bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome Analysis of Archived Tumor Tissues by Visium, GeoMx DSP, and Chromium Methods Reveals Inter- and Intra-Patient Heterogeneity
Authors: Dong Yixing , Saglietti Chiara , Bayard Quentin , Perez Almudena Espin , Carpentier Sabrina , Buszta Daria , Tissot Stephanie , Dubois Rémy , Kamburov Atanas , Kang Senbai , Haignere Carla , Sarkis Rita , Andre Sylvie , Gaveta Marina Alexandre , Lastra Silvia Lopez , Piazzon Nathalie , Santos Rita , Von Loga Katharina , Hoffmann Caroline , Coukos George , Peters Solange , Soumelis Vassili , Durand Eric Y. , De Leval Laurence , Gottardo Raphael , Homicsko Krisztian , Madissoon Elo 
Published: November 2024

AbstractRecent advancements in probe-based, full-transcriptome, high-resolution technologies for Formalin-Fixed Paraffin-Embedded (FFPE) tissues, such as Visium CytAssist, Chromium Flex (10X Genomics), and GeoMx DSP (Nanostring), have opened new opportunities for studying decades-old archival samples in biobanks, facilitating the generation of data from extensive cohorts. However, the experimental protocols can be labor-intensive and costly; therefore, it is thus essential for researchers to carefully evaluate the strengths and limitations of each technology in relation to their specific research objectives.Here, we report the results of a comparative analysis of the three methods mentioned above on FFPE archival tumor samples from four non-small cell lung cancer, four breast cancer and six diffuse large B-cell lymphoma. We highlight some relative advantages and disadvantages of each method in the context of operational challenges, bioinformatic analysis and biological discovery. Our results show that: 1) all three methods yielded good-quality, highly reproducible transcriptomic data from serial sections of the same FFPE block; 2) GeoMx data contained mixtures of cell types, even when pre-selecting areas with cell type-specific markers; 3) high-throughput spot-level (Visium) or cell-level (Chromium) data enabled the identification of tumor heterogeneity within and between patients, which could be used to identify targeted therapies.Our data support the use of Visium and Chromium for high-throughput and discovery-driven projects, while the GeoMx platform could be suited for addressing specialized questions on targeted regions. All data generated from this study, including GeoMx, Visium, Chromium, H&E, and expert annotations are publicly available.
C1q in non-immune human serum has a non-redundant complement function towards clinical Mycobacterium tuberculosis complex strains
Authors: Duque Mario Alejandro , Götz Maximilian Peter , Rousseau Emilie , Homolka Susanne , Niemann Stefan , Garred Peter , Hölscher Christoph , Walter Kerstin , Rosbjerg Anne 
Published: November 2024

AbstractTheMycobacterium tuberculosiscomplex (MTBC) includes three human-adapted species:Mycobacterium tuberculosis,Mycobacterium africanum, andMycobacterium canettii. With their genetic diversity and inherent virulence, these bacteria interact with host factors to influence tuberculosis (TB) transmission and pathogenesis. A critical yet poorly understood aspect of the immune response in TB involves the role of the complement system. Our study aimed to assess the general interaction between the complement system and key clinical MTBC strains representing the principal lineages known to vary in virulence. We found that not only mannose binding lectin (MBL) from the lectin pathway, but also C1q from the classical pathway directly recognize mycobacteria. While MBL generally showed a higher level of binding than C1q, the binding interactions varied across different MTBC strains. We further observed that complement activation products C4b, C3b and the terminal complement complex (TCC) were deposited on the surface of MTBC strains. Inhibition of MBL alone did not substantially alter complement activation, whereas C1q inhibition ceased activation for most strains investigated. Exposure to human serum did not impact the viability or growth of the MTBC strains. In conclusion, both the classical and lectin pathways of complement via C1q and MBL are activated by a broad range of lineages of the MTBC. The classical pathway is the main complement activator in non-immune serum across diverse MTBC lineages, with C1q playing a potentially novel role in the immune response in TB.
A novelPbunavirusphage from the Ganges River in biocontrol of multidrug-resistantPseudomonas aeruginosain wastewater by downregulation oflas/rhlsystems and reduction of KPC carbapenemases
Authors: Samson Rachel , Joshi Sai , Pramanik Rinka , Khairnar Krishna , Dharne Mahesh 
Published: November 2024

