bluuebunny/crossref_metadata_2025 huggingface dataset:
Transcription promotes the restoration of chromatin following DNA replication
Authors: Bandau Susanne , Alvarez Vanesa , Jiang Hao , Graff Sarah , Sundaramoorthy Ramasubramanian , Toman Matt , Owen-Hughes Tom , Sidoli Simone , Lamond Angus , Alabert Constance
Published: April 2023

DNA replication results in the transient eviction of nucleosomes, RNAPII and transcription regulators. How chromatin organization is duplicated on the two daughter strands is a central question in epigenetics. In mammals, transcription restarts on newly replicated DNA within a couple of hours, promoting chromatin accessibility. However, the role of transcription in the restoration of other chromatin determinants following DNA replication remains unclear. Here we have monitored protein re-association to newly replicated DNA upon inhibition of transcription using iPOND coupled to quantitative mass spectrometry. We show that nucleosome assembly and the re-establishment of most histone modifications are uncoupled from transcription restart. However, upon transcription inhibition, the re-association of many proteins was altered, including ATP-dependent remodellers, transcription regulators, the histone variant H2A.Z, histone modifiers as well as the restoration of H3.3K36me2. Finally, transcription also provoked the recruitment of several DNA repair proteins, revealing that transcription promotes chromatin reestablishment post-replication but is also a potential source of genotoxic stress.
A chromosome scale genome assembly and evaluation of mtDNA variation in the willow leaf beetleChrysomela aeneicollis
Authors: Bracewell Ryan R. , Stillman Jonathon H. , Dahlhoff Elizabeth P. , Smeds Elliott , Chatla Kamalakar , Bachtrog Doris , Williams Caroline , Rank Nathan E.
Published: April 2023

The leaf beetleChrysomela aeneicollishas a broad geographic range across Western North America, but is restricted to cool habitats at high elevations along the west coast. Central California populations occur only at high altitudes (2900-3450 m) where they are limited by reduced oxygen supply and recent drought conditions that are associated with climate change. Here we report a chromosome-scale genome assembly alongside a complete mitochondrial genome, and characterize differences among mitochondrial genomes along a latitudinal gradient over which beetles show substantial population structure and adaptation to fluctuating temperatures. Our scaffolded genome assembly consists of 21 linkage groups; one of which we identified as the X chromosome based on female/male whole genome sequencing coverage and orthology withTribolium castaneum. We identified repetitive sequences in the genome and found them to be broadly distributed across all linkage groups. Using a reference transcriptome, we annotated a total of 12,586 protein coding genes. We also describe differences in putative secondary structures of mitochondrial RNA molecules, which may generate functional differences important in adaptation to harsh abiotic conditions. We document substitutions at mitochondrial tRNA molecules and substitutions and insertions in the 16S rRNA region that could affect intermolecular interactions with products from the nuclear genome. This first chromosome-level reference genome will enable genomic research in this important model organism for understanding the biological impacts of climate change on montane insects.
OpenABC Enables Flexible, Simplified, and Efficient GPU Accelerated Simulations of Biomolecular Condensates
Authors: Liu Shuming , Wang Cong , Latham Andrew , Ding Xinqiang , Zhang Bin
Published: April 2023

Biomolecular condensates are important structures in various cellular processes but are challenging to study using traditional experimental techniques. In silico simulations with residue-level coarse-grained models strike a balance between computational efficiency and chemical accuracy. They could offer valuable insights by connecting the emergent properties of these complex systems with molecular sequences. However, existing coarse-grained models often lack easy-to-follow tutorials and are implemented in software that is not optimal for condensate simulations. To address these issues, we introduce OpenABC, a software package that greatly simplifies the setup and execution of coarse-grained condensate simulations with multiple force fields using Python scripting. OpenABC seamlessly integrates with the OpenMM molecular dynamics engine, enabling efficient simulations with performances on a single GPU that rival the speed achieved by hundreds of CPUs. We also provide tools that convert coarse-grained configurations to all-atom structures for atomistic simulations. We anticipate that Open-ABC will significantly facilitate the adoption of in silico simulations by a broader community to investigate the structural and dynamical properties of condensates. Open-ABC is available athttps://github.com/ZhangGroup-MITChemistry/OpenABC
Identifying antisense oligonucleotides to disrupt small RNA regulated antibiotic resistance via a cell-free transcription-translation platform
Authors: Tsai Min Jen , Zambrano Raphael Angelo I. , Susas Jeremiah Lyn , Silva Lizette , Takahashi Melissa K.
Published: April 2023

Bacterial small RNAs (sRNAs) regulate many important physiological processes in cells including antibiotic resistance and virulence genes through base pairing interactions with mRNAs. Antisense oligonucleotides (ASOs) have great potential as therapeutics against bacterial pathogens by targeting sRNAs such as MicF, which regulates outer membrane protein OmpF expression and limits permeability of antibiotics. Here, we devise a cell-free transcription-translation (TX-TL) assay to identify ASO designs that sufficiently sequester MicF. ASOs were then ordered as peptide nucleic acids conjugated to cell-penetrating peptides (CPP-PNA) to allow for effective delivery into bacteria. Subsequent minimum inhibitory concentration (MIC) assays demonstrated that simultaneously targeting the regions of MicF responsible for sequestering the start codon and the Shine-Dalgarno sequence ofompFwith two different CPP-PNAs synergistically reduced the MIC for a set of antibiotics. This investigation offers a TX-TL based approach to identify novel therapeutic candidates to combat intrinsic sRNA-mediated antibiotic resistance mechanisms.
Genomic markers of drug resistance inMycobacterium tuberculosispopulations with minority variants
Authors: Zhang Xiaomei , Lam Connie , Martinez Elena , Sim Eby , Crighton Taryn , Marais Ben J , Sintchenko Vitali
Published: April 2023

