bluuebunny/crossref_metadata_2025 huggingface dataset:
Genes of the fatty acid oxidation pathway are upregulated in female as compared to male cardiomyocytes
Authors: Talukdar Maya , Chmátal Lukáš , Mao Linyong , Reichart Daniel , Murashige Danielle , Skaletsky Yelena , DeLaughter Daniel M. , Arany Zoltan , Seidman Jonathan G. , Seidman Christine , Page David C.
Published: June 2024

Human females and males differ in cardiac physiology and pathology, even after controlling for sex differences in anthropometrics, lifestyle, and environment. For example, females and males differ in cardiac stroke volume and ventricular thickness, and they exhibit different rates and symptoms of cardiovascular disease. Less is understood about molecular differences in female and male hearts, such as sex differences in gene expression. Here we present an integrative framework utilizing bulk and single-nucleus RNA-sequencing data to study sex differences in the cardiac transcriptome. We show that genes of the fatty acid oxidation (FAO) pathway, the primary source of energy in the heart, are expressed more highly in healthy female than in healthy male hearts. We demonstrate that this sex difference is due to cardiomyocyte-specific, female-biased expression of FAO genes and cannot be explained by sex differences in cardiac cellular composition or number of mitochondria, where FAO takes place. Finally, we observe increased cardiac flux and energetic utilization of free fatty acids in female compared to male hearts. Overall, our results demonstrate that male and female human hearts exhibit fundamental differences in metabolism that likely contribute to sex differences in cardiac physiology and pathology.
Drug-Induced p53 Activation Limits Pancreatic Cancer Initiation
Authors: Twardowski Jennifer J , Heist Thomas I , Soares Zamira Guerra , Berry Emily S , Ruffolo Luis I , Pröschel Christoph , Mello Stephano S
Published: June 2024

Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal disease, initiated predominantly by mutations inKras, which induce acinar-to-ductal metaplasia (ADM) and subsequent formation of precursor lesions, such as pancreatic intraepithelial neoplasia (PanIN). Progression to PDAC is frequently associated with mutations in the tumor suppressorTP53, presumably via disrupting p53-mediated cellular senescence of PanINs. WhetherTP53also has tumor-suppressive activity in earlier phases of PDAC initiation has been less clear. In this study, we investigate the impact of pharmacological stabilization of the wild-type p53 protein on the formation of ADM in aKrasG12D-driven mouse model of PDAC. Our findings demonstrate that p53 stabilization via Nutlin-3a significantly reduces both ADM and PanIN formation by promoting the differentiation of ADM into acinar cells. This differentiation coincides with p53-dependent upregulation of the transcription factor Mist1 (Bhlha15), a critical inducer of acinar cell identity. Our results reveal a role for p53 in tissue repair and maintenance of homeostasis in tumor suppression and suggest pharmacological engagement of p53 as an intervention strategy to prevent PDAC initiation.
Bioinformatics analysis of the potential biomarkers of Multiple Sclerosis and Guillain-Barré syndrome
Authors: Kwok Tyler , Huerta-White Tajah , Briegel Karl , Singh Aaisha , Yeguvapalli Suneetha , Chitrala Kumaraswamy Naidu
Published: June 2024

Recent research emphasizes the intricate interplay of genetics and epigenetics in neurological disorders, notably Multiple Sclerosis (MS) and Guillain-Barre Syndrome (GBS), both of which exhibit cardiovascular dysregulation, with GBS often featuring serious bradyarrhythmias requiring prompt recognition and treatment. While cardiovascular autonomic dysfunction in MS is typically less severe, orthostatic intolerance affects around half of MS patients. Their distinction lies in their autoimmune responses, MS is an autoimmune disease affecting the central nervous system, causes demyelination and axon damage, leading to cognitive, ocular, and musculoskeletal dysfunction. In contrast, GBS primarily affects the peripheral nervous system, resulting in paralysis and respiratory complications. Despite their differences, both diseases share environmental risk factors such as viral infections and Vitamin D deficiency. This study aims to explore shared gene expression pathways, functional annotations, and molecular pathways between MS and GBS to enhance diagnostics, pathogenesis understanding, and treatment strategies through molecular analysis techniques. Through the gene expression analysis, five significant genes were found UTS2, TNFSF10, GBP1, VCAN, FOS. Results shows that Common DEGs are linked to apoptosis, bacterial infections, and atherosclerosis. Molecular docking analysis suggests Aflatoxin B1 as a potential therapeutic compound due to its high binding affinity with common differentially expressed proteins.
Real-time Biomechanical Characterisation of Cytoskeletal Remodelling
Authors: Zhang Kaiwen , Reeves Chayla , Berry Joseph D. , Fox Kate , Elbourne Aaron , Gelmi Amy
Published: June 2024

As progenitors for tissue, human mesenchymal stem cells (hMSCs) with ability of self-proliferation and differentiation into various cell types such as osteocytes and adipocytes show great potential applications for tissue engineering. Stem cell fate regulation is highly affected by the cytoskeleton structure and mechanical properties. In this paper, quantitative Atomic Force Microscopy (Q-AFM) was used to continuously characterise topography and biomechanical properties while applying cytoskeleton disruptors to hMSCs. The cell stiffness (quantified by Young’s modulus), primarily governed by the cytoskeleton network, had quantifiable changes associated with cytoskeleton polymerisation and depolymerisation when treatments were applied. Furthermore, with Q-AFM measurements, these changes were tracked in real time over a period of minutes to hours, and the biomechanical properties of the cells were tracked through the applied treatment and subsequent recovery post treatment. Here we present the capability of Q-AFM to perform real time biomechanical characterisation of living cells, directly correlated to intracellular structure and cytoskeletal remodelling.
Phylogeny and species delimitation of ciliates in the genusSpirostomum(Class, Heterotrichea) using single-cell transcriptomes
Authors: Shazib Shahed Uddin Ahmed , Cote-L’Heureux Auden , Ahsan Ragib , Muñoz-Gómez Sergio A. , Lee JunMo , Katz Laura A. , Shin Mann Kyoon
Published: June 2024