AbstractWastewater systems are reservoirs of multidrug-resistant (MDR) pathogens, includingPseudomonas aeruginosa, mirroring those found in the hospital effluents. Effective treatment of raw sewage for MDRP. aeruginosaabatement is critical for safe effluent disposal. This study reports the isolation of a novel phage (ɸPRS-1) within thePbunavirusgenus from a pristine stretch of the Ganges River, targeting the MDR strain ofP. aeruginosa. Antibacterial and antibiofilm assays of ɸPRS-1 againstP. aeruginosaPAO1 demonstrated robust efficacy, achieving log10reductions of 8.14 in planktonic cells, 9.83 in biofilm inhibition, and 7.01 in biofilm disruption after 24 hours. Additionally, ɸPRS-1 effectively disrupted the preformed biofilm of various other MDRP. aeruginosastrains with >5 log10reductions. Mechanistically, ɸPRS-1 downregulated quorum-sensing genes and reduced the carbapenemase resistance KPC cluster, validated through qRT-PCR analysis. Evaluation of ɸPRS-1 in raw sewage revealed a 4.2 log10CFU/mL reduction in theP. aeruginosacounts, highlighting its efficacy in complex environmental matrices.In vitro,cytotoxicity assays confirmed the phage’s safety. The use of ɸPRS-1 for tackling MDRP. aeruginosain the wastewater offers a sustainable alternative, potentially reducing reliance on other treatment methods. The findings have attempted to deliver SDGs 3, 6, 11, 14, and 15.HighlightsA novel phage (ɸPRS-1) from an untapped location of the Ganges RiverɸPRS-1 reduces planktonic cells of MDRP. aeruginosaby 8.14 log10in 24 hoursAntibiofilm potentials: 9.83 log10reduction (inhibition) >5 log10reduction (disruption)Downregulates quorum-sensing genes and reduces KPC resistance in MDRP. aeruginosaɸPRS-1 shows 4.2 log10CFU/mL reduction of MDRP. aeruginosain raw sewageGraphical Abstract
Proton selective conductance and gating of lysosomal cation channel TMEM175
Authors: Schulze Tobias , Sprave Timon , Groebe Carolin , Krumbach Jan , Behringer Magnus , Hamacher Kay , Thiel Gerhard , Grimm Christian , Rauh Oliver 
Published: November 2024

AbstractThe lysosomal cation channel TMEM175 is crucial for maintaining lysosomal function and pH homeostasis, and its aberrant function is linked to Parkinson’s disease (PD). While TMEM175 activity was first interpreted in the context of its potassium (K+) selective conductance, subsequent studies revealed also a substantial permeability to protons (H+). Here we dissect the complex changes in TMEM175 conductance and current reversal voltages in response to pH jumps on the luminal side of the channel protein. In whole-cell patch clamp experiments with plasma membrane redistributed TMEM175 we show that a pH jump from symmetrical pH 7.4 to pH 4.7 on the luminal side triggers a continuous rise in inward and outward current, concomitant with a transient positive excursion of the reversal voltage (Erev). The peak Erevshift remains almost 100 mV below the estimated equilibrium voltage for protons and shows little sensitivity to the K+gradient. The data are consistent with a scenario in which a TMEM175 mediated proton flux elicits a fast collapse of the pH gradient. In MD simulations we identify the luminal H57 as titratable partner for the formation of intra- and inter-subunit salt bridges with D279 and E282 for stabilizing the channel open state. This presumed gating function is confirmed by mutational studies and lysosomal patch-clamp experiments in which a H57Y mutant exhibits a reduced pH dependency of activation. Our findings contribute to a better comprehension of TMEM175’s complex electrophysiological properties and foster understanding of TMEM175 as a pharmacological target for neurodegenerative disease therapy.
Kudoagenomes from contaminated hosts reveal extensive gene order conservation and rapid sequence evolution
Authors: Weber Claudia C , Paulini Michael ,   Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team,   Wellcome Sanger Institute Tree of Life Core Informatics team, Blaxter Mark L 
Published: November 2024

