bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic Insights into Sepsis: Mendelian Randomization Analysis of Cerebrospinal Fluid Metabolites
Authors: Xuan Xin , Huang Zhihao , Kong Zhiqian , Li Ruoyu , Li Jianfeng , Huang Haiyan
Published: October 2024

Background

Sepsis, a life-threatening response to infection leading to systemic inflammation and organ dysfunction, has been hypothesized to be influenced by metabolic alterations in cerebrospinal fluid (CSF). Despite extensive research, the specific metabolic pathways contributing to sepsis remain unclear. This study aims to elucidate the causal relationships between CSF metabolites and sepsis risk using Mendelian Randomization (MR), offering insights that could lead to novel therapeutic strategies.

Methods

We conducted a two-sample MR analysis using genetic variants as instrumental variables (IVs) to investigate 338 CSF metabolites identified through a genome-wide association study. Data on sepsis-related outcomes were extracted from the genome-wide association study (GWAS) catalog encompassing 486,484 individuals of European descent. IVs were rigorously selected based on stringent genetic association and linkage disequilibrium criteria. Statistical analyses, including inverse variance weighting (IVW) and weighted median methods, were performed using the 'TwoSampleMR' package in R software, supplemented by comprehensive sensitivity analyses to ensure the robustness of our findings.

Results

Our analysis identified 19 CSF metabolites causally associated with sepsis risk. Notably, metabolites such as 1-palmitoyl-2-stearoyl-gpc (16:0/18:0) and 2-hydroxyglutarate showed significant negative correlations with sepsis risk. The reverse MR analysis further revealed that sepsis could negatively impact certain CSF metabolite levels, particularly Ribonate, suggesting a bidirectional relationship. These relationships were substantiated by rigorous statistical testing and sensitivity analyses confirming the absence of horizontal pleiotropy and the stability of our results across various MR methods.

Conclusions

This study demonstrates significant causal associations between specific CSF metabolites and the risk of developing sepsis, highlighting the potential for these metabolites to serve as biomarkers or therapeutic targets. The bidirectional nature of these findings also suggests that sepsis itself may alter metabolic profiles, offering further avenues for intervention.
Activation of Wnt/β-catenin signalling by mutually exclusiveFBXW11andCTNNB1hotspot mutations drives salivary gland basal cell adenoma
Authors: Wong Kim , Bishop Justin A. , Weinreb Ilan , Motta Marialetizia , Del Castillo Velasco-Herrera Martin , Bellacchio Emanuele , Ferreira Ingrid , van der Weyden Louise , Boccacino Jacqueline M. , Rotundo Giovannina , Ciolfi Andrea , Cheema Saamin , Olvera-León Rebeca , Offord Victoria , Droop Alastair , Vermes Ian , Allgaeuer Michael , Hyrcza Martin , Anderson Elizabeth , Smith Katie , de Saint Aubain Nicolas , Mogler Carolin , Stenzinger Albrecht , Arends Mark J. , Brenn Thomas , Tartaglia Marco , Adams David J.
Published: October 2024

Wnt signalling must be ‘just right’ to promote tumour growth. Basal cell adenoma (BCA) and basal cell adenocarcinoma (BCAC) of the salivary gland are rare tumours that can be difficult to distinguish from each other and other salivary gland tumour subtypes. Due to their rarity, the genetic profiles of BCA and BCAC have not been extensively explored. Using whole-exome and transcriptome sequencing of BCA and BCAC cohorts, we identify a novel recurrentFBXW11missense mutation (p.F517S) in BCA, that was mutually exclusive with the previously reportedCTNNB1p.I35T gain-of-function (GoF) mutation. These driver events collectively accounted for 94% of BCAs.In vitro, mutant FBXW11 had a dominant negative affect, characterised by defective binding to β-catenin and the accumulation of β-catenin in cells. This was consistent with the nuclear expression of β-catenin observed in BCA cases harbouring theFBXW11p.F517S mutation and activation of the Wnt/β-catenin pathway. The genomic profiles of BCAC were distinct from BCA, with hotspotDICER1andHRASmutations and putative driver mutations affecting PI3K/AKT and NF-κB signalling pathway genes. A single BCAC, which may represent a malignant transformation of BCA, harboured the recurrentFBXW11mutation. These findings have important implications for the diagnosis and treatment of BCA and BCAC, which, despite histopathologic overlap, may be unrelated entities.
RBP4 functions as an antagonistic ligand of orphan DR6
Authors: Kim Taeyun , Lee Wonhee John , Nguyen Thy N. C. , Jang Juhee , Kim Kiwook , Kim Min-Sik , Seo Daeha , Lee Young-Sam , Lee Yun-Il
Published: October 2024

Death receptor (DR) is a unique transmembrane receptor mediating extrinsic factor-induced programmed cell death pathways. For most DRs, the regulatory mechanism has been revealed to involve agonistic death ligand (e.g., TRAIL, TNF-α)-driven receptor clustering and activation, offering an in-depth understanding of the mechanistic basis for cell death regulation and therapeutic strategies. However, only death receptor 6 (DR6) remains orphan, and its molecular mechanism is poorly understood. Here, we identified retinol binding protein 4 (RBP4), a major vitamin-A carrier protein, as an antagonistic ligand of DR6. Single-molecule photobleaching and single-receptor tracking analyses revealed that RBP4 drives DR6 dimerization on the plasma membrane to prevent DR6 prodegenerative heterointeractions and consequent neurodegenerative processes. DR6 homodimerization predominantly depends on an extracellular intrinsically disordered region, allowing the agonistic propensity of increasing Ca2+levels. Collectively, our study establishes the distinct molecular mechanism of DR6 and highlights the non-canonical role of RBP4 as a cell death regulator.
Conserved sites on the influenza H1 and H3 hemagglutinin recognized by human antibodies
Authors: Maurer Daniel P. , Vu Mya , Ramos Ana Sofia Ferreira , Dugan Haley L. , Khalife Paul , Geoghegan James C. , Walker Laura M. , Bajic Goran , Schmidt Aaron G.
Published: October 2024

