bluuebunny/crossref_metadata_2025 huggingface dataset:
Aberrant accumulation of NIK promotes tumorigenicity by dysregulating post-translational modifications in breast cancer
Authors: Hayashi Yusuke , Nakayama Jun , Yamamoto Mizuki , Maekawa Masashi , Watanabe Shinya , Higashiyama Shigeki , Inoue Jun-ichiro , Yamamoto Yusuke , Semba Kentaro
Published: August 2021

Post-translational modifications and mRNA translation are frequently altered in human cancers. However, investigations to understand their roles in the cancer progression mechanism remain insufficient. In this research, we explored protein levels altered by translational or post-translational regulation by analyzing transcriptome and western blotting data of the highly malignant breast cancer cell lines. From these analyses, NIK was found to be upregulated at the protein level to predominantly activate the non-canonical NF-κB pathway in a breast cancer cell line. Furthermore, the increase in NIK protein production was attributed to the dysregulation of ubiquitin-proteasome system caused by a decrease in the translation of cIAP1. NIK upregulation contributed to tumorigenicity by regulating the expression of inflammatory response-related genes. Collectively, our study suggests that NIK is post-translationally modified and has the potential to be a therapeutic target and diagnostic marker for breast cancer.
The mechanical regulation of RNA binding protein hnRNPC in the failing heart
Authors: Martino Fabiana , Varadarajan Nandan Mysore , Perestrelo Ana Rubina , Hejret Vaclav , Durikova Helena , Horvath Vladimir , Cavalieri Francesca , Caruso Frank , Albihlal Waleed S. , Gerber André P. , O’Connell Mary A. , Vanacova Stepanka , Pagliari Stefania , Forte Giancarlo
Published: August 2021

Cardiac pathologies are characterized by intense remodeling of the extracellular matrix (ECM) that eventually leads to heart failure. Cardiomyocytes respond to the ensuing biomechanical stress by re-expressing fetal contractile proteins via transcriptional and post-transcriptional processes, like alternative splicing (AS). Here, we demonstrate that the heterogeneous nuclear ribonucleoprotein C (hnRNPC) is upregulated and relocates to the sarcomeric Z-disk upon ECM pathological remodeling. We show that this is an active site of localized translation, where the ribonucleoprotein associates to the translation machinery. Alterations in hnRNPC expression and localization can be mechanically determined and affect the AS of numerous mRNAs involved in mechanotransduction and cardiovascular diseases, like Hippo pathway effector YAP1. We propose that cardiac ECM remodeling serves as a switch in RNA metabolism by impacting an associated regulatory protein of the spliceosome apparatus. These findings offer new insights on the mechanism of mRNAs homeostasis mechanoregulation in pathological conditions.
Stress Evaluation of Various Breeding Environments in Mouse
Authors: Lee Gwang-Hoon , Choi Hye-Yoon , Jo Woori , Kim Kil-Soo
Published: August 2021

Laboratory animals are raised in a fixed space during the study period and are environmentally bound. Laboratory animal may be under stress on the constrained environment, which changes physiological indicators, affecting the reproducibility and accuracy of animal study. Therefore, reducing animal stress by providing proper breeding environment and environmental enrichment can be the basis for animal study. In this study, the stress level was assessed according to the mouse breeding environment. According to the results of the experiment, it was determined that the individual ventilation cage had less cortisol concentration in serum and body weight increased in the individual ventilation cage than individual isolated cage, when providing environmental enrichment rather than group breeding or not providing environmental enrichment. The results will provide appropriate guidelines for laboratory animal welfare.
Age-related neural dedifferentiation for individual stimuli: An across-participant pattern similarity analysis
Authors: Koen Joshua D.
Published: August 2021

Age-related neural dedifferentiation – reductions in the regional specificity and precision of neural representations – is proposed to compromise the ability of older adults to form sufficiently distinct neural representations to support episodic memory encoding. The computational model that spurred investigations of age-related neural dedifferentiation initially characterized this phenomenon as a reduction in the specificity of neural patterns for individual items or stimuli. Most investigations have focused on reductions in neural differentiation for patterns of neural activity associated with category level information, such as reduced neural selectivity between categories of visual stimuli (e.g., scenes, objects, and faces). Here, I report a novel across-participant pattern similarity analysis method to measure neural distinctiveness for individual stimuli that were presented to participants on a single occasion. Measures of item level pattern similarity during encoding showed a graded positive subsequent memory effect in younger, with no significant subsequent memory effect in older adults. These results suggest that age-related reductions in the distinctiveness of neural patterns for individual stimuli during age differences in memory encoding. Moreover, a measure of category level similarity demonstrated a significant subsequent memory effect associated with item recognition (regardless of an object source memory detail), whereas the effect in older was associated with source memory. These results converge with predictions of computational models of dedifferentiation showing age-related reductions in the distinctiveness of neural patterns across multiple levels of representation.
Three-dimensional microenvironment regulates gene expression, function, and tight junction dynamics of iPSC-derived blood-brain barrier microvessels
Authors: Linville Raleigh M. , Sklar Matthew B. , Grifno Gabrielle N. , F. Nerenberg Renée , Zhou Justin , Ye Robert , DeStefano Jackson G. , Guo Zhaobin , Jha Ria , Jamieson John J. , Zhao Nan , Searson Peter C.
Published: August 2021

