bluuebunny/crossref_metadata_2025 huggingface dataset:
ConcurrentPIK3CAmutant drives cachexia through inflammatory signaling inEGFRmutant lung cancer
Authors: Yue Meiting , Qin Zhen , Tang Shijie , Cai Xinlei , Zhao Yikai , Chen Liang , Chen Luonan , Ji Hongbin
Published: January 2025

PIK3CAmutation is frequently concurrent with known oncogenic drivers such asEGFRmutation in lung cancer, raising an interesting question about its real function. Cachexia is a systemic disease involving complex interaction between primary tumors and distant organs, significantly contributing to cancer-related mortality. Through integrative study of genetically engineered mouse models (GEMMs) and clinical data, we find concurrentPIK3CAmutant preferentially drives cachexia inEGFR-mutant lung cancer, promoting malignant progression instead of cancer initiation.PIK3CAmutant-mediated cachexia could be overcome by osimertinib (Osi) treatment in Osi-sensitive GEMM. In contrast, chemotherapy, routinely used in clinic for those relapsed from Osi therapy, fails to ameliorate cachexia in Osi-resistant GEMM despite notable tumor suppression.PIK3CAmutant-driven cachexia is mediated through NF-κB activation and could be dampened by combined aspirin treatment. This work uncovers the biological function ofPIK3CAmutant and mechanism behinds its clinical impacts, and proposes a potentially effective strategy for clinical management.
Single-cell decoding of human islet cell type-specific alterations in type 2 diabetes reveals converging genetic- and state-driven β-cell gene expression defects
Authors: Bandesh Khushdeep , Motakis Efthymios , Nargund Siddhi , Kursawe Romy , Selvam Vijay , Bhuiyan Redwan M , Eryilmaz Giray Naim , Krishnan Sai Nivedita , Spracklen Cassandra N. , Ucar Duygu , Stitzel Michael L.
Published: January 2025

Pancreatic islets maintain glucose homeostasis through coordinated action of their constituent endocrine and affiliate cell types and are central to type 2 diabetes (T2D) genetics and pathophysiology. Our understanding of robust human islet cell type-specific alterations in T2D remains limited. Here, we report comprehensive single cell transcriptome profiling of 245,878 human islet cells from a 48-donor cohort spanning non-diabetic (ND), pre-diabetic (PD), and T2D states, identifying 14 distinct cell types detected in every donor from each glycemic state. Cohort analysis reveals ∼25-30% loss of functional beta cell mass in T2D vs. ND or PD donors resulting from (1) reduced total beta cell numbers/proportions and (2) reciprocal loss of ‘high function’ and gain of senescent β-cell subpopulations. We identify in T2D β-cells 511 differentially expressed genes (DEGs), including new (66.5%) and validated genes (e.g.,FXYD2, SLC2A2, SYT1), and significant neuronal transmission and vitamin A metabolism pathway alterations. Importantly, we demonstrate newly identified DEG roles in human β-cell viability and/or insulin secretion and link 47 DEGs to diabetes-relevant phenotypes in knockout mice, implicating them as potential causal islet dysfunction genes. Additionally, we nominate as candidate T2D causal genes and therapeutic targets 27 DEGs for which T2D genetic risk variants (GWAS SNPs) and pathophysiology (T2D vs. ND) exert concordant expression effects. We provide this freely accessible atlas for data exploration, analysis, and hypothesis testing. Together, this study provides new genomic resources for and insights into T2D pathophysiology and human islet dysfunction.
Recruiting ESCRT to single-chain heterotrimer peptide-MHCI releases antigen-presenting vesicles that stimulate T cells selectively
Authors: Olson Blade A. , Huey-Tubman Kathryn E. , Mao Zhiyuan , Hoffmann Magnus A. G. , Murray Richard M. , Mayo Stephen L.
Published: January 2025

Immune cells naturally secrete extracellular antigen-presenting vesicles (APVs) displaying peptide:MHC complexes to facilitate the initiation, expansion, maintenance, or silencing of immune responses. Previous work has sought to manufacture and purify these vesicles for cell-free immunotherapies. In this study, APV assembly and release is achieved in non-immune cells by transfecting HEK293T or Expi293F cells with a single-chain heterotrimer (SCT) peptide/major histocompatibility complex I (pMHCI) construct containing an ESCRT- and ALIX-binding region (EABR) sequence appended to the cytoplasmic tail; this EABR sequence recruits ESCRT proteins to induce the budding of APVs displaying SCT pMHCI. A comparison of multiple pMHCI constructs shows that inducing the release of APVs by the addition of an EABR sequence generalizes across SCT pMHCI constructs. Purified pMHCI/EABR APVs selectively stimulate IFN-γ release from T cells presenting their cognate T cell receptor, demonstrating the potential use of these vesicles as a form of cell-free immunotherapy.