Myxozoans are obligate endoparasites that belong to the phylumCnidaria. Compared to their closest free-living relatives, they have evolved highly simplified body plans and reduced genomes.Kudoa iwatai, for example, has lost upwards of two thirds of genes thought to have been present in its ancestors. However, little is known about myxozoan genome architecture because of a lack of sufficiently contiguous genome assemblies.This work presents two new, near-chromosomalKudoagenomes, built entirely from low-coverage long reads from infected fish samples. The results illustrate the potential of using unsupervised learning methods to disentangle sequences from different sources, and facilitate producing genomes from undersampled taxa. Extracting distinct components of chromatin interaction networks allows scaffolds from mixed samples to be assigned to their source genomes. Meanwhile, low-dimensional embeddings of read composition permit targeted assembly of potential parasite reads.Despite drastic changes in genome architecture in the lineage leading toKudoaand considerable sequence divergence between the two genomes, gene order is highly conserved. Although parasitic cnidarians show rapid protein evolution compared to their free-living relatives, there is limited evidence of less efficient selection. While deleterious substitutions may become fixed at a higher rate, large evolutionary distances between species make robustly analysing patterns of molecular evolution challenging. These observations highlight the importance of filling in taxonomic gaps, to allow a comprehensive assessment of the impacts of parasitism on genome evolution.
Leukemia confers a durable imprint on healthy hematopoietic stem and progenitor cells
Authors: Chen Ding-Wen , Schrey Julie M. , Fan Jian-Meng , Adams Sarah E. , Taylor Deanne M. , Wafula Eric K. , Kurre Peter 
Published: November 2024

AbstractRecent models of infection and experimental inflammation reveal that hematopoietic stem and progenitor cells (HSPCs) can generate a memory of the exposure that heightens the response to subsequent stimulation, a process termed central trained immunity. Inflammation is also a constitutive feature of cancer, including hematologic malignancies. Here, we adapt a translationally relevant model of acute myeloid leukemia (AML) to determine if inflammation in the bone marrow (BM) niche durably reprograms resident healthy HSPCs. To simulate the onset of malignancy along with the associated inflammatory surge as well as the subsequent remission, we generated hematopoietic chimera with healthy HSPCs and HSPCs bearing a doxycycline-responsive oncogene (hMLL-AF9) expression cassette, a validated model of AML. Results show that the exposure to AML blasts in the BM leaves healthy HSPCs during experimental remission with broad transcriptomic, epigenetic changes and enhanced reliance on glycolysis. A heterologous secondary challenge of AML-experienced animals resulted in pronounced gene expression changes in inflammatory and metabolic pathways. These augmented responses coincided with altered chromatin accessibility in AML-experienced HSPCs. Motif analysis of the epigenome in AML trained HSPC points to the involvement of core hematopoietic transcription factors. Altogether, these observations provide first evidence for the durable inflammatory reprogramming of healthy HSPCs in the cancer microenvironment.
Tumoral hypoxic extracellular vesicles create a protective microenvironment for triple-negative breast cancer
Authors: Pachane Bianca C. , Bottaro Pedro H. T. , Machado Aline M. , de Castro Cynthia A. , Guerra Gabriela , Gozzer Larissa T. , Grigoli Marina M. , Zutião Artur D. , Fuzer Angelina M. , Cominetti Marcia R. , Altei Wanessa F. , Selistre-de-Araujo Heloisa S. 
Published: November 2024

AbstractBackgroundThe highly metastatic triple-negative breast cancer (TNBC) relies on its tumor microenvironment (TME) to maintain phenotypic heterogeneity and progression. Extracellular vesicles from hypoxic TNBC were previously shown to aid tumoral invasion but their function in the tumor microenvironment is still unclear.MethodsWe used a novel method to investigate the TMEin vitrocalled multicellular circulating co-culture, to characterize how TNBC-derived hypoxic EVs (EVh) interfere with tumoral and endothelial cells, fibroblasts, monocytes and macrophages.ResultsEVh promoted monocyte differentiation to M2-like macrophages and inhibited macrophage-derived phagocytosis in endothelial and tumoral cells. The protection of endothelial, tumoral and stromal cellular integrity by EVh increased pro-tumoral and pro-angiogenic signaling, collagen matrix synthesis and a potential differentiation to cancer-associated fibroblasts.ConclusionOur findings highlighted the critical role of EVh in protecting tumor cells, indicating its cooperation towards a protective TME, which was demonstrated by the multicellular circulating co-culture and conventional co-culture protocols, leading to an adequate system with potential for investigating other tumor-related processes, including circulating tumor cells and metastasis.Graphical Abstract
FIBOS: R and Python packages for analyzing protein packing and structure
Authors: Soares Herson H. M. , Romanelli João P. R. , Fleming Patrick J. , Silveira Carlos H. da 
Published: November 2024

