bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fibroblast-induced mammary epithelial branching depends on fibroblast contractility
Authors: Sumbal Jakub , Fre Silvia , Koledova Zuzana Sumbalova 
Published: March 2023

AbstractEpithelial branching morphogenesis is an essential process in living organisms, through which organ-specific epithelial shapes are created. Interactions between epithelial cells and their stromal microenvironment instruct branching morphogenesis but remain incompletely understood. Here we employed fibroblast-organoid or fibroblast-spheroid co-culture systems and time-lapse imaging to reveal that physical contact between fibroblasts and epithelial cells and fibroblast contractility are required to induce mammary epithelial branching. Pharmacological inhibition of ROCK or non-muscle myosin II, or fibroblast-specific knock-out ofMyh9abrogate fibroblast-induced epithelial branching. Furthermore, fibroblast-induced branching requires epithelial proliferation and is associated with distinctive epithelial patterning of YAP and ERK activity along organoid branches, which is dependent on fibroblast contractility. Together, we identify fibroblast contractility as a novel stromal factor driving mammary epithelial morphogenesis. Our study contributes to comprehensive understanding of overlapping but divergent employment of mechanically active fibroblasts in developmental versus tumorigenic programs.
Total RNA sequencing reveals gene expression and microbial alterations shared by oral pre-malignant lesions and cancer
Authors: Khan Mohammed Muzamil , Frustino Jennifer , Villa Alessandro , Nguyen Bach-Cuc , Woo Sook-Bin , Johnson William Evan , Varelas Xaralabos , Kukuruzinska Maria , Monti Stefano 
Published: March 2023

ABSTRACTHead and neck cancers are a complex malignancy comprising multiple anatomical sites, with cancer of the oral cavity ranking among the deadliest and most disfiguring cancers globally. Oral cancer (OC) constitutes a subset of head and neck cancer cases, presenting primarily as tobacco-and alcohol-associated oral squamous cell carcinoma (OSCC), with a 5-year survival rate of ∼65%, partly due to the lack of early detection and effective treatments. OSCC arises from premalignant lesions (PMLs) in the oral cavity through a multi-step series of clinical and histopathological stages, including varying degrees of epithelial dysplasia. To gain insights into the molecular mechanisms associated with the progression of PMLs to OSCC, we profiled the whole transcriptome of 66 human PMLs comprising leukoplakia with dysplasia and hyperkeratosis non-reactive (HkNR) pathologies, alongside healthy controls and OSCC. Our data revealed that PMLs were enriched in gene signatures associated with cellular plasticity, such as partial EMT (p-EMT) phenotypes, and with immune response. Integrated analyses of the host transcriptome and microbiome further highlighted a significant association between differential microbial abundance and PML pathway activity, suggesting a contribution of the oral microbiome towards PML evolution to OSCC. Collectively, this study reveals molecular processes associated with PML progression that may help early diagnosis and disease interception at an early stage.AUTHOR SUMMARYPatients harboring oral premalignant lesions (PMLs) have an increased risk of developing oral squamous cell carcinoma (OSCC), but the underlying mechanisms driving transformation of PMLs to OSCC remain poorly understood. In this study, Khan et al., analyzed a newly generated dataset of gene expression and microbial profiles of oral tissues from patients diagnosed with PMLs from differing histopathological groups, including hyperkeratosis not reactive (HkNR) and dysplasia, comparing these profiles with OSCC and normal oral mucosa. Significant similarities between PMLs and OSCC were observed, with PMLs manifesting several cancer hallmarks, including oncogenic and immune pathways. The study also demonstrates associations between the abundance of multiple microbial species and PML groups, suggesting a potential contribution of the oral microbiome to the early stages of OSCC development. The study offers insights into the nature of the molecular, cellular and microbial heterogeneity of oral PMLs and suggests that molecular and clinical refinement of PMLs may provide opportunities for early disease detection and interception.
A soft tick vector ofBabesiasp. YLG in Yellow-legged gull (Larus michahellis) nests
Authors: Bonsergent Claire , Vittecoq Marion , Leray Carole , Jouglin Maggy , Buysse Marie , McCoy Karen D. , Malandrin Laurence 
Published: March 2023

