bluuebunny/crossref_metadata_2025 huggingface dataset:
CD68+Follicular Macrophages Harbor HIV Reservoirs in Human Lymph Node Tissues During Suppressive ART
Authors: Moodley Merantha , Chasara Caroline , Khaba Trevor , Mahlobo Bongiwe , Reddy Nicole , Nxele Sifundo , Msipa Sibongiseni , Reddy Kavidha , Ngubane Thandekile , Jajbhay Ismail , Pansegrouw Johan , Ndung’u Thumbi , Ndhlovu Zaza M.
Published: February 2025

Uncertainty persists regarding the contribution of tissue macrophages to HIV reservoirs, largely due to insufficient characterization of these reservoirs within their native tissue microenvironments. This study aimed to characterize and quantify macrophage reservoirs in human lymph node (LN) tissues in terms of their phenotype, location, and their potential for sustained productive infection during suppressive antiretroviral therapy.

We examined the topology, nature, and size of macrophage reservoirs in lymph nodes (LNs) from 45 PLWH subtype C on suppressive ART and 14 matched controls usingin situimaging and multiplexed immunofluorescence microscopy. Germinal center CD68+macrophages harbored HIVgag-polDNA, HIVgag-polRNA and Gagp24 protein. Digital droplet PCR confirmed the presence of proviral reservoirs in myeloid cells within LNs. High-resolution imaging techniques revealed that infected macrophages within GCs displayed distinct morphological characteristics, featuring larger and irregular shapes. In contrast, phagocytic macrophages exhibited intracellular staining for CD4+T cells, had regular shapes, and were predominantly found outside the GCs.

Our findings provide detailed quantitative, spatial, and phenotypic characterization of macrophage reservoirs in LNs, offering a clear estimation of the extent to which macrophages contribute to persistent HIV reservoirs in these tissues. These findings establish a basis for developing targeted strategies aimed at the elimination of these reservoirs in LN tissues.

Author summary

HIV hides in reservoirs within immune cells across the body in the blood and various tissues, making it a complex challenge to cure. Therefore, it is essential to identify and understand all sources of HIV reservoirs aid the development of an HIV cure. Macrophages are increasingly recognized as key contributors of viral reservoir persistence. However, the role of macrophages as latent HIV reservoirs remains unclear due to limited studies in human tissues. In this study we investigated macrophage reservoirs in human lymph nodes to answer key questions: where do they hide, how can we identify them, what is their contribution to the lymph node reservoir burden, and are they truly able to support productive viral replication? We found that macrophages residing within lymph node germinal centers, identified by CD68 expression, contained HIV DNA, RNA, and Gagp24 protein. Moreover, using high resolution microscopy, we were able to distinguish between productively infected macrophages from those that engulfed T cells. By unveiling these unique features of macrophage reservoirs, our research paves the way for the design of targeted therapy aimed at eliminating these reservoirs, towards an HIV cure.
The Winner Takes It All: a single genotype ofKalanchoe×houghtoniiis a global invader
Authors: Pascual-Díaz Joan Pere , Besolí Neus , López-Pujol Jordi , Nualart Neus , Pérez-Lorenzo Iván , Shtein Ronen , Valenzuela Laura , Garcia Sònia , Vitales Daniel
Published: February 2025

Background and Aims

Invasive alien plant species pose a global challenge, and their impact is amplified by globalisation and the accelerating pace of climate change. In mild-climate regions, drought-tolerant invasive plants showing broad environmental tolerance have a competitive advantage. One example isKalanchoe×houghtonii(Crassulaceae), popularly known as “mother of millions”. It is a hybrid resulting from the interploid cross betweenK. daigremontianaandK. delagoensis, both native to Madagascar.Kalanchoe×houghtonii, propagated as an ornamental plant, has emerged as a global invader in less than a century. Four morphotypes of this hybrid have been identified, with different ploidy levels and varying invasive capacities. Here we aim to investigate the genomic variability behind the invasion success ofKalanchoe×houghtonii.

Methods

We sampled 57 accessions ofKalanchoe×houghtonii, K. daigremontiana, K. delagoensisand closely related taxa, including old herbarium materials, from all over the world. We analysed genome size, chromosome numbers, sequenced the whole genome, analysed the complete plastome sequence of each accession, and studied the diversity of the ribosomal RNA genes. We also performed a detailed phylogenomic study using nuclear BUSCO genes.

Key Results

Our study reveals the genetic and cytogenetic variability between morphotypes, and shows that a single tetraploid genotype (morphotype A) dominates all populations, emerging as the first reported clonal hybrid capable of worldwide colonisation. Morphotype A shows a striking genetic uniformity, high phenotypic plasticity, and extremely high rates of vegetative reproduction, representing an example of a “general-purpose genotype”.