Minority variants ofMycobacterium tuberculosisharbouring mutations conferring resistance can become dominant populations during tuberculosis (TB) treatment, leading to treatment failure. Our understanding of drug resistant within-host sub-populations and the frequency of resistance conferring mutations in minority variants remains limited.

M. tuberculosissequences recovered from liquid cultures of culture-confirmed TB cases notified between January 2017 and December 2021 in New South Wales, Australia were examined. Potential drug resistance conferring minority variants were identified using LoFreq, and mixed populations of differentM. tuberculosisstrains (≥100 SNPs apart) were examined using QuantTB.

A total of 1831 routinely sequencedM. tuberculosisstrains were included in the analysis. Drug resistance conferring minority variants were detected in 3.5% (65/1831) of sequenced cultures; 84.6% (55/65) had majority strains that were drug susceptible and 15.4% (10/65) had majority strains that were drug resistant. Minority variants with high confidence drug resistance conferring mutations were 1.5 times more common when the majority strains were drug resistant. MixedM. tuberculosisstrain populations were documented in 10.0% (183/1831) of specimens. Minority variants with high confidence drug resistance conferring mutations were more frequently detected in mixedM. tuberculosisstrain populations (2.7%, 5/183) than in single strain populations (0.6%, 10/1648; p=0.01).

Drug resistant minority variants require careful monitoring in settings that implement routineM. tuberculosissequencing. The frequency with which drug resistant minority variants are detected is influenced by selective culture methods and culture-independent sequencing should provide a more accurate picture.
Nuclear growth and import can be uncoupled
Authors: Chen Pan , Mishra Sampada , Levy Daniel L.
Published: April 2023

What drives nuclear growth? Studying nuclei assembled inXenopusegg extract and focusing on importin α/β–mediated nuclear import, we show that, while nuclear growth depends on nuclear import, nuclear growth and import can be uncoupled. Nuclei containing fragmented DNA grew slowly despite exhibiting normal import rates, suggesting nuclear import itself is insufficient to drive nuclear growth. Nuclei containing more DNA grew larger but imported more slowly. Altering chromatin modifications caused nuclei to grow less while still importing to the same extent or to grow larger without increasing nuclear import. Increasing heterochromatin in vivo in sea urchin embryos increased nuclear growth but not import. These data suggest that nuclear import is not the primary driving force for nuclear growth. Instead, live imaging showed that nuclear growth preferentially occurred at sites of high chromatin density and lamin addition, whereas small nuclei lacking DNA exhibited less lamin incorporation. Our hypothesized model is that lamin incorporation and nuclear growth are driven by chromatin mechanical properties, which depend on and can be tuned by nuclear import.
Contrasting walking styles map to discrete neural substrates in the mouse brainstem
Authors: Worley Audrey , Kirby Alana , Luks Sophie , Samardzic Tamara , Ellison Brian , Broom Lauren , Latremoliere Alban , VanderHorst Veronique G
Published: April 2023

Walking is a slow gait which is particularly adaptable to meet internal or external needs and is prone to maladaptive alterations that lead to gait disorders. Alterations can affect speed, but also style (the way one walks). While slowed speed may signify the presence of a problem, style represents the hallmark essential for clinical classification of gait disorders. However, it has been challenging to objectively capture key stylistic features while uncovering neural substrates driving these features. Here we revealed brainstem hotspots that drive strikingly different walking styles by employing an unbiased mapping assay that combines quantitative walking signatures with focal, cell type specific activation. We found that activation of inhibitory neurons that mapped to the ventromedial caudal pons induced slow motion-like style. Activation of excitatory neurons that mapped to the ventromedial upper medulla induced shuffle-like style. Contrasting shifts in walking signatures distinguished these styles. Activation of inhibitory and excitatory neurons outside these territories or of serotonergic neurons modulated walking speed, but without walking signature shifts. Consistent with their contrasting modulatory actions, hotspots for slow-motion and shuffle-like gaits preferentially innervated different substrates. These findings lay the basis for new avenues to study mechanisms underlying (mal)adaptive walking styles and gait disorders.

