bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural Knowledge Transfer of Panoptic Kidney Segmentation to Other Stains, Organs, and Species
Authors: Ginley Brandon , Jen Kuang-Yu , Sarder Pinaki
Published: October 2021

Background

Panoptic segmentation networks are a newer class of image segmentation algorithms that are constrained to understand the difference between instance-type objects (objects that are discrete countable entities, such as renal tubules) and group-type objects (uncountable, amorphous regions of texture such as renal interstitium). This class of deep networks has unique advantages for biological datasets, particularly in computational pathology.

Methods

We collected 126 periodic acid Schiff whole slide images of native diabetic nephropathy, lupus nephritis, and transplant surveillance kidney biopsies, and fully annotated them for the following micro-compartments: interstitium, glomeruli, globally sclerotic glomeruli, tubules, and arterial tree (arteries/arterioles). Using this data, we trained a panoptic feature pyramid network. We compared performance of the network against a renal pathologist’s annotations, and the method’s transferability to other computational pathology domain tasks was investigated.

Results

The panoptic feature pyramid networks showed high performance as compared to renal pathologist for all of the annotated classes in a testing set of transplant kidney biopsies. The network was not only able to generalize its object understanding across different stains and species of kidney data, but also across several organ types.

Conclusions

Panoptic networks have unique advantages for computational pathology; namely, these networks internally model structural morphology, which aids bootstrapping of annotations for new computational pathology tasks.
Real-Time Structure Search and Structure Classification for AlphaFold Protein Models
Authors: Aderinwale Tunde , Bharadwaj Vijay , Christoffer Charles , Terashi Genki , Zhang Zicong , Jahandideh Rashidedin , Kagaya Yuki , Kihara Daisuke
Published: October 2021

AlphaFold2 showed a substantial improvement in the accuracy of protein structure prediction. Following the release of the software, whole-proteome protein structure predictions by AlphaFold2 for 21 organisms were made publicly available. Here, we developed the infrastructure, 3D-AF-Surfer, to enable real-time structure-based search for the AlphaFold2 models by combining molecular surface representation with 3D Zernike descriptors and deep neural networks.
Developing a Biomimetic Evaluation Method for Antiviral Coatings Using Artificial Saliva Droplets
Authors: Tanaka Naoki , Miyamae Nobuhiro
Published: October 2021

Respiratory infections pose a serious threat worldwide, and many new antiviral agents and coatings have been developed to reduce the overall risk of viral infection. Here, we evaluate the methodology used to test these antiviral coatings and developed a novel system that is more similar to “real-world” conditions. Contact infection is largely mediated via contact with saliva containing the active virus released as droplets by coughing or sneezing, with these droplets adhering to objects and surfaces and subsequently entering the human body via indirect contact with the mucous membranes. Here, we evaluated the antiviral effect of a known antiviral coating agent using an artificial saliva based system, where artificial saliva containing phages were sprayed onto the antiviral coating under various conditions associated with viral replication and infectious spread. We used a commercially available antiviral coating in this evaluation, and M13 bacteriophages as model viruses. This method enables simple biomimetic evaluations of any product’s antiviral effects.
Evaluating test-retest reliability and sex/age-related effects on temporal clustering coefficient of dynamic functional brain networks
Authors: Long Yicheng , Yan Chaogan , Wu Zhipeng , Huang Xiaojun , Cao Hengyi , Liu Zhening , Palaniyappan Lena
Published: October 2021

The multilayer dynamic network model has been proposed as an effective method to understand how the brain functions dynamically. Specially, derived from the definition of clustering coefficient in static networks, the temporal clustering coefficient provides a direct measure of topological stability of dynamic brain networks and shows potential in predicting altered brain functions in both normal and pathological conditions. However, test–retest reliability and demographic-related effects on this measure remain to be evaluated. Using a publicly available dataset from the Human Connectome Project consisting of 337 young healthy adults (157 males/180 females; 22 to 37 years old), the present study investigated: (1) the test-retest reliability of temporal clustering coefficient across four repeated resting-state functional magnetic resonance imaging scans as measured by intraclass correlation coefficient (ICC); and (2) sex- and age-related effects on temporal clustering coefficient. The results showed that (1) the temporal clustering coefficient had overall moderate test-retest reliability (ICC > 0.40 over a wide range of densities) at both global and subnetwork levels; (2) female subjects showed significantly higher temporal clustering coefficient than males at both global and subnetwork levels, in particular within the default-mode and subcortical regions; (3) temporal clustering coefficient of the subcortical subnetwork was negatively correlated with age in young adults. Our findings suggest that temporal clustering coefficient is a reliable and reproducible approach for the identification of individual differences in brain function, and provide evidence for sex and age effects on human brain dynamic connectome.
Zika virus infection drives epigenetic modulation of immunity by the histone acetyltransferase CBP of Aedes aegypti
Authors: de Mendonça Amarante Anderson , de Abreu da Silva Isabel Caetano , Carneiro Vitor Coutinho , Revoredo Vicentino Amanda Roberta , de Amorim Pinto Marcia , Higa Luiza Mendonça , Moharana Kanhu Charan , Talyuli Octávio Augusto C. , Venancio Thiago Motta , de Oliveira Pedro Lagerblad , Fantappié Marcelo Rosado
Published: October 2021