Conclusions

The astonishing reproductive capacity, broad adaptability and the speed at whichK.×houghtoniiis colonising new regions by clonal spread highlight the importance of understanding hybridisation and polyploidy in the invasion of ecosystems. Our findings call for the need for risk assessments before developing new hybrids for ornamental plant breeding that may exhibit invasive characteristics.
Systematic identification of regions where DNA methylation is correlated with transcription refines regulatory logic in normal and tumour tissues
Authors: Heery Richard , Schaefer Martin H
Published: February 2025

DNA methylation at gene promoters is generally considered to be associated with transcriptional repression. However, lack of a clear picture of where promoter methylation is most important for transcriptional regulation has hindered our understanding of this relationship and resulted in the use of a wide variety of arbitrary promoter definitions. We demonstrate here that the use of different promoter definitions can lead to contradictory results between studies of promoter methylation. In response, we have developed Methodical, a computational method that combines RNA-seq and whole genome bisulfite sequencing (WGBS) data to identify genomic regions where DNA methylation is highly correlated with transcriptional activity. We refer to these regions as transcript-proximal methylation-associated regulatory sites (TMRs). We applied Methodical to one normal prostate tissue data set, one prostate tumour dataset and one prostate metastases dataset and characterized the identified TMRs. We show that the region just downstream of the TSS, particularly within the first exon and intron, is the most common location for TMRs and that TMRs are enriched for particular genomic features, chromatin states and transcription factor binding sites. Finally, we demonstrate that the methylation of TMRs is generally strongly correlated with transcription in diverse cancer types and that TMRs are highly subject to altered DNA methylation in cancer.
Unraveling the inbreeding depression patterns in a self-pollinated eucalyptus population
Authors: Ferreira Filipe Manoel , Ferreira Vieira Netto João Amaro , Melchert Guilherme Ferreira , Benatti Thiago Romanos , de Matos José Wilacildo , Muniz Fabiana Rezende , Baracuhy Brum Itaraju Junior , do Nascimento André Vieira , Bhering Leonardo Lopes , da Graças Dias Kaio Olimpio , Tambarussi Evandro Vagner
Published: February 2025

Genetic improvement greatly contributed to the success of the forest industry in Brazil. While past selection efforts inEucalyptusspp. have yielded satisfactory genetic gains, the response to selection in the last decade has fallen below expectations. Recent research suggests that inbreeding-based selection strategies, well-established in crops such as rice and maize, could be adapted to enhance perennial species such as guava and can be expanded to forest species, such as eucalypt. In this context, 20 eliteEucalyptusspp. genotypes were self-pollinated, producing 30 progenies per family. A total of 600 individuals were planted in an experimental trial and evaluated for growth traits at 3 years of age. Both the progeny and the 20 parent geno-types were genotyped using SNP chips. This research aims to unravel the patterns of inbreeding depression in thisS0:1population ofEucalyptusspp., by examining autozygosity and genomic inbreeding patterns, estimating in-breeding depression (ID) and genetic parameters, and studying the impact of the unbalance between selfed and crossed individuals on the inbreeding depression estimator. The results revealed that dominance variance accounted for a notable portion of the phenotypic variation, demonstrating the significance of non-additive genetic effects in diameter at breast height (DBH).IDwas evident, with reductions inDBHobserved in most families as ho- mozygosity increased. Simulations highlighted that unbalanced sample sizes of selfed and crossbred individuals could bias estimates ofID. By integrating genomic data and advanced quantitative methods, this study brings new information into the genetic consequences of self-pollination in eucalyptus, offering a foundation for managing inbreeding and enhancing genetic gains in perennial breeding.
Partially differentiated enterocytes in ileal and distal-colonic human F508del-CF-enteroids secrete fluid in response to forskolin and linaclotide
Authors: Rong Yan , Zhang Zixin , de Jonge Hugo R. , Lin Ruxian , Yu Huimin , Sarker Rafiq , Boffelli Dario , Zwick Rachel K. , Klein Ophir D. , Tse Ming , Donowitz Mark , Singh Varsha
Published: February 2025

Constipation causes significant morbidity in Cystic Fibrosis (CF) patients. Using CF patient (F508del) derivedex vivoileal and distal colonic/rectal enteroids as a model and the Forskolin Induced Swelling Assay (FIS), we compared CFTR mediated fluid secretion in human enterocytes across the crypt-villus axis.CFTR expression and FIS decreased as enterocytes differentiated from crypt to become partially differentiated and then mature villus cells. While there was no FIS response in undifferentiated (crypt enterocytes) F508del-CF enteroids, partially differentiated F508del-CF enteroids had a swelling response to forskolin (cAMP) and linaclotide (cGMP) which was ∼48%, and ∼67% of the response in healthy enteroids, respectively and was prevented by a CFTR inhibitor. Also, linaclotide and a general PDE inhibitor independently enhanced combined CFTR-modulator-induced FIS response from partially differentiated F508del-CF enteroids. These findings demonstrate that partially differentiated ileal and distal colonic F508del-CFTR enteroids can be stimulated to secrete fluid by cAMP and cGMP.
CK2 directly controls CARD9 protein homeostasis
Authors: Kelly Aya M. , Merselis Leidy C. , Causton Benjamin , Calder Olivia K. , Chao Hoson , Prack Margaret , Stine Laurel B. , Amako Yuka , Wang Tao , Yesilkanal Ali E. , Condon Kendall J. , Pierce Meekyum O. , Watterson Scott H. , Guernon Jason , Anand Amit , Selvam Sabariya , Dagde Sayali , Holzinger Emily , Piasecki Lauren , Pemberton Travis A. , Fu Emily , Joint McKenna , Sandt Hayden , Singh Ashish K. , Wang Tai , Cobb Denise , Ni Xiaochun , Davies Geraint H. M. , Corin Alan F. , Roy Sophie , Wilson Stephen C.
Published: February 2025