Graphical abstract
CRACD suppresses neuroendocrinal plasticity of lung adenocarcinoma
Authors: Kim Bongjun , Zhang Shengzhe , Huang Yuanjian , Ko Kyung-Pil , Zou Gengyi , Zhang Jie , Jun Sohee , Kim Kee-Beom , Jung Youn-Sang , Park Kwon-Sik , Park Jae-Il
Published: April 2023

Tumor cell plasticity contributes to intratumoral heterogeneity and therapy resistance. Through cell plasticity, lung adenocarcinoma (LUAD) cells transform into neuroendocrinal (NE) tumor cells. However, the mechanisms of NE cell plasticity remain unclear. CRACD, a capping protein inhibitor, is frequently inactivated in cancers.CRACDknock-out (KO) de-represses NE-related gene expression in the pulmonary epithelium and LUAD cells. In LUAD mouse models,CracdKO increases intratumoral heterogeneity with NE gene expression. Single-cell transcriptomic analysis showed thatCracdKO-induced NE plasticity is associated with cell de-differentiation and activated stemness-related pathways. The single-cell transcriptomes of LUAD patient tumors recapitulate that the distinct LUAD NE cell cluster expressing NE genes is co-enriched with SOX2, OCT4, and NANOG pathway activation, and impaired actin remodeling. This study reveals an unexpected role of CRACD in restricting NE cell plasticity that induces cell de-differentiation, providing new insights into cell plasticity of LUAD.
A millisecond coarse-grained simulation approach to decipher allosteric cannabinoid binding at the glycine receptorα1
Authors: Bartocci Alessio , Grazzi Andrea , Awad Nour , Corringer Pierre-Jean , Souza Paulo C.T. , Cecchini Marco
Published: April 2023

Glycine receptors (GlyR) are regulated by small-molecule binding at several allosteric sites. Cannabinoids like tetrahydrocannabinol (THC) and N-arachidonyl-ethanol-amide (AEA) potentiate GlyR but their mechanism of action is not fully established. By combining millisecond coarse-grained MD simulations powered by Martini 3 with backmapping to all-atom representations, we characterize the cannabinoid-binding sites at zebrafish GlyR-α1 with atomic resolution. Based on hundreds of thousand ligand-binding events, we find that cannabinoids bind to the transmembrane domain of the receptor at both intrasubunit and intersubunit sites. For THC, the intrasubunit binding mode predicted in simulation is in excellent agreement with recent cryo-EM structures, while intersubunit binding recapitulates in full previous mutagenesis experiments. Intriguingly, AEA is predicted to bind at the same intersubunit site despite the strikingly different chemistry. Statistical analyses of the receptor-ligand interactions highlight potentially relevant residues for GlyR potentiation, offering experimentally testable predictions. The predictions for AEA are validated by electrophysiology recordings of rationally designed mutants. The results highlight the existence of multiple cannabinoid-binding sites for the allosteric regulation of GlyR and put forward an effective strategy for the identification and structural characterization of allosteric sites in transmembrane proteins.
The ATP-exporting channel Pannexin-1 promotes CD8+T cell effector and memory responses
Authors: Vardam-Kaur Trupti , Banuelos Alma , Gabaldon-Parish Maria , Macedo Bruna Gois , Salgado Caio Loureiro , Wanhainen Kelsey Marie , Zhou Maggie Hanqi , van Dijk Sarah , Santiago-Carvalho Igor , Beniwal Angad S. , Leff Chloe L. , Peng Changwei , Tran Nhan L. , Jameson Stephen C. , Borges da Silva Henrique
Published: April 2023

Sensing of extracellular ATP (eATP) controls CD8+T cell function. Their accumulation can occur through export by specialized molecules, such as the release channel Pannexin-1 (Panx1). Whether Panx1 controls CD8+T cell immune responsesin vivo, however, has not been previously addressed. Here, we report that T cell-specific Panx1 is needed for CD8+T cell responses to viral infections and cancer. We found that CD8-specific Panx1 promotes both effector and memory CD8+T cell responses. Panx1 favors initial effector CD8+T cell activation through extracellular ATP (eATP) export and subsequent P2RX4 activation, which helps promote full effector differentiation through extracellular lactate accumulation and its subsequent recycling. In contrast, Panx1 promotes memory CD8+T cell survival primarily through ATP export and subsequent P2RX7 engagement, leading to improved mitochondrial metabolism. In summary, Panx1-mediated eATP export regulates effector and memory CD8+T cells through distinct purinergic receptors and different metabolic and signaling pathways.
Pharmacological Induction of mesenchymal-epithelial transition chemosensitizes breast cancer cells and prevents metastatic progression
Authors: Bagheri Meisam , Mohamed Gadisti Aisha , Ashick Mohammed , Saleem Mohamed , Ognjenovic Nevena B. , Lu Hanxu , Kolling Fred W. , Wilkins Owen M. , Das Subhadeep , Croix Ian S. La , Nagaraj Shivashankar H. , Muller Kristen E. , Gerber Scott A. , Miller Todd W. , Pattabiraman Diwakar R.
Published: April 2023

The epithelial-mesenchymal transition (EMT) is a developmental program co-opted by tumor cells that aids the initiation of the metastatic cascade. Tumor cells that undergo EMT are relatively chemoresistant, and there are currently no therapeutic avenues specifically targeting cells that have acquired mesenchymal traits. We show that treatment of mesenchymal-like triple-negative breast cancer (TNBC) cells with the microtubule-destabilizing chemotherapeutic eribulin, which is FDA-approved for the treatment of advanced breast cancer, leads to a mesenchymal-epithelial transition (MET). This MET is accompanied by loss of metastatic propensity and sensitization to subsequent treatment with other FDA-approved chemotherapeutics. We uncover a novel epigenetic mechanism of action that supports eribulin pretreatment as a path to MET induction that curtails metastatic progression and the evolution of therapy resistance.

