Biology subjects

Bock, C.

Publications and source records attributed to Bock, C..

At least 19 recordsLinked to original sources

bioRxiv2026

Mutanome-guided immunopeptidomics of blood plasma for neoepitope detection in solid tumors is constrained by cfDNA variant calling sensitivity and MS detection limits

Introduction: Neoepitopes form the basis of tumor-specific immune responses. Tissue biopsy, the primary source for neoepitope detection, is limited and invasive. Therefore, we aimed to identify neoepitopes by mutanome-guided immunopeptidomics from plasma of cancer patients. Methods: Mass spectrometry (MS) data analysis of HLA ligands from plasma (n = 4) was guided by patient-specific mutanomes of cell-free DNA (cfDNA) from plasma or tumor genomic DNA (tgDNA) from tissue. Matched tumor tissue and healthy donor plasma served as controls. Neoepitopes were validated with synthetic peptides, and immunogenicity was assessed using IFN-gamma ELISpot and intracellular cytokine staining. Results: Wild-type immunopeptidomes from tissue and plasma overlapped by 58%, with 91% of plasma HLA ligands rediscovered in tissue. 13 out of 15 tumor-associated HLA ligands detected in plasma were rediscovered in the matching tissue. However, no neoepitopes in plasma were identified by immunopeptidomics guided by cfDNA mutanomes, likely reflecting the limited overlap between cfDNA and tgDNA mutanomes (15%). Using the tgDNA mutanome as a complementary reference, two neoepitopes were detected in one patient's plasma, albeit at the MS detection limit. Both neoepitopes were also discovered in tissue, along with three tissue-exclusive neoepitopes. Two tissue-exclusive neoepitopes induced antigen-specific T cell responses in healthy donor PBMCs. Conclusion: In summary, plasma immunopeptidomics enables profiling of HLA ligands from wild-type proteins, including TAAs. In principle, neoepitope detection from plasma at the peptide level is feasible, but tissue remains the gold standard for variant calling and neoepitope identification. Improved detection methods may enable minimally invasive approaches in the future.

immunology↗

bioRxiv2026

Novel biologically relevant small RNA-sequencing alignment tool LevenMap for alignment to database of non-coding RNAs

A crucial aspect of the bioinformatics workflow in small RNA-sequencing is the alignment of reads to a database of reference ncRNAs. Alignment algorithms such as Bowtie, Burrows-Wheeler Aligner (BWA), and Spliced Transcripts Alignment to a Reference (STAR) - which are designed for aligning reads to a reference genome - are typically used. Aligning short RNA-sequenced reads to a database of non-coding RNAs (ncRNAs) is fundamentally a different task than aligning longer reads to a genome due to ncRNAs (i) having roughly the same number of nucleotides as the reads being aligned and (ii) being subsequences of other ncRNAs. To account for these differences, we developed the novel alignment algorithm LevenMap. Of all reads which exactly matched a reference ncRNA in a publicly available dataset, LevenMap aligned 100.0% of them to their respective ncRNA while all other aligners mapped less than 40% of these reads to their corresponding ncRNA. Furthermore, the mean ratio (length of read) / (length of corresponding reference ncRNA) of all aligned reads was 1.0 and 0.998 for LevenMap with at most zero and one mismatch(es) allowed, respectively; this ratio was no more than 0.51 for all other aligners. Overall, LevenMap is designed to account for the nuances of aligning small RNA-sequencing data to a database of reference ncRNAs and yields more biologically relevant counts compared to traditional aligners in this context. LevenMap is free and publicly available on GitHub: https://github.com/hdlugas/LevenMap.

bioinformatics↗

bioRxiv2026

Mtor/Rptor Function Globally Prevents Cortical Microcephaly and Cell-autonomously Promotes Postnatal Neuron Survival in Cell Type Specific Manner

