bluuebunny/crossref_metadata_2025 huggingface dataset:
Widespread deviant patterns of heterozygosity in whole-genome sequencing due to autopolyploidy, repeated elements, and duplication
Authors: Dallaire Xavier , Bouchard Raphael , Hénault Philippe , Ulmo-Diaz Gabriela , Normandeau Eric , Mérot Claire , Bernatchez Louis , Moore Jean-Sébastien
Published: July 2023

Most population genomic tools rely on accurate SNP calling and filtering to meet their underlying assumptions. However, genomic complexity, due to structural variants, paralogous sequences and repetitive elements, presents significant challenges in assembling contiguous reference genomes. Consequently, short-read resequencing studies can encounter mismapping issues, leading to SNPs that deviate from Mendelian expected patterns of heterozygosity and allelic ratio. In this study, we employed the ngsParalog software to identify such deviant SNPs in whole-genome sequencing data from four species: Arctic Char (Salvelinus alpinus), Lake Whitefish (Coregonus clupeaformis), Atlantic Salmon (Salmo salar), and the American Eel (Anguilla rostrata), with low (2X) to intermediate (6X) coverage. The analyses revealed that deviant SNPs accounted for up to 62% of all SNPs in salmonid datasets and approximately 10% in the American Eel dataset. These deviant SNPs were particularly concentrated within repetitive elements and genomic regions that had recently undergone rediploidization in salmonids. Additionally, narrow peaks of elevated coverage were ubiquitous along all four reference genomes, encompassed most deviant SNPs and could be partially attributed to transposons and tandem repeats. Including these deviant SNPs in genomic analyses led to highly distorted site frequency spectra, apparent homogenization of populations and underestimating pairwise FSTvalues. Considering the widespread occurrence of deviant SNPs arising from a variety of source, their important impact in estimating population parameters, and the availability of effective tools to identify them, we propose that excluding deviant-SNPs from WGS datasets is required to improve genomic inferences for a wide range of taxa and sequencing depths.

Significance: Genomes can be very repetitive and hard to assemble into a reference, which can lead to biases when genotyping genetic markers in complex genomic regions. Here, we draw attention to this issue in various whole-genome datasets and validate a method to identify problematic SNPs at low coverage. We also explore processes creating such SNPs and their consequences on common population genomics analyses.
Transfer learning to leverage larger datasets for improved prediction of protein stability changes
Authors: Dieckhaus Henry , Brocidiacono Michael , Randolph Nicholas , Kuhlman Brian
Published: July 2023

Amino acid mutations that lower a protein’s thermodynamic stability are implicated in numerous diseases, and engineered proteins with enhanced stability are important in research and medicine. Computational methods for predicting how mutations perturb protein stability are therefore of great interest. Despite recent advancements in protein design using deep learning,in silicoprediction of stability changes has remained challenging, in part due to a lack of large, high-quality training datasets for model development. Here we introduce ThermoMPNN, a deep neural network trained to predict stability changes for protein point mutations given an initial structure. In doing so, we demonstrate the utility of a newly released mega-scale stability dataset for training a robust stability model. We also employ transfer learning to leverage a second, larger dataset by using learned features extracted from a deep neural network trained to predict a protein’s amino acid sequence given its three-dimensional structure. We show that our method achieves competitive performance on established benchmark datasets using a lightweight model architecture that allows for rapid, scalable predictions. Finally, we make ThermoMPNN readily available as a tool for stability prediction and design.
Genetic Architectures of Medical Images Revealed by Registration and Fusion of Multiple Modalities
Authors: Friedman Sam Freesun , Moran Gemma Elyse , Rakic Marianne , Phillipakis Anthony
Published: July 2023

The advent of biobanks with vast quantities of medical imaging and paired genetic measurements creates huge opportunities for a new generation of genotype-phenotype association studies. However, disentangling biological signals from the many sources of bias and artifacts remains difficult. Using diverse types of medical imaging (i.e. MRIs, ECGs and DXAs), we develop registered and cross-modal generative models. In all cases, we show how registration, both spatial and temporal, guided by domain knowledge or learned de novo, uncovers rich biological information. Remarkably, our findings demonstrate that even extremely lossy transformations, such as registering images onto a single 1D curve (e.g. a circle), can yield robust signals. Conversely, we demonstrate that increasing data dimensionality by integrating multiple modalities can also result in richer representations. Through genome- and phenome-wide association studies (GWAS and PheWAS) of learned embeddings, we uncover significantly more associations with registered and fused modalities than with equivalently trained and sized representations learned from native coordinate spaces. Our findings systematically reveal the crucial role registration plays in enhancing the characterization of physiological states across a broad range of medical imaging data types.
Correlations reveal the hierarchical organization of networks with latent binary variables
Authors: Häusler Stefan
Published: July 2023

Deciphering the functional organization of large biological networks is a major challenge for current mathematical methods. A common approach is to decompose networks into largely independent functional modules, but inferring these modules and their organization from network activity is difficult, given the uncertainties and incompleteness of measurements. Typically, some parts of the overall functional organization, such as intermediate processing steps, are latent. We show that the hidden structure can be determined from the statistical moments of observable network components alone, as long as the functional relevance of the network components lies in their mean values and the mean of each latent variable maps onto a scaled expectation of a binary variable. Whether the function of biological networks permits a hierarchical modularization can be falsified by a correlation-based statistical test that we derive. We apply the test to three biological networks at different spatial scales, i.e., gene regulatory networks, dendrites of pyramidal neurons, and networks of spiking neurons.
Clade-wise alignment integration improves co-evolutionary signals for protein-protein interaction prediction
Authors: Fang Tao , Szklarczyk Damian , Hachilif Radja , von Mering Christian
Published: July 2023

Background

Protein-protein interactions play essential roles in almost all biological processes. The binding interfaces between interacting proteins impose evolutionary constraints, leading to co-evolutionary signals that have successfully been employed to predict protein interactions from multiple sequence alignments (MSAs). During the construction of MSAs for this purpose, critical choices have to be made: how to ensure the reliable identification of orthologs, how to deal with paralogs, and how to optimally balance the need for large alignments versus sufficient alignment quality.