While the advent of targeted therapy has led to vast improvements in outcomes for certain types of breast cancer, a mainstay for triple-negative breast cancer (TNBC) remains cytotoxic chemotherapy. A major clinical hurdle in successfully managing this disease is the eventual development of therapeutic resistance and disease relapse in more aggressive forms. Our data reveal that epigenetic modulation of EMT state using the FDA-approved therapeutic eribulin curtails metastatic propensity of breast tumors and, when administered in the treatment-naïve setting, sensitizes to subsequent treatment with other chemotherapeutics.
Individual vocal recognition in the black-headed spider monkey (Ateles fusciceps)
Authors: Nagle D. , Power T. , Quinn J. L. , Troisi C. A.
Published: April 2023

Individual vocal recognition – the ability to discriminate between individuals based on sound – is thought to be particularly useful for social species that regularly lose visual contact between group members. For instance, individuals living in a fission-fusion group that feed on patchily distributed food in a complex physical environment (e.g., dense forest) are likely to depend heavily on vocalisation to identify individuals that are good at finding food. Spider monkeys (Ateles spp.) live in such environments and have distinctive individual contact calls (whinnies). We used a habituation-dishabituation playback-paradigm to investigate whether black-headed spider monkeys (A. fusciceps) are able to discriminate between female individuals in their group. We found that a group of captive spider monkeys was able to discriminate between individuals using those contact calls. Although many primate species have been found to have individual characteristics in their calls, this is one of the few direct experimental evidence of vocal recognition using a habituation-dishabituation paradigm.
Mapping rhodopsin trafficking in rod photoreceptors with quantitative super-resolution microscopy
Authors: Haggerty Kristen N. , Eshelman Shannon C. , Sexton Lauren A. , Frimpong Emmanuel , Rogers Leah M. , Agosto Melina A. , Robichaux Michael A.
Published: April 2023

Photoreceptor cells in the vertebrate retina have a highly compartmentalized morphology for efficient long-term phototransduction. Rhodopsin, the visual pigment in rod photoreceptors, is densely packaged into the rod outer segment sensory cilium and continuously renewed through essential synthesis and trafficking pathways housed in the rod inner segment. Despite the importance of this region for rod health and maintenance, the subcellular organization of rhodopsin and its trafficking regulators in the mammalian rod inner segment remain undefined. We used super-resolution fluorescence microscopy with optimized retinal immunolabeling techniques to perform a single molecule localization analysis of rhodopsin in the inner segments of mouse rods. We found that a significant fraction of rhodopsin molecules was localized at the plasma membrane in an even distribution along the entire length of the inner segment, where markers of transport vesicles also colocalized. Thus, our results collectively establish a model of rhodopsin trafficking through the inner segment plasma membrane as an essential subcellular pathway in mouse rod photoreceptors.

Photoreceptor cells of the retina are maintained through a complex protein trafficking network. This study applies quantitative super-resolution microscopy to uncover localization details about the trafficking of the essential visual pigment rhodopsin in the inner segment region of rod photoreceptors.
A multi-scale digital twin for adiposity-driven insulin resistance in humans: diet and drug effects
Authors: Herrgårdh Tilda , Simonsson Christian , Ekstedt Mattias , Lundberg Peter , Stenkula Karin G. , Nyman Elin , Gennemark Peter , Cedersund Gunnar
Published: April 2023

Aims

The increased prevalence of insulin resistance is one of the major health risks in society today. Insulin resistance involves both short-term dynamics, such as altered meal responses, and long-term dynamics, such as development of type 2 diabetes. Insulin resistance also occurs on different physiological levels, ranging from disease phenotypes to organ-organ communication and intracellular signaling. To better understand the progression of insulin resistance, an analysis method is needed that can combine different timescales and physiological levels. One such method is digital twins, consisting of combined mechanistic multi-scale and multi-level mathematical models. We have previously developed a multi-level model for short-term glucose homeostasis and intracellular insulin signaling, and there exists long-term weight regulation models. However, no one has combined these kinds of models into an interconnected, multi-level and multi-timescale digital twin model. Herein, we present a first such multi-scale digital twin for the progression of insulin resistance in humans.

Methods

The model is based on ordinary differential equations representing biochemical and physiological processes, in which unknown parameters were fitted to data using a MATLAB toolbox.

Results

The connected twin correctly predicts independent data from a weight increase study, both for weight-changes, for fasting plasma insulin and glucose levels, as well as for intracellular insulin signaling. Similarly, the model can predict independent weight-change data in a weight loss study, involving diet and the weight loss drug topiramate. These independent validation tests are confirmed by a chi-square test (𝑉(𝜃) = 4.8 < 21 = 𝜒2𝑐𝑢𝑚,𝑖𝑛𝑣(12,0.05)). In both these cases, the model can also predict non-measured variables, such as activity of intracellular intermediaries, glucose tolerance responses, and organ fluxes.

Conclusions

We present a first multi-level and multi-timescale model, describing dynamics on the whole-body, organ and cellular levels, ranging from minutes to years. This model constitutes the basis for a new digital twin technology, which in the future could potentially be used to aid medical pedagogics and increase motivation and compliance and thus aid in prevention and treatment of insulin resistance.
Dosimetric and biologic intercomparison between electron and proton FLASH beams
Authors: Almeida A , Togno M , Ballesteros-Zebadua P , Franco-Perez J , Geyer R , Schaefer R , Petit B , Grilj V , Meer D , Safai S , Lomax T , Weber DC , Bailat C , Psoroulas S , Vozenin MC
Published: April 2023

Background and purpose

The FLASH effect has been validated in different preclinical experiments with electrons (eFLASH) and protons (pFLASH) operating at a mean dose rate above 40 Gy/s. However, no systematic intercomparison of the FLASH effect produced by evs. pFLASH has yet been performed and constitutes the aim of the present study.