AbstractSummaryAdvances in prediction of the 3D structures of most known proteins through machine learning methods have achieved unprecedented accuracies. However, although these computed structure models (CSMs) are overall remarkably good, they still challenge accuracy at the atomic level, especially in refinement of interatomic packing. The Occluded Surface (OS) algorithm is widely used for atomic packing analysis. But it lacks implementations in high-level languages like R and Python, limiting its accessibility. We introduce FIBOS, an R and Python package incorporating the OS methodology with enhancements. It embeds efficient Fortran code from the original OS. It also improves the original algorithm by using Fibonacci spirals to distribute surface dots, reducing anisotropy and ensuring a more even point distribution. As a case study using FIBOS, we compared packing densities between experimental protein structures and AlphaFold predictions. While average packing densities are similar, AlphaFold models exhibit comparatively greater variability and less homogeneity, potentially reflecting local inaccuracies. The FIBOS package provides an accessible tool for protein packing density analysis in R and Python, facilitating structural assessment in the era of extensive computational protein models.Availability and implementationThe R and Python packages code are available athttps://github.com/insilico-unifei/fibos-Randhttps://github.com/insilico-unifei/fibos-py.
Integrative analysis of CAM photosynthesis reveals its impact on primary metabolism inYucca
Authors: Wickell David , Field Richard , Weitz Karl , Chu Rosalie , Trejo Jesse , Tolic Nikola , Munoz Nathalie Munoz , Hundley Hope , Savage Emily , Lipzen Anna , Leebens-Mack Jim , Heyduk Karolina 
Published: November 2024

AbstractCrassulacean Acid Metabolism (CAM) is an adaptation that temporally separates carbon uptake at night from photosynthesis during the day. CAM has evolved repeatedly across vascular plants, perhaps, in part, because it does not involve any novel gene functions and instead relies on regulatory modification of existing C3pathways. The co-option of established processes and corresponding alteration of metabolic flux is likely to impact other primary metabolic pathways such as nitrogen metabolism and photorespiration. However, the majority of CAM research to date has focused on a handful of genes in the core CAM pathway. Understanding the complex downstream effects associated with the emergence of CAM is essential to explaining its convergent evolution as well as efforts to engineer carbon concentrating mechanisms in crops. In this study, we integrate genomic, transcriptomic, proteomic, and metabolomic data to compare primary metabolism between the CAM speciesYucca aloifoliaand closely related C3species,Y. filamentosa. Despite substantial differences in metabolite abundance across multiple pathways, including citrate and nitrogen metabolism, we observe relatively few gene expression differences outside of the core CAM pathway. Additionally, we observe minimal correlation between protein abundance and mRNA expression, suggesting significant post-transcriptional regulation in CAM species. Our findings provide insights into the metabolic shifts associated with CAM evolution and highlight the complexity of its regulation at multiple biological levels.
Characterizing a Low-Density Neutrophil gene signature in acute and chronic infections and its impact on disease severity
Authors: de Toledo Matheus Aparecido , de Lima João Victor Souza , Salomão Reinaldo , Leite Giuseppe G. F. 
Published: November 2024

AbstractLow-density neutrophils (LDNs) or polymorphonuclear myeloid-derived suppressor cells (PMN-MDSC) are involved in the pathogenesis of cancer, autoimmune and infectious diseases. They are crucial in the host-response to invading pathogens, especially during acute illness, and are associated with poor prognosis in many infectious diseases. However, their gene expression profile and contribution to disease outcomes are not well described. We conducted a meta-analysis of gene expression datasets from peripheral blood mononuclear cells (PBMCs), focusing on patients with viral and bacterial infections. We identified a consensus set of 2,798 differentially expressed genes. Among these, 49 genes were commonly found in both the neutrophil degranulation pathway and the granule lumen-specific community. To validate this signature, we evaluated its expression in RNA-seq datasets, finding consistent upregulation of 24 genes in severe infections, 17 of them overlapped with genes overexpressed in CD16intcells. We also investigated the abundance of LDN-related proteins in a PBMC proteomics dataset from a cohort of sepsis and septic shock patients, identifying 13 proteins with significantly higher levels in sepsis and septic shock patients compared to healthy controls. In conclusion, our study identified a pattern of 17 upregulated LDN genes, common to PBMC-transcriptome and RNA-seq, and up-regulated in CD16int, associated with acute infections and severe clinical outcomes, marking the first time these genes have been collectively presented as a potential signature of LDNs in relation to disease severity. Further research with prospective cohorts is needed to validate this LDN signature and explore its clinical implications.Summary SentenceMeta-analysis revealed a 17-gene LDN signature associated with severity in acute infections, providing potential biomarkers for clinical outcomes in infectious diseases.
Structural Basis of GPCR-G Protein Pre-coupling and Activation: Insights from CCR1-Gi Complex
Authors: Shao Zhehua , Dong Yingjun , Jia Ruixin , Shen Qingya , Yao Bingpeng , He Xinheng , Yuan Qingning , Shen Dandan , Mao Chunyou , Zhang Chao , Chen Zhihua , Eric Xu H. , Ying Songmin , Zhang Yan , Li Wen 
Published: November 2024