The blood-brain barrier (BBB) plays a pivotal role in brain health and disease. In the BBB, brain microvascular endothelial cells (BMECs) are connected by tight junctions which regulate paracellular transport, and express specialized transporter systems which regulate transcellular transport. However, existingin vitromodels of the BBB display variable physiological accuracy across a wide range of characteristics including gene/protein expression and barrier function. Here, we use an isogenic family of fluorescently-labeled iPSC-derived BMEC-like cells (iBMECs) and brain pericyte-like cells (iPCs) within two-dimensional confluent monolayers (2D) and three-dimensional (3D) tissue-engineered microvessels to explore how 3D microenvironment regulates gene expression and function of thein vitroBBB. We show that 3D microenvironment (shear stress, cell-ECM interactions, and cylindrical geometry) increases BBB phenotype and endothelial identity, and alters angiogenic and cytokine responses in synergy with pericyte co-culture. Tissue-engineered microvessels incorporating junction-labeled iBMECs enable study of the real-time dynamics of tight junctions during homeostasis and in response to physical and chemical perturbations.
Transposable element diversity remains high in gigantic genomes
Authors: Haley Ava Louise , Mueller Rachel Lockridge
Published: August 2021

Transposable elements (TEs) are repetitive sequences of DNA that replicate and proliferate throughout genomes. Taken together, all the TEs in a genome form a diverse community of sequences, which can be studied to draw conclusions about genome evolution. TE diversity can be measured using models for ecological community diversity that consider species richness and evenness. Several models predict TE diversity decreasing as genomes expand because of selection against ectopic recombination and/or competition among TEs to garner host replicative machinery and evade host silencing mechanisms. Salamanders have some of the largest vertebrate genomes and highest TE loads. Salamanders of the genus Plethodon, in particular, have genomes that range in size from 20 to 70 Gb. Here, we use Oxford Nanopore sequencing to generate low-coverage genomic sequences for four species of Plethodon that encompass two independent genome expansion events, one in the eastern clade (P. cinereus, 29.3 Gb vs. P. glutinosus, 38.9 Gb) and one in the western clade (P. vehiculum, 46.4 Gb vs P. idahoensis, 67.0 Gb). We classified the TEs in these genomes and found ~52 TE superfamilies, accounting for 27-32% of the genomes. We calculated Simpson’s and Shannon’s diversity indices to quantify overall TE diversity. In both pairwise comparisons, the diversity index values for the smaller and larger genome were almost identical. This result indicates that, when genomes reach extremely large sizes, they maintain high levels of TE diversity at the superfamily level, in contrast to predictions made by previous studies on smaller genomes.
Pattern separation and tuning shift in human sensory cortex underlie fear memory
Authors: You Yuqi , Novak Lucas R. , Clancy Kevin , Li Wen
Published: August 2021

Animal research has recognized the role of the sensory cortex in fear memory and two key underlying mechanisms—pattern separation and tuning shift. We interrogated these mechanisms in the human sensory cortex in an olfactory differential conditioning study with a delayed (9-day) retention test. Combining affective appraisal and olfactory psychophysics with functional magnetic resonance imaging (fMRI) multivoxel pattern analysis and voxel-based tuning analysis over a linear odor-morphing continuum, we confirmed affective and perceptual learning and memory and demonstrated associative plasticity in the human olfactory (piriform) cortex. Specifically, the piriform cortex exhibited immediate and lasting enhancement in pattern separation (between the conditioned stimuli/CS and neighboring non-CS) and late-onset yet lasting tuning shift towards the CS, especially in anxious individuals. These findings highlight an evolutionarily conserved sensory cortical system of fear memory, which can underpin sensory encoding of fear/threat and confer a sensory mechanism to the neuropathophysiology of anxiety.
Successive remodeling of IgG glycans using a solid-phase enzymatic platform
Authors: Hsu Yen-Pang , Verma Deeptak , Sun Shuwen , McGregor Caroline , Mangion Ian , Mann Benjamin F.
Published: August 2021

The success of glycoprotein-based drugs in various disease treatments has become widespread. Frequently, therapeutic glycoproteins exhibit a heterogeneous array of glycans that are intended to mimic human glycopatterns. While immunogenic responses to biologic drugs are uncommon, enabling exquisite control of glycosylation with minimized microheterogeneity would improve their safety, efficacy and bioavailability. Therefore, close attention has been drawn to the development of glycoengineering strategies to control the glycan structures. With the accumulation of knowledge about the glycan biosynthesis enzymes, enzymatic glycan remodeling provides a potential strategy to construct highly ordered glycans with improved efficiency and biocompatibility. In this study, we quantitatively evaluate more than 30 enzymes for glycoengineering immobilized immunoglobulin G, an impactful glycoprotein class in the pharmaceutical field. We demonstrate successive glycan remodeling in a solid-phase platform, which enabled IgG glycan harmonization into a series of complex-type N-glycoforms with high yield and efficiency while retaining native IgG binding affinity.

Significance

Glycosylation plays critical functional and structural roles in protein biology. However, our understanding of how discrete glycan structures affect protein behaviors remains extremely limited due to the naturally occurring microheterogeneity. Through the use of characterized glycoengineering enzyme combination, we report a solid-phase glycan remodeling (SPGR) platform that enables efficient IgG glycan harmonization into several glycoforms of interest with high biocompatibility to the substrates. It provides an efficient strategy to screen the biological behavior of distinct glycoforms, building a fundamental understanding of glycosylation.
A base-resolution panorama of the in vivo impact of cytosine methylation on transcription factor binding
Authors: Hernandez-Corchado Aldo , Najafabadi Hamed S.
Published: August 2021

While methylation of CpG dinucleotides is traditionally considered antagonistic to the DNA-binding activity of most transcription factors (TFs), recent in vitro studies have revealed a more complex picture, suggesting that over a third of TFs may preferentially bind to methylated sequences. Expanding these in vitro observations to in vivo TF binding preferences, however, is challenging, as the effect of methylation of individual CpG sites cannot be easily isolated from the confounding effects of DNA accessibility and regional DNA methylation. As a result, the in vivo methylation preferences of most TFs remain uncharacterized.