The generation of faithful cell-type diversity and correct projection neuron numbers is essential for cerebral cortex development. Corticogenesis is however susceptible to genetic interference of critical signaling pathways, including mutations in Mtor/Rptor that lead to microcephaly. How the loss of Rptor/mTORC1 function affects cortical developmental programs, at single cell level, is still unknown. Here, we utilized Mosaic Analysis with Double Markers (MADM) technology to probe Rptor gene function upon sparse single cell- or global tissue-wide ablation. We found that tissue-wide effects drive the etiology of cortical microcephaly upon loss of Rptor, rather than deficits in projection neuron genesis. Conversely, Rptor function is cell-autonomously required for postnatal projection neuron survival in a highly cell-type-specific manner. Collectively, our results suggest that the fine balance of precise cell-type-specific cell-autonomous Rptor/mTORC1 function in concert with non-cell-autonomous tissue-wide effects is essential for the development of a properly-sized cerebral cortex with accurate projection neuron diversity.

neuroscience↗

bioRxiv2025

Leveraging species-wide variation and patterns of adaptation to inform pecan crop improvement efforts

The genetic basis of adaptation is a fundamental question in evolutionary biology, and understanding how species will be able to adapt to changing conditions across their range has important implications for conservation and agriculture. To accurately interrogate the genetics of adaptation and assess the adaptive capacity of a species requires also characterizing the ways other mechanisms, including geographic distance and population dynamics, shape genetic variation. Pecan is an ecologically, culturally, and economically important North American tree, and a broader understanding of the genetics of environment adaptation will aid pecan conservation, breeding, and commercial management. Here, we use an expansive set of more than 700 pecan genotypes in combination with the first haplotype-resolved genome assembly for pecan to assess species-wide genetic variation and evaluate environmental adaptation across the native distribution. We identify five gene pools in pecan, with the lowest diversity in southern gene pools, and present evidence that gene pools began differentiating during multiple glacial cycles. Using complementary genotype-environment association approaches, we infer species-wide patterns of environmental adaptation. With these results, we predict mismatches in adaptation for pecan genotypes to different environments, including future environment scenarios. We see that in all locations, present-day genotypes incur some level of predicted maladaptation to simulated future environments, but current genetic diversity may provide a valuable source of resilience to future conditions through assisted migration. These results expand the understanding of environmental adaptation in pecan and provide insight into how long-lived species will be able to adapt to future conditions.

evolutionary biology↗

bioRxiv2025

Uncovering the transcriptional hallmarks of endothelial cell aging via integrated single-cell analysis

Endothelial cells (ECs) are critical regulators of vascular function and exhibit specialized, organ-specific roles across tissues. During aging, these cells become dysfunctional, resulting in increased susceptibility to cardiovascular disease and its associated mortality. While single-cell transcriptomics studies have revealed extensive endothelial heterogeneity across tissues and conditions, a comprehensive atlas of human EC transcriptomes over the course of the adult human lifespan is still lacking. Here, we present the Human Aging Endothelial Cell Atlas (HAECA), a harmonized single-cell transcriptomic compendium of over 375,000 ECs from 12 human tissues throughout adulthood. Using HAECA, we identified age-associated transcriptional shifts, including a decline in angiogenic gene expression in venous ECs and widespread alterations in extracellular matrix (ECM)- and mechanotransduction-associated pathways. We validated these findings in aging human skin and further uncovered a p21-linked transcriptional program in ECs, confirmed in both in vitro and in vivo models and linked to cellular senescence. Together, our study provides a high-resolution transcriptome reference across spatial as well as temporal axes of the human endothelium.

