bluuebunny/crossref_metadata_2025 huggingface dataset:
Proteogenomics guided identification of functional neoantigens in non-small cell lung cancer
Authors: Nicholas Ben , Bailey Alistair , McCann Katy J , Wood Oliver , Currall Eve , Johnson Peter , Elliott Tim , Ottensmeier Christian , Skipp Paul
Published: June 2024

Non-small cell lung cancer (NSCLC) has poor survival even for those receiving modern checkpoint inhibitor therapies. Personalised vaccines based on short peptide neoantigens containing tumour mutations, presented to cytotoxic T-cells by human leukocyte antigen (HLA) molecules, are an attractive strategy. However, identifying therapeutically relevant neoantigens is challenging, with existing methods yielding positive responses in only 6% of candidates tested, and neoantigen-based vaccines in melanoma, glioblastoma and pancreatic cancer producing an immune responses in about 50% of patients. Here we report a proteogenomics approach to identify neoantigens in tumours from a cohort of 24 NSCLC patients: 15 adenocarcinoma, 9 squamous cell carcinoma. We characterised the mutational and HLA immunopeptide landscapes of NSCLC using whole exome sequencing, transcriptomics and mass spectrometry immunopeptidomics. We directly identified one neoantigen, and additional predicted neoantigens were generated using an existing in silico neoantigen prediction workflow. Using the immunopeptidomes to filter for candidate predicted neoantigens we identified positive functional assay responses for 5 out of the 6 patients we tested, with an overall success rate of 13%, inclusive of the directly observed neoantigen. Finally, for one patient using scRNAseq we identified a CD8+ effector T-cell clonotype expanded only in response to the putative class I HLA neoantigen. These results represent an improvement in both the quantity of neoantigens identified and the specificity of immune responses to neoantigens, utilising knowledge of the HLA peptides presented on a tumour. Thus immunopeptidomics has the potential to improve the efficacy of neoantigen based personalised cancer vaccine workflows.
Disentangling Cobionts and Contamination in Long-Read Genomic Data using Sequence Composition
Authors: Weber Claudia C
Published: June 2024

The recent acceleration in genome sequencing targeting previously unexplored parts of the tree of life presents computational challenges. Samples collected from the wild often contain sequences from several organisms, including the target, its cobionts, and contaminants. Effective methods are therefore needed to separate sequences. Though advances in sequencing technology make this task easier, it remains difficult to taxonomically assign sequences from eukaryotic taxa that are not well-represented in databases. Therefore, reference-based methods alone are insufficient. Here, I examine how we can take advantage of differences in sequence composition between organisms to identify symbionts, parasites and contaminants in samples, with minimal reliance on reference data. To this end, I explore data from the Darwin Tree of Life project, including hundreds of high-quality HiFi read sets from insects. Visualising two-dimensional representations of read tetranucleotide composition learned by a Variational Autoencoder can reveal distinct components of a sample. Annotating the embeddings with additional information, such as coding density, estimated coverage, or taxonomic labels allows rapid assessment of the contents of a dataset. The approach scales to millions of sequences, making it possible to explore unassembled read sets, even for large genomes. Combined with interactive visualisation tools, it allows a large fraction of cobionts reported by reference-based screening to be identified. Crucially, it also facilitates retrieving genomes for which suitable reference data are absent.
Dissolution of Phosphate and Precipitation of Carbonate in the Biomineralization of the Bivalve Shell Limnoperna fortunei
Authors: Valadão Cardoso Antonio , Novaes Ferreira Rodrigo
Published: June 2024

Abstract

The mantle of bivalves plays a crucial role in the formation and maintenance of their shells through biomineralization. Detailed studies using scanning electron microscopy (SEM) and energy dispersive spectroscopy (EDS) analysis have revealed the presence of phosphorus (P) compounds as the primary phase during biomineralization at the growing edge of the periostracum of the bivalve shell Limnoperna fortunei (Dunker, 1857). The presence of a crystal morphology like hydroxyapatite (HAp) at the growing edge of the shell has also been identified, and the Ca/P ratio compatible with HAp. Carbonic anhydrase (CA), whose presence in the shell was investigated in this work, and/or bivalve proteins with identical capability are likely responsible for the dissolution phosphate and calcium carbonate precipitation. Other experimental techniques (ICP-OES, WDXRF) were used to quantify the main chemical elements in the shell of L. fortunei and the marine bivalve P. perna. The concentration of P in the shells suggests that phosphate is confined to the growing regions. FTIR and FTIR-ATR spectroscopies indicate aragonite as the main phase at the shell edges but also show the presence of phosphate absorption bands. X-ray diffraction (XRD) analyses revealed aragonite and calcite phases at the shell edges, with the presence of one of the main peaks of crystalline calcium phosphate both in L. fortunei and P. perna. The presence of phosphate as the primary phase in the biomineralization process of L. fortunei rekindles the discussion about the importance of the co-occurrence of phosphate and carbonate in the bivalve biomineralization dynamics and suggests an important evolutionary advantage in acquiring phosphate compounds essential for energy production and organism function.
Evolutionary modes ofwtfmeiotic driver genes inSchizosaccharomyces pombe
Authors: Xu Yan-Hui , Suo Fang , Zhang Xiao-Ran , Du Tong-Yang , Hua Yu , Jia Guo-Song , Zheng Jin-Xin , Du Li-Lin
Published: June 2024

