bluuebunny/crossref_metadata_2025 huggingface dataset:
Chemoenzymatic Synthesis Planning Guided by Reaction Type Score
Authors: Li Hongxiang , Liu Xuan , Jiang Guangde , Zhao Huimin
Published: October 2024

Thanks to the growing interests in computer-aided synthesis planning (CASP), a wide variety of retrosynthesis and retrobiosynthesis tools have been developed in the past decades. However, synthesis planning tools for multi-step chemoenzymatic reactions are still rare despite the widespread use of enzymatic reactions in chemical synthesis. Herein we report a reaction type score (RTscore)-guided chemoenzymatic synthesis planning (RTS-CESP) strategy. Briefly, the RTscore is trained using a text-based convolutional neural network (TextCNN) to distinguish synthesis reactions from decomposition reactions and evaluate synthesis efficiency. Once multiple chemical synthesis routes are generated by a retrosynthesis tool for a target molecule, RTscore is used to rank them and find the step(s) that can be replaced by enzymatic reactions to improve synthesis efficiency. As proof of concept, RTS-CESP was applied to 10 molecules with known chemoenzymatic synthesis routes in literature and was able to predict all of them with six being the top-ranked routes. Moreover, RTS-CESP was employed for 1000 molecules in the boutique database and was able to predict the chemoenzymatic synthesis routes for 554 molecules, outperforming ASKCOS, a state-of-the-art chemoenzymatic synthesis planning tool. Finally, RTS-CESP was used to design a new chemoenzymatic synthesis route for the FDA-approved drug Alclofenac, which was shorter than literature-reported route and have been experimentally validated.
Ice and air: Visualisation of freeze-thaw embolism and freezing spread in youngL. tulipiferaleaves
Authors: Johnson Kate M. , Scherer Muriel , Gerber Dominic , Style Robert W. , Dufresne Eric R. , Brodersen Craig R.
Published: October 2024

Spring freezing is an unforgiving stress for young leaves, often leading to death, with consequences for tree productivity and survival. While both the plant water transport system and living tissues are vulnerable to freezing, we do not know whether damage to one or both of these systems causes death in leaves exposed to freezing. Whole saplings ofLiriodendron tulipiferawere exposed to freezing and thawing trajectories designed to mimic natural spring freezes. We monitored the formation of freeze-thaw xylem embolism and damage to photosynthetic tissues to reveal a predictable progression of ice formation across the leaf surface that is strongly influenced by leaf vein architecture, notably the presence or absence of bundle sheath extensions. Our data also show that freeze-thaw embolism occurs only in the largest vein orders where mean vessel diameter exceeds 30µm. With evidence of both freeze-thaw embolism and damage to photosynthetic tissue, we conclude that this dual-mode lethality may be common among other wide-vesseled angiosperm-leaves, potentially playing a role in limiting geographic distributions, and show that bundle sheath extensions may stall or even prevent freezing spread.

Highlight

Both ice and air lead likely lead to death in youngL.tulipferaleaves exposed to freezing, with the spread of both governed by physical characteristics of these leaves.
DNMT3AR882H Is Not Required for Disease Maintenance in Primary Human AML, but Is Associated With Increased Leukemia Stem Cell Frequency
Authors: Koehnke Thomas , Karigane Daiki , Hilgart Eleanor , Fan Amy C. , Kayamori Kensuke , Miyauchi Masashi , Collins Cailin T. , Suchy Fabian P. , Rangavajhula Athreya , Feng Yang , Nakauchi Yusuke , Martinez-Montes Eduardo , Fowler Jonas , Loh Kyle M. , Nakauchi Hiromitsu , Koldobskiy Michael A. , Feinberg Andrew P. , Majeti Ravindra
Published: October 2024

Genetic mutations are being thoroughly mapped in human cancers, yet a fundamental question in cancer biology is whether such mutations are functionally required for cancer initiation, maintenance of established cancer, or both. Here, we study this question in the context of human acute myeloid leukemia (AML), where DNMT3AR882 missense mutations often arise early, in pre-leukemic clonal hematopoiesis, and corrupt the DNA methylation landscape to initiate leukemia. We developed CRISPR-based methods to directly correct DNMT3AR882 mutations in leukemic cells obtained from patients. Surprisingly, DNMT3AR882 mutations were largely dispensable for disease maintenance. Replacing DNMT3AR882 mutants with wild-type DNMT3A did not impair the ability of AML cells to engraft in vivo, and minimally altered DNA methylation. Taken together, DNMT3AR882 mutations are initially necessary for AML initiation, but are largely dispensable for disease maintenance. The notion that initiating oncogenes differ from those that maintain cancer has important implications for cancer evolution and therapy.
DNA methylation memory of pancreatic acinar-ductal metaplasia transition state altering Kras-downstream PI3K and Rho GTPase signaling in the absence of Kras mutation
Authors: Lo Emily K.W. , Idrizi Adrian , Tryggvadottir Rakel , Zhou Weiqiang , Hou Wenpin , Ji Hongkai , Cahan Patrick , Feinberg Andrew P.
Published: October 2024

