bluuebunny/crossref_metadata_2025 huggingface dataset:
Predicting identity-preserving object transformations across the human ventral visual stream
Authors: Mocz Viola , Vaziri-Pashkam Maryam , Chun Marvin , Xu Yaoda
Published: August 2020

In everyday life, we have no trouble recognizing and categorizing objects as they change in position, size, and orientation in our visual fields. This phenomenon is known as object invariance. Previous fMRI research suggests that higher-level object processing regions in the human lateral occipital cortex may link object responses from different affine states (i.e. size and viewpoint) through a general linear mapping function with the learned mapping capable of predicting responses of novel objects. In this study, we extended this approach to examine the mapping for both Euclidean (e.g. position and size) and non-Euclidean (e.g. image statistics and spatial frequency) transformations across the human ventral visual processing hierarchy, including areas V1, V2, V3, V4, ventral occipitotemporal cortex (VOT), and lateral occipitotemporal cortex (LOT). The predicted pattern generated from a linear mapping could capture a significant amount, but not all, of the variance of the true pattern across the ventral visual pathway. The derived linear mapping functions were not entirely category independent as performance was better for the categories included in the training. Moreover, prediction performance was not consistently better in higher than lower visual regions, nor were there notable differences between Euclidean and non-Euclidean transformations. Together, these findings demonstrate a near-orthogonal representation of object identity and non-identity features throughout the human ventral visual processing pathway, with the non-identity features largely untangled from the identity features early in the visual processing.

Significance Statement

Presently we still do not fully understand how object identity and non-identity (e.g. position, size) information are simultaneously represented in the primate ventral visual system to form invariant representations. Previous work suggests that the human lateral occipital cortex may be linking different affine states of object representations through general linear mapping functions. Here we show that across the entire human ventral processing pathway, we could link object responses in different states of non-identity transformations through linear mapping functions for both Euclidean and non-Euclidean transformations. These mapping functions are not identity-independent, suggesting that object identity and non-identity features are represented in a near, rather than a completely, orthogonal manner.
Intercellular Arc signaling regulates vasodilation
Authors: Barragan-Iglesias Paulino , de la Peña June Bryan , Lou Tzu-Fang , Loerch Sarah , Kunder Nikesh , Shukla Tarjani , Basavarajappa Lokesh , Song Jane , Megat Salim , Moy Jamie K. , Wanghzou Andi , Ray Pradipta R. , Shepherd Jason , Hoyt Kenneth , Steward Oswald , Price Theodore J. , Campbell Zachary T.
Published: August 2020

Injury responses require communication between different cell types in the skin. Sensory neurons contribute to inflammation and can secrete signaling molecules that affect non-neuronal cells. Despite the pervasive role of translational regulation in nociception, the contribution of activity-dependent protein synthesis to inflammation is not well understood. To address this problem, we examined the landscape of nascent translation in DRG neurons treated with inflammatory mediators using ribosome profiling. We identified the activity-dependent gene, Arc, as a target of privileged translationin vitroandin vivo. Inflammatory cues promote local translation of Arc in the skin. Arc deficient mice display exaggerated paw temperatures and vasodilation in response to an inflammatory challenge. Since Arc has recently been shown to be released from neurons in extracellular vesicles, we hypothesized that intercellular Arc signaling regulates the inflammatory response in skin. We found that the excessive thermal responses and vasodilation observed in Arc defective mice are rescued by injection of Arc-containing extracellular vesicles into the skin. Our findings suggest that activity-dependent production of Arc in afferent fibers regulates neurogenic inflammation through intercellular signaling.

HIGHLIGHTS

Ribosome profiling identifies Arc as a target of activity-dependent translation

Arc is present in the DRG, spinal cord, and skin

Induced Arc biosynthesis in skin requires the presence of afferent fibers

Arc-deficient mice have exaggerated inflammation that is rescued by Arc-containing extracellular vesicles
Hydroxychloroquine: mechanism of action inhibiting SARS-CoV2 entry
Authors: Yuan Zixuan , Pavel Mahmud Arif , Wang Hao , Hansen Scott B.
Published: August 2020

Hydroxychloroquine (HCQ) has been proposed in the treatment of SARS-coronavirus 2 (SARS-CoV-2) infection, albeit with much controversy.In vitro, HCQ effectively inhibits viral entry, but its use in the clinic has been hampered by conflicting results. A better understanding of HCQ’s mechanism of actionsin vitrois needed to resolve these conflicts. Recently, anesthetics were shown to disrupt ordered monosialotetrahexosylganglioside1 (GM1) lipid rafts. These same lipid rafts recruit the SARS-CoV-2 surface receptor angiotensin converting enzyme 2 (ACE2) to an endocytic entry point, away from phosphatidylinositol 4,5 bisphosphate (PIP2) domains. Here we employed super resolution imaging of cultured mammalian cells to show HCQ directly perturbs GM1 lipid rafts and inhibits the ability of ACE2 receptor to associate with the endocytic pathway. HCQ also disrupts PIP2domains and their ability to cluster and sequester ACE2. Similarly, the antibiotic erythromycin inhibits viral entry and both HCQ and erythromycin decrease the antimicrobial host defense peptide amyloid beta in cultured cells. We conclude HCQ is an anesthetic-like compound that disrupts GM1 lipid rafts similar to anesthetics. The disruption likely decreases viral clustering at both endocytic and putative PIP2entry points.

KEY POINTS

Question:What is the molecular basis for antiviral activity of hydroxychloroquine?