Significance Statement

Immune cells are known to naturally release pMHC-displaying extracellular vesicles (EVs), called antigen-presenting vesicles (APVs), which can orchestrate immune responses either directly or with the aid of antigen-presenting cells (APCs). For decades, researchers have pursued ways to replicate these APVs for immunotherapy by using chemically modified nanoparticles or by engineering the increased expression of APVs from immune cells which are typically low yield. Here we presents a broadly applicable platform for generating high concentrations of pMHCI-displaying APVs that can selectively modulate T cells, demonstrating a significant advance in the engineering of APVs for cell-free immunotherapy. The APVs presented here, and related APVs, could be translated into clinical therapies for modulating cancer progression or regulating autoimmunity in addition to their use as a tool to help characterize how endogenous extracellular vesicles influence the immune system.
Multi-scale structure of chromatin condensates rationalizes phase separation and material properties
Authors: Zhou Huabin , Huertas Jan , Maristany M. Julia , Russell Kieran , Hwang June Ho , Yao Run-wen , Hutchings Joshua , Shiozaki Momoko , Zhao Xiaowei , Doolittle Lynda K. , Gibson Bryan A. , Riggi Margot , Espinosa Jorge R. , Yu Zhiheng , Villa Elizabeth , Collepardo-Guevara Rosana , Rosen Michael K.
Published: January 2025

Biomolecular condensates, compartments that concentrate molecules without surrounding membranes, are integral to numerous cellular processes. The structure and interaction networks of molecules within condensates remain poorly understood. Using cryo-electron tomography and molecular dynamics simulations we elucidated the structure of phase separated chromatin condensates across scales, from individual amino acids to network architecture. We found that internucleosomal DNA linker length controls nucleosome arrangement and histone tail interactions, shaping the structure of individual chromatin molecules both within and outside condensates. This structural modulation determines the balance between intra- and intermolecular interactions, which in turn governs the molecular network, thermodynamic stability, and material properties of chromatin condensates. Mammalian nuclei contain dense clusters of nucleosomes whose non-random organization is mirrored by the reconstituted condensates. Our work explains how the structure of individual chromatin molecules ultimately determines physical properties of chromatin condensates, with implications for cellular chromatin organization.
Phyla: Towards a Foundation Model for Phylogenetic Inference
Authors: Shen Andrew , Ektefaie Yasha , Jain Lavik , Farhat Maha , Zitnik Marinka
Published: January 2025

Deep learning has made strides in modeling protein sequences but often struggles to generalize beyond its training distribution. Current models focus on learning individual sequences through masked language modeling, but effective protein sequence analysis demands the ability to reason across sequences, a critical step in phylogenetic analysis. Training biological foundation models explicitly for intersequence reasoning could enhance their generalizability and performance for phylogenetic inference and other tasks in computational biology. Here, we report an ongoing development of PHYLA, an architecture that operates on an explicit, higher-level semantic representation of phylogenetic trees. PHYLA employs a hybrid state-space transformer architecture and a novel tree loss function to achieve state-of-the-art performance on sequence reasoning benchmarks and phylogenetic tree reconstruction. To validate PHYLA’s capabilities, we applied it to reconstruct the tree of life, where PHYLA accurately reclassified archaeal organisms, such as Lokiarchaeota, as more closely related to bacteria—aligning with recent phylogenetic insights. PHYLA represents a step toward molecular sequence reasoning, emphasizing structured reasoning over memorization and advancing protein sequence analysis and phylogenetic inference.
Accurate tiling of spatial single-cell data with Tessera
Authors: Stein Daniel J. , Tran Miles , Korsunsky Ilya
Published: January 2025

Single-cell spatial transcriptomics reveals how cells organize in healthy and diseased tissues. From these data, tissue segmentation analysis defines discrete compartments that organize cells into functional multicellular units. Existing methods for automated tissue segmentation rely on spatial smoothing to define spatially coherent regions but often blur the boundaries between adjacent tissue compartments. We describe Tessera, an algorithm that approaches tissue segmentation through a novel approach, dividing the tissue into small multicellular tiles whose edges track with natural tissue boundaries. Tessera achieves this by incorporating successful tools from edge-preserving smoothing, topological data analysis, and morphology-aware agglomerative spatial clustering. We show that Tessera identifies a range of known anatomical structures, in healthy mouse brain and human lymph nodes, and novel disease-associated niches, in human brain and in lung cancer. Tessera is a general-purpose tool that returns spatially coherent spatial structures with accurate boundaries across a range of spatial transcriptomics and proteomics technologies.
Novel pink-spot disease in North American kelp nurseries
Authors: Schenk Siobhan , Jackman Andrea Sarah , Clark Jennifer , Parfrey Laura Wegener
Published: January 2025

Macroalgal cultivation is a growing industry in North America, but is well established in Asia and Africa, where macroalgal disease cause crop losses, placing a significant economic burden on farmers. As kelp cultivation intensifies in North America, kelp disease prevalence is expected to increase in tandem. With input from the kelp-growing community through an online survey, we describe the prevalence of a novel kelp disease, pink-spot disease, which has been observed in Canada and the United States onSaccharina latissima, Alaria marginata, Nereocystis luetkeana, andMacrocystis tenuifolia. Eight of the fourteen (57%) surveyed kelp growers report bright pink spots (pink-spot disease) on their kelp spools in the land-based nursery stage. Along with the grower survey, we conducted 16S rRNA amplicon sequencing in 2021 and 2022 to investigate the causative agent of pink-spot disease and associated bacterial community changes on infectedSaccharina latissima(sugar kelp) spools. Our data in both years show that a member of the genusAlgicolais enriched on visibly diseased spool regions compared to asymptomatic spool regions and may be the causative agent of pink-spot disease. As macroalgal cultivation continues to intensify, monitoring diseases is important to mitigate potential negative impacts.
Notes on the diet and size ofCassiopea
Authors: Muffett Kaden , Mammone Marta , Morejón-Arrojo Ramón D. , Toso Andrea , Fumarola Lara M. , Klovrza Anabelle Marques , Cardona Valentina , Geson Serafin Mendez , Rowe Claire E. , Bellantuono Anthony , Miglietta Maria Pia , Collin Rachel
Published: January 2025