A critical area of recent cancer research is the emergence of transition states between normal and cancer that exhibit increased cell plasticity which underlies tumor cell heterogeneity. Pancreatic ductal adenocarcinoma (PDAC) can arise from the combination of a transition state termed acinar-to-ductal metaplasia (ADM) and a gain-of-function mutation in the proto-oncogeneKRAS. During ADM, digestive enzyme-producing acinar cells acquire a transient ductal epithelium-like phenotype while maintaining their geographical acinar organization. One route of ADM initiation is the overexpression of theKrüppel-like factor 4gene (KLF4) in the absence of oncogenic driver mutations. Here, we asked to what extent cells acquire and retain an epigenetic memory of the ADM transition state in the absence of oncogene mutation. We identified differential DNA methylation at Kras-downstreamPI3KandRho/Rac/Cdc42GTPase pathway genes during ADM, as well as a corresponding gene expression increase in these pathways. Importantly, differential methylation persisted after gene expression returned to normal. Caerulein exposure, which induces widespread digestive system changes in addition to ADM, showed similar changes in DNA methylation in ADM cells. Regions of differential methylation were enriched for motifs of KLF and AP-1 family transcription factors, as were those of human pancreatic intraepithelial neoplasia (PanIN) samples, demonstrating the relevance of this epigenetic transition state memory in human carcinogenesis. Finally, single-cell spatial transcriptomics revealed that these ADM transition cells were enriched for PI3K pathway and AP1 family members, linking epigenetic memory to cancer cell plasticity even in the absence of oncogene mutation.
In-depth investigation of genome to refine QTL positions for spontaneous sex-reversal in XX rainbow trout
Authors: Dehaullon Audrey , Fraslin Clémence , Bestin Anastasia , Poncet Charles , Guiguen Yann , Quillet Edwige , Phocas Florence
Published: October 2024

Sex determination is a flexible process in fish, controlled by genetics or environmental factors or a combination of both depending on the species. Revealing the underlying molecular mechanisms may have important implications for research on reproductive development in vertebrates, as well as sex-ratio control and selective breeding in fish. Phenotypic sex in rainbow trout is primarily controlled by a XX/XY male heterogametic sex determination system. Unexpectedly in genetically XX all-female farmed populations, a small proportion of males or intersex individuals are regularly observed. This spontaneous masculinisation is a highly heritable trait, controlled by minor sex-modifier genes that remain unknown, although several QTL regions were detected in previous studies. In this work we used genome-based approaches and various statistical methods to investigate these QTL regions. We validated in six different French farmed populations DNA markers we had previously identified in a different commercial population on chromosomes Omy1, Omy12 and Omy20. We also identified functional candidate genes located that may be involved in spontaneous masculinisation by reducing germ cell proliferation and repressing oogenesis of XX-rainbow trout in the absence of the master sex determining gene. In particular,syndig1,tlx1andhellson Omy1, as well askhdrbs2andcsmd1on Omy20 deserve further investigation as potential sex-modifier genes to precise their functional roles as well as their interaction with rearing temperature. Those findings could be used to produce all-female populations that are preferred by farmers due to a delayed maturation of females and higher susceptibility of male trout to diseases.
Light activatespsbAtranslation in plants by relieving inhibition of translation factor HCF173 by thepsbAORF incis
Authors: Williams-Carrier Rosalind , Chotewutmontri Prakitchai , Perkel Sarah , Rojas Margarita , Belcher Susan , Barkan Alice
Published: October 2024

The D1 reaction center protein of photosystem II is subject to photooxidative damage. Photodamaged D1 must be replaced with newly synthesized D1 to maintain photosynthesis. In plant chloroplasts, D1 synthesis is coupled to D1 photodamage via regulated translation initiation onpsbAmRNA, which encodes D1. Mechanisms underlying this coupling are unclear. We show by analysis of reporter constructs in tobacco that thepsbAtranslational activators HCF173 and HCF244 activate viacis-elements in thepsbAUTRs and that the 5’ UTR sequence bound by HCF173 is essential forpsbAexpression. However, thepsbAUTRs are not sufficient to program light-regulated translation. Instead, thepsbAopen reading frame acts incisto repress translation initiation, and D1 photodamage relieves this repression. A truncated HCF173 mutant conditions constitutively highpsbAribosome occupancy in the dark, implicating HCF173 as a mediator of the repressive signal. We propose a model that is informed by structures of the Complex I assembly factor CIA30/NDUFAF1 positing that D1 photodamage relieves a repressive cotranslational interaction between nascent D1 and HCF173’s CIA30 domain, and that the D1 assembly factor HCF136 promotes this interaction. These findings elucidate a translational rheostat that maintains photosynthesis in the face of inevitable photosystem II photodamage.
In silico design of a multi-epitope vaccine against tick-borne encephalitis virus via immunoinformatic analysis
Authors: Wang Bingjie
Published: October 2024