CARD9 is an attractive target for therapeutic intervention because the human genetic data provides strong evidence for the causal role of CARD9 in both protection and susceptibility to autoimmune disease. Expression quantitative trait loci (eQTLs) link higher CARD9 expression to increased disease risk and lower CARD9 expression to protection. Additionally, a rare allele variant leading to a C-terminal truncation of CARD9 (CARD9Δ11) and subsequent loss-of-function is also protective for inflammatory bowel disease (IBD). The mechanism of CARD9-driven inflammation through scaffold assembly with BCL10 and MALT1 (CBM complex) suggests a durable inflammatory signal driven by increasing levels of CARD9. Therefore, CARD9 depletion is a desired therapeutic strategy for drug discovery, yet a difficult one due to the nature of CARD9 as an adaptor protein target and the limited number of chemical tools available to engage it. Here, we uncover through a protein homeostasis screen that casein kinase 2 (CK2/CSNK2) inhibition leads to cellular CARD9 depletion. Following up with arrayed CRISPR screening, we identify key casein kinase isoforms/subunits responsible for CARD9 depletion. We find that CK2 directly binds to CARD9 and phosphorylates S424/S425 as well as S483/S484. Orthosteric CK2 inhibition prevents CK2 binding to CARD9 and leads to CARD9 destabilization. We show that the interaction between CK2 and CARD9Δ11 is significantly attenuated and not sensitive to CK2-mediated protein stabilization. The CK2-driven CARD9 depletion mechanism is preserved outside of immortalized cell lines and conserved between primary, differentiated mouse and human dendritic cells. Finally, we demonstrate therapeutic proof of conceptin vivousing CK2 inhibition to deplete CARD9 in murine whole blood, peritoneum, and colon. Our study expands the scope of cellular consequences dealt by kinase inhibition, offers an unconventional approach for engaging a therapeutically intractable target, and identifies a novel mechanism that could contribute to disease protection conferred by the CARD9Δ11 allele.
Accurate PROTAC targeted degradation prediction with DegradeMaster
Authors: Liu Jie , Roy Michael , Isbel Luke , Li Fuyi
Published: February 2025

Motivation

Proteolysis-targeting chimeras (PROTACs) are heterobifunctional molecules that can degrade ‘undruggable’ protein of interest (POI) by recruiting E3 ligases and hijacking the ubiquitin-proteasome system. Some efforts have been made to develop deep learning-based approaches to predict the degradation ability of a given PROTAC. However, existing deep learning methods either simplify proteins and PROTACs as 2D graphs by disregarding crucial 3D spatial information or exclusively rely on limited labels for supervised learning without considering the abundant information from unlabeled data. Nevertheless, considering the potential to accelerate drug discovery, it is critical to develop more accurate computational methods for PROTAC-targeted protein degradation prediction.

Results

This study proposes DegradeMaster, a semi-supervised E(3)-equivariant graph neural network-based predictor for targeted degradation prediction of PROTACs. DegradeMaster leverages an E(3)-equivariant graph encoder to incorporate 3D geometric constraints into the molecular representations and utilises a memory-based pseudo-labeling strategy to enrich annotated data during training. A mutual attention pooling module is also designed for interpretable graph representation. Experiments on both supervised and semi-supervised PROTAC datasets demonstrate that DegradeMaster outperforms state-of-the-art baselines, with substantial improvement of AUROC by 10.5%. Case studies show DegradeMaster achieves 88.33% and 77.78% accuracy in predicting the degradability of VZ185 candidates on BRD9 and ACBI3 on KRAS mutants. Visualization of attention weights on 3D molecule graph demonstrates that DegradeMaster recognises linking and binding regions of warhead and E3 ligands and emphasizes the importance of structural information in these areas for degradation prediction. Together, this shows the potential for cutting-edge tools to highlight functional PROTAC components, thereby accelerating novel compound generation.

Availability

The source code and datasets are available athttps://github.com/Jackson117/DegradeMasterandhttps://zenodo.org/records/14715718.
Identifying Sex Differences in Lung Adenocarcinoma Using Multi-Omics Integrative Protein Signaling Networks
Authors: Chen Chen , Saha Enakshi , Fischer Jonas , Ben Guebila Marouen , Fanfani Viola , Shutta Katherine H. , Padi Megha , Glass Kimberly , DeMeo Dawn L. , Lopes-Ramos Camila M. , Quackenbush John
Published: February 2025

Lung adenocarcinoma (LUAD) exhibits differences between the sexes in incidence, prognosis, and therapy, suggesting underexplored molecular mechanisms. We conducted an integrative multi-omics analysis using the Clinical Proteomic Tumor Analysis Consortium (CPTAC) and The Cancer Genome Atlas (TCGA) datasets to contrast transcriptomes and proteomes between sexes. We used TIGER to analyze TCGA-LUAD expression data and found sex-biased activity of transcription factors (TFs); we used PTM-SEA with CPTAC-LUAD proteomics data and found sex-biased kinase activity. We combined these to construct a kinase-TF signaling network and discovered druggable pathways linked to cancer-related processes. We also found significant sex biases in clinically relevant TFs and kinases, including NR3C1, AR, and AURKA. Using the PRISM drug screening database, we identified potential sex-specific drugs, such as glucocorticoid receptor agonists and aurora kinase inhibitors. Our findings emphasize the importance of considering sex and using multi-omics network methods to discover personalized cancer therapies.
Assessing Genotype-Phenotype Correlations with Deep Learning in Colorectal Cancer: A Multi-Centric Study
Authors: Gustav Marco , van Treeck Marko , Reitsam Nic G. , Carrero Zunamys I. , Loeffler Chiara M. , Meneghetti Asier Rabasco , Märkl Bruno , Boardman Lisa A. , French Amy J. , Goode Ellen L. , Gsur Andrea , Brezina Stefanie , Gunter Marc J. , Murphy Neil , Hönscheid Pia , Sperling Christian , Foersch Sebastian , Steinfelder Robert , Harrison Tabitha , Peters Ulrike , Phipps Amanda , Kather Jakob Nikolas
Published: February 2025

Background

Deep Learning (DL) has emerged as a powerful tool to predict genetic biomarkers directly from digitized Hematoxylin and Eosin (H&E) slides in colorectal cancer (CRC). However, few studies have systematically investigated the predictability of biomarkers beyond routinely available alterations such as microsatellite instability (MSI), andBRAFandKRASmutations.