Here, we introduce joint accessibility-methylation-sequence (JAMS) models, which connect the strength of the binding signal observed in ChIP-seq to the DNA accessibility of the binding site, regional methylation level, DNA sequence, and base-resolution cytosine methylation. We show that JAMS models quantitatively explain the TF binding strength, recapitulate cell type-specific TF binding, and have high precision for inferring intra-motif methylation effects. Analysis of 2209 ChIP-seq experiments resulted in high-confidence JAMS models for 260 TFs, revealing that 45% of TFs are inhibited by intra-motif methylation in vivo. In contrast, only 16 TFs (6%) preferentially bind to methylated sites, including 11 novel methyl-binding TFs that are mostly from the multi-zinc finger family of TFs.

Our study substantially expands the repertoire of in vivo methyl-binding TFs, but also suggests that most TFs that prefer methylated CpGs in vitro present themselves as methylation agnostic in vivo, potentially due to the balancing effect of competition with other methyl-binding proteins.
Enhancement of the immunogenicity of a Mycobacterium tuberculosis fusion protein using ISCOMATRIX and PLUSCOM nano-adjuvants after nasal administration in mice
Authors: Avarvand Arshid Yousefi , Meshkat Zahra , Khademi Farzad , Aryan Ehsan , Sankian Mojtaba , Tafaghodi Mohsen
Published: August 2021

Background

Tuberculosis (TB), a contagious disease caused by Mycobacterium tuberculosis (M. tuberculosis), remains a health problem worldwide and this infection has the highest mortality rate among bacterial infections. Current studies suggest that intranasal administration of new tuberculosis vaccines could enhance the immunogenicity of M. tuberculosis antigens. Hence, we aim to evaluate the protective efficacy and immunogenicity of HspX/EsxS fusion protein of M. tuberculosis along with ISCOMATRIX and PLUSCOM nano-adjuvants and MPLA through the intranasal administration in mice model.

Methods

In present study, the recombinant fusion protein was expressed in Escherichia coli and purified and used to prepare different nanoparticle formulations in combination with ISCOMATRIX and PLUSCOM nano-adjuvants and MPLA. Mice were intranasally vaccinated with each formulation three times at an interval of 2 weeks. Finally, IFN-γ, IL-4. IL-17 and TGF-β concentration in supernatant of cultured splenocytes of vaccinated mice as well as serum titers of IgG1 and IgG2a and sIgA titers in nasal lavage were determined.

Results

According to obtained results, intranasally vaccinated mice with formulations containing ISCOMATRIX and PLUSCOM nano-adjuvants and MPLA could effectively induced IFN-γ and sIgA responses. Moreover, both HspX/EsxS/ISCOMATRIX/MPLA and HspX/EsxS/PLUSCOM/MPLA and their BCG booster formulation could strongly stimulate the immune system and enhance the immunogenicity of M. tuberculosis antigens.

Conclusion

The results demonstrate the potential of HspX/EsxS-fused protein in combination with ISCOMATRIX, PLUSCOM and MPLA after nasal administration in enhancing immune response against of M. tuberculosis antigens. So, nasal immunization with these formulations, could induce immune responses and considered as new TB vaccine or as BCG booster.
Mechanistic basis for SNX27-Retromer coupling to ESCPE-1 in promoting endosomal cargo recycling
Authors: Simonetti Boris , Guo Qian , Gimenez-Andres Manuel , Chen Kai-En , Moody Edmund R.R. , Evans Ashley J. , Danson Chris M. , Williams Tom A. , Collins Brett M. , Cullen Peter J.
Published: August 2021

Sorting nexin-27 (SNX27)-Retromer is an endosomal sorting complex that orchestrates endosome-to-plasma membrane recycling of hundreds of internalized receptors, channels and transporters, enzymes and adhesion molecules. While SNX27-Retromer is essential for development, subtle functional defects are observed in human disease, most notably neurodegenerative and neurological disorders. Achieving a thorough mechanistic dissection of SNX27-Retromer is central to understanding endosomal sorting in health and disease. Here we combine biochemical, structural and cellular analyses to establish the mechanistic basis through which SNX27-Retromer couples to the membrane tubulating ESCPE-1 complex (Endosomal SNX-BAR sorting complex for promoting exit 1). We show that a conserved surface in the FERM (4.1/ezrin/radixin/moesin) domain of SNX27 directly binds acidic-Asp-Leu-Phe (aDLF) motifs in the disordered amino-termini of the SNX1 and SNX2 subunits of ESCPE-1. This interaction hands-over SNX27-Retromer captured integral membrane proteins into ESCPE-1 tubular profiles to promote their cell surface recycling. Through phylogenetic analysis, we reveal that SNX27:Retromer:ESCPE-1 assembly evolved in a stepwise manner during the early evolution of metazoans, which reflects the increasing complexity of endosomal sorting from the ancestral opisthokont to modern animals.
Preclinical models of human multiple myeloma subgroups
Authors: Winkler Wiebke , Díaz Carlota Farré , Blanc Eric , Napieczynska Hanna , Langner Patrick , Werner Marvin , Walter Barbara , Wollert-Wulf Brigitte , Yasuda Tomoharu , Heuser Arnd , Beule Dieter , Mathas Stephan , Anagnostopoulos Ioannis , Rosenwald Andreas , Rajewsky Klaus , Janz Martin
Published: August 2021