Materials and methods

The electron eRT6/Oriatron/CHUV/5.5 MeV and proton Gantry1/PSI/170 MeV were used to deliver conventional (0.1 Gy/s eCONV and pCONV) and FLASH (≥100 Gy/s eFLASH and pFLASH) irradiation. Protons were delivered in transmission. Dosimetric and biologic intercomparisons were performed with previously validated models.

Results

Doses measured at Gantry1 were in agreement (± 2.5%) with reference dosimeters calibrated at CHUV/IRA. The neurocognitive capacity of e and pFLASH irradiated mice was indistinguishable from the control while both e and pCONV irradiated cohorts showed cognitive decrements. Complete tumor response was obtained with the two beams and was similar between e and pFLASHvs. e and pCONV. Tumor rejection was similar indicating that T-cell memory response is beam-type and dose-rate independent.

Conclusion

Despite major differences in the temporal microstructure, this study shows that dosimetric standards can be established. The sparing of brain function and tumor control produced by the two beams were similar, suggesting that the most important physical parameter driving the FLASH effect is the overall time of exposure which should be in the range of hundreds of milliseconds for WBI in mice. In addition, we observed that immunological memory response is similar between electron and proton beams and is independent off the dose rate.
Tuning social interactions’ strength drives collective response to light intensity in schooling fish
Authors: Xue Tingting , Li Xu , Lin GuoZheng , Escobedo Ramón , Han Zhangang , Chen Xiaosong , Sire Clément , Theraulaz Guy
Published: April 2023

Schooling fish heavily rely on visual cues to interact with neighbors and avoid obstacles. The availability of sensory information is influenced by environmental conditions and changes in the physical environment that can alter the sensory environment of the fish, which in turn affects individual and group movements. In this study, we combine experiments and data-driven modeling to investigate the impact of varying levels of light intensity on social interactions and collective behavior in rummy-nose tetra fish. The trajectories of single fish and groups of fish swimming in a tank under different lighting conditions were analyzed to quantify their movements and spatial distribution. Interaction functions between two individuals and the fish interaction with the tank wall were reconstructed and modeled for each light condition. Our results demonstrate that light intensity strongly modulates social interactions between fish and their reactions to obstacles, which then impact collective motion patterns that emerge at the group level.
Key common genes and pathways in ulcerative colitis and ankylosing spondylitis based on bioinformatics analysis
Authors: Li Lin , Li Fuzhen , Xie Kunpeng , Zhou Pengyi , Zhu Haiyan , Du Liping , Yang Peizeng , Jin Xuemin
Published: April 2023

Associations between ulcerative colitis (UC) and ankylosing spondylitis (AS) have been observed in multiple studies, but the common etiology of UC and AS remain unknown. Thus, the current research was conducted to investigate the shared genes and relevant mechanisms in UC and AS. GSE87466 and GSE25101 datasets were used to identify DEGs involved in UC and AS, respectively. The clusterProfiler R package was utilized to detect the biological processes of DEGs in UC and AS. The performance of common DEGs in distinguishing UC or AS samples from control ones were evaluated by ROC curves. The miRWalk, Cistrome and TransmiR database were utilized to construct the network of TF-miRNA-diagnostic biomarker. GSEA method and CTD database were used to investigate the common KEGG pathways shared by UC and AS. In addition, CTD database was also used to detect the interaction score between diagnostic biomarkers and diseases associated with UC or AS. Moreover, prospective diagnostic biomarker-targeting drugs were identified using the DGIdb database. A total of 20 common DEGs were obtained by analyzing data in GSE97466 and GSE25101 datasets. ROC curves revealed that GMFG, GNG11, CLEC4D, CMTM2, VAMP5, S100A8, S100A12 and DGKQ may serve as diagnostic biomarkers for the individuals with AS and UC. A network of TF-miRNA-diagnostic biomarker, composed of 212 nodes and 721 edges, was constructed and visualized by Cytoscape software. Toll-like receptor signaling pathway, antigen processing and presentation, allograft rejection, viral myocarditis, pathways in cancer, graft versus host disease and natural killer cell mediated cytotoxicity were identified as common pathways in UC and AS. For the first time, our study identified 8 common key genes and 7 common pathways in UC and AS. These findings may help to clarify the relationship between UC and AS, and provide guidance in the diagnosis and treatment of UC and AS patients.