Monoclonal antibodies (mAbs) targeting the influenza hemagglutinin (HA) have the potential to be used as prophylactics or templates for next-generation vaccines that provide broad protection. Here, we isolated broad, subtype-neutralizing mAbs from human B cells targeting the H1 or H3 HA head as well as a unique mAb targeting the stem. The H1 mAbs target the previously defined lateral patch epitope on H1 HAs and recognize HAs from 1933 to 2021 in addition to a swine H1N1 virus with pandemic potential. Using directed evolution, we improved the neutralization potency of these H1 mAbs towards a contemporary H1 strain. Using deep mutational scanning of four antigenically distinct H1N1 viruses, we identified potential viral escape pathways. For the H3 mAbs we used cryo-EM to define the targeted epitopes: one mAb recognizes the side of the H3 head, accommodating the N133 glycan and a pocket underneath the receptor binding site. The other H3 mAb recognizes an epitope in the HA stem that overlaps with previously characterized mAbs, but with distinct antibody variable genes and mode of recognition. Collectively, these mAbs identify common sites recognized by broad, subtype-specific mAbs that may be elicited by next-generation vaccines.
Genomes ofWiebesiafig wasps reveal the adaptation and codiversification in fig-fig wasp mutualism
Authors: Lo Bai-Wei , Lin Hsin-Fu , Kong Siu-Wah , Wu Wen-Jer , Wang Selina Cai-Ling , Lu Xuemei , Wang Hurng-Yi
Published: October 2024

Figs and fig wasps represent one of the most intimate examples of plant-pollinator coevolution. As figs diversified into geographically isolated populations, both figs and fig wasps underwent selective pressures driven by local adaptation and coevolution.Ficus pumilacomprises two ecologically distinct varieties: the creeping fig (F. pumilavar.pumila), which is widely distributed across the lowlands of East Asia, and the jelly fig (F. pumilavar.awkeotsang), endemic to Taiwan and found at mid-elevations. To elucidate how codiversification with fig hosts influences the evolutionary trajectories of fig wasps, we analyzed the genomes ofWiebesiasp. 2 and sp. 3, the respective pollinators of creeping fig and jelly fig. Our demographic analysis indicates that vicariance during the Last Glacial Period facilitated ecological differentiation between these two fig-fig wasp pairs. Through comparative and population genomic analyses, we identified selection signals linked to habitat adaptation, with evolutionary rates corresponding to the life history traits of their host figs. Variations in host preference behavior, chemosensory gene expression, and adaptive duplications in olfactory receptors highlight potential mechanisms for adaptation to host floral scents. These findings collectively underscore how the obligate mutualism between figs and their pollinating wasps allows the ecological traits and habitat preferences of fig hosts to shape the evolutionary pathways of their pollinators, leaving distinct molecular imprints in the fig wasp genomes. This study demonstrates the capacity of tightly intertwined life cycles between plants and pollinators to drive adaptation and diversification.
Degradation of fish food webs in the anthropocene
Authors: Carvajal-Quintero Juan D. , Dornelas Maria , Comte Lise , Herrrera-Pérez Juliana , Tedesco Pablo A. , Giam Xingli , Brose Ulrich , Chase Jonathan M.
Published: October 2024

The Anthropocene is marked by profound changes in biodiversity and the ecosystems in which species live1–4. A primary signature of this change is the often rapid change in species composition through time (i.e., species turnover) rather than changes in the numbers of species per se5–7. Less well known, however, is which types of species are ‘winning’ and which are ‘losing’ as ecosystems change through time8,9, as well as whether and how these changes influence higher-level processes in the food webs in which species are embedded10,11. Here, we combine a compilation of long-term observations of ∼15,000 freshwater and marine fish communities surveyed for 1949-2019 years, together with information about their diets and trophic status in order to evaluate how the food webs in which these fish communities are embedded are changing through time. We found widespread alteration to fish food web topology and functioning. This includes an increase in connectance and generalism in food webs, which has led to greater predation pressure, as indicated by higher diet overlap and increased prey vulnerability. We also identified a decrease in modularity, which has reduced the compartmentalization within local networks. These changes extend across the trophic structure of food webs, causing a cascading shift in the proportion of species across trophic levels. Our study highlights the complex responses of biodiversity change of fish food webs in the Anthropocene, which can ultimately influence the functions of these ecosystems and human well-being12,13.
Changes in the cellular composition of the endometrium during the implantation window are associated with recurrent pregnancy loss
Authors: Reddin Ian G. , Pearson-Farr Jennifer E. , Turaj Anna H. , Lim Sean H. , Lewis Rohan M. , Cheong Ying C , Cleal Jane K.
Published: October 2024