Multiple myeloma (MM), a tumor of germinal center (GC)-experienced plasma cells, comprises distinct genetic subgroups, such as the t(11;14)/CCND1 and the t(4;14)/MMSET subtype. We have generated subgroup-specific MM models by the GC B cell-specific co-activation of Ccnd1 or MMSET with a constitutively active Ikk2 mutant, mimicking the secondary NFκB activation frequently seen in human MM. Ccnd1/Ikk2ca and MMSET/Ikk2ca mice developed a pronounced, clonally restricted plasma cell outgrowth with age, accompanied by serum M spikes, bone marrow insufficiency and bone lesions. The transgenic plasma cells could be propagated in vivo and showed transcriptional profiles resembling their human counterparts. Thus, we show that Ccnd1 and MMSET cooperate with NFκB in MM pathogenesis, considering for the first time the genetic heterogeneity of MM for the generation of preclinical models.
Sex–associated differences between body mass index and SARS-CoV-2 antibody titers following the BNT162b2 vaccine among 2,435 healthcare workers in Japan
Authors: Yamamoto Shohei , Mizoue Tetsuya , Tanaka Akihito , Oshiro Yusuke , Inamura Natsumi , Konishi Maki , Ozeki Mitsuru , Miyo Kengo , Sugiura Wataru , Sugiyama Haruhito , Ohmagari Norio
Published: September 2021

Obesity may downregulate vaccine-induced immunogenicity, but the epidemiological evidence for the COVID-19 vaccine is limited, and the sex-associated difference is unknown. It was observed that a higher body mass index was associated with lower titers of spike IgG antibodies against SARS-CoV-2 in men but not in women.
Maximum-likelihood model fitting for quantitative analysis of SMLM data
Authors: Wu Yu-Le , Hoess Philipp , Tschanz Aline , Matti Ulf , Mund Markus , Ries Jonas
Published: September 2021

Quantitative analysis is an important part of any single-molecule localization microscopy (SMLM) data analysis workflow to extract biological insights from the coordinates of the single fluorophores, but current approaches are restricted to simple geometries or do not work on heterogenous structures.

Here, we present LocMoFit (Localization Model Fit), an open-source framework to fit an arbitrary model directly to the localization coordinates in SMLM data. Using maximum likelihood estimation, this tool extracts the most likely parameters for a given model that best describe the data, and can select the most likely model from alternative models. We demonstrate the versatility of LocMoFit by measuring precise dimensions of the nuclear pore complex and microtubules. We also use LocMoFit to assemble static and dynamic multi-color protein density maps from thousands of snapshots. In case an underlying geometry cannot be postulated, LocMoFit can perform single-particle averaging of super-resolution structures without any assumption about geometry or symmetry. We provide extensive simulation and visualization routines to validate the robustness of LocMoFit and tutorials based on example data to enable any user to increase the information content they can extract from their SMLM data.
Analogs of TIQ-A as inhibitors of human mono-ADP-ribosylating PARPs
Authors: Maksimainen Mirko M. , Murthy Sudarshan , Sowa Sven T. , Galera-Prat Albert , Rolina Elena , Heiskanen Juha P. , Lehtiö Lari
Published: September 2021

The scaffold of TIQ-A, a previously known inhibitor of human poly-ADP-ribosyltransferase PARP1, was utilized to develop inhibitors against human mono-ADP-ribosyltransferases through structure-guided design and activity profiling. By supplementing the TIQ-A scaffold with small structural changes, based on a PARP10 inhibitor OUL35, selectivity changed from poly-ADP-ribosyltransferases towards mono-ADP-ribosyltransferases. Binding modes of analogs were experimentally verified by determining complex crystal structures with mono-ADP-ribosyltransferase PARP15 and with poly-ADP-ribosyltransferase TNKS2. The best analogs of the study achieved 10 – 20-fold selectivity towards mono-ADP-ribosyltransferases PARP10 and PARP15 while maintaining micromolar potencies. The work demonstrates a route to differentiate compound selectivity between mono- and poly-ribosyltransferases of the human ARTD family.
Multiple Sclerosis Patients have an Altered Gut Mycobiome and Increased Fungal to Bacterial Richness
Authors: Yadav Meeta , Ali Soham , Shrode Rachel L. , Shahi Shailesh K. , Jensen Samantha N. , Hoang Jemmie , Cassidy Samuel , Olalde Heena , Guseva Natalya , Paullus Mishelle , Cherwin Catherine , Wang Kai , Cho Tracey , Kamholz John , Mangalam Ashutosh K.
Published: September 2021

Trillions of microbes such as bacteria, fungi, and viruses exist in the healthy human gut microbiome. Although gut bacterial dysbiosis has been extensively studied in multiple sclerosis (MS), the significance of the fungal microbiome (mycobiome) is an understudied and neglected part of the intestinal microbiome in MS. The aim of this study was to characterize the gut mycobiome of patients with relapsing-remitting multiple sclerosis (RRMS), compare it to healthy controls, and examine its association with changes in the bacterial microbiome. We characterized and compared the mycobiome of 20 RRMS patients and 33 healthy controls (HC) using Internal Transcribed Spacer 2 (ITS2) and compared mycobiome interactions with the bacterial microbiome using 16S rRNA sequencing. Our results demonstrate an altered mycobiome in RRMS patients compared with HC. RRMS patients showed an increased abundance of Basidiomycota and decreased Ascomycota at the phylum level with an increased abundance of Candida and Epicoccum genera along with a decreased abundance of Saccharomyces compared to HC. We also observed an increased ITS2/16S ratio, altered fungal and bacterial associations, and altered fungal functional profiles in MS patients compared to HC.