Epigenetic mechanisms are responsible for a wide range of biological phenomena in insects, controlling embryonic development, growth, aging and nutrition. Despite this, the role of epigenetics in shaping insect-pathogen interactions has received little attention. Gene expression in eukaryotes is regulated by histone acetylation/deacetylation, an epigenetic process mediated by histone acetyltransferases (HATs) and histone deacetylases (HDACs). In this study, we explored the role of the Aedes aegypti histone acetyltransferase CBP (AaCBP) after infection with Zika virus (ZIKV), focusing on the two main immune tissues, the midgut and fat body. We showed that the expression and activity of AaCBP could be positively modulated by blood meal and ZIKV infection. Nevertheless, Zika-infected mosquitoes that were silenced for AaCBP revealed a significant reduction in the acetylation of H3K27 (CBP target marker), followed by downmodulation of the expression of immune genes, higher titers of ZIKV and lower survival rates. Importantly, in Zika-infected mosquitoes that were treated with sodium butyrate, a histone deacetylase inhibitor, their capacity to fight virus infection was rescued. Our data point to a direct correlation among histone hyperacetylation by AaCBP, upregulation of antimicrobial peptide genes and increased survival of Zika-infected-A. aegypti.

Author summary

Pathogens have coevolved with mosquitoes to optimize transmission to hosts. As natural vectors, mosquitoes are permissive to and allow systemic and persistent arbovirus infection, which intriguingly does not result in dramatic pathological sequelae that affect their lifespan. In this regard, mosquitoes have evolved mechanisms to tolerate persistent infection and develop efficient antiviral strategies to restrict viral replication to nonpathogenic levels. There is a great deal of evidence supporting the implication of epigenetics in the modulation of the biological interaction between hosts and pathogens. This study reveals that Zika virus infection positively modulates the expression and activity of A. aegypti histone acetyltransferase CBP (AaCBP). This study shows that AaCBP plays a role in the activation of immune-responsive genes to limit Zika virus replication. This first description that Zika virus infection has epigenomic consequences in the regulation of A. aegypti immunity opens a new avenue for research on mosquito factors that can drive vector competence.
High-precision spatial analysis of mouse courtship vocalization behavior reveals sex and strain differences
Authors: Oliveira-Stahl G. , Farboud S. , Sterling M. L. , Heckman J. J. , van Raalte B. , Lenferink D. , van der Stam A. , Smeets C. J. L. M. , Fisher S. E. , Englitz B.
Published: October 2021

Mice display a wide repertoire of vocalizations that varies with sex, strain, and context. Especially during social interaction, mice emit sequences of ultrasonic vocalizations (USVs) of high complexity. As animals of both sexes vocalize, a reliable attribution of USVs to their emitter is essential.

The state-of-the-art in sound localization for USVs in 2D allows spatial localization at a resolution of multiple centimeters. However, animals interact at closer ranges, e.g. snout-to-snout. Hence, improved algorithms are required to reliably assign USVs. We present a novel algorithm, SLIM (Sound Localization via Intersecting Manifolds), that achieves a 3-fold improvement in accuracy (12-14.3mm) using only 4 microphones and extends to many microphones and localization in 3D. This accuracy allows reliable assignment of 84.3% of all USVs in our dataset.

We apply SLIM to courtship interactions between adult C57Bl/6J wildtype mice and those carrying a heterozygous Foxp2 variant (R552H). The improved spatial accuracy reveals detailed vocalization preferences for specific spatial relations between the mice. Specifically, vocalization probability, duration, Wiener entropy, and frequency level differed in particular spatial relations between WT females, Foxp2-R552H and WT males.

In conclusion, the improved attribution of vocalizations to their emitters provides a foundation for better understanding social vocal behaviors.
Dissecting tumor cell programs through group biology estimation in clinical single-cell transcriptomics
Authors: Johri Shreya , Bi Kevin , Titchen Breanna M. , Fu Jingxin , Conway Jake , Crowdis Jett P. , Volkes Natalie I. , Fan Zenghua , Fong Lawrence , Park Jihye , Liu David , He Meng Xiao , Van Allen Eliezer M.
Published: October 2021

Given the growing number of clinically integrated cancer single-cell transcriptomic studies, robust differential enrichment methods for gene signatures to dissect tumor cellular states for discovery and translation are critical. Current analysis strategies neither adequately represent the hierarchical structure of clinical single-cell transcriptomic datasets nor account for the variability in the number of recovered cells per sample, leading to results potentially confounded by sample-driven biology with high false positives instead of accurately representing true differential enrichment of group-level biology (e.g., treatment responders vs. non-responders). This problem is especially prominent for single-cell analyses of the tumor compartment, because high intra-patient similarity (as opposed to inter-patient similarity) results in stricter hierarchical structured data that confounds enrichment analysis. Furthermore, to identify signatures which are truly representative of the entire group, there is a need to quantify the robustness of otherwise statistically significant signatures to sample exclusion. Here, we present a new nonparametric statistical method, BEANIE, to account for these issues, and demonstrate its utility in two cancer cohorts stratified by clinical groups to reduce biological hypotheses and guide translational investigations. Using BEANIE, we show how the consideration of sample-specific versus group biology greatly decreases the false positive rate and guides identification of robust signatures that can also be corroborated across different cell type compartments.
PRMT1 regulates EGFR and Wnt signaling pathways and is a promising target for combinatorial treatment of breast cancer
Authors: Suresh Samyuktha , Huard Solène , Brisson Amélie , Némati Fariba , Poulard Coralie , Ye Mengliang , Martel Elise , Reyes Cécile , Silvestre David C. , Meseure Didier , Nicolas André , Gentien David , Le Romancer Muriel , Decaudin Didier , Roman-Roman Sergio , Dubois Thierry
Published: October 2021