Recurrent pregnancy loss (RPL) affects 1-2% of women trying to conceive, yet in many cases the causes remain unclear. Endometrial function is central to the establishment and maintenance of pregnancy, and endometrial dysfunction may underlie RPL. A greater understanding of the endometrial cell populations and their interactions in women with and without RPL may identify markers of endometrial receptivity and the likelihood of pregnancy success. Single cell RNA sequencing was performed on RPL (n = 3) and control (n = 4) endometrial biopsies collected at days 21-24 of the menstrual cycle, the window of implantation. 10,022 cells were clustered and nine major individual cell types were characterised. Further analysis identified six distinct endometrial stromal cell (EnSCs) and three natural killer (NK) cell sub-populations. In RPL, there were changes in the abundance of specific endometrial stromal and NK cell subpopulations with associated differences in cellular communication between the cell types related to the Wnt pathway and angiogenesis. This is consistent with NK cell signalling orchestrating the difference in abundance of stromal cells and regulating processes needed for successful implantation. These changes in RPL endometrium provide further evidence for an endometrial cause of RPL and identify specific mechanisms for future study.
CRB2 Depletion Induces YAP Signaling and Disrupts Mechanosensing in Podocytes
Authors: Sun Yingyu , Kronenberg Nils M. , Sethi Sidharth K. , Dash Surjya N. , Kovalik Maria E. , Sempowski Benjamin , Strickland Shelby , Raina Rupresh , John Sperati C. , Tian Xuefei , Ishibe Shuta , Hall Gentzon , Gather Malte C.
Published: October 2024

Focal Segmental Glomerulosclerosis (FSGS) is a histologic lesion caused by a variety of injurious stimuli that lead to dysfunction/loss of glomerular visceral epithelial cells (i.e. podocytes). Pathogenic mutations in CRB2, encoding the type 1 transmembrane protein Crumb 2 Homolog Protein, have been shown to cause early-onset corticosteroid-resistant nephrotic syndrome (SRNS)/FSGS. Here, we identified a 2-generation East Asian kindred (DUK40595) with biopsy-proven SRNS/FSGS caused by a compound heterozygous mutation in CRB2 comprised of the previously described truncating mutation p.Gly1036_Alafs*43 and a rare 9-bp deletion mutation p.Leu1074_Asp1076del. Because compound heterozygous mutations involving the truncating p.Gly1036_Alafs*43 variant have been associated with reduced CRB2 expression in podocytes and autosomal recessive SRNS/FSGS, we sought to define the pathogenic effects of CRB2 deficiency in podocytes. We show that CRB2 knockdown induces YAP activity and target gene expression in podocytes. It upregulates YAP-mediated mechanosignaling and increases the density of focal adhesion and F-actin. Using Elastic Resonator Interference Stress Microscopy (ERISM), we demonstrate that CRB2 knockdown also enhances podocyte contractility in a substrate stiffness-dependent manner. The knockdown effect decreases with increasing substrate stiffness, indicating impaired mechanosensing in CRB2 knockdown cells at low substrate stiffness. While the mechanical activation of CRB2 knockdown cells is associated with increased YAP activity, the enhanced cell contractility is not significantly reduced by the selective YAP inhibitors K-975 and verteporfin, suggesting that multiple pathways may be involved in mechanosignaling downstream of CRB2. Taken together, these studies provide the first evidence that CRB2 deficiency may impair podocyte mechanotransduction via disruption of YAP signaling in podocytes.
In siliconanoscope to study the interplay of genome organization and transcription regulation
Authors: Gopi Soundhararajan , Brandani Giovanni B , Tan Cheng , Jung Jaewoon , Gu Chenyang , Mizutani Azuki , Ochiai Hiroshi , Sugita Yuji , Takada Shoji
Published: October 2024

In eukaryotic genomes, regulated access and communication between cis-regulatory elements (CREs) are necessary for enhancer-mediated transcription of genes. The molecular framework of the chromatin organization underlying such communication remains poorly understood. To better understand it, we develop a multiscale modeling pipeline to build near-atomistic models of the 200 kbNanoggene locus in mouse embryonic stem cells comprising nucleosomes, transcription factors, co-activators, and RNA polymerase II-Mediator complexes. By integrating diverse experimental data, including protein localization, genomic interaction frequencies, cryo-electron microscopy, and single-molecule fluorescence studies, our model offers novel insights into chromatin organization and its role in enhancer-promoter communication. The models equilibrated by high-performance molecular dynamics simulations span a scale of ∼350 nm, revealing an experimentally consistent local and global organization of chromatin and transcriptional machinery. Our models elucidate that the sequence-regulated chromatin accessibility facilitates the recruitment of transcription regulatory proteins exclusively at CREs, guided by the contrasting nucleosome organization compared to other regions. By constructing an experimentally consistent near-atomic model of chromatin in the cellular environment, our approach provides a robust framework for future studies on nuclear compartmentalization, chromatin organization, and transcription regulation.
Efficient Inference, Training, and Fine-tuning of Protein Language Models
Authors: Çelik Muhammed Hasan , Xie Xiaohui
Published: October 2024