Tick-borne encephalitis virus (TBEV) is a serious pathogen that poses a significant threat to humans, causing encephalitis that can result in lifelong sequelae. In this study, we focused on the complete proteomes of the five current TBEV subtypes to identify dominant epitopes. Immunoinformatics tools were employed to screen for LBL, HTL, and CTL epitopes. These epitopes were then linked using various linkers and combined with adjuvants and histidine tag. The vaccine underwent a series of physicochemical property analyses, including secondary structure prediction, three-dimensional structure prediction, molecular docking, molecular dynamics simulation, immune simulation, and in silico cloning. The results indicate that the vaccine is highly conserved, strongly immunogenic, stable, non-allergenic, and non-toxic. Molecular docking and molecular dynamics simulation demonstrate that the vaccine can form a stable binding complex with TLR3. Immune simulation analysis shows that the vaccine effectively stimulates both cellular and humoral immune responses, accompanied by an increase in cytokine titers. Furthermore, through codon optimization and in silico cloning, the vaccine can be stably and effectively expressed in theEscherichia colisystem. As an effective candidate for TBEV vaccination, the multi-epitope vaccine developed in this study has promising application prospects and provides a new approach for the research, development, and improvement of vaccines targeting TBEV.
Deficient QPRT drives trans-Golgi NAD+hyperinflation and pathological protein secretion in rheumatoid arthritis
Authors: Njunge Lucy Wanjiru , Liu Kaijing , Xiong Chenghe , Chen Liuqing , He Qifei , Wang Pei , Huang Guan , Li Yong , Abhulimen Peace Osebhue , Cheng Wenxiang , Yu Qiuliyang
Published: October 2024

Aberrant protein secretion is a central driver of tissue inflammation and destruction in rheumatoid arthritis (RA). While RA fibroblast-like synoviocytes (FLSs) exhibit prominent endoplasmic reticulum (ER) and Golgi, the mechanism underlying their excessive protein secretion is not fully understood. Here, we identified the deficiency ofde novoNAD+synthesis enzyme, quinolinate phosphoribosyltransferase (QPRT), as a significant abnormality in RA synovium. QPRT loss counterintuitively inflates NAD+in the trans-Golgi network (TGN) while decreasing NAD+in the cytoplasm, ER and cis/medial-Golgi. QPRT knockdown promoted Golgi membrane expansion and epithelial-to-mesenchymal-transition (EMT)-associated secretome production in RA FLSs by suppressing TGN-residing PARP12, resulting in mTORC1-mediated protein translation and Golgi expansion. Furthermore, QPRT gene therapy restored NAD+balance, corrected Golgi dysfunction, reduced cytokine production, and improved RA severity in mouse models. These findings underscore QPRT’s role in coordinating protein secretion and the regulatory dynamics of compartmentalized NAD+, proposing QPRT targeting as a therapeutic strategy for inflammatory, secretory and Golgi-related diseases.
Correlation Between Enzymatic and Non-Enzymatic Genes inAcinetobacter baumanniiIsolates
Authors: Rahi Alya Amer , Al-Hasnawy Huda H.
Published: October 2024

Abstracts

Background

Acinetobacter baumanniiis a multidrug-resistant bacterium responsible for severe infections, particularly in hospital settings. Its resistance is driven by enzymatic genes such as those encoding beta-lactamases and carbapenemases, which degrade antibiotics, and non-enzymatic genes that modify mechanisms like efflux pumps and membrane permeability, further enhancing its defence against treatments. Together, these factors allowA. baumanniito thrive in clinical environments, complicating infection management.

Objective

This study aimed to explore the relationships between beta-lactamases, carbapenemases, efflux pumps, and membrane permeability changes, to understand their collective contribution toA. baumannii’smultidrug resistance.

Materials and Methods

Among 300 clinical isolates from urine, blood, wounds, and burns, 25 (8.33%) were identified asA. baumannii. These included 8% from urine, 12% from blood, and 40% each from wound and burn swabs. all specimens were taken from patients who have different symptoms in hospital of Al-Hilla Teaching Hospital/ Babylon. The research was carried out through the period January and June 2024. Bacterial identification was conducted using the VITEK-2 system and HI-Chromoagar®A. baumannii. Enzymatic genes were detected using conventional PCR, while non-enzymatic genes were analyzed via RT-qPCR.

Results

Molecular analysis revealed the presence of beta-lactamase (blaOXA-51, blaOXA-23) and metallo-beta-lactamase genes (blaVIM, blaIMP), with high antibiotic resistance rates. Gene expression analysis highlighted efflux pump upregulation (adeB) and altered permeability (CarO), reinforcing multidrug resistance mechanisms.

Conclusion

The combined action of enzymatic and non-enzymatic resistance genes inA. baumanniipresents a significant treatment challenge, necessitating multi-target therapeutic approaches.
Disruption of molecular interactions between G3BP1 stress granule host protein and nucleocapsid (NTD-N) protein impedes SARS-CoV-2 virus replication
Authors: Dhaka Preeti , Singh Ankur , Nehul Sanketkumar , Choudhary Shweta , Panda Prasan Kumar , Sharma Gaurav Kumar , Kumar Pravindra , Tomar Shailly
Published: October 2024