Identifying new therapeutic strategies for triple-negative breast cancer (TNBC) patients is a priority as these patients are highly prone to relapse after chemotherapy. Here, we found that protein arginine methyltransferase 1 (PRMT1) is highly expressed in all breast cancer subtypes. Its depletion decreases cell survival by inducing DNA damage and apoptosis in various breast cancer cell lines. Transcriptomic analysis and chromatin immunoprecipitation revealed that PRMT1 regulates the epidermal growth factor receptor (EGFR) and the Wnt signaling pathways, reported to be activated in TNBC. The enzymatic activity of PRMT1 is also required to stimulate the canonical Wnt pathway. Recently developed type I PRMT inhibitors decrease breast cancer cell proliferation and show anti-tumor activity in a TNBC xenograft model. These inhibitors display synergistic interactions with some chemotherapies used to treat TNBC patients, as well as the EGFR inhibitor, erlotinib. Therefore, targeting PRMT1 in combination with drugs used in the clinic may improve current treatments for TNBC patients.

Significance

This study highlights the requirement of PRMT1 for breast cancer cell survival and demonstrates the potential of targeting type I PRMTs in combination with chemotherapies in triple-negative breast cancer.
FABP7 Binds to Fatty Acid Micelles: Implications for Lipid Transport
Authors: Lenz Stefan , Bodnariuc Iulia , Renaud-Young Margaret , Shandro Tanille M. , MacCallum Justin L.
Published: October 2021

The transport of hydrophobic molecules, including long-chain fatty acids, within cells is highly dynamic. Hydrophobic molecules are unable to freely diffuse through the aqueous cytoplasm without a transporter. Fatty acid binding proteins (FABP) transport these molecules to different cellular compartments. As part of their transport, FABPs often associate with cell membranes to acquire and deliver their bound cargo. Understanding the nature of this transport is becoming increasingly important because lipid signaling functions are associated with metabolic pathways impacting disease pathologies such as carcinomas, autism and schizophrenia. Herein, we focus on Brain fatty acid binding protein (FABP7), which demonstrates localization to the cytoplasm and nucleus, influencing transcription and fatty acid metabolism. We use a combined biophysical approach to elucidate the interaction between FABP7 and model membranes. Specifically, we use microscale thermophoresis to show that FABP7 can bind oleic acid (OA) and docosahexaenoic acid (DHA) micelles, while differential scanning fluorimetry experiments show binding lowers the melting temperature of FABP7. Structural data from NMR and multiscale molecular dynamics simulations reveals that the interaction between FABP7 and micelles is through FABP7’s portal region residues. Our simulations also capture binding events where fatty acids dissociate from the model membrane and bind to FABP7. Overall, our data reveals a novel interaction between FABP7 and OA or DHA micelles and provides key structural insight into the transport of hydrophobic molecules.

Significance

This study examines how FABP7 binds to fatty acids at low and high fatty acid concentrations. Our binding assays, including microscale thermophoresis (MST) and Nile red fluorescence establish that FABP7 binds to both free fatty acids in solution and fatty acid micelles. NMR and computational experiments show that FABP7 specifically interacts with micelles through the portal region of the protein, thereby mediating ligand transfer into the binding cavity.
Extrachromosomal Amplification of Human Papillomavirus Episomes as a Mechanism of Cervical Carcinogenesis
Authors: Rossi Nicole M. , Dai Jieqiong , Xie Yi , Lou Hong , Boland Joseph F. , Yeager Meredith , Orozco Roberto , Alvirez Enrique , Mirabello Lisa , Gharzouzi Eduardo , Dean Michael
Published: October 2021

Integration of Human Papillomaviruses (HPV) is an important mechanism of carcinogenesis but is absent in a significant fraction of HPV16+ tumors. We applied long-read whole-genome sequencing (WGS) to cervical cancer cell lines and tumors. In two HPV16+ cell lines, we identified large tandem arrays of full-length and truncated viral genomes integrated into multiple locations indicating formation as extrachromosomal DNA (HPV superspreading). An HPV16+ cell line with episomal DNA has tandem arrays of full-length, truncated, and rearranged HPV16 genomes (multimer episomes). WGS of HPV16+ cervical tumors revealed that 11/20 with only episomal HPV (EP) have intact monomer episomes. The remaining nine EP tumors have multimer and rearranged HPV genomes. Most HPV rearrangements disrupt the E1 and E2 genes, and EP tumors overexpress the E6 and E7 viral oncogenes. Tumors with both episomal and integrated HPV16 display multimer episomes and concatemers of human and viral sequences. One tumor has a recurrent deletion of an inhibitory site regulating E6 and E7 expression, and another has a recurrent duplication consistent with HPV superspreading. Therefore, HPV16 can cause cancer without integration through aberrant episomal replication, forming rearranged and multimer episomes.
Clostridioides difficileinfection increases circulating p-cresol levels and dysregulates brain dopamine metabolism: linking gut-brain axis to autism spectrum disorders?
Authors: Vinithakumari Akhil A. , Padhi Piyush , Hernandez Belen , Je-Han Lin Susanne , Dunkerson-Kurzhumov Aaron , Showman Lucas , Breitzman Matthew , Stokes Caroline , Sulaiman Yousuf , Tangudu Chandra , Kuttappan Deepa Ashwarya , Muyyarikkandy Muhammed Shafeekh , Phillips Gregory , Anantharam Vellareddy , Perera Ann , Sponseller Brett , Kanthasamy Anumantha , Mooyottu Shankumar
Published: October 2021

