bluuebunny/crossref_metadata_2025 huggingface dataset:
Post-EMT: Cadherin-11 mediates cancer hijacking fibroblasts
Authors: Kang Weirong , Fan Yibo , Du Yinxiao , Tonkova Elina A. , Hsu Yi-Hsin , Tan Kel Vin , Alexander Stephanie , Wong Bin Sheng , Yang Haocheng , Luo Jingyuan , Yao Kuo , Yang Jiayao , Hu Xin , Liu Tingting , Gan Yu , Zhang Jian , Zhao Jean J. , Konstantopoulos Konstantinos , Friedl Peter , Khong Pek Lan , Lu Aiping , Hung Mien-Chie , Brenner Michael B. , Segall Jeffrey E. , Gu Zhizhan
Published: August 2019

Current prevailing knowledge on EMT (epithelial mesenchymal transition) deems epithelial cells acquire the characters of mesenchymal cells to be capable of invading and metastasizing on their own. One of the signature events of EMT is called “cadherin switch”, e.g. the epithelial E-cadherin switching to the mesenchymal Cadherin-11. Here, we report the critical events after EMT that cancer cells utilize cadherin-11 to hijack the endogenous cadherin-11 positive fibroblasts. Numerous 3-D cell invasion assays with high-content live cell imaging methods reveal that cadherin-11 positive cancer cells adhere to and migrate back and forth dynamically on the cell bodies of fibroblasts. By adhering to fibroblasts for co-invasion through 3-D matrices, cancer cells acquire higher invasion speed and velocity, as well as significantly elevated invasion persistence, which are exclusive characteristics of fibroblast invasion. Silencing cadherin-11 in cancer cells or in fibroblasts, or in both, significantly decouples such physical co-invasion. Additional bioinformatics studies and PDX (patient derived xenograft) studies link such cadherin-11 mediated cancer hijacking fibroblasts to the clinical cancer progression in human such as triple-negative breast cancer patients. Further animal studies confirm cadherin-11 mediates cancer hijacking fibroblasts in vivo and promotes significant solid tumor progression and distant metastasis. Moreover, overexpression of cadherin-11 strikingly protects 4T1-luc cells from implant rejection against firefly luciferase in immunocompetent mice. Overall, our findings report and characterize the critical post-EMT event of cancer hijacking fibroblasts in cancer progression and suggest cadherin-11 can be a therapeutic target for solid tumors with stroma. Our studies hence provide significant updates on the “EMT” theory that EMT cancer cells can hijack fibroblasts to achieve full mesenchymal behaviors in vivo for efficient homing, growth, metastasis and evasion of immune surveillance. Our studies also reveal that cadherin-11 is the key molecule that helps link cancer cells to stromal fibroblasts in the “Seed & Soil” theory.

Graphical Abstract
Global transcriptomic profiling of the bone marrow stromal microenvironment during postnatal development, aging and inflammation
Authors: Helbling Patrick M. , Piñeiro-Yáñez Elena , Gerosa Rahel , Boettcher Steffen , Al-Shahrour Fátima , Manz Markus G. , Nombela-Arrieta César
Published: August 2019

Bone marrow (BM) stromal cells provide the structural and regulatory framework for hematopoiesis and contribute to developmental-stage specific niches, such as those preserving hematopoietic stem cell (HSCs). Despite recent advances in our understanding of stromal composition and function, little is known on the dynamic transcriptional remodeling that this compartment undergoes over time and during adaptation to stress. Similarly, how molecular changes in stroma are linked to age-related modulation of hematopoiesis is poorly understood. Using RNA-sequencing, we performed a longitudinal comparison of the transcriptional profile of four principal mesenchymal and endothelial stromal subsets, namely CXCL12-abundant reticular (CARc), PDGFR-α+Sca-1+, sinusoidal (SECs) and arterial endothelial cells (AECs), isolated from early postnatal, adult and aged mice. Our data i) provide molecular fingerprints defining novel, cell-specific anatomical and functional features ii) reveal radical reprogramming of pro-hematopoietic, immune and matrisomic transcriptional programs during the narrow temporal transition from juvenile to adult stages iii) demonstrate that homeostatic aging is characterized by a progressive and pronounced upregulation of pro-inflammatory gene-expression and loss of stromal cell fitness. By profilingin vivoresponses of stromal cells to infection-mimicking agents, we finally demonstrate that transcriptomic pathways elicited by sterile inflammation are largely recapitulated during aging, thereby supporting the inflammatory basis of aging-related adaptations of BM hematopoietic function.
Augmenting protein network embeddings with sequence information
Authors: Kané Hassan , Coulibali Mohamed , Abdalla Ali , Ajanoh Pelkins
Published: August 2019