Killer meiotic drivers (KMDs) are a class of selfish genetic elements that defy Mendel's law and bias transmission in their favor by destroying meiotic progeny that do not carry them. How KMDs evolve is not well understood. In the fission yeastSchizosaccharomyces pombe, the largest gene family, known as thewtfgenes, is a KMD family that causes intraspecific hybrid sterility. Here, we investigate howwtfgenes evolve using long-read-based genome assemblies of 31 distinctS. pombenatural isolates, which encompass the known genetic diversity ofS. pombe. Our analysis, involving nearly 1,000wtfgenes in these isolates, yields a comprehensive portrayal of the intraspecific diversity ofwtfgenes. Leveraging single-nucleotide polymorphisms in adjacent unique sequences, we pinpointwtf-gene-containing loci that have recently undergone gene conversion events and infer their pre-gene-conversion state. These events include the revival ofwtfpseudogenes, lending support to the notion that gene conversion plays a role in preserving this gene family from extinction. Moreover, our investigation reveals that solo long terminal repeats (LTRs) of retrotransposons, frequently found nearwtfgenes, can act as recombination arms, influencing the upstream regulatory sequences ofwtfgenes. Additionally, our exploration of the outer boundaries ofwtfgenes uncovers a previously unrecognized type of directly oriented repeats flankingwtfgenes. These repeats may have facilitated the early expansion of thewtfgene family inS. pombe. Our findings enhance the understanding of the mechanisms influencing the evolution of this KMD gene family.
Antinociceptive synergy in a peripheral hyperalgesia model: interplay of cannabinoidergic, adrenergic, and opioidergic systems and their antagonism
Authors: Lopes Caio Fabio Baeta , Santos-Silva Thamyris , Fonseca Flávia Cristina , de Queiroz Bárbara Formiga Gonçalves , Duarte Igor Dimitri Gama , Romero Thiago Roberto Lima
Published: June 2024

There is growing interest in co-administering know analgesics for pain management, to reduce side effects and maximize therapeutic effects by pharmacological synergism, defined as supra-additive effects to biological stimuli. This work aimed to evaluate, using isobolgraphic analysis, synergistic effects of three antinociceptive substances— anandamide (AEA), a cannabinoid CB1 receptor agonist; xylazine (XYL), an adrenergic α2-receptor agonist; and DAMGO, an µ-opioid receptor agonist—administered in binary doses in a prostaglandin E2 (PGE2)-induced peripheral pain model. Hyperalgesia was induced in Swiss male mice, and subsequently, animals were treated with binary agonist combinations administered to the hind paw. Mechanical nociceptive thresholds were measured using an algesimetric task, and the results obtained were compared with additive predicted effects. For AEA+XYL and AEA+DAMGO combinations, the observed effects were significantly greater than those predicted by Loewe’s additivity principles at all tested effect levels (10%, 30%, and 50% maximum possible effect, MPE). DAMGO+XYL combination showed significant synergistic effects at 10% and 30% MPE but not at 50% MPE. Confirming these findings, combination indexes (CI) for AEA+XYL and AEA+DAMGO were less than 1, indicating synergism, while CI for DAMGO+XYL was near 1, indicating additivity. Notably, single-system antagonism with either AM251, a CB1 antagonist, yohimbine, an α2C-receptor antagonist or naloxone, pan-opioid receptor antagonist, could prevent synergy or any analgesia at all for AEA+XYL and AEA+DAMGO. Furthermore, the binary agonist combinations did not produce systemic effects, sedation, or motor impairments. The results suggest synergistic antinociceptive effects for AEA+XYL and AEA+DAMGO, which are dependent on concomitant agonism upon known metabotropic receptors.
Lipid metabolic reprogramming drives triglyceride storage and variable sensitivity to FASN inhibition in endocrine-resistant breast cancer cells
Authors: Ward Ashley V. , Riley Duncan , Cosper Kirsten E. , Finlay-Schultz Jessica , Brechbuhl Heather M. , Libby Andrew E. , Hill Kaitlyn B. , Varshney Rohan R. , Kabos Peter , Rudolph Michael C. , Sartorius Carol A.
Published: June 2024

Background

Lipid metabolic reprogramming is increasingly recognized as a hallmark of endocrine resistance in estrogen receptor-positive (ER+) breast cancer. In this study, we investigated alterations in lipid metabolism in ER+ breast cancer cell lines with acquired resistance to common endocrine therapies and evaluated the efficacy of a clinically relevant fatty acid synthase (FASN) inhibitor.

Methods

ER+ breast cancer cell lines resistant to Tamoxifen (TamR), Fulvestrant (FulvR), and long-term estrogen withdrawal (EWD) were derived. Global gene expression and lipidomic profiling were performed to compare parental and endocrine resistant cells. Lipid storage was assessed using Oil Red O (ORO) staining. The FASN inhibitor TVB-2640 was tested for its impact on lipid storage and cell growth.13C2-acetate tracing was used to evaluate FASN activity and the efficacy of TVB-2640.

Results

Endocrine resistant cells showed significant enrichment in lipid metabolism pathways and distinct lipidomic profiles, characterized by elevated triglyceride levels and enhanced cytoplasmic lipid droplets.13C2-acetate tracing revealed increased FASN activity in endocrine resistant cells, which was effectively reduced by TVB-2640. While TVB-2640 reduced lipid storage in most but not all cell lines, this did not correlate with decreased cell growth.