Protein language models have shown great promise in predicting protein structure, function, and the effects of missense variants on protein fitness. However, their use has been limited by the substantial computational resources required. In this work, we focus on improving the computational efficiency of protein language models (PLMs), specifically the Evolutionary Scale Modeling (ESM) family, to increase the accessibility of PLMs. By implementing optimizations such as FlashAttention and Partition-Attention, a novel technique designed to handle proteins of variable length, we achieved a 16-fold speedup in inference time and reduced memory usage by 3 to 14 times for long proteins. Additionally, 4-bit quantization applied to billion-parameter models led to a 2 to 3 times reduction in memory consumption with minimal performance loss in the missense variant effect prediction task. Training efficiency was also improved, with a 6-fold reduction in runtime achieved through activation checkpointing and the DeepSpeed Zero-Offload strategy. For fine-tuning, we employed parameter-efficient methods, enabling state-of-the-art predictions of protein properties and functions by training only the model head or a small fraction of adapter weights. For instance, we achieved a Spearman’s correlation coefficient of 70% in melting point prediction and an 87% area under the precision-recall curve (AU-PRC) for transcription factor prediction. Our efficient ESM (ESME) implementation significantly lowers the barrier to using these powerful models, making them accessible to academic laboratories with limited computational resources. The ESME implementation is available on PyPI (pypi.org/project/esm-efficient) and GitHub (github.com/uci-cbcl/esm-efficient).
Divergent biosynthesis of monoterpene indole alkaloids from geissoschizine
Authors: Kamileen Mohamed O. , Hong Benke , Gase Klaus , Kunert Maritta , Caputi Lorenzo , Lichman Benjamin R. , O’Connor Sarah E.
Published: October 2024

Plants can generate structural diversity by enzymatic rearrangement of a central intermediate. 19E-geisssochizine is one such chemically versatile intermediate that plays a central role in the biosynthesis of monoterpene indole alkaloids such as strychnine, ibogaine and vinblastine. Here we report how 19E-geissoschizine undergoes oxidative transformations to generate four distinct alkaloid scaffolds through the action of three biosynthetic enzymes. Using in vitro enzymatic assays and gene silencing, we demonstrate how these three cytochrome P450 enzymes in the medicinal plantCatharanthus roseustransform 19E-geisssochzine intostrychnos, sarpagan, akuammiline-type, andmavacurane-type alkaloids. We use mutational analysis to show how minimal changes to the active site of these similar enzymes modulate product specificity. This work highlights how substrate reactivity and enzyme mutations work synergistically to generate chemical diversity.
The population structure of invasiveLantana camarais shaped by its mating system
Authors: Praveen P. , Gopal Rajesh , Ramakrishnan Uma
Published: October 2024

Over the last century, invasive species have emerged as an important driver of global biodiversity loss. Many invasive species have low genetic diversity in the invaded habitats, owing to the demographic bottleneck during introduction.Lantana camarais one of the hundred most problematic invasive species globally. Despite its ecological importance in many countries, our understanding of the genetic diversity patterns of this plant remains poor. Previous studies hypothesize that invasiveL. camarais a species complex with a hybrid origin, but this remains untested. We investigated the population genetic patterns of this invasive species by sampling 359 plants that represented a spectrum of flower colour variants across 36 locations, spanning most of the biogeographic regions across India. Analyses of the population structure using 19,008 SNPs revealed thatL. camarain India exhibits a strong genetic structure. Interestingly, the structuring pattern does not exhibit a strong correlation with geography. In the structure analysis, individuals with similar flower colours clustered together regardless of their location of origin. The genetic distance between most of the individuals was low, indicating the absence of multiple species. A high inbreeding coefficient and a low proportion of heterozygous sites observed suggested that the strong structure could be due to self-fertilization. Thus we infer thatL. camaraexists as homozygous inbred lines formed by self-fertilization and that these inbred lines could be associated with distinct flower colours. Together, this would explain the correlation between flower colour and genetic structure, and the lack of geographic structure. These results refute the argument thatL. camarais a species complex and emphasize the importance of the mating system in shaping the patterns of diversity in this invasive species. Our findings highlight a hitherto unknown role for mating systems in invasive species, furthering our understanding of evolution in invasive species.
Phylogenetic Study of Long Non-Coding RNANEAT1andMALAT1to Infer Structural-Functional Connection
Authors: Arkhipova Ksenia , Drukker Micha
Published: October 2024

NEAT1andMALAT1are the only two lncRNAs that utilise the tRNA-processing machinery for their maturation, coded very close to each other yet differing in function and evolutionary conservation. Here, we identifiedNEAT1andMALAT1orthologs in 545 mammals and studied their conservation patterns to gain functional insights. In the functional basis ofNEAT1Long, we found G-quadruplexes and short sequence motifs that interact with the DSHS family of proteins and TDP-43, as well as gene length and self-complementary regions that further stabilise paraspeckle integrity. We found that transposable elements play a crucial role inNEAT1evolution by contributing structures recognised by DSHS proteins. We identified theNEAT1Shortisoform in allNEAT1orthologs, and our results suggest its distinct functional role. Our findings also support the conservation of the isoform switch mechanism mediated by TDP-43. The function ofMALAT1is likely based on its highly conserved primary sequence, and we demonstrated the gene regions under stronger purifying selection. This is the first large-scale phylogenetic study ofNEAT1– a lncRNAs that lack sequence similarity between orthologs while maintaining functional and syntenic conservation.
Quantitative light element (sodium and potassium) profiling in plant tissues using monochromatic X-ray fluorescence analysis
Authors: Kahlon Parvinderdeep S. , Kokkinopoulou Pinelopi , Alfageme Silvia Bugallo , Leong Cheuk Ka , Chen Zewu , Testerink Christa , van der Ent Antony
Published: October 2024