Computational methods that infer the function of proteins are key to understanding life at the molecular level. In recent years, representation learning has emerged as a powerful paradigm to discover new patterns among entities as varied as images, words, speech, molecules. In typical representation learning, there is only one source of data or one level of abstraction at which the learned representation occurs. However, proteins can be described by their primary, secondary, tertiary, and quaternary structure or even as nodes in protein-protein interaction networks. Given that protein function is an emergent property of all these levels of interactions in this work, we learn joint representations from both amino acid sequence and multilayer networks representing tissue-specific protein-protein interactions. Using these hybrid representations, we show that simple machine learning models trained using these hybrid representations outperform existing network-based methods on the task of tissue-specific protein function prediction on 13 out of 13 tissues. Furthermore, these representations outperform existing ones by 14% on average.
Quantification of malaria antigens PfHRP2 and pLDH by quantitative suspension array technology in whole blood, dried blood spot and plasma
Authors: Martiáñez-Vendrell Xavier , Jiménez Alfons , Vásquez Ana , Campillo Ana , Incardona Sandra , González Raquel , Gamboa Dionicia , Torres Katherine , Oyibo Wellington , Faye Babacar , Macete Eusebio , Menéndez Clara , Ding Xavier C. , Mayor Alfredo
Published: August 2019

Background

Malaria diagnostics by rapid diagnostic tests (RDTs) relies primarily on the qualitative detection ofPlasmodium falciparumhistidine-rich protein 2 (PfHRP2) andPlasmodium splactate dehydrogenase (pLDH). As novel RDTs with increased sensitivity are being developed and implemented as point of care diagnostics, highly sensitive laboratory based assays are needed for evaluating RDTs performance. Here, a quantitative suspension array technology (qSAT) was developed, validated and applied for the simultaneous detection of PfHRP2 and pLDH in a variety of clinical samples (whole blood, plasma and dried blood spots) from different endemic countries.

Results

The qSAT was specific for the target antigens, with analytical ranges of 6.8 to 762.8 pg/ml for PfHRP2 and 78.1 to 17076.6 pg/ml forP. falciparum(Pf-LDH). The assay detectedP. vivaxLDH (Pv-LDH) at a lower sensitivity than Pf-LDH (analytical range of 1093.20 to 187288.5 pg/ml). Both PfHRP2 and pLDH levels determined using the qSAT showed to positively correlate with parasite densities determined by quantitative PCR (Spearman r=0.59 and 0.75, respectively) as well as microscopy (Spearman r=0.40 and 0.75, respectively), suggesting the assay to be a good predictor of parasite density.

Conclusion

This immunoassay can be used as a reference test for the detection and quantification of PfHRP2 and pLDH, and could serve for external validation of RDTs performance, to determine antigen persistence after parasite clearance, as well as a complementary tool to assess malaria burden in endemic settings.
Quantifying genetic effects on disease mediated by assayed gene expression levels
Authors: Yao Douglas W. , O’Connor Luke J. , Price Alkes L. , Gusev Alexander
Published: August 2019

Disease variants identified by genome-wide association studies (GWAS) tend to overlap with expression quantitative trait loci (eQTLs). However, it remains unclear whether this overlap is driven by mediation of genetic effects on disease by expression levels, or whether it primarily reflects pleiotropic relationships instead. Here we introduce a new method, mediated expression score regression (MESC), to estimate disease heritability mediated by the cis-genetic component of assayed steady-state gene expression levels, using summary association statistics from GWAS and eQTL studies. We show that MESC produces robust estimates of expression-mediated heritability across a wide range of simulations. We applied MESC to GWAS summary statistics for 42 diseases and complex traits (averageN= 323K) and cis-eQTL data across 48 tissues from the GTEx consortium. We determined that a statistically significant but low proportion of disease heritability (mean estimate 11% with S.E. 2%) is mediated by the cis-genetic component of assayed gene expression levels, with substantial variation across diseases (point estimates from 0% to 38%). We further partitioned expression-mediated heritability across various gene sets. We observed an inverse relationship between cis-heritability of expression and disease heritability mediated by expression, suggesting that genes with weaker eQTLs have larger causal effects on disease. Moreover, we observed broad patterns of expression-mediated heritability enrichment across functional gene sets that implicate specific gene sets in disease, including loss-of-function intolerant genes and FDA-approved drug targets. Our results demonstrate that eQTLs estimated from steady-state expression levels in bulk tissues are informative of regulatory disease mechanisms, but that such eQTLs are insufficient to explain the majority of disease heritability. Instead, additional assays are necessary to more fully capture the regulatory effects of GWAS variants.
Antibody Targeting of B7-H4 Enhances the Immune Response in Urothelial Carcinoma
Authors: Podojil Joseph R. , Glaser Alexander P. , Baker Dylan , Courtois Elise T. , Fantini Damiano , Yu Yanni , Eaton Valerie , Sivajothi Santhosh , Robson Paul , Miller Stephen D. , Meeks Joshua J.
Published: August 2019

