. The spatial analyses showed little difference between subspecies, both in microbiome composition and in individual bacterial lineages. Similarly, the degree of admixture had minimal effects on the gut bacteriome and mycobiome and was caused by changes in a few microbial lineages that correspond to the common symbionts of free-living house mice. In contrast to previous studies, these data do not support the hypothesis that the microbiota plays an important role in host reproductive isolation in this particular model system.
Droplet-based bisulfite sequencing for high-throughput profiling of single-cell DNA methylomes
Authors: Zhang Qiang , Ma Sai , Liu Zhengzhi , Zhu Bohan , Zhou Zirui , Li Gaoshan , Meana J. Javier , González-Maeso Javier , Lu Chang 
Published: May 2023

AbstractGenome-wide DNA methylation profile, or DNA methylome, is a critical component of the overall epigenomic landscape that modulates gene activities and cell fate. Single-cell DNA methylomic studies offer unprecedented resolution for detecting and profiling cell subsets based on methylomic features. However, existing single-cell methylomic technologies are all based on use of tubes or well plates and these platforms are not easily scalable for handling a large number of single cells. Here we demonstrate a droplet-based microfluidic technology, Drop-BS, to construct single-cell bisulfite sequencing libraries for DNA methylome profiling. Drop-BS takes advantage of the ultrahigh throughput offered by droplet microfluidics to prepare bisulfite sequencing libraries of up to 10,000 single cells within 2 d. We applied the technology to profile mixed cell lines, mouse and human brain tissues to reveal cell type heterogeneity. Drop-BS will pave the way for single-cell methylomic studies requiring examination of a large cell population.
The combination of differential expression and differential network connectivity analyses identifies RNA splicing and processing as common pathways altered with age across human tissues
Authors: Batalha Caio M.P.F. , Fujita André , de Souza-Pinto Nadja C. 
Published: May 2023

ABSTRACTTranscriptomic changes occur with age, but the extent of their similarities across tissues is not clear. Previous studies have identified no similarity in age-modulated genes in different tissues. In this study, we sought to identify transcriptional changes with age across tissues using differential network analysis, with the premise that differential expression analysis alone is not capable of detecting all the changes in the transcriptional landscape that occur in tissues with age. Our results show major transcriptional alterations not detected by differential expression analysis that can be detected by differential connectivity analysis. Combining these two analyses, we detected genes changing across tissues, enriched in “RNA splicing” and “RNA processing”, and highly connected in protein-protein interaction networks. Co-expression module analyses demonstrated that other genes with tissue-specific variations with age are enriched in pathways that combat accumulation of aberrant RNAs and proteins, which are caused by defective splicing. Additionally, tissues displayed a major reorganization of their genes’ connectivities with age, with most demonstrating convergent connectivity patterns. Our analyses identify genes and processes which transcriptional changes are conserved across tissues, demonstrating a central role for RNA splicing and processing genes and highlighting the importance of differential network analysis for understanding the ageing transcriptome.
A potent MAPK13-14 inhibitor prevents airway inflammation and mucus production
Authors: Keeler Shamus P. , Wu Kangyun , Zhang Yong , Mao Dailing , Li Ming , Iberg Courtney A. , Austin Stephen R. , Glaser Samuel A. , Yantis Jennifer , Podgorny Stephanie , Brody Steven L. , Chartock Joshua R. , Han Zhenfu , Byers Derek E. , Romero Arthur G. , Holtzman Michael J. 
Published: May 2023

ABSTRACTCommon respiratory diseases continue to represent a major public health problem, and much of the morbidity and mortality is due to airway inflammation and mucus production. Previous studies indicated a role for mitogen-activated protein kinase 14 (MAPK14) in this type of disease, but clinical trials are unsuccessful to date. Our previous work identified a related but distinct kinase known as MAPK13 that is activated in respiratory airway diseases and is required for mucus production in human cell-culture models. Support for MAPK13 function in these models came from effectiveness ofMAPK13versusMAPK14gene-knockdown and from first-generation MAPK13-14 inhibitors. However, these first-generation inhibitors were incompletely optimized for blocking activity and were untested in vivo. Here we report the next generation and selection of a potent MAPK13-14 inhibitor (designated NuP-3) that more effectively down-regulates type-2 cytokine-stimulated mucus production in air-liquid interface and organoid cultures of human airway epithelial cells. We also show that NuP-3 treatment prevents respiratory airway inflammation and mucus production in new minipig models of airway disease triggered by type-2 cytokine challenge or respiratory viral infection. The results thereby provide the next advance in developing a small-molecule kinase inhibitor to address key features of respiratory disease.New and noteworthyThis study describes the discovery of a potent MAPK13-14 inhibitor and its effectiveness in models of respiratory airway disease. The findings thereby provide a scheme for pathogenesis and therapy of lung diseases (e.g., asthma, COPD, Covid-19, post-viral and allergic respiratory disease) and related conditions that implicate MAPK13-14 function. The findings also refine a hypothesis for epithelial and immune cell functions in respiratory disease that features MAPK13 as a possible component of this disease process.
TGF-β1 activates neutrophil signaling and gene expression but not migration
Authors: Hein Lauren E. , SenGupta Shuvasree , Gunasekaran Gaurie , Johnson Craig , Parent Carole A. 
Published: May 2023