Accurately determining the elemental composition of plant tissues is essential for physiological studies on plant stress, including salinity tolerance. However, high-throughput routine analysis of light elements (range of sodium to calcium) in plant samples is challenging due to the need for complete sample dissolution and expensive inductively coupled plasma-mass-spectrometry (ICP-MS) analysis. Lower costs method (ion chromatography, ion selective electrodes) exists, but also require sample dissolution and lack sensitivity for very small samples (<10 mg). This study reports on a new method for the quantitative analysis of light elements in plant tissues using monochromatic X-ray fluorescence (XRF) instrumentation and innovative sample preparation and mounting. We used this approach to assess elemental uptake, distribution, and accumulation inArabidopsis thalianaandOryza sativaplants subjected to salt stress. The method can be used on samples as small as 1 mg making it suitable for smallArabidopsis thalianaplants. We systematically evaluated different sample preparations methods, repeatability, and measurement times to confirm the robustness of the technique. The results show that the monochromatic XRF method delivers rapid, non-destructive, and extraction-free analysis, strongly correlating with ICP-MS acquired data. As such, the monochromatic XRF method is a reliable and efficient alternative for studying salinity tolerance ideally suited for investigating elemental composition of early plant developmental stages, offering new possibilities for research into early stimuli sensing, perception and nutrient efficiency.
Uncovering pre-sensitizing agents to FLT3 inhibitors in acute myeloid leukemia with ReSisTrace lineage tracing
Authors: Eriksson Johanna , Zheng Shuyu , Bao Jie , Dai Jun , Wang Wenyu , Vähärautio Anna , Tang Jing
Published: October 2024

While FLT3 inhibitors have significantly improved the treatment of aggressive FLT3-mutated acute myeloid leukemia (AML), the emergence of resistance remains as a major challenge. Here, we applied our recently developed single-cell lineage-tracing method ReSisTrace to identify cells that are pre-resistant or pre-sensitive to FLT3 inhibitors midostaurin and quizartinib in FLT3-ITD-positive AML. By comparing the gene expression profiles of these cells, we unraveled the transcriptional pre-resistance signatures, including G1 to S phase transition 1 (GSPT1) gene. Targeting GSPT1 with the small molecule CC-90009 exhibited strong synergistic effect when combined with FLT3 inhibitors in the FLT3-ITD-mutated MOLM-13 and MV4-11 cell lines and primary AML patient samples. Further, we identified novel compounds that induced transcriptomic changes opposite to the pre-resistance signatures, thereby driving cells to FLT3 inhibitor-sensitive states. Vistusertib (mTOR inhibitor), linsitinib (IGF1R and insulin receptor inhibitor), and meisoindigo (IGF1R and Src family kinase inhibitor), all inhibiting pathways parallel to or downstream of oncogenic FLT3 signaling, were predicted and validated to pre-sensitize the FLT3-ITD-mutated cell lines and primary cells to FLT3 inhibitors. Collectively, these findings demonstrate the validity of our lineage-tracing method in unveiling pre-existing transcriptional features of treatment vulnerability in hematological cancers, and elucidate novel strategies for enhancing FLT3 inhibitor treatment efficacy in FLT3-ITD-positive AML by preventing the emergence of treatment resistance.
IRE1-dependent GOLIM4 expression controls protein secretion to modulate glioblastoma cell adhesion and migration
Authors: Bakambamba Ketsia , Nivet Manon , Sauzay Chloé , Martin Sophie , Lafont Elodie , Négroni Luc , Chevet Eric , Avril Tony
Published: October 2024

One of the main glioblastoma (GB) features is the diffuse migration of the tumor cells within the surrounding brain parenchyma, rendering almost impossible the complete tumor resection and irradiation, leading to inexorable lethal relapse of the disease. In the past years, we demonstrated that IRE1α (hereafter IRE1), one of the Endoplasmic Reticulum (ER) stress sensors, plays a key role in GB biology by impacting on immune infiltration, angiogenesis and tumor cell migration/invasion, all these features being linked to an alteration of protein secretion. In the present study, we investigated if and how IRE1 could regulate the functionality of the secretory machinery in GB cells and identified GOLIM4, a Golgi-associated molecule whose expression is regulated downstream of IRE1 through the transcription of XBP1s. Interestingly, GOLIM4 silencing led to decreased surface expression of multiple molecules including MHC class I molecules, growth factor receptors (PDGFRA and IL13RA2) and proteins involved in cell-cell adhesion (CD44, CD54, NCAM1), adhesion to matrix (ITGB1) or cell migration (CD90) without alteration of their encoding transcripts’ expression levels. Moreover, GOLIM4 silencing phenotypically affected GB cell-cell adhesion and cell migration in multiple models. Overall, we have described a novel IRE1/XBP1s/GOLIM4 operon that controls the secretion of specific proteins and impacts the tumor aggressiveness.