Polyunsaturated fatty acids (PUFAs) containing 6 or more double bonds were elevated in endocrine resistant cells and remained unaffected or increased with TVB-2640.

Conclusion

Endocrine resistant breast cancer cells undergo a metabolic shift toward increased triglyceride storage and PUFAs with high degrees of desaturation. While TVB-2640 reduced lipid storage in most conditions, it had limited effects on the growth of endocrine resistant breast cancer cells. Targeting specific lipid metabolic dependencies, particularly pathways that produce PUFAs, represents a potential therapeutic strategy in endocrine resistant breast cancer.
Antibacterial effectors inDictyostelium discoideum: specific activity against different bacterial species
Authors: Munoz-Ruiz Raphael , Lamrabet Otmane , Jauslin Tania , Guilhen Cyril , Bourbon Alixia , Cosson Pierre
Published: June 2024

Dictyostelium discoideumis a phagocytic amoeba continuously eating, killing and digesting bacteria. Previous studies have detected inD. discoideumcell extracts a bacteriolytic activity effective againstKlebsiella pneumoniaebacteria.

In this study we characterized bacteriolytic activities found inD. discoideumcell extracts against five different bacteria (K. pneumoniae,Escherichia coli,Pseudomonas aeruginosa,Staphylococcus aureus, andBacillus subtilis).We first analyzed the bacteriolytic activity against these five bacteria in parallel over a range of pH values. We then measured the remaining bacteriolytic activity inD. discoideum kil1andmodAKO mutants. We also performed partial fractionation ofD. discoideumextracts and assessed activity against different bacteria. Together our results indicate that optimal bacteriolytic activity against different bacteria results from the action of different effectors. Proteomic analysis allowed us to propose a list of potential bacteriolytic effectors.

IMPORTANCE

Many antibacterial effectors have been characterized over the last decades, and their biological importance, mode of action and specificity is often still under study. Here we characterizedin vitrobacteriolytic activity inD. discoideumextracts against five species of gram-negative and gram-positive bacteria. Our results reveal that optimal lysis of different bacteria mobilizes different effectors. Proteomic analysis generated a list of potential bacteriolytic effectors. This work opens the way for future analysis of the role of individual effectors in livingD. discoideumcells.
Studies ofCrHCF244reveal similarities and differences inpsbAtranslation betweenChlamydomonas reinhardtiiandArabidopsis thaliana
Authors: Wang Xiaozhuo , Wang Guannan , Cheramie Lexi A. , Zhao Cuiping , Dassanayake Maheshi , Moroney James V. , Vinyard David J.
Published: June 2024

Translation ofpsbA, the chloroplast gene that encodes the D1 subunit of Photosystem II (PSII), is important for both PSII biogenesis and repair. The translation of thepsbAtranscript in the chloroplast is under the control of nuclear gene products. Using aChlamydomonasforward genetic screen and whole genome sequencing, we found a mutant defective in PSII activity and mapped the causative gene to be the homolog ofArabidopsis High Fluorescence(HCF244) gene, orCrHCF244. We then demonstrated that CrHCF244 is required forpsbAtranslation in the alga, consistent with the function of HCF244 inArabidopsis. TheArabidopsis HCF244gene also complemented the algal mutant. These results experimentally support the functional conservation of the homologs in green algae and land plants. However, these studies also revealed differences inpsbAtranslation inChlamydomonasandArabidopsis. Loss of HCF244 inArabidopsisresults in a large decrease in chlorophyll. In contrast, there is no significant loss of chlorophyll inChlamydomonaswhenCrHCF244is knocked out. This observation supports the uncoupling of D1 translation and chlorophyll association in algae as reported recently in anohp2mutant, which is defective in chlorophyll delivery. Intriguingly, theCrHCF244mutant also exhibited a relatively high rate of suppressor mutants, pointing to the presence of alternative pathway(s) for D1 translation control. The characterization of both the conserved aspects and the differences inpsbAtranslation control between algae and plants will help elucidate how this process is regulated.

Highlight

We identified CrHCF244 as a translation factor ofpsbAinChlamydomonas. Characterization of this protein and genetic examinations of other previously identifiedpsbAtranslation factors inChlamydomonasreveal similarities and differences inpsbAtranslation betweenChlamydomonasandArabidopsis.
The reparative immunologic consequences of stem cell transplantation as a cellular therapy for refractory Crohn’s disease
Authors: Guisado Daniela , Talware Sayali , Wang Xiaoli , Davis Andrew , Fozilov Elbek , Etra Aaron , Colombel Jean-Frederic , Schaniel Christoph , Tastad Christopher , Levine John E. , Ferrara James L. M. , Chuang Ling-Shiang , Sabic Ksenija , Singh Shishir , Marcellino Bridget K. , Hoffman Ronald , Cho Judy , Cohen Louis J.
Published: June 2024

Background

Treatment strategies for Crohn’s disease (CD) suppress diverse inflammatory pathways but many patients remain refractory to treatment. Autologous hematopoietic stem cell transplantation (SCT) has emerged as a therapy for medically refractory CD. SCT was developed to rescue cancer patients from myelosuppressive chemotherapy but its use for CD and other immune diseases necessitates reimagining SCT as a cellular therapy that restores appropriately responsive immune cell populations from hematopoietic progenitors in the stem cell autograft (i.e. immune “reset”). Here we present a paradigm to understand SCT as a cellular therapy for immune diseases and reveal how SCT re-establishes cellular immunity utilizing high-dimensional cellular phenotyping and functional studies of the stem cell grafts.