Gastrointestinal illnesses are one of the most common comorbidities reported in patients with neurodevelopmental diseases, including autism spectrum disorders (ASD). Gut dysbiosis, overgrowth ofC. difficile, and gut microbiota-associated alterations in central neurotransmission have been implicated in ASD, where the dopaminergic axis plays an important role in the disease pathogenesis. HumanC. difficilestrains produce a significant amount of the toxic metabolite p-cresol, an inhibitor of dopamine beta-hydroxylase (DBH), which catalyzes the conversion of dopamine (DA) to norepinephrine (NE). p-Cresol is known to precipitate and exacerbate autistic behavior in rodents by increasing DA levels and altering DA receptor sensitivity in brain regions relevant to ASD. Therefore, we hypothesized thatC. difficileinfection dysregulates dopaminergic metabolism by increasing p-cresol levels in the gut and systemic circulation, and by inhibiting brain DBH, ultimately leading to elevated DA in different brain regions. For testing this hypothesis, we induced antibiotic-associatedC. difficileinfection in mice and determined the gut and serum p-cresol levels, serum DBH activity, and dopamine and its metabolite levels in different brain regions relevant to ASD. The results showed thatC. difficileinfection causes a significant increase in striatal DA, accompanied by significantly altered levels of DA metabolites and NE in different brain regions (p < 0.05). In addition, significantly increased circulating p-cresol levels and reduced DBH activity were observed inC. difficileinfected mice (p < 0.05). Therefore, the results from this study suggest a potential link betweenC. difficileinfection and alterations in the dopaminergic axis implicated in the precipitation and aggravation of ASD.
The mechanosensitive TRPV2 calcium channel controls human melanoma invasiveness and metastatic potential
Authors: Shoji Kenji F. , Bayet Elsa , Devedec Dahiana Le , Mallavialle Aude , Marionneau-Lambot Séverine , Leverrier-Penna Sabrina , Rambow Florian , Perret Raul , Joussaume Aurélie , Viel Roselyne , Fautrel Alain , Khammari Amir , Constantin Bruno , Tartare-Deckert Sophie , Penna Aubin
Published: October 2021

Discovery of therapeutic targets against metastasis is of primary importance since being the main cause of cancer-related death. Melanoma is a highly aggressive cancer endowed with a unique capacity of rapidly metastasizing. Deregulation of calcium homeostasis has been involved in numerous cellular metastatic behaviors, although the molecular determinants supporting these processes often remain unclear. Here, we evidenced a prominent expression of the plasma membrane TRPV2 calcium channel as a distinctive feature of melanoma tumors, directly related to melanoma metastatic progression and dissemination. In vitro as well as in vivo, TRPV2 activity was sufficient to confer both migratory and invasive phenotypes to non-invasive melanoma cells, while conversely upon TRPV2 silencing, highly metastatic melanoma cells failed to retain their malignant behaviors. We established a model whereupon activation of the mechanosensitive TRPV2 channel, localized in highly dynamic nascent adhesion clusters, directly regulates calpain-dependent cleavage of the adhesive protein talin together with F-actin network. By operating at the crossroad of the tumor microenvironment and the intracellular machinery, mechanosensitive TRPV2 channel controls melanoma cells aggressiveness. Finally in human melanoma tumor samples, TRPV2 overexpression represents a molecular marker of advanced malignancy and bad prognosis, highlighting a new therapeutic option for migrastatics in the treatment of metastatic melanoma.

Significance

One essential feature of metastatic cells is enhanced motility and invasiveness. This study evidences TRPV2 channel control over metastatic melanoma invasiveness, highlights new migration regulatory mechanisms, and reveals this channel as a biomarker and migrastatic target for the treatment of advanced melanoma.
Retinal self-organization: a model of RGC and SAC mosaic formation
Authors: de Montigny Jean , Sernagor Evelyne , Bauer Roman
Published: October 2021

Individual retinal cell types exhibit semi-regular spatial patterns called retinal mosaics. These mosaics enable uniform sampling of visual information and are formed to varying degrees across cell types. Retinal ganglion cells (RGC) and amacrine cells (including starburst amacrine cells (SAC)) are notably known to exhibit such layouts. Mechanisms responsible for the formation of such organised structures and their requirements are still not well understood. Mosaic formation follows three main principles: (1) homotypic cells prevent nearby cells from adopting the same type, (2) cell tangential migration, with homotypic cell repulsion, (3) cell death (with RGCs exhibiting high rates of apoptosis).

Here, we use BioDynaMo, an agent-based simulation framework, to build a detailed and mechanistic model of mosaic formation. In particular, we investigate the implications of the three theories for RGC’s mosaic formation. We report that the cell migration mechanism yields the most regular mosaics and that cell death can create regular mosaics only if the death rate is kept below 30%, after which cell death has a negative impact on mosaic regularity. In addition, and in accordance with recent studies, we propose here that low density RGC type mosaics exhibit on average low regularities, and thus we question the relevance of regular spacing as a criterion for a group of RGCs to form a RGC type.