The Ras GTPase-activating protein SH3-domain-binding protein 1 (G3BP1) serves as a formidable barrier to viral replication by generating stress granules (SGs) in response to viral infections. Interestingly, viruses, including SARS-CoV-2, have evolved defensive mechanisms to hijack SG proteins like G3BP1 for the dissipation of SGs that lead to the evasion of host’s immune responses. Previous research has demonstrated that the interaction between the NTF2-like domain of G3BP1 (G3BP1NTF-2) and the intrinsically disordered N-terminal domain (NTD-N1-25) of the N protein plays a crucial role in regulating viral replication and pathogenicity. Interestingly, the current study identified an additional upstream stretch of residues (128KDGIIWVATEG138) (N128-138) within the N-terminal domain of the N protein (NTD-N41-174) that also forms molecular contacts with the G3BP1 protein, as revealed throughin silicoanalysis, site-directed mutagenesis and biochemical analysis. Remarkably, WIN-62577, and fluspirilene, the small molecules targeting the conserved peptide binding pocket in G3BP1NTF-2,not only disrupted the protein-protein interactions (PPIs) between the NTD-N41-174and G3BP1NTF-2but also exhibited significant antiviral efficacy against SARS-CoV-2 replication with EC50values of ∼1.8 µM and ∼1.3 µM, respectively. The findings of this study, validated by biophysical thermodynamics and biochemical investigations, advance the potential of developing therapeutics targeting the SG host protein against SARS-CoV-2, which may also serve as a broad-spectrum antiviral target.
A multi-subunit autophagic capture complex facilitates degradation of ER stalled MHC-I in pancreatic cancer
Authors: Berquez Marine , Li Alexander L. , Luy Matthew A. , Venida Anthony C. , O’Loughlin Thomas , Rademaker Gilles , Barpanda Abhilash , Hu Jingjie , Yano Julian , Wiita Arun , Gilbert Luke A. , Bruno Peter M. , Perera Rushika M.
Published: October 2024

Pancreatic ductal adenocarcinoma (PDA) evades immune detection partly via autophagic capture and lysosomal degradation of major histocompatibility complex class I (MHC-I). Why MHC-I is susceptible to capture via autophagy remains unclear. By synchronizing exit of proteins from the endoplasmic reticulum (ER), we show that PDAC cells display prolonged retention of MHC-I in the ER and fail to efficiently route it to the plasma membrane. A capture-complex composed of NBR1 and the ER-phagy receptor TEX264 facilitates targeting of MHC-I for autophagic degradation, and suppression of either receptor is sufficient to increase total levels and re-route MHC-I to the plasma membrane. Binding of MHC-I to the capture complex is linked to antigen presentation efficiency, as inhibiting antigen loading via knockdown of TAP1 or beta 2-Microglobulin led to increased binding between MHC-I and the TEX264-NBR1 capture complex. Conversely, expression of ER directed high affinity antigenic peptides led to increased MHC-I at the cell surface and reduced lysosomal degradation. A genome-wide CRISPRi screen identified NFXL1, as an ER-resident E3 ligase that binds to MHC-I and mediates its autophagic capture. High levels of NFXL1 are negatively correlated with MHC-I protein expression and predicts poor patient prognosis. These data highlight an ER resident capture complex tasked with sequestration and degradation of non-conformational MHC-I in PDAC cells, and targeting this complex has the potential to increase PDAC immunogenicity.
Early detection of non-small cell lung cancer using electronic health record data
Authors: Li Xiudi , Yuan Erin Y. , Kuperberg Stephen J. , Bonzel Clara-Lea , Jeffway Mary I. , Cai Tianrun , Liao Katherine P. , Aguiar-Ibáñez Raquel , Kao Yu-Han , Santorelli Melissa L. , Christiani David C. , Cai Tianxi , Duan Rui
Published: October 2024

Rationale

Specific patient characteristics increase the risk of cancer, necessitating personalized healthcare approaches. For high-risk individuals, tailored clinical management ensures proactive monitoring and timely interventions. Electronic Health Records (EHR) data are crucial for supporting these personalized approaches, improving cancer prevention and early diagnosis.

Objectives

We leverage EHR data and build a prediction model for early detection of non-small cell lung cancer (NSCLC).

Methods

We utilize data from Mass General Brigham’s EHR and implement a three-stage ensemble learning approach. Initially, we generate risk scores using multivariate logistic regression in a self-control and case-control design to distinguish between cases and controls. Subsequently, these risk scores are integrated and calibrated using a prospective Cox model to develop the risk prediction model.

Results

We identified 127 EHR-derived features predictive for early detection of NSCLC. The highly predictive features include smoking, relevant lab test results, and chronic lung diseases. The predictive model reached area under the ROC curve (AUC) of 0.801 (positive predictive value (PPV) 0.0173 with specificity 0.02) for predicting one-year NSCLC risk in a population aged 18 and above, and AUC of 0.757 (PPV 0.0196 with specificity 0.02) in a population aged 40 and above.

Conclusions

This study identified EHR derived features which are predictive of early NSCLC diagnosis. The developed risk prediction model exhibits superior performance for early detection of NSCLC compared to a baseline model that only relies on demographic and smoking information, demonstrating the potential of incorporating EHR derived features for personalized cancer screening recommendations and early detection.
Revisiting Aristotle’s observation on bees: High floral constancy is common among bees but it is shaped by the locally abundant flowering species
Authors: Shrotri Saket , Kaur Sukhraj , Nawge Viraj , Sandhya S , Dandavate Rohan , Gowda Vinita
Published: October 2024

Floral constancy is the tendency of a pollinator to sequentially visit flowers of the same species despite the availability of other rewarding plants. In a phytodiverse community, resource assurance may lead to pollinators displaying floral constancy to the most abundant plant species. We tested this by investigating if pollinators are floral constant on the abundant or the non-abundant plants within a seasonally flowering tropical community. We quantified floral constancy in three social (Apisspp.) and two solitary (non-Apis) Indian native bees using three approaches, that is by manually tracking the bees, analysing their pollen load, and examining pollen sacs of returning bees at their hive. We next examined inApis cerana indicaif constancy in individual bees translated to hive-level constancy. We found that in our community with distinct co-flowering patches, bees were constant to the most abundant species within a localised patch, and not to the most abundant species in the landscape. While the pollen loads from both the social and solitary bees suggested that they show high floral constancy (> 70% uni-dominant pollen), their values differed significantly (p< 0.0001). Finally, approximately 90% of individuals within a hive showed floral constancy (monolectic), but collectively, a hive displayed polylectic foraging. Our findings highlight that the foraging patterns of native pollinators has been understudied and is a critical first step towards connecting reproductive assurances to plant-pollinator dependencies in large landscapes.
TreeFormer: A transformer-based tree rearrangement operation for phylogenetic reconstruction
Authors: Ly-Trong Nhan , Matsen Frederick A. , Minh Bui Quang
Published: October 2024