Ciliates are single-celled microbial eukaryotes that diverged from other eukaryotic lineages over a billion years ago. The extensive evolutionary timespan of ciliate has led to enormous genetic and phenotypic changes, contributing significantly to their high level of diversity. Recent analyses based on molecular data have revealed numerous cases of cryptic species complexes in different ciliate lineages, demonstrating the need for a robust approach to delimit species boundaries and elucidate phylogenetic relationships. Heterotrich ciliate species of the genusSpirostomumare abundant in freshwater and brackish environments and are commonly used as biological indicators for assessing water quality. However, someSpirostomumspecies are difficult to identify due to a lack of distinguishable morphological characteristics, and the existence of cryptic species in this genus remains largely unexplored. Previous phylogenetic studies have focused on only a few loci, namely the ribosomal RNA genes, alpha-tubulin, and mitochondrial CO1. In this study, we obtained single-cell transcriptome of 25Spirostomumspecies populations (representing six morphospecies) sampled from South Korea and the USA, and used concatenation- and coalescent-based methods for species tree inference and delimitation. Phylogenomic analysis of 37Spirostomumpopulations and 265 protein-coding genes provided a robustious insight into the evolutionary relationships amongSpirostomumspecies and confirmed that species with moniliform and compact macronucleus each form a distinct monophyletic lineage. Furthermore, the multispecies coalescent (MSC) model suggests that there are at least nine cryptic species in theSpirostomumgenus, three inS. minus, two inS. ambiguum, S. subtilis, andS. tereseach. Overall, our fine sampling of closely relatedSpirostomumpopulations and wide scRNA-seq allowed us to demonstrate the hidden crypticity of species within the genusSpirostomum, and to resolve and provide much stronger support than hitherto to the phylogeny of this important ciliate genus.
Housing temperature dictates the systemic and tissue-specific molecular responses to cancer in mice
Authors: Irazoki Andrea , Frank Emma , Phung Pham Tang Cam , Braun Jessica L , Ehrlich Amy M. , Haid Mark , Riols Fabien , Friis Hansen Camilla Hartmann , Rydal Jørgensen Anne-Sofie , Andersen Nicoline Resen , Hidalgo-Corbacho Laura , Meneses-Valdes Roberto , Ali Mona Sadek , Raun Steffen Henning , Modvig Johanne Louise , Gallero Samantha , Larsen Steen , Gerhart-Hines Zach , Jensen Thomas Elbenhardt , Rohm Maria , Treebak Jonas T. , Fajardo Val Andrew , Sylow Lykke
Published: June 2024

Cancer cachexia is a metabolic condition affecting up to 80% of patients with cancer. Cachexia is mediated by reduced muscle and fat mass and impaired function, and it lowers survival for patients. With no approved drugs to treat cachexia, preclinical efforts focus on understanding the molecular mechanisms underlying this condition to reveal treatment targets. Housing laboratory mice at ambient temperature imposes cold stress, leading to induced thermogenic activity and consequent whole-body metabolic adaptations. Yet, the impact of housing temperature inin vivopreclinical cachexia remains unknown. We found that thermoneutral (TN) housing in C26 carcinoma-bearing (C26) mice affected lean and fat mass, but not muscle weight or force. TN housing improved glucose tolerance in C26 mice, while enhancing circulating abundance of FGF21 and IL-6. Thermogenic tissues, especially brown adipose tissue, exhibited housing temperature-dependent molecular responses to cancer in oxygen consumption, ATP levels and SERCA ATPase activity, which are all crucial for cancer-induced whole-body metabolic adaptations. We conclude that molecular and systemic adaptations to cancer in mice critically depend on housing temperature, which should be considered in the design and interpretation of preclinical cancer studies.
Painting the diversity of a world’s favourite fruit: A next generation catalogue of cultivated bananas
Authors: Sardos Julie , Cenci Alberto , Martin Guillaume , Breton Catherine , Guignon Valentin , Van den Houwe Ines , Mendez Yaleidis , Sachter-Smith Gabriel L. , Chase Rachel , Ruas Max , Rivallan Ronan , Paofa Janet , Wigmore William , Hunter David Tilafono , D’Hont Angélique , Yahiaoui Nabila , Jenny Christophe , Perrier Xavier , Roux Nicolas , Rouard Mathieu
Published: June 2024

Societal impact statement

Bananas are nutritious fruits of major importance in the tropics and subtropics. Characterizing their diversity is essential to ensure their conservation and use. A catalogue showcasing cultivated bananas genomic diversity was compiled and is to be used as a tool to support the classification of banana cultivars. This research revealed that cultivated banana groups are not all made of identical clones. Materials from recent collecting missions indicated that more banana diversity is expected to be found as the exploration of the banana gene pool continues. These discoveries will drive dynamic conservation strategies for banana genetic resources and will increase their use.

