bluuebunny/crossref_metadata_2025 huggingface dataset:
Biomaterial based implants caused remote liver fatty deposition through activated blood-derived Kupffer cells
Authors: Peng Zhi , Xie Chang , Jin Shucheng , Hu Jiajie , Yao Xudong , Ye Jinchun , Zhang Xianzhu , Lim Jia Xuan , Wu Bingbing , Wu Haoyu , Liang Renjie , Wen Ya , Huang Jiahui , Zou Xiaohui , Ouyang Hongwei
Published: April 2023

Understanding the foreign-body response (FBR) of biomaterials is a prerequisite for the prediction of its clinical application, and the present assessments mainly rely on in vitro cell culture and in situ histopathology. However, remote organs responses after biomaterials implantation is unclear. Here, by leveraging body-wide-transcriptomics data, we performed in-depth systems analysis of biomaterials - remote organs crosstalk after abdominal implantation of polypropylene and silk fibroin using a rodent model, demonstrating local implantation caused remote organs responses dominated by acute-phase responses, immune system responses and lipid metabolism disorders. Of note, liver function was specially disturbed, defined as hepatic lipid deposition. Combining flow cytometry analyses and liver monocyte recruitment inhibition experiments, we proved that blood derived monocyte-derived Kupffer cells in the liver underlying the mechanism of abnormal lipid deposition induced by local biomaterials implantation. Moreover, from the perspective of temporality, the remote organs responses and liver lipid deposition of silk fibroin group faded away with biomaterial degradation and restored to normal at end, which highlighted its superiority of degradability. These findings were further indirectly evidenced by human blood biochemical examination from 141 clinical cases of hernia repair using silk fibroin mesh and polypropylene mesh. In conclusion, this study provided knowledge of biomaterials-body interactions. It is of great important for future development of biomaterial devices for clinical application.

One Sentence Summary

Abdominal local biomaterials implantation induces remote organ fatty deposition through activated blood-derived Kupffer cells.
Ginsentide TP1 Protects Hypoxia-Induced Dysfunction and ER Stress-Linked Apoptosis
Authors: Dutta Bamaprasad , Loo Shining , Kam Antony , Sze Siu Kwan , Tam James P.
Published: April 2023

Hypoxia-induced vascular endothelial dysfunction (VED) is a significant contributor to several severe human conditions, including heart disease, stroke, dementia, and cancer. However, current treatment options for VED are limited due to a lack of understanding of the underlying disease mechanisms and therapeutic leads. We recently discovered a heat-stable microprotein in ginseng, known as ginsentide TP1 that has been shown to reduce vascular dysfunction in cardiovascular disease models. In this study, we use a combination of functional assays and quantitative pulsed SILAC proteomics to determine new proteins synthesized in hypoxia and to show that ginsentide TP1 provides protection for human endothelial cells against hypoxia and ER stress. We found that hypoxia activates various pathways related to endothelium activation and monocyte adhesion, which in turn, impairs nitric oxide (NO) synthase activity, reduces NO bioavailability, and increases the production of reactive oxygen species that contribute to VED. Additionally, hypoxia triggers endoplasmic reticulum stress and initiates apoptotic signaling pathways associated with cardiovascular pathology. Treatment with ginsentide TP1 reduced surface adhesion molecule expression prevented activation of the endothelium and leukocyte adhesion, restored protein hemostasis, and reduced ER stress to protect against hypoxia-induced cell death. Ginsentide TP1 also restored NO signaling and bioavailability, reduced oxidative stress, and protected endothelial cells from endothelium dysfunction. In conclusion, this study shows that the molecular pathogenesis of VED induced by hypoxia can be mitigated by treatment with ginsentide TP1, which could be one of the key bioactive compounds responsible for the “cure-all” effect of ginseng. This research may lead to the development of new therapies for cardiovascular disorders.
The Impact of Chronic Phthalate Exposure on Rodent Anxiety and Cognition
Authors: Yu Zhe , Iyer Laxmi , Swiercz Adam P. , Paronett Elizabeth , Ramadan Manelle , Marvar Paul J. , Posnack Nikki Gillum
Published: April 2023

There is a growing importance for environmental contributions to psychiatric disorders and understanding the impact of the exposome (i.e., pollutants and toxins). Increased biomonitoring and epidemiological studies, for example, suggest that daily phthalate chemical exposure contribute to neurological and behavioral abnormalities, however these mechanisms remain poorly understood. The current study therefore aimed to examine the effects of chronic phthalate exposure on rodent anxiety behaviors, cognition, and the impact on hypothalamic-pituitary­ adrenal (HPA)-axis function. Adult male mice (C57BL6/J) were administered mono-2-ethylhexyl phthalate (MEHP) via drinking water (1 mg/ml), and anxiety-like behavior, cognition combined with HPA- axis and inflammatory assays were assessed after 3 weeks of MEHP exposure. MEHP-treated mice exhibited enhanced generalized anxiety-like behaviors, as demonstrated by reduced time spent in the open-arm of the elevated plus maze (EPM) and center exploration in the open field (OF). Tests of spatial, cognition and memory function were unchanged. Following MEHP administration, circulating levels of corticosterone and pro­ inflammatory cytokines were significantly increased, while at the tissue level, MEHP-dependent reductions in glucocorticoid metabolism genes 11β-hydroxysteroid dehydrogenase (11β-HSD) 1 and 2. These data suggest that chronic MEHP exposure leads to enhanced generalized-anxiety behaviors independent of rodent measures of cognition and memory, which maybe driven by MEHP-dependent effects on HPA-axis and peripheral glucocorticoid metabolism function.
An integrated single-cell RNA-seq map of human neuroblastoma tumors and preclinical models uncovers divergent mesenchymal-like gene expression programs
Authors: Chapple Richard H. , Liu Xueying , Natarajan Sivaraman , Alexander Margaret I.M. , Kim Yuna , Patel Anand G. , LaFlamme Christy W. , Pan Min , Wright William C. , Lee Hyeong-Min , Zhang Yinwen , Lu Meifen , Koo Selene C. , Long Courtney , Harper John , Savage Chandra , Johnson Melissa D. , Confer Thomas , Akers Walter J. , Dyer Michael A. , Sheppard Heather , Easton John , Geeleher Paul
Published: April 2023