This study demonstrates that RRMS patients had a distinct mycobiome with associated changes in the bacterial microbiome compared to HC. There is an increased fungal to bacterial ratio as well as more diverse fungal-bacterial interactions in RRMS patients compared to HC. Our study is the first step towards future studies in delineating the mechanisms through which the fungal microbiome can influence MS disease.
Temporal inhibition of chromatin looping and enhancer accessibility during neuronal remodeling
Authors: Chen Dahong , McManus Catherine E. , Radmanesh Behram , Matzat Leah H. , Lei Elissa P.
Published: September 2021

During development, looping of an enhancer to a promoter is frequently observed in conjunction with temporal and tissue-specific transcriptional activation. The chromatin insulator-associated protein Shep promotes Drosophila post-mitotic neuronal remodeling by repressing transcription of master developmental regulators, such as brain tumor (brat), specifically in maturing neurons. Since insulator proteins can promote looping, we hypothesized that Shep antagonizes brat promoter interaction with an as yet unidentified enhancer. Using chromatin conformation capture and reporter assays, we identified two novel enhancer regions that increase in looping frequency with the brat promoter specifically in pupal brains after Shep depletion. The brat promoters and enhancers function independently of Shep, ruling out direct repression of these elements. Moreover, ATAC-seq in isolated neurons demonstrated that Shep restricts chromatin accessibility of a key brat enhancer as well as other enhancers genome-wide in remodeling pupal but not larval neurons. These enhancers are enriched for chromatin targets of Shep and are located at Shep-inhibited genes, suggesting direct Shep inhibition of enhancer accessibility and gene expression during neuronal remodeling. Our results provide evidence for temporal regulation of chromatin looping and enhancer accessibility during neuronal maturation.
Diurnal activity budget and conservation implication of Hippopotamus amphibius at Bui National Park, Ghana
Authors: Bempah Godfred , Osei Marie , Gyimah Alice , Nsoah Winnifred
Published: September 2021

Animals apportion time for their daily behavioral activities. We studied the activity budget of Hippopotamus amphibius at the Black Volta River in the Bui National Park, Ghana. We performed instantaneous scan sample using ground count survey between August 2020 to July 2021. We observed that H. amphibius spent most of their day time resting (54.75 %), followed by feeding (22.93 %), walking (19.2 %) and touching (3.12 %). We found significant difference in the time spent between the daily activities (H = 41.67; p < 0.0001). Except activities involving touching, we found no significant seasonal differences in feeding, resting and walking activities by H. amphibius. Understanding the behavioral activities of H. amphibius will enhance management and conservation of the animals.
β-glucan imprinting remodels macrophage function in response to environmental cues
Authors: Piffer Alícia C. , Camilli Giorgio , Bohm Mathieu , Lavenir Rachel , Quintin Jessica
Published: September 2021

In vitro, exposure of human primary monocytes to the fungal β-glucan enhances their pro-inflammatory responsiveness towards several pathogens. Yet, the role of environmental condition of this process remains unclear. Here we found that β-glucan-induced innate immune memory counteract the anti-inflammatory status of the macrophages. In response to β-glucan imprinting, M-CSF-(M2-like-) macrophages increase their pro-inflammatory responsiveness to secondary stimuli associated with decrease of the M-CSF differentiation hallmarks. In contrast, in GM-CSF-(M1-like-) environment, β-glucan imprinting reduced the pro-inflammatory canonical feature of the macrophages, together with their terminal differentiation marks. Comparing M-CSF and GM-CSF environment, we observed that β-glucan-imprinted macrophages present comparable functions in terms of cytokine responses, phagocytosis, oxidative burst, and angiogenesis. This effect is mediated through Dectin-1 and associated with altered expression of the master regulators of macrophage terminal differentiation, IRF5 and IRF3. β-glucan-induced innate immune memory skews the commitment of the macrophages in complex environment towards similar and less terminally differentiated cells. Together, these observations suggest a potential therapeutic role for β-glucan-induced modulation of innate memory in different pathological contexts.
“Axonal Length Determines distinct homeostatic phenotypes in human iPSC derived motor neurons on a bioengineered platform”
Authors: Hagemann Cathleen , Gonzalez Carmen Moreno , Guetta Ludovica , Tyzack Giulia , Chiappini Ciro , Legati Andrea , Patani Rickie , Serio Andrea
Published: September 2021

Stem cell-based experimental platforms for neuroscience can effectively model key mechanistic aspects of human development and disease. However, conventional culture systems often overlook the engineering constraints that cells face in vivo. This is particularly relevant for neurons covering long range connections such as spinal motor neurons (MNs). The axons of these neurons extend up to 1m in length and require a complex interplay of mechanisms to maintain cellular homeostasis. It follows that shorter axons in conventional cultures may not faithfully capture important aspects of their longer counterparts. Here we directly address this issue by establishing a bioengineered platform to assemble arrays of human axons ranging from micrometers to centimeters, permitting systematic investigation of the effects of length on human axonal biology for the first time. With this approach, we reveal a link between length and metabolism in human MNs in vitro, where axons above a “threshold” size induce specific molecular adaptations in cytoskeleton composition, functional properties, local translation and mitochondrial homeostasis. Our findings specifically demonstrate the existence of a length-dependent mechanism that switches homeostatic processes within human MNs in order to sustain long axons. Our findings have critical implications for in vitro modelling of several neurodegenerative disorders and reinforce the importance of modelling cell shape and biophysical constraints with fidelity and precision in vitro.
Mutually Antagonistic Protein Pairs of Cancer
Authors: Dalgıç Ertuğrul
Published: September 2021