Findings:Hydroxychloroquine disrupt lipid rafts similar to general anesthetics.

Meaning:Since lipids cluster ACE2 and facilitate viral entry, hydroxychloroquine appears to inhibit viral entry by disrupting the lipid clustering of the SARS-CoV2 receptor.
Genome-wide predictions of genetic redundancy inArabidopsis thaliana
Authors: Cusack Siobhan A. , Wang Peipei , Moore Bethany M. , Meng Fanrui , Conner Jeffrey K. , Krysan Patrick J. , Lehti-Shiu Melissa D. , Shiu Shin-Han
Published: August 2020

Genetic redundancy refers to a situation where an individual with a loss-of-function mutation in one gene (single mutant) does not show an apparent phenotype until one or more paralogs are also knocked out (double/higher-order mutant). Previous studies have identified some characteristics common among redundant gene pairs, but a predictive model of genetic redundancy incorporating a wide variety of features has not yet been established. In addition, the relative importance of these characteristics for genetic redundancy remains unclear. Here, we establish machine learning models for predicting whether a gene pair is likely redundant or not in the model plantArabidopsis thaliana. Benchmark gene pairs were classified based on six feature categories: functional annotations, evolutionary conservation including duplication patterns and mechanisms, epigenetic marks, protein properties including post-translational modifications, gene expression, and gene network properties. The definition of redundancy, data transformations, feature subsets, and machine learning algorithms used affected model performance significantly. Among the most important features in predicting gene pairs as redundant were having a paralog(s) from recent duplication events, annotation as a transcription factor, downregulation during stress conditions, and having similar expression patterns under stress conditions. Predictions were then tested using phenotype data withheld from model building and validated using well-characterized, redundant and nonredundant gene pairs. This genetic redundancy model sheds light on characteristics that may contribute to long-term maintenance of paralogs that are seemingly functionally redundant, and will ultimately allow for more targeted generation of functionally informative double mutants, advancing functional genomic studies.
Maternalschistosomiasisimpairs offspring IL-4 production and B cell expansion
Authors: Cortes-Selva Diana , Gibbs Lisa , Ready Andrew , Ekiz H. Atakan , Rajwa Bartek , Fairfax Keke C.
Published: August 2020

Maternal helminth infections are a global public health concern and correlate with altered infant immune responses to some childhood immunizations, but a mechanistic understanding of how maternal helminth infection alters the cellular immune responses of offspring is lacking. Here we establish a model of maternalSchistosoma mansoniinfection in dual IL-4 reporter mice. We find that offspring born to mothers infected withS. mansonihave impaired production of IL-4 during homoeostasis, and following immunization with a Tetanus-Diphtheria vaccine. We identified that iNKT cells are the dominant source of IL-4 during early life homeostasis, and that diminished IL-4 production was associated with both reduced B cell and follicular dendritic cell responses. These defects were maintained long-term, affecting memory B and T cell responses. Single-cell RNASeq analysis of immunized offspring identified egg antigen-dependent reductions in B-cell cell cycle and proliferation-related genes. These data reveal that maternal infection leads to long-lasting defects in the cellular responses to heterologous antigens and provide vital insight into the influence of maternal infection on offspring immunity.
Transient delivery of A-C/EBP protein perturbs differentiation of 3T3-L1 cells and induces preadipocyte marker genes
Authors: Sharma Nishtha , Kaur Raminder , Yadav Binduma , Shah Koushik , Pandey Harshita , Choudhary Diksha , Jain Prateek , Aggarwal Aanchal , Vinson Charles , Rishi Vikas
Published: August 2020

Transformation of committed 3T3-L1 preadipocytes to lipid-laden adipocytes involves timely appearance of numerous transcription factors (TFs), foremost among them C/EBPβ, is expressed during early phases of differentiation. Here we describe liposome-mediated protein transfection approach to rapidly downregulate C/EBPβ by A-C/EBP protein inhibitor. Signals from tagged A-C/EBP were observed in 3T3-L1 cells within 2hrs of protein inhibitor transfections whereas for gene transfection signals appeared in 48hrs. Following transient transfections, expression profiles of 24 marker genes belonging to pro- and anti-adipogenic, cell cycle, and preadipocytes pathways was analyzed. mRNA and protein expression profiles of adipocyte-marker genes showed lower expression in both A-C/EBP protein and gene transfected samples. Interestingly, for preadipocytes and cell fate determinant genes, striking differences were observed between protein and gene transfected samples. Preadipocyte differentiation factors Stat5a and Creb were downregulated in A-C/EBP protein samples. Five preadipocyte markers, namely,Pdgfrα, Pdgfrβ, Ly6A, CD34 Itgb1showed high expression in protein samples whereas onlyLy6AandCD34were expressed in gene transfected samples.PdgfrαandPdgfrβ, two known cell fate markers were expressed in protein transfected samples 5-days post-differentiation suggesting a possible reversal of differentiation. Our study provides evidences for the robust and efficient knockdown of C/EBPβ protein to understand time-dependent gene regulation during adipogenesis.
At least seven distinct rotavirus genotype constellations in bats with evidence of reassortment and zoonotic transmissions
Authors: Simsek Ceren , Corman Victor Max , Everling Hermann Ulrich , Lukashev Alexander N. , Rasche Andrea , Maganga Gael Darren , Binger Tabea , Jansen Daan , Beller Leen , Deboutte Ward , Gloza-Rausch Florian , Seebens-Hoyer Antje , Yordanov Stoian , Sylverken Augustina , Oppong Samuel , Sarkodie Yaw Adu , Vallo Peter , Leroy Eric M. , Bourgarel Mathieu , Yinda Kwe Claude , Van Ranst Marc , Drosten Christian , Drexler Jan Felix , Matthijnssens Jelle
Published: August 2020