Neuroblastoma is a common pediatric cancer, where preclinical studies suggest that a mesenchymal-like gene expression program contributes to chemotherapy resistance. However, clinical outcomes remain poor, implying we need a better understanding of the relationship between patient tumor heterogeneity and preclinical models. Here, we generated single-cell RNA-seq maps of neuroblastoma cell lines, patient-derived xenograft models (PDX), and a genetically engineered mouse model (GEMM). We developed an unsupervised machine learning approach (‘automatic consensus nonnegative matrix factorization’ (acNMF)) to compare the gene expression programs found in preclinical models to a large cohort of patient tumors. We confirmed a weakly expressed, mesenchymal-like program in otherwise adrenergic cancer cells in some pre-treated high-risk patient tumors, but this appears distinct from the presumptive drug-resistance mesenchymal programs evident in cell lines. Surprisingly however, this weak-mesenchymal-like program was maintained in PDX and could be chemotherapy-induced in our GEMM after only 24 hours, suggesting an uncharacterized therapy-escape mechanism. Collectively, our findings improve the understanding of how neuroblastoma patient tumor heterogeneity is reflected in preclinical models, provides a comprehensive integrated resource, and a generalizable set of computational methodologies for the joint analysis of clinical and pre-clinical single-cell RNA-seq datasets.
Identification of Mirror Repeats in Viral Genomes using FPCB Analysis
Authors: Yadav Pooja , Kumari Jyoti , Yadav Priyanka , Yadav Rachna , Yadav Shivani , Sharma Dinesh , Singh Amrita , Sehrawat Barkha , Yadav Manisha , Yadav Sandeep
Published: April 2023

The majority of living domains consist of DNA as genetic material with the minor exception of viruses. The unique nature of every species determines by its unique pattern of genome or gene products. The genomic features become an evident example of evolutionary study also. Different types of repeat patterns are observed in genomes of living domains including human beings whose two third portion of the genome is repetitive. Among the varied type of repeat sequences Mirror Repeats (MR) play crucial roles at the genetic level in every species. The major focus of our research is on identification & to check the distribution of mirror repeat. For this, we employed a bioinformatics-based approach refer as FASTA PARALLEL COMPLEMENT BLAST (FPCB) to identify unique mirror repeat (MR) sequences in some selected viral genomes from three different categories (Animal, Plant & Human). The identified repeats vary in their length as well as found to be distributed throughout the selected viral genomes. The maximum no of MR were reported in the case of Dengue virus (229) & minimum is in the case of TMV (97). In the remaining selected viruses - HCV, HPV, HTLV-1, PVY, Rabies virus 178, 156, 175, 203 & 204 MR sequences were reported. These sequences can be utilized in many ways like in molecular diagnosis, drug delivery target as well as evolutionary study, etc. The present research also helps in the development of novel tools of bioinformatics to study mirror repeats and their functional perspective in the context of their occurrence in all domains.
A cell-free strategy for profiling intracellular antibiotic sensitivity and resistance
Authors: Chengan Kameshwari , Hind Charlotte , Nagappa Lakshmeesha , Wand Matthew E. , Hanson Tanith , Escolano Ruben Martin , Tsaousis Anastasios , Bengoechea José A , Mark Sutton J. , Smales Christopher M , Moore Simon J
Published: April 2023

Antimicrobial resistance (AMR) is a pandemic spread across multiple priority infectious disease threats. While the cell envelope plays a key role in AMR, this also makes it challenging to study how antibiotics function inside the cell. Herein, we present aKlebsiella pneumoniaecell-free gene expression (CFE) platform for the rapid profiling of intracellular antibiotic sensitivity and resistance. This cell-free approach provides the unique macromolecular and metabolite components from this microbe, which include multiple antibiotic targets from transcription, translation, and metabolic processes. First, we compare theK. pneumoniaeCFE system to whole cell antimicrobial assays. We find that several antibiotic classes show higher sensitivity in the CFE system, suggesting limitations in antibiotic transport in the whole cell assay. Next, we evolvedK. pneumoniaestrains with resistance to specific antibiotics and use whole genome sequencing analysis for genotyping. As an exemplary case, we show that a single RNA polymerase beta subunit variant H526L (also frequently found in multidrug resistantMycobacterium tuberculosis) confers a 58-fold increase in CFE resistance to rifampicin. Overall, we describe a safe (i.e., non-living, non-pathogenic) platform suitable for studying an infectious disease model in a Containment Level 1 laboratory. Our CFE strategy is generalisable to laboratory and clinicalK. pneumoniaestrains and provides a new experimental tool to profile intracellular AMR variants. In conclusion, our CFE tool provides a significant advance towards understanding AMR and complements wider infectious disease studies.
Pan-cancer analysis reveals tumor microbiome associations with host molecular aberrations
Authors: Ma Chenchen , Su Changxing , Li Jiaxuan , Qu Jiuxin , Shuai Shimin
Published: April 2023