cell biology↗

bioRxiv2025

Purine nucleobases enhance CD8+ T cell effector function

During antiviral immune responses, activated immune cells remodel metabolic pathways towards uptake and utilization of biosynthetic and bioenergetic metabolites. Concurrently, viral infections alter metabolic environments, impacting metabolite availability for the establishment of an effective immune response. Here, we integrated in vivo metabolomics data from murine and human viral infections with in vitro metabolite screens, identifying purine nucleobases as novel immunometabolites that enhance CD8+ T cell effector function. We found that CD8+ T cells can switch from resource-intensive purine de novo synthesis to purine salvage pathway, to produce nucleotides from purine nucleobases. This strategy of metabolic adaptation allows diversion of biosynthetic and bioenergetic resources towards enhancing effector molecule production. Our findings unveil an adaptation strategy by CD8+ T cells to manage metabolic challenges in dynamic organismal environments and suggest pharmacological targets in purine metabolism as potential targets for immunotherapy. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=144 SRC="FIGDIR/small/669899v1_ufig1.gif" ALT="Figure 1"> View larger version (65K): org.highwire.dtl.DTLVardef@17b4b15org.highwire.dtl.DTLVardef@17e57a3org.highwire.dtl.DTLVardef@1abc36aorg.highwire.dtl.DTLVardef@1aa704a_HPS_FORMAT_FIGEXP M_FIG C_FIG Instead of producing nucleotides via purine de novo synthesis, CD8+ T cells can import and utilize purine nucleobases via the purine salvage pathway to divert bioenergetic and biosynthetic resources towards effector function. By shifting from purine de novo synthesis to the purine salvage pathway, cells save significant resources: 5 moles of the key bioenergetic metabolite ATP, and biosynthetic metabolites including 2 moles of glutamine, 1 mole each of serine or glycine, and 1 mole of aspartate.

immunology↗

bioRxiv2025

Molecularly informed analysis of histopathology images using natural language

Histopathology refers to the microscopic examination of diseased tissues and routinely guides treatment decisions for cancer and other diseases. Currently, this analysis focuses on morphological features but rarely considers gene expression information, which can add an important molecular dimension. Here, we introduce SpotWhisperer, an AI method that links histopathological images to spatial gene expression profiles and their text annotations, enabling molecularly grounded histopathology analysis through natural language. Our method outperforms pathology vision-language models on a newly curated benchmark dataset, dedicated to spatially resolved H&E annotation. Integrated into a web interface, SpotWhisperer enables interactive exploration of cell types and disease mechanisms using free-text queries with access to inferred spatial gene expression profiles. In summary, SpotWhisperer analyzes cost-effective pathology images with spatial gene expression and natural-language AI, demonstrating a path for routine integration of microscopic molecular information into histopathology.

bioinformatics↗

bioRxiv2025

Time-resolved immune dynamics in rheumatoid arthritis under Methotrexate therapy

Rheumatoid arthritis (RA) is characterized by immune dysregulation, including alterations in peripheral blood mononuclear cell (PBMC) populations and aberrant cytokine signaling. Methotrexate (MTX) is the preferred first-line treatment for RA, yet its precise mechanisms of action remain incompletely understood. This study employed a multi-omics strategy--combining single-cell RNA sequencing (scRNA-seq) and immunophenotyping--to identify key effector peripheral immune cells and their cellular responses in RA patients over 12 weeks of MTX treatment. In our study, MTX was associated with significant immune modulation, including the restoration of naive T and B cells and reductions in T cell memory subsets with these effects detectable as early as three weeks post-treatment. Plasmablast levels also emerged as a potential biomarker for early therapeutic response, reflecting MTXs impact on immune homeostasis. Transcriptional analysis revealed modulation of key pathways, including TNF- signaling, B cell receptor signaling, and T cell receptor-mediated apoptosis. Network analysis identified critical regulatory hubs, such as EGR1, JAK2, and SOCS1, in monocytes and CD4 memory T cells, highlighting these cell types as key mediators of MTXs effects. In conclusion, these findings advance our understanding of MTXs effects on immune cell dynamics at different stages of treatment, showing for the first time the early cellular changes leading to immune modulation in RA. Altogether, our results provide the foundation for further mechanistic investigations into MTX.