Graphical abstract
Cannabidiol Toxicity Driven by Hydroxyquinone Formation
Authors: Montero Metzli I. , Rajaram Pravien S. , Alvarado Jose E. Zamora , McCloskey Kara E. , Baxter Ryan D. , Eguiluz Roberto C. Andresen
Published: October 2024

Oxidative byproducts of cannabidiol (CBD) are known to be cytotoxic. However, CBD susceptibility to oxidation and resulting toxicity dissolved in two common solvents, ethanol (EtOH) and dimethyl sulfoxide (DMSO), is seldom discussed. Furthermore, CBD products contain a wide range of concentrations, making it challenging to link general health risks associated with CBD cytotoxicity. Here, we report on the effect of CBD and CBD analogs dissolved in EtOH or DMSO at various concentrations. The cells used in these studies were human umbilical vascular endothelial cells (HUVECs). Our findings show that significant CBD oxidation of CBD to form cannabidiol-quinone (CBD-Q) and subsequent cytotoxicity, occurring at 10 µM concentration regardless of the solution delivery vehicle. Moreover, a new analog of CBD, cannabidiol-diacetate (CBD-DA), exhibits significantly more stability and reduced toxicity compared with CBD or CBD-Q. This knowledge is important for determining concentration-dependent health risks of complex cannabinoid mixtures and establishing legal limits.
Cooperation maximizes biodiversity
Authors: Godoy Oscar , Soler-Toscano Fernando , Portillo José R. , Suárez Antonio , Langa José A.
Published: October 2024

Cooperation, the mutual benefit that individuals of different species obtain when they interact together, is ubiquitous in nature. Despite their importance, most of all current ecological theories have been formalized focusing on negative interactions such as competition or predation. The role of cooperation, or other types of positive interactions including facilitation and mutualism, has not been fully addressed, or, if so, always in combination with negative interactions. This fact limits our understanding of the unique features by which cooperation as opposed to competition promotes biodiversity. To address this gap, we introduce here cooperation into structural stability, a general framework to understand how species interactions and environmental variability determine the long-term persistence of species within communities. Compared to a pure competitive case, cooperation promotes three distinctive features. First, cooperation increases the opportunities for species to coexist. This feature increases the persistence of species with contrasted phylogenetic, functional, and demographic strategies that the environment would otherwise filter. Second, cooperation creates intertwined biodiversity where the existence of some species begets the presence of others. Third, cooperation promotes multistability by changing the dynamics of community assembly due to variations in environmental conditions. In conclusion, we present a fully operational framework to understand the unique ecological roles of cooperation in nature. It indicates that cooperation as opposed to competition maximizes the maintenance of biodiversity.
Equi-Under-Dispersed Possion Distribution (EUPoisson)
Authors: Hassan Mohamed Y.
Published: October 2024

In this study, we propose an Equi-Under-dispersed Poisson distribution derived from a finite mixture of weighted Poisson distributions. This probability distribution is a simple, parsimonious, and flexible option suitable for modeling under-dispersed count data. It aims to overcome some of the weaknesses of existing methods in modeling Equi-Under-dispersed count data. Explicit expressions for the moment-generating function, mean, variance, and index of dispersion are derived. Real count data are used to compare its performance with that of the zero-inflated Poisson distribution and the finite mixture of Poisson distributions. Maximum likelihood estimation is implemented to estimate the parameters of the distribution, and goodness-of-fit statistical techniques are used to compare the fit of the competing distributions.
Adult diet strongly affects cuticle thickness and its injury resistance in the insectNarnia femorata(Hemiptera: Coreidae)
Authors: Greenway EV(Ginny) , Woodman Tamsin , Emberts Zachary , Chen Simon , Federle Walter , Miller Christine W.
Published: October 2024

Arthropods are the most diverse phylum on earth, accounting for up to 90% of animal species. The cuticular exoskeleton has played a vital role in their evolutionary success, but we know surprisingly little about the factors influencing its development, structure, and biomechanical properties. In this study, we examined whether and how nutrition affects the cuticle after an insect has completed its final molt into the adult stage. We found that a high-quality adult diet provided to the leaf-footed cactus bug,Narnia femorata(Hemiptera: Coreidae), over three weeks led to 4.1-times thicker cuticle with 3.7-times greater injury resistance relative to those that consumed a poor, but still ecologically relevant, diet. We further discovered that a high-quality adult diet allowed compensation for a sub-optimal juvenile diet. The cuticle of males was more injury resistant than that of females, as expected due to the aggressive male competition in this species. Altogether, our results show that, even after the final molt, nutrition can strongly influence the development and properties of the arthropod cuticle, a phenomenon that likely has drastic fitness-related consequences for locomotion, predator-prey interactions, and resource acquisition.
The maintenance of multiple ecDNA types in single cancer cells
Authors: Scanu Elisa , Werner Benjamin , Huang Weini
Published: October 2024

Extrachromosomal DNA (ecDNA) emerges as a crucial promoter of rapid intra-tumour heterogeneity and oncogene amplification, contributing to tumour progression and adaptability to resistance. Multiple types of ecDNA are often observed within the same cancer cell, promoting high levels of complexity. While the study of multiple ecDNA types is still in its early stages with exciting new clinical and experimental studies in human cancers, few theoretical models have been proposed to understand the mechanisms enabling the maintenance of multiple ecDNA types (mix cells). Here, based on our general framework of modeling multiple ecDNA types, we explore the conditions that allow for a stable coexistence of multiple ecDNA types within single cancer cells. We study how genetic mutations or phenotypic switching among different ecDNA types contribute to the maintenance of ecDNA diversity under different fitness regimes. We show that either positive epistasis or switching is required to stably maintain mix cell populations. Counter-intuitively, intermediate rather than high switching rates lead to the highest fraction of mix cells, which is further confirmed by our analysis of sub-population compositions, transition probabilities between pure and mix states as well as single-cell Shannon indices.
Discovery of Novel Targets for Important Human and Plant Fungal Pathogens via Automated Computational Pipeline HitList
Authors: Condon David E. , Schroeder Brenda K. , Rowley Paul A. , Ytreberg F. Marty
Published: October 2024