Locally advanced urothelial carcinoma has a poor survival despite a response to immunotherapy in approximately 25% of patients. To develop new therapies targeting other immune checkpoints, we identified increased expression of the T cell inhibitor protein, B7-H4 (VTCN1, B7S1, B7X), during tumor development of murine bladder cancer. Evaluation of B7-H4 in human bladder cancer by single-cell RNA-Seq and immune mass cytometry showed that B7-H4 is expressed by luminal tumors that are not normally responsive to PD-1 inhibitors. Additionally, overexpression B7-H4 was associated with significantly worse patient survival. In support of clinical translation, treatment of human monocyte and T cell co-cultures with a B7-H4 blocking antibody resulted in enhanced IFN-γ secretion by CD4+and CD8+T cell. While the study of B7-H4 in mouse cancer models has been difficult using tumor cell lines, our findings show that B7-H4 expression increased at 3 months after exposure to BBN on CD11b+monocytes/macrophages and delivery of anti-B7-H4 antibody resulted in decreased tumor size and increased CD8 immune cell infiltration with increased CD8+/IFN-γ-producing T cells and a complimentary decrease in tumor infiltrating T regulatory cells (Tregs). Furthermore, treatment with a combination of anti-PD-1 and anti-B7-H4 antibodies resulted in a significant reduction in tumor stage. This data suggests that novel anti-B7-H4 antibodies maybe a viable target for bladder cancers unresponsive to PD-1 checkpoint inhibitors.
Silencing epigenetic writer DOT1L attenuates intimal hyperplasia
Authors: Huang Yitao , Urabe Go , Zhang Mengxue , Li Jing , Wang Bowen , Craig Kent K. , Guo Lian-Wang
Published: August 2019

Objective

Histone methyltransferases are emerging targets for epigenetic therapy. DOT1L (disruptor of telomeric silencing 1-like) is the H3K79 methylation writer. We investigated its role in the development of intimal hyperplasia (IH).

Approach and Results

IH was induced via balloon angioplasty in rat carotid arteries. DOT1L and its catalytic products H3K79me2 and H3K79me3 (immunostaining) increased by 4.69 ±0.34, 2.38 ±0.052, and 3.07 ±0.27 fold, respectively, in injured (versus uninjured) carotid arteries at post-injury day 7. DOT1L silencing via shRNA-lentivirus infusion in injured arteries reduced DOT1L, H3K79me2, and IH at day 14 by 54.5%, 37.1%, and 76.5%, respectively. Moreover, perivascular administration of a DOT1L-selective inhibitor (EPZ5676) reduced H3K79me2, H3K79me3, and IH by 56.1%, 58.6%, and 39.9%, respectively.

Conclusions

DOT1L inhibition mitigates the development of IH.
Transferrin binding protein B and Transferrin binding protein A 2 expand the transferrin recognition range ofHistophilus somni
Authors: Pogoutse Anastassia K. , Moraes Trevor F.
Published: August 2019

The bacterial bipartite transferrin receptor is an iron acquisition system that is required for survival by several key human and animal pathogens. It consists of the TonB-dependent transporter Transferrin binding protein A (TbpA) and the surface lipoprotein Transferrin binding protein B (TbpB). Curiously, the Tbps are only found in host specific pathogens, and are themselves host specific, meaning that they will bind to the transferrin of their host species, but not to those of other animal species. While this phenomenon has long been established, neither the steps in the evolutionary process that led to this exquisite adaptation for the host, nor the steps that could alter it, are known. We sought to gain insight into these processes by studying Tbp specificity inHistophilus somni, a major pathogen of cattle. A past study showed that whole cells ofH. somnispecifically bind bovine transferrin, but not transferrin from sheep and goats, two bovids whose transferrins share 93% amino acid sequence identity with bovine transferrin. To our surprise, we found thatH. somnican use sheep and goat transferrins as iron sources for growth, and thatHsTbpB, but notHsTbpA, has detectable affinity for sheep and goat transferrins. Furthermore, a third transferrin binding protein,HsTbpA2, also showed affinity for sheep and goat transferrins. Our results show thatH. somniTbpB and TbpA2 act to broaden the host transferrin recognition range ofH. somni.

Importance

Host restricted pathogens infect a single host species or a narrow range of host species.Histophilussomni, a pathogen that incurs severe economic losses for the cattle industry, infects cattle, sheep, and goats, but not other mammals. The transferrin binding proteins, TbpA and TbpB, are thought to be a key iron acquisition system inH. somni, however, surprisingly, they were also shown to be cattle transferrin-specific. In our study we find thatH. somniTbpB, and another little-studied Tbp, TbpA2, bind sheep and goat transferrins as well as bovine transferrin. Our results suggest that TbpA2 may have allowed for host range expansion, and provide a mechanism for how host specificity in Tbp containing pathogens can be altered.
A Dysbiotic Gut Microbiome Suppresses Antibody Mediated-Protection AgainstVibrio cholerae
Authors: Macbeth John , Hsiao Ansel
Published: August 2019

Vibrio choleraeis the etiologic agent of cholera, a severe diarrheal disease that represents a significant burden on global health and productivity. Despite the pressing need, available preventative measures such as oral cholera vaccines exhibit highly variable protective efficacy. We hypothesized that one contributor to vaccine efficacy variability across geographical regions may be due to differences in gut microbiome, which in cholera-endemic areas is strongly and repeatedly modulated by malnutrition, cholera, and non-cholera infectious diarrhea. Here, we assemble representative model communities of either human gut microbes resembling those of healthy individuals or those of individuals recovering from diarrhea or malnutrition. We establish these communities in a murine immunization model, and show that the dysbiotic gut microbiome, commonly present in areas where malnutrition and diarrhea are common, suppresses the immune response againstVibrio choleraethrough the action of CD4+cells. Our findings suggest that the composition of the gut microbiome at time of immunization may be pivotal for providing robust immunity from oral cholera vaccines, and highlight the importance of the gut microbiome on mucosal immunization responses and vaccine development strategies.

