Display omitted
•Our study underscores the significance of integrating microgastropoda taxa into molecular phylogenetic analyses of gastropod subgroups.•Pomatias’s placement outside of Littorinoidea ...challenges traditional classification.•Lacuna’s placement indicates a close relationship with Naticidae, prompting consideration for its removal from Littorinidae.•Peasiella may belong to a distinct family separate from Littorinidae.•Pteropods is situated phylogenetically between Littorinoidea and Naticoidea.
Littorinoidea is one of the most diverse radiations and the most successful group that evolutionary transitions from marine to terrestrial within Littorinimorpha. With such an unmatched diversity, few phylogenetic investigations have attempted to understand their evolutionary relationships, and existing research has primarily focused on typical intertidal species. To address this gap, we conducted the first phylogenomic analysis of the Littorinoidea, leveraging 35 transcriptomes to investigate their internal relationships. Our analyses revealed significant revisions necessary within the Littorinoidea: 1) Pomatias appears distantly related to Littorinidae, suggesting a potential ancestral origin outside of Littorinoidea, challenging traditional classification. The homology of penial innervation within Littorinoidea warrants reevaluation. 2) Lacuna’s placement indicates a close relationship with Naticidae, prompting consideration for its removal from Littorinidae. 3) Based on the current phylogenetic research, Peasiella may belong to a distinct family separate from Littorinidae. 4) Our findings support revising the placement of Pteropods within the Littorinimorpha, which is situated phylogenetically between the families Littorinoidea and Naticoidea. Additionally, we highlight the impact of site heterogeneity and evolutionary rate variation on phylogenetic inference. Our study provides a robust phylogenomic framework for the Littorinoidea, emphasizing the importance of including microgastropoda taxa in molecular phylogenetic reconstructions of gastropod subgroups.
Epstein-Barr virus (EBV)-related nasopharyngeal carcinoma (NPC) is an epithelial malignancy arising from the nasopharyngeal mucosal lining. A high incidence was recorded in EBV-endemic areas (EA) ...such as East and Southeast Asia 1 while in Europe, a non-endemic area (NEA), is low (1/105/year); however, the estimated survival rate is much lower than that recorded in Asian EA (5-year age-standardized relative survival = 54–57% vs. 74%) 2. Risk factors of NPC include genetic, ethnic and environmental factors 3. Differences in incidence and survival rates between EA and NEA NPCs could involve several factors, including EBV-related factors, genetic susceptibility of the population to EBV infections, and environmental factors such as diet and pollution 4-7. Nevertheless, all proposed models of NPC pathogenesis are based on data derived from EA in Asia. Furthermore, clinical, pathogenic, and microenvironmental characteristics may play additional roles. EBV-related NPC in EA has already been characterized using genomic and transcriptomic data analysis 8-9. However, gene expression analysis data 10 of NEA NPC is limited. Comparing gene expression data from EA and NEA diseases allows the recognition of similarities and differences in incidence and outcome among diseases arising in different geographical areas. We investigated the transcriptomic patterns of genes involved in EA NPC to interpret these differences and verifying them to an Italian cohort with available tumor tissue and clinical data. The immune and biological/functional characterization of EA and NEA NPC could improve the identification of new therapeutic strategies. Currently, the treatment for localized NPC includes radiotherapy, which is often combined with platinum-based chemotherapy, especially for locally advanced cancer. Neoadjuvant chemotherapy with cisplatin and gemcitabine was administered in the case of high-risk disease 11 -12. Immunotherapy with checkpoint inhibitors has shown clinical efficacy in recurrent/metastatic advanced NPC and is currently under evaluation to define its mechanism of action 13. Our study aimed to dissect the gene expression (GE) and microenvironment of NPC, leading to the identification of the molecular subtypes of EA and NEA NPC. We also aimed to elucidate the biological and functional differences within EA NPC and between EA NPC and NEA NPC to eventually provide new insights into novel treatment strategies.