Switch-like behavior of tumorigenesis could be governed by antagonistic gene and protein pairs with mutual inhibition. Unlike extensive analysis of gene expression, search for protein level antagonistic pairs has been limited. Here, potential cancer type specific antagonist protein pairs with mutual inhibition were obtained from large scale datasets. Cancer samples or cancer types were compared to retrieve potential protein pairs with contrasting differential expression patterns. Analysis of two different protein expression datasets showed that a few proteins participate in most of the mutually antagonistic relationships. Some proteins with highly antagonistic profile were identified, which could not be attained from a differential expression or a correlation based analysis. The antagonistic protein pairs are sparsely connected by molecular interactions. Glioma, melanoma, and cervical cancer, are more frequently associated with antagonistic proteins than most of the other cancer types. Integrative analysis of mutually antagonist protein pairs contributes to our understanding of systems level changes of cancer.
Yap/Taz-Activated Tert-Expressing Acinar Cells Are Required for Pancreatic Regeneration
Authors: Suh Han Na , Kim Moon Jong , Lee Sung Ho , Jun Sohee , Zhang Jie , Johnson Randy L. , Park Jae-Il
Published: September 2021

The expression of TERT (telomerase reverse transcriptase) has been implicated in stem and progenitor cells, which are essential for tissue homeostasis and regeneration. However, the roles of TERT-expressing cells in the pancreas remain elusive. Employing genetically engineered Tert knock-in mouse model, herein, we located a rare population of Tert+ acinar cells. While Tert+ cells are quiescent in normal conditions, acinar cell injury leads to mitotic activation of Tert+ cells and subsequent generation of new acinar cells. Moreover, the genetic ablation of Tert+ cells impairs pancreatic regeneration. We further found that Yap/Taz activation is required for the expansion of Tert+ acinar cells. Our results identified Tert+ acinar cells as a distinct subset of acinar cells, which contributes to pancreatic regeneration via Yap/Taz activation.
Efficient ancestry and mutation simulation with msprime 1.0
Authors: Baumdicker Franz , Bisschop Gertjan , Goldstein Daniel , Gower Graham , Ragsdale Aaron P. , Tsambos Georgia , Zhu Sha , Eldon Bjarki , Ellerman E. Castedo , Galloway Jared G. , Gladstein Ariella L. , Gorjanc Gregor , Guo Bing , Jeffery Ben , Kretzschmar Warren W. , Lohse Konrad , Matschiner Michael , Nelson Dominic , Pope Nathaniel S. , Quinto-Cortés Consuelo D. , Rodrigues Murillo F. , Saunack Kumar , Sellinger Thibaut , Thornton Kevin , van Kemenade Hugo , Wohns Anthony W. , Wong Yan , Gravel Simon , Kern Andrew D. , Koskela Jere , Ralph Peter L. , Kelleher Jerome
Published: September 2021

Stochastic simulation is a key tool in population genetics, since the models involved are often analytically intractable and simulation is usually the only way of obtaining ground-truth data to evaluate inferences. Because of this necessity, a large number of specialised simulation programs have been developed, each filling a particular niche, but with largely overlapping functionality and a substantial duplication of effort. Here, we introducemsprimeversion 1.0, which efficiently implements ancestry and mutation simulations based on the succinct tree sequence data structure andtskitlibrary. We summarisemsprime’s many features, and show that its performance is excellent, often many times faster and more memory efficient than specialised alternatives. These high-performance features have been thoroughly tested and validated, and built using a collaborative, open source development model, which reduces duplication of effort and promotes software quality via community engagement.
Only females show a stable association between neuroticism and microstructural asymmetry of the cingulum across childhood and adolescence: A longitudinal DTI study
Authors: Plachti Anna , Baaré William FC , Johansen Louise Baruël , Thompson Wesley K. , Siebner Hartwig R. , Madsen Kathrine Skak
Published: September 2021

Neuroticism is characterized by a tendency to experience negative and anxious emotions. This personality trait is linked to an increased risk of anxiety and mood disorders. In a cross-sectional 3T diffusion tensor imaging (DTI) study in children and adolescents, we found an association between neuroticism and a relative imbalance between left and right (i.e., asymmetry) fractional anisotropy (FA) in the cingulum and white matter underlying the ventromedial prefrontal cortex with opposite directions in females and males. Here we analyzed the longitudinal follow-up DTI data, which was acquired in 76 typically-developing 7- to 18-year-olds, including up to 11 scans per subject. Neuroticism was assessed up to four times. Our longitudinal DTI measurements substantiate robust associations between higher neuroticism scores and increased left relative to right cingulum FA in females and decreased left relative to right cingulum FA in males. In females, the association was already present in late childhood and with a stable expression across childhood and adolescence. In males, the association gradually emerged during adolescence. Future longitudinal studies should clarify which neurobiological factors (e.g., genetic variation, prenatal stress, sex hormones) contribute to the sex-specific associations in the relationship between neuroticism and interhemispheric microstructural asymmetry of the cingulum.

Highlight

We analyzed a unique longitudinal DTI dataset covering late childhood and adolescence.