Banana is an important food crop cultivated in many tropical and subtropical regions around the world. Due to their low fertility, banana landraces are clonally propagated. However, different factors, such as synonymy and the effects of environment, make their assignment to described sets of clones, or cultivar groups, difficult. Consequently, passport data of accessions in genebanks is often uncomplete and sometimes inaccurate.

With the recent advances in genomics, a new powerful tool was developed enabling the fine-scale characterization of banana’s ancestry along chromosomes, i.e.in silicochromosome painting. We applied this method to a high-throughput genotyping data set obtained from 317 banana accessions spanning most of the known cultivar groups. This set included both genebank and new uncharacterized materials.

By comparing curated morphological assignation to the genomic patterns resulting fromin silicochromosome painting, we were able to compile a catalogue referencing the chromosome painting patterns of most of the described cultivar groups.

Examining the genomic patterns obtained, we discovered intra-cultivar group variability. In some cultivar groups, mitotic recombination or deletions were clonally accumulated in cultivars. In addition, we identified at least 4 cultivar groups in which cultivars likely resulting from distinct sexual events co-existed, notably Pisang Awak in which 5 distinct genomic patterns of two ploidy levels were identified. New patterns were also discovered in the newest materials of the set, showing that a wider diversity of clones still existon farm.
An active electronic, high-density epidural paddle array for chronic spinal cord neuromodulation
Authors: Parker Samuel R. , Calvert Jonathan S. , Darie Radu , Jang Jaeson , Govindarajan Lakshmi Narasimhan , Angelino Keith , Chitnis Girish , Iyassu Yohannes , Shaaya Elias , Fridley Jared S. , Serre Thomas , Borton David A. , McLaughlin Bryan L.
Published: June 2024

Objective

Epidural electrical stimulation (EES) has shown promise as both a clinical therapy and research tool for studying nervous system function. However, available clinical EES paddles are limited to using a small number of contacts due to the burden of wires necessary to connect each contact to the therapeutic delivery device, limiting the treatment area or density of epidural electrode arrays. We aimed to eliminate this burden using advanced on-paddle electronics.

Approach

We developed a smart EES paddle with a 60-electrode programmable array, addressable using an active electronic multiplexer embedded within the electrode paddle body. The electronics are sealed in novel, ultra-low profile hermetic packaging. We conducted extensive reliability testing on the novel array, including a battery of ISO 10993-1 biocompatibility tests and determination of the hermetic package leak rate. We then evaluated the EES device in vivo, placed on the epidural surface of the ovine lumbosacral spinal cord for 15 months.

Main results

The active paddle array performed nominally when implanted in sheep for over 15 months and no device-related malfunctions were observed. The onboard multiplexer enabled bespoke electrode arrangements across, and within, experimental sessions. We identified stereotyped responses to stimulation in lower extremity musculature, and examined local field potential responses to EES using high-density recording bipoles. Finally, spatial electrode encoding enabled machine learning models to accurately perform EES parameter inference for unseen stimulation electrodes, reducing the need for extensive training data in future deep models.

Significance

We report the development and chronic large animalin vivoevaluation of a high-density EES paddle array containing active electronics. Our results provide a foundation for more advanced computation and processing to be integrated directly into devices implanted at the neural interface, opening new avenues for the study of nervous system function and new therapies to treat neural injury and dysfunction.
Structure-specific variation in per- and polyfluoroalkyl substances toxicity among genetically diverseCaenorhabditis elegansstrains
Authors: Leuthner Tess C. , Zhang Sharon , Kohrn Brendan F , Stapleton Heather M. , Baugh L. Ryan
Published: June 2024

Background

There are >14,500 structurally diverse per- and polyfluoroalkyl substances (PFAS). Despite knowledge that these “forever chemicals” are in 99% of humans, mechanisms of toxicity and adverse health effects are incompletely known. Furthermore, the contribution of genetic variation to PFAS susceptibility and health consequences is unknown.

Objectives

We determined the toxicity of a structurally distinct set of PFAS in twelve genetically diverse strains of the genetic model systemCaenorhabditis elegans.

Methods

Dose-response curves for four perfluoroalkyl carboxylic acids (PFNA, PFOA, PFPeA, and PFBA), two perfluoroalkyl sulfonic acids (PFOS and PFBS), two perfluoroalkyl sulfonamides (PFOSA and PFBSA), two fluoroether carboxylic acids (GenX and PFMOAA), one fluoroether sulfonic acid (PFEESA), and two fluorotelomers (6:2 FCA and 6:2 FTS) were determined in theC. eleganslaboratory reference strain, N2, and eleven genetically diverse wild strains. Body length was quantified by image analysis at each dose after 48 hr of developmental exposure of L1 arrest-synchronized larvae to estimate effective concentration values (EC50).

Results

There was a significant range in toxicity among PFAS: PFOSA > PFBSA ≈ PFOS ≈ PFNA > PFOA > GenX ≈ PFEESA > PFBS ≈ PFPeA ≈ PFBA. Long-chain PFAS had greater toxicity than short-chain, and fluorosulfonamides were more toxic than carboxylic and sulfonic acids. Genetic variation explained variation in susceptibility to PFBSA, PFOS, PFBA, PFOA, GenX, PFEESA, PFPeA, and PFBA. There was significant variation in toxicity amongC. elegansstrains due to chain length, functional group, and between legacy and emerging PFAS.