AbstractGPCR-mediated G protein activation cycle contains obligated step of the receptor-G protein assembly before G protein activation (pre-coupling state). However, transient nature of this pre-coupling state has prevented structural and mechanistic understanding of this essential step of G protein activation cycle. In this study, we discover that CCR1 has high level of pre-coupling state, which allows its rapid response to chemokines. Taking advantage of this observation, we uncover molecular mechanism of the pre-coupling state by solving the cryo-electron microscopy structure of the chemokine receptor CCR1 in complex with its cognate G protein (Gi) in a pre-coupled, inactivated state. This structure reveals that CCR1 adopts a conformation distinct from both its fully active and inactive states, with the G protein’s α5 helix partially inserted into the receptor’s intracellular cavity. Notably, the C-terminal four residues of the Gα subunit are disordered in this pre-coupled state, contrasting with their well-defined α-helical structure in the fully active complex. Functional assays demonstrate that while deletion of these four C-terminal Gα residues does not affect pre-coupling, it abolishes G protein activation upon agonist binding. This finding highlights the critical role of these residues in GPCR-mediated G protein activation, but not in initial recruitment. Furthermore, our studies indicate that the ability to form pre-coupled complexes is conserved among chemokine receptors, suggesting a common mechanism for rapid signal transduction in this GPCR subfamily. These results provide the first structural evidence for GPCR-G protein pre-coupling and offer molecular insights into the transition from inactive to active states. Our findings fill the long-missing gap in understanding GPCR-mediated G protein activated cycle.
Deep Gaussian Process with Uncertainty Estimation for Microsatellite Instability and Immunotherapy Response Prediction Based on Histology
Authors: Park Sunho , Pettigrew Morgan F. , Cha Yoon Jin , Kim In-Ho , Kim Minji , Banerjee Imon , Barnfather Isabel , Clemenceau Jean R. , Jang Inyeop , Kim Hyunki , Kim Younghoon , Pai Rish K , Park Jeong Hwan , Samadder Jewel J. , Song Kyo Young , Sung Ji-Youn , Cheong Jae-Ho , Kang Jeonghyun , Lee Sung Hak , Wang Sam C. , Hwang Tae Hyun 
Published: November 2024

AbstractDetermining tumor microsatellite status has significant clinical value because tumors that are microsatellite instability-high (MSI-H) or mismatch repair deficient (dMMR) respond well to immune check-point inhibitors (ICIs) and oftentimes not to chemotherapeutics. We propose MSI-SEER, a deep Gaussian process-based Bayesian model that analyzes H&E whole-slide images in weakly-supervised-learning to predict microsatellite status in gastric and colorectal cancers. We performed extensive validation using multiple large datasets comprised of patients from diverse racial backgrounds. MSI-SEER achieved state-of-the-art performance with MSI prediction, which was by integrating uncertainty prediction. We achieved high accuracy for predicting ICI responsiveness by combining tumor MSI status with stroma-to-tumor ratio. Finally, MSI-SEER’s tile-level predictions revealed novel insights into the role of spatial distribution of MSI-H regions in the tumor microenvironment and ICI response.
A generic pipeline for CADD Score generation: chickenCADD and turkeyCADD
Authors: Lensing K. , van Schipstal JGC. , de Ridder D. , Groenen MAM. , Derks MFL. 
Published: November 2024

AbstractCombined Annotation Dependent Depletion (CADD) is a machine learning approach used to predict the deleteriousness of genetic variants across a genome. By integrating diverse genomic features, CADD assigns a PHRED-like rank score to each potential variant. Unlike other methods, CADD does not rely on limited datasets of known pathogenic or benign variants but uses larger and less biased training sets. The rapid increase in high-quality genomes and functional annotations across species highlights the need for an automated, non-species-specific pipeline to generate CADD scores. Here, we introduce such a pipeline, facilitating the generation of CADD scores for various species using only a high-quality genome with gene annotation and a multi-species alignment. Additionally, we present updated chickenCADD scores and newly generated turkeyCADD scores, both generated with the pipeline.