ABSTRACTBabesiasp. YLG has recently been described in Yellow-legged gull (Larus michahellis) chicks and belongs to the Peircei clade in the new classification of Piroplasms. Here, we studiedBabesiasp. YLG vectorial transmission by ticks in the simplified environment of a single seabird breeding colony where the Yellow-legged gull is the sole vertebrate host,Ornithodoros maritimus(syn.Alectorobius maritimus) the sole tick species, andBabesiasp. YLG is the only blood parasite species detected in chicks of the colony. We collected ticks over four years, maintained certain individuals through moulting or oviposition, and dissected fresh ticks to isolate different organs and test for the presence of the parasite using molecular assays. We report the first strong evidence of a Piroplasmidae transmitted by a soft tick. Indeed,Babesiasp. YLG DNA was detected in the salivary glands of nymphs, females and males, a necessary organ to infect for transmission to a new vertebrate host. Parasite DNA was also found in tick ovaries, which could indicate possible transovarial transmission. Our detection ofBabesiasp. YLG DNA in several male testes and in endospermatophores, and notably in a parasite-free female (uninfected ovaries and salivary glands), raise the interesting possibility of sexual transmission from infected males to uninfected females. Future work in this system will now need to focus on the degree to which the parasite can be maintained locally by ticks and the epidemiological consequences of infection for bothO. maritimusand its avian host.
Immune cell type signature discovery and random forest classification for analysis of single cell gene expression datasets
Authors: Aybey Bogac , Zhao Sheng , Brors Benedikt , Staub Eike 
Published: March 2023

AbstractBackgroundRobust immune cell gene expression signatures are central to the analysis of single cell studies. Nearly all known sets of immune cell signatures have been derived by making use of only single gene expression datasets. Utilizing the power of multiple integrated datasets could lead to high-quality immune cell signatures which could be used as superior inputs to machine learning-based cell type classification approaches.ResultsWe established a novel gene expression similarity-based workflow for the discovery of immune cell type signatures that leverages multiple datasets, here four single cell expression datasets from three different cancer types. We used our immune cell signatures to train random forest classifiers for immune cell type assignment of single-cell RNA-seq datasets. We obtained similar or better prediction results compared to commonly used methods for cell type assignment in two independent benchmarking datasets. Our gene signature set yields higher prediction scores than other published immune cell type gene sets in our random forest approach.Discussion and conclusionWe demonstrated the quality of our immune cell signatures and their strong performance in a random forest-based cell typing approach. We argue that classifying cells based on our comparably slim sets of genes accompanied by a random forest-based approach not only matches or outperforms widely used published approaches. It also facilitates unbiased downstream statistical analyses of differential gene expression between cell types for 90% of all genes whose expression profiles have not been used for cell type classification.
Absence of Telomerase Leads to Immune Response and Tumor Regression in Zebrafish Melanoma
Authors: Lopes-Bastos Bruno , Nabais Joana , Ferreira Tânia , El Maï Mounir , Bird Malia , Targen Seniye , Kang Da , Yue Jia-Xing , Carvalho Tânia , Ferreira Miguel Godinho 
Published: March 2023

AbstractMost cancers reactivate telomerase to maintain telomere length to acquire immortality. The importance of this process is well illustrated by the fact that telomerase promoter mutations are found at a high frequency in many cancer types, including melanoma. However, it is unclear when and if telomerase is strictly required during tumorigenesis. Here, we show that melanoma can occur in the absence of telomerase but is required to sustain later growth and to avoid tumor regression. We combined telomerase mutant zebrafish (tert-/-) with two established melanoma models and found equal melanoma incidence and invasiveness as tumors became visible. Later, however, whiletert+/+fish develop increasing larger tumors,tert-/-tumors stagnate growth and regress.tert-/-tumors showed lower cell proliferation, higher apoptosis and melanocyte differentiation. We also detected an immune response directed attert-/-tumors.tert-/-tumors exhibited increased immune cell infiltrates and resume growth when transplanted into immunocompromised hosts. We propose that telomerase is required for melanoma in zebrafish, albeit at later stages of progression, to sustain growth while avoiding immune rejection and regression. Thus, absence of telomerase restricts melanoma through tumor-autonomous mechanisms (cell cycle arrest, apoptosis and melanocyte differentiation) and a non-tumor-autonomous mechanisms (immune rejection).
Dopamine D1-receptor Organization Contributes to Functional Brain Architecture
Authors: Pedersen Robin , Johansson Jarkko , Nordin Kristin , Rieckmann Anna , Wåhlin Anders , Nyberg Lars , Bäckman Lars , Salami Alireza 
Published: March 2023