Methods

Immunophenotyping using CyTOF, single cell RNA sequencing (scRNA-seq) and T cell receptor (TCR) sequencing was performed on peripheral blood and intestinal tissue samples from refractory CD patients who underwent SCT. The stem cell graft from these patients was analyzed using flow cytometry and functionally interrogated using a murine model for engraftment.

Results

Our study revealed a remodeling of intestinal macrophages capable of supporting mucosal healing that was independently validated using multimodal studies of immune reconstitution events including CyTOF and scRNA-seq. Functional interrogation of hematopoietic stem cells (HSCs) using a xenograft model demonstrated that HSCs shape the timing of immune reconstitution, the selected reconstitution of specific cell lineages and potentially the clinical efficacy of SCT.

Conclusions

These studies indicate that SCT serves as a myeloid-directed cellular therapy re-establishing homeostatic intestinal macrophages that support intestinal healing and suggest refractory CD evolves from impairment of restorative functions in myeloid cells. Furthermore, we report heterogeneity among HSCs from CD patients which may drive SCT outcomes and suggests an unrecognized impact of CD pathophysiology on HSC in the marrow niche.
Data-driven modeling ofE. colitranscriptional regulation
Authors: Dalldorf Christopher G. , Hughes Griffith , Li Gaoyuan , Palsson Bernhard O. , Zielinski Daniel C.
Published: June 2024

The growth of bacterial gene expression datasets has offered unprecedented coverage of achievable transcriptomes, reflecting diverse activity states of the transcription regulatory network. Machine learning methods like Independent Component Analysis (ICA) can decompose gene expression datasets into regulatory modules and condition-specific regulator activities. Here, we present a workflow to utilize inferred regulator activities to construct quantitative models of promoter regulation inE. coli. Resulting models are validated by predicting condition-specific TF effector concentrations and binding site motif strength based on differential gene expression data alone. We show how reconstructed promoter models can capture multi-scale regulation and disentangle regulator interactions, including resolving the apparent paradox whereargRexpression is positively correlated with its regulon despite being a repressor. We applied the workflow for all regulator-linked components extracted by ICA, demonstrating the scalability of the workflow to capture theE. coliTRN. This work suggests a path toward systematic, quantitative reconstruction of transcription regulatory networks driven by the large-scale databases that are now available for many organisms.
A phased chromosome-level genome assembly provides insights into the evolution of sex chromosomes inAmaranthus tuberculatus
Authors: Raiyemo Damilola A. , Cutti Luan , Patterson Eric L. , Llaca Victor , Fengler Kevin , Montgomery Jacob S. , Morran Sarah , Gaines Todd A. , Tranel Patrick J.
Published: June 2024

Amaranthus tuberculatus(waterhemp) is a troublesome weed species of agronomic importance that is dioecious with an XY sex-determination system. The evolution of sex chromosomes, the contiguity of sex-determining region (SDR) and the expression pattern of genes within the SDR remain poorly understood.

We assembled the genome of a maleA. tuberculatus, phased the genome into two chromosome-level haplotypes, and performed restriction site-associated DNA genome- wide association (RAD-GWA) analysis, comparative genomics, adaptive evolution analysis, and, with existing data, transcriptomic profiling to characterize the species’ sex chromosomes.

Comparative analysis enabled the identification of a ∼32.8 Mb SDR on chromosome 1 that is gene-poor, abundant in long terminal repeat (LTR) retrotransposons, and harbors two inversions. Synteny analysis revealed that chromosome 1 likely originated from the fusion of two ancestral chromosomes, and mRNA data indicated 93 genes out of the 531 protein-coding genes within the SDR of haplome 2 were differentially expressed between mature male and female flowers, with several of the genes enriched for Gene Ontology (GO) terms involved in floral development.

Beyond adding to our understanding of sex chromosome evolution, the genomic resource provided here will be valuable for addressing further questions on adaptive trait evolution inAmaranthus.
A High-quality Oxford Nanopore Assembly of the Hourglass Dolphin (Lagenorhynchus cruciger) Genome
Authors: McGrath Nick , le Roux Jamie , Whibley Annabel , Alexander Alana , Stewart Ramari Oliphant , Johnstone Muriel , Stockin Karen A. , Silander Olin K.
Published: June 2024

The hourglass dolphin (Lagenorhynchus cruciger) is a small cetacean species of the Southern Ocean, with significance to iwi Māori (Māori tribes) of Aotearoa New Zealand as taonga (treasured/valued). Due to the remoteness and difficulty of surveying Antarctic waters, it remains one of the least-studied dolphin species. A recent stranding of an hourglass dolphin represented a rare opportunity to generate a genome assembly as a resource for future study into the conservation and evolutionary biology of this species. In this study, we present a high-quality genome assembly of an hourglass dolphin individual using a single sequencing platform, Oxford Nanopore Technologies, coupled with computationally efficient assembly methods. Our assembly strategy yielded a genome of high contiguity (N50 of 8.07 Mbp) and quality (98.3% BUSCO completeness). Compared to other Delphinoidea reference genomes, this assembly has fewer missing BUSCOs than any exceptOrcinus orca, more single-copy complete BUSCOs than any exceptPhocoena sinus, and 20% fewer duplicated BUSCOs than the average Delphinoidea reference genome. This suggests that it is one of the most complete and accurate marine mammal genomes to date. This study showcases the feasibility of a cost-effective mammalian genome assembly method, allowing for genomic data generation outside the traditional confines of academia and/or resource-rich genome assembly hubs, and facilitating the ability to uphold Indigenous data sovereignty. In the future the genome assembly presented here will allow valuable insights into the past population size changes, adaptation, vulnerability to future climate change of the hourglass dolphin and related species.
THE DUAL-SPECIFICITY KINASE DYRK1A INTERACTS WITH THE HEPATITIS B VIRUS GENOME AND REGULATES THE PRODUCTION OF VIRAL RNA
Authors: Pastor Florentin , Charles Emilie , Di Vona Chiara , Chapelle Maëlys , Rivoire Michel , Passot Guillaume , Chabot Benoit , de la Luna Susana , Lucifora Julie , Durantel David , Salvetti Anna
Published: June 2024