Importance

Diarrhea caused by enteric bacterial pathogens is a recurring and important issue for worldwide health. Cholera, the severe watery diarrhea caused by the bacteriumVibrio cholerae, affects millions of people annually. Currently, there is a lack of effective preventative measures for cholera, due to the uneven performance of oral cholera vaccines. Thus, it is essential to better understand the factors that may affect vaccine efficacy. One aspect may be variations in the resident community of gut microbes, the gut microbiome, across populations living in developed versus developing regions as a function of host genetics, diet, and infection. Our findings suggest that specific structures of the gut microbiome are involved in disrupting the immune responses toV. choleraevaccination.
Thinking like a naturalist: enhancing computer vision of citizen science images by harnessing contextual data
Authors: Terry J. Christopher D. , Roy Helen E. , August Tom A.
Published: August 2019

The accurate identification of species in images submitted by citizen scientists is currently a bottleneck for many data uses. Machine learning tools offer the potential to provide rapid, objective and scalable species identification for the benefit of many aspects of ecological science. Currently, most approaches only make use of image pixel data for classification. However, an experienced naturalist would also use a wide variety of contextual information such as the location and date of recording.

Here, we examine the automated identification of ladybird (Coccinellidae) records from the British Isles submitted to the UK Ladybird Survey, a volunteer-led mass participation recording scheme. Each image is associated with metadata; a date, location and recorder ID, which can be cross-referenced with other data sources to determine local weather at the time of recording, habitat types and the experience of the observer. We built multi-input neural network models that synthesise metadata and images to identify records to species level.

We show that machine learning models can effectively harness contextual information to improve the interpretation of images. Against an image-only baseline of 48.2%, we observe a 9.1 percentage-point improvement in top-1 accuracy with a multi-input model compared to only a 3.6% increase when using an ensemble of image and metadata models. This suggests that contextual data is being used to interpret an image, beyond just providing a prior expectation. We show that our neural network models appear to be utilising similar pieces of evidence as human naturalists to make identifications.

Metadata is a key tool for human naturalists. We show it can also be harnessed by computer vision systems. Contextualisation offers considerable extra information, particularly for challenging species, even within small and relatively homogeneous areas such as the British Isles. Although complex relationships between disparate sources of information can be profitably interpreted by simple neural network architectures, there is likely considerable room for further progress. Contextualising images has the potential to lead to a step change in the accuracy of automated identification tools, with considerable benefits for large scale verification of submitted records.
Low rank mechanisms underlying flexible visual representations
Authors: Ruff Douglas A. , Xue Cheng , Kramer Lily E. , Baqai Faisal , Cohen Marlene R.
Published: August 2019

Neuronal population responses to sensory stimuli are remarkably flexible. The responses of neurons in visual cortex depend on stimulus properties (e.g. contrast), processes that affect all stages of visual processing (e.g. adaptation), and cognitive processes (e.g attention or task switching). The effects of all of these processes on trial-averaged responses of individual neurons are well-described by divisive normalization, in which responses are scaled by the total stimulus drive. Normalization describes how a staggering variety of sensory, cognitive, and motor processes affect individual neurons (1), but whether different normalization processes could be mediated by the same mechanism remains poorly understood. We and others recently showed that attention has low rank effects on the covariability of populations of neurons in visual area V4 (2–4), which strongly constrains mechanistic models mechanism (2). We hypothesized that measuring changes in population covariability associated with other normalization processes could clarify whether they might share a mechanism. Our experimental design included measurements in multiple visual areas using four normalization processes. We found that contrast, adaptation, attention, and task switching affect the responses of populations of neurons in primate visual cortex in a similarly low rank way. These results suggest that a given circuit uses a common mechanism to perform many forms of normalization and likely reflect a general principle that applies to a wide range of brain areas and sensory, cognitive, or motor processes.
Orbit Image Analysis: An open-source whole slide image analysis tool
Authors: Stritt Manuel , Stalder Anna K. , Vezzali Enrico
Published: August 2019

We describe the open-source whole slide image analysis tool Orbit Image Analysis. It is a generic tile-processing engine which allows the execution of various image analysis algorithms provided by either Orbit itself or other open-source solutions using a tile-based map-reduce execution framework. We show its sophisticated machine-learning approach for WSI quantification, and its flexibility by integrating a deep learning segmentation method for complex object detection. It can run locally standalone or connect to the open-source image server OMERO, and provides scale-out functionality to use the Spark framework for distributed computing. We demonstrate the application of Orbit in three real-world use-cases: Idiopathic lung fibrosis, nerve fibre density quantification, and glomeruli detection in kidney.