Medusae of the genusCassiopeaare common components of tropical and subtropical coastlines globally. Despite the broad distribution of this benthic scyphozoan, much about their ecology remains poorly described. Here, we collected over 100 adultCassiopeaindividuals from Panama, the eastern United States, Cuba, the Philippines, Italy and Australia to examine continuity and differences in their diet across space, and to investigate whether their unique lifestyle is reflected in their diet. We found the majority of prey items to be associated with the epibenthos. The recovered prey were supermajority crustaceans, mainly harpacticoid copepods, with pteropods, nematodes, and miscellaneous eggs common as secondary components. Within the gastrovascular cavity of a single medusa, we found up to 379 items. There was a limited relationship between medusa size and prey items. Location had an impact on gut content diversity and medusa size had a small impact on the number of taxa found within the gut. In some sites, prey were scarce or absent from all medusae sampled. Overall, we reaffirm the diet previously recorded for small medusae in Puerto Rico and show that similar components are common in large and small medusae from throughout the East and West Atlantic and the Philippines.
siRNA complexation with Galactose-Functionalized Dendrimer: PAMAM vs PETIM
Authors: Maity Tarun , Kumar Yogendra , Maiti Prabal K.
Published: January 2025

siRNA-based therapies hold promise for treating various diseases, but efficient and targeted delivery remains challenging. This study explored the potential of galactose-functionalized poly(amidoamine) (Gal-PAMAM) and poly(propyl ether amine) (Gal-PETIM) dendrimers as siRNA carriers using all-atom molecular dynamics simulations. This study revealed distinct complexation behavior for both the system in physiological (pH ∼ 7) and high (pH ∼ 10) environments. Electrostatic interactions dominated complexation, with PMF profiles revealing stronger binding affinity for Gal-PAMAM/siRNA at pH 7. siRNA displayed lower flexibility at pH 7 for both complexes, indicating enhanced stability. These findings suggest that Gal-PAMAM dendrimers at physiological pH hold promise for efficient siRNA delivery due to their superior complex stability and interaction strength. However, in polar solvents, Gal-PETIM exhibits hydrophobic behavior, enabling rapid delivery.
When neighbours play a role: a systems-level analysis of protein interactions conditioning cancer driver mutation effects
Authors: Vital Márcia FS , Miranda João AI , Carrolo Margarida , Quintela António , Pinto Francisco R
Published: January 2025

Background

Cancer is driven by the accumulation of somatic mutations, including driver mutations that confer a selective advantage to cancer cells. Driver proteins operate within complex interaction networks, and their activity is conditioned by neighbour proteins. Understanding the interplay between driver mutations and the expression of their neighbour proteins can provide insights into cancer biology and potential therapeutic targets.

Methods

We assessed associations between expression of neighbour proteins and driver mutation status, comparing both between and within cancer types. We further evaluated if neighbours were enriched in significant associations with multiple drivers and characterised the impact of neighbour expression on overall survival for all cancer types.

Results

We found a significant correlation between the number of driver associations a neighbour gene has and the number of sign-coherent survival associations, particularly for neighbours enriched in positive associations, where high neighbour expression correlated with increased driver mutations and poorer survival. We identified 247 neighbours simultaneously enriched in positive driver and survival associations and 39 neighbours simultaneously enriched in negative driver and survival associations.

Conclusions

Our study systematically identified neighbours associated with driver mutation status. Complementary evidence from survival analysis and the literature suggests that neighbours enriched in driver associations are promising drug target candidates.
Fibroblast Density is a Risk Factor for Drug-induced Arrhythmias
Authors: Hirose Kayo , Umezu Shinjiro , Sato Daisuke
Published: January 2025

A recent study by Kawatouet al. has shown that the local heterogeneity of ion channel conductance is a critical substrate for focal or reentrant arrhythmias. However, the role of fibroblasts with repolarization heterogeneity in the initiation and maintenance of arrhythmias remains unknown. In this study, we investigated how diffuse fibrosis contributes to the formation of focal and reentrant arrhythmias under drug-induced heterogeneity using physiologically detailed mathematical models of the human heart. To simulate drug-induced heterogeneity, we varied the maximum conductance of transmembrane potassium and calcium currents, leading to heterogeneity in action potential duration (APD). Then, we assessed the effects of different fibrosis densities (FD) on the occurrence of premature ventricular complexes (PVCs). Fibroblasts were randomly and evenly inserted into the tissue, and various FD levels ranging from 0 to 35% were examined. We found a biphasic relationship between FD and drug-induced PVCs. Within a certain range of FD, FD positively correlated with PVC susceptibility. However, excessively high fibrosis levels were associated with reduced susceptibility to PVCs. In addition, the self-sustainability of arrhythmias exhibited a positive correlation with FD. This study demonstrates the interplay between the diffuse fibrosis and the drug-induced heterogeneity of APD in the genesis of ventricular arrhythmias.