Methods

Our primary dataset comprised H&E slides of CRC tumors across five cohorts totaling 1,376 patients who underwent comprehensive panel sequencing, with an additional 536 patients from two public datasets for validation. We developed a DL model using a single transformer model to predict multiple genetic alterations directly from the slides. The model’s performance was compared against conventional single-target models, and potential confounders were analyzed.

Findings

The multi-target model was able to predict numerous biomarkers from pathology slides, matching and partly exceeding single-target transformers. The Area Under the Receiver Operating Characteristic curve (AUROC, mean ± std) on the primary external validation cohorts was:BRAF(0·78 ± 0·01), hypermutation (0·88 ± 0·01), MSI (0·93 ± 0·01),RNF43(0·86 ± 0·01); this biomarker predictability was mirrored across metrics and co-occurrence analyses. However, biomarkers with high AUROCs largely correlated with MSI, with model predictions depending considerably on MSI-associated morphology upon pathological examination.

Interpretation

Our study demonstrates that multi-target transformers can predict the biomarker status for numerous genetic alterations in CRC directly from H&E slides. However, their pre-dictability is mainly associated with MSI phenotype, despite indications of slight biomarker-inherent contributions to a phenotype. Our findings underscore the need to analyze confounders in AI-based oncology biomarkers. To enable this, we developed a validated model applicable to other cancers and larger, diverse datasets.

Funding

The German Federal Ministry of Health, the Max-Eder-Programme of German Cancer Aid, the German Federal Ministry of Education and Research, the German Academic Exchange Service, and the EU.
Transcription factor 19 is an androgen responsive gene that modulates vessel homeostasis and sustains metastatic prostate cancer
Authors: Ercilla Amaia , Crespo Jana R. , Garcia-Longarte Saioa , Fidalgo Marta , Martin-Martin Natalia , Carlevaris Onintza , Astobiza Ianire , Fernández-Ruiz Sonia , Guiu Marc , Bárcena Laura , Mendizabal Isabel , Aransay Ana M. , Graupera Mariona , Gomis Roger R. , Carracedo Arkaitz
Published: February 2025

Prostate cancer is a prevalent tumor type that, despite being highly curable, progresses to metastatic disease in a fraction of patients, thus accounting for more than 350.000 annual deaths worldwide. In turn, uncovering the molecular insights of metastatic disease is instrumental to improve the survival rate of prostate cancer patients. By means of gene expression metanalysis in multiple prostate cancer patient cohorts, we identified a set of genes that are differentially expressed in aggressive prostate cancer.Transcription factor 19 (TCF19)stood out as an unprecedented epithelial gene upregulated in metastatic disease, with prognostic potential and associated with the activity of androgen receptor. By combining computational and empiric approaches, our data revealed that TCF19 is required for full metastatic capacity and its depletion influences core cancer-related processes, such as vascular permeability, supporting the role of this gene in the dissemination of prostate tumor cells.
scKAN: Interpretable Single-cell Analysis for Cell-type-specific Gene Discovery and Drug Repurposing via Kolmogorov-Arnold Networks
Authors: He Haohuai , Tang Zhenchao , Chen Guanxing , Xu Fan , Hu Yao , Feng Yinglan , Wu Jibin , Huang Yu-An , Huang Zhi-An , Tan Kay Chen
Published: February 2025

Single-cell analysis has revolutionized our understanding of cellular heterogeneity, yet current approaches face challenges in efficiency and interpretability. In this study, we present scKAN, a framework that leverages Kolmogorov-Arnold Networks for interpretable single-cell analysis through three key innovations: efficient knowledge transfer from large language models through a lightweight distillation strategy; systematic identification of cell-type-specific functional gene sets through KAN’s learned activation curves; and precise marker gene discovery enabled by KAN’s importance scores with potential for drug repurposing applications. The model achieves superior performance on cell-type annotation with a 6.63% improvement in macro F1 score compared to state-of-the-art methods. Furthermore, scKAN’s learned activation curves and importance scores provide interpretable insights into cell-type-specific gene patterns, facilitating both gene set identification and marker gene discovery. We demonstrate the practical utility of scKAN through a case study on pancreatic ductal adenocarcinoma, where it successfully identified novel therapeutic targets and potential drug candidates, including Doconexent as a promising repurposing candidate. Molecular dynamics simulations further validated the stability of the predicted drug-target complexes. Our approach offers a comprehensive framework for bridging single-cell analysis with drug discovery, accelerating the translation of single-cell insights into therapeutic applications.
Dynamicµ-PBWT: Dynamic Run-length Compressed PBWT for Biobank Scale Data
Authors: Shakya Pramesh , Sanaullah Ahsan , Zhi Degui , Zhang Shaojie
Published: February 2025