genomics↗

bioRxiv2024

PHLPP2 is a pseudophosphatase that lost activity in the metazoan ancestor

The phosphoinositide 3-kinase (PI3K) pathway is a major regulator of cell and organismal growth. Consequently, hyperactivation of PI3K and its downstream effector kinase, Akt, is observed in many human cancers. PH domain leucine-rich repeat-containing protein phosphatases (PHLPP), two paralogous members of the metal-dependent protein phosphatase family, have been reported as negative regulators of Akt signaling and, therefore, tumor suppressors. However, the stoichiometry and identity of the bound metal ion(s), mechanism of action, and enzymatic specificity of these proteins are not known. Seeking to fill these gaps in our understanding of PHLPP biology, we unexpectedly discovered that PHLPP2 has no catalytic activity against the regulatory phosphorylation sites of Akt, nor the generic substrate para -nitrophenylphosphate. Instead, we found that PHLPP2 is a pseudophosphatase with a single zinc ion bound in its catalytic center. Furthermore, we found that current cancer genomics data do not support the proposed role of PHLPP1 or PHLPP2 as tumor suppressors. Phylogenetic analyses revealed an ancestral phosphatase that arose more than 1 Mya, but that lost activity at the base of the metazoan lineage. In summary, our results provide a molecular explanation for the inconclusive results that have hampered research on PHLPP and argue for a new focus on non-catalytic roles of PHLPP1 and PHLPP2. Significance StatementPHLPP1 and PHLPP2 have previously been reported as protein phosphatases that specifically inactivate Akt, a pro-growth and survival kinase hyperactivated in many human cancers. Unexpectedly, we found that purified PHLPP2 has no detectable enzymatic activity in vitro, an observation which can be rationalized by its unusual active site, which has diverged significantly from that of canonical metal-dependent phosphatases. Furthermore, we show that cancer genomics do not support a role for either PHLPP1 or PHLPP2 in cancer. Our findings argue for the exploration of alternative hypotheses regarding the role of PHLPP in Akt signaling and cancer, with a focus on its non-catalytic functions.

biochemistry↗

bioRxiv2024

Reconstitution of Human Brain Cell Diversity in Organoids via Four Protocols

Human brain organoids are powerful in vitro models for brain development and disease. However, their variability can complicate use in biomedical research and drug discovery. Both the specific protocol as well as the pluripotent starting cell line influence organoid variability and can result in incomplete representation of brain cell types in an organoid experiment. Here, we systematically analyze the cellular and transcriptional landscape of brain organoids grown from multiple cell lines using four different protocols recapitulating dorsal and ventral forebrain, midbrain, and striatum. We establish the NEST-Score as a quantitative readout for cell line-driven and protocol-driven differentiation propensities by comparing cellular states across multiple cell lines and to in vivo reference data sets. Thereby, we establish a set of organoid protocols that together recreate the vast majority of cell types in the developing human brain and provide a reference for how well cell types are recapitulated across cell lines in each protocol. Additionally, we survey factors contributing to variability during organoid development and identify early gene expression signatures predicting protocol-driven organoid generation at later stages. We provide easy online access to our data through a web-based analysis tool, creating a reference for brain organoid research that allows rapid, straightforward validation of protocol and cell line performance.

developmental biology↗

bioRxiv2024

Comparative RT-qPCR and qPCR reveals early infection, low-titer infection, and relative cell activity of the HLB bacterium, Candidatus Liberibacter asiaticus

Candidatus Liberibacter asiaticus (Las) is one of the causal agents of citrus huanglongbing (HLB) epidemics worldwide. Due to its fastidious nature, intracellular and systemic infection, detecting Las at early and/or low-titer infection, as well as differentiating between live or dead cells in the host psyllids and citrus plants is critical for effective HLB management. To achieve both sensitive Las detection and differentiation, we employed one-step reverse transcription-quantitative PCR (RT-qPCR) using total nucleic acids as template. This method allows use of both Las 16S rRNA and rDNA as template in the same reaction and increases detection sensitivity by up to 1000-fold in comparison with quantitative PCR (qPCR). The increased sensitivity significantly reduces false negative detection and detects the otherwise undetectable low-titer Las infections. Furthermore, the greater the abundance of 16S rRNA present in the samples, the bigger the Ct gap obtained between RT-qPCR and qPCR results. The numerical Ct gap can be used to deduce relative Las cellular activity and indirectly infer whether cells are alive or dead. In addition, this comparative detection method also can be used to select inoculum and monitor relative cell activity during in vitro Las culture and evaluate the effectiveness of antimicrobial treatments against Las bacteria.