The genome of Hepatitis B virus (HBV) persists in infected hepatocytes as a nuclear episome (cccDNA) that is responsible for the transcription of viral genes and viral rebound, following antiviral treatment arrest in chronically infected patients. Beside pegylated interferon-alpha, there is currently no clinically approved therapeutic protocol able to target cccDNA [1]. The development of alternative strategies aiming at permanently abrogating HBV RNA production requires a thorough understanding of cccDNA transcriptional and post-transcriptional regulation. In a previous study, we discovered that 1C8, a compound that inhibits the phosphorylation of some cellular RNA-binding proteins (RBPs), could decrease the level of HBV RNAs. Here, we aimed at identifying kinases responsible for this effect. Among the kinases targeted by 1C8, we focused on DYRK1A, a dual-specificity kinase that controls the transcription of cellular genes by phosphorylating transcription factors, histones, chromatin regulators as well as RNA polymerase II. The results of a combination of genetic and chemical approaches using HBV-infected hepatocytes, indicated that DYRK1A positively regulates the production of HBV RNAs. In addition, we found that DYRK1A associates with cccDNA, and stimulates the production of HBV nascent RNAs. Finally, reporter gene assays showed that DYRK1A up-regulates the activity of the HBV enhancer 1/X promoter in a sequence-dependent manner. Altogether, these results indicate that DYRK1A is a proviral factor that may participate in the the HBV life cycle by stimulating the production of HBx, a viral factor absolutely required to trigger the complete cccDNA transcriptional program.
Meta TCT: Towards Interpretable Treatment Effects in Clinical Trials for Progressive Diseases
Authors: Stijven Florian , Mallinckrodt Craig , Molenberghs Geert , Alonso Ariel , Dickson Sam , Hendrix Suzanne
Published: June 2024

In progressive diseases, like Alzheimer’s disease, treatments that slow progression should start early in the disease course to longer maintain higher levels of functioning. In corresponding clinical trials, the treatment effect is usually expressed in terms of mean differences on a clinical scale. Early in the disease course, however, treatment effects expressed on a clinical scale are often small but may nonetheless correspond to an important slowing of disease progression. This complicates the appreciation of the relevance of observed treatment effects. For example, it may be difficult to determine whether a 2-point improvement on a clinical scale is relevant for clinical practice. In this paper, we propose the meta Time-Component Tests (meta TCT). This new approach leads to estimators of treatment effects on the time scale, in terms of time saved or percentage slowing of progression, that are easy to interpret. This approach is based on estimates obtained from an arbitrary model for longitudinal data and is, therefore, very flexible. Asymptotic properties of the Meta TCT estimators are derived and evaluated in an extensive simulation study. Meta TCT is then applied to a phase 2/3 clinical trial for Alzheimer’s disease, which was first analyzed with a mixed model. In this trial, meta TCT leads to important additional insights into the treatment effect. We believe that meta TCT will facilitate the estimation of interpretable treatment effects in clinical trials for progressive diseases, and that this, in turn, will fine-tune the evaluation of the clinical relevance of new treatments.
Inequalities in relative cancer survival by race, immigration status, income, and education for 22 cancer sites in Canada, a cohort study
Authors: Malagón Talía , Botting-Provost Sarah , Moore Alissa , El-Zein Mariam , Franco Eduardo L.
Published: June 2024

Introduction

There is a paucity of disaggregated data to monitor cancer health inequalities in Canada. We used data linkage to estimate site-specific cancer relative survival by race, immigration status, household income, and education level in Canada.

Methods

We pooled the Canadian Census Health and Environment Cohorts, which are linked datasets of 5.9 million respondents of the 2006 long-form census and 6.5 million respondents of the 2011 National Household Survey. Individual-level respondent data from these surveys were probabilistically linked with the Canadian Cancer Registry up to 2015 and with the Canadian Vital Statistics Database up to 2019. We used propensity score matching and Poisson models to calculate age-standardized relative survival by equity stratifiers for all cancers combined and for 22 individual cancer sites for the period 2006-2019.

Results

There were 757,485 primary cancer cases diagnosed over follow-up included in survival analyses; the age-standardized period relative survival was 72.5% at 5 years post-diagnosis. Relative survival was higher in immigrants (74.6%, 95%CI 74.3-74.8) than in Canadian-born persons (70.4%, 95%CI 70.2-70.6), and higher in racial groups with high proportions of immigrants. There was a marked social gradient by household income and education level, with 11-12% lower relative survival in cancer patients in the lowest household income and education levels than in the highest levels. Socioeconomic gradients were observed for most cancer sites, though the magnitude varied.