AbstractDecades of research on functional brain mapping have highlighted the importance of understanding the functional organization of the cerebral cortex. Recent advances have revealed a gradient of functional organization spanning from primary sensory to transmodal cortices. This gradient-like axis of connectivity has been hypothesized to be aligned with regional differences in the density of neuromodulatory receptors. Recent work in non-human primates supports this notion, revealing a gradient of dopamine D1-like receptor (D1DR) density along the cortical hierarchy. Given the importance of dopaminergic modulation for synaptic activity and neural gain, we tested whether D1DRs shares the same organizational principles as brain function in humans, and whether inter-regional relationships in D1 expression modulate functional crosstalk. Using the world’s largest combined dopamine D1DR-PET and MRI database, we provided empirical support for the first time in humans that the landscape of D1DR availability follows a unimodal-transmodal cortical hierarchy, with greater D1DR expression in associative cortical regions. We found an organization of inter-regional D1DR co-expression spanning unimodal to transmodal brain regions, expressing a high spatial correspondence to the principal macroscale gradient of functional connectivity. Critically, we found that individual differences in D1DR density between unimodal and transmodal regions was associated with greater differentiation of default-mode and somatosensory networks. Finally, inter-regional D1DR co-expression was found to modulate couplings within, but not between, functional networks. Together, our results show that D1DR co-expression provides a biomolecular layer to the functional organization of the brain.Significance StatementWe found a high correspondence between the organization of the most abundantly expressed dopamine receptor subtype and a macroscale unimodal-to-transmodal functional gradient. Differences in D1 density between unimodal and transmodal regions were related to the shape of the functional gradient, contributing to greater differentiation of somatomotor and default mode networks. Finally, we observed that the covariance structure of dopamine D1 receptors is associated with the strength of connectivity within functional networks. The discovery of a dopaminergic layer of brain organization represents a crucial first step towards an understanding of how dopamine, with close ties to behavior and neuropsychiatric conditions, potentially contribute to the emergence of functional brain organization.
Retigabine and gabapentin restore channel function and neuronal firing of an epilepsy-associated dominant-negativeKCNQ5variant
Authors: Krüger Johanna , Lerche Holger 
Published: March 2023

AbstractObjectiveKCNQ5encodes the voltage-gated potassium channel KV7.5, a member of the KV7 channel family, which conducts the M-current. This current was shown to be a potent regulator of neuronal excitability by mediating the medium and slow afterhyperpolarization. Recently, we have identified five loss-of-function variants inKCNQ5in patients with genetic generalized epilepsy. Using the most severe dominant-negative variant p.(Arg359Cys) (R359C), we set out to investigate pharmacological therapeutic intervention by KV7 channel openers on channel function and neuronal firing.MethodsWhole-cell patch clamp recordings were conducted in human embryonic kidney cells to investigate the immediate effect of retigabine, gabapentin and intracellular application of zinc on the R359C variant in absence and presence of KV7.5-WT subunits. Transfected primary hippocampal cultures were used to examine the effect of R359C on neuronal firing and whether this effect could be reversed by drug application.ResultsRetigabine and gabapentin both increased R359C-derived K+current density and M-current amplitudes in both homomeric and heteromeric mutant KV7.5 channels. Retigabine was most effective in restoring K+currents. Ten µM retigabine was sufficient to reach the level of WT currents without retigabine, whereas 100 µM of gabapentin showed less than half of this effect and application of 50 µM zinc only significantly increased M-current amplitude in heteromeric channels. Overexpression of KV7.5-WT potently inhibited neuronal firing by increasing the M-current, and medium afterhyperpolarization, whereas R359C overexpression had the opposite effect. All three aforementioned drugs reversed the effect of R359C reducing firing to nearly normal levels at high current injections.SignificanceOur study shows that a dominant-negative complete loss-of-function variant in KV7.5 leads to largely increased neuronal firing indicating a neuronal hyperexcitability. KV7 channel openers, such as retigabine or gabapentin, could be treatment options for otherwise pharmacoresistant epilepsy patients carrying loss-of-function variants inKCNQ5.
Positive and biphasic extracellular waveforms correspond to return currents and axonal spikes
Authors: Someck Shirly , Levi Amir , Sloin Hadas E. , Spivak Lidor , Gattegno Roni , Stark Eran 
Published: March 2023