molecular biology↗

bioRxiv2024

Multimodal learning of transcriptomes and text enables interactive single-cell RNA-seq data exploration with natural-language chats

Single-cell RNA-seq characterizes biological samples at unprecedented scale and detail, but data interpretation remains challenging. Here we introduce CellWhisperer, a multimodal machine learning model and software that connects transcriptomes and text for interactive single-cell RNA-seq data analysis. CellWhisperer enables the chat-based interrogation of transcriptome data in English language. To train our model, we created an AI-curated dataset with over a million pairs of RNA-seq profiles and matched textual annotations across a broad range of human biology, and we established a multimodal embedding of matched transcriptomes and text using contrastive learning. Our model enables free-text search and annotation of transcriptome datasets by cell types, states, and other properties in a zero-shot manner and without the need for reference datasets. Moreover, Cell-Whisperer answers questions about cells and genes in natural-language chats, using a biologically fluent large language model that we fine-tuned to analyze bulk and single-cell transcriptome data across various biological applications. We integrated CellWhisperer with the widely used CELLxGENE browser, allowing users to in-teractively explore RNA-seq data through an integrated graphical and chat interface. Our method demonstrates a new way of working with transcriptome data, leveraging the power of natural language for single-cell data analysis and establishing an important building block for future AI-based bioinformatics research assistants.

bioinformatics↗

bioRxiv2024

Mechanical Centrosome Fracturing during Cell Navigation

The centrosome is the primary microtubule orchestrator in most eukaryotic cells, nucleating and anchoring microtubules that grow radially and exert forces on cargos. At the same time, mechanical stresses from the microenvironment and cellular shape changes compress and bend microtubules. Yet, centrosomes are membrane-less organelles, raising the question of how centrosomes withstand mechanical forces. Here we discover that centrosomes in non-dividing cells can mechanically fracture. We reveal that centrosomes experience mechanical deformations during microenvironmental confinement and navigational pathfinding by motile cells. Coherence of the centrosome is maintained by Dyrk3, preventing fracturing by mechanical forces. Centrosome fracturing impedes cellular function by generating coexisting microtubule organizing centers that compete during path navigation and thereby cause cellular entanglement in the microenvironment. Our findings show that non-dividing cells actively maintain the integrity of the centrosome to withstand mechanical forces. Given that almost all cells in multicellular organism experience forces, these results suggest that centrosome stability preservation is fundamental during development, tissue maintenance, immunology, and disease. One-Sentence SummaryPathfinding during cellular motility causes centrosome breakage counteracted by Dyrk3 activity.

cell biology↗

bioRxiv2024

Pipeline Olympics: continuable benchmarking of computational workflows for DNA methylation sequencing data against an experimental gold-standard

DNA methylation is a widely studied epigenetic mark and a powerful biomarker of cell type, age, environmental exposures, and disease. Whole-genome sequencing following selective conversion of unmethylated cytosines into thymines via bisulfite treatment or enzymatic methods remains the reference method for DNA methylation profiling genome-wide. While numerous software tools facilitate processing of DNA methylation sequencing reads, a comprehensive benchmarking study has been lacking thus far. In this study, we systematically compared complete computational workflows for processing DNA methylation sequencing data using a dedicated benchmarking dataset generated with five genome-wide profiling protocols. As an evaluation reference, we employed highly quantitative locus-specific measurements from our preceding benchmark of targeted DNA methylation assays. Based on this experimental gold-standard assessment and several comprehensive metrics, we identified workflows that consistently demonstrated superior performance and revealed major workflow development trends. To facilitate the sustainability of our benchmark, we implemented an interactive workflow execution and data presentation platform, adaptable to user-defined criteria and seamlessly expandable to future software.

bioinformatics↗

bioRxiv2024

HDAC1 controls the generation and maintenance of effector-like CD8+ T cells during chronic viral infection