In the cingulum, left-right fractional anisotropy (FA) asymmetry scaled with neuroticism.

Females displayed a stable association of neuroticism with increased cingulum asymmetry.

Males showed an association between neuroticism and decreased cingulum FA asymmetry.

The association in males became more accentuated during adolescence
The sensitivity of magnetic particle imaging and fluorine-19 magnetic resonance imaging for cell tracking
Authors: Sehl Olivia C. , Foster Paula J.
Published: September 2021

Purpose

Magnetic particle imaging (MPI) and fluorine-19 (19F) MRI produce images which allow for quantification of labeled cells. MPI is an emerging instrument for cell tracking, which is expected to have superior sensitivity compared to 19F MRI. Our objective is to assess the cellular sensitivity of MPI and 19F MRI for detection of mesenchymal stem cells (MSC) and breast cancer cells.

Methods

Cells were labeled with ferucarbotran or perfluoropolyether, for imaging on a preclinical MPI system or 3 Tesla clinical MRI, respectively. In vivo sensitivity with MPI and 19F MRI was evaluated by imaging MSC that were administered by different routes.

Results

Using the same imaging time, as few as 4000 MSC (76 ng iron) and 8000 breast cancer cells (74 ng iron) were reliably detected with MPI, and 256,000 MSC (9.01 × 101619F atoms) were detected with 19F MRI, with SNR > 5. In vivo imaging revealed reduced sensitivity compared to ex vivo cell pellets of the same cell number.

Conclusion

MPI has the potential to be more sensitive than 19F MRI for cell tracking. We attribute reduced MPI and 19F MRI cell detection in vivo to the effect of cell dispersion among other factors, which are described.
Synergistic Effect of Serotonin 1A and Serotonin 1B/D Receptor Agonists in the Treatment of L-DOPA-Induced Dyskinesia in 6-Hydroxydopamine-Lesioned Rats
Authors: Thomsen Mikael , Stoica Anca , Christensen Kenneth Vielsted , Mikkelsen Jens , Hansen John Bondo
Published: September 2021

Background

The gold standard for symptomatic relief of Parkinson’s disease is L-DOPA. However, long-term treatment often leads to motor complications such as L-DOPA-induced dyskinesia (LID). While amantadine (Gocovri™) is the only approved therapy for dyskinesia in people with Parkinson’s disease on the American market, it is associated with neurological side effects and limited efficacy. Thus, there remains a high unmet need for addressing LID in Parkinson’s disease patients worldwide.

Objective

The objective of this study was to evaluate the efficacy, safety and performance compared to approved treatments of the serotonin receptor 1A (5-HT1A) and 5-HT1B/D agonists buspirone and zolmitriptan in the 6-hydroxydopamine unilaterally lesioned rat model for Parkinson’s disease.

Methods

The hemi-parkinsonian 6-OHDA lesioned rats underwent chronic treatment with L-DOPA to induce dyskinesia and were subsequently used for efficacy testing of buspirone, zolmitriptan and comparison with amantadine, measured as abnormal involuntary movement (AIM) scores after L-DOPA challenge. Safety testing was performed in model and naive animals using forelimb adjusting, rotarod and open field tests.

Results

5-HT1A and 5-HT1B/D agonism effectively reduced AIM scores in a synergistic manner. The drug combination of buspirone and zolmitriptan was safe and did not lead to tolerance development following sub-chronic administration. Head-to-head comparison with amantadine showed superior performance of buspirone and zolmitriptan in the model.

Conclusions

The strong anti-dyskinetic effect found with combined 5-HT1A and 5-HT1B/D agonism renders buspirone and zolmitriptan a potential clinical candidate for LID in Parkinson’s disease.
Structure-guided glyco-engineering of ACE2 for improved potency as soluble SARS-CoV-2 decoy receptor
Authors: Capraz Tümay , Kienzl Nikolaus F. , Laurent Elisabeth , Perthold Jan W. , Föderl-Höbenreich Esther , Grünwald-Gruber Clemens , Maresch Daniel , Monteil Vanessa , Niederhöfer Janine , Wirnsberger Gerald , Mirazimi Ali , Zatloukal Kurt , Mach Lukas , Penninger Josef M. , Oostenbrink Chris , Stadlmann Johannes
Published: September 2021

Infection and viral entry of SARS-CoV-2 crucially depends on the binding of its Spike protein to angiotensin converting enzyme 2 (ACE2) presented on host cells. Glycosylation of both proteins is critical for this interaction. Recombinant soluble human ACE2 can neutralize SARS-CoV-2 and is currently undergoing clinical tests for the treatment of COVID-19. We used 3D structural models and molecular dynamics simulations to define the ACE2 N-glycans that critically influence Spike-ACE2 complex formation. Engineering of ACE2 N-glycosylation by site-directed mutagenesis or glycosidase treatment resulted in enhanced binding affinities and improved virus neutralization without notable deleterious effects on the structural stability and catalytic activity of the protein. Importantly, simultaneous removal of all accessible N-glycans from recombinant soluble human ACE2 yields a superior SARS-CoV-2 decoy receptor with promise as effective treatment for COVID-19 patients.
Impending anthropogenic threats and protected area prioritization for the largest Neotropical apex predator in its Amazonian stronghold
Authors: Bogoni Juliano A. , Boron Valeria , Peres Carlos A. , Coelho Maria Eduarda M. S. , Morato Ronaldo G. , Oliveira-da-Costa Marcelo
Published: September 2021