Abstract

Host-microbiome interaction is known to play a pivotal role in the cancer ecosystem, yet the associations have not been systematically investigated at the pan-cancer and the multi-omics level. Here, we evaluated nearly 10,000 samples across 32 cancer types collected from The Cancer Genome Atlas (TCGA), to investigate the association between the tumor microbiome (taxa, n=1,630) and tumor microenvironment composition (cell types, n=20), epigenome (CpG island methylation, n=30,716), transcriptome (gene expression, n=10,216) and proteome (protein expression, n=193). We identified 836,738 candidate associations between the tumor microbiome and host molecular aberrations across multiple cancers. Besides cancer-specific associations, we also revealed recurrent pan-cancer associations between microbes (Lachnoclostridium,Flammeovirga,TerrabacterandCampylobacter) and immune cells, as well as between microbes (CollimonasandSutterella) and fibroblasts, which were further validated by cell type estimations derived from pathological images and methylation data. We also identified several potential microbe and gene/protein expression associations mediated by DNA methylation using the sequential mediation analysis. Furthermore, our survival analysis demonstrated that tumor microbes may affect the patient’s overall survival and progression-free survival. Finally, a user-friendly web portal, Multi-Omics and Microbiome Associations in Cancer (MOMAC) was constructed for users to explore potential host-microbe interactions in cancer.

Graphical abstract
What is a rhythm for the brain? The impact of contextual temporal variability on auditory perception
Authors: Bonnet Pierre A , Bonnefond Mathilde , Kösem Anne
Published: April 2023

Temporal predictions can be formed and impact perception when sensory timing is fully predictable: for instance, the detection of a target sound is enhanced if it is presented on the beat of an isochronous rhythm. However, natural sensory stimuli, like speech or music, are not entirely predictable, but still possess statistical temporal regularities. We investigated whether temporal expectations can be formed in non-fully predictable contexts, and how the temporal variability of sensory contexts affects auditory perception. Specifically, we asked how “rhythmic” an auditory stimulation needs to be in order to observe temporal predictions effects on auditory discrimination performances. In this behavioral auditory oddball experiment, participants listened to auditory sound sequences where the temporal interval between each sound was drawn from gaussian distributions with distinct standard deviations. Participants were asked to discriminate sounds with a deviant pitch in the sequences. Auditory discrimination performances, as measured with deviant sound discrimination accuracy and response times, progressively declined as the temporal variability of the sound sequence increased. Temporal predictability effects ceased to be observed only for the more variable contexts. Moreover, both global and local temporal statistics impacted auditory perception, suggesting that temporal statistics are promptly integrated to optimize perception. Altogether, these results suggests that temporal predictions can be set up quickly based on the temporal statistics of past sensory events and are robust to a certain amount of temporal variability. Therefore, temporal predictions can be built on sensory stimulations that are not purely periodic nor temporally deterministic.

Significance statement

The perception of sensory events is known to be enhanced when their timing is fully predictable. However, it is unclear whether temporal predictions are robust to temporal variability, which is naturally present in many auditory signals such as speech and music. In this behavioral experiment, participants listened to auditory sound sequences where the timing between each sound was drawn from distinct gaussian distributions. Participant’s ability to discriminate deviant sounds in the sequences was function of the temporal statistics of past events: auditory deviant discrimination progressively declined as the temporal variability of the sound sequence increased. Results therefore suggest that auditory perception is sensitive to prediction mechanisms that are involved even if temporal information is not totally predictable.
Biomechanics Characterization of Autonomic and Somatic Nerves by High Dynamic Closed-Loop MEMS force sensing
Authors: González-González María Alejandra , Alemansour Hammed , Maroufi Mohammad , Coskun Mustafa Bulut , Lloyd David , Moheimani S. O. Reza , Romero-Ortega Mario I.
Published: April 2023

The biomechanics of peripheral nerves are determined by the blood-nerve barrier (BNB), together with the epineural barrier, extracellular matrix, and axonal composition, which maintain structural and functional stability. These elements are often ignored in the fabrication of penetrating devices, and the implant process is traumatic due to the mechanical distress, compromising the function of neuroprosthesis for sensory-motor restoration in amputees. Miniaturization of penetrating interfaces offers the unique opportunity of decoding individual nerve fibers associated to specific functions, however, a main issue for their implant is the lack of high-precision standardization of insertion forces. Current automatized electromechanical force sensors are available; however, their sensitivity and range amplitude are limited (i.e. mN), and have been tested onlyin-vitro. We previously developed a high-precision bi-directional micro-electromechanical force sensor, with a closed-loop mechanism (MEMS-CLFS), that while measuring with high-precision (−211.7μN to 211.5μN with a resolution of 4.74nN), can be used in alive animal. Our technology has an on-chip electrothermal displacement sensor with a shuttle beam displacement amplification mechanism, for large range and high-frequency resolution (dynamic range of 92.9 dB), which eliminates the adverse effect of flexural nonlinearity measurements, observed with other systems, and reduces the mechanical impact on delicate biological tissue. In this work, we use the MEMS-CLFS forin-vivobidirectional measurement of biomechanics in somatic and autonomic nerves. Furthermore we define the mechanical implications of irrigation and collagen VI in the BNB, which is different for both autonomic and somatic nerves (∼ 8.5-8.6 fold density of collagen VI and vasculature CD31+ in the VN vs ScN). This study allowed us to create a mathematical approach to predict insertion forces. Our data highlights the necessity of nerve-customization forces to prevent injury when implanting interfaces, and describes a high precision MEMS technology and mathematical model for their measurements.
Fibronectin, DHPS and SLC3A2 Signaling Cooperate to Control Tumor Spheroid Growth, Subcellular eIF5A1/2 Distribution and CDK4/6 Inhibitor Resistance
Authors: Geller Cameron , Maddela Joanna , Tuplano Ranel , Runa Farhana , Adamian Yvess , Güth Robert , Soto Gabriela Ortiz , Tomaneng Luke , Cantor Joseph , Kelber Jonathan A.
Published: April 2023