CD8+ T cell exhaustion is a complex process that involves the differentiation of persistently activated CD8+ T cells into functionally distinct cell subsets. Here, we investigated the role of the key epigenetic regulator histone deacetylase 1 (HDAC1) in the differentiation of exhausted T (Tex) cells during chronic viral infection. We uncovered that HDAC1 controls the generation and maintenance of effector-like CX3CR1+ Tex cells in a CD8+ T cell-intrinsic manner. Deletion of HDAC1 led to expansion of an alternative Tex cell subset characterized by high expression of T cell exhaustion markers, and this was accompanied by elevated viremia. HDAC1 knockout altered the chromatin landscape in progenitor Tex cells, abrogated the expression of effector-like signature genes and interfered with cell fate specification toward the CX3CR1+ Tex cell subset. We conclude that HDAC1 is functionally required for controlling viral load during chronic infection by ensuring adequate CX3CR1+ Tex cell subset differentiation. HighlightsO_LIHDAC1 promotes the generation of CX3CR1+ effector-like Tex cell subsets in chronic viral infection in a CD8+ T cell-intrinsic manner. C_LIO_LIDeletion of HDAC1 leads to an increase of a cell subset enriched in exhaustion markers and is accompanied with elevated viremia. C_LIO_LIHDAC1 is required for the maintenance of the CX3CR1+ Tex cell pool. C_LIO_LIHDAC1 deletion alters the chromatin landscape at effector-like signature gene loci in progenitor Tex cells. C_LI

immunology↗

bioRxiv2024

Altered spawning seasons of Atlantic salmon broodstock genetically and epigenetically influence cell cycle and lipid-mediated regulations in their offspring

Manipulating spawning seasons of Atlantic salmon (Salmo salar) is a common practice to facilitate year-round harvesting in salmon aquaculture. This process involves adjusting water temperature and light regime to control female broodstock maturation. However, recent studies have indicated that altered spawning seasons can significantly affect the nutritional status and growth performance of the offspring. Therefore, gaining a deeper understanding of the biological regulations influenced by these alterations is crucial to enhance the growth performance of fish over multiple generations. In this study, we investigated omics data from four different spawning seasons achieved through recirculating aquaculture systems (RAS) and sea-pen-based approaches. In addition to the normal spawning season in November (sea-pen), three altered seasons were designated: off-season (five-month advance, RAS), early season (two-month advance, sea-pen), and late season (two-month delay, sea-pen). We conducted comprehensive gene expression and DNA methylation analysis on liver samples collected from the start-feeding larvae of the next generation. Our results revealed distinct gene expression and DNA methylation patterns associated with the altered spawning seasons. Specifically, offspring from RAS-based off-season exhibited altered lipid-mediated regulation, while those from sea-pen-based early and late seasons showed changes in cellular processes, particularly in cell cycle regulation when compared to the normal season. The consequences of our findings are significant for growth and health, potentially providing information for developing valuable tools for assessing growth potential and optimizing production strategies in aquaculture. Author SummaryThis study examines the impact of manipulating Atlantic salmon spawning seasons in aquaculture on genetic and epigenetic regulations in their offspring. Manipulating water temperature and light cycles during broodstock rearing allows for year-round harvesting. In aquaculture, altering spawning seasons is a common practice; however, recent research suggests that these changes affect the nutritional status and growth of offspring. To understand these effects at the molecular level, we analysed transcriptomic and epigenetic data from salmon offspring born to broodstock with four different spawning seasons. Our results reveal distinct transcriptomic and epigenetic patterns associated with altered seasons, influencing lipid metabolism and cell cycle regulation. These findings hold significant implications for improving aquaculture practices, potentially enhancing growth performance and nutritional quality of farmed salmon across generations as temperature and light are crucial abiotic factors influencing the next generation. Furthermore, our study potentially contributes to understanding the impact of climate change on the spawning behaviour of aquatic vertebrates, particularly in relation to increasing global ocean temperatures and the resulting changes in photoperiod as species migrate northward in the Northern Hemisphere, experiencing longer daylight in summer and shorter daylight in winter.

genomics↗

bioRxiv2023

One-carbon metabolism nutrients impact the interplay between DNA methylation and gene expression in liver, enhancing protein synthesis in Atlantic Salmon