Durbin’s positional Burrows-Wheeler transform (PBWT) supports efficient haplotype matching and queries given a panel of haplotypes. It has been widely used for statistical phasing, imputation and identity-by-descent (IBD) detection. However, the original PBWT panel doesn’t support dynamic updates when haplotypes need to be added or deleted from the panel. Dynamic-PBWT (d-PBWT) solved this problem but it is not memory efficient. While the memory constraint problem of the PBWT has been tackled by Syllable-PBWT andµ-PBWT, these are static data structures that do not allow updates. Additionally, Syllable-PBWT only supports long-match query andµ-PBWT only supports set-maximal match query, limiting their functionality in the compressed form. In this paper, we present Dynamicµ-PBWT (which can also be seen as compressed d-PBWT) that is memory efficient and supports dynamic updates. We run-length compress PBWT to achieve better compression rate and store the runs in the self-balancing trees to enable dynamic updates. We show that the number of updates per insertion or deletion in the tree at each site is constant regardless of the number of haplotypes in the panel and the updates can be made without decompressing the index. In addition, we use orders of magnitude less memory than d-PBWT. We also provide a long match query algorithm that can easily be extended back to the originalµ-PBWT. Overall, the flexibility and space-efficiency of Dynamicµ-PBWT makes it a potential index data structure for biobank scale genetic data analyses. The source code for Dynamicµ-PBWT is available athttps://github.com/ucfcbb/Dynamic-mu-PBWT.
Peptide-induced hydration of lipid bilayers modulates packing pattern and conformations of hydrocarbon chains – a potential pathway for peptide translocation?
Authors: Pašalić Lea , Pem Barbara , Jakas Andreja , Čikoš Ana , Groznica Nikolina , Mlinarić Tihana , Accorsi Matilde , Mangiarotti Agustín , Dimova Rumiana , Bakarić Danijela
Published: February 2025

Cell-penetrating peptides (CPPs) with a cationic-hydrophobic character are recognized as carriers for delivering various therapeutics and diagnostic agents across cell membranes and into the cells. Among the most studied CPPs, nona-arginine (R9) exhibits superior penetration compared to nona-lysine (K9), suggesting that the penetration ability depends not only on charge, distribution and concentration of peptides but also on the lipid membrane composition. However, for heptapeptides composed of arginine (R), lysine (K) and phenylalanine (F) residues, which show some CPPs properties, these interactions remain unexplored. This study sheds light on the adsorption of R5F2/K5F2 on model prokaryotic (PRO) and eukaryotic (EU) lipid membranes containing a zwitterionic lipid (phosphatidylcholine; PC) and an anionic lipid (either phosphatidylglycerol, PG, in the PRO model, or phosphatidylserine, PS in EU) at the 90:10 molar ratio. Using differential scanning calorimetry (DSC) and temperature-dependent UV-Vis spectroscopy, we observed peptide-induced changes in the interfacial water layer that affect the fluidity and rigidity of lipid bilayers. The distinct adsorption behavior of R5F2/K5F2 on PRO and EU lipid bilayers revealed the changes in lipid packing and hydrocarbon chain conformations as exclusively peptide-dependent features. The peptide-induced formation of vacancies in the non-polar bilayer part is consistent with partial leakage observed in giant unilamellar vesicles. The synchronized arrangement could represent a mechanism for the concerted translocation of CPPs, along with their potential cargo across the lipid membrane. This study provides new insights into the peptide-lipid interactions underlying CPPs functionality.
A Benchmarking Study of Random Projections and Principal Components for Dimensionality Reduction Strategies in Single Cell Analysis
Authors: Abdelnaby Mohamed , Moussa Marmar R.
Published: February 2025

Principal Component Analysis (PCA) has long been a cornerstone in dimensionality reduction for high-dimensional data, including single-cell RNA sequencing (scRNA-seq). However, PCA’s performance typically degrades with increasing data size, can be sensitive to outliers, and assumes linearity. Recently, Random Projection (RP) methods have emerged as promising alternatives, addressing some of these limitations. This study systematically and comprehensively evaluates PCA and RP approaches, including Singular Value Decomposition (SVD) and randomized SVD, alongside Sparse and Gaussian Random Projection algorithms, with a focus on computational efficiency and downstream analysis effectiveness. We benchmark performance using multiple scRNA-seq datasets including labeled and unlabeled publicly available datasets. We apply Hierarchical Clustering and Spherical K-Means clustering algorithms to assess downstream clustering quality. For labeled datasets, clustering accuracy is measured using the Hungarian algorithm and Mutual Information. For unlabeled datasets, the Dunn Index and Gap Statistic capture cluster separation. Across both dataset types, the Within-Cluster Sum of Squares (WCSS) metric is used to assess variability. Additionally, locality preservation is examined, with RP outperforming PCA in several of the evaluated metrics. Our results demonstrate that RP not only surpasses PCA in computational speed but also rivals and, in some cases, exceeds PCA in preserving data variability and clustering quality. By providing a thorough benchmarking of PCA and RP methods, this work offers valuable insights into selecting optimal dimensionality reduction techniques, balancing computational performance, scalability, and the quality of downstream analyses.
Blender tissue cartography: an intuitive tool for the analysis of dynamic 3D microscopy data
Authors: Claussen Nikolas , Regis Cécile , Wopat Susan , Streichan Sebastian
Published: February 2025