Author Summary

Ankylosing spondylitis (AS) and Ulcerative colitis (UC) are two types of autoimmune diseases that often co-occur. The simultaneous onset of both diseases often results in severe clinical manifestations and limited therapeutic efficacy. So there is an urgent need to gain a deeper understanding of the causes of UC and AS in order to develop more effective treatment strategies. In this study, we explored the genes and pathways commonly involved in two diseases, constructed a transcriptional network, and further investigated potential drugs. The discoveries could potentially offer insights into the connection between UC and AS, and assist in identifying and managing patients with UC and AS.
Ulk4 promotes Shh signaling by regulating Stk36 ciliary localization and Gli2 phosphorylation
Authors: Zhou Mengmeng , Han Yuhong , Jiang Jin
Published: April 2023

The Hedgehog (Hh) family of secreted proteins governs embryonic development and adult tissue homeostasis through the Gli family of transcription factors. Gli is thought to be activated at the tip of primary cilium, but the underlying mechanism has remained poorly understood. Here, we show thatUnc-51-likekinase 4 (Ulk4), a pseudokinase and a member of the Ulk kinase family, acts in conjunction with another Ulk family member Stk36 to promote Gli2 phosphorylation and Hh pathway activation. Ulk4 interacts with Stk36 through its N-terminal region containing the pseudokinase domain and Gli2 via its regulatory domain to bridge the kinase and substrate. Although dispensable for Hh-induced Stk36 kinase activation, Ulk4 is essential for Stk36 ciliary tip localization, Gli2 phosphorylation and activation. In response to Hh, both Ulk4 and Stk36 colocalize with Gli2 at ciliary tip, and Ulk4 and Stk36 depend on each other for their ciliary tip accumulation. We further show that ciliary localization of Ulk4 depends on Stk36 kinase activity and phosphorylation of Ulk4 on Thr1023, and that ciliary tip accumulation of Ulk4 is essential for its function in the Hh pathway. Taken together, our results suggest that Ulk4 regulates Hh signaling by promoting Stk36-mediated Gli2 phosphorylation and activation at ciliary tip.
Single-cell temporal dynamics reveals the relative contributions of transcription and degradation to cell-type specific gene expression in zebrafish embryos
Authors: Fishman Lior , Nechooshtan Gal , Erhard Florian , Regev Aviv , Farrell Jeffrey A. , Rabani Michal
Published: April 2023

Abstract

During embryonic development, pluripotent cells assume specialized identities by adopting particular gene expression profiles. However, systematically dissecting the underlying regulation of mRNA transcription and degradation remains a challenge, especially within whole embryos with diverse cellular identities. Here, we collect temporal cellular transcriptomes of zebrafish embryos, and decompose them into their newly-transcribed (zygotic) and pre-existing (maternal) mRNA components by combining single-cell RNA-Seq and metabolic labeling. We introduce kinetic models capable of quantifying regulatory rates of mRNA transcription and degradation within individual cell types during their specification. These reveal different regulatory rates between thousands of genes, and sometimes between cell types, that shape spatio-temporal expression patterns. Transcription drives most cell-type restricted gene expression. However, selective retention of maternal transcripts helps to define the gene expression profiles of germ cells and enveloping layer cells, two of the earliest specified cell-types. Coordination between transcription and degradation restricts expression of maternal-zygotic genes to specific cell types or times, and allows the emergence of spatio-temporal patterns when overall mRNA levels are held relatively constant. Sequence-based analysis links differences in degradation to specific sequence motifs. Our study reveals mRNA transcription and degradation events that control embryonic gene expression, and provides a quantitative approach to study mRNA regulation during a dynamic spatio-temporal response.
Dynamic calcium-mediated stress response and recovery signatures in the fungal pathogen,Candida albicans
Authors: Giuraniuc CV , Parkin C , Almeida MC , Fricker M , Shadmani P , Nye S , Wehmeier S , Chawla S , Bedekovic T , Lehtovirta-Morley L , Richards D , Gow NA , Brand AC
Published: April 2023

Calcium (Ca2+) is an important second messenger for activating stress response signalling and cell adaptation in eukaryotic cells yet intracellular Ca2+-dynamics in fungi is poorly understood due to lack of effective real-time Ca2+reporters. We engineered the GCaMP6f construct for use in the fungal pathogen,Candida albicans, and used live-cell imaging to observe dynamic Ca2+spiking as well as slower changes in ambient Ca2+-GCaMP levels elicited by stress or gene deletion. Short-term exposure to membrane, osmotic or oxidative stress generated immediate stress-specific responses and repeated exposure revealed differential recovery signatures. Osmotic stress caused yeast cell shrinkage and no adaptation response, where Ca2+-GCaMP spiking was inhibited by 1 M NaCl but not by 0.66 M CaCl2.Treatment with SDS caused a spike-burst, raised ambient Ca2+-GCaMP levels and significant cell death, but surviving cells adapted over subsequent exposures. Treatment with 5 mM H2O2abolished spiking and caused transient autofluorescence but cells adapted such that spiking returned and autofluorescence diminished on repeated exposure. Adaptation to H2O2was dependent on Cap1, extracellular Ca2+and calcineurin, but not on its downstream target, Crz1. Ca2+-dynamics were not affected by H2O2in thehog1Δ oryvc1Δ mutants, suggesting a pre-adapted, resistant state, possibly due to changes in membrane permeability. Live-cell imaging of Ca2+-GCaMP responses in individual cells has therefore revealed the dynamics of Ca2+-influx, signalling and homeostasis and their role in the temporal stress response signatures ofC. albicans.
Nanoparticle Enrichment Mass-Spectrometry Proteomics Identifies Protein Altering Variants for Precise pQTL Mapping
Authors: Suhre Karsten , Venkataraman Guhan Ram , Guturu Harendra , Halama Anna , Stephan Nisha , Thareja Gaurav , Sarwath Hina , Motamedchaboki Khatereh , Donovan Margaret , Siddiqui Asim , Batzoglou Serafim , Schmidt Frank
Published: April 2023