Phylogenetic inference is a fundamental problem in biology, which studies the origins and evolutionary relationships among species. Popular phylogenetic inference methods, such as IQ-TREE, RAxML, and PHYML, typically utilize heuristic tree search algorithms to seek a phylogenetic tree that maximizes the likelihood of the observed genetic data. However, tree search is time-consuming and often prone to local optima. To address these issues, we introduce TreeFormer, a new Transformer-based tree rearrangement operation for tree search. Experimental results show that TreeFormer achieves higher accuracy than FastTree 2 when reconstructing trees from real alignments with fewer than 1000 sites.
Clathrin-independent endocytosis and retrograde transport in cancer cells promote cytotoxic CD8 T cell activation
Authors: Xu Shiqiang , Buridant Alix , Hirsch Thibault , Shafaq-Zadah Massiullah , Dransart Estelle , Ledoux Benjamin , Johannes Ludger , van der Bruggen Pierre , Morsomme Pierre , Renard Henri-François
Published: October 2024

Endophilin A3-mediated clathrin-independent endocytosis (EndoA3-mediated CIE) mediates the internalization of immunoglobulin-like proteins, including key immune synapse components. Here, we identify ICAM1 as a novel EndoA3-dependent cargo, alongside ALCAM. We demonstrate that both proteins subsequently undergo retromer-dependent retrograde transport to thetrans-Golgi network (TGN) in cancer cells. From there, they undergo polarized redistribution to the plasma membrane, where they contribute to immune synapse formation between cancer cells and cytotoxic CD8 T cells. Disruption of EndoA3 or retromer components significantly impairs the activation of autologous cytotoxic CD8 T cells, as demonstrated by decreased cytokine production. Concomitantly, we observed a reduced localization of ICAM1 at the immune synapse, indicating impaired immune synapse integrity. Indeed, cancer cells lacking EndoA3-mediated CIE or retromer form enlarged immune synapses that fail to restore full T cell activation, suggesting a compensatory attempt by T cells to overcome the defective synapse. Together, these findings reveal that EndoA3-mediated CIE and retrograde transport act in concert in cancer cells to relocate immune synapse components via the Golgi, thereby promoting the activation of cytotoxic CD8 T cells. Our study paves the way for the design of future therapeutic strategies targeting these pathways to enhance T cell-mediated anti-tumor immunity.

Significance Statement

This study uncovers a novel mechanism by which clathrin-independent endocytosis (CIE) and retrograde transport collaborate to regulate immune synapse dynamics in cancer cells. We identify ICAM1 as a new cargo of Endophilin A3-mediated CIE, highlighting its role in the polarized redistribution of immune synapse components critical for cytotoxic CD8 T cell activation. By linking a specific CIE mechanism and retrograde transport to immune synapse function, our findings provide new insights into cancer-immunity interactions and suggest potential therapeutic strategies to enhance immune responses by targeting protein trafficking pathways.
Exploring the adhesion properties of extracellular vesicles for functional assays
Authors: Pachane Bianca C. , Carlson Bess , Queen Suzanne E. , Selistre-de-Araujo Heloisa S. , Witwer Kenneth W.
Published: October 2024

The “stickiness” of extracellular vesicles (EVs) can pose challenges for EV processing and storage, but adhesive properties may also be exploited to immobilize EVs directly on surfaces for various measurement techniques, including super-resolution microscopy. Direct adhesion to surfaces may allow examination of broader populations of EVs than molecular affinity approaches, which can also involve specialized, expensive affinity reagents. Here, we report on the interaction of EVs with borosilicate glass and quartz coverslips and on the effects of pre-coating coverslips with poly-L-lysine (PLL), a reagent commonly used to facilitate interactions between negatively charged surfaces of cells and amorphous surfaces. Additionally, we compared two mounting media conditions for super-resolution microscopy (SRM) imaging and used immobilized EVs for a B-cell interaction test. Our findings suggest that borosilicate glass coverslips immobilize EVs better than quartz glass coverslips. We also found that PLL is not strictly required for EV retention but contributes to the uniform distribution of EVs on borosilicate glass coverslips. Overall, these findings suggest that standard lab materials like borosilicate glass coverslips, with or without PLL, can be effectively used for the immobilization of EVs in specific imaging techniques.
Identification of distinct subtypes of post-stroke and neurotypical gait behaviors using neural network analysis of kinematic time series data
Authors: Kuch Andrian , Schweighofer Nicolas , Finley James M. , McKenzie Alison , Wen Yuxin , Sánchez Natalia
Published: October 2024

Background

Heterogeneous types of gait impairment are common post-stroke. Studies used supervised and unsupervised machine learning on discrete biomechanical features to summarize the gait cycle and identify common patterns of gait behaviors. However, discrete features cannot account for temporal variations that occur during gait. Here, we propose a novel machine-learning pipeline to identify subgroups of gait behaviors post-stroke using kinematic time series data.