Results

Here, we propose a divide-and-conquer strategy for MSA generation: instead of building a single, large alignment for each protein, multiple distinct alignments are constructed, each covering only a single clade in the tree of life. Co-evolutionary signals are searched separately within these clades, and are only subsequently integrated into a final interaction prediction using machine learning. We find that this strategy markedly improves overall prediction performance, concomitant with better alignment quality. Using the popular DCA algorithm to systematically search pairs of such alignments, a genome-wide all-against-all interaction scan in a bacterial genome is demonstrated.

Conclusions

Given the recent successes of AlphaFold in predicting protein-protein interactions at atomic detail, a discover-and-refine approach is proposed: our method could provide a fast and accurate strategy for pre-screening the entire genome, submitting to AlphaFold only promising interaction candidates - thus reducing false positives as well as computation time.
Actin-Driven Nanotopography Promotes Stable Integrin Adhesion Formation in Developing Tissue
Authors: Chen Tianchi , Huertas Fernández-Espartero Cecilia , Illand Abigail , Tsai Ching-Ting , Yang Yang , Klapholz Benjamin , Jouchet Pierre , Fabre Mélanie , Rossier Olivier , Cui Bianxiao , Lévêque-Fort Sandrine , Brown Nicholas H. , Giannone Grégory
Published: July 2023

Morphogenesis requires building stable macromolecular structures from highly dynamic proteins. Muscles are anchored by long-lasting integrin adhesions to resist contractile force. However, the mechanisms governing integrin diffusion, immobilization, and activation within developing tissues remain elusive. Here, we show that actin polymerisation-driven membrane protrusions form nanotopographies that enable strong adhesion at Drosophila muscle attachment sites (MAS). Super-resolution microscopy revealed that integrins assemble adhesive belts around Arp2/3-dependent actin protrusions, forming invadosome-like structures with membrane nanotopographies. Single protein tracking showed that, during MAS development, integrins became immobile and confined within diffusion traps formed by the membrane nanotopographies. Actin filaments also displayed restricted motion and confinement, indicating strong mechanical connection with integrins. Using isolated muscles cells, we show that substrate nanotopography, rather than rigidity, drives adhesion maturation by regulating actin protrusion, integrin diffusion and immobilization. These results thus demonstrate that actin-polymerisation driven membrane protrusions are essential for the formation of strong integrin adhesions sites in the developing embryo, and highlight the important contribution of geometry to morphogenesis.
The shared ancestry between the C9orf72 hexanucleotide repeat expansion and intermediate-length alleles using haplotype sharing trees and HAPTK
Authors: Rautila Osma S. , Kaivola Karri , Rautila Harri , Hokkanen Laura , Launes Jyrki , Strandberg Timo E. , Laaksovirta Hannu , Palmio Johanna , Tienari Pentti J.
Published: July 2023

The C9orf72 hexanucleotide repeat expansion (HRE) is a common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The inheritance is autosomal dominant, but a high proportion of cases are sporadic. One possible explanation isde novoexpansions of unstable intermediate-length alleles (IAs). Using haplotype sharing trees (HST) with the novel haplotype analysis tool kit (HAPTK), we derived majority-based ancestral haplotypes of HRE carriers and discovered that IAs containing ≥18-20 repeats share large haplotypes in common with the HRE. Using HSTs of HRE and IA carriers, we demonstrate that the longer IA haplotypes are largely indistinguishable from HRE haplotypes. These analysis tools allow physical understanding of the haplotype blocks shared with the ancestral haplotype. Our results demonstrate that the haplotypes with longer IAs belong to the same pool of haplotypes as the HRE and suggest that longer IAs represent potential premutation alleles.
Predictive microbial community changes across a temperature gradient
Authors: Sun Xin , Folmar Jacquelyn , Favier Ariel , Pyenson Nora , Sanchez Alvaro , Rebolleda-Gomez María
Published: July 2023

A central challenge in community ecology is predicting the effects of abiotic factors on community assembly. In particular, microbial communities play a central role in the ecosystem, but we do not understand how changing factors like temperature are going to affect community composition or function. One of the challenges is that we do not understand the mechanistic impacts of temperature on different metabolic strategies, nor how this metabolic plasticity could impact microbial interactions. Dissecting the contribution of environmental factors on microbial interactions in natural ecosystems is hindered by our understanding of microbial physiology and our ability to disentangle interactions from sequencing data. Studying the self-assembly of multiple communities in synthetic environments, here we are able to predict changes in microbial community composition based on metabolic responses of each functional group along a temperature gradient. This research highlights the importance of metabolic plasticity and metabolic trade-offs in predicting species interactions and community dynamics across abiotic gradients.
Structure and function of bacterial YeeE-YeeD complex in thiosulfate uptake pathway
Authors: Ikei Mai , Miyazaki Ryoji , Monden Keigo , Naito Yusuke , Takeuchi Azusa , Takahashi Yutaro S. , Tanaka Yoshiki , Murata Keina , Mori Takaharu , Ichikawa Muneyoshi , Tsukazaki Tomoya
Published: July 2023