We also investigate SAC mosaics formation and possible interactions between the ganglion cell layer (GCL) and inner nuclear layer (INL) populations. Investigations are conducted both experimentally and by applying our simulation model to the SAC population. We report that homotypic interactions between the GCL and INL populations during mosaics creation are required to reproduce the observed SAC mosaics’ characteristics. This suggests that the GCL and INL populations of SACs might not be independent during retinal development.

Author Summary

Retinal function depends on cells self-organisation during early development. Understanding the mechanisms underlying this self-organisation could improve not only our comprehension of the retina and its development but also of the cortex. Ultimately, this could lead to novel therapeutic approaches for developmental diseases. Computational models can be of precious help to study this process of self-organisation, given that they are biologically plausible. In this sense, it is important that implemented developmental mechanisms follow the principle of locally available information, without any global knowledge or external supervisor. Here, we follow this principle to investigate mosaic formation during retinal development. In this work, we demonstrate that tangential migration is the only mechanism able to form regular mosaics and that the GCL/INL SAC populations might not be independent during their mosaic formation. More, we question the relevance of regular spacing for RGC types classification.
Allosteric stabilization of calcium and phosphoinositide dual binding engages three synaptotagmins in fast exocytosis
Authors: Kobbersmed Janus R. L. , Berns Manon M. M. , Ditlevsen Susanne , Sørensen Jakob B. , Walter Alexander M.
Published: October 2021

Synaptic communication relies on the fusion of synaptic vesicles with the plasma membrane, which leads to neurotransmitter release. This exocytosis is triggered by brief and local elevations of intracellular Ca2+ with remarkably high sensitivity. How this is molecularly achieved is unknown. While synaptotagmins confer the Ca2+ sensitivity of neurotransmitter exocytosis, biochemical measurements reported Ca2+ affinities too low to account for synaptic function. However, synaptotagmin’s Ca2+ affinity increases upon binding the plasma membrane phospholipid PI(4,5)P2 and, vice versa, Ca2+-binding increases synaptotagmin’s PI(4,5)P2 affinity, indicating a stabilization of the Ca2+/PI(4,5)P2 dual-bound syt. We here devise a molecular exocytosis model based on this positive allosteric stabilization and the assumptions that (1.) synaptotagmin Ca2+/PI(4,5)P2 dual binding lowers the energy barrier for vesicle fusion and that (2.) the effect of multiple synaptotagmins on the energy barrier is additive. The model, which relies on biochemically measured Ca2+/PI(4,5)P2 affinities and protein copy numbers, reproduced the steep Ca2+ dependency of neurotransmitter release. Our results indicate that each synaptotagmin dual binding Ca2+/PI(4,5)P2 lowers the energy barrier for vesicle fusion by 4.85 kBT and that allosteric stabilization of this state enables the synchronized engagement of three synaptotagmins for fast exocytosis. Furthermore, we show that mutations altering synaptotagmin’s allosteric properties may show dominant-negative effects, even though synaptotagmins act independently on the energy barrier, and that dynamic changes of local PI(4,5)P2 (e.g. upon vesicle movement) dramatically impact synaptic responses. We conclude that allosterically stabilized Ca2+/PI(4,5)P2 dual binding enables synaptotagmins to exert their coordinated function in neurotransmission.
Quantitative fragmentomics allow affinity mapping of interactomes
Authors: Gogl Gergo , Zambo Boglarka , Kostmann Camille , Cousido-Siah Alexandra , Morlet Bastien , Durbesson Fabien , Negroni Luc , Eberling Pascal , Jane Pau , Nomine Yves , Zeke Andras , Østergaard Søren , Monsellier Elodie , Vincentelli Renaud , Trave Gilles
Published: October 2021

Human protein networks have been widely explored but most binding affinities remain unknown, hindering quantitative interactome-function studies. Yet interactomes rely on minimal interacting fragments displaying quantifiable affinities. Here we measured the affinities of 65,000 interactions involving PDZ domains and their target PDZ-binding motifs (PBM) within a human interactome region particularly relevant for viral infection and cancer. We calculate interactomic distances, identify hot spots for viral interference, generate binding profiles and specificity logos, and explain selected cases by crystallographic studies. Mass spectrometry experiments on cell extracts and literature surveys show that quantitative fragmentomics effectively complement protein interactomics by providing affinities and completeness of coverage, putting a full human interactome affinity survey within realistic reach. Finally, we show that interactome hijacking by the viral PBM of human papillomavirus (HPV) E6 oncoprotein deeply impacts the host cell proteome way beyond immediate E6 binders, illustrating the complex system-wide relationship between interactome and function.
Potential genetic robustness of Prnp and Sprn double knockout mouse embryos towards ShRNA-lentiviral inoculation
Authors: Rau Andrea , Passet Bruno , Castille Johan , Asset Alexandre , Lecardonnel Jérome , Moroldo Marco , Jaffrézic Florence , Laloë Denis , Moazami-Goudarzi Katayoun , Vilotte Jean-Luc
Published: October 2021

Shadoo, encoded by Sprn, and PrP, encoded by Prnp, are related proteins whose biological functions are still incompletely understood. Although previous knockdown experiments have suggested the necessity of Shadoo in the absence of PrP during early mouse embryogenesis, little impact of the double-knockout of these two loci was reported. To further investigate this apparent discrepancy, we compared the transcriptome of WT, Prnp0/0 and Prnp0/0, Sprn0/0 E6.5 mouse embryos following inoculation by Sprn-ShRNA or Prnp-ShRNA lentiviral vectors at the one-cell stage. Our results highlighted a significant induction of an apoptotic pathway in Prnp0/0 E6.5 mouse embryos inoculated with Sprn-ShRNA vectors alongside interferon and to a lesser extent inflammatory responses, confirming previous reported experiments. On the contrary, ShRNA vector inoculation in Prnp0/0, Sprn0/0 embryos did not induce apoptosis and resulted in lower interferon responses. Finally, comparisons of the transcriptome of WT and Prnp0/0, Sprn0/0 embryos revealed only slight differences, which may in part explain the genetic robustness observed in the latter genotype.