Bats host many viruses pathogenic to humans, and increasing evidence suggests that Rotavirus A (RVA) also belongs to this list. Rotaviruses cause diarrheal disease in many mammals and birds, and their segmented genomes allow them to reassort and increase their genetic diversity. Eighteen out of 2,142 bat fecal samples (0.8%) collected from Europe, Central America and Africa were PCR-positive for RVA and 11 of those were fully characterized using viral metagenomics. Upon contrasting their genomes with publicly available data, at least 7 distinct bat RVA genotype constellations (GCs) were identified, including evidence of reassortments and 6 novel genotypes. Some of these constellations are spread across the world, whereas others appear to be geographically restricted. Our analyses also suggest that several unusual human and equine RVA strains might be of bat RVA origin, based on their phylogenetic clustering, despite varying levels of nucleotide sequence identities between them. Although SA11 is one of the most widely used reference strains for RVA research and forms the backbone of a reverse genetics system, its origin remained enigmatic. Remarkably, the majority of the genotypes of SA11-like strains were shared with Gabonese bat RVAs, suggesting a potential common origin. Overall, our findings suggest an underexplored genetic diversity of RVAs in bats, which is likely only the tip of the iceberg. Increasing contact between humans and bat wildlife will further increase the zoonosis risk, which warrants closer attention to these viruses.

Importance

The increased research on bat coronaviruses after SARS-CoV and MERS-CoVallowed the very rapid identification of SARS-CoV-2. This is an excellent example of the importance of knowing viruses harbored by wildlife in general and bats in particular, for global preparedness against emerging viral pathogens. The current effort to characterize bat rotavirus strains from 3 continents shed light on the vast genetic diversity of rotaviruses and also hinted at a bat origin for several atypical rotaviruses in humans and animals, implying that zoonoses of bat rotaviruses might occur more frequently than currently realized.
The proteasome-related Connectase is a fast and specific protein ligase
Authors: Fuchs Adrian C. D. , Ammelburg Moritz , Martin Jörg , Hartmann Marcus D. , Lupas Andrei N.
Published: August 2020

Genetic methods allow the recombinant production of any protein of interest, but yield the full-length construct in one step and are limited to native amino acids. For the “on demand” generation of chimeric, immobilized, fluorophore-conjugated or segmentally labeled proteins, these proteins must be modified using chemical1,2, (split) intein2,3, split domain4or enzymatic methods5. While each of these options comes with its own advantages and drawbacks, ligase enzymes are often used where small ligation motifs and good chemoselectivity are required. However, applications with the reference enzyme Sortase A are impeded by poor catalytic efficiencies, low substrate specificities and side reactions6,7. Here, we present the discovery of Connectase, a monomeric proteasome homolog that ligates substrates via a highly conserved KDPGA motif originally identified in methyltransferase A (MtrA), a key enzyme in archaeal methanogenesis. Connectase displays nanomolar affinity and thus great specificity for its substrates, allowing efficient protein-protein ligations even in complex solutions and at low substrate concentrations. Compared to an optimized Sortase variant, Connectase catalyzes such ligations at substantially higher rates, with higher yields but without detectable side reactions and thus presents a valuable new tool for protein conjugations.
Identifying causes of social evolution: The Price approach, contextual analysis, and multilevel selection
Authors: Thies Christoph , Watson Richard A.
Published: August 2020

Kin selection theory and multilevel selection theory are different approaches to explaining the evolution of social traits. The latter claims that it is useful to regard selection as a process that can occur on multiple levels of organisation such as the level of individuals and the level of groups. This is reflected in a decomposition of fitness into an individual component and a group component. However, the two major statistical tools to determine the coefficients of such a decomposition, the multilevel Price equation and contextual analysis, are inconsistent and may disagree on whether group selection is present. Here we show that the reason for the discrepancies is that underlying the multilevel Price equation and contextual analysis are two nonequivalent causal models for the generation of individual fitness effects (thus leaving different ‘remainders’ explained by group effects). While the multilevel Price equation assumes that the individual effect of a trait determines an individual’s relative success within a group, contextual analysis posits that the individual effect is context-independent. Since these different assumptions reflect claims about the causal structure of the system, the correct approach cannot be determined on general theoretical or statistical grounds but must be identified by experimental intervention. We outline interventions that reveal the underlying causal structure and thus facilitate choosing the appropriate approach. We note that the reductionist viewpoint of kin selection theory with its focus on the individual is immune to such inconsistency because it does not address causal structure with respect to levels of organisation. In contrast, our analysis of the two approaches to measuring group selection demonstrates that multilevel selection theory adds meaningful (falsifiable) causal structure to explain the sources of individual fitness and thereby constitutes a proper refinement of kin selection theory.
Cdc42 reactivation at growth sites is regulated by local cell-cycle-dependent loss of its GAP Rga4
Authors: Rich-Robinson Julie , Russell Afton , Mancini Eleanor , Das Maitreyi
Published: August 2020