Tissue cartography extracts and cartographically projects surfaces from volumetric biological image data. This turns 3D-into 2D data which is much easier to visualize, analyze, and computationally process. Tissue cartography has proven particularly useful in developmental biology by taking advantage of the sheet-like organization of many biological tissues. However, existing software tools for tissue cartography are limited in the type of geometries they can handle and difficult for non-experts to use and extend. Here, we describeblender_tissue_cartography(btc), a tissue cartography add-on for the popular 3D creation software Blender.btcmakes tissue cartography user-friendly via a graphical user interface and harnesses powerful algorithms from the computer graphics community for biological image analysis. ThebtcGUI enables interactive analysis and visualization without requiring any programming expertise, while an accompanying Python library allows expert users to create custom analysis pipelines. Both the add-on and the Python library are highly modular and fully documented, including interactive Jupyter Notebook tutorials.btcfeatures a general-purpose pipeline for time-lapse data in which the user graphically defines a cartographic projection for a singlekey frame, which is propagated to all other frames via surface-to-surface alignment algorithms. Thebtcdifferential geometry module allows mathematically correcting for cartographic distortion, enabling faithful 3D measurements in 2D cartographic projections, including for vector fields like tissue flow fields. We demonstratebtcon diverse and complex tissue shapes fromDrosophila, stem-cell-based organoids,Arabidopsis, and zebrafish.
Loss of intestinal endosome associated protein sorting nexin 27 disrupts epithelial barrier and promotes inflammation
Authors: Deb Shreya , Zhang Yong-guo , Xia Yinglin , Sun Jun
Published: February 2025

Backgrounds and aims: SNX27, member of the sorting nexin (SNX) family, carries a unique PDZ domain and mediates recycling of endocytosed transmembrane proteins. SNX27 is critical for neurodevelopmental processes, however its role in intestine remains unexplored. We aim to determine the previously unknown roles of SNX27 in regulating intestinal homeostasis, epithelial barrier integrity, and inflammatory responses. Methods: We used available datasets to analyze SNX27 expression in human IBD. We generated a novel mouse model of SNX27 conditional deletion from intestinal epithelial cells (SNX27ΔIEC) and challenged these mice with Dextran Sulfate Sodium (DSS). Results: SNX27 expression was significantly lower in human IBD, including UC and CD. SNX27ΔIEC mice had significantly lower bodyweight and exhibited increased proliferation and poor differentiation of secretory Paneth and Goblet cells. We found reduced mucin layer and downregulation of crucial epithelial barrier proteins β-catenin, E-cadherin, ZO-1, and Claudin10 in SNX27ΔIEC mice. SNX27ΔIEC mice showed high intestinal permeability and spontaneously developed intestinal inflammation. Moreover, SNX27ΔIEC mice were more susceptible towards DSS-induced colitis, compared to the SNX27Loxp mice. Conclusion: Overall, deletion of intestinal epithelial SNX27 weakens barrier functions and promotes inflammation. Our results indicate a novel role of SNX27 in regulating intestinal physiology and protecting against intestinal disorders. Thus, understanding the mechanisms of SNX27 downregulation in IBD will provide insights into new prevention and targets against chronic inflammation.
Life history evolution of insects in response to climate variation: seasonal timing versus thermal physiology
Authors: Gotthard Karl , Berger David , Rohner Patrick
Published: February 2025

Climate adaptation in insects can proceed via responses in life history traits and their thermal plasticity, and through phenological shifts mediated by responses to photoperiodic cues (“photoperiodism”). While, experimental studies demonstrate evolutionary potential for both modes of adaptation, it remains unclear how evolution will unfold in natural populations, limiting our ability to predict how insects will respond to climate change. Here we review the literature and perform an analysis of published studies revealing that photoperiodism for diapause induction evolves predictably along latitude, with high-latitude populations entering diapause earlier. In contrast, although a few species showed clinal variation in life history and thermal plasticity, the direction of these clines were not consistent across taxa. This suggests that while life history traits sometime evolve rapidly, photoperiodism is a more predictable response to climate, and thus, climate adaptation is more likely to proceed via phenological shifts than physiological adaptations to changing temperatures.
The Cause of Most Common Antler Abnormality is Not a Fracture But an Osteomyelitis Like Disease the Pedunculitis Chronica Deformans
Authors: Sukosd Farkas , Lakatos Istvan , Urmos Adam , Babarczi Bianka , Skoda Gabriella , Molnar Zsofia , Pankotai Tibor , Borsos Barbara N , Karkas Reka , Sukosd Akos , Palanki Gabor , Dobrosy Szabolcs , Toth Attila Arany , Erdelyi Karoly , Horvath Gyozo , Horvath Adrienn , Toth Daniel , Maurer Mate , Miso Mihaly , Plank Patrik , Czeh Arpad , Nagyeri Gyorgy , Ferenczi Szilamer , Gobolos Peter , Kemenesi Gabor , Posta Katalin , Kovacs Ferenc , Mezes Miklos , Szemethy Laszlo , Szoke Zsuzsanna
Published: February 2025

Climate change is increasing the incidence of certain diseases in wildlife, offering a deeper understanding of their underlying causes. Traditionally, the most common antler abnormalities have been attributed to trauma, based on their morphology. However, this explanation does not account for the epidemic-like spread of abnormalities in specific regions, suggesting that they might be a previously undescribed aspect of this anomaly. In fallow deer (Dama dama), using advanced medical diagnostic tools, we identified an osteomyelitis-like condition, Pedunculitis Chronica Deformans (PCD) which is also observed in otherCervidae. The incidence of this disease shows a strong correlation with the production of mycotoxins by molds that are becoming more prevalent with global warming. Mycotoxins can inhibit wound healing through scar formation after the antlers are cast, leading to the development of PCD. In this report we characterize PCD pathomorphology and introduce a scoring system to differentiate it from other deformities. Moreover, we argue that the most common anomalies such as fractures, antler losses, fatal meningoencephalitis and brain abscesses are complications of PCD. Our research underscores the potential of antlers to serve as biomarkers for mycotoxin exposure.
PARP inhibitors elicit distinct transcriptional programs in homologous recombination competent castration-resistant prostate cancer
Authors: Cunningham Moriah L. , Vasquez-Gonzalez Jasibel , Barnada Samantha , Tchotorlishvili Salome , Jones Latese , Shankle Hailey , Mulders Tessa , Ajmal Namra , Solomides Charalambos , Shafi Ayesha A. , Gomella Leonard G. , Kelly Wm Kevin , McMahon Steven B. , Schiewer Matthew J.
Published: February 2025