Highlights

Sprn-ShRNA lentivirus vector inoculation in Prnp knockout one-cell mouse embryos results in the induction of an apoptosis pathway at E6.5, alongside interferon and to a lesser extent inflammatory responses.

Sprn- or Prnp-ShRNA lentivirus vector inoculations in Prnp/Sprn knockout one-cell mouse embryos induce lower interferon responses and no apoptotic pathway at E6.5.

Although wild type and Prnp/Sprn knockout E6.5 mouse embryos are transcriptomically similar, some differences might explain this apparent resilience of the double knockout genotype.
Pattern Recognition Receptor for Bacterial Lipopolysaccharide in the Cytosol of Human Macrophages
Authors: Rojas-Lopez Maricarmen , Zajac Amanda S. , Wood Thomas E. , Miller Kelly A. , Gil-Marqués María Luisa , Hachey Austin C. , Kharbanda Vritti , Egger Keith T. , Goldberg Marcia B.
Published: October 2021

Endotoxin - bacterial lipopolysaccharide (LPS) - is a driver of the lethal infection sepsis through activation of innate immune responses. When delivered to the cytosol of macrophages, LPS (cLPS) induces the assembly of an inflammasome that contains caspases-4/5 in humans or caspase-11 in mice. Whereas activation of all other inflammasomes is triggered by sensing of pathogen products by a specific host cytosolic pattern recognition receptor protein, whether pattern recognition receptors for cLPS exist has been doubted by many investigators, as caspases-4, -5, and -11 bind and activate LPS directlyin vitro. Here we show that the primate-specific protein NLRP11 is a pattern recognition receptor for cLPS required for efficient activation of the caspase-4 inflammasome in human macrophages.NLRP11is present in humans and other primates, but absent in mice, likely explaining why it has been missed in screens looking for innate immune signaling molecules, most of which have been carried out in mice. NLRP11 is a previously missing link and a component of the human caspase-4 inflammasome activation pathway.

One Sentence Summary

Discovery that human macrophages contain a cytosolic receptor for bacterial lipopolysaccharide.
Novel regulation of the transcription factor ZHX2 by N-terminal methylation
Authors: Conner Meghan M. , Parker Haley V. , Falcone Daniela R. , Chung Gehoon , Schaner Tooley Christine E.
Published: October 2021

N-terminal methylation (Nα-methylation) by the methyltransferase NRMT1 is an important post-translational modification that regulates protein-DNA interactions. Accordingly, its loss impairs functions that are reliant on such interactions, including DNA repair and transcriptional regulation. Global loss of Nα-methylation results in severe developmental and premature aging phenotypes, but given over 300 predicted substrates, it is hard to discern which physiological substrates contribute to each phenotype. One of the most striking phenotypes in NRMT1 knockout (Nrmt1-/-) mice is early liver degeneration. To identify the disrupted signaling pathways leading to this phenotype and the NRMT1 substrates involved, we performed RNA-sequencing analysis of control and Nrmt1-/- adult mouse livers. We found both a significant upregulation of transcripts in the cytochrome P450 (CYP) family and downregulation of transcripts in the major urinary protein (MUP) family. Interestingly, transcription of both families is inversely regulated by the transcription factor zinc fingers and homeoboxes 2 (ZHX2). ZHX2 contains a non-canonical NRMT1 consensus sequence, indicating its function could be directly regulated by Nα-methylation. We confirmed misregulation of CYP and MUP mRNA and protein levels in Nrmt1-/- livers and verified NRMT1 can methylate ZHX2 in vitro. In addition, we used mutants of ZHX2 that cannot be methylated to directly demonstrate Nα-methylation promotes ZHX2 transcription factor activity. Finally, we show Nrmt1-/- mice also exhibit early postnatal de-repression of ZHX2 targets involved in fetal liver development. Taken together, these data implicate continual ZHX2 misregulation as a driving force behind the liver phenotype seen in Nrmt1-/- mice.
Drift on holey landscapes as a dominant evolutionary process
Authors: Dochtermann Ned A. , Klock Brady , Roff Derek A. , Royauté Raphaël
Published: October 2021

An organism’s phenotype has been shaped by evolution but the specific processes have to be indirectly inferred for most species. For example, correlations among traits imply the historical action of correlated selection and, more generally, the expression and distribution of traits is expected to be reflective of the adaptive landscapes that have shaped a population. However, our expectations about how quantitative traits—like most behaviors, physiological processes, and life-history traits—should be distributed under different evolutionary processes is not clear. Here we show that genetic variation in quantitative traits is not distributed as would be expected under dominant evolutionary models. Instead, we found that genetic variation in quantitative traits across 6 phyla and 60 species (including both Plantae and Animalia) is consistent with evolution across high dimensional “holey landscapes”. This suggests that the leading conceptualizations and modeling of the evolution of trait integration fail to capture how phenotypes are shaped and that traits are integrated in a manner contrary to predictions of dominant evolutionary theory. Our results demonstrate that our understanding of how evolution has shaped phenotypes remains incomplete and these results provide a starting point for reassessing the relevance of existing evolutionary models.