Genome-wide association studies (GWAS) with proteomics generate hypotheses on protein function and offer genetic evidence for drug target prioritization. Although most protein quantitative loci (pQTLs) have so far been identified by high-throughput affinity proteomics platforms, these methods also have some limitations, such as uncertainty about target identity, non-specific binding of aptamers, and inability to handle epitope-modifying variants that affect affinity binding. Mass spectrometry (MS) proteomics has the potential to overcome these challenges and broaden the scope of pQTL studies. Here, we employ the recently developed MS-based Proteograph™ workflow (Seer, Inc.) to quantify over 18,000 unique peptides from almost 3,000 proteins in more than 320 blood samples from a multi-ethnic cohort. We implement a bottom-up MS-proteomics approach for the detection and quantification of blood-circulating proteins in the presence of protein altering variants (PAVs). We identify 184 PAVs located in 137 genes that are significantly associated with their corresponding variant peptides in MS data (MS-PAVs). Half of these MS-PAVs (94) overlap withcis-pQTLs previously identified by affinity proteomics pQTL studies, thus confirming the target specificity of the affinity binders. An additional 54 MS-PAVs overlap withtrans-pQTLs (and notcis-pQTLs) in affinity proteomics studies, thus identifying the putatively causalcis-encoded protein and providing experimental evidence for its presence in blood. The remaining 36 MS-PAVs have not been previously reported and include proteins that may be inaccessible to affinity proteomics, such as a variant in the incretin pro-peptide (GIP) that associates with type 2 diabetes and cardiovascular disease. Overall, our study introduces a novel approach for analyzing MS-based proteomics data within the GWAS context, provides new insights relevant to genetics-based drug discovery, and highlights the potential of MS-proteomics technologies when applied at population scale.

Highlights

This is the first pQTL study that uses the Proteograph™(Seer Inc.) mass spectrometry-based proteomics workflow.

We introduce a novel bottom-up proteomics approach that accounts for protein altering variants in the detection of pQTLs.

We confirm the target and potential epitope effects of affinity binders forcis-pQTLs from affinity proteomics studies.

We establish putatively causal proteins for known affinity proteomicstrans-pQTLs and confirm their presence in blood.

We identify novel protein altering variants in proteins of clinical relevance that may not be accessible to affinity proteomics.

Graphical abstract
Neural patterns of conscious visual awareness in the Riddoch syndrome
Authors: Beyh Ahmad , Rasche Samuel E , Leff Alexander , ffytche Dominic , Zeki Semir
Published: April 2023

The Riddoch syndrome is one in which patients blinded by lesions to their primary visual cortex can consciously perceive visual motion in their blind field, an ability that correlates with activity in motion area V5. Our assessment of the characteristics of this syndrome in patient ST, using multimodal MRI, showed that: 1. ST’s V5 is intact, receives direct subcortical input, and decodable neural patterns emerge in it only during the conscious perception of visual motion; 2. moving stimuli activate medial visual areas but, unless associated with decodable V5 activity, they remain unperceived; 3. ST’s high confidence ratings when discriminating motion at chance levels, is associated with inferior frontal gyrus activity. Finally, we report that ST’s Riddoch Syndrome results in hallucinatory motion with hippocampal activity as a correlate. Our results shed new light on perceptual experiences associated with this syndrome and on the neural determinants of conscious visual experience.
Bayesian inference of spike-timing dependent plasticity learning rules from single neuron recordings in humans
Authors: Hem Ingeborg , Ledergerber Debora , Battistin Claudia , Dunn Benjamin
Published: April 2023

Spike-timing dependent plasticity (STDP) learning rules are popular in both neuroscience and artificial neural networks due to their ability to capture the change in neural connections arising from the correlated activity of neurons. Recent technological advances have made large neural recordings common, substantially increasing the probability that two connected neurons are simultaneously observed, which we can use to infer functional connectivity and associated learning rules. We use a Bayesian framework and assume neural spike recordings follow a binary data model to infer the connections and their evolution over time from data using STDP rules. We test the resulting method on simulated and real data, where the real case study consists of human electrophysiological recordings. The simulated case study allows validation of the model, and the real case study shows that we are able to infer learning rules from awake human data.
Metabolic Reprogramming via targeting ACOD1 promotes polarization and anti-tumor activity of human CAR-iMACs in solid tumors
Authors: Wang Xudong , Su Siyu , Zhu Yuqing , Cheng Xiaolong , Cheng Chen , Chen Leilei , Lei Anhua , Zhang Li , Xu Yuyan , Li Wei , Zhang Yi , Ye Dan , Zhang Jin
Published: April 2023