Fungi are a major threat to human health and agricultural productivity, causing 1.7 million human deaths and billions of dollars in crop losses and spoilage annually. While various antifungal compounds have been developed to combat these fungi in medical and agricultural settings, but there are concerns that treatment effectiveness is waning due to the emergence of acquired drug resistance and to novel pathogens. Effectiveness is further hampered due to the limited number of modes of action for available antifungal compounds.To develop new strategies for the control and mitigation of fungal disease and spoilage, new antifungals are needed with novel fungal-specific protein targets that can overcome resistance and prevent host toxicity. New antifungals can add new methods of targeting fungi that have no effective control measures. The increasing availability of complete genomes of pathogenic and spoilage fungi has enabled identification of novel protein and RNA targets essential for viability and not found in host plants or humans. In this study, an automated bioinformatics pipeline utilizing BLAST, ClustalΩ, and subtractive genomics was created and used to identify potential new targets for any system of hosts and pathogens with available genomic or proteomic data. This pipeline called HitList allowsin silicoscreening of thousands of possible targets. HitList was then used to generate a list of potential antifungal targets for the World Health Organization fungal priority pathogens list and the top 10 agricultural fungal pathogens. Known antifungal targets were found, validating the approach, and an additional eight novel protein targets were discovered that could be used for the rational design of antifungal compounds.
Heterogeneity Assessment and Protein Pathway Prediction via Spatial Lipidomic and Proteomic Correlation: Advancing Dry Proteomics concept for Human Glioblastoma Prognosis
Authors: Lagache Laurine , Zirem Yanis , Rhun Émilie Le , Fournier Isabelle , Salzet Michel
Published: October 2024

Prediction of proteins and associated biological pathways from lipid analyses via MALDI MSI is a pressing challenge. We introduced “dry proteomics,” using MALDI MSI to validate spatial localization of identified optimal clusters in lipid or protein imaging. Consistent cluster appearance across omics images suggests association with specific lipid and protein pathways, forming the basis of dry proteomics. The methodology was refined using rat brain tissue as a model, then applied to human glioblastoma, a highly heterogeneous cancer. Sequential tissue sections underwent omics MALDI MSI and unsupervised clustering. Differentiated lipid and protein clusters, with distinct spatial locations, were identified. Spatial omics analysis facilitated lipid and protein characterization, leading to a predictive model identifying clusters in any tissue based on unique lipid signatures and predicting associated protein pathways. Application to rat brain slices revealed diverse tissue subpopulations, including successfully predicted cerebellum areas. Similar analysis on 50 glioblastoma patients confirmed lipid-protein associations, correlating with patient prognosis.

GRAPHICAL ABSTRACT
Functional yeast promoter sequence design using temporal convolutional generative language models
Authors: Alsaggaf Ibrahim , Wan Cen
Published: October 2024

Promoter sequence design is the key to accurately control gene expression processes that play a crucial role in biological systems. Thanks to the recent community effort, we are now able to elucidate the associations between yeast promoter sequences and their corresponding expression levels using advanced deep learning methods. This milestone boosts the further development of many downstream biological sequence research tasks like synthetic DNA design. In this work, we propose a novel synthetic promoter sequence design method, namely Gen-DNA-TCN, which exploits a pre-trained sequence-to-expression predictive model to facilitate its temporal convolutional neural networks-based generative model training. A large-scale evaluation suggests that Gen-DNA-TCN successfully generated diverse synthetic promoter sequences that also encode similar distributions of transcription factor binding sites to real promoter sequences.
Annexin A6 modulates the secretion of pro-inflammatory cytokines and exosomes via interaction with SNAP23 in triple negative breast cancer cells
Authors: Sakwe Nobelle I. , Vuong Ngoc B. , Black Perrin J. , Ball Destiny D. , Thomas Portia , Beasley Heather K. , Hinton Antentor , Ochieng Josiah , Sakwe Amos M.
Published: October 2024

Pro-inflammatory cytokines are secreted via the classical pathway from secretory vesicles or the non-classical pathway via extracellular vesicles (EVs), that together, play critical roles in triple-negative breast cancer (TNBC) progression. Annexin A6 (AnxA6) is a Ca2+-dependent membrane-binding protein that in TNBC is implicated in cell growth and invasiveness. AnxA6 is associated with EVs, but whether it affects the secretion of proinflammatory cytokines and/or EVs remains to be fully elucidated. To assess if AnxA6 influences the secretion of cytokines and extracellular vesicles, we used cytokine arrays to analyze secreted factors in cleared culture supernatants from control AnxA6 expressing and AnxA6 downregulated MDA-MB-468 TNBC cells. This revealed the diminished secretion of monocyte chemoattractant protein 1 (MCP-1/CCL2), interleukin 8 (IL-8), dickkopf1 (DKK1), throbospondin-1 (TSP-1), and osteopontin (OPN) following AnxA6 downregulation. We also show that the secretion of small EVs is strongly reduced in AnxA6 downregulated cells and that upregulation of AnxA6 promoted the secretion of treatment was also associated with increased EVs associated Rab7, cholesterol, and MCP-1 levels. Moreover, cholesterol content in EVs was significantly higher in AnxA6-expressing cells than in AnxA6 downregulated cells and following chronic lapatinib induced upregulation of AnxA6. Mechanistically, we demonstrate that the secretion of MCP-1 and/or EVs is AnxA6 dependent and that this requires the translocation of AnxA6 to cellular membranes and its interaction with SNAP23. AnxA6 neutralizing antibodies strongly diminished the survival of AnxA6 low TNBC cells but had minimal effects on the survival of TNBC cells expressing relatively high levels of the protein. Together, these data suggest that AnxA6 facilitates the secretion of EVs and proinflammatory cytokines that may be critical for TNBC progression.
CXADR is a Human IgG Fc Receptor
Authors: Emig Christopher J. , Vitug Adela A.
Published: October 2024