Methods

We analyzed ankle and knee kinematic data during treadmill walking data in 39 individuals post- stroke and 28 neurotypical controls. The data were first input into a supervised dual-stage Convolutional Neural Network-Temporal Convolutional Network, trained to extract temporal and spatial gait features. Then, we used these features to find clusters of different gait behaviors using unsupervised time series k-means. We repeated the clustering process using 10,000 bootstrap training data samples and a Gaussian Mixture Model to identify stable clusters representative of our dataset. Finally, we assessed the kinematic differences between the identified clusters using 1D statistical parametric mapping ANOVA. We then compared gait spatiotemporal and clinical characteristics between clusters using one-way ANOVA.

Results

We obtained five clusters: two clusters of neurotypical individuals (C1 and C2) and three clusters of individuals post-stroke (S1, S2, S3). C1 had kinematics that resembled the normative gait pattern. Individuals in C2 had a shorter stride time than C1. Individuals in S1 had mild impairment and walked with increased bilateral knee flexion during the loading response. Individuals in S2 had moderate impairment, were the slowest among the clusters, took shorter steps, had increased knee flexion during stance bilaterally and reduced paretic knee flexion during swing. Individuals in S3 had mild impairment, asymmetric swing time, had increased ankle abduction during the gait cycle and reduced dorsiflexion bilaterally during loading response and stance. Every individual was assigned to a cluster with a cluster membership likelihood above 93%.

Conclusions

Our results indicate that joint kinematics in individuals post-stroke are distinct from controls, even in those individuals with mild impairment. The three subgroups post-stroke showed distinct kinematic impairments during specific phases in the gait cycle, providing additional information to clinicians for gait retraining interventions.
Improving GWAS performance in underrepresented groups by appropriate modeling of genetics, environment, and sociocultural factors
Authors: Cataldo-Ramirez Chelsea C. , Lin Meng , Mcmahon Aislinn , Gignoux Christopher R. , Weaver Timothy D. , Henn Brenna M.
Published: October 2024

Genome-wide association studies (GWAS) and polygenic score (PGS) development are typically constrained by the data available in biobank repositories in which European cohorts are vastly overrepresented. Here, we increase the utility of non-European participant data within the UK Biobank (UKB) by characterizing the genetic affinities of UKB participants who self-identify as Bangladeshi, Indian, Pakistani, “White and Asian” (WA), and “Any Other Asian” (AOA), towards creating a more robust South Asian sample size for future genetic analyses. We assess the relationships between genetic structure and self-selected ethnic identities resulting in consistent patterns of clustering used to train a support vector machine (SVM). The SVM model was utilized to reassignn= 1,853 AOA and WA participants at the subcontinental level, and increase the sample size of the UKB South Asian group by 1,381 additional participants. We then leverage these samples to assess GWAS performance and PGS development. We further include environmental covariates in the height GWAS by implementing a rigorous covariate selection procedure, and compare the outputs of two GWAS models: GWASnulland GWASenv. We show that PGS performance derived from environmentally adjusted GWAS yields comparable prediction to PGS models developed with an order of magnitude larger training dataset (R2=0.021 vs 0.026). Models with 7 - 8 environmental covariates double the variance explained by PGS alone. In summary, we demonstrate how GWAS performance can be improved by leveraging ambiguous ethnicity codes, ancestry matched imputation panels, and including environmental covariates.
Comparative spatiotemporal single cell transcriptomes reveal rewiring of pre-existing regulations during emergence of Kranz anatomy in C4grasses
Authors: Zhao Caiyao , Yang Jianzhao , Ni Anting , Chen Hanyang , Su Hong , Cheng Yating , Li Xiaoya , Zhong Liyuan , Fang Dongming , Sun Hao-Ran , Yi Juan , Wang Ying , Wang Yanjie , Lyu Ming-ju Amy , Ni Xiaoxiang , Chen Lichuan , Li Huanjin , Yu Guichao , Wang Yumeng , Chen Rulei , Yu Hanyue , Shao Wenwen , Sun Haixi , Bai Yinqi , Li Chuanshun , Dong Yang , Zou Changsong , Tu Xiaoyu , Ma Shisong , Guo Xing , Zhang Gengyun , Wang Peng , Liu Huan , Wei Tong , Gu Ying , Xu Xun , Zhu Xin-Guang
Published: October 2024

Many of the world’s most productive food and bioenergy crops use C4photosynthesis, which have high photosynthetic efficiency due to a Kranz anatomy-based CO2concentrating mechanism. Here, we took a comparative transcriptomics approach using single cell spatial transcriptomes of leaf primordia for maize (Zea mays) and single cell RNA-seq (scRNA-seq) atlases of corresponding leaf tissues for three C4species (Zea mays,Sorghum bicolor,Setaria viridis) and one C3rice (Oryza sativa) to study regulatory networks involved in the development and evolution of Kranz anatomy. We show that the formation of Kranz anatomy involves extensive recruitment and modification of pre-existing regulatory modules, especially the SHR-SCR module and the auxin signaling pathway. Members of theINDETERMINATE DOMAIN(IDD) family transcription factors, includingIDD7andIDDP1, contribute to the modification of the involved modules. These extensive recruitment and modification of existing genetic regulatory programs underlie the repeated emergence of C4photosynthesis during evolution.
Unraveling the genetic landscape of susceptibility to multiple primary cancers
Authors: Middha Pooja , Kachuri Linda , Nierenberg Jovia L. , Graff Rebecca E. , Cavazos Taylor B. , Hoffmann Thomas J. , Zhang Jie , Alexeeff Stacey , Habel Laurel , Corley Douglas A. , Van Den Eeden Stephen , Kushi Lawrence H. , Ziv Elad , Sakoda Lori C. , Witte John S.
Published: October 2024