Author summary

Sudden cardiac death remains a leading cause of death worldwide. Understanding the mechanisms underlying arrhythmia and its precursors is critical for the development of effective therapies and drugs. Repolarization heterogeneity plays a crucial role in both the initiation and maintenance of arrhythmias. Fibroblasts constitute a vital component of cardiac structure, originating from the remodeling of ventricular wall cells or the transformation of injured myocardial cells. Fibroblasts are known to couple with and alter the electrical properties of myocardial cells. However, our understanding of the role of fibroblasts in the development of arrhythmia remains limited. In this study, we employed a physiologically detailed mathematical model of cardiac tissue to investigate the roles of drug-induced heterogeneity and diffuse fibrosis in the initiation and maintenance of arrhythmias. We used 2D and 3D computational models to simulate various levels of drug-induced heterogeneity conditions with normal to pathological levels of fibroblast density (FD). We found that within a certain range of FD, fibroblasts promote PVCs under drug-induced heterogeneity. However, if FD exceeds 30%, the occurrence of PVCs decreases (biphasic relationship). On the other hand, the self-sustainability of VF (ventricular fibrillation) consistently increases with FD. This study implies that fibroblasts in cardiac tissue may play different roles in the initiation and maintenance of arrhythmia.
A comprehensive comparison on clustering methods for multi-slide spatially resolved transcriptomics data analysis
Authors: Xiong Caiwei , Shuai Huang , Zhou Muqing , Zhang Yiyan , Wu Wenrong , Li Xihao , Yao Huaxiu , Chen Jiawen , Li Yun
Published: January 2025

Spatial transcriptomics (ST) data, by providing spatial information, enables simultaneous analysis of gene expression distributions and their spatial patterns within tissue. Clustering or spatial domain detection represents an essential methodology for ST data, facilitating the exploration of spatial organizations with shared gene expression or histological characteristics. Traditionally, clustering algorithms for ST have focused on individual tissue sections. However, the emergence of numerous contiguous tissue sections derived from the same or similar tissue specimens within or across individuals has led to the development of multi-slide clustering methods. In this study, we assess seven single-slide and three multi-slide clustering methods on two simulated datasets and three real datasets. Additionally, we investigate the effectiveness of pre-processing techniques, including spatial coordinate alignment (for example, PASTE) and gene expression batch effect removal (for example, Harmony), on clustering performance. Our study provides a comprehensive comparison of clustering methods for multi-slide ST data, serving as a practical guide for method selection in various scenarios.
Light induces Phytochrome B SUMOylation to recruit the immune regulator NPR1 in nuclear condensates to control immunity in plants
Authors: Ghosh Srayan , Ghosh Shraboni , Mansi Mansi , Long Xian , Clark Lisa , Srivastava Anjil , Kakkunath Sumesh , Orosa Beatriz , Bailey Mark , Bhagat Prakash Kumar , Gough Catherine , Zhang Cunjin , de Lucas Miguel , Sadanandom Ari
Published: January 2025

It has long been observed that light perception by phytochromes control plant immunity, however, the underpinning molecular mechanism is less well understood. We demonstrate that light mediated SUMO conjugation to Phytochrome B (PhyB) is critical for increasing cellular salicylic-acid (SA) levels to orchestrate systemic acquired resistance (SAR) upon avirulent bacterial infection. SUMOylation is critical for PhyB nuclear condensate formation during light activated immunity. Light induced PhyB SUMOylation recruits NPR1, through its SUMO interacting motif to nuclear condensates to elevate SA levels for immune responses. In the dark during SAR, elevated SA levels substitute for light to maintain PhyB SUMOylation and immune-related photobody formation by stimulating the degradation of PhyB targeting deSUMOylase, OTS1. SUMOylated PhyB-NPR1 immune photobodies associate with TGA transcription factor associated chromatin to trigger immune gene expression. We unravel a mechanism where SUMOylation can enable light to recruit NPR1 to PhyB nuclear condensates to form immune photobodies to regulate plant immunity.

Highlights

Light-dependent immunity in plants relies on the SUMO mediated interaction between the photoreceptor PhyB and the Salicylic Acid (SA) receptor NPR1.

Light induced PhyB SUMOylation recruits NPR1 to nuclear condensates which we identify as immune photobodies that elevate SA levels for immune responses.

In darkness, SA can replace light in enabling PhyB-NPR1 immune photobody formation by regulating SUMOylation revealing a SA mediated mechanism for controlling PhyB liquid-liquid phase separation.

SUMO-modified PhyB-NPR1 immune photobodies regulate transcriptional activity of immune associated chromatin to shape defence responses in plants.
Identification of Two Elusive Human Ribonuclease MRP-Specific Protein Components
Authors: Che Rui , Mirani Bhoomi , Panah Monireh , Chen Xiaotong , Luo Hong , Alexandrov Andrei
Published: January 2025

All known protein components of one of the longest-studied human ribonucleoprotein ribozyme nuclear Ribonuclease MRP (RNase MRP), which processes pre-rRNA at ITS1 site 2, are shared with Ribonuclease P (RNase P), which cleaves pre-tRNA 5′ leader sequences. Our genome-wide forward genetic screening identified two poorly characterized human genes, which we named RPP24 and RPP64. We show that these two genes are required for pre-rRNA ITS1 site 2 processing and their protein products efficiently associate with RNA MRP. Unlike all other human RNase MRP protein components, RPP24 and RPP64 are not required for RNase P activity and do not associate with RNase P-specific RNA H1. Despite extremely limited sequence homology, RPP24 and RPP64 exhibit predicted structural similarities to two RNase MRP-specific components inS. cerevisiae, with specific differences in RPP64 regions of substrate recognition. Collectively, our functional screening and validation revealed the first two protein components unique to human nuclear RNase MRP.
To hybridise or not to hybridise? Systematic review and meta-analysis of woodpeckers
Authors: Bakai Antonii , Fuchs Jérôme , Gorman Gerard , Sajdak Dominika , Kajtoch Łukasz
Published: January 2025