Extracellular matrix (ECM) protein expression/deposition within and stiffening of the breast cancer microenvironment facilitates disease progression and correlates with poor patient survival. However, the mechanisms by which ECM components control tumorigenic behaviors and responses to therapeutic intervention remain poorly understood. Fibronectin (FN) is a major ECM protein controlling multiple processes. In this regard, we previously reported that DHPS-dependent hypusination of eIF5A1/2 is necessary for fibronectin-mediated breast cancer metastasis and epithelial to mesenchymal transition (EMT). Here, we explored the clinical significance of an interactome generated using hypusination pathway components and markers of intratumoral heterogeneity. Solute carrier 3A2 (SLC3A2 or CD98hc) stood out as an indicator of poor overall survival among patients with basal-like breast cancers that express elevated levels of DHPS. We subsequently discovered that blockade of DHPS or SLC3A2 reduced triple negative breast cancer (TNBC) spheroid growth. Interestingly, spheroids stimulated with exogenous fibronectin were less sensitive to inhibition of either DHPS or SLC3A2 – an effect that could be abrogated by dual DHPS/SLC3A2 blockade. We further discovered that a subset of TNBC cells responded to fibronectin by increasing cytoplasmic localization of eIF5A1/2. Notably, these fibronectin-induced subcellular localization phenotypes correlated with a G0/G1 cell cycle arrest. Fibronectin-treated TNBC cells responded to dual DHPS/SLC3A2 blockade by shifting eIF5A1/2 localization back to a nucleus-dominant state, suppressing proliferation and further arresting cells in the G2/M phase of the cell cycle. Finally, we observed that dual DHPS/SLC3A2 inhibition increased the sensitivity of both Rb-negative and -positive TNBC cells to the CDK4/6 inhibitor palbociclib. Taken together, these data identify a previously unrecognized mechanism through which extracellular fibronectin controls cancer cell tumorigenicity by modulating subcellular eIF5A1/2 localization and provides prognostic/therapeutic utility for targeting the cooperative DHPS/SLC3A2 signaling axis to improve breast cancer treatment responses.
Reproducible and fully automated testing of nocifensive behavior in mice
Authors: Dedek Christopher , Azadgoleh Mehdi A. , Prescott Steven A.
Published: April 2023

Pain in rodents is often inferred from their withdrawal to noxious stimulation, using the threshold stimulus intensity or response latency to quantify pain sensitivity. This usually involves applying stimuli by hand and measuring responses by eye, which limits reproducibility and throughput to the detriment of preclinical pain research. Here, we describe a device that standardizes and automates pain testing by providing computer-controlled aiming, stimulation, and response measurement. Optogenetic and thermal stimuli are applied to the hind paw using blue and infrared light, respectively. Red light delivered through the same light path assists with aiming, and changes in its reflectance off the paw are used to measure paw withdrawal latency with millisecond precision at a fraction of the cost and data processing associated with high-speed video. Using standard video, aiming was automated by training a neural network to recognize the paws and move the stimulator using motorized linear actuators. Real-time data processing allows for closed-loop control of stimulus initiation and termination. We show that stimuli delivered with this device are significantly less variable than hand-delivered stimuli, and that reducing stimulus variability is crucial for resolving stimulus-dependent variations in withdrawal. Slower stimulus waveforms whose stable delivery is made possible with this device reveal details not evident with typical photostimulus pulses. Moreover, the substage video reveals a wealth of “spontaneous” behaviors occurring before and after stimulation that can considered alongside withdrawal metrics to better assess the pain experience. Automation allows comprehensive testing to be standardized and carried out efficiently.
A time for every purpose: using time-dependent sensitivity analysis to help understand and manage dynamic ecological systems
Authors: Ng Wee Hao , Myers Christopher R. , McArt Scott , Ellner Stephen P.
Published: April 2023

Sensitivity analysis is often used to help understand and manage ecological systems, by assessing how a constant change in vital rates or other model parameters might affect the management outcome. This allows the manager to identify the most favorable course of action. However, realistic changes are often localized in time—for example, a short period of culling leads to a temporary increase in the mortality rate over the period. Hence, knowing when to act may be just as important as knowing what to act upon. In this article, we introduce the method of time-dependent sensitivity analysis (TDSA) that simultaneously addresses both questions. We illustrate TDSA using three case studies: transient dynamics in static disease transmission networks, disease dynamics in a reservoir species with seasonal life-history events, and endogenously-driven population cycles in herbivorous invertebrate forest pests. We demonstrate how TDSA often provides useful biological insights, which are understandable on hindsight but would not have been easily discovered without the help of TDSA. However, as a caution, we also show how TDSA can produce results that mainly reflect uncertain modeling choices and are therefore potentially misleading. We provide guidelines to help users maximize the utility of TDSA while avoiding pitfalls.
Benchmarking cassette-based deep mutagenesis by Golden Gate assembly
Authors: Daffern Nicolas , Francino-Urdaniz Irene , Baumer Zachary T. , Whitehead Timothy A.
Published: April 2023