With advances in cancer screening and treatment, there is a growing population of cancer survivors who may develop subsequent primary cancers. While hereditary cancer syndromes account for only a portion of multiple cancer cases, we sought to explore the role of common genetic variation in susceptibility to multiple primary tumors. We conducted a cross-ancestry genome-wide association study (GWAS) and transcriptome-wide association study (TWAS) of 10,983 individuals with multiple primary cancers, 84,475 individuals with single cancer, and 420,944 cancer-free controls from two large-scale studies.

Our GWAS identified six lead variants across five genomic regions that were significantly associated (P<5×10-8) with the risk of developing multiple primary tumors (overall and invasive) relative to cancer-free controls (at 3q26, 8q24, 10q24, 11q13.3, and 17p13). We also found one variant significantly associated with multiple cancers when comparing to single cancer cases (at 22q13.1). Multi-tissue TWAS detected associations with genes involved in telomere maintenance in two of these regions (ACTRT3in 3q26 andSLKandSTN1in 10q24) and the development of multiple cancers. Additionally, the TWAS also identified several novel genes associated with multiple cancers, including two immune-related genes,IRF4andTNFRSF6B. Telomere maintenance and immune dysregulation emerge as central, common pathways influencing susceptibility to multiple cancers. These findings underscore the importance of exploring shared mechanisms in carcinogenesis, offering insights for targeted prevention and intervention strategies.
Dynamics and ecology of a multi-stage expansion of Oropouche virus in Brazil
Authors: Tegally Houriiyah , Dellicour Simon , Poongavanan Jenicca , Mavian Carla , Dor Graeme , Fonseca Vagner , Tagliamonte Massimiliano S. , Dunaiski Marcel , Moir Monika , Wilkinson Eduan , de Albuquerque Carlos Frederico Campelo , Frutuoso Livia C. V. ,   CLIMADE Consortium, Holmes Edward C. , Baxter Cheryl , Lessells Richard , Kraemer Moritz U.G. , Lourenço José , Alcantara Luiz Carlos Junior , de Oliveira Tulio , Giovanetti Marta
Published: October 2024

In March 2024, the Pan American Health Organization (PAHO) issued an alert in response to a rapid increase in Oropouche fever cases across South America. Brazil has been particularly affected, reporting a novel reassortant lineage of the Oropouche virus (OROV) and expansion to previously non-endemic areas beyond the Amazon Basin. Utilising phylogeographic approaches, we reveal a multi-scale expansion process with both short and long-distance dispersal events, and diffusion velocities in line with human-mediated jumps. We identify forest cover, banana and cocoa cultivation, temperature, and human population density as key environmental factors associated with OROV range expansion. Using ecological niche modelling, we show that OROV circulated in areas of enhanced ecological suitability immediately preceding its explosive epidemic expansion in the Amazon. This likely resulted from the virus being introduced into simultaneously densely populated and environmentally favourable regions in the Amazon, such as Manaus, leading to an amplified epidemic and spread beyond the Amazon. Our study provides valuable insights into the dispersal and ecological dynamics of OROV, highlighting the role of human mobility in colonisation of new areas, and raising concern over high viral suitability along the Brazilian coast.
Isoform-level analyses of 6 cancers uncover extensive genetic risk mechanisms undetected at the gene-level
Authors: Chang Yung-Han , Head S. Taylor , Harrison Tabitha , Yu Yao , Huff Chad D. , Pasaniuc Bogdan , Lindström Sara , Bhattacharya Arjun
Published: October 2024

Integrating genome-wide association study (GWAS) and transcriptomic datasets can help identify potential mediators for germline genetic risk of cancer. However, traditional methods have been largely unsuccessful because of an overreliance on total gene expression. These approaches overlook alternative splicing, which can produce multiple isoforms from the same gene, each with potentially different effects on cancer risk.

Here, we integrate genetic and multi-tissue isoform-level gene expression data from the Genotype Tissue-Expression Project (GTEx, N = 108-574) with publicly available European-ancestry GWAS summary statistics (all N > 20,000 cases) to identify both isoform- and gene-level risk associations with six cancers (breast, endometrial, colorectal, lung, ovarian, prostate) and six related cancer subtype classifications (N = 12 total). Compared to traditional methods leveraging total gene expression, directly modeling isoform expression through transcriptome-wide association studies (isoTWAS) substantially increases discovery of transcriptomic mechanisms underlying genetic associations. Using the same RNA-seq datasets, isoTWAS identified 164% more significant unique gene associations compared to TWAS (6,163 and 2,336, respectively), with isoTWAS-prioritized genes enriched 4-fold for evolutionarily-constrained genes (P = 6.1 × 10−13). isoTWAS tags transcriptomic associations at 52% more independent GWAS loci compared to TWAS across the six cancers. Additionally, isoform expression mediates an estimated 63% greater proportion of cancer risk SNP heritability compared to gene expression when evaluating cis-genetic influence on isoform expression. We highlight several notable isoTWAS associations that demonstrate GWAS colocalization at the isoform level but not at the gene level, including,CLPTM1L(lung cancer),LAMC1(colorectal), andBABAM1(breast). These results underscore the critical importance of modeling isoform-level expression to maximize discovery of genetic risk mechanisms for cancers.
Validation of the PREDICT Breast Version 3.0 Prognostic Tool in US Breast Cancer Patients
Authors: Hsiao Yi-Wen , Wishart Gordon C. , Pharoah Paul D.P. , Peng Pei-Chen
Published: October 2024