In fission yeast, polarized cell growth stops during division and resumes after cell separation. We uncoupled these sequential events by delaying cytokinesis with a temporary Latrunculin A treatment. Mitotic cells recovering from treatment initiate end growth without cell separation, displaying apolar elongationsansseparation (PrESS) phenotype. PrESS cell ends reactivate Cdc42, a major regulator of polarized growth, before cell separation, but at a fixed time after anaphase B. A candidate screen implicates Rga4, a negative regulator of Cdc42, in this process. We show that Rga4 appears punctate at the cell sides during G2, but is diffuse during mitosis, extending to the ends. While the Morphogenesis Orb6 (MOR) pathway is known to promote cell separation and growth by activating protein synthesis, we find that for polarized growth, removal of Rga4 from the ends is also necessary. Therefore, we propose that growth resumes after division once the MOR pathway is activated and the ends lose Rga4 in a cell-cycle-dependent manner.
A combined proteomics and Mendelian randomization approach to investigate the effects of aspirin-targeted proteins on colorectal cancer
Authors: Nounu Aayah , Greenhough Alexander , Heesom Kate J , Richmond Rebecca C , Zheng Jie , Weinstein Stephanie J , Albanes Demetrius , Baron John A , Hopper John L , Figueiredo Jane C , Newcomb Polly A , Lindor Noralane M , Casey Graham , Platz Elizabeth A , Le Marchand Loïc , Ulrich Cornelia M , Li Christopher I , van Duijnhoven Fränzel JB , Gsur Andrea , Campbell Peter T , Moreno Víctor , Vodicka Pavel , Vodickova Ludmila , Brenner Hermann , Chang-Claude Jenny , Hoffmeister Michael , Sakoda Lori C , Slattery Martha L , Schoen Robert E , Gunter Marc J , Castellví-Bel Sergi , Kim Hyeong Rok , Kweon Sun-Seog , Chan Andrew T , Li Li , Zheng Wei , Bishop D Timothy , Buchanan Daniel D , Giles Graham G , Gruber Stephen B , Rennert Gad , Stadler Zsofia K , Harrison Tabitha A , Lin Yi , Keku Temitope O , Woods Michael O , Schafmayer Clemens , Van Guelpen Bethany , Gallinger Steven J , Hampel Heather , Berndt Sonja I , Pharoah Paul D P , Lindblom Annika , Wolk Alicja , Wu Anna H , White Emily , Peters Ulrike , Drew David A , Scherer Dominique , Bermejo Justo Lorenzo , Williams Ann C , Relton Caroline L
Published: August 2020

Background

Evidence for aspirin’s chemopreventative properties on colorectal cancer (CRC) is substantial, but its mechanism of action is not well-understood. We combined a proteomic approach with Mendelian randomization (MR) to identify possible new aspirin targets that decrease CRC risk.

Methods

Human colorectal adenoma cells (RG/C2) were treated with aspirin (24 hours) and a stable isotope labelling with amino acids in cell culture (SILAC) based proteomics approach identified altered protein expression. Protein quantitative trait loci (pQTLs) from INTERVAL (N=3,301) and expression QTLs (eQTLs) from the eQTLGen Consortium (N=31,684) were used as genetic proxies for protein and mRNA expression levels. Two-sample MR of mRNA/protein expression on CRC risk was performed using eQTL/pQTL data combined with CRC genetic summary data from the Colon Cancer Family Registry (CCFR), Colorectal Transdisciplinary (CORECT), Genetics and Epidemiology of Colorectal Cancer (GECCO) consortia and UK Biobank (55,168 cases and 65,160 controls).

Results

Altered expression was detected for 125/5886 proteins. Of these, aspirin decreased MCM6, RRM2 and ARFIP2 expression and MR analysis showed that a standard deviation increase in mRNA/protein expression was associated with increased CRC risk (OR:1.08, 95% CI:1.03-1.13, OR:3.33, 95% CI:2.46-4.50 and OR:1.15, 95% CI:1.02-1.29, respectively).

Conclusion

MCM6 and RRM2 are involved in DNA repair whereby reduced expression may lead to increased DNA aberrations and ultimately cancer cell death, whereas ARFIP2 is involved in actin cytoskeletal regulation indicating a possible role in aspirin’s reduction of metastasis.

Impact

Our approach has shown how laboratory experiments and population-based approaches can combine to identify aspirin-targeted proteins possibly affecting CRC risk.
A non-canonical function for Centromere-associated protein-E (CENP-E) controls centrosome integrity and orientation of cell division
Authors: Owa Mikito , Dynlacht Brian
Published: August 2020

Centromere-associated protein-E (CENP-E) is a kinesin motor localizing at kinetochores. Although its mitotic functions have been well studied, it has been challenging to investigate direct consequences of CENP-E removal using conventional methods because CENP-E depletion results in mitotic arrest. In this study, we harnessed an auxin-inducible degron system to achieve acute degradation of CENP-E. We revealed a kinetochore-independent role for CENP-E that removes pericentriolar material 1 (PCM1) from centrosomes in G2phase. After acute loss of CENP-E, centrosomal Polo-like kinase 1 (Plk1) is sequestered by accumulated PCM1, resulting in aberrant phosphorylation and destabilization of centrosomes, which triggers loss of astral microtubules and oblique cell divisions. Furthermore, we also observed centrosome and cell division defects in cells from a microcephaly patient with mutations inCENPE. Orientation of cell division is deregulated in some microcephalic patients, and our unanticipated findings provide a unifying principle that explains how microcephaly can result from centrosomal defects.
DPP9 directly sequesters the NLRP1 C-terminus to repress inflammasome activation
Authors: Hollingsworth L. Robert , Sharif Humayun , Griswold Andrew R. , Fontana Pietro , Mintseris Julian , Dagbay Kevin B. , Paulo Joao A. , Gygi Steven P. , Bachovchin Daniel A. , Wu Hao
Published: August 2020