The pro-inflammatory state of macrophages is crucial in conferring its role in combating tumor cells. That state is closely associated with metabolic reprogramming. Here we identified key metabolic genes regulating macrophage pro-inflammatory activation in a pooled metabolic gene knockout CRISPR screen. We found thatKEAP1 andACOD1are strong regulators of the pro-inflammatory state, and therefore developed humanACOD1knockout macrophages with our induced pluripotent stem cell-derived CAR-macrophage (CAR-iMAC) platform. The engineered iMACs showed stronger and more persistent polarization toward the pro-inflammatory state, more ROS production, and more potent phagocytosis and cytotoxic functions against cancer cellsin vitro. Upon transplantation to ovarian or pancreatic cancer mouse models,ACOD1depleted CAR-iMACs exhibited enhanced capacity in repressing tumorsin vivoand prolonged the lifespan of mice. In addition, combiningACOD1-depleted CAR-iMACs with immune check point inhibitors (ICIs), such as the anti-CD47 antibody or anti-PD1 antibody resulted in stronger tumor suppressing effect. Mechanistically, the depletion of ACOD1 reduced the immunometabolite itaconate, allowing KEAP1 to prevent NRF2 from entering the nucleus to activate the anti-inflammatory program. This study demonstrates that ACOD1 is a new myeloid target for cancer immunotherapy and metabolically engineered human iPSC-derived CAR-iMACs exhibit enhanced polarization and anti-tumor functions in adoptive cell transfer therapies.
Early-life stress exposure impacts the hippocampal synaptic proteome in a mouse model of Alzheimer’s disease: age- and pathology-dependent effects on mitochondrial proteins
Authors: Kotah Janssen M. , Kater Mandy S.J. , Hoeijmakers Lianne , Brosens Niek , Lesuis Sylvie L. , Tandari Roberta , Marchetto Luca , Yusaf Ella , Smit August B. , Lucassen Paul J. , Krugers Harm , Verheijen Mark H.G. , Korosi Aniko
Published: April 2023

Epidemiological evidence indicates that early life stress (ES) exposure increases the risk for later-life diseases, such as Alzheimer’s disease (AD). Accordingly, we and others have shown that ES aggravates the development of, and response to, amyloid-beta (Aβ) pathology in animal models. Moreover, ES-exposed transgenic APP/PS1 mice display deficits in both cognitive flexibility and synaptic function. As the mechanisms behind these changes were unclear, we here investigated how exposure to ES, using the limited nesting and bedding model, affects the synaptic proteome across 2 different ages in both wildtype and APP/PS1 transgenic mice.

We found that, compared to wildtype mice, the hippocampal synaptosomes of APP/PS1 mice at an early pathological stage (4 months) showed a higher abundance of mitochondrial proteins and lower levels of proteins involved in actin dynamics. Interestingly, ES exposure in wildtype mice had similar effects on the level of mitochondrial and actin-related synaptosomal proteins at this age, whereas ES exposure had no additional effect on the synaptosomal proteome of early-stage APP/PS1 mice. Accordingly, ultrastructural analysis of the synapse using electron microscopy in a follow-up cohort showed fewer mitochondria in pre- and post-synaptic compartments of APP/PS1 and ES-exposed mice, respectively.

At a later pathological stage (10 months), the hippocampal synaptic proteome of APP/PS1 mice revealed an upregulation of proteins related to Aβ processing, that was accompanied by a downregulation of proteins related to postsynaptic receptor endocytosis. ES exposure no longer affected the synaptic proteome of wildtype animals by this age, whereas it affected the expression of astrocytic proteins involved in lipid metabolism in APP/PS1 mice. We confirmed a dysregulation of astrocyte protein expression in a separate cohort of 12-month-old mice, by immunostaining for the alpha subunit of the mitochondrial trifunctional protein and fatty acid synthase in astrocytes.

In conclusion, our data suggest that ES and amyloidosis share pathogenic pathways involving synaptic mitochondrial dysfunction and astrocytic lipid metabolism. These pathways might be underlying contributors to the long-term aggravation of the APP/PS1 phenotype by ES, as well as to the ES-associated risk for AD progression.

These data are publicly accessible online as a web app viahttps://amsterdamstudygroup.shinyapps.io/ES_Synaptosome_Proteomics_Visualizer/.
Altered X-chromosome inactivation predisposes to autoimmunity
Authors: Huret Christophe , Férrayé Léa , David Antoine , Mohamed Myriame , Valentin Nicolas , Charlotte Frédéric , Savignac Magali , Goodhardt Michele , Guéry Jean-Charles , Rougeulle Claire , Morey Céline
Published: April 2023

In mammals, males and females show marked differences in immune responses. Males are globally more sensitive to infectious diseases while females are more susceptible to systemic autoimmunity. X-chromosome inactivation (XCI), the epigenetic mechanism that ensures the silencing of one X in females, may participate in these sex-biases. Here, we perturbed the expression of the trigger of XCI, the non-coding RNAXist,in female mice. This resulted in reactivation of genes on the inactive X, including members of the Toll-like receptor 7 (TLR7) signalling pathway, in monocyte/macrophages, dendritic and B cells. Consequently, female mice spontaneously developed inflammatory signs typical of lupus, including anti-nucleic acid autoantibodies, increased frequencies of age-associated and germinal centre B cells and expansion of monocyte/macrophages and dendritic cells. Mechanistically, TLR7 signalling is dysregulated in macrophages, which leads to sustained expression of target genes upon stimulation. These findings provide a direct link between maintenance of XCI and female-biased autoimmune manifestations and highlight altered XCI as a cause of autoimmunity.

Teaser

The reason why autoimmunity mostly affects women is unclear. Here, we show that aberrant expression of genes on the X induces signs of lupus in female mice.