Author summary

Whole slide images (WSI) are digital scans of samples, e.g. tissue sections. It is very convenient to view samples in this digital form, and with the increasing computation power it can also be used for quantification. These images are often too large to be analysed with standard tools. To overcome this issue, we created on open-source tool called Orbit Image Analysis which divides the images into smaller parts and allows the analysis of it with either embedded algorithms or the integration of existing tools. It also provides mechanisms to process huge amounts of images in distributed computing environments such as clusters or cloud infrastructures. In this paper we describe the Orbit system and demonstrate its application based on three real-word use-cases.
SAPH-ire TFx – A Recommendation-based Machine Learning Model Captures a Broad Feature Landscape Underlying Functional Post-Translational Modifications
Authors: English Nolan , Torres Matthew
Published: August 2019

Protein post-translational modifications (PTMs) are a rapidly expanding feature class of significant importance in cell biology. Due to a high burden of experimental proof, the number of functional PTMs in the eukaryotic proteome is currently underestimated. Furthermore, not all PTMs are functionally equivalent. Therefore, computational approaches that can confidently recommend the functional potential of experimental PTMs are essential. To address this challenge, we developed SAPH-ire TFx (https://saphire.biosci.gatech.edu/): a multi-feature neural network model and web resource optimized for recommending experimental PTMs with high potential for biological impact. The model is rigorously benchmarked against independent datasets and alternative models, exhibiting unmatched performance in the recall of known functional PTM sites and the recommendation of PTMs that were later confirmed experimentally. An analysis of feature contributions to model outcome provides further insight on the need for multiple rather than single features to capture the breadth of functional data in the public domain.

Contact

mtorres35@gatech.edu

Supplementary Information

See Tables S1-S6 & Figures S1-S4.
The effect of overnight consolidation in the perceptual learning of non-native tonal contrasts
Authors: Qin Zhen , Zhang Caicai
Published: August 2019

Sleep-mediated overnight consolidation was found to facilitate perceptual learning by promoting learners’ generalization across talkers in their perception of novel segmental categories. Lexical tone differs from most segmental contrasts in that it is highly variable across talkers, and displays dynamic change over time. It remains unclear whether a similar (or a larger) effect of overnight consolidation would be found for perceptual learning of novel tonal contrasts. Thus, this study aims to examine whether overnight consolidation facilitates generalization across talkers in the discrimination and identification of novel Cantonese level tones by Mandarin listeners. Two groups of Mandarin listeners were perceptually trained either in the morning or in the evening. Listeners were trained in a tone identification (ID) task using stimuli produced by a trained talker. Their development was then tested in the ID and AX discrimination tasks using stimuli produced by trained and untrained talkers in three posttests following training: immediately after training, 12-hour delay, and 24-hour delay. While the evening group slept between the first and second posttests, the morning group did not. The results of accuracy rates in the ID task showed that while Mandarin listeners trained in the evening showed an improved trend, predicted by their individual sleep time, in identifying the level tones produced by both the trained and untrained talkers, Mandarin listeners trained in the morning showed a declining trend. In contrast, the results of d-prime scores in the AX discrimination task did not show different developmental patterns between the two groups. Consistent with previous studies on segmental learning, the finding suggests that overnight consolidation might have assisted the evening trainees’ formation of a more abstract (talker-independent) representation of novel tone categories in memory traces. The results are discussed regarding the features of lexical tones to shed light on the mechanism of phonetic learning.
Prebiotically Plausible ‘Patching’ of RNA Backbone Cleavage Through a 3′-5′ Pyrophosphate Linkage
Authors: Wright Tom H. , Giurgiu Constantin , Radakovic Aleksandar , O’Flaherty Derek K. , Zhou Lijun , Szostak Jack W.
Published: August 2019

Achieving multiple cycles of RNA replication within a model protocell would be a critical step towards demonstrating a path from prebiotic chemistry to cellular biology. Any model for early life based on an ‘RNA world’ must account for RNA strand cleavage and hydrolysis, which would degrade primitive genetic information and lead to an accumulation of truncated, phosphate-terminated strands. We show here that cleavage of the phosphodiester backbone is not an endpoint for RNA replication. Instead, 3′ -phosphate terminated RNA strands are able to participate in template-directed copying reactions with activated ribonucleotide monomers. These reactions form a pyrophosphate linkage, the stability of which we have characterized in the context of RNA copying chemistry. We found that the pyrophosphate bond is relatively stable within an RNA duplex and in the presence of chelated magnesium. Under these conditions, pyrophosphate-RNA can act as a temporary ‘patch’ to template the polymerization of canonical ribonucleotides, suggesting a plausible non-enzymatic pathway for the salvage and recovery of genetic information following strand cleavage.
WAPL maintains dynamic cohesin to preserve lineage specific distal gene regulation
Authors: Liu Ning Qing , Maresca Michela , van den Brand Teun , Braccioli Luca , Schijns Marijne M.G.A. , Teunissen Hans , Bruneau Benoit G. , Nora Elphège P. , de Wit Elzo
Published: August 2019

The cohesin complex plays essential roles in sister chromatin cohesin, chromosome organization and gene expression. The role of cohesin in gene regulation is incompletely understood. Here, we report that the cohesin release factor WAPL is crucial for maintaining a pool of dynamic cohesin bound to regions that are associated with lineage specific genes in mouse embryonic stem cells. These regulatory regions are enriched for active enhancer marks and transcription factor binding sites, but largely devoid of CTCF binding sites. Stabilization of cohesin, which leads to a loss of dynamic cohesin from these regions, does not affect transcription factor binding or active enhancer marks, but does result in changes in promoter-enhancer interactions and downregulation of genes. Acute cohesin depletion can phenocopy the effect of WAPL depletion, showing that cohesin plays a crucial role in maintaining expression of lineage specific genes. The binding of dynamic cohesin to chromatin is dependent on the pluripotency transcription factor OCT4, but not NANOG. Finally, dynamic cohesin binding sites are also found in differentiated cells, suggesting that they represent a general regulatory principle. We propose that cohesin dynamically binding to regulatory sites creates a favorable spatial environment in which promoters and enhancers can communicate to ensure proper gene expression.