Uptake of thiosulfate ions as an inorganic sulfur source from the environment is important for bacterial sulfur assimilation. Recently, a selective thiosulfate uptake pathway involving a membrane protein YeeE (TsuA) inEscherichia coliwas characterized. YeeE-like proteins are conserved in some bacteria, archaea, and eukaryotes. However, the precise function of YeeE, along with its potential partner protein in the thiosulfate ion uptake pathway, remained unclear. Here, we assessed selective thiosulfate transport viaSpirochaeta thermophilaYeeE in vitro and characterizedE. coliYeeD (TsuB) as an adjacent and essential protein for YeeE-mediated thiosulfate uptake in vivo. We further showed thatS. thermophilaYeeD possesses thiosulfate decomposition activity and that a conserved cysteine in YeeD was modified to several forms in the presence of thiosulfate. Finally, the crystal structures ofS. thermophilaYeeE-YeeD fusion proteins at 3.34-Å and 2.60-Å resolutions revealed their interactions. The association was evaluated by a binding assay using purifiedS. thermophilaYeeE and YeeD. Based on these results, a model of the sophisticated uptake of thiosulfate ions by YeeE and YeeD is proposed.

125-character sentence

The structural study of the YeeE-YeeD membrane protein complex provides insight into the thiosulfate uptake and degradation mechanism.
Dynamic simulations of feeding and respiration of the early Cambrian periderm-bearing cnidarian polyps
Authors: Zhang Yiheng , Wang Xing , Han Jian , Xiao Juyue , Yong Yuanyuan , Yu Chiyang , Yue Ning , Sun Jie , He Kaiyue , Hao Wenjing , Zhang Tao , Wang Bin , Wang Deng , Yang Xiaoguang
Published: July 2023

Although fossil evidence suggests the existence of an early muscular system in the ancient cnidarian jellyfish from the early Cambrian Kuanchuanpu biota (ca.535 Ma), south China, the mechanisms underlying the feeding and respiration of the early jellyfish are conjectural. Recently, the polyp inside the periderm of olivooids was demonstrated to be a calyx-like structure, most likely bearing short tentacles and bundles of coronal muscles at the edge of the calyx, thus presumably contributing to feeding and respiration. Here, we simulate the contraction and expansion of the microscopic periderm-bearing olivooidQuadrapyrgitesvia the fluid-structure interaction computational fluid dynamics (CFD) method to investigate their feeding and respiratory activities. The simulations show that the rate of water inhalation by the polyp subumbrella is positively correlated with the rate of contraction and expansion of the coronal muscles, consistent with the previous feeding and respiration hypothesis. The dynamic simulations also show that the frequent inhalation/exhalation of water through the periderm polyp expansion/contraction conducted by the muscular system ofQuadrapyrgitesmost likely represents the ancestral feeding and respiration patterns of Cambrian sedentary medusozoans that predated the rhythmic jet-propelled swimming of the modern jellyfish. Most importantly for these Cambrian microscopic sedentary medusozoans, the increase of body size and stronger capacity of muscle contraction may have been indispensable in the stepwise evolution of active feeding and subsequent swimming in a higher flow (or higher Reynolds number) environment.

Impact statement

To the best of our knowledge, our study is the first to simulate the feeding and respiration patterns ofQuadrapyrgitesby introducing a dynamic fluid-structure coupling method, revealing the relationship between the ancient medusozoans and modern jellyfish.
mAFiA: Detecting m6A at single-molecular resolution via direct-RNA sequencing
Authors: Chan Adrian , Naarmann-de Vries Isabel S. , Scheitl Carolin P. M. , Höbartner Claudia , Dieterich Christoph
Published: July 2023

Direct-RNA sequencing offers the possibility to simultaneously identify canonical bases and epi-transcriptomic modifications in each single RNA molecule. Thus far, the development of computational methods has been hampered by the lack of biologically realistic training data that carries modification labels at molecular resolution. Here, we report on the synthesis of such samples and the development of a bespoke algorithm that accurately detects single m6A nucleotides on single molecules in both synthetic RNAs and natural mRNA.
Circadian proteomics reveal rampant tuning of post-transcriptional apparatus byChlamydomonasclock
Authors: Jadhav Dinesh Balasaheb , Roy Sougata
Published: July 2023