Protocols for the construction of large, deeply mutagenized protein encoding libraries via Golden Gate assembly of synthetic DNA cassettes employ disparate, system specific methodology. Here we benchmark a broadly applicable Golden Gate method for building user-defined libraries. We demonstrate that a 25 μl reaction, using 40 fmol of input DNA, can generate a library on the order of 1×106members and that reaction volume or input DNA concentration can be scaled up with no losses in transformation efficiency. Such libraries can be constructed from dsDNA cassettes generated either by degenerate oligonucleotides or oligo pools. We demonstrate its real-world effectiveness by building custom, user-defined libraries on the order of 104to 107unique protein encoding variants for two orthogonal protein engineering systems. We include a detailed protocol and provide several general-use destination vectors.
Assessing transcriptomic re-identification risks using discriminative sequence models
Authors: Sadhuka Shuvom , Fridman Daniel , Berger Bonnie , Cho Hyunghoon
Published: April 2023

Gene expression data provides molecular insights into the functional impact of genetic variation, for example through expression quantitative trait loci (eQTL). With an improving understanding of the association between genotypes and gene expression comes a greater concern that gene expression profiles could be matched to genotype profiles of the same individuals in another dataset, known as a linking attack. Prior works demonstrating such a risk could analyze only a fraction of eQTLs that are independent due to restrictive model assumptions, leaving the full extent of this risk incompletely understood. To address this challenge, we introduce the discriminative sequence model (DSM), a novel probabilistic framework for predicting a sequence of genotypes based on gene expression data. By modeling the joint distribution over all known eQTLs in a genomic region, DSM improves the power of linking attacks with necessary calibration for linkage disequilibrium and redundant predictive signals. We demonstrate greater linking accuracy of DSM compared to existing approaches across a range of attack scenarios and datasets including up to 22K individuals, suggesting that DSM helps uncover a substantial additional risk overlooked by previous studies. Our work provides a unified framework for assessing the privacy risks of sharing diverse omics datasets beyond transcriptomics.
“Antimicrobial Properties and Physical Characteristics of Essential Oil Extracted fromArtemisia herba albaCollected in El Bayadh, Algeria”
Authors: Dif Mustapha mahmoud , Fatima zohra Djaadane
Published: April 2023

Artemisia herba-albais a white mugwort harvested in the Bougtobe region of the El-Bayad province. Essential oils were extracted from the plant using hydrodistillation. The antibacterial study ofArtemisia herba-albaessential oils revealed a significant inhibitory action on the growth of tested microorganisms includingBacillus cereus, Staphylococcus aureus. These results demonstrated significant activity compared to the positive control penicillin, amoxicillin, and spiramycin. Overall, the results showed that the tested essential oil possesses interesting antimicrobial activities, and therefore, opens up new perspectives in the field of natural applications as a promising alternative to chemical products and for industrial exploitation.
WITHDRAWN: LonP1 Drives Proneural Mesenchymal Transition in IDH1-R132H Diffuse Glioma
Authors: Douglas Christopher , Lomeli Naomi , Vu Thao , Pham James , Bota Daniela A.
Published: April 2023

Withdrawal Statement

The authors have withdrawn their manuscript owing to massive revision and data validation. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Computational pathology infers clinically relevant protein levels and drug response in breast cancer by weakly supervised contrastive learning
Authors: Liu Hui , Xie Xiaodong , Wang Bin
Published: April 2023

Visual inspection of histopathology slides via optical microscope is the routine medical examination for clinical diagnosis of tumors. Recent studies have demonstrated that computational pathology not only automate the tumor diagnosis, but also showed great potential to uncover tumor-related genetic alterations and transcriptomic patterns. In this paper, we propose wsi2rppa, a weakly supervised contrastive learning framework to infer the protein levels of tumor biomarkers from whole slide images (WSIs) in breast cancer. We firstly conducted contrastive learning-based pre-training on tessellated tiles to extract histopathological features, which are then aggregated by attention pooling and adapted to downstream tasks. Our extensive experiments showed that our method achieved state-of-the-art performance in tumor diagnostic task, and also performed well in predicting clinically relevant protein levels and drug response. To show the model interpretability, we spatially visualized the WSIs colored the tiles by their attention scores, and found that the regions with high scores were highly consistent with the tumor and necrotic regions annotated by a 10-year experienced pathologist. Moreover, spatial transcriptomic data further verified that the heatmap generated by attention scores agree greatly with the spatial expression landscape of two typical tumor biomarker genes. In particular, our method achieved 0.79 AUC value in predicting the response of breast cancer patients to the drug trastuzumab treatment. These findings showed the remarkable potential of deep learning-based morphological feature is very indicative of clinically relevant protein levels, drug response and clinical outcomes.
Evaluation of the disease-modifying effects of Aureobasidium pullulans AFO-202 strain produced Beta-Glucan in Parkinson’s disease – Results of a pilot clinical study
Authors: Vetrievel Chockanathan , Nithyanandam Allimuthu , Srinivasan Subramaniam , Bharatidasan Sudhakar S , Dedeepiya Vidyasagar Devaprasad , Ikewaki Nobunao , Iwasaki Masaru , Senthilkumar Rajappa , Preethy Senthilkumar , Abraham Samuel JK
Published: April 2023