Hybridisation is a common phenomenon among birds in general. Woodpeckers (Picidae) are no exception, as approximately 20% of species are known to hybridise and for many others interspecific mating is suspected. However, the mechanisms and consequences (phenotypic and genetic) of hybridisation are known for only a fraction of woodpecker species. Here, we conduct a systematic review on the literature that deals with hybridisation in woodpeckers and use a meta-analytical approach to examine the available geographical and genetic data. According to available published data, the majority of woodpeckers that hybridise inhabit the Neotropics, followed by the Nearctic and the Palearctic. Hybridisation appears to be less common in the Afrotropic and Oriental regions. As expected, genetic distances are substantially lower between hybridising species pairs than between non hybridising congenerics. This implies that hybridisation is typical for “young” (sister) pairs of species, that typically have similarities in their respective reproductive biology, ecology and ethology, and thus had less time for genetic incompatibilities to build up. These similarities also explain the difficulties experienced in studies on hybrid woodpeckers, but these could be overcome by the use of modern techniques (remote sensing and/or citizen science combining with AI identification and genomic identification). As hybridisation plays a role in woodpecker evolution and ecology it should be considered when conservation policies for rare species are drafted.
Mining the endogenous peptidome for peptide binders with deep learning-driven optimization and molecular simulations
Authors: Hartman Erik , Samsudin Firdaus , Bond Peter J. , Schmidtchen Artur , Malmström Johan
Published: January 2025

The endogenous peptidome is the complete set of naturally occurring peptides, some of which are involved in processes like intercellular communication, and in innate immunity. The peptidome is also a potential source of uncharacterized peptide-based therapeutics, which has remained largely unexplored due to challenges in identifying bioactive peptides in vast peptidomic datasets. Here, we present a generalized computational pipeline that mines datasets for peptides with high affinity binding capacities. The approach employs protein-peptide docking, binding interface scoring and a deep ensemble model to dynamically learn the mapping between peptide embeddings and binding capacity. We demonstrate the utility of the pipeline by identifying endogenous peptide binders for the LPS-binding site of CD14 using experimentally defined wound fluid peptidomes. Promising candidates underwent conformational refinement and validation through all-atom molecular dynamics simulations. This pipeline offers a systematic way to uncover novel peptide binders within large peptidomes, paving the way for accelerated discovery of peptide-based therapeutics.
A comprehensive quality control pipeline in human microbiome research for large population studies
Authors: Li Ruolin , Verlouw Joost A.M. , Boer Cindy G. , Arp Pascal , van Meurs Joyce , Uitterlinden Andre G. , Kraaij Robert , Medina-Gomez Carolina
Published: January 2025

Abstract

The widespread application of high-throughput Next Generation Sequencing (NGS) technologies has made microbiome research an emerging field in public health and biomedical sciences. However, there are still many challenges that need to be addressed in this field. Pipelines available to generate microbiome data across cohorts are diverse, and sources of variation to be recorded and evaluated during microbiome profiling have not been standardized. Moreover, meticulous quality control of the microbiome data processing, from collection to computational quantification is still challenging, especially in large population studies. Innovative approaches are required to handle samples and to minimize the potential bias introduced by logistic hurdles in biobanking. In this paper, we describe the methodological steps surrounding the optimization of the 16s rRNA gut microbiome profiling in two large prospective cohorts the Generation R Study (mean age 9.83 ± 0.32 years) and the Rotterdam Study (mean age 62.67 ± 5.66 years). This paper also highlights potential solutions to sample mislabeling in large-scale microbiome analysis. To summarize, our study addresses common problems in human microbiome research. It aims to improve the research quality and reliability by integrating more stringent quality control standards into microbiome research.
A self-supervised deep learning pipeline for segmentation in two-photon fluorescence microscopy
Authors: Ntiri Emmanuel Edward , Xu Tony , Rozak Matthew , Attarpour Ahmadreza , Dorr Adrienne , Stefanovic Bojana , Goubran Maged
Published: January 2025

Two-photon fluorescence microscopy (TPFM) allows in situ investigation of the structure and function of the brain at a cellular level, but the conventional image analyses of TPFM data are labour-intensive. Automated deep learning (DL)-based image processing pipelines used to analyze TPFM data require large labeled training datasets. Here, we developed a self supervised learning (SSL) pipeline to test whether unlabeled data can be used to boost the accuracy and generalizability of DL models for image segmentation in TPFM. We specifically developed four pretext tasks, including shuffling, rotation, axis rotation, and reconstruction, to train models without supervision using the UNet architecture. We validated our pipeline on two tasks (neuronal soma and vasculature segmentation), using large 3D microscopy datasets. We introduced a novel density-based metric, which provided more sensitive evaluation to downstream analysis tasks. We further determined the amount of labeled data required to reach performance on par with fully supervised learning (FSL) models. SSL-based models that were fine-tuned with only 50% of data were on par or superior (e.g., Dice increase of 3% for neuron segmentation and Dice score of 0.88 ± 0.09 for vessel segmentation) to FSL models. We demonstrated that segmentation maps generated by SSL models pretrained on the reconstruction and rotation tasks can be better translated to downstream tasks than can other SSL tasks. Finally, we benchmarked all models on a publicly available out-of-distribution dataset, demonstrating that SSL models outperform FSL when trained with clean data, and are more robust than FSL models when trained with noisy data.
Contribution of DNA breathing to physical interactions with transcription factors
Authors: Butt Waqaas , Lai Ben , Chiu Tsu-Pei , Bhattarai Manish , Qian Sheng , Bishop Alan R. , Duan Jubao , Alexandrov Boian S. , Rohs Remo , He Xin
Published: January 2025