Significance Statement

We found that empirical estimations of how quantitative genetic variation is distributed do not correspond to typical Gaussian representations of fitness landscapes. These Gaussian landscapes underpin major areas of evolutionary biology and how selection is estimated in natural populations. Rather than being consistent with evolution on Gaussian landscapes, empirical estimates of genetic variation are, instead, consistent with evolution on high-dimensional “holey” landscapes. These landscapes represent situations where specific combinations of trait values are either viable or not and populations randomly drift among the viable combinations. This finding suggests that we have substantially misunderstood how selection actually shapes populations and thus how evolution typically proceeds.
Optimal confidence for unaware visuomotor deviations
Authors: Pereira Michael , Skiba Rafal , Cojan Yann , Vuilleumier Patrik , Bègue Indrit
Published: October 2021

Numerous studies have shown that humans can successfully correct deviations to ongoing movements without being aware of them, suggesting limited conscious monitoring of visuomotor performance. Here, we ask whether such limited monitoring impairs the capacity to judiciously place confidence ratings to reflect decision accuracy (metacognitive sensitivity). To this end, we recorded functional magnetic resonance imaging data while thirty-one participants reported visuomotor cursor deviations and rated their confidence retrospectively. We show that participants use a summary statistic of the unfolding visual feedback (the maximum cursor error) to detect deviations but that this information alone is insufficient to explain detection performance. The same summary statistics is used by participants to optimally adjust their confidence ratings, even for unaware deviations. At the neural level, activity in the ventral striatum tracked high confidence, whereas a broad network including the anterior prefrontal cortex encoded cursor error but not confidence, shedding new light on a role of the anterior prefrontal cortex for action monitoring rather than confidence. Together, our results challenge the notion of limited action monitoring and uncover a new mechanism by which humans optimally monitor their movements as they unfold, even when unaware of ongoing deviations.
Melanoma Addiction to GCDH is Mediated by NRF2 Tumor Suppressor Function
Authors: Verma Sachin , Crawford David , Khateb Ali , Feng Yongmei , Sergienko Eduard , Pathria Gaurav , Ma Chen-Ting , Olson Steven H , Scott David , Murad Rabi , Ruppin Eytan , Jackson Michael , Ronai Ze’ev A
Published: October 2021

Tumor dependency on specific metabolic signals has guided numerous therapeutic approaches. Here we identify melanoma addiction to the mitochondrial protein Glutaryl-CoA dehydrogenase (GCDH), a component in lysine metabolism which controls protein glutarylation. GCDH knockdown promoted apoptotic Unfolded Protein Response signaling and cell death in melanoma cells, an activity blocked by knockdown of the upstream lysine catabolism enzyme DHTKD1. Correspondingly, reduced GCDH expression correlated with improved survival of melanoma patients. A key mediator of GCDH-dependent melanoma cell death programs is the transcription factor NRF2, which induces ATF3, CHOP, and CHAC1 transcription linking lysine catabolism with the UPR signaling. NRF2 glutarylation upon GCDH KD increased its stability and DNA binding activity, which coincided with increased transcriptional activity, promoting apoptotic UPR signaling and tumor suppression. In vivo, genetic GCDH inhibition effectively inhibited melanoma tumor growth. Overall, these findings demonstrate an addiction of melanoma cells to GCDH, which by controlling NRF2 glutarylation limits apoptotic UPR signaling. Inhibiting the GCDH pathway could represent a novel therapeutic modality to treat melanoma.
selscan 2.0: scanning for sweeps in unphased data
Authors: Szpiech Zachary A.
Published: October 2021

Several popular haplotype-based statistics for identifying recent or ongoing positive selection in genomes require knowledge of haplotype phase. Here we provide an update to selscan which implements a re-definition of these statistics for use in unphased data.

Availability and Implementation

Source code and binaries freely available athttps://github.com/szpiech/selscan, implemented in C/C++ and supported on Linux, Windows, and MacOS.

Contact

szpiech@psu.edu

Supplemental Information

Online supplemental information available
NanoSplicer: Accurate identification of splice junctions using Oxford Nanopore sequencing
Authors: You Yupei , Clark Michael B. , Shim Heejung
Published: October 2021

Motivation

Long read sequencing methods have considerable advantages for characterising RNA isoforms. Oxford nanopore sequencing records changes in electrical current when nucleic acid traverses through a pore. However, basecalling of this raw signal (known as a squiggle) is error prone, making it challenging to accurately identify splice junctions. Existing strategies include utilising matched short-read data and/or annotated splice junctions to correct nanopore reads but add expense or limit junctions to known (incomplete) annotations. Therefore, a method that could accurately identify splice junctions solely from nanopore data would have numerous advantages.