Prostate cancer (PCa) is the second most lethal cancer in men in the United States. African American (AA) men have twice the incidence and death rate from the disease than European American (EA) men. Early-stage PCa is treated with hormone deprivation therapy, although patients frequently experience relapse. Advanced stage PCa is associated with increased expression and activity of the DNA damage/repair pathway enzyme, poly (ADP-ribose) polymerase 1 (PARP1). Furthermore, PARP1 inhibitors are FDA-approved for the treatment of advanced PCa tumors that carry mutations in components of a specific DNA damage/repair pathway termed homologous recombination repair (HRR). However, PARPi also provide benefit in model systems without HRR incompetencies.

A number of different PARPi have now been developed, tested and approved for use in PCa. These inhibitors utilize multiple biochemical mechanisms of action and exhibit distinct potencies and toxicity profiles. While there is emerging evidence of differences in DNA damage/repair pathway enzyme expression between EA and AA men, PARP1 itself has not been fully explored in the context of race.

This study hypothesized that 1) AA and EA PCa may respond differently to PARPi and 2) different PARPi may differentially impact the transcriptome, irrespective of HRR status.

To test these hypotheses, PCa patient samples from a racially diverse cohort were examined to define race-based differences in PARP activity/expression. Additionally, biologically relevant doses of five clinically relevant PARPi were established across multiple PCa lines carrying different genetic backgrounds, HRR status, and hormone therapy sensitivities. Collectively, these findings demonstrate a link between racial background and PARP1 expression/activity and define a core transcriptional response that lies downstream of all five PARPi, while simultaneously defining transcriptional programs unique to each inhibitor. These findings broaden our understanding of the effector pathways downstream of individual PARPi and provide a compelling rationale for a broader exploration of the impact of race on the response to PARPi. They may also help refine personalized recommendations for use of specific PARPi.
Actin Painting: a multicolor fluorescence staining method highlighting cell type-specific differences in the composition of filamentous actin architectures
Authors: Nagasaki Akira , Kijima Saku T. , Shinkai Yoichi , Ohtsuka Yukio , Ochiishi Tomoyo , Sasaki Yasnory T.F. , Hata Saori , Hirano Kazumi , Kato Yoshio , Doi Motomichi , Uyeda Taro Q.P.
Published: February 2025

Actin is a major structural component of the cytoskeleton in eukaryotic cells, and filamentous actin (F-actin) forms a variety of types of cellular structures. Many actin probes have been developed to visualize F-actin architectures in eukaryotic cells. However, it is known that double-stained images of F-actin obtained by two different types of actin probes often show partial inconsistencies. While developing actin probes, we observed that the merged images of three distinct actin probes, each labeled with a different fluorescent dye (red, green and blue), enabled various F-actin architectures to be distinguished based on color. This differentiation arises from slight variations in the distribution of each actin probe, and results in a unique color combination of actin probes that reflects the relative intensities of the three fluorescent dyes. In this report, we introduce a new cell staining method, named Actin Painting, which exploits the unique affinity of actin-binding molecules in each actin probe to F-actin architectures. This technique allows the classification of various cell types based on their specific actin cytoskeleton.
Functional diversity of soil microbial communities increases with ecosystem development
Authors: Ranheim Sveen Tord , Viketoft Maria , Bengtsson Jan , Lejoly Justine , Buegger Franz , Pritsch Karin , Strengbom Joachim , Fritscher Joachim , Hildebrand Falk , Osburn Ernest , Hannula Emilia , Bahram Mo
Published: February 2025

Land abandonment is the single largest process of land-use change in the Global North driving succession and afforestation at continental scales, but assessing its impacts on soil microbial communities remains a challenge. Here, we established a nationwide successional gradient of paired grassland and forest sites to track developments in microbial structure and functioning following land abandonment and gradually changing plant communities. We show that microbes generally respond through threshold dynamics, leading to increasing functional but decreasing taxonomic diversity. Succession also increased the specialization of microbial nutrient (C-N-P) cycling genes while decreasing genetic redundancy, highlighting a putative trade-off between two desirable ecosystem properties: functional diversity and functional redundancy. Increasing fungal functional diversity underpinned higher microbial C-cycling capacity, underscoring the causal link between functional traits and ecosystem processes. Changing litter quality similarly provided a mechanistic link between plant and microbial communities despite otherwise largely decoupled successional developments. Land abandonment is frequently touted as an opportunity to increase biodiversity and carbon storage. Our results show that deeper knowledge about the multifaceted development of soil microbial communities and its links to plant communities during succession may be needed to fully grasp the impacts of global land abandonment processes.
Fast and Accuratein silicoAntigen Typing with Kaptive 3
Authors: Stanton Thomas D. , Hetland Marit A.K. , Löhr Iren H. , Holt Kathryn E. , Wyres Kelly L.
Published: February 2025

Surface polysaccharides are common antigens in priority pathogens and therefore attractive targets for novel control strategies such as vaccines, monoclonal antibody and phage therapies. Distinct serotypes correspond to diverse polysaccharide structures that are encoded by distinct biosynthesis gene clusters, e.g. theKlebsiella pneumoniaespecies complex (KpSC) K- and O-loci encode the synthesis machinery for the capsule (K) and outer-lipopolysaccharides (O), respectively. We previously presented Kaptive and Kaptive 2, programs to identify K and O-loci directly from KpSC genome assemblies (later adapted forAcinetobacter baumannii), enabling sero-epidemiological analyses to guide vaccine and phage therapy development. However, for some KpSC genome collections, Kaptive (v≤2) was unable to type a high proportion of K-loci. Here we identify the cause of this issue as assembly fragmentation, and present a new version of Kaptive (v3) to circumvent this problem, reduce processing times and simplify output interpretation.