Interaction between transcription factors (TFs) and DNA plays a key role in regulating gene expression. It is generally believed that these interactions are controlled through recognition of DNA core motifs by TFs. Nevertheless, several studies pointed out the limitation of this view, in particular, DNA sequence variants influencing TF binding are often located outside of core motifs. One possible explanation is that the physical properties of DNA may play a role in TF-DNA interactions. Recent studies have supported the importance of DNA shape features, especially in flanking regions of core motifs. Another important physical property of DNA is DNA breathing, the spontaneous opening of double-stranded DNA through thermal motions. But there have been few genomic studies of the role of DNA breathing in TF-DNA interactions. In this work, we analyzed in vitro TF-DNA binding data of three TFs and found that DNA breathing features inside or near core motifs are correlated with binding affinity. This suggests that these TFs may prefer locally and temporally melted DNA formed through breathing. We extended the analysis to 44 TFs with in vivo ChIP-seq binding data. We found that for a large proportion of TFs, their breathing features in or near core motifs are associated with binding, but the sign and magnitude of these associations vary substantially across TF families. Altogether, our study supports the hypothesis that DNA breathing features near binding motifs contribute to TF-DNA interactions.

Author Summary

Proper regulation of when and where genes are expressed is crucial to biological development and function. This process is largely controlled by interaction of transcription factors (TFs) with DNA sequences. The recognition of specific DNA sequences by TFs is important to ensure that only the correct genes are activated. Extensive work has shown that TFs prefer to bind certain DNA sequence patterns of 6-20 bp, known as motifs. However, the structure of DNA molecules may also play a role. In this work, we explored the role of DNA breathing, which refers to spontaneous opening of double strand DNA due to thermal motions. This process creates transient, single-strand “bubbles” in DNA. Through examining TF-DNA binding data of >60 TFs, we found that the propensity of DNA forming bubbles near motifs is often associated with binding affinity of DNA sequence. Interestingly the patterns of these associations seem to vary with TFs. Altogether, our results highlighted the potential of DNA breathing in influencing TF-DNA interactions.
Multimodal Neuroimaging Reveals Distinct Characteristics of Levodopa-Induced Dyskinesias inde novoParkinson’s Disease Patients
Authors: Shukla Sakshi , Patnaik Mantosh , Kumar Aditya , Tinaz Sule , Thirugnanasambandam Nivethida
Published: January 2025

Levodopa-induced dyskinesia (LID) is a significant treatment complication that affects a substantial proportion of Parkinson’s disease (PD) patients. Our understanding of the neural basis of LID remains limited, partly due to the small sample sizes in existing neuroimaging studies.

In this study, we utilized structural MRI data from the Parkinson’s Progression Markers Initiative (PPMI) database, including de novo PD patients (104 non-dyskinetic for a least 3 years after diagnosis and 120 who developed dyskinesia) and 100 age- and sex-matched healthy controls. Additionally, we analyzed resting-state functional MRI data from a subset of these participants to investigate connectivity differences among the groups.

Our analysis revealed no significant baseline volumetric differences between dyskinetic and non-dyskinetic PD patients. However, the thickness of frontal and sensorimotor cortices were significantly greater in dyskinetic patients. In the subcortical regions, vertex-based shape analysis identified localized surface growth in the left caudate and left pallidum, as well as surface morphology changes in the bilateral pallidum in dyskinetics. Resting-state functional connectivity analysis revealed stronger connectivity between the putamen, inferior frontal gyrus, and sensory cortex in dyskinetic PD patients compared to non-dyskinetics.

These findings suggest that specific morphological and functional changes in the motor cortical-basal ganglia circuitry of de novo PD patients may predispose them to LID over time. Additionally, the altered functional connectivity patterns reinstate the role of the inferior frontal gyrus in the pathophysiology of dyskinesia and suggest that it might be a suitable target for neuromodulatory interventions, consistent with previous reports.
Cell atlases and the Developmental Foundations of the Phenotype
Authors: Lou Alicia , Chagoyen Mónica , Poyatos Juan F
Published: January 2025