AbstractTumor-associated neutrophils are found in many types of cancer and are often reported to contribute to negative outcomes. The presence of transforming growth factor-beta (TGF-β) in the tumor microenvironment reportedly contributes to the skewing of neutrophils to a more pro-tumor phenotype. The effects of TGF-β on neutrophil signaling and migration are, however, unclear. We sought to characterize TGF-β signaling in both primary human neutrophils and the neutrophil-like cell line HL-60 and determine whether it directly induces neutrophil migration. We found that TGF-β1 does not induce neutrophil chemotaxis in transwell or underagarose migration assays. TGF-β1 does activate canonical signaling through SMAD3 and noncanonical signaling through ERK1/2 in neutrophils in a time-and dose-dependent manner. Additionally, TGF-β1 present in the tumor-conditioned media (TCM) of invasive breast cancer cells results in SMAD3 activation. We discovered that TCM induces neutrophils to secrete leukotriene B4(LTB4), which is a lipid mediator important for amplifying the range of neutrophil recruitment. However, TGF-β1 alone does not induce secretion of LTB4. RNA-sequencing revealed that TGF-β1 and TCM alter gene expression in HL-60 cells, including the mRNA levels of the pro-tumor oncostatin M (OSM) and vascular endothelial growth factor A (VEGFA). These new insights into the role and impact of TGF-β1 on neutrophil signaling, migration, and gene expression have significant implications in the understanding of the changes in neutrophils that occur in the tumor microenvironment.
ATR kinase supports normal proliferation in the early S phase by preventing replication resource exhaustion
Authors: Menolfi Demis , Lee Brian J. , Zhang Hanwen , Jiang Wenxia , Bowen Nicole E. , Wang Yunyue , Zhao Junfei , Holmes Antony , Gershik Steven , Rabadan Raul , Kim Baek , Zha Shan 
Published: May 2023

AbstractThe ATR kinase, which coordinates cellular responses to DNA replication stress, is also essential for the proliferation of normal unstressed cells. Although its role in the replication stress response is well defined, the mechanisms by which ATR supports normal cell proliferation remain elusive. Here, we show that ATR is dispensable for the viability of G0-arrested naïve B cells. However, upon cytokine-induced proliferation, Atr-deficient B cells initiate DNA replication efficiently in early S phase, but by mid-S phase they display dNTP depletion, fork stalling, and replication failure. Nonetheless, productive DNA replication can be restored in Atr-deficient cells by pathways that suppress origin firing, such as downregulation of CDC7 and CDK1 kinase activities. Together, these findings indicate that ATR supports the proliferation of normal unstressed cells by tempering the pace of origin firing during the early S phase to avoid exhaustion of dNTPs and other replication factors.
Divergent evolution of sleep functions
Authors: Joyce Michaela , Falconio Federica A. , Blackhurst Laurence , Prieto-Godino Lucia , French Alice S. , Gilestro Giorgio F. 
Published: May 2023

AbstractMost living organisms have evolved to synchronize their biological activities with the earth’s rotation, a daily regulation of biology and behaviour controlled by an evolutionary conserved molecular machinery known as the circadian clock. For most animals, circadian mechanisms are meant to maximize their exposure to positive activities (e.g.:social interactions, mating, feeding – generally during the day) and minimize their exposure to peril (e.g.:predation, weather, darkness – generally during the night1). On top of circadian regulation, some behaviours also feature a second layer of homeostatic control acting as a fail-safe to ensure important activities are not ignored. Sleep is one of these behaviours: largely controlled by the circadian clock for its baseline appearance, it is at the same time modulated by a – poorly understood – homeostatic regulator ensuring animals obey their species-specific amount of daily sleep2. An evolutionary conserved homeostatic control is often considered the main evidence for a core biological function of sleep beyond the trivial one (that is: keeping us out of trouble by limiting our energy expenditure and exposure to danger3,4) and it is hypothesized that sleep evolved around this mysterious basic biological function. Here we characterize sleep regulation in a group of seven species of theDrosophilagenus at key evolutionary distances and representing a variety of ecological niche adaptations. We show that the spontaneous circadian-driven aspects of sleep are conserved among all species but the homeostatic regulation, unexpectedly, is not. We uncover differences in the behavioural, cell-biological and neuro-pharmacological aspects of sleep and suggest that, in Drosophilids, sleep primarily evolved to satisfy a circadian role, keeping animals immobile during dangerous hours of the day. The homeostatic functions of sleep evolved independently, in a species-specific fashion, and are not conserved.
Does stress make males? An experiment on the role of glucocorticoids in anuran sex reversal
Authors: Bókony Veronika , Kalina Csenge , Ujhegyi Nikolett , Mikó Zsanett , Lefler Kinga Katalin , Vili Nóra , Gál Zoltán , Gabor Caitlin R. , Hoffmann Orsolya Ivett 
Published: May 2023