AbstractMultiple biophysical mechanisms may generate non-negative extracellular waveforms during action potentials, but the origin and prevalence of positive spikes and biphasic spikes in the intact brain are unknown. Using extracellular recordings from densely-connected cortical networks in freely-moving mice, we find that a tenth of the waveforms are non-negative. Positive phases of non-negative spikes occur in synchrony or just before wider same-unit negative spikes. Narrow positive spikes occur in isolation in the white matter. Isolated biphasic spikes are narrower than negative spikes, occurring right after spikes of verified inhibitory units. In CA1, units with dominant non-negative spikes exhibit place fields, phase precession, and phase-locking to ripples. Thus, near-somatic narrow positive extracellular potentials correspond to return currents, and isolated non-negative spikes correspond to axonal potentials. Identifying non-negative extracellular waveforms that correspond to non-somatic compartments during spikes can enhance the understanding of physiological and pathological neural mechanisms in intact animals.
Intronic TNR-RetainedIsopropylmalate Isomerase Large Subunit1transcripts impair leaf development in Arabidopsis
Authors: Li Yimeng , Li Rui , Kawade Kensuke , Sato Muneo , Kuwahara Ayuko , Sasaki Ryosuke , Oikawa Akira , Tsukaya Hirokazu , Hirai Masami Yokota 
Published: March 2023

AbstractIntronic trinucleotide repeat (TNR) is widely distributed in plant genomes. In Arabidopsis accession Bur-0, abnormally expanded TTC repeat in intron-3 of theISOPROPYLMALATE ISOMERASE LARGE SUBUNIT1(IIL1) gene causes growth defects called theirregularly impaired leaves(iil) phenotype, triggered by DNA methylation-mediatedIIL1gene silencing at elevated temperature. However, little is known about how the reduced expression ofIIL1causes theiilphenotype. We demonstrated that theiilphenotype was resulted from the relative increase of intron-3-retainedIIL1transcripts through the experiments where theiilphenotype was reproduced by introducing theIIL1gene harboring 100 copies of TTC repeat into Col-0. Theiilphenotype appeared when the total amount of theIIL1transcripts was decreased by co-suppression and the percentage of intron-3-retainedIIL1transcripts was increased. TheIIL1gene encodes an isopropylmalate isomerase large subunit, forming heterodimers with small subunits (AtLeuD1, AtLeuD2, or AtLeuD3). In themyb28 myb29mutant lacking AtLeuD1 and AtLeuD2, theiilphenotype was almost completely suppressed regardless of higher percentage of intron-3-retainedIIL1transcripts. The results indicated that theiilphenotype was associated with interaction with AtLeuDs, suggesting that intronic TNR-containing transcripts were translated into abnormal proteins and perturbed the metabolic pathway supporting the leaf development.
Oligodendrocytes in human iPS cell-derived cortical grafts remyelinate adult rat and human cortical neurons
Authors: Martinez-Curiel Raquel , Jansson Linda , Tsupykov Oleg , Avaliani Natalia , Aretio-Medina Constanza , Hidalgo Isabel , Monni Emanuela , Bengzon Johan , Skibo Galyna , Lindvall Olle , Kokaia Zaal , Palma-Tortosa Sara 
Published: March 2023