It is widely acknowledged that development shapes phenotypes, yet the extent to which genes with similar expression patterns during development lead to equivalent organismal phenotypes when mutated remains unclear. Here, we propose addressing this issue, which we term the 𝒟evelopment–to– 𝒫henotype, or 𝒟–𝒫, rule, by leveraging single-cell gene expression atlases and phenotypic ontologies, usingCaenorhabditis elegansas a model system. This framework quantifies the proportionality between developmental expression and phenotypic similarities, demonstrating that the relationship holds on average. Genes that strongly fulfill the rule exhibit broad “housekeeping” expression and are associated with systemic phenotypes, whereas weak similarities correspond to specific expression patterns and specialized phenotypes. Deviations from the 𝒟–𝒫 rule provide insights into developmental divergence and phenotypic degeneracy, highlighting genes with narrow functional roles but systemic phenotypic impact. Furthermore, genes that closely adhere to the rule exhibit the highest pleiotropic impact on organismal traits. Our analysis also identifies cell types, such as ASK neurons, as key mediators of phenotype-specific gene contributions, exemplified by their association with chemosensory behavior and chemotaxis. These findings validate the 𝒟–𝒫 rule and underscore the role of cells as critical mediators of the genotypephenotype map, offering a unified framework to understand the developmental origins of phenotypic complexity.
Treatment outcomes of bedaquiline-resistant tuberculosis: a retrospective and matched cohort study
Authors: Mdlenyani Lindokuhle , Mohamed Zahraa , Stadler Jacob AM , Mtwa Nomfuneko , Meintjes Graeme , Warren Robin , Kuhlin Johanna , Wasserman Sean
Published: January 2025

Background

Rising prevalence of bedaquiline resistance undermines benefits from this life-saving drug for rifampicin-resistant tuberculosis (RR-TB). Despite increasing awareness, patient-level outcomes for bedaquiline-resistant TB have not been well-characterised and case management poorly defined.

Methods

We conducted a retrospective cohort study with matched controls at a TB referral hospital in South Africa. Cases included patients ≥13 years with a phenotypic bedaquiline-resistantMycobacterium tuberculosisisolate identified between January 2018 and June 2023. Matched controls (1:1) with bedaquiline-susceptible RR-TB were selected from a prospective observational study conducted at the same facility. Primary outcomes included time to sputum culture conversion (SCC), a modified WHO-defined unfavourable outcome, and TB-free survival (alive, with SCC, and in care or treatment completed) through 18 months. Adjusted analyses used Cox proportional hazards models.

Findings

Eighty-two patients with bedaquiline-resistant TB were included; 57 (70%) were HIV-positive and 17 (21%) had no prior exposure to bedaquiline or clofazimine. Bedaquiline was prescribed for 72 (88%) and meropenem (plus amoxicillin-clavulanate) for 32 (39%) after submission of the sputum sample with the first bedaquiline-resistantMycobacterium tuberculosisisolate. At 18 months, 43 (52%) patients achieved TB-free survival; 17 (20%) failed to achieve sustained SCC, there were 19 (23%) deaths, and 50 (80%) survivors (n=63) were still on treatment. WHO treatment outcomes following treatment initiation were unfavourable in 54 (67%) patients, driven by treatment failure in 35 (43%). Median time to SCC after treatment initiation was 175 (IQR 100–254) days in the bedaquiline resistant cohort and 32 days (IQR 30–42 days) in the matched bedaquiline susceptible cohort. Baseline smear microscopy grade (HR 0·41, 95% CI 0·23–0·73, p=0·003) and bedaquiline resistance (HR 0·06, 95% CI 0·02–0·23, p<0·001) were associated with reduced SCC.

Interpretation

Current treatment options for bedaquiline-resistant TB result in prolonged therapy, delayed microbiological responses, and poor clinical outcomes.

Funding

This work was partially supported by the South African Medical Research Council (grant number MRC-RFA-SHIP 02–2018). JK was funded by Swedish Heart & Lung Foundation (20220859 and 20240774) Swedish Society of Medicine (SLS-985976). SW was supported by the National Institutes of Health (U01AI170426) and the Bill & Melinda Gates Foundation. GM was supported by the Wellcome Trust (214321/Z/18/Z, and 203135/Z/16/Z), and the South African Research Chairs Initiative of the Department of Science and Technology and National Research Foundation (NRF) of South Africa (Grant No 64787).
Integrating Macroeconomic and Public Health Impacts in Social Planning Policies for Pandemic Response
Authors: Cornfeld Ofer , Niu Kaicheng , Neeman Oded , Roswell Michael , Steinbach Gabi , Beckett Stephen J. , Wardi Yorai , Weitz Joshua S. , Yashiv Eran
Published: January 2025

Infectious disease outbreaks with pandemic potential present challenges for mitigation and control. Policymakers make decisions to reduce disease-associated morbidity and mortality while also minimizing socioeconomic costs of control. Despite ongoing efforts and widespread recognition of the challenge, there remains a paucity of decision tool frameworks that integrate epidemic and macroeconomic dynamics. Here, we propose and analyze an econo-epidemic model to identify robust planning policies to limit epidemic impacts while maintaining economic activity. The model couples epidemic dynamics, behavioral change, economic activity, and feasible policy plans informed by respiratory disease threats of pandemic concern. We compare alternative fixed, dynamic open-loop optimal control, and feedback control policies via a welfare loss framework. We find that open loop policies that adjust employment dynamically while maintaining a flat epidemic curve in advance of the uncertain arrival of population-scale vaccination outperform fixed employment reduction policies. However, open loop policies are highly sensitive to misestimation of parameters associated with intrinsic disease strength and feedback between economic activity and transmission, leading to potentially significant increases in welfare loss. In contrast, feedback control policies guided by open loop dynamical targets of the time-varying reproduction number perform near-optimally when parameters are well-estimated, while significantly outperforming open loop policies whenever disease features and population-scale behavioral response are misestimated – as they inevitably are. These findings present a template for integrating principled economic models with epidemic scenarios to identify vulnerabilities in policy responses and expand policy options in preparation for future pandemics.
Detection of anti–SARS-CoV-2 mucosal IgA in clinical saliva samples after a dose of Novavax COVID-19 vaccine
Authors: Zhu Mingzhu , Massuda Edmond , Patel Urvashi , Chau Gordon , Kalkeri Raj , Cloney-Clark Shane , Smith Katherine , Neal Susan , Plested Joyce S. , Mallory Raburn M. , Bennett Chijioke
Published: January 2025