Conclusion

C. elegansrespond to legacy and emerging PFAS of diverse structures, and this depends on specific structures and genetic variation. Harnessing the natural genetic diversity ofC. elegansand the structural complexity of PFAS is a powerful New Approach Methodology (NAM) to investigate structure-activity relationships and mechanisms of toxicity which may inform regulation of other PFAS to improve human and environmental health.
The theory of massively repeated evolution and full identifications of Cancer Driving Nucleotides (CDNs)
Authors: Zhang Lingjie , Deng Tong , Liufu Zhongqi , Liu Xueyu , Chen Bingjie , Hu Zheng , Liu Chenli , Tracy Miles E. , Lu Xuemei , Wen Haijun , Wu Chung-I
Published: June 2024

Tumorigenesis, like most complex genetic traits, is driven by the joint actions of many mutations. At the nucleotide level, such mutations are Cancer Driving Nucleotides (CDNs). The full sets of CDNs are necessary, and perhaps even sufficient, for the understanding and treatment of each cancer patient. Currently, only a small fraction of CDNs is known as most mutations accrued in tumors are not drivers. We now develop the theory of CDNs on the basis that cancer evolution is massively repeated in millions of individuals. Hence, any advantageous mutation should recur frequently and, conversely, any mutation that does not is either a passenger or deleterious mutation. In the TCGA cancer database (sample size n = 300 - 1000), point mutations may recur iniout ofnpatients. This study explores a wide range of mutation characteristics to determine the limit of recurrences (i*) driven solely by neutral evolution. Since no neutral mutation can reachi*= 3, all mutations recurring ati≥ 3 are CDNs. The theory shows the feasibility of identifying almost all CDNs ifnincreases to 100,000 for each cancer type. At present, only < 10% of CDNs have been identified. When the full sets of CDNs are identified, the evolutionary mechanism of tumorigenesis in each case can be known and, importantly, gene targeted therapy will be far more effective in treatment and robust against drug resistance.
On the discovered Cancer Driving Nucleotides (CDNs)–Distributions across genes, cancer types and patients
Authors: Zhang Lingjie , Deng Tong , Liufu Zhongqi , Chen Xiangnyu , Wu Shijie , Liu Xueyu , Shi Changhao , Chen Bingjie , Hu Zheng , Cai Qichun , Liu Chenli , Li Mengfeng , Tracy Miles E. , Lu Xuemei , Wu Chung-I , Wen Haijun
Published: June 2024

A central goal of cancer genomics is to identify, in each patient, all the cancer driving mutations. Among them, point mutations are referred to as Cancer Driving Nucleotides (CDNs), which recur in cancers. The companion study shows that the probability ofirecurrent hits innpatients would decrease exponentially withi; hence, any mutation withi≥ 3 hits in the TCGA database is a high-probability CDN. This study characterizes the 50∼150 CDNs identifiable for each cancer type of TCGA (while anticipating 10 times more undiscovered ones) as follows:i) CDNs tend to code for amino acids of divergent chemical properties.ii) At the genic level, far more CDNs (>5-fold) fall on non-canonical than canonical cancer driving genes (CDGs). Most undiscovered CDNs are expected to be on unknown CDGs.iii) CDNs tend to be more widely shared among cancer types than canonical CDGs, mainly because of the higher resolution at the nucleotide than the whole-gene level.iv) Most important, among the 50∼100 coding region mutations carried by a cancer patient, 5∼8 CDNs are expected but only 0∼2 CDNs have been identified at present. This low level of identification has hampered functional test and gene targeted therapy. We show that, by expanding the sample size to 105, most CDNs can be identified. Full CDN identification will then facilitate the design of patient-specific targeting against multiple CDN-harboring genes.
Stochastic foraging paths primarily drives within-species variations of prey consumption rates
Authors: Bansaye Vincent , Berthelot Geoffroy , Bachari Amina El , Chazottes Jean-René , Billiard Sylvain
Published: June 2024

The speed at which individuals interact, in particular prey and predators, affects ecological processes at all scales, including how fast matter and energy flow through ecosystems, and how stable communities are. Environmental heterogeneity and individual variabilities are generally believed to be the main factors underlying the variation of consumption rates of prey by predators. We challenge this view by comparing predicted variability from a stochastic model to experimental data. We first analyze a stochastic model of a simple random walk with elementary ecological processes involved in prey consumption, including prey depletion, predator movements and prey handling. We provide sharp approximations of the distribution of the consumption rate and a quantitative prediction of the coefficient of variation when stochastic foraging is the only source of variability. Predictions are then compared to the coefficients of variation estimated from data from dozens of various species and experimental contexts. We show that the predictions only accounting for intrinsic stochasticity in foraging are compatible with the range of observed values, in particular in 1 or 2 dimensional space. After evaluating the robustness of our model’s predictions through stochastic computer simulations, we conclude that the main driver of the variation of the consumption rate is the foraging process itself rather than environmental or between-individual variabilities. Our approach lays the foundations for unifying foraging theory and population ecology, and as such has many empirical and theoretical implications for both fields.
Pre-TCR-Targeted Immunotherapy for T-cell Acute Lymphoblastic Leukemia
Authors: Fuentes Patricia , García-Peydró Marina , Mosquera Marta , Cela Carmela , Alcain Juan , Camós Mireia , Alarcón Balbino , Toribio María L.
Published: June 2024