SUMMARYNeuronal loss and axonal demyelination underlie long-term functional impairments in patients affected by brain disorders such as ischemic stroke. Stem cell-based approaches reconstructing and remyelinating brain neural circuitry, leading to recovery, are highly warranted. Here we demonstrate thein vitroandin vivoproduction of myelinating oligodendrocytes from a human induced pluripotent stem (iPS) cell-derived long-term neuroepithelial stem (lt-NES) cell line, which also gives rise to neurons with the capacity to integrate into stroke-injured, adult rat cortical networks. Most importantly, the generated oligodendrocytes survive and form myelin ensheathing human axons in the host tissue after grafting onto adult human cortical organotypic cultures. This lt-NES cell line is the first human stem cell source that after intracerebral delivery can repair both injured neural circuitries and demyelinated axons. Our findings provide supportive evidence for the potential future use of human iPS cell-derived cell lines to promote effective clinical recovery following brain injuries.
Proteomic survey of the DNA damage response inCaulobacter crescentus
Authors: Tashjian Tommy F. , Zeinert Rilee D. , Eyles Stephen J. , Chien Peter 
Published: March 2023

ABSTRACTThe bacterial DNA damage response is a critical, coordinated response to endogenous and exogenous sources of DNA damage. Response dynamics are dependent on coordinated synthesis and loss of relevant proteins. While much is known about its global transcriptional control, changes in protein abundance that occur upon DNA damage are less well characterized at the system level. Here, we perform a proteome-wide survey of the DNA damage response inCaulobacter crescentus. We find that while most protein abundance changes upon DNA damage are readily explained by changes in transcription, there are exceptions. The survey also allowed us to identify the novel DNA damage response factor, YaaA, which has been overlooked by previously published, transcription- focused studies.A similar survey in a Δlonstrain was performed to explorelon’srole in DNA damage survival. The Δlonstrain had a smaller dynamic range of protein abundance changes in general upon DNA damage compared to the wild type strain. This system-wide change to the dynamics of the response may explain this strain’s sensitivity to DNA damage. Our proteome survey of the DNA damage response provides additional insight into the complex regulation of stress response and nominates a novel response factor that was overlooked in prior studies.IMPORTANCEThe DNA damage response helps bacteria to react to and potentially survive DNA damage. The mutagenesis induced during this stress response contributes to the development of antibiotic resistance. Understanding how bacteria coordinate their response to DNA damage could help us to combat this growing threat to human health. While the transcriptional regulation of the bacterial DNA damage response has been characterized, this study is the first to our knowledge to assess the proteomic response to DNA damage inCaulobacter.
A novel paradigm for operant social learning in rats
Authors: Rautio Ida V. , Holmberg Ella Holt , Kurup Devika , Dunn Benjamin A. , Whitlock Jonathan R. 
Published: March 2023

AbstractThe ability to learn by observing the behavior of others is both energy efficient and brings high survival value, making it an important learning tool for many species in the animal kingdom. As such, several forms of observational learning have been documented in a myriad of species. In the laboratory, rodents have proven useful models for studying different forms of observational learning, however, the most robust learning paradigms typically rely on aversive stimuli, like foot shocks, to drive the social acquisition of fear. Non-fear-based tasks have also been developed, but these rarely succeed in having observer animals perform a new behaviorde novo. Consequently, much less is known regarding the cellular mechanisms supporting non-fear-based types of learning, such as visuomotor skill acquisition. To address this we developed a reward-based social learning paradigm in adult rats, in which observer animals learn to tap lit spheres in a specific sequence by watching skilled demonstrators, with successful trials leading to rewarding intracranial stimulation in both observers and performers. Following three days of observation and a 24-hour delay, observer animals outperformed control animals on several metrics of task performance and efficiency, with a subset of observers demonstrating correct performance immediately when tested. This paradigm thus introduces a novel tool to investigate the neural circuits supporting observational learning and memory for visuomotor behavior, a phenomenon about which little is understood, particularly in rodents.