Immunoglobulin (Ig) A acts as a first line of defense against respiratory pathogens. Mucosal IgA in salivary and nasal passages has a rapid response to antigens and can play a protective role against reinfection. The mainstay for analyzing SARS-CoV-2 infection and vaccine efficacy has been assessment of serum IgG levels; however, validated assays for assessment of mucosal IgA in clinical samples are necessary as new and adapted measures are generated to combat immune-evasive viral variants. A mucosal IgA assay was developed and tested through assessment of IgA levels in salivary samples from participants of the 2019nCoV-314/NCT05973006study. These participants had previously received ≥2 mRNA-based COVID-19 vaccinations prior to enrollment and received a single intramuscular study dose of NVX-CoV2601 (XBB.1.5) or bivalent vaccine (NVX-CoV2601 + NVX-CoV2373 [Wuhan]). Salivary samples were collected prior to vaccination on day 0 and on day 28 to assess response post vaccination. Both vaccine groups elicited a significant increase in anti–SARS-CoV-2 spike IgA against XBB.1.5. Furthermore, cross-reactivity via identification of anti-JN.1 and anti-Wuhan IgA was also observed. The detection of IgA in clinical mucosal samples through this assay will be a valuable tool in supporting vaccine development.
De novo design of epitope-specific antibodies against soluble and multipass membrane proteins with high specificity, developability, and function
Authors:   Nabla Bio, Biswas Surojit
Published: January 2025

We present JAM, a generative protein design system that enables fully computational design of antibodies with therapeutic-grade properties for the first time. JAM generates antibodies de novo in both single-domain (VHH) and paired (scFv/mAb) antibody formats that achieve double-digit nanomolar affinities, strong early-stage developability profiles, and precise epitope targeting without experimental optimization. We demonstrate JAM's capabilities across multiple therapeutic contexts, including the first fully computationally designed antibodies to multipass membrane proteins - Claudin-4 and CXCR7. Against SARS-CoV-2, JAM-designed antibodies achieved sub-nanomolar pseudovirus neutralization potency, with early stage developability metrics achieving established clinical benchmarks. We show that increasing test-time computation by allowing JAM to iteratively introspect on its outputs substantially improves both binding success rates and affinities, representing the first evidence that test-time compute scaling may extend to physical protein design systems. The entire process from design to recombinant characterization requires <6 weeks, and multiple targets can be pursued in parallel with minimal additional experimental overhead. These results establish de novo antibody design as a practical approach for therapeutic discovery, offering paths to both improved efficiency in standard workflows and new opportunities for previously intractable targets. Disclaimer: While we provide detailed descriptions of experimental methods and success metrics, we choose not disclose methodological details of JAM for commercial reasons.
Reduced levels of synaptic vesicle protein 2A in the extracellular vesicles and brain of Alzheimer’s disease- associations with Aβ, tau and synaptophysin
Authors: Nussbaumer Jana , Barve Aatmika , Zufferey Valentin , Espourteille Jeanne , Kirabali Tunahan , Konietzko Uwe , Razansky Daniel , Rominger Axel , Nordberg Agneta , Buée Luc , Colin Morvane , Nitsch Roger M. , Hock Christoph , Richetin Kevin , Ni Ruiqing
Published: January 2025

Background

Synaptic dysfunction plays an important role in Alzheimer’s disease (AD) and is an emerging imaging and fluid biomarker. Here, we aimed to assess the regional expression of synaptic vesicle glycoprotein 2A (SV2A) in the brain and extracellular vesicles of AD patients and its associations with the APOE ε4 allele, amyloid-β, tau pathologies, and other synaptic markers.

Methods

Mass spectrometry-based synaptosome proteomics was performed on brain-derived extracellular vesicles (BdEVs) isolated from the frontal cortex of 17 AD patients and 4 NCs. Immunohistochemical staining for SV2A, synaptophysin, amyloid-β and phospho-tau was performed on postmortem tissue from the frontal, temporal, and entorhinal cortices and hippocampus of 40 AD patients and 44 nondemented controls (NCs).

Results

Reduced levels of synaptic proteins, including synaptotagamin, GAP43, SYT1, SNAP25 and 14-3-3ζ, were positively correlated with SV2A and negatively correlated with GFAP and NEFL in BdEVs from AD patients and NCs. We detected lower levels of SV2A in the hippocampus and entorhinal cortex of AD compard to NCs, and in APOE ε4 carriers than in noncarriers. SV2A levels were positively correlated with synaptophysin and negatively correlated with the levels of the amyloid-β, phospho-tau, and Braak stages.

Conclusions

This study provides postmortem evidence of synaptic markers and reduced regional levels of SV2A in brain tissue slices and BdEVs from AD patients compared with NCs and in APOE ε4 carriers compared to non-carriers. SV2A could serve as a valuable marker for monitoring synaptic degeneration in AD.