Conclusions

Despite the availability of universal healthcare in Canada, the observed differences in relative survival suggest there remain important inequities in cancer control and care.
Gone but not forgotten: dynamics of sperm storage and potential ejaculate digestion in the black soldier flyHermetia illucens
Authors: Manas Frédéric , Piterois Harmony , Labrousse Carole , Beaugard Laureen , Uzbekov Rustem , Bressac Christophe
Published: June 2024

When it comes to describe reproduction in internally fertilized species, understanding the dynamics of sperm storage is crucial to unravel the complexity of post-copulatory sexual selection processes. This physiological process goes from sperm transfer to its use for fertilization. In this framework, the spatiotemporal dynamics of sperm storage were described in the black soldier fly (BSF) with fluorescence and transmission electron microscopy (TEM). Besides being of great economic interest, BSF females have highly compartmentalized spermathecae. Spermatozoa were counted both during and after mating in two successive spermathecae compartments: the fishnet canals and the reservoirs. In addition to seminal fluids, male transfers a sperm plug in the fishnet canals, then only some spermatozoa reach the reservoirs over 2 days. TEM observations of the fishnet canals revealed potential digestive functions, explaining the decline in the number and the viability of spermatozoa that have not been stored in the reservoirs. After one mating, females laid up to three fertile clutches, evidencing no constraints on sperm quantity or quality. Spermatic and ultrastructural investigations strongly suggest that BSF ejaculate acts both as a sperm plug and a as nuptial gift, reinforcing the interest in studying this insect as a model for sexual selection.
Early development of the glucocorticoid stress response in dyeing poison frog tadpoles
Authors: Surber-Cunningham Lisa L. , Jimenez Lucas S. , Mobo Lauren W. , Westrick Sarah E. , Fischer Eva K.
Published: June 2024

In vertebrates, the glucocorticoid “stress” response (corticosterone or cortisol) through the hypothalamic-pituitary-adrenal (HPA) axis influences many essential functions, including behavior, metabolism, immunity, and ontogenetic transitions. During development, stress responses can be adaptive if they facilitate antipredator behavior and modulate developmental speed to adjust to environmental conditions; however, these same responses can be maladaptive when energetic costs become too high and developmental speed trades-off with size and health at maturity. Thus, the timing of HPA-axis development may be aligned with specific developmental challenges and opportunities presented by a species’ life history strategy. In anurans (frogs and toads), corticosterone plays critical roles in development and behavior, and concentrations can fluctuate in response to environmental stressors. Given the role of corticosterone in ontogenetic changes and behaviors, we studied the development of the HPA axis in tadpoles of the dyeing poison frog (Dendrobates tinctorius), a species with a unique life history that includes transport to water after hatching on land and aggressive and cannibalistic behavior. We measured the excretion rate and whole-body concentration of corticosterone and the corticosterone response to adrenocorticotropic hormone (ACTH) in free-swimming tadpoles after transport and throughout metamorphosis. We found no significant differences across development in excretion rates or whole-body concentration of corticosterone, nor corticosterone response to ACTH, indicating that that the glucocorticoid response develops early in ontogeny. This pattern differs from those in other species of tadpoles, suggesting the unique ecological pressures faced byD. tinctoriushave shaped the development of its HPA axis. More broadly, this study illustrates how life history strategies and tradeoffs impact the timing of the HPA axis development.
Adenomyosis and fibrosis define the morphological memory of the postpartum uterus of dairy cows previously exposed to metritis
Authors: Sellmer Ramos I , Caldeira MO , Poock SE , Moraes JGN , Lucy MC , Patterson AL
Published: June 2024

Optimal reproductive success following parturition in lactating dairy cows is dependent upon adequate completion of uterine involution. Failure to resolve pathogenic bacterial contamination within the first week postpartum can lead to uterine disease (metritis). Metritis is associated with decreased fertility and a failure or delay to establish pregnancy. We hypothesized that the inflammation resulting from early postpartum metritis would be associated with long-term changes in uterine morphology due to impaired uterine involution within the first 30 days postpartum (dpp). First parity Holstein cows were diagnosed with or without metritis at 7-10 dpp and uterine tissue were analyzed at 30 (Exp. 1), or 80 and 165 (Exp. 2) dpp for the presence of abnormal morphology, including abnormal invasion of endometrial glands and stroma into the myometrium (adenomyosis) using immunohistochemistry for FOXA2 (uterine gland specific marker) and presence of late postpartum endometrial fibrosis using mason’s trichrome stain (MTS). Severity of adenomyosis was determined by the number and size of adenomyotic foci, distance of foci from the endometrium-myometrium interface (EMI), and degree of fibrosis (MTS stain intensity). The presence, size, and distance from the EMI of adenomyotic foci were greater later postpartum and in cows with early postpartum diagnosis of metritis. Endometrial fibrosis was greater at the stratum basalis (at EMI) compared to the stratum compactum endometrium (near lumen) for all Exp. 2 cows, but greater endometrial fibrosis (regardless of endometrial region) was observed in cows that were diagnosed with metritis. Taken together, these data indicate that early postpartum metritis is associated with long-term modifications to the postpartum uterine morphology, including aberrant endometrial invasion into the myometrium (adenomyosis) and increased pathological fibrogenesis, leading to the presence of late postpartum endometrial fibrosis (scar tissue). Additionally, increased collagen fiber at the EMI suggests a correlation between the development of adenomyosis and fibrosis, which could possibly result from sustained endometrial inflammation caused by uterine disease.
Circulating miR-126-3p is a mechanistic biomarker for knee osteoarthritis
Authors: Wilson Thomas G. , Baghel Madhu , Kaur Navdeep , Datta Indrani , Loveless Ian , Potla Pratibha , Mendez Devin , Hansen Logan , Baker Kevin , Lynch T. Sean , Moutzouros Vasilios , Davis Jason , Ali Shabana Amanda
Published: June 2024