Supplementation of one-carbon (1C) metabolism micronutrients, which include B-vitamins and methionine, is essential for the healthy growth and development of Atlantic salmon (Salmo salar). However, the recent shift towards non-fish meal diets in salmon aquaculture has led to the need for reassessments of recommended micronutrient levels. Despite the importance of 1C metabolism in growth performance and various cellular regulations, the molecular mechanisms affected by these dietary alterations are less understood. To investigate the molecular effect of 1C nutrients, we analysed gene expression and DNA methylation using two types of omics data: RNA sequencing (RNA-seq) and reduced-representation bisulfite sequencing (RRBS). We collected liver samples at the end of a feeding trial that lasted 220 days through the smoltification stage, where fish were fed three different levels of four key 1C nutrients: methionine, vitamin B6, B9, and B12. Our results indicate that the dosage of 1C nutrients significantly impacts genetic and epigenetic regulations in the liver of Atlantic salmon, particularly in biological pathways related to protein synthesis. The interplay between DNA methylation and gene expression in these pathways may play an important role in the mechanisms underlying growth performance affected by 1C metabolism. Author SummaryAtlantic salmon rely on one-carbon (1C) metabolism micronutrients like B-vitamins and methionine, which they acquire through their diets. Small pelagic fish are the primary source in the wild, but finding sustainable alternatives such as plants, insects, and algae is challenging as salmon aquaculture expands. Adjusting nutrient levels when changing base ingredients further complicates the task. Understanding the molecular mechanisms affected by these micronutrients is crucial for aquaculture sustainability. In this study, we investigated the molecular effects of 1C metabolism micronutrients on Atlantic salmon. Liver samples from salmon fed varying levels of key 1C nutrients over a 220-day trial were analysed using RNA sequencing (RNA-seq) and reduced-representation bisulfite sequencing (RRBS) to assess gene expression and DNA methylation, respectively. Our results revealed significant impacts of 1C nutrient dosage on genetic and epigenetic regulations in the salmon liver, particularly in protein synthesis pathways. The interplay between DNA methylation and gene expression in these pathways influences growth performance under 1C metabolism. Uncovering molecular changes resulting from dietary alterations provides valuable insights to optimize nutritional requirements in salmon aquaculture, supporting sustainable production and welfare of this important species.

genetics↗

bioRxiv2023

Single-cell profiling uncovers regulatory programs of pathogenic Th2 cells in allergic asthma

Lung pathogenic T helper type 2 (pTh2) cells are important drivers of allergic asthma, but fundamental questions remain regarding their regulation and heterogeneity. The differentiation and effector functions of immune cells are tightly regulated by epigenetic processes. Histone deacetylase 1 (HDAC1) is an important epigenetic regulator of T cells, however, its role in pTh2 cells is yet to be determined. Here we investigate immune regulation in allergic asthma by single-cell RNA sequencing (scRNA-seq) in mice challenged with house dust mite, in the presence and absence of HDAC1 function. Our analyses reveal two distinct subsets of lung pTh2 cells: pathogenic effector Th2 (peTh2) and pathogenic Th2 tissue-resident memory (Th2 Trm) cells. Both pTh2 cell subsets are highly proinflammatory and exhibit distinct transcriptional and phenotypic signatures as compared with other lung Th subsets. Based on our scRNA-seq analysis, we identify conditions to generate pTh2 cells in vitro and confirm that these in vitro generated pTh2 cells have a similar transcriptional profile as lung peTh2 cells. Using our new in vitro model, we demonstrate that the p38 mitogen-activated protein kinase pathway is critical for interleukin-5 (IL-5) and IL-13 expression in pTh2 cells. Our data further underline the importance of HDAC1 in limiting the pathogenicity of lung and in vitro pTh2 cells and in the formation of lung Th2 Trm cells. In summary, we have generated novel insights into pTh2 cell biology and established a new in vitro model for investigating pTh2 cells that will be useful for discovering molecular mechanisms involved in pTh2-mediated allergic asthma.

immunology↗