HIGHLIGHTS

The cohesin release factor WAPL is crucial for maintaining a pluripotency-specific phenotype.

Dynamic cohesin is enriched at lineage specific loci and overlaps with binding sites of pluripotency transcription factors.

Expression of lineage specific genes is maintained by dynamic cohesin binding through the formation of promoter-enhancer associated self-interaction domains.

CTCF-independent cohesin binding to chromatin is controlled by the pioneer factor OCT4.
DeepBCR: Deep learning framework for cancer-type classification and binding affinity estimation using B cell receptor repertoires
Authors: Hu Xihao , Liu X Shirley
Published: August 2019

We developed a deep learning framework to model the binding specificity of B-cell receptors (BCRs). The DeepBCR framework can predict the cancer type from a repertoire of BCRs and estimate the binding affinity of a single BCR. We designed a peptide encoding network that includes an amino acid encoding layer, k-mer motif layer, and immunoglobulin isotype layer, and used transfer learning to reduce parameters and over-fitting. When we applied the framework to evaluate the three commercial anti-PD1 drugs (Opdivo, Keytruda, and Libtayo), the predicted binding affinities correlate with the real affinities measured in kD values. This validates the prediction and indicates that we can use the framework to select strong antigen-specific binders.
Predicting metabolism during growth by osmotic cell expansion
Authors: Shameer Sanu , Vallarino José G. , Fernie Alisdair R. , Ratcliffe R. George , Sweetlove Lee J
Published: August 2019

Cell expansion is a significant contributor to organ growth and is driven by the accumulation of osmolytes to increase cell turgor pressure. Metabolic modelling has the potential to provide insights into the processes that underpin osmolyte synthesis and transport, but the main computational approach for predicting metabolic network fluxes, flux balance analysis (FBA), typically uses biomass composition as the main output constraint and ignores potential changes in cell volume. Here we present GrOE-FBA (Growth by Osmotic Expansion-Flux Balance Analysis), a framework that accounts for both the metabolic and ionic contributions to the osmotica that drive cell expansion, as well as the synthesis of protein, cell wall and cell membrane components required for cell enlargement. Using GrOE-FBA, the metabolic fluxes in dividing and expanding cell were analyzed, and the energetic costs for metabolite biosynthesis and accumulation in the two scenarios were found to be surprisingly similar. The expansion phase of tomato fruit growth was also modelled using a multi-phase single optimization GrOE-FBA model and this approach gave accurate predictions of the major metabolite levels throughout fruit development as well as revealing a role for transitory starch accumulation in ensuring optimal fruit development.
Fibroblast growth factor receptor facilitates recurrence of minimal residual disease following trastuzumab emtansine therapy
Authors: Akhand Saeed S. , Purdy Stephen Connor , Liu Zian , Anderson Joshua C. , Willey Christopher D. , Wendt Michael K.
Published: August 2019

Trastuzumab-emtansine (T-DM1) is an antibody-drug conjugate (ADC) that efficiently delivers a potent microtubule inhibitor into HER2 overexpressing tumor cells. However, resistance to T-DM1 is emerging as a significant clinical problem. Continuous in vitro treatment of HER2-transformed mammary epithelial cells with T-DM1 did not elicit spontaneously resistant cells. However, induction of epithelial-mesenchymal transition (EMT) via pretreatment with TGF-β1 facilitated acquisition of T-DM1 resistance. Flow cytometric analyses indicated that induction of EMT decreased trastuzumab binding, prior to overt loss of HER2 expression. Kinome analyses of T-DM1 resistant cells indicated increased phosphorylation of ErbB1, ErbB4, and fibroblast blast growth factor receptor 1 (FGFR1). T-DM1 resistant cells failed to respond to the ErbB kinase inhibitors lapatinib and afatinib, but they acquired sensitivity to FIIN4, a covalent FGFR kinase inhibitor. In vivo, T-DM1 treatment led to robust regression of HER2-transformed tumors, but minimal residual disease (MRD) was still detectable via bioluminescent imaging. Upon cessation of the ADC relapse occurred and secondary tumors were resistant to additional rounds of T-DM1, but this recurrent tumor growth could be inhibited by FIIN4. Expression of FGFR1 was upregulated in T-DM1 resistant tumors, and ectopic overexpression of FGFR1 was sufficient to enhance tumor growth, diminish trastuzumab binding, and promote recurrence following T-DM1-induced MRD. Finally, patient-derived xenografts from a HER2+ breast cancer patient who had progressed on trastuzumab failed to respond to T-DM1, but tumor growth was significantly inhibited by FIIN4. Overall, our studies strongly support therapeutic combination of TDM1 and FGFR targeted agents in HER2+ breast cancer.
A Game of Thrones at Human Centromeres II. A new molecular/evolutionary model
Authors: Rice William R.
Published: August 2019