As a chronic joint disease, osteoarthritis (OA) is a major contributor to pain and disability worldwide, and yet there are currently no validated soluble biomarkers or disease-modifying treatments. Since microRNAs are promising mechanistic biomarkers that can be therapeutically targeted, we aimed to prioritize reproducible circulating microRNAs in knee OA. We performed secondary analysis on two microRNA-sequencing datasets and found circulating miR-126-3p to be elevated in radiographic knee OA compared to non-OA individuals. This finding was validated in an independent cohort (N=145), where miR-126-3p showed an area under the receiver operating characteristic curve of 0.91 for distinguishing knee OA. Measuring miR-126-3p in six primary human knee OA tissues, subchondral bone, fat pad and synovium exhibited the highest levels, and cartilage the lowest. Following systemic miR-126-3p mimic treatment in a surgical mouse model of knee OA, we found reduced disease severity. Following miR-126-3p mimic treatment in human knee OA tissue explants, we found direct inhibition of genes associated with angiogenesis and indirect inhibition of genes associated with osteogenesis, adipogenesis, and synovitis. These findings suggest miR-126-3p becomes elevated during knee OA and mitigates disease processes to attenuate severity.
Cellular and biophysical barriers to lipid nanoparticle mediated delivery of RNA to the cytosol
Authors: Johansson Johanna M. , Du Rietz Hampus , Hedlund Hampus , Eriksson Hanna C. , Oude Blenke Erik , Pote Aditya , Harun Said , Nordenfelt Pontus , Lindfors Lennart , Wittrup Anders
Published: June 2024

Lipid nanoparticle (LNP) formulation was the first approved delivery strategy for liver-targeted siRNA delivery and currently represent the most advanced platform for delivery of therapeutic mRNA in clinical use, after the approval of mRNA-based vaccines against the SARS-CoV-2 coronavirus. Still, poor efficiency of LNPs to promote cytosolic delivery of both mRNA and siRNA after internalization by target cells limits their potency and thus clinical application as RNA delivery vehicles - especially in extrahepatic tissues and tumors. It is still unclear how endosomal escape of LNP-delivered RNA cargo occurs, and why only a minute proportion of all therapeutic molecules reach the cytoplasm. Here, we explored the intracellular sorting, integrity and endosomal escape of both mRNA and siRNA loaded LNPs to characterize the nature of RNA release from endosomal compartments and pinpoint current bottlenecks. Using live-cell imaging and super-resolution microscopy of LNPs with fluorescently labeled RNA payload, we identify multiple distinct steps of substantial inefficiency in the cytosolic delivery of nucleic acid cargoes. We demonstrate that membrane damages marked by recruitment of galectins are conducive to cytosolic RNA delivery, while membrane perturbations recruiting the ESCRT machinery do not permit endosomal escape. By quantitative single-vesicle analysis, we show that only a small fraction of the nucleic acid cargo contained in the endosome is released to the cytosol upon LNP-triggered membrane damage detected by galectins. Unexpectedly, we also observe that only a subset of damaged endosomes contain RNA payload. Through FRET and super-resolution microscopy, using LNPs formulated with both fluorescently labeled ionizable lipid (MC3-BODIPY) and RNA, we find that RNA cargo and ionizable lipid segregate during endosomal sorting - both within single endosomes and to different endosomal compartments. Finally, we visualize localized MC3-BODIPY enrichment in endosomal membranes and membrane damage in direct proximity to siRNA-LNPs tethered to the luminal vesicle membrane. Taken together, this work has identified multiple mechanistically distinct barriers limiting intracellular RNA delivery by LNPs.
Personalizing computational models to construct medical digital twins
Authors: Knapp Adam C. , Cruz Daniel A. , Mehrad Borna , Laubenbacher Reinhard C.
Published: June 2024

Digital twin technology, pioneered for engineering applications, is being adapted to biomedicine and healthcare; however, several problems need to be solved in the process. One major problem is that of dynamically calibrating a computational model to an individual patient, using data collected from that patient over time. This kind of calibration is crucial for improving model-based forecasts and realizing personalized medicine. The underlying computational model often focuses on a particular part of human biology, combines different modeling paradigms at different scales, and is both stochastic and spatially heterogeneous. A commonly used modeling framework is that of an agent-based model, a computational model for simulating autonomous agents such as cells, which captures how system-level properties are affected by local interactions. There are no standard personalization methods that can be readily applied to such models. The key challenge for any such algorithm is to bridge the gap between the clinically measurable quantities (the macrostate) and the fine-grained data at different physiological scales which are required to run the model (the microstate). In this paper we develop an algorithm which applies a classic data assimilation technique, the ensemble Kalman filter, at the macrostate level. We then link the Kalman update at the macrostate level to an update at the microstate level that produces microstates which are not only compatible with desired macrostates but also highly likely with respect to model dynamics.