Background

PREDICT Breast v3 is the latest updated prognostication tool, developed from the breast cancer registry of approximately 35,000 women diagnosed between 2000 and 2018 in the United Kingdom. However, its performance in the United States (US) population is unknown. This study aims to validate PREDICT Breast v3 using newly released Surveillance, Epidemiology, and End Results (SEER) outcome data for US breast cancer patients and to address potential health disparities.

Methods

Over 860,000 female patients diagnosed between 2000 and 2018 with primary breast cancer and followed for at least 10 years were selected from the SEER database. Predicted and observed 10- and 15-year breast cancer-specific survival outcomes were compared for the overall cohort, stratified by estrogen receptor (ER) status, and predefined subgroups. Discriminatory accuracy was determined through the area under the receiver-operator curves (AUC).

Results

PREDICT Breast v3 demonstrated good calibration and discrimination for long-term breast cancer-specific mortality. It provided accurate mortality estimates (within a ±10% error range) across the entire US population for 10-year (−8% in ER-positive and 4% in ER-negative patients) and 15-year (−3 % in ER-positive and 5% in ER-negative patients) all-cause mortality, for both ER statuses. The model also showed good performance for 10- and 15-year all-cause mortality across the U.S. population, with AUC of 0.769 and 0.793 for ER-positive breast cancer as well as AUC of 0.738 and 0.746 for ER-negative breast cancer. However, recalibration is needed for specific groups, such as non-Hispanic Asian and non-Hispanic Black patients with ER-negative status.

Conclusions

PREDICT v3 accurately predicts 10- and 15-year overall survival in contemporary US breast cancer patients. Future work should focus on promoting equitable care by addressing disparities that are observed in predictive tools.
Notch, β-catenin and MAPK signaling segregate endoderm and mesoderm in the diploblastNematostella vectensis
Authors: Haillot Emmanuel , Lebedeva Tatiana , Steger Julia , Genikhovich Grigory , Montenegro Juan D. , Cole Alison G. , Technau Ulrich
Published: October 2024

Cnidaria are typically considered diploblastic (i.e. consisting of two germ layers) in contrast to their triploblastic sister clade, the Bilateria. However, a recent study suggested that sea anemones and other cnidarians have three segregated germ layer identities, corresponding to the bilaterian germ layers1. Here, we investigated, how the three germ layer identities are specified during early development of the sea anemoneNematostella vectensis. First, the mesodermal territory is specified at the animal pole at 6 hours postfertilization, followed by the specification of a ring of endodermal territory between mesoderm and ectoderm. We then assessed the role of β-catenin, MAPK and Notch signaling pathways during mesoderm and endoderm formation. Our results show that the mesoderm is initiated by MAPK signaling and simultaneously restricted to the future oral side by mutually exclusive nuclear β-catenin signaling. The mesodermal cells then express the Delta ligand, while the ectodermal cells express the Notch receptor. Inhibition of Notch signaling as well as ectopic expression of the Notch intracellular domain showed that endodermal tissue identity is induced by Notch signaling at the boundary between mesoderm and ectoderm. We propose a new model that outlines the different steps leading to the segregation of mesoderm and endoderm identities inNematostella, confirming the presence of 3 distinct germ layer identities in this cnidarian. Notably, the observed crosstalk of MAPK, β-catenin and Notch signaling in the specification of three germ layers inNematostellais highly reminiscent to early stage gastrulae of sea urchins suggesting that triploblasty may predate the split of cnidarians and bilaterians.
NINJ1 is a restriction factor for HSV-1 in mouse macrophages
Authors: Hartenian Ella , Agustoni Magalie , Broz Petr
Published: October 2024

Restriction factors block multiple stages of viral infection. Here we describe how NINJ1 controls HSV-1 infection of mouse macrophages, a key cell type during systemic and local acute infection. We observed thatNinj1−/–macrophages are more susceptible to infection than WT cells.Ninj1−/–macrophages exhibited earlier and stronger expression of all kinetic classes of viral proteins, resulting in higher production of infectious viral particles, with initial differences seen in the first few hours post infection. Given the important role of NINJ1 during cell death, we next investigated if NINJ1 restricts HSV-1 in a manner related to its role in cell death. However, infectedNinj1-deficient cells did not exhibit differences in cell death compared to WT controls at early time points in infection where we observe a difference in infection rates. Instead, the higher infection rate inNinj1−/–macrophages correlated to enhancement in the average numbers of viral particles entering each cell. Finally, we determined the consequences of the altered entry and found higher ISG RNA expression in infectedNinj1−/–cells, which we ascribe to both TLR signaling and STING-mediated recognition. Together, this indicates that the NINJ1 present on WT macrophages reduces HSV-1 entry, which has consequences for the inflammatory phenotype associated with HSV-1 infection.