NLRP1 is a cytosolic inflammasome sensor that mediates activation of caspase-1, which in turn induces cytokine maturation and pyroptotic cell death1-6. Gain-of-function NLPR1 mutations cause skin inflammatory diseases including carcinoma, keratosis, and papillomatosis7-14. NLRP1 contains a unique function-to-find domain (FIIND) that autoproteolyzes into noncovalently associated subdomains15-18. Proteasomal degradation of the autoinhibitory N-terminal fragment (NT) activates NLRP1 by releasing the inflammatory C-terminal fragment (CT)19,20. Cytosolic dipeptidyl peptidases 8 and 9 (DPP8/9) interact with NLRP1, and small-molecule DPP8/9 inhibitors activate NLRP1 by poorly characterized mechanisms11,19,21. Here, we report cryo-EM structures of the human NLRP1-DPP9 complex, alone and in complex with the DPP8/9 inhibitor Val-boroPro (VbP). Surprisingly, the NLRP1-DPP9 complex is a ternary complex comprised of DPP9, one intact FIIND of a non-degraded full-length NLRP1 (NLRP1-FL) and one NLRP1-CT freed by NT degradation. The N-terminus of the NLRP1-CT unfolds and inserts into the DPP9 active site but is not cleaved by DPP9, and this binding is disrupted by VbP. Structure-based mutagenesis reveals that the binding of NLRP1-CT to DPP9 requires NLRP1-FL and vice versa, and inflammasome activation by ectopic NLRP1-CT expression is rescued by co-expressing autoproteolysis-deficient NLRP1-FL. Collectively, these data indicate that DPP9 functions as a “bomb-diffuser” to prevent NLRP1-CTs from inducing inflammation during homeostatic protein turnover.
Single-cell dynamics of pannexin-1-facilitated programmed ATP loss during apoptosis
Authors: Imamura Hiromi , Sakamoto Shuichiro , Yoshida Tomoki , Matsui Yusuke , Penuela Silvia , Laird Dale W. , Mizukami Shin , Kikuchi Kazuya , Kakizuka Akira
Published: August 2020

ATP is essential for all living cells. However, how dead cells lose ATP has not been well investigated. In this study, we developed new FRET biosensors for dual imaging of intracellular ATP level and caspase-3 activity in single apoptotic cultured human cells. We show that the cytosolic ATP level starts to decrease immediately after the activation of caspase-3, and this process is completed typically within 2 hours. The ATP decrease was facilitated by caspase-dependent cleavage of the plasma membrane channel pannexin-1, indicating that the intracellular decrease of the apoptotic cell is a “programmed” process. Apoptotic cells deficient of pannexin-1 sustained the ability to produce ATP through glycolysis and to consume ATP, and did not stop wasting glucose much longer period than normal apoptotic cells. Thus, the pannexin-1 plays a role in arresting the metabolic activity of dead apoptotic cells, most likely through facilitating the loss of intracellular ATP. (148 words)
PRG2 and AQPEP are misexpressed in fetal membranes in placenta previa and percreta
Authors: Zhang Elisa T. , Hannibal Roberta L. , Badillo Rivera Keyla M. , Song Janet H.T. , McGowan Kelly , Zhu Xiaowei , Meinhardt Gudrun , Knöfler Martin , Pollheimer Jürgen , Urban Alexander E. , Folkins Ann K. , Lyell Deirdre J. , Baker Julie C.
Published: August 2020

The obstetrical conditions placenta accreta spectrum (PAS) and placenta previa are a significant source of pregnancy-associated morbidity and mortality, yet the specific molecular and cellular underpinnings of these conditions are not known. In this study, we identified misregulated gene expression patterns in tissues from placenta previa and percreta (the most extreme form of PAS) compared with control cases. By comparing this gene set with existing placental single-cell and bulk RNA-Seq datasets, we show that the upregulated genes predominantly mark extravillous trophoblasts. We performed immunofluorescence on several candidate molecules and found that PRG2 and AQPEP protein levels are upregulated in both the fetal membranes and the placental disk in both conditions. While this increased AQPEP expression remains restricted to trophoblasts, PRG2 is mislocalized and is found throughout the fetal membranes. Using a larger patient cohort with a diverse set of gestationally aged-matched controls, we validated PRG2 as a marker for both previa and PAS and AQPEP as a marker for only previa in the fetal membranes membranes. Our findings suggest that the extraembryonic tissues surrounding the conceptus, including both the fetal membranes membranes and the placental disk, harbor a signature of previa and PAS that reflects increased trophoblast invasiveness.

Summary sentence

3SEQ and immunofluorescence reveal that extravillous trophoblast factors, most notably PRG2 and AQPEP, define the diseases placenta previa and placenta accreta spectrum (PAS) in both the chorioamniotic membranes and the placental disk.
The origins and consequences ofUPF1variants in pancreatic adenosquamous carcinoma
Authors: Polaski Jacob T. , Udy Dylan B. , Escobar-Hoyos Luisa F. , Askan Gokce , Leach Steven D. , Ventura Andrea , Kannan Ram , Bradley Robert K.
Published: August 2020