The aetiology of Parkinson’s disease (PD) has been linked to the aggregation and spread of misfolded alpha-synuclein via the gut-brain axis. We previously reported the effects of a biological response modifier, beta-glucan, produced by the AFO-202 strain ofAureobasidium Pullulans, which improves clinical symptoms and controls gutEnterobacteriaceaeassociated with curli and amyloid-alpha-synuclein production. In this study, we report the effects of beta-glucan on PD. Eight patients with PD were recruited, five of whom completed the study. Each participant was administered 3 g of AFO-202 B-glucan orally daily for 90 days in addition to their regular prescription drugs. Pre- and post-study comparison revealed that the mean UPDRS decreased from 43.25 ± 13.75 at baseline to 40 ± 13.65 post intervention. Improvements in cognition, walking and balance, postural stability, and constipation scales were observed. The mean constipation severity score decreased from 3 ± 1.73 to 1.75 ± 0.43 post intervention. The serum creatinine kinase levels decreased and the blood glucose and lipid levels normalised. The MRI Parkinson’s index (MRPI) improved in one patient. This safe AFO-202 B-glucan produced beneficial disease-modifying improvements in the UPDRS and MRI that were clinically significant in the short timeframe of 90 days. Further validation in larger, longer-term clinical trials will help confirm the use of beta-glucan as a potential adjuvant treatment for PD which may pave way for future evaluations of these beta-glucans in other synculeinopathies as well Lewy-body related pathogenesis.
Whole-brain deactivations precede uninduced mind-blanking reports
Authors: Boulakis Paradeisios Alexandros , Mortaheb Sepehr , Calster Laurens van , Majerus Steve , Demertzi Athena
Published: April 2023

Mind-blanking (MB) is termed as the inability to report our immediate-past mental content. In contrast to mental states with reportable content, such as mind-wandering or sensory perceptions, the neural correlates of MB started getting elucidated only recently. A notable particularity that pertains to MB studies is the way MB is instructed for reporting, like by deliberately asking participants to “empty their minds”. Such instructions were shown to induce fMRI activations in frontal brain regions, typically associated with metacognition and self-evaluative processes, suggesting that MB may be a result of intentional mental content suppression. Here, we aim at examining this hypothesis by determining the neural correlates of MB without induction. Using fMRI combined with experience-sampling in 31 participants (22 female), univariate analysis of MB reports revealed deactivations in occipital, frontal, parietal, and thalamic areas, but no activations in prefrontal regions. These findings were confirmed using Bayesian region-of-interest analysis on areas previously shown to be implicated in induced MB, where we report evidence for frontal deactivations during MB reports compared to other mental states. Contrast analysis between reports of MB and content-oriented mental states also revealed deactivations in the left angular gyrus. We propose that these effects characterize a neuronal profile of MB, where key thalamocortical nodes are unable to communicate and formulate reportable content. Collectively, we show that study instructions for MB lead to differential neural activation. These results provide mechanistic insights linked to the phenomenology of MB and point to the possibility of MB being expressed in different forms.
Marine transmissible cancer navigates urbanised waters, threatening to spillover
Authors: Hammel M. , Touchard F. , Burioli E. A. V. , Paradis L. , Cerqueira F. , Chailler E. , Bernard I. , Cochet H. , Simon A. , Thomas F. , Destoumieux-Garzón D. , Charrière G. M. , Bierne N.
Published: April 2023

Inter-individual transmission of cancer cells represents a unique form of microparasites increasingly reported in marine bivalves. In this study, we sought to understand the ecology of the propagation ofMytilus trossulusBivalve Transmissible Neoplasia 2 (MtrBTN2), a transmissible cancer affecting fourMytilusmussel species worldwide. We investigated the prevalence of MtrBTN2 in the mosaic hybrid zone ofM. edulisandM. galloprovincialisalong the French Atlantic coast, sampling contrasting natural and anthropogenic habitats. We observed a similar prevalence in both species, likely due to the spatial proximity of the two species in this region. Our results showed that ports had higher prevalence of MtrBTN2, with a possible hotspot observed at a shuttle landing dock. No cancer was found in natural beds except for two sites close to the hotspot, suggesting spillover. Ports may provide favourable conditions for the transmission of MtrBTN2, such as high mussel density, stressful conditions, sheltered and confined shores, or buffered temperatures. Ships may also spread the disease through biofouling. Our results suggest ports may serve as epidemiological hubs, with maritime routes providing artificial gateways for MtrBTN2 propagation. This highlights the importance of preventing biofouling on docks and ship hulls to limit the spread of marine pathogens hosted by fouling species.
Targeting the catalytic activity of HDAC1 in T cells protects against experimental autoimmune encephalomyelitis
Authors: Zhu Ci , Stolz Valentina , Simonovic Natalija , Al-Rubaye Osamah , Vcelkova Terezia , Moos Verena , Hess Lena , Hagelkruys Astrid , Madern Moritz , Reiter Wolfgang , Meixner Arabella , Bock Christoph , Hartl Markus , Ellmeier Ellmeier , Seiser Christian
Published: April 2023