Timing of biological processes enable organisms to sustain the diurnal fluctuations resulting from earth’s rotation. Circadian clocks execute this temporal regulation by modulating temporal expression of genes. Clock regulation of mRNAs was envisioned as the primary driver of daily rhythms. However, mRNA oscillations often don’t concur with the downstream protein oscillations. To assess the contribution from post-transcriptional processes, we quantitatively probed theChlamydomonasproteome for two circadian cycles. Our study suggests rampant role of posttranscriptional processes in clock regulation ofChlamydomonasmetabolism. We quantified >1000 proteins, half of which demonstrate circadian rhythms. Among these rhythmic proteins, >40% originate from non-rhythmic mRNAs and > 90% peak around midday or midnight. Accumulation rhythms of proteins rather than their encoding mRNAs shows extreme coordination. We uncovered new rhythms and accounted for physiological rhythms whose mechanistic details remained undocumented from earlier transcriptomic studies. We envisage our study will refine and enrich the evaluation of temporal metabolic processes inChlamydomonas.Owing toChlamydomonas’sunique phylogeny this study can lead to new insights into evolution of clock regulation across kingdoms.
Fruitless mating with the exes: the irreversible parthenogenesis in a stick insect
Authors: Nozaki Tomonari , Chikami Yasuhiko , Yano Koki , Sato Ryuta , Suetsugu Kenji , Kaneko Shingo
Published: July 2023

Parthenogenetic lineages, common in many animals, have sparked debate about their evolutionary persistence. While asexuality is expected to ensure reproductive assurance and provide a demographic advantage, parthenogens should suffer from the lack of gene shuffling with other individuals. On the other hand, occasional sexual reproduction has been theoretically predicted to be enough to mitigate the long-term costs of parthenogenesis. Recent studies have revealed instances of cryptic sex in some old parthenogenetic lineages, which is most likely mediated by rarely occurring males. Unlike female traits that rapidly become vestigial under asexuality, traits in males have been predicted to slowly decay due to the accumulation of neutral mutations over long evolutionary times. In fact, rare males often retain sexual functions, raising questions about the asexuality of these long-standing parthenogenetic lineages. Here, we intensively examined the possibility of sexual reproduction in the Japanese common stick insect,Ramulus mikado, which was also suggested to be an old parthenogen in our previous work. While asexual female reproduction appears to be quite predominant throughout Japan, we fortunately obtained the rare males from the field. These males exhibited typical stick insect male morphology and engaged in mating behaviors with conspecific females. However, no paternal-specific alleles were detected in the offspring; all embryos showed genotypes identical to their mothers. Our histological observations on a few males revealed that they had no sperm in their reproductive organs, although the degree of decay may be different among the lineages. We also found that females have sexual organs with signs of degeneration. All these results demonstrate the irreversible asexual reproduction ofR. mikadoand indicate their long history as a parthenogenetic species. Our present study provides unique insights into the maintenance of parthenogenesis and degenerative evolution of sexual traits in ancient asexual lineages.
Heterogenous Biofilm Mass-Transport Model Replicates Periphery Sequestration of Antibiotics inP. aeruginosaPAO1 Microcolonies
Authors: Prince Joshua , Jones A-Andrew D.
Published: July 2023

1

A spatiotemporal model for antibiotic accumulation in bacterial biofilm microcolonies which leverages heterogenous porosity and attachment site profiles replicated the periphery sequestration phenomena reported in prior experimental studies onPseudomonas aeruginosa PAO1biofilm cell clusters. TheseP. aeruginosacell clusters arein vitromodels of the chronicP. aeruginosainfections found in adult cystic fibrosis patients, which display resistance to antibiotic treatments, leading to exacerbated morbidity and mortality. This resistance has been partially attributed to periphery sequestration, where antibiotics are unable to penetrate biofilm cell clusters. The underlying physical phenomena driving this periphery sequestration have not been definitively established. This paper introduces mathematical models to account for two proposed physical phenomena driving periphery sequestration: biofilm matrix attachment and volume-exclusion due to variable biofilm porosity. An antibiotic accumulation model which incorporated these phenomena was able to better fit observed periphery sequestration data compared to previous models.
Global Pannexin 1-deletion increases tumor-infiltrating lymphocytes in the BRAF/Pten mouse melanoma model
Authors: Sanchez-Pupo Rafael E. , Finch Garth A. , Johnston Danielle E. , Craig Heather , Abdo Rober , Barr Kevin , Kerfoot Steven , Dagnino Lina , Penuela Silvia
Published: July 2023

Immunotherapies for malignant melanoma seek to boost the anti-tumoral response of CD8+T cells but have a limited patient response rate, in part due to limited tumoral immune cell infiltration. Genetic or pharmacological inhibition of Pannexin 1 (PANX1) channel-forming protein is known to decrease melanoma cell tumorigenic propertiesin vitroandex vivo. Here, we crossedPanx1knockout (Panx1−/−) mice with the inducible melanoma model:BrafCA,PtenloxP,Tyr::CreERT2(BPC). We found that deleting thePanx1gene in mice does not reduce BRAF(V600E)/Pten-driven primary tumor formation or improve survival. However, BPC-Panx1−/-mice tumors exhibited a significant increase in infiltration of CD8+T lymphocytes with no changes in the expression of early T cell activation marker CD69, LAG-3 checkpoint receptor or PD-L1 in tumors when compared to BPC-Panx1+/+genotype. Our results suggest that although aPanx1deletion does not overturn the aggressiveBRAF/Pten-driven melanoma progressionin vivo, it does increase the infiltration of effector immune T cell populations in the tumor microenvironment. We propose that PANX1-targeted therapy could be explored as a strategy to increase tumor-infiltrating lymphocytes to boost anti-tumor immunity.
Look4LTRs: A Long terminal repeat retrotransposon detection tool capable of cross species studies and discovering recently nested repeats
Authors: Garza Anthony B. , Lerat Emmanuelle , Girgis Hani Z.
Published: July 2023