Pancreatic adenosquamous carcinoma (PASC) is a rare and aggressive subtype of pancreatic cancer whose mutational origins are poorly understood. An early study reported somatic mutations inUPF1, which encodes a core component of the nonsense-mediated mRNA decay (NMD) pathway, as a common signature of PASC, but subsequent studies did not observe these lesions in other PASC cohorts. The corresponding controversy about whetherUPF1mutations are important contributors to PASC has been exacerbated by a paucity of functional studies of these lesions. Here, we systematically assessed the potential roles ofUPF1mutations in PASC. We modeled two reportedUPF1mutations to find no consistent effects on pancreatic cancer growth, acquisition of adenosquamous features,UPF1splicing, UPF1 protein levels, or NMD efficiency. We subsequently discovered that ~40% ofUPF1mutations reportedly present in PASCs are identical to standing genetic variation in the human population, suggesting that they are likely non-pathogenic inherited variation rather than pathogenic mutations. Our data suggest thatUPF1is not a common functional driver of PASC and motivate further attempts to identify unique genetic features defining these malignancies.
Multicellular Organoids of the Neurovascular Blood-Brain Barrier: A New Platform for Precision Neuronanomedicine
Authors: Kumarasamy Murali , Sosnik Alejandro
Published: August 2020

The treatment of neurological disorders (NDs) is challenged by low drug permeability from the systemic circulation into the central nervous system (CNS) owing to the presence of the blood-brain barrier (BBB). Neuronanomedicine investigates nanotechnology strategies to target the brain and improve the therapeutic outcome in NDs. Two-dimensional adherent cell BBB models show substantial phenogenomic heterogeneity and their ability to predict the permeability of molecules and nanoparticles into the brain is extremely limited. Thus, the high-throughput screening of CNS nanomedicines relies on the use of animal models. To address this dearth, 3D organoids that mimic thein vivophysiology are under development. Still, there exist concerns about the standardization and scale-up of the production process, their proper characterisation, and their industrial application. In this work, we report on a novel multicellular organoid of the neurovascular blood–brain barrier (NV-BBB) that recapitulates the regulated syncytium of human endothelial cells and the function of the human BBB. For this, an advanced organoid comprising human brain microvascular endothelial cells, brain vascular pericytes and human astrocytes combined with primary neurons and microglia isolated from neonate rats is bio-fabricated without the use of an extracellular matrix. The structure and function are fully characterized by confocal laser scanning fluorescence microscopy, light sheet fluorescence microscopy, scanning transmission electron microscopy, cryogenic-scanning electron microscopy, western blotting, RNA-sequencing and quantitative gene expression by quantitative polymerase chain reaction analysis. This bulk of these self-assembloids is comprised of neural cells and microglia and the surface covered by endothelial cells that act as a biological barrier that resembles the BBB endothelium. In addition, the formation of neuron-microglia morphofunctional communication sites is confirmed. Analysis of key transcriptomic expressions show the up-regulation of selected BBB-related genes including tight junction proteins, solute carriers, transporters of the ATP-binding cassette superfamily, metabolic enzymes, and prominent basement membrane signatures. Results confirmed the more efficient cell-cell communication in 3D organoids made of multiple neural-tissue cells than in 2D endothelial cell monocultures. These multicellular organoids are utilized to screen the permeability of different polymeric, metallic, and ceramic nanoparticles. Results reveal penetration through different mechanisms such as clathrin-mediated endocytosis and distribution patterns in the organoid that depend on the nanoparticle type, highlighting the promise of this simple, reproducible and scalable multicellular NV-BBB organoid platform to investigate the BBB permeability of different nanomaterials in nanomedicine, nanosafety, and nanotoxicology.
Mathematical Modeling of Multiple Pathways in Colorectal Carcinogenesis using Dynamical Systems with Kronecker Structure
Authors: Haupt Saskia , Zeilmann Alexander , Ahadova Aysel , von Knebel Doeberitz Magnus , Kloor Matthias , Heuveline Vincent
Published: August 2020

Like many other tumors, colorectal cancers develop through multiple pathways containing different driver mutations. This is also true for colorectal carcinogenesis in Lynch syndrome, the most common inherited colorectal cancer syndrome. However, a comprehensive understanding of Lynch syndrome tumor evolution which allows for tailored clinical treatment and even prevention is still lacking.

We suggest a linear autonomous dynamical system modeling the evolution of the different pathways. Starting with the gene mutation graphs of the driver genes, we formulate three key assumptions about how these different mutations might be combined. This approach leads to a dynamical system that is built by the Kronecker sum of the adjacency matrices of the gene mutation graphs. This Kronecker structure makes the dynamical system amenable to a thorough mathematical analysis and medical interpretation, even if the number of incorporated genes or possible mutation states is increased.

For the case that some of the mathematical key assumptions are not satisfied, we explain possible extensions to our model. Additionally, improved bio-medical measurements or novel medical insights can be integrated into the model in a straightforward manner, as all parameters in the model have a biological interpretation. Modifications of the model are able to account for other forms of colorectal carcinogenesis, such as Lynch-like and familial adenomatous polyposis cases.

Graphical Abstract:

From the Medical Hypothesis Over the Modeling Approach To the Mathematical Structure.