AbstractEnvironmentally sensitive sex determination may help organisms adapt to environmental change but also makes them vulnerable to anthropogenic stressors, with diverse consequences for population dynamics and evolution. The mechanisms translating environmental stimuli to sex are controversial: although several fish experiments supported the mediator role of glucocorticoid hormones, results on some reptiles challenged it. We tested this hypothesis in amphibians by investigating the effect of corticosterone on sex determination in agile frogs (Rana dalmatina). This species is liable to environmental sex reversal whereby genetic females develop into phenotypic males. After exposing tadpoles during sex determination to waterborne corticosterone, the proportion of genetic females with testes or ovotestes increased from 11% to up to 32% at 3 out of 4 concentrations. These differences were not statistically significant except for the group treated with 10 nM corticosterone, and there was no monotonous dose-effect relationship. These findings suggest that corticosterone is unlikely to mediate sex reversal in frogs. Unexpectedly, animals originating from urban habitats had higher sex-reversal and corticosterone-release rates, reduced body mass and development speed, and lower survival compared to individuals collected from woodland habitats. Thus, anthropogenic environments may affect both sex and fitness, and the underlying mechanisms may vary across ectothermic vertebrates.
Elevated sleep need in a stress-resilientDrosophilaspecies
Authors: Yano Jessica , Nave Ceazar , Larratt Katherine , Honey Phia , Jingco Cassandra , Roberts Makayla , Trotter Damion , He Xin , Elezi Gazmend , Whitelegge Julian P. , Wasserman Sara , Donlea Jeffrey M. 
Published: May 2023

AbstractSleep is broadly conserved across the animal kingdom, but can vary widely between species. It is currently unclear which types of selective pressures and sleep regulatory mechanisms influence differences in sleep between species. The fruit flyDrosophila melanogasterhas become a successful model system for examining sleep regulation and function, but little is known about the sleep patterns and need for sleep in many related fly species. Here, we find thatDrosophila mojavensis, a fly species that has adapted to extreme desert environments, exhibits strong increases in sleep compared toD. melanogaster.Long-sleepingD. mojavensisshow intact sleep homeostasis, indicating that these flies carry an elevated need for sleep. In addition,D. mojavensisexhibit altered abundance or distribution of several sleep/wake related neuromodulators and neuropeptides that are consistent with their reduced locomotor activity, and increased sleep. Finally, we find that in a nutrient-deprived environment, the sleep responses of individualD. mojavensisare correlated with their survival time. Our results demonstrate thatD. mojavensisis a novel model for studying organisms with high sleep need, and for exploring sleep strategies that provide resilience in extreme environments.
Gene editing withoutex vivoculture evades genotoxicity in human hematopoietic stem cells
Authors: Zeng Jing , Nguyen My Anh , Liu Pengpeng , Ferreira da Silva Lucas , Lin Linda Y. , Justus David G. , Petri Karl , Clement Kendell , Porter Shaina N. , Verma Archana , Neri Nola R. , Rosanwo Tolulope , Ciuculescu Marioara-Felicia , Abriss Daniela , Mintzer Esther , Maitland Stacy A. , Demirci Selami , Tisdale John F. , Williams David A. , Zhu Lihua Julie , Pruett-Miller Shondra M. , Pinello Luca , Joung J. Keith , Pattanayak Vikram , Manis John P. , Armant Myriam , Pellin Danilo , Brendel Christian , Wolfe Scot A. , Bauer Daniel E. 
Published: May 2023

SUMMARYGene editing theBCL11Aerythroid enhancer is a validated approach to fetal hemoglobin (HbF) induction for β-hemoglobinopathy therapy, though heterogeneity in edit allele distribution and HbF response may impact its safety and efficacy. Here we compared combined CRISPR-Cas9 endonuclease editing of theBCL11A+58 and +55 enhancers with leading gene modification approaches under clinical investigation. We found that combined targeting of theBCL11A+58 and +55 enhancers with 3xNLS-SpCas9 and two sgRNAs resulted in superior HbF induction, including in engrafting erythroid cells from sickle cell disease (SCD) patient xenografts, attributable to simultaneous disruption of core half E-box/GATA motifs at both enhancers. We corroborated prior observations that double strand breaks (DSBs) could produce unintended on- target outcomes in hematopoietic stem and progenitor cells (HSPCs) such as long deletions and centromere-distal chromosome fragment loss. We show these unintended outcomes are a byproduct of cellular proliferation stimulated by ex vivo culture. Editing HSPCs without cytokine culture bypassed long deletion and micronuclei formation while preserving efficient on-target editing and engraftment function. These results indicate that nuclease editing of quiescent hematopoietic stem cells (HSCs) limits DSB genotoxicity while maintaining therapeutic potency and encourages efforts for in vivo delivery of nucleases to HSCs.