Targeted immunotherapy for T-cell acute lymphoblastic leukemia (T-ALL), an aggressive tumor of developing T-cell progenitors, is an urgent unmet need, especially for relapsed/refractory (r/r) disease. Selective T-ALL targeting is challenging due to the shared antigen expression between leukemic and normal T cells. Here we identify the pre-TCR, a surface receptor essential for T-cell development, as a biomarker of leukemia-initiating cells (LICs) in human T-ALL. Loss-of-function genetic approaches demonstrate that pre-TCR signaling is necessary for LIC activity and tumor progression in pre-TCR+T-ALL patient’s xenografts. Furthermore, we demonstrate the specific therapeutic targeting of pre-TCR with a monoclonal antibody against the invariant pTα subunit of the human pre-TCR, and validate an anti-pTα antibody-drug conjugate treatment as a potent immunotherapy for inhibiting LIC activity and tumor progression of T-ALLin vivo. These findings reveal the suitability of pre-TCR targeting as a promising therapy for the treatment of (r/r) patients with T-ALL expressing the pre-TCR.
Genome-wide conditional degron libraries for functional genomics
Authors: Gameiro Eduardo , Juárez-Núñez Karla A. , Fung Jia Jun , Shankar Susmitha , Luke Brian , Khmelinskii Anton
Published: June 2024

The yeast knockout library, comprised of strains carrying precise deletions of individual open reading frames (ORFs), has been a vital resource to understand gene function. However, accumulation of suppressor mutations in knockout strains can lead to erroneous functional annotations. Moreover, the library is limited to non-essential ORFs, and must be complemented with hypomorphic alleles of essential ORFs for genome- wide studies. To address these limitations, we constructed genome-wide libraries of conditional alleles based on the auxin-inducible degron (AID) system for conditional degradation of AID-tagged proteins. First, we determined that N-terminal tagging is at least twice more likely to inadvertently impair protein function across the proteome. We thus constructed two genome-wide libraries with over 5600 essential and non-essential proteins fused at the C-terminus with an AID tag and an optional fluorescent protein. Almost 90% of AID- tagged proteins were degraded in the presence of the auxin analog 5-Ph-IAA, with initial protein abundance and tag accessibility as limiting factors. Genome-wide screens for DNA damage response factors with the AID libraries revealed a role for the glucose signaling factorGSF2in resistance to hydroxyurea, highlighting how these resources extend the toolbox for functional genomics in yeast.
Ancient genomes reveal Avar-Hungarian transformations in the 9th-10th centuries CE Carpathian Basin
Authors: Gerber Dániel , Csáky Veronika , Szeifert Bea , Borbély Noémi , Jakab Kristóf , Mező György , Petkes Zsolt , Szücsi Frigyes , Évinger Sándor , Líbor Csilla , Rácz Piroska , Kiss Krisztián , Mende Balázs Gusztáv , Szőke Béla Miklós , Szécsényi-Nagy Anna
Published: June 2024

During the Early Medieval period, the Carpathian Basin witnessed significant demographic shifts, notably under the Avar dominance for approximately 250 years, followed by the settlement of early Hungarians in the region during the late 9th century CE. This study presents the genetic analysis of 296 ancient samples, including 103 shotgun-sequenced genomes, from present-day Western Hungary. By employing identity-by-descent (IBD) segment sharing networks, this research offers detailed insights into the population structure and dynamics of the region from the 5th to the 11th centuries CE, with specific focus on certain microregions. Our evaluations reveal spatially different histories in Transdanubia even between communities in close geographical proximity, highlighting the importance of dense sampling and analyses. Our findings highlight extensive homogenisation and reorganization processes, discontinuities between Hun, Avar, and Conquest period immigrant groups, alongside the spread and integration of ancestry related to the Hungarian conquerors.

Teaser

Genetic formation of medieval Hungary, discontinuity between immigrant groups in the first millennium CE
TIMS2Rescore: A DDA-PASEF optimized data-driven rescoring pipeline based on MS2Rescore
Authors: Declercq Arthur , Devreese Robbe , Scheid Jonas , Jachmann Caroline , Den Bossche Tim Van , Preikschat Annica , Gomez-Zepeda David , Rijal Jeewan Babu , Hirschler Aurélie , Krieger Jonathan R , Srikumar Tharan , Rosenberger George , Trede Dennis , Carapito Christine , Tenzer Stefan , Walz Juliane S , Degroeve Sven , Bouwmeester Robbin , Martens Lennart , Gabriels Ralf
Published: June 2024

The high throughput analysis of proteins with mass spectrometry (MS) is highly valuable for understanding human biology, discovering disease biomarkers, identifying therapeutic targets, and exploring pathogen interactions. To achieve these goals, specialized proteomics subfields – such as plasma proteomics, immunopeptidomics, and metaproteomics – must tackle specific analytical challenges, such as an increased identification ambiguity compared to routine proteomics experiments. Technical advancements in MS instrumentation can counter these issues by acquiring more discerning information at higher sensitivity levels, as is exemplified by the incorporation of ion mobility and parallel accumulation - serial fragmentation (PASEF) technologies in timsTOF instruments. In addition, AI-based bioinformatics solutions can help overcome ambiguity issues by integrating more data into the identification workflow. Here, we introduce TIMS2Rescore, a data-driven rescoring workflow optimized for DDA-PASEF data from timsTOF instruments. This platform includes new timsTOF MS2PIP spectrum prediction models and IM2Deep, a new deep learning-based peptide ion mobility predictor. Furthermore, to fully streamline data throughput, TIMS2Rescore directly accepts Bruker raw mass spectrometry data, and search results from ProteoScape and many other search engines, including MS Amanda and PEAKS. We showcase TIMS2Rescore performance on plasma proteomics, immunopeptidomics (HLA class I and II), and metaproteomics data sets. TIMS2Rescore is open-source and freely available athttps://github.com/compomics/tims2rescore.
FinaleToolkit: Accelerating Cell-Free DNA Fragmentation Analysis with a High-Speed Computational Toolkit
Authors: Li James Wenhan , Bandaru Ravi , Liu Yaping
Published: June 2024