Plant genomes include large numbers of transposable elements. One particular type of these elements is flanked by two Long Terminal Repeats (LTRs) and can translocate using RNA. Such elements are known as LTR-retrotransposons; they are the most abundant type of transposons in plant genomes. They have many important functions involving gene regulation and the rise of new genes and pseudo genes in response to severe stress. Additionally, LTR-retrotransposons have several applications in biotechnology. Due to the abundance and the importance of LTR-retrotransposons, multiple computational tools have been developed for their detection. However, none of these tools take advantages of the availability of related genomes; they process one chromosome at a time. Further, recently nested LTR-retrotransposons (multiple elements of the same family are inserted into each other) cannot be annotated accurately — or cannot be annotated at all — by the currently available tools. Motivated to overcome these two limitations, we builtLook4LTRs, which can annotate LTR-retrotransposons in multiple related genomes simultaneously and discover recently nested elements. The methodology ofLook4LTRsdepends on techniques imported from the signal-processing field, graph algorithms, and machine learning with a minimal use of alignment algorithms. Four plant genomes were used in developingLook4LTRsand eight plant genomes for evaluating it in contrast to three related tools.Look4LTRsis the fastest while maintaining better or comparable F1 scores (the harmonic average of recall and precision) to those obtained by the other tools. Our results demonstrate the added benefit of annotating LTR-retrotransposons in multiple related genomes simultaneously and the ability to discover recently nested elements. Expert human manual examination of six elements — not included in the ground truth — revealed that three elements belong to known families and two elements are likely from new families. With respect to examining recently nested LTR-retrotransposons, three out of five were confirmed to be valid elements.Look4LTRs— with its speed, accuracy, and novel features — represents a true advancement in the annotation of LTR-retrotransposons, opening the door to many studies focused on understanding their functions in plants.
The predicted acetoin dehydrogenase pathway represses sporulation ofClostridioides difficile
Authors: Wetzel Daniela , Rizvi Arshad , Edwards Adrianne N. , McBride Shonna M.
Published: July 2023

Clostridioides difficileis a major gastrointestinal pathogen that is transmitted as a dormant spore. As an intestinal pathogen,C. difficilemust contend with variable environmental conditions, including fluctuations in pH and nutrient availability. Nutrition and pH both influence growth and spore formation, but how pH and nutrition jointly influence sporulation are not known. In this study, we investigated the dual impact of pH and pH-dependent metabolism onC. difficilesporulation. Specifically, we examined the impacts of pH and the metabolite acetoin onC. difficilegrowth and sporulation. We found that expression of the predicted acetoin dehydrogenase operon,acoRABCL, was pH-dependent and regulated by acetoin. Regulation of theC. difficile acolocus is distinct from other characterized systems and appears to involve a co-transcribed DeoR-family regulator rather than the sigma54-dependent activator. In addition, anacoAnull mutant produced significantly more spores and initiated sporulation earlier than the parent strain. However, unlike other Firmicutes, growth and culture density ofC. difficilewas not increased by acetoin availability or disruption of theacopathway. Together, these results indicate that acetoin, pH, and theacopathway play important roles in nutritional repression of sporulation inC. difficile, but acetoin metabolism does not support cell growth as a stationary phase energy source.

IMPORTANCE

Clostridioides difficile,orC. diff, is an anaerobic bacterium that lives within the gut of many mammals and causes infectious diarrhea.C. difficileis able to survive outside of the gut and transmit to new hosts by forming dormant spores. It is known that the pH of the intestine and the nutrients available both affect the growth and sporulation ofC. diffiicile,but the specific conditions that result in sporulation in the host are not clear. In this study, we investigated how pH and the metabolite acetoin affect the ability ofC. difficileto grow, proliferate, and form spores. We found that a mutant lacking the predicted acetoin metabolism pathway form more spores, but their growth is not impacted. These results show thatC. difficileuses acetoin differently than many other species and that acetoin has an important role as an environmental metabolite that influences spore formation.
A Non-Coding Variant inSLC15A4Modulates Enhancer Activity and Lysosomal Deacidification Linked to Lupus Susceptibility
Authors: Singh Manish Kumar , Maiti Guru Prashad , Reddy-Rallabandi HariKrishna , Fazel-Najafabadi Mehdi , Looger Loren L. , Nath Swapan K.
Published: July 2023

Systemic lupus erythematosus (SLE) is a complex autoimmune disease with a strong genetic basis. Despite the identification of several single nucleotide polymorphisms (SNPs) near theSLC15A4gene that are significantly associated with SLE across multiple populations, specific causal SNP(s) and molecular mechanisms responsible for disease susceptibility are unknown. To address this gap, we employed bioinformatics, expression quantitative trait loci (eQTLs), and 3D chromatin interaction analysis to nominate a likely functional variant, rs35907548, in an active intronic enhancer ofSLC15A4. Through luciferase reporter assays followed by chromatin immunoprecipitation (ChIP)-qPCR, we observed significant allele-specific enhancer effects of rs35907548 in diverse cell lines. The rs35907548 risk allele T is associated with increased regulatory activity and target gene expression, as shown by eQTLs and chromosome conformation capture (3C)-qPCR. The latter revealed long-range chromatin interactions between the rs35907548 enhancer and the promoters ofSLC15A4, GLTLD1, and an uncharacterized lncRNA. The enhancer-promoter interactions and expression effects were validated by CRISPR/Cas9 knock-out (KO) of the locus in HL60 promyeloblast cells. KO cells also displayed dramatically dysregulated endolysosomal pH regulation. Together, our data show that the rs35907548 risk allele affects multiple aspects of cellular physiology and may directly contribute to SLE.
Unraveling cell differentiation mechanisms through topological exploration of single-cell developmental trajectories
Authors: Flores-Bautista Emanuel , Thomson Matt
Published: July 2023