Results

We developed “NanoSplicer” to identify splice junctions using raw nanopore signal (squiggles). For each splice junction the observed squiggle is compared to candidate squiggles representing potential junctions to identify the correct candidate. Measuring squiggle similarity enables us to compute the probability of each candidate junction and find the most likely one. We tested our method using 1. synthetic mRNAs with known splice junctions 2. biological mRNAs from a lung-cancer cell-line. The results from both datasets demonstrate NanoSplicer improves splice junction identification, especially when the basecalling error rate near the splice junction is elevated. Our method is implemented in the software package NanoSplicer, available at https://github.com/shimlab/NanoSplicer.
Spatiotemporal transcriptome at single-cell resolution reveals key radial glial cell population in axolotl telencephalon development and regeneration
Authors: Wei Xiaoyu , Fu Sulei , Li Hanbo , Liu Yang , Wang Shuai , Feng Weimin , Yang Yunzhi , Liu Xiawei , Zeng Yan-Yun , Cheng Mengnan , Lai Yiwei , Qiu Xiaojie , Wu Liang , Zhang Nannan , Jiang Yujia , Xu Jiangshan , Su Xiaoshan , Peng Cheng , Han Lei , Lou Wilson Pak-Kin , Liu Chuanyu , Yuan Yue , Ma Kailong , Yang Tao , Pan Xiangyu , Gao Shang , Chen Ao , Esteban Miguel A. , Yang Huanming , Wang Jian , Fan Guangyi , Liu Longqi , Chen Liang , Xu Xun , Fei Ji-Feng , Gu Ying
Published: October 2021

Brain regeneration requires a precise coordination of complex responses in a time- and region-specific manner. Identifying key cell types and molecules that direct brain regeneration would provide potential targets for the advance of regenerative medicine. However, progress in the field has been hampered largely due to limited regeneration capacity of the mammalian brain and understanding of the regeneration process at both cellular and molecular level. Here, using axolotl brain with extrodinary regeneration ability upon injury, and the SpaTial Enhanced REsolution Omics-sequencing (Stereo-seq), we reconstructed the first architecture of axolotl telencephalon with gene expression profiling at single-cell resolution, and fine cell dynamics maps throughout development and regeneration. Intriguingly, we discovered a marked heterogeneity of radial glial cell (RGC) types with distinct behaviors. Of note, one subtype of RGCs is activated since early regeneration stages and proliferates while other RGCs remain dormant. Such RGC subtype appears to be the major cell population involved in early wound healing response and gradually covers the injured area before presumably transformed into the lost neurons. Altogether, our work systematically decoded the complex cellular and molecular dynamics of axolotl telencephalon in development and regeneration, laying the foundation for studying the regulatory mechanism of brain regeneration in the future.
Retraction ATPase motors from three orthologous type IVa pilus systems support promiscuous retraction of the Vibrio cholerae competence pilus
Authors: Couser Evan , Chlebek Jennifer L. , Dalia Ankur B.
Published: October 2021

Bacterial surface appendages called type IVa pili (T4aP) promote diverse activities including DNA uptake, twitching motility, and virulence. These activities rely on the ability of T4aP to dynamically extend and retract from the cell surface. Dynamic extension relies on a motor ATPase commonly called PilB. Most T4aP also rely on specific motor ATPases, commonly called PilT and PilU, to dynamically and forcefully retract. Here, we systematically assess whether motor ATPases from three orthologous T4aP can functionally complement Vibrio cholerae mutants that lack their endogenous motors. We found that the PilT and PilU retraction ATPases from the three T4aP systems tested are promiscuous and promote retraction of the V. cholerae competence T4aP despite a high degree of sequence divergence. In contrast, the orthologous extension ATPases from the same T4aP systems were not able to mediate extension of the V. cholerae competence T4aP despite exhibiting a similar degree of sequence divergence. Also, we show that one of the PilT orthologs characterized does not support PilU-dependent retraction and provide some data to indicate that the C-terminus of PilT is important for PilU-dependent retraction. Together, our data suggest that retraction ATPases may have maintained a high degree of promiscuity for promoting retraction of T4aP, while extension ATPases may have evolved to become specific for their cognate systems.

IMPORTANCE

One way that bacteria interact with their environments is via hair-like appendages called type IVa pili (T4aP). These appendages dynamically extend and retract from the cell surface via the action of distinct ATPase motors. T4aP are present in diverse bacterial species. Here, we demonstrate that retraction motors from three T4aP are promiscuous, and capable of promoting retraction of a heterologous T4aP system. By contrast, the extension ATPase motors from these same T4aP systems are specific and cannot promote extension of a heterologous T4aP. Thus, these results suggest that T4aP extension may be more tightly regulated compared to T4aP retraction.
Loss-of-function, gain-of-function and dominant-negative mutations have profoundly different effects on protein structure: implications for variant effect prediction
Authors: Gerasimavicius Lukas , Livesey Benjamin J , Marsh Joseph A.
Published: October 2021

Most known pathogenic mutations occur in protein-coding regions of DNA and change the way proteins are made. Taking protein structure into account has therefore provided great insight into the molecular mechanisms underlying human genetic disease. While there has been much focus on how mutations can disrupt protein structure and thus cause a loss of function (LOF), alternative mechanisms, specifically dominant-negative (DN) and gain-of-function (GOF) effects, are less understood. Here, we have investigated the protein-level effects of pathogenic missense mutations associated with different molecular mechanisms. We observe striking differences between recessive vs dominant, and LOF vs non-LOF mutations, with dominant, non-LOF disease mutations having much milder effects on protein structure, and DN mutations being highly enriched at protein interfaces. We also find that nearly all computational variant effect predictors underperform on non-LOF mutations, even those based solely on sequence conservation. However, we do find that non-LOF mutations could potentially be identified by their tendency to cluster in three-dimensional space. Overall, our work suggests that many pathogenic mutations that act via DN and GOF mutations are likely being missed by current variant prioritisation strategies, but that there is considerable scope to improve computational predictions through consideration of molecular disease mechanisms.