Human centromeres are remarkable in four ways: they are i) defined epigenetically by an elevated concentration of the histone H3 variant CENP-A, ii) inherited epigenetically by trans-generational cary-over of nucleosomes containing CENP-A, iii) formed over unusually long and complex tandem repeats (Higher Order Repeats, HORs) that extend over exceptionally long arrays of DNA (up to 8 Mb), and iv) evolve in such a rapid and punctuated manner that most HORs on orthologous chimp and human chromosomes are in different clades. What molecular and evolutionary processes generated these distinctive characteristics? Here I motivate and construct a new model for the formation, expansion/contraction, homogenization and rapid evolution of human centromeric repeat arrays that is based on fork-collapse during DNA replication (in response to proteins bound to DNA and/or collisions between DNA and RNA polymerases) followed by out-of-register re-initiation of replication via Break-Induced Repair (BIR). The model represents a new form of molecular drive. It predicts rapid and sometimes punctuated evolution of centromeric HORs due to a new form of intragenomic competition that is based on two features: i) the rate of tandem copy number expansion, and ii) resistance to invasion by pericentric heterochromatin within a centromere’s HOR array. These features determine which variant array elements will eventually occupy a pivotal region within a centromeric repeat array (switch-point) that gradually expands to populate the entire array. In humans, continuous HOR turnover is predicted due to intra-array competition between three repeat types with an intransitive hierarchy: A < B < C < A, where A = short, single-dimer HORs containing one monomer that binds centromere protein-B (CENP-B) and another that does not, B = moderately longer HORs composed of ≥ 2 dimers, and C = substantially longer HORs that lose their dimeric modular structure. Continuous turnover of proteins that bind centromeric DNA (but these proteins are not constituents of the kinetochore) and polygenic variation influencing position-effect variegation are predicted to cause rapid turnover of centromeric repeats in species lacking HORs and/or CENP-B binding at centromeres. Evolution at centromeres is a molecular ‘Game-of-Thrones’ because centromeric sequences ‘reign’ due to an epigenetic ‘crown’ of CENP-A that is perpetually ‘usurped’ by new sequences that more rapidly assemble large ‘armies’ of tandem repeats and/or resist ‘invasion’ from a surrounding ‘frontier’ of percentric heterochromatin. These ‘regal transitions’ occur in a backdrop of slashing and decapitation (fork-collapse generating truncated sister chromatids) in the context of promiscuous sex that is frequently incestuous (out-of-register BIR between sibling chromatids).
Quantifying and engineering mucus adhesion of probiotics
Authors: Mays Zachary J. S. , Chappell Todd C. , Nair Nikhil U.
Published: August 2019

Mucus in the gastrointestinal (GI) tract is the primary point-of-interaction between humans and their gut microbiota. This not only intimates that mucus ensures protection against endogenous and ex-ogenous opportunists but provision for the human microbiota to reside and flourish. With the emergence of living therapeutics, engineered microbes can deliver and produce increasingly complex medicine, and controlling the mucoadhesive properties of different microbial chassis can dictate dose-response in a patient. Here we present a redesigned, in vitro, plate-based assay to measure the mucus adhesion of various probiotics. Cell-mucus interactions were isolated by immobilizing mucus to the plate surface. Binding parameters were derived for each probiotic strain by measuring cell adhesion over a wide range of cell concentrations, providing dose-dependent adhesion metrics. Surface proteins and cell components known to influence mucoadhesion were then heterologously expressed or altered in Lactococcus lactis MG1363 and E. coli Nissle 1917 to control mucus-binding capacity, avidity, and cooperativity.
High-Accuracy Protein Structures by Combining Machine-Learning with Physics-Based Refinement
Authors: Heo Lim , Feig Michael
Published: August 2019

Protein structure prediction has long been available as an alternative to experimental structure determination, especially via homology modeling based on templates from related sequences. Recently, models based on distance restraints from co-evoluttionary analysis via machine learning have significantly expanded the ability to predict structures for sequences without templates. One such method, AlphaFold, also performs well on sequences were templates are available but without using such information directly. Here we show that combining machine-learning based models from AlphaFold with state-of-the-art physics-based refinement via molecular dynamics simulations further improves predictions to outperform any other prediction method tested during the latest round of CASP. The resulting models have highly accurate global and local structure, including high accuracy at functionally important interface residues, and they are highly suitable as initial models for crystal structure determination via molecular replacement.
Assessing the motivational effects of ethanol in mice using a discrete-trial current-intensity intracranial self-stimulation procedure
Authors: Barkley-Levenson Amanda M. , Der-Avakian Andre , Palmer Abraham A.
Published: August 2019

Background

Alcohol (ethanol) produces both rewarding and aversive effects, and sensitivity to these effects is associated with risk for an alcohol use disorder (AUD). Measurement of these motivational effects in animal models is an important but challenging aspect of preclinical research into the neurobiology of AUD. Here, we evaluated whether a discrete-trial current-intensity intracranial self-stimulation (ICSS) procedure can be used to assess both reward-enhancing and aversive responses to ethanol in mice.