Histone deacetylases are key epigenetic regulators that control T cell-mediated immunity. A T cell-specific deletion ofHdac1(HDAC1cKO) protects mice against experimental autoimmune encephalomyelitis (EAE). However, it remains elusive whether inhibition of HDAC1 enzymatic activity, which could be achieved therapeutically by HDAC1 inhibitor treatment, is sufficient to block EAE induction. In order to address this question, we generated a novel mouse strain that expresses catalytically inactive HDAC1 (HDAC1Off) from theRosa26locus in HDAC1cKOCD4+T cells to mimic selective inhibition of HDAC1 enzymatic activityin vivo. Mice expressing wildtype HDAC1 in HDAC1cKOCD4+T cells (HDAC1On) were generated as corresponding controls. In contrast to HDAC1Onmice, HDAC1Offmice did not develop EAE, and this correlated with diminished leukocyte CNS infiltration. HDAC1OffCD4+T cells in the CNS displayed a severe reduction of IFNγ, IL-17A and TNFα proinflammatory cytokine expression, andin vivoactivated HDAC1OffCD4+T cells downregulated gene sets associated with T cell activation, cytokine expression and cell migration. This indicates impaired effector functions of HDAC1OffCD4+T cells. Taken together, our study demonstrates that the inhibition of the catalytic activity of HDAC1 in T cells is sufficient to achieve a clinical benefit in EAE disease development. This raises the translational perspective of pharmacological HDAC1 inhibition for treating human T cell-mediated autoimmune diseases.

Highlights

Successful generation of a novel mouse model that expresses enzymatic-inactive HDAC1 to mimic HDAC1 inhibitor treatmentin vivo.

Mice expressing enzymatically inactive HDAC1 instead of WT HDAC1 in T cells do not develop EAE and display diminished leukocyte CNS infiltration.

In vivoactivated CD4+T cells expressing enzymatic inactive HDAC1 downregulate pathways important for T cell activation, cytokine expression and cell migration.

Demonstrate the proof-of-principle that targeting the enzymatic activity of HDAC1 is a promising treatment strategy for autoimmune diseases.
Data-Driven Modelling of Gene Expression States in Breast Cancer and their Prediction from Routine Whole Slide Images
Authors: Dawood Muhammad , Eastwood Mark , Jahanifar Mostafa , Young Lawrence , Ben-Hur Asa , Branson Kim , Jones Louise , Rajpoot Nasir , Minhas Fayyaz ul Amir Afsar
Published: April 2023

Identification of gene expression state of a cancer patient from routine pathology imaging and characterization of its phenotypic effects have significant clinical and therapeutic implications. However, prediction of expression of individual genes from whole slide images (WSIs) is challenging due to co-dependent or correlated expression of multiple genes. Here, we use a purely data-driven approach to first identify groups of genes with co-dependent expression and then predict their status from (WSIs) using a bespoke graph neural network. These gene groups allow us to capture the gene expression state of a patient with a small number of binary variables that are biologically meaningful and carry histopathological insights for clinically and therapeutic use cases. Prediction of gene expression state based on these gene groups allows associating histological phenotypes (cellular composition, mitotic counts, grading, etc.) with underlying gene expression patterns and opens avenues for gaining significant biological insights from routine pathology imaging directly.

Graphical Abstract

Highlights

Data-driven discovery of co-expressing gene groups in breast caner

Histological imaging based prediction of gene groups via deep learning

Identification of phenotypic correlates of gene-expression in histological imaging

Clinical and therapeutic impact of gene groups and their visual patterns identified
EOGT Enables Residual Notch Signaling in Mouse Intestinal Cells Lacking POFUT1
Authors: Nauman Mohd , Varshney Shweta , Choi Jiahn , Augenlicht Leonard H. , Stanley Pamela
Published: April 2023

Notch signaling determines cell fates in mouse intestine. Notch receptors contain multiple epidermal growth factor-like (EGF) repeats modified by O-glycans that regulate Notch signaling. Conditional deletion of protein O-fucosyltransferase 1 (Pofut1) substantially reduces Notch signaling and markedly perturbs lineage development in mouse intestine. However, mice with inactivatedPofut1are viable, whereas complete elimination of Notch signaling in intestine is lethal. Here we investigate whether residual Notch signaling enabled by EOGT permits mice lackingPofut1in intestine to survive. Mice globally lackingEogtalone were grossly unaffected in intestinal development. In contrast, mice lacking bothEogtandPofut1died at ∼28 days after birth with greater loss of body weight, a greater increase in the numbers of goblet and Paneth cells, and greater downregulation of Notch target genes, compared toPofut1deletion alone. These data establish that both O-fucose and O-GlcNAc glycans are fundamental to Notch signaling in the intestine and provide new insights into roles for O-glycans in regulating Notch ligand binding. Finally, EOGT and O-GlcNAc glycans provide residual Notch signaling and support viability in mice lackingPofut1in the intestine.
A maturation defective HIV-1 activates cGAS
Authors: Sumner Rebecca P. , Blest Henry , Lin Meiyin , Maluquer de Motes Carlos , Towers Greg J.
Published: April 2023

Background

Detection of viruses by host pattern recognition receptors induces the expression of type I interferon (IFN) and IFN-stimulated genes (ISGs), which suppress viral replication. Retroviruses such as HIV-1 are subject to sensing by both RNA and DNA sensors, and whether there are any particular features of the viral genome or reverse transcripts that facilitate or enhance this sensing is currently unknown.