The medical hypothesis of multiple pathways in carcinogenesis is widely known for various types of cancer.Left:We present a model for this phenomenon at the example of Lynch syndrome, the most common inherited colorectal cancer syndrome, with specific key driver events in the MMR genes,CTNNB1,APC,KRASandTP53.Middle:This current medical understanding of carcinogenesis is translated into a mathematical model using a specific dynamical system, which can be represented by a graph structure, where each vertex in the graph represents a genotypic state and the edges correspond to the transition probabilities between those states. Starting with all colonic crypts in the state of all genes being wild-type and a single MMR germline mutation due to Lynch syndrome, we are interested in the distribution of the crypts among the graph at different ages of the patient in order to obtain estimates for the number of crypts in specific states, e.g. adenomatous or cancerous states.Right:The underlying matrix of the dynamical system makes use of the Kronecker sum and product. It is a sparse upper triangular matrix accounting for the assumption that mutations cannot be reverted. This allows fast numerical solving by using the matrix exponential. Each nonzero entry of the matrix represents a connection between genotypic states in the graph.
Discovery of Clioquinol and Analogues as Novel Inhibitors of Severe Acute Respiratory Syndrome Coronavirus 2 Infection, ACE2 and ACE2 - Spike Protein InteractionIn Vitro
Authors: Olaleye Omonike A. , Kaur Manvir , Onyenaka Collins , Adebusuyi Tolu
Published: August 2020

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the etiological agent for coronavirus disease 2019 (COVID-19), has emerged as an ongoing global pandemic. Presently, there are no clinically approved vaccines nor drugs for COVID-19. Hence, there is an urgent need to accelerate the development of effective antivirals. Here in, we discovered Clioquinol (5-chloro-7-iodo-8-quinolinol (CLQ)), a FDA approved drug and two of its analogues (7-bromo-5-chloro-8-hydroxyquinoline (CLBQ14); and 5, 7-Dichloro-8-hydroxyquinoline (CLCQ)) as potent inhibitors of SARS-CoV-2 infection induced cytopathic effectin vitro. In addition, all three compounds showed potent anti-exopeptidase activity against recombinant human angiotensin converting enzyme 2 (rhACE2) and inhibited the binding of rhACE2 with SARS-CoV-2 Spike (RBD) protein. CLQ displayed the highest potency in the low micromolar range, with its antiviral activity showing strong correlation with inhibition of rhACE2 and rhACE2-RBD interaction. Altogether, our findings provide a new mode of action and molecular target for CLQ and validates this pharmacophore as a promising lead series for clinical development of potential therapeutics for COVID-19.
CREB mediates theC. elegansdauer polyphenism through direct and cell-autonomous regulation of TGF-β expression
Authors: Park Jisoo , Oh Hyekyung , Kim Do-Young , Cheon YongJin , Park Yeon-Ji , Neal Scott J. , Dar Abdul Rouf , Butcher Rebecca A. , Sengupta Piali , Kim Daewon , Kim Kyuhyung
Published: August 2020

Animals can adapt to dynamic environmental conditions by modulating their developmental programs. Understanding the genetic architecture and molecular mechanisms underlying developmental plasticity in response to changing environments is an important and emerging area of research. Here, we show a novel role of cAMP response element binding protein (CREB)-encodingcrh-1gene in developmental polyphenism ofC. elegans. Under conditions that promote normal development in wild-type animals,crh-1mutants inappropriately form transient pre-dauer (L2d) larva and express the L2d marker gene. L2d formation incrh-1mutants is specifically induced by the ascaroside pheromone ascr#5 (asc-ωC3; C3), andcrh-1functions autonomously in the ascr#5-sensing ASI neurons to inhibit L2d formation. Moreover, we find that CRH-1 directly binds upstream of thedaf-7TGF-β locus and promotes its expression in the ASI neurons. Taken together, these results provide new insight into how animals alter their developmental programs in response to environmental changes.
A benchmarking model for validation and standardization of traction force microscopy analysis tools
Authors: Pardon Gaspard , Castillo Erica , Pruitt Beth L.
Published: August 2020

Traction Force Microscopy (TFM) has become a well-established technique to assay the biophysical force produced by cells cultured on soft substrates of controlled stiffness. However, experimental conditions as well as computational implementations can have a large impact on the analysis results accuracy and reproducibility. While this can be alleviated using appropriate controls and a rigorous analytical approach, the comparison of results across studies remains difficult and there is a need for validation and benchmarking tools. To validate the accuracy of and compare various computational TFM analysis algorithms, we developed a virtualin silicomodel of a cell contracting on a soft substrate of controlled stiffness. The model utilizes user-defined parameters for the cell dimensions as well as for the strength and spatial distribution of a contraction dipole to calculate the deformation that would result on a soft substrate due to the cell contraction. The deformation is computed using the forward analytical stress-strain tensor calculation in the Fourier space. The resulting displacement field is used to apply, using image processing, a deformation on a real or simulated image of fluorescent microspheres embedded into a soft hydrogel, which is normally obtain experimentally by TFM imaging. The deformation field and resulting image then serve as input in the PIV and TFM analysis. The model also enables to create movies of a dynamic cell contraction, such as that of a cardiomyocyte, to validate the time accuracy of the TFM analysis after application of image processing algorithm, such as denoising. Our tool therefore addresses the need for validation and standardization of TFM analytical algorithms and its experimental implementations.
Propagation and update of auditory perceptual priors through alpha and theta rhythms
Authors: Ho Hao Tam , Burr David C. , Alais David , Morrone Maria Concetta
Published: August 2020