CXADR is a membrane protein present in epithelial tight junctions and other tissues with a variety of known functions, in addition to its role as entry receptor for coxsackie B virus and adenovirus 2 and 5. We identified a previously unknown function of CXADR as a binding partner for human IgG but not IgA, IgE, IgM, or ScFv in a non paratope specific manner. Binding was specific to human and rabbit IgG, and not observed for mouse, rat, donkey, or goat IgG. Binding of Ig to CXADR is inhibited by FcBlock (BD), and is competitive with anti-Fc binding secondary antibodies, but not anti-Fab secondary antibodies, indicating that CXADR binds the Fc portion of IgG. CXADR, being a member of the immune superfamily of proteins, has similar structural homology to other Ig binding proteins, including Fc receptors. We conclude that CXADR has a previously unknown function as a human Fc receptor, serving as a direct link between the humoral adaptive immune system and many cell types in the human body previously unknown to express FcR.
Identification of immunogenic and cross-reactive chikungunya virus-specific CD4+T cell epitopes in chronic chikungunya viral arthritic disease in humans
Authors: Agarwal Rimjhim , Ha Calvin , Cortes Fernanda H. , Lee Yeji , Martínez-Pérez Amparo , Gálvez Rosa Isela , Castillo Izabella N. , Balmaseda Angel , Harris Eva , Romero-Vivas Claudia M , Premkumar Lakshmanane , Falconar Andrew K , Grifoni Alba , Sette Alessandro , Weiskopf Daniela
Published: October 2024

Chikungunya virus (CHIKV), a mosquito-borne alphavirus, causes acute febrile illness that can progress into chronic chikungunya virus disease (CHIKVD) marked by persistent debilitating arthralgia. At present, the exact cause of chronic CHIKVD is not understood, and in humans, the targets of CD4+T cells in CHIKV are currently unknown. Here, by stimulating peripheral blood mononuclear cells (PBMCs) collected from patients suffering from chronic CHIKVD with peptides spanning the entire CHIKV genome, we provide a comprehensive landscape of CHIKV CD4+T cell epitopes. We identified 123 novel CD4+T cell epitopes and three immunodominant regions in E1, nsP1 and CP proteins. The immunodominance of these E1, nsP1 and CP regions was mapped to optimal epitopes, characterized by the capacity to bind to many common HLA class II allelic variants. In addition, we designed and validated a new CHIKV-specific CD4+T cell epitope megapool, spanning both structural and non-structural proteins, which can be a useful tool to study CHIKV-specific T cell responses in small blood volumes, typically available in pediatric or clinical samples. Finally, byin silicoassessment of the conservation of the CHIKV proteome in a diverse set of alphaviruses, we defined CHIKV epitopes conserved across arthritogenic and encephalitic viruses. Overall, our work is the first to identify CD4+T cell targets of CHIKV in humans, expanding our capacity to study the role of T cells in CHIKV pathogenesis and mapping targets of alphaviruses for vaccine design.
Universal function of WRI1 involved in integrated regulation of multiple latex metabolism pathways inHevea brasiliensisandTaraxacum kok-saghyz
Authors: Fan Ruisheng , wan Jiong , Yang Wenfeng , Wei Fang , Gao Honghua , Qu Peng , Du Huabo , Qiu Jian
Published: October 2024

Hevea brasiliensisandTaraxacum kok-saghyzare sources of nature rubber (NR) and recent research has focused on finding a method to increase NR quality and production. NR consists mainly ofcis-1,4-polyisoprene, which is synthesized from sucrose by a series of reactions during carbon metabolism. WRINKLED1 (WRI1) is a transcription factor (TF) that coordinates many genes involved in carbon metabolism and lipid biosynthesis. Here, we isolated and characterized two orthologues ofWRIin rubber-producing plantsH. brasiliensisa andT. kok-saghyz, which are highly expressed in their latex. Subcellular localization and ectopic expression inArabidopsis thalianaindicated that the TFs,HbWRI1andTkWRI1, are involved in lipid accumulation. Overexpression ofHbWRI1andTkWRI1inT. kok-saghyzsubstantially enhanced NR quality and production, including dry rubber content, molecular weight, and the diameter of rubber particles in the latex. Conversely, they were decreased inTkWRI1repression. Furthermore, based on the activated expression in transgenicT. kok-saghyzlatex and the existence of AW-box element in the promoter regions, 16 direct downstream genes of HbWRI1 and TkWRI1 were identified by a dual-luciferase reporter assay and yeast one-hybrid assay, and their products were responsible for both NR biosynthesis and lipid metabolism. These results reveal a regulatory module that HbWRI1 and TkWRI1 TFs can positively regulate NR quality and production inT. kok-saghyzlatex by synergistically regulating the entire NR biosynthesis. This module is expected to be utilized to develop superior varieties to enhance NR quality and production.