Results

Whilst investigating the determinants of innate detection of HIV-1 we noticed that infection of THP-1 cells or primary macrophages with a virus expressing Gag fused to a reporter gene (luciferase or GFP) induced a robust IFN and ISG response that was not observed with an equivalent virus with similar genome length and composition, but expressing wild-type Gag. Innate immune activation by Gag-fusion HIV-1 was dependent on reverse transcription and DNA sensor cGAS, suggesting activation of an IFN response by viral DNA. Further investigation of the Gag-fusion viral particles revealed maturation defects, as evidenced by incomplete Gag cleavage and a diminished capacity to saturate restriction factor TRIM5α, likely due to aberrant particle formation. We propose that expression of the Gag fusion protein disturbs the correct cleavage and maturation of wild-type Gag, yielding viral particles that are unable to effectively shield viral DNA from detection by innate sensors including cGAS.

Conclusions

These data highlight the crucial role of capsid in innate evasion and support growing literature that disruption of Gag cleavage and capsid formation induces a viral DNA- and cGAS-dependent innate immune response. Together these data demonstrate a protective role for capsid and suggest that antiviral activity of capsid-targeting antivirals may benefit from enhanced innate and adaptive immunityin vivo.
During heat stress inMyxococcus xanthus, the CdbS PilZ domain protein, along with two PilZ-DnaK chaperones, perturbs chromosome organization and accelerates cell death
Authors: Seidel Michael , Skotnicka Dorota , Glatter Timo , Søgaard-Andersen Lotte
Published: April 2023

C-di-GMP is a bacterial second messenger that regulates diverse processes in response to environmental or cellular cues. The nucleoid-associated protein (NAP) CdbA inMyxococcus xanthusbinds c-di-GMP and DNA in a mutually exclusive mannerin vitro. CdbA is essential for viability, and CdbA depletion causes defects in chromosome organization, leading to a block in cell division and, ultimately, cell death. Most NAPs are not essential; therefore, to explore the paradoxicalcdbAessentiality, we isolated suppressor mutations that restored cell viability without CdbA. Most mutations mapped tocdbS, which encodes a stand-alone c-di-GMP binding PilZ domain protein, and caused loss-of-function ofcdbS. Cells lacking CdbA and CdbS or only CdbS were fully viable and had no defects in chromosome organization. CdbA depletion caused post-transcriptional upregulation of CdbS accumulation, and this CdbS over-accumulation was sufficient to disrupt chromosome organization and cause cell death. CdbA depletion also caused increased accumulation of CsdK1 and CsdK2, two unusual PilZ-DnaK chaperones. During CdbA depletion, CsdK1 and CsdK2, in turn, stabilized CdbS, thereby enabling its increased accumulation and toxicity. Moreover, we demonstrate that heat stress, possibly involving an increased cellular c-di-GMP concentration, induces the CdbA/CsdK1/CsdK2/CdbA system, causing a CsdK1- and CsdK2-dependent increase in CdbS accumulation. Thereby this system accelerates heat stress-induced chromosome mis-organization and cell death. Collectively, this work describes a unique system that contributes to regulated cell death inM. xanthusand suggests a link between c-di-GMP signaling and regulated cell death in bacteria.

Author summary

The nucleotide-based second messenger c-di-GMP in bacteria controls numerous processes in response to environmental or cellular cues. Typically, these processes are related to lifestyle transitions between motile and sessile behaviors. However, c-di-GMP also regulates other processes. InMyxococcus xanthus, CdbA is a DNA-binding and nucleoid-associated protein that helps to organize the large chromosome. CdbA binds c-di-GMP and DNA in a mutually exclusive manner. While other nucleoid-associated proteins are not essential, CdbA is essential. Here, we show that the crucial function of CdbA is to maintain the level of the c-di-GMP-binding PilZ-domain protein CdbS appropriately low. The CdbS level is not only increased upon depletion of CdbA but also in response to heat stress. Under both conditions, the increased CdbS level perturbs chromosome organization and ultimately causes cell death. The CdbA/CdbS system represents a unique system that contributes to regulated cell death inM. xanthusand suggests a link between c-di-GMP signaling and regulated cell death.
Ultraconformable cuff implants for long-term bidirectional interfacing of peripheral nerves at sub-nerve resolutions
Authors: Carnicer-Lombarte Alejandro , Boys Alexander J. , Güemes Amparo , Gurke Johannes , Velasco-Bosom Santiago , Hilton Sam , Barone Damiano G. , Malliaras George G.
Published: April 2023

Implantable devices interfacing with peripheral nerves exhibit limited longevity and resolution. Poor nerve-electrode interface quality, invasive surgical placement and development of foreign body reaction combine to limit research and clinical application of these devices. Here, we develop cuff implants with an ultraconformable design that achieve high-quality and stable interfacing with nerves in chronic implantation scenarios. When implanted in sensorimotor nerves of the arm in awake rats for 21 days, the devices recorded nerve action potentials with fascicle-specific resolution and extracted from these the conduction velocity and direction of propagation. The ultraconformable cuffs exhibited high biocompatibility, producing lower levels of fibrotic scarring than clinically equivalent PDMS silicone cuffs. In addition to recording nerve activity, the devices were able to modulate nerve activity at sub-nerve resolution to produce a wide range of paw movements. The developed implantable devices represent a platform enabling new forms of fine nerve signal sensing and modulation, with applications in physiology research and closed-loop therapeutics.