Cell-free DNA (cfDNA) fragmentation pattern represents a promising non-invasive biomarker for disease diagnosis and prognosis. Numerous fragmentation features, such as end motif and window protection score (WPS), have been characterized in cfDNA genomic sequencing. However, the analytical tools developed in these studies are often not released to the liquid biopsy community or are inefficient for genome-wide analysis in large datasets. To address this gap, we have developed FinaleToolkit, a fast and memory-efficient Python package designed to generate comprehensive fragmentation features from large cfDNA genomic sequencing data. For instance, FinaleToolkit can generate genome-wide WPS features from a ∼100X cfDNA whole-genome sequencing (WGS) dataset with over 1 billion fragments in 1.2 hours, offering up to a ∼50-fold increase in processing speed compared to original implementations in the same dataset. We have benchmarked FinaleToolkit against original approaches or implementations where possible, confirming its efficacy. Furthermore, FinaleToolkit enabled the genome-wide analysis of fragmentation patterns over arbitrary genomic intervals, significantly boosting the performance for cancer early detection. FinaleToolkit is open source and thoroughly documented with both command line interface and Python application programming interface (API) to facilitate its widespread adoption and use within the research community:https://github.com/epifluidlab/FinaleToolkit
Lineage-specific microbial protein prediction enables large-scale exploration of protein ecology within the human gut
Authors: Schmitz Matthias , Dimonaco Nicholas J. , Clavel Thomas , Hitch Thomas C.A.
Published: June 2024

Microbes use a range of genetic codes and gene structures, yet these are ignored during metagenomic analysis. This causes spurious protein predictions, preventing functional assignment which limits our understanding of ecosystems. To resolve this, we developed a lineage-specific gene prediction approach that uses the correct genetic code based on the taxonomic assignment of genetic fragments, removes partial predictions, and optimises prediction of small proteins. Applied to 9,634 metagenomes and 3,594 genomes from the human gut, this approach increased the landscape of captured expressed microbial proteins by 78.9%, including previously hidden functional groups. Optimised small protein prediction captured 3,772,658 small protein clusters, many with antimicrobial activity. Integration of the protein sequences and sample metadata into a tool, InvestiGUT, enables association of protein prevalence with host parameters. Accurate prediction of proteins is critical for understanding the functionality of microbiomes, hence this work will enhance understanding mechanistic interactions between microbes and hosts.
Systematic genetic characterization of the human PKR kinase domain highlights its functional malleability to escape a poxvirus substrate mimic
Authors: Chambers Michael J. , Scobell Sophia B. , Sadhu Meru J.
Published: June 2024

Evolutionary arms races can arise at the contact surfaces between host and viral proteins, producing dynamic spaces in which genetic variants are continually pursued. However, the sampling of genetic variation must be balanced with the need to maintain protein function. A striking case is given by protein kinase R (PKR), a member of the mammalian innate immune system. PKR detects viral replication within the host cell and halts protein synthesis to prevent viral replication by phosphorylating eIF2α, a component of the translation initiation machinery. PKR is targeted by many viral antagonists, including poxvirus pseudosubstrate antagonists that mimic the natural substrate, eIF2α, and inhibit PKR activity. Remarkably, PKR has several rapidly evolving residues at this interface, suggesting it is engaging in an evolutionary arms race, despite the surface’s critical role in phosphorylating eIF2α. To systematically explore the evolutionary opportunities available at this dynamic interface, we generated and characterized a library of 426 SNP-accessible nonsynonymous variants of human PKR for their ability to escape inhibition by the model pseudosubstrate inhibitor K3, encoded by the vaccinia virus geneK3L. We identified key sites in the PKR kinase domain that harbor K3-resistant variants, as well as critical sites where variation leads to loss of function. We find K3-resistant variants are readily available throughout the interface and are enriched at sites under positive selection. Moreover, variants beneficial against K3 were also beneficial against an enhanced variant of K3, indicating resilience to viral adaptation. Overall, we find that the eIF2α-binding surface of PKR is highly malleable, potentiating its evolutionary ability to combat viral inhibition.
Multi-task benchmarking of spatially resolved gene expression simulation models
Authors: Liang Xiaoqi , Cao Yue , Hwa Yang Jean Yee
Published: June 2024