To maintain a continuous and coherent percept over time, the brain makes use of past sensory information to anticipate forthcoming stimuli. We recently showed that auditory experience in the immediate past is propagated through ear-specific reverberations, manifested as rhythmic fluctuations of decision bias at alpha frequency. Here, we apply the same time-resolved behavioural method to investigate how perceptual performance changes over time under conditions of high stimulus expectation, and to examine the effect of unexpected events on behaviour. As in our previous study, participants were required to discriminate the ear-of-origin of a brief monaural pure tone embedded in uncorrelated dichotic white noise. We manipulated stimulus expectation by increasing the target probability in one ear to 80%. Consistent with our earlier findings, performance did not remain constant across trials, but varied rhythmically with delay from noise onset. Specifically, decision bias showed a similar oscillation at ~9 Hz that depended on ear congruency between successive targets. This suggests rhythmic communication of auditory perceptual history occurs early and is not readily influenced by top-down expectations. In addition, we report a novel observation specific to infrequent, unexpected stimuli that gave rise to oscillations in accuracy at ~7.6 Hz one trial after the target occurred in the non-anticipated ear. This new behavioural oscillation may reflect a mechanism for updating the sensory representation once a prediction error has been detected.
ERAP2 increases the abundance of a peptide submotif highly selective for the Birdshot Uveitis-associated HLA-A29
Authors: Venema W.J. , Hiddingh S. , de Boer J.H. , Claas F.H.J. , Mulder A , Den Hollander A.I. , Stratikos E. , Sarkizova S. , van der Veken L.T. , Janssen G.M.C. , van Veelen P.A. , Kuiper J.J.W.
Published: August 2020

Birdshot Uveitis (BU) is a blinding inflammatory eye condition that only affects HLA-A29-positive individuals. Genetic association studies linkedERAP2with BU, an aminopeptidase which trims peptides before their presentation by HLA class I at the cell surface, which suggests that ERAP2-dependent peptide presentation by HLA-A29 drives the pathogenesis of BU. However, it remains poorly understood whether the effects of ERAP2 on the HLA-A29 peptidome are distinct from its effect on other HLA allotypes. To address this, we focused on the effects of ERAP2 on the immunopeptidome in patient-derived antigen presenting cells. Using complementary HLA-A29-based and pan-class I immunopurifications, isotope-labelled naturally processed and presented HLA-bound peptides were sequenced by mass spectrometry. We show that the effects of ERAP2 on the N-terminus of ligands of HLA-A29 are shared across endogenous HLA allotypes, but discover and replicate that one peptide motif generated in the presence of ERAP2 is specifically bound by HLA-A29. This motif can be found in the amino acid sequence of putative autoantigens. We further show evidence for internal sequence specificity for ERAP2 imprinted in the immunopeptidome. These results reveal that ERAP2 can generate an HLA-A29-specific antigen repertoire, which supports that antigen presentation is a key disease pathway in BU.
DeepKhib: a deep-learning framework for lysine 2-hydroxyisobutyrylation sites prediction
Authors: Zhang Luna , Zou Yang , He Ningning , Chen Yu , Chen Zhen , Li Lei
Published: August 2020

As a novel type of post-translational modification, lysine 2-Hydroxyisobutyrylation (Khib) plays an important role in gene transcription and signal transduction. In order to understand its regulatory mechanism, the essential step is the recognition of Khibsites. Thousands of Khibsites have been experimentally verified across five different species. However, there are only a couple traditional machine-learning algorithms developed to predict Khib sites for limited species, lacking a general prediction algorithm. We constructed a deep-learning algorithm based on convolutional neural network with the one-hot encoding approach, dubbed CNNOH. It performs favorably to the traditional machine-learning models and other deep-learning models across different species, in terms of cross-validation and independent test. The area under the ROC curve (AUC) values for CNNOHranged from 0.82 to 0.87 for different organisms, which is superior to the currently-available Khibpredictors. Moreover, we developed the general model based on the integrated data from multiple species and it showed great universality and effectiveness with the AUC values in the range of 0.79 to 0.87. Accordingly, we constructed the on-line prediction tool dubbed DeepKhib for easily identifying Khibsites, which includes both species-specific and general models. DeepKhib is available athttp://www.bioinfogo.org/DeepKhib.
MRLocus: identifying causal genes mediating a trait through Bayesian estimation of allelic heterogeneity
Authors: Zhu Anqi , Matoba Nana , Wilson Emmaleigh , Tapia Amanda L. , Li Yun , Ibrahim Joseph G. , Stein Jason L. , Love Michael I.
Published: August 2020

Expression quantitative trait loci (eQTL) studies are used to understand the regulatory function of non-coding genome-wide association study (GWAS) risk loci, but colocalization alone does not demonstrate a causal relationship of gene expression affecting a trait. Evidence for mediation, that perturbation of gene expression in a given tissue or developmental context will induce a change in the downstream GWAS trait, can be provided by two-sample Mendelian Randomization (MR). Here, we introduce a new statistical method, MRLocus, for Bayesian estimation of the gene-to-trait effect from eQTL and GWAS summary data for loci displaying allelic heterogeneity, that is, containing multiple LD-independent eQTLs. MRLocus makes use of a colocalization step applied to each eQTL, followed by an MR analysis step across eQTLs. Additionally, our method involves estimation of allelic heterogeneity through a dispersion parameter, indicating variable mediation effects from each individual eQTL on the downstream trait. Our method is evaluated against state-of-the-art methods for estimation of the gene-to-trait mediation effect, using an existing simulation framework. In simulation, MRLocus often has the highest accuracy among competing methods, and in each case provides more accurate estimation of uncertainty as assessed through interval coverage. MRLocus is then applied to five causal candidate genes for mediation of particular GWAS traits, where gene-to-trait effects are concordant with those previously reported. We find that MRLocus’ estimation of the causal effect across eQTLs within a locus provides useful information for determining how perturbation of gene expression or individual regulatory elements will affect downstream traits. The MRLocus method is implemented as an R package available athttps://mikelove.github.io/mrlocus.