Jaguars (Panthera onca) exert critical top-down control over large vertebrates across the Neotropics and have been declining due to multiple threats. Based on geospatial layers, we extracted socio-environmental variables for 447 protected areas across the Brazilian Amazon to identify protected areas that merit short-term high-priority efforts to maximize jaguar persistence. Data were analyzed using descriptive statistics, structural equations and regression modeling. Our results reveal that areas containing the largest jaguar densities and estimated population sizes are precisely those confronting most anthropogenic threats. We reveal that jaguars in the world’s largest tropical forest biome are threatened by deforestation associated with anthropogenic fires, and subsequent establishment of pastures. We provide a shortlist of protected areas that should be prioritized for short-term jaguar conservation. The future predicament of jaguar populations can only be ensured if protected areas can be proofed against downgrading and downsizing geopolitical pressures and external anthropogenic threats.
Systematic discovery of gene fusions in pediatric cancer by integrating RNA-seq and WGS
Authors: van Belzen Ianthe A.E.M. , Cai Casey , van Tuil Marc , Badloe Shashi , Strengman Eric , Janse Alex , Verwiel Eugène T. , van der Leest Douwe F.M. , Kester Lennart , Molenaar Jan J. , Meijerink Jules , Drost Jarno , Peng Weng Chuan , Kerstens Hinri H.D. , Tops Bastiaan B.J. , Holstege Frank C.P. , Kemmeren Patrick , Hehir-Kwa Jayne Y.
Published: September 2021

Background

Gene fusions are important cancer drivers in pediatric cancer and their accurate detection is essential for diagnosis and treatment. Clinical decision-making requires high confidence and precision of detection. Recent developments show RNA sequencing (RNA-seq) is promising for genome-wide detection of fusion products, but hindered by many false positives that require extensive manual curation and impede discovery of pathogenic fusions.

Results

We developed Fusion-sq to detect tumor-specific gene fusions by integrating and “fusing” evidence from RNA-seq and whole genome sequencing (WGS) using intron-exon gene structure. In a pediatric pan-cancer cohort of 130 patients, we identified 165 high confidence tumor-specific gene fusions and their underlying structural variants (SVs). This includes all clinically relevant fusions known to be present in this cohort (30 patients). Fusion-sq distinguishes healthy-occurring from tumor-specific fusions, and resolves fusions in amplified regions and copy number unstable genomes. A high gene fusion burden is associated with copy number instability. We identified 27 potentially pathogenic fusions involving oncogenes or tumor-suppressor genes characterised by underlying SVs or expression changes indicative of activating or disruptive effects.

Conclusions

Our results indicate how clinically relevant and potentially pathogenic gene fusions can be identified and their functional effects investigated by combining WGS and RNA-seq. Integrating RNA fusion predictions with underlying SVs advances fusion detection beyond extensive manual filtering. Taken together, we developed a method for identifying candidate fusions that is suitable for precision oncology applications. Our method provides multi-omics evidence for assessing the pathogenicity of tumor-specific fusions for future clinical decision making.
The cause of on-target point mutations generated by CRISPR-Cas9 treatment in the yeast Xanthophyllomyces dendrorhous
Authors: Hong Jixuan , Meng Ziyue , Zhang Zixi , Su Hang , Fan Yuxuan , Huang Ruilin , Ding Ruirui , Zhang Ning , Li Fuli , Wang Shi’an
Published: September 2021

Recognizing outcomes of DNA repair induced by CRISPR-Cas9 cutting is vital for precise genome editing. Reported DNA repair outcomes after Cas9 cutting include deletions/insertions and low frequency of genomic rearrangements and nucleotide substitutions. Thus far, substitution mutations caused by CRISPR-Cas9 has not attracted much attention. Here, we identified on-target point mutations induced by CRISPR-Cas9 treatment in the yeast Xanthophyllomyces dendrorhous by Sanger and Illumina sequencing. Different from previous studies, our findings suggested that the on-target mutations are not random and they cannot render the gRNA effective. Moreover, these point mutations showed strong sequence dependence that is not consistent with the observations in Hela cells, in which CRISPR-mediated substitutions were considered lacking sequence dependence and conversion preferences. Furthermore, this study demonstrated that the NHEJ components Ku70, Ku80, Mre11, or RAD50, and the overlapping roles of non-essential DNA polymerases were necessary for the emergence of point mutations, increasing the knowledge on CRISPR-Cas9 mediated DNA repair.
Multicenter reverse-phase protein array data integration
Authors: de Koning Leanne , Bernhardt Stephan , Macleod Kenneth G. , Ouine Bérengère , Cartier Aurélie , Sibut Vonick , Carragher Neil O. , Korf Ulrike , Serrels Bryan , Byron Adam
Published: September 2021

Among the technologies available for protein biomarker discovery and validation, reverse-phase protein array (RPPA) benefits from unequalled sample throughput. Panels of high-quality antibodies enable the quantification by RPPA of protein abundance and posttranslational modifications in biological specimens with high precision and sensitivity. Incorporation of RPPA technology into clinical and drug development pipelines requires robust assays that generate reproducible results across multiple laboratories. We implemented the first international multicenter pilot study to investigate RPPA workflow variability. We characterized the proteomic responses of a series of breast cancer cells to two cancer drugs. This analysis quantified 86,832 sample spots, representing 108 biological samples, arrayed at three independent RPPA platforms. This unique integrated set of data is publicly available as a resource to the proteomic and cancer research communities to catalyse further analysis and investigation. We anticipate that this dataset will form a reference for the comparison of RPPA workflows and reagents, which can be expanded in the future, and will aid the identification of platform-robust treatment-marker antigens in breast cancer cells.