Computational methods for spatially resolved transcriptomics (SRT) are frequently developed and assessed through data simulation. The effectiveness of these evaluations relies on the simulation methods’ ability to accurately reflect experimental data. However, a systematic evaluation framework for spatial simulators is lacking. Here, we present SpatialSimBench, a comprehensive evaluation framework that assesses 13 simulation methods using 10 distinct STR datasets. We introduce simAdaptor, a tool that extends single-cell simulators to incorporate spatial variables, thus enabling them to simulate spatial data. SimAdaptor enables SpatialSimBench to be “back-wards” compatible. That is, it facilitates direct comparison between spatially aware simulators and existing non-spatial single-cell simulators through the adaption. Through SpatialSimBench, we demonstrate the feasibility of leveraging existing single-cell simulators for SRT data and highlight performance differences among methods. Additionally, we evaluate the simulation methods based on a total of 35 metrics across data property estimation, various downstream analysis and scalability. In total, we generated 4550 results from 13 simulation methods, 10 spatial datasets and 35 metrics. Our findings reveal that model estimation can be impacted by distribution assumptions and dataset characteristics. In summary, our evaluation and the evaluation framework will provide guidelines for selecting appropriate methods for specific scenarios and informing future method development.
Toxicity of nitrification inhibitors to soil-living animals
Authors: Bruus Marianne , Krogh Paul Henning
Published: June 2024

The toxicity of four substances appearing in nitrification inhibitors (DMPP, nitrapyrin, triazole and methylpyrazole) was tested towards three selected soil fauna species, i.e. the springtailFolsomia candida, the enchytraeidEnchytraeus albidusand the earthwormEisenia fetida. Range-finding and definitive tests were performed according to OECD standard protocols. Test results were compared to expected exposure in order to assess the risk of using nitrification inhibitors. Especially nitrapyrin was estimated to pose a potential risk to soil fauna.
Extracellular vesicle mobility in collagen I hydrogels is influenced by RGD-binding integrins
Authors: Tam Nicky W. , Becker Alexander , Mangiarotti Agustín , Cipitria Amaia , Dimova Rumiana
Published: June 2024

Extracellular vesicles (EVs) are a diverse population of membrane structures produced and released by cells into the extracellular space for the intercellular trafficking of cargo molecules. They are implicated in various biological processes, including angiogenesis, immunomodulation, and cancer cell signaling. While much research has focused on their biogenesis or their effects on recipient cells, less is understood about how EVs are capable of traversing diverse tissue environments and crossing biological barriers. Their interactions with extracellular matrix components are of particular interest, as such interactions govern diffusivity and mobility, providing a potential basis for organotropism. To start to untangle how EV-matrix interactions affect diffusivity, we use highspeed epifluorescence microscopy, single particle tracking, and confocal reflectance microscopy to analyze particle mobility and localization in extracellular matrix-mimicking hydrogels composed of collagen I. EVs are compared with synthetic liposomes and extruded plasma membrane vesicles to better understand the importance of membrane composition on these interactions. By treating EVs with trypsin to digest surface proteins, we determine that proteins are primarily responsible for EV immobilization in collagen I hydrogels. We next use a synthetic peptide competitive inhibitor to narrow down the identity of the proteins involved to argynylglycylaspartic acid (RGD) motif-binding integrins, which interact with unincorporated or denatured non-fibrillar collagen. Moreover, the effect of integrin inhibition with RGD peptides has strong implications for the use of RGD-peptide-based drugs to treat certain cancers, as integrin inhibition appears to increase EV mobility, improving their ability to infiltrate tissue-like environments.
Selective illumination on line-scanning confocal mesoscope enhances background rejection in cortex-wide mouse brain imaging
Authors: Xie Hao
Published: June 2024

Confocal microscope has optical sectioning that is accessible for structural and dynamic imaging in in vivo mouse brain. With the requirement of brain-wide field-of-view (FOV) in many neuroscience researches, existing confocal microscope fails to fulfill the requirement. Here, we proposed the brain-wide, high resolution line-scan confocal mesoscope (LSCM) for in vivo mouse imaging, achieving 6.6-mm-FOV, 3.2-μm-resolution and video-rate acquisition. To further enhance the background rejection ability, we introduced the selective illumination method into our system. We demonstrated that the proposed technique is s able to image the neurodynamics in in vivo mouse brain. Comparing to the LSCM and wide-field mesoscope, our selective illumination line-scan confocal mesoscope improves more than 25% and 3 times background rejection ability, respectively.
Embedding bioprinting of low viscous, photopolymerizable blood-based bioinks in a self-healing transparent supporting bath
Authors: Decarli Monize Caiado , Ferreira Helena P. , Sobreiro-Almeida Rita , Teixeira Filipa C. , Correia Tiago R. , Babilotte Joanna , Olijve Jos , Custódio Catarina A. , Gonçalves Inês C. , Mota Carlos , Mano João F. , Moroni Lorenzo
Published: June 2024

Protein-based hydrogels have great potential to be used as bioinks for biofabrication-driven tissue regeneration strategies due to their innate bioactivity. Nevertheless, their use as bioinks in conventional 3D bioprinting is impaired due to their intrinsic low viscosity. Using embedding bioprinting, a liquid bioink is printed whithin a support that physically holds the patterned filament. Inspired by the recognized microencapsulation technique complex coacervation, we introduce crystal self-healing embedding bioprinting (CLADDING) based on a highly transparent crystal supporting bath. The suitability of distinct classes of gelatins was evaluated (i.e., molecular weight distribution, isoelectric point and ionic content), as well as the formation of gelatin-gum arabic microparticles as a function of pH, temperature, solvent and mass ratios. Characterizing and controlling this parametric window resulted in high yields of support bath with ideal self-healing properties for interaction with protein-based bioinks during bioprinting. This support bath achieved transparency, which boosted light permeation within the bath. CLADDING bioprinted constructs fully composed of platelet lysates encapsulating a co-culture of human mesenchymal stem cells and endothelial cells were obtained, demonstrating high-dense cellular network with excellent cell viability and stability over a month. CLADDING broadens the spectrum of photocrosslinkable materials with extremely low viscosity that can now be bioprinted with sensitive cells using embedding bioprinting without any additional support.
Multicompartmentalized microvascularized tumor-on-a-chip to study tumor-stroma interactions and drug resistance in ovarian cancer
Authors: Plesselova Simona , Calar Kristin , Axemaker Hailey , Sahly Emma , de la Puente Pilar
Published: June 2024