Significance Statement

To realize the promise of personalized medicine, we need to be able to integrate different types of data collected from a given patient into a computational framework that enables decision making about optimal interventions to help this patient to either maintain or regain health. Digital twins represent such a framework, once the technology is sufficiently developed. A fundamental problem that currently does not have a widely applicable solution is how to calibrate a generic computational model of human biology to a given patient at a given time. This paper presents a solution to this problem for the agent-based model framework, commonly used to capture stochastic and spatially heterogeneous biological processes, such as tumor growth or immune system dynamics.
Collaboration between IL-7 and IL-15 enables adaptation of tissue-resident and circulating memory CD8+T cells
Authors: Jarjour Nicholas N. , Dalzell Talia S. , Maurice Nicholas J. , Wanhainen Kelsey M. , Peng Changwei , DePauw Taylor A. , Block Katharine E. , Valente William J. , Ashby K. Maude , Masopust David , Jameson Stephen C.
Published: June 2024

Interleukin-7 (IL-7) is considered a critical regulator of memory CD8+T cell homeostasis, but this is primarily based on analysis of circulating and not tissue-resident memory (TRM) subsets. Furthermore, the cell-intrinsic requirement for IL-7 signaling during memory homeostasis has not been directly tested. Using inducible deletion, we found thatIl7raloss had only a modest effect on persistence of circulating memory and TRMsubsets and that IL-7Rα was primarily required for normal basal proliferation. Loss of IL-15 signaling imposed heightened IL-7Rα dependence on memory CD8+T cells, including TRMpopulations previously described as IL-15-independent. In the absence of IL-15 signaling, IL-7Rα was upregulated, and loss of IL-7Rα signaling reduced proliferation in response to IL-15, suggesting cross-regulation in memory CD8+T cells. Thus, across subsets and tissues, IL-7 and IL-15 act in concert to support memory CD8+T cells, conferring resilience to altered availability of either cytokine.

Highlights

Tissue-resident and circulating memory CD8+T cells modestly decline after loss of IL-7Rα IL-7Rα is required for normal self-renewal of memory CD8+T cells

Combined loss of IL-7 and IL-15 causes a profound defect across memory CD8+T cell subsets Cross-regulation of IL-7 and IL-15 signaling occurs in memory CD8+T cells

Abstract Figure
High-Resolution In Silico Painting with Generative Models
Authors: Le Trang , Lundberg Emma
Published: June 2024

Label-free organelle prediction presents a longstanding challenge in cellular imaging, given the promise to to circumvent the numerous drawbacks associated with fluorescent microscopy, including its high costs, cytotoxicity, and time-consuming nature. Recent advancements in deep learning have introduced numerous effective algorithms, primarily deterministic, for predicting fluorescent patterns from transmitted light microscopy images. However, existing models frequently suffer from poor performance or are limited to specific datasets, image modalities, and magnifications, thus lacking a universal solution. In this paper, we present a simplified VQGAN training scheme that is easily adapted with different input/output channels for image-to-image translation tasks. We applied the algorithm to generate multi-channel organelle staining outputs from bright field inputs, equivalent to the popular Cell Painting assay. The same algorithm also participated and placed first in the ISBI 2024 Light My Cell challenge.
Developing and Benchmarking Sulfate and Sulfamate Force Field Parameters for Glycosaminoglycans via Ab Initio Molecular Dynamics Simulations
Authors: Riopedre-Fernandez Miguel , Kostal Vojtech , Martinek Tomas , Martinez-Seara Hector , Biriukov Denys
Published: June 2024

Glycosaminoglycans (GAGs) are negatively charged polysaccharides found on cell surfaces, where they regulate transport pathways of foreign molecules toward the cell. The structural and functional diversity of GAGs is largely attributed to varied sulfa-tion patterns along the polymer chains, which makes understanding their molecular recognition mechanisms crucial. Molecular dynamics (MD) simulations, with their un-matched microscopic perspective, have the potential to be a reference tool for exploring the patterns responsible for biologically relevant interactions. However, the capability of molecular dynamics models (i.e., force fields) used in biosimulations to accurately capture sulfation-specific interactions is not well established. In this work, we evalu-ate the performance of molecular dynamics force fields for sulfated GAGs by studying ion pairing of Ca2+to sulfated moieties — N-methylsulfamate and methylsulfate — that resemble N- and O-sulfation found in GAGs, respectively. We tested nonpolariz-able (CHARMM36 and GLYCAM06), explicitly polarizable (Drude and AMOEBA), and implicitly polarizable through charge scaling (prosECCo75 and GLYCAM-ECC75) force fields. The Ca–sulfamate/sulfate interaction free energy profiles obtained with the tested force fields were compared against reference ab initio molecular dynamics (AIMD) simulations. AIMD reveals that the preferential Ca2+binding mode to sul-fated GAG groups is solvent-shared pairing, and only the charge-scaled models agree satisfactorily with the AIMD data. All other force fields exhibit poorer performance, sometimes even qualitatively. Surprisingly, even explicitly polarizable force fields dis-play a notable shortfall in their performance, attributed to difficulties in their optimiza-tion and possible inherent limitations in depicting high-charge-density ion interactions accurately. Finally, the underperforming force fields lead to unrealistic aggregation of sulfated saccharides, qualitatively distorting our understanding of the soft glycocalyx environment. Our results highlight the importance of accurately treating electronic polarization in MD simulations of sulfated GAGs and caution against over-reliance on currently available models without thorough validation and optimization.