Methods

C57BL/6J mice were surgically implanted with bipolar stimulating electrodes targeting the medial forebrain bundle and trained on a discrete-trial current-intensity ICSS procedure. Mice were tested for changes in response thresholds after various doses of ethanol (0.5 g/kg-1.75 g/kg), using a Latin square design.

Results

A 1 g/kg dose of ethanol produced a significant reward-enhancement (i.e., lowered response thresholds), whereas a 1.75 g/kg dose produced an aversive effect (elevated response thresholds).

Conclusions

The discrete-trial current-intensity ICSS procedure is an effective assay for measuring both reward-enhancing responses to ethanol as well as aversive responses in the same animal. This should prove to be a useful tool for assessing the effects of experimental manipulations on the motivational effects of ethanol in mice.
Development and evaluation of a rapid on-site water pathogen detection system for water quality monitoring
Authors: Chia Joel Y. , Tay Yu Pei , Poh Daniel , Tay Boon Hunt , Koh Eileen , Teo Joshua , Yap Hoi Ming , Lim Merrill , Soh Li Ting , Lee Yuan Kun , Lee Chi-Lik Ken
Published: August 2019

Timely response to outbreak of water-borne diseases caused by bacteria requires efficient monitoring and rapid detection strategies. Herein, we report a rapid DNA-based on-site detection system for specific detection of Pseudomonas aeruginosa. To evaluate the test performance of our method against spiked water samples, parallel tests based on real-time PCR and standard culture methods were concurrently performed. Test sensitivities of between 96.7% and 92.3% were obtained, based on the calculation obtained from qPCR and culture test, respectively, with a corresponding level of specificity of 92.9% and 83.3%. Time-to-result is around 45 min, with a detection limit of 1 CFU/100 mL. Here, a fully-deployable detection method where bacteria of-interest can be detected rapidly with high accuracy was described. This test method can be modified to detect other bacteria of-interest and can also be used in different applications. The test results can be obtained on-site and can therefore be particularly useful in public facilities health surveillance, where regulators can quickly determine if a site is safe or if other emergency response measures are required.

IMPORTANCE

Pseudomonas aeruginosa is a well-established water quality biomarker, known to be associated to humans’ health risks. To ascertain the presence of this pathogen, relevant stakeholders currently rely on standard quantitative ISO methods (APHA 9213E) which require 6 days from sampling to results. This window could potentially lead to waterborne outbreaks if the contaminated water features are not shut down for proper and urgent mitigation. This manuscript describes a method to detect this disease-causing microorganism in its viable forms under 1 hour, with a sensitivity of 1 CFU/100mL. Besides providing valuable information of the quality of water system, this direct monitoring of pathogens can reduce substantial time needed from sampling to reporting. This method can be established as a platform technology for other pathogenic microorganisms. On-going work to develop economic point-of-care prototypes could facilitate quick screening of targeted waterborne pathogens and results in better assessment of public health risk and quick in devising emergency response measures and other management strategies.
Norovirus replication in human intestinal epithelial cells is restricted by the interferon-induced JAK/STAT signalling pathway and RNA Polymerase II mediated transcriptional responses
Authors: Hosmillo Myra , Chaudhry Yasmin , Nayak Komal , Sorgeloos Frederic , Koo Bon-Kyoung , Merenda Alessandra , Lillestol Reidun , Drumright Lydia , Zilbauer Matthias , Goodfellow Ian
Published: August 2019

Human noroviruses (HuNoV) are a leading cause of viral gastroenteritis worldwide and a significant cause of morbidity and mortality in all age groups. The recent finding that HuNoV can be propagated in B cells and mucosa derived intestinal epithelial organoids (IEOs), has transformed our capability to dissect the life cycle of noroviruses. Using RNA-Seq of HuNoV infected intestinal epithelial cells (IECs), we have found that replication of HuNoV in IECs results in interferon-induced transcriptional responses and that HuNoV replication in IECs is sensitive to IFN. This contrasts with previous studies that suggest that the innate immune response may play no role in the restriction of HuNoV replication in immortalised cells. We demonstrate that the inhibition of JAK1/JAK2 enhances HuNoV replication in IECs. Surprisingly, targeted inhibition of cellular RNA polymerase II-mediated transcription was not detrimental to HuNoV replication, but enhanced replication to a greater degree compared to blocking of JAK signalling directly. Furthermore, we demonstrate for the first time that IECs generated from genetically modified intestinal organoids, engineered to be deficient in the interferon response, are more permissive to HuNoV infection. Together our work identifies the IFN-induced transcriptional responses restrict HuNoV replication in IECs and demonstrates that the inhibition of these responses by modifications to the culture conditions can greatly enhance the robustness of the norovirus culture system.

Importance

Noroviruses are a major cause of gastroenteritis worldwide yet the challenges associated with their growth culture has greatly hampered the development of therapeutic approaches and has limited our understanding of cellular pathways that control infection. Here we show that human intestinal epithelial cells, the first point of entry of human noroviruses into the host, limit virus replication by the induction of the innate responses. Furthermore we show that modulating the ability of intestinal epithelial cells to induce transcriptional responses to HuNoV infection can significantly enhance human norovirus replication in culture. Collectively our findings provide new insights into the biological pathways that control norovirus infection but also identify mechanisms to enhance the robustness of norovirus culture.