Introduction

The majority of ovarian cancer (OC) patients receiving standard of care chemotherapy develop chemoresistance within 5 years. The tumor microenvironment (TME) is a dynamic and influential player in disease progression and therapeutic response. However, there is a lack of models that allow us to elucidate the compartmentalized nature of TME in a controllable, yet physiologically relevant manner and its critical role in modulating drug resistance.

Methods

We developed a 3D microvascularized multiniche tumor-on-a-chip formed by five chambers (central cancer chamber, flanked by two lateral stromal chambers and two external circulation chambers) to recapitulate OC-TME compartmentalization and study its influence on drug resistance. Stromal chambers included endothelial cells alone or cocultured with normal fibroblasts or cancer-associated fibroblasts (CAF).

Results

The tumor-on-a-chip recapitulated spatial TME compartmentalization including vessel-like structure, stromal-mediated extracellular matrix (ECM) remodeling, generation of oxygen gradients, and delayed drug diffusion/penetration from the circulation chamber towards the cancer chamber. The cancer chamber mimicked metastasis-like migration and increased drug resistance to carboplatin/paclitaxel treatment in the presence of CAF when compared to normal fibroblasts. CAF-mediated drug resistance was rescued by ECM targeted therapy. Critically, these results demonstrate that cellular crosstalk recreation and spatial organization through compartmentalization are essential to determining the effect of the compartmentalized OC-TME on drug resistance.

Conclusions

Our results present a functionally characterized microvascularized multiniche tumor-on-a-chip able to recapitulate TME compartmentalization influencing drug resistance. This technology holds the potential to guide the design of more effective and targeted therapeutic strategies to overcome chemoresistance in OC.
Widespread temporal niche partitioning in an adaptive radiation of cichlid fishes
Authors: Nichols Annika L. A. , Shafer Maxwell E. R. , Indermaur Adrian , Rüegg Attila , Gonzalez-Dominguez Rita , Malinsky Milan , Sommer-Trembo Carolin , Fritschi Laura , Salzburger Walter , Schier Alexander F.
Published: June 2024

The partitioning of ecological niches is a fundamental component of species diversification in adaptive radiations. However, it is presently unknown if and how such bursts of organismal diversity are influenced by temporal niche partitioning, wherein species avoid competition by being active during different time windows. Here, we address this question through profiling temporal activity patterns in the exceptionally diverse fauna of cichlid fishes from African Lake Tanganyika. By integrating week-long longitudinal behavioural recordings of over 500 individuals from 60 species with eco-morphological and genomic information, we provide two lines of evidence that temporal niche partitioning facilitated this massive adaptive radiation. First, Tanganyikan cichlids exhibit all known circadian temporal activity patterns (diurnal, nocturnal, crepuscular, and cathemeral) and display substantial inter-specific variation in daily amounts of locomotion. Second, many species with similar habitat and diet niches occupy distinct temporal niches. Moreover, our results suggest that shifts between diurnal and nocturnal activity patterns are facilitated by a crepuscular intermediate state. In addition, genome-wide association studies indicate that the genetics underlying activity patterns is complex, with different clades associated with different combinations of variants. The identified variants were not associated with core circadian clock genes but with genes implicated in synapse function. These observations indicate that temporal niche partitioning contributed to adaptive radiation in cichlids and that many genes are associated with the diversity and evolution of temporal activity patterns.
Complement Biosensors Identify a Classical Pathway Stimulus in Complement-Mediated Hemolytic Uremic Syndrome
Authors: Cole Michael A. , Ranjan Nikhil , Gerber Gloria F. , Pan Xiang-Zuo , Flores-Guerrero Daniel , Chaturvedi Shruti , Sperati C. John , McCrae Keith R. , Brodsky Robert A.
Published: June 2024

Complement-mediated hemolytic uremic syndrome (CM-HUS) is a thrombotic microangiopathy characterized by germline variants or acquired antibodies to complement proteins and regulators. Building upon our prior experience with the modified Ham (mHam) assay for ex vivo diagnosis of complementopathies, we have developed an array of cell-based complement “biosensors’’ by selective removal of complement regulatory proteins (CD55 and CD59, CD46, or a combination thereof) in an autonomously bioluminescent HEK293 cell line. These biosensors can be used as a sensitive method for diagnosing CM-HUS and monitoring therapeutic complement blockade. Using specific complement pathway inhibitors, this model identifies IgM-driven classical pathway stimulus during both acute disease and in many patients during clinical remission. This provides a potential explanation for ~50% of CM-HUS patients who lack an alternative pathway “driving” variant and suggests at least a subset of CM-HUS is characterized by a breakdown of IgM immunologic tolerance.

Key Points

CM-HUS has a CP stimulus driven by polyreactive IgM, addressing the mystery of why 40% of CM-HUS lack complement specific variants

Complement biosensors and the bioluminescent mHam can be used to aid in diagnosis of CM-HUS and monitor complement inhibitor therapy