Understanding the circuits that control cell differentiation is a fundamental problem in developmental biology. Single-cell RNA sequencing has emerged as a powerful tool for investigating this problem. However, the reconstruction of developmental trajectories is based on the assumption that cell states traverse a tree-like structure, which may bias our understanding of critical developmental mechanisms. To address this limitation, we developed a framework, TopGen, that enables identifying topological signatures of functional biological circuits as persistent homology groups in transcriptome space. First, we show that TopGen can identify genetic drivers of topological structures in simulated datasets. We then applied our approach to more than ten single-cell developmental atlases and found that topological transcriptome spaces are predominantly path-connected and only sometimes simply connected. Finally, we applied TopGen to analyze gene expression patterns in topological loops representing stem-like, transdifferentiation, and convergent cell circuits, found inC. elegans, H. vulgaris, andN. vectensis, respectively. Our results show that some essential differentiation mechanisms use non-trivial topological motifs, and that these motifs can be conserved in a cell-type–specific manner. Thus, our approach to studying the topological properties of developmental transcriptome atlases opens new possibilities for understanding cell development and differentiation.
An adaptive biomolecular condensation response is conserved across environmentally divergent species
Authors: Kik Samantha Keyport , Christopher Dana , Glauninger Hendrik , Hickernell Caitlin Wong , Bard Jared A. M. , Ford Michael , Sosnick Tobin R. , Drummond D. Allan
Published: July 2023

Cells must sense and respond to sudden maladaptive environmental changes—stresses—to survive and thrive. Across eukaryotes, stresses such as heat shock trigger conserved responses: growth arrest, a specific transcriptional response, and biomolecular condensation of protein and mRNA into structures known as stress granules under severe stress. The composition, formation mechanism, adaptive significance, and even evolutionary conservation of these condensed structures remain enigmatic. Here we provide an unprecedented view into stress-triggered condensation, its evolutionary conservation and tuning, and its integration into other well-studied aspects of the stress response. Using three morphologically near-identical budding yeast species adapted to different thermal environments and diverged by up to 100 million years, we show that proteome-scale biomolecular condensation is tuned to species-specific thermal niches, closely tracking corresponding growth and transcriptional responses. In each species, poly(A)-binding protein—a core marker of stress granules—condenses in isolation at species-specific temperatures, with conserved molecular features and conformational changes modulating condensation. From the ecological to the molecular scale, our results reveal previously unappreciated levels of evolutionary selection in the eukaryotic stress response, while establishing a rich, tractable system for further inquiry.
Reliable protein-protein docking with AlphaFold, Rosetta, and replica-exchange
Authors: Harmalkar Ameya , Lyskov Sergey , Gray Jeffrey J.
Published: July 2023

Despite the recent breakthrough of AlphaFold (AF) in the field of protein sequence-to-structure prediction, modeling protein interfaces and predicting protein complex structures remains challenging, especially when there is a significant conformational change in one or both binding partners. Prior studies have demonstrated that AF-multimer (AFm) can predict accurate protein complexes in only up to 43% of cases.1In this work, we combine AlphaFold as a structural template generator with a physics-based replica exchange docking algorithm to better sample conformational changes. Using a curated collection of 254 available protein targets with both unbound and bound structures, we first demonstrate that AlphaFold confidence measures (pLDDT) can be repurposed for estimating protein flexibility and docking accuracy for multimers. We incorporate these metrics within our ReplicaDock 2.0 protocol2to complete a robust in-silico pipeline for accurate protein complex structure prediction. AlphaRED (AlphaFold-initiated Replica Exchange Docking) successfully docks failed AF predictions including 97 failure cases in Docking Benchmark Set 5.5. AlphaRED generates CAPRI acceptable-quality or better predictions for 63% of benchmark targets. Further, on a subset of antigen-antibody targets, which is challenging for AFm (20% success rate), AlphaRED demonstrates a success rate of 43%. This new strategy demonstrates the success possible by integrating deep-learning based architectures trained on evolutionary information with physics-based enhanced sampling. The pipeline is available atgithub.com/Graylab/AlphaRED.
Epigenomic Analyses Identify FOXM1 As a Key Regulator of Anti-Tumor Immune Response in Esophageal Adenocarcinoma
Authors: Ziman Benjamin , Yang Qian , Zheng Yueyuan , Sheth Megha , Nam Chehyun , Zhao Hua , Sinha Uttam K , Lin De-Chen
Published: July 2023