We compared the performance of Kaptive v2 and Kaptive v3 for typing genome assemblies generated from subsampled Illumina read sets (decrements of 10x depth), for which a corresponding high quality completed genome was also available to determine the ‘true’ loci (n=549 KpSC, n=198A. baumannii). Both versions of Kaptive showed high rates of agreement to the matched true locus among ‘typeable’ locus calls (≥96% for ≥20x read depth), but Kaptive v3 was more sensitive, particularly for low depth assemblies (at <40x depth, v3 ranged 0.85-1 vs v2 0.09-0.94) and/or typing KpSC K-loci (e.g. 0.97 vs 0.82 for non-subsampled assemblies). Overall, Kaptive v3 was also associated with a higher rate of optimal outcomes i.e. loci matching those in the reference database were correctly typed and genuine novel loci were reported as untypeable (73-98% for v3 vs 7-77% for v2 for KpSC K-loci).

Kaptive v3 was >1 order of magnitude faster than Kaptive v2 making it easy to analyse thousands of assemblies on a desktop computer, facilitating broadly accessible in silico serotyping that is both accurate and sensitive. The Kaptive v3 source code is freely available on GitHub (https://github.com/klebgenomics/Kaptive), and has been implemented in Kaptive Web (https://kaptive-web.erc.monash.edu).
The ABCG1 transporter facilitates sesquiterpene accumulation inMarchantia polymorphaoil bodies
Authors: Forestier Edith C. F. , Asprilla Paola , Romani Facundo , Bonter Ignacy , Frangedakis Eftychios , Haseloff Jim
Published: February 2025

Marchantia polymorphaoil bodies (OBs) are specialised cell structures housing a diverse array of C15-terpenes, called sesquiterpenes. These compounds are known for their roles as herbivore repellents, yet the enzymes responsible for the biosynthesis of their precursors (C5 isoprenoid units) remain poorly characterized. Discrepancies remain between enzyme localizations suggested by computational predictions and those observed in earlier experimental studies, complicating our understanding of terpene biosynthesis. We investigated the localization of isoprenoid biosynthetic enzymes using translational and transcriptional reporters, coupled with confocal microscopy. Most enzymes localized as predicted (e.g., cytosol, chloroplast and the endoplasmic reticulum), and OB cells were identified as the primary sites of terpene biosynthesis.

To explore OBs as potential storage sites for terpenes, we attempted to produce exogenous but easily identifiable compounds inMarchantia, such as the diterpene taxadiene and the triterpene β-amyrin. Targeting to OB cells resulted in measurable amounts of these compounds, but their yields remained unaffected by the over-expression of key precursor genes, underscoring challenges in redirecting metabolic flux.

To further investigate terpene accumulation in OBs, we focused on ABCG1, an ABC transporter previously reported to localize at the OB membrane. Overexpression of ABCG1 in OB cells, alongside an exogenous sesquiterpene synthase, only increased the levels of endogenous sesquiterpenes, while CRISPR-mediated disruption of ABCG1 resulted in a dramatic reduction in sesquiterpene accumulation. These findings establish ABCG1 as a critical factor for sesquiterpene retention within OBs and provide new insights into the mechanisms governing terpene metabolism and storage inMarchantia polymorpha.
MethylProphet: A Generalized Gene-Contextual Model for Inferring Whole-Genome DNA Methylation Landscape
Authors: Huang Xiaoke , Liu Qi , Zhao Yifei , Tang Xianfeng , Zhou Yuyin , Hou Wenpin
Published: February 2025

DNA methylation (DNAm), an epigenetic modification, regulates gene expression, influences phenotypes, and encodes inheritable information, making it critical for disease diagnosis, treatment, and prevention. While human genome contains approximately28 millionCpG sites where DNAm can be measured, only 1–3% of these sites are typically available in most datasets due to complex experimental protocols and high costs, hindering insights from DNAm data. Leveraging the relationship between gene expression and DNAm offers promise for computational inference, but existing statistical, machine learning, and masking-based generative Transformers face critical limitations: they cannot infer DNAm at unmeasured CpGs or in new samples effectively. To overcome these challenges, we introduce MethylProphet, a gene-guided, context-aware Transformer model designed for DNAm inference. MethylProphet employs a Bottleneck MLP for efficient gene profile compression and a specialized DNA sequence tokenizer, integrating global gene expression patterns with local CpG context through a Transformer encoder architecture. Trained on whole-genome bisulfite sequencing data from ENCODE (1.6B training CpG-sample pairs; 322B tokens), MethylProphet demonstrates strong performance in hold-out evaluations, effectively inferring DNAm for unmeasured CpGs and new samples. In addition, its application to 10842 pairs of gene expression and DNAm samples at TCGA chromosome 1 (450M training CpGsample pairs; 91B tokens) highlights its potential to facilitate pan-cancer DNAm landscape inference, offering a powerful tool for advancing epigenetic research and precision medicine. All codes, data, protocols, and models are publicly available viahttps://github.com/xk-huang/methylprophet/.