Unlike most cancer types, the incidence of esophageal adenocarcinoma (EAC) has rapidly escalated in the western world over recent decades. Using whole genome bisulfite sequencing (WGBS), we identify the transcription factor (TF) FOXM1 as an important epigenetic regulator of EAC. FOXM1 plays a critical role in cellular proliferation and tumor growth in EAC patient-derived organoids and cell line models. We identify ERBB2 as an upstream regulator of the expression and transcriptional activity of FOXM1. Unexpectedly, Gene Set Enrichment Analysis (GSEA) unbiased screen reveals a prominent anti-correlation between FOXM1 and immune response pathways. Indeed, syngeneic mouse models show that FOXM1 inhibits the infiltration of CD8+T cells into the tumor microenvironment. Consistently, FOXM1 suppresses CD8+T cell chemotaxisin vitroand antigen-dependent CD8+T cell killing. This study characterizes FOXM1 as a significant EAC-promoting TF and elucidates its novel function in regulating anti-tumor immune response.
Multiplexed functional assessments ofMYH7variants in human cardiomyocytes at scale
Authors: Friedman Clayton E. , Fayer Shawn , Pendyala Sriram , Chien Wei-Ming , Tran Linda , Chao Leslie S. , McKinstry Ashley , Ahmed Dania , Loiben Alexander , Farris Stephen D. , Stempien-Otero April , Jonlin Erica , Murry Charles E. , Starita Lea M. , Fowler Douglas M. , Yang Kai-Chun
Published: July 2023

Background

Single, autosomal-dominant missense mutations inMYH7, which encodes a sarcomeric protein (MHC-β) in cardiac and skeletal myocytes, are a leading cause of hypertrophic cardiomyopathy and are clinically-actionable. However, ∼75% ofMYH7variants are of unknown significance (VUS), causing diagnostic challenges for clinicians and emotional distress for patients. Deep mutational scans (DMS) can determine variant effect at scale, but have only been utilized in easily-editable cell lines. While human induced pluripotent stem cells (hiPSCs) can be differentiated to numerous cell types that enable the interrogation of variant effect in a disease-relevant context, DMS have not been executed using diploid hiPSC derivates. However, CRaTER enrichment has recently enabled the pooled generation of a saturated five positionMYH7variant hiPSC library suitable for DMS for the first time.

Results

As a proof-of-concept, we differentiated thisMYH7variant hiPSC library to cardiomyocytes (hiPSC-CMs) for multiplexed assessment of MHC-β variant abundance by massively parallel sequencing (VAMP-seq) and hiPSC-CM survival. We confirm MHC-β protein loss occurs in a failing human heart with a pathogenicMYH7mutation. We find the multiplexed assessment of MHC-β abundance and hiPSC-CM survival both accurately segregate all pathogenic variants from synonymous controls. Overall, functional scores of 68 amino acid substitutions across these independent assays are ∼50% consistent.

Conclusions

This study leverages hiPSC differentiation into disease-relevant cardiomyocytes to enable multiplexed assessments ofMYH7missense variants at scale for the first time. This proof-of-concept demonstrates the ability to DMS previously restricted, clinically-actionable genes to reduce the burden of VUS on patients and clinicians.
Mistletoe as a Therapeutic Option in Cancer Patients: a scoping review protocol
Authors: Cordeiro Milena Mendes , Malta Felipe Aguiar Pupo Seabra , Gonçalves Daniela Caetano
Published: July 2023

Objective

This scoping review aims to identify, map and provide an overview of the studies investigating the therapeutic use of Viscum Album L. (mistletoe) in cancer patients. By identifying pivotal patterns and research gaps in the existing literature on Viscum therapy, this review intends to offer valuable insights and supportive information to better inform future research efforts in this field.

Introduction

Cancer exerts a significant impact on global mortality, posing numerous challenges to public policies. The disease progression and the conventional treatment itself presents multifaceted health adversities to subjects. In response to these complexities, researchers have been exploring non-conventional therapeutic approaches, including phytotherapy. Mistletoe, a widely-used herbal medicine in oncology, is currently undergoing investigation for its potential adjuvant roles in both curative and palliative cancer care.

Inclusion criteria

We will consider studies that include individuals with cancer, irrespective of participant’s age or cancer type/stage, and who were subjected/exposed to interventions based on or incorporating Viscum album L. The review will consider clinical, quasi-experimental, and analytical observational studies, with no limitations on the time of intervention/exposure, treatment stage or geographic region.

Methods

This review will follow the methodological guidance of the JBI Manual for Evidence Synthesis for scoping reviews. The searches will be conducted in the following databases: MEDLINE (via PubMed), CENTRAL (via Cochrane Library), Embase (via Elsevier), Scopus, Web of Science Core Collection, CINAHL (via EBSCO), LILACS and SciELO. The search strategy will be adapted to the specificities of each of these databases, using thesaurus terms and synonyms related to the intervention (mistletoe) and the population (cancer), without restrictions on language or date of publication. The search for unpublished studies will be done in Google Scholar, preprint servers (medRxiv and bioRxiv) and trial registry platforms (Clinical Trials and International Clinical Trials Registry Platform), along grey literature in OpenGrey. Initially, eligibility criteria will be screened by two independent reviewers, assessing article titles and abstracts. Following finishing the full reading and inclusion determination, data extraction will be carried out by two independent reviewers. The results will be presented in narrative form and through tables and graphs.
Adjunctive Vasopressors in Patients with Septic Shock: Protocol for a Systematic Review and Meta-Analysis
Authors: Bauer Seth R. , Wieruszewski Patrick M. , Bissell Brittany D. , Dugar Siddharth , Sacha Gretchen L. , Sato Ryota , Siuba Matthew T. , Schleicher Mary , Vachharajani Vidula , Falck-Ytter Yngve , Morgan Rebecca L.
Published: July 2023

Background

Over one-third of patients with septic shock have adjunctive vasopressors added to first-line vasopressors. However, no randomized trial has detected improved mortality with adjunctive vasopressors. Published systematic reviews and meta-analysis have sought to inform the use of adjunctive vasopressors, yet each published review has limitations that hinder its interpretation. This review aims to overcome the limitations of previous reviews by systematically synthesizing the direct evidence for adjunctive vasopressor therapy use in adult patients with septic shock.

Methods

We will conduct a systematic review and meta-analysis of randomized controlled trials evaluating adjunctive vasopressors (vasopressin analogues, angiotensin II, hydroxocobalamin, methylene blue, and catecholamine analogues) in adult patients with septic shock. Relevant studies will be identified through comprehensive searches of MEDLINE, Embase, CENTRAL, and reference lists of previous systematic reviews. Only randomized trials comparing adjunctive vasopressors (>75% of subjects on vasopressors at enrollment) to standard care vasopressors in adults with septic shock (>75% of subjects having septic shock) will be included. Titles and abstracts will be screened, full-text articles assessed for eligibility, and data extracted from included studies. Outcomes of interest include short-term mortality, intermediate-term mortality, kidney replacement therapy, digital/peripheral ischemia, and venous thromboembolism. Pairwise meta-analysis using a random-effects model will be utilized to estimate the risk ratio for the outcomes. Risk of bias will be adjudicated with the Cochrane Risk of Bias 2 tool, and GRADE will be used to rate the certainty of the body of evidence.

Discussion

Although adjunctive vasopressors are commonly used in patients with septic shock their effect on patient-important outcomes is unclear. This study is planned to use rigorous systematic review methodology, including strict adhere to established guidelines, in order to overcome limitations of previously-published reviews and inform clinical practice and treatment guidelines for the use of adjunctive vasopressors in adults with septic shock.

Systematic review registration

PROSPERO CRD4202327984
Bacterial pathogens deliver water/solute-permeable channels as a virulence strategy
Authors: Nomura Kinya , Andreazza Felipe , Cheng Jie , Dong Ke , Zhou Pei , He Sheng Yang
Published: July 2023

Many animal and plant pathogenic bacteria utilize a type III secretion system to deliver effector proteins into the host cell1,2. Elucidation of how these effector proteins function in the host cell is critical for understanding infectious diseases in animals and plants3–5. The widely conserved AvrE/DspE-family effectors play a central role in the pathogenesis of diverse phytopathogenic bacteria6. These conserved effectors are involved in the induction of “water-soaking” and host cell death that are conducive to bacterial multiplication in infected tissues. However, the exact biochemical functions of AvrE/DspE-family effectors have been recalcitrant to mechanistic understanding for three decades. Here we show that AvrE/DspE-family effectors fold into a β-barrel structure that resembles bacterial porins. Expression of AvrE and DspE inXenopusoocytes results in (i) inward and outward currents, (ii) permeability to water and (iii) osmolarity-dependent oocyte swelling and bursting. Liposome reconstitution confirmed that the DspE channel alone is sufficient to allow the passage of small molecules such as fluorescein dye. Targeted screening of chemical blockers based on the predicted pore size (15-20 Å) of the DspE channel identified polyamidoamine (PAMAM) dendrimers as inhibitors of the DspE/AvrE channels. Remarkably, PAMAMs broadly inhibit AvrE/DspE virulence activities inXenopusoocytes and duringErwinia amylovoraandPseudomonas syringaeinfections. Thus, we have unraveled the enigmatic function of a centrally important family of bacterial effectors with significant conceptual and practical implications in the study of bacterial pathogenesis.
Metabolic arms race between a plant and a fungal pathogen
Authors: Liu Y. , Mahdi L.K. , Porzel A. , Stark P. , Esposto D. , Scherr-Henning A. , Bathe U. , Acosta I.F. , Zuccaro A. , Balcke G.U. , Tissier A.
Published: July 2023

In this work, we uncover a metabolite interaction between barley and the fungal pathogenBipolaris sorokiniana(Bs), involving hordedanes, a previously undescribed set of labdane-related diterpenoids with antimicrobial properties.Bsinfection of barley roots elicits hordedane synthesis from a 600-kb gene cluster. Heterologous reconstruction of the synthesis pathway in yeast produced several hordedanes, including one of the most advanced products 19-b-hydroxy-hordetrienoic acid (19-OH-HTA). Barley mutants in the diterpene synthase genes of the cluster are unable to produce hordedanes but, unexpectedly, show reducedBscolonization. Accordingly, 19-OH-HTA enhances both germination and growth ofBs, while it inhibits other fungi, andBschemically modifies 19-OH-HTA. Thus, plant and pathogen molecular interactions extend beyond protein-protein recognition and the simple detoxification of plant antimicrobial metabolites.

One-Sentence Summary

A fungal pathogen uses barley diterpenoid phytoalexins to facilitate root colonization.
Gradient-based implementation of linear model outperforms deep learning models
Authors: Hamidi Hamid , Wang Dinghao , Long Quan , Greenberg Matthew
Published: July 2023

Deep learning has been widely considered more effective than traditional statistical models in modeling biological complex data such as single-cell omics. Here we show the devil is hidden in details: by adapting a modern gradient solver to a traditional linear mixed model, we showed that conventional models can outperform deep models in terms of both speed and accuracy. This work reveals the potential of re-implementing traditional models with modern solvers.