Six GE datasets of NPC-EA transcriptomic repositories, including tumor and normal samples (GSE12452, GSE34573, GSE132112, GSE53819, GSE68799, GSE102349) and one validation dataset including both EA and NEA (https://doi.org/10.5281/zenodo.5347891) were retrieved. Four GE signatures associated to EBV related NPC prognosis (PMID: 24297049, 35262435, 32596151, 33096113), genes/pathways and gene sets (PMID: 35846746, 35394843, 35105963) were applied on EA and NEA NPC cohorts (Liu_NPC, Wood EBV EBNA1 Targets Down, Sengupta NPC_with LMP1 UP, REACTOME DNA Repair; Hallmarks). A bioinformatic meta-analysis approach was used to integrate the six EA datasets, and the classifier method was applied to the validation dataset in order to identify the subtype with worst prognosis. Moreover, RNA sequencing was performed on 50 Italian NEA NPC samples (study number: INT188/19; GSE208281). Biological and functional profiling of EA and NEA were performed using xCell, Gene set enrichment analyses, and treatment prediction methods (radiosensitivity index PMID: 16103067, pRRophetic R package, Immunophenoscore PMID: 28052254).
Through the meta-analysis of EA-NPC datasets, four clusters (Cl) were identified. Prognostic analyses revealed that Cl3 had the worst prognosis (P=0.0476), confirmed by three of the four prognostic signatures and in the validation dataset (P=0.0368). The biological and functional characterization of these clusters disclosed the relative GE subtypes: Cl1, Immune-active; Cl2, Defense-response; Cl3, Proliferation;Cl4, Perineural-interaction/EBV-exhaustion. According to the treatment prediction methods, the sensitivity of each cluster was radiotherapy and immunotherapy for immune-active, radiochemotherapy and immunotherapy for defense-response, chemotherapy for proliferation, and cisplatin treatment for perineural-interaction/EBV-exhaustion. Only three clusters, excluding perineural-interaction/EBV-exhaustion, were expressed in our NEA cohort. Immune/biological characterization and treatment prediction analyses of NEA partially replicated the EA results.
Our study provides a relevant biological overview of EBV-related NPC in both EA and NEA. The immune microenvironment plays a critical role in NPC owing to the viral etiology of this malignancy. The presence of a perineural-interaction/EBV-exhaustion cluster in EA suggests an inactive EBV infection according to the viral related “hit and run theory”. Evaluation of miRNAs is ongoing along with miRNA/gene expression integration. Well characterized EA- and NEA-NPC retrospective and prospective cohorts are needed to validate the obtained results and can help designing future clinical studies.
Background
Atopic dermatitis (AD) is the most common chronic inflammatory skin disease with complex pathogenesis for which the cellular and molecular crosstalk in AD skin has not been fully ...understood.
Methods
Skin tissues examined for spatial gene expression were derived from the upper arm of 6 healthy control (HC) donors and 7 AD patients (lesion and nonlesion). We performed spatial transcriptomics sequencing to characterize the cellular infiltrate in lesional skin. For single‐cell analysis, we analyzed the single‐cell data from suction blister material from AD lesions and HC skin at the antecubital fossa skin (4 ADs and 5 HCs) and full‐thickness skin biopsies (4 ADs and 2 HCs). The multiple proximity extension assays were performed in the serum samples from 36 AD patients and 28 HCs.
Results
The single‐cell analysis identified unique clusters of fibroblasts, dendritic cells, and macrophages in the lesional AD skin. Spatial transcriptomics analysis showed the upregulation of COL6A5, COL4A1, TNC, and CCL19 in COL18A1‐expressing fibroblasts in the leukocyte‐infiltrated areas in AD skin. CCR7‐expressing dendritic cells (DCs) showed a similar distribution in the lesions. Additionally, M2 macrophages expressed CCL13 and CCL18 in this area. Ligand–receptor interaction analysis of the spatial transcriptome identified neighboring infiltration and interaction between activated COL18A1‐expressing fibroblasts, CCL13‐ and CCL18‐expressing M2 macrophages, CCR7‐ and LAMP3‐expressing DCs, and T cells. As observed in skin lesions, serum levels of TNC and CCL18 were significantly elevated in AD, and correlated with clinical disease severity.
Conclusion
In this study, we show the unknown cellular crosstalk in leukocyte‐infiltrated area in lesional skin. Our findings provide a comprehensive in‐depth knowledge of the nature of AD skin lesions to guide the development of better treatments.
Single‐cell RNA‐ and spatial RNA‐seq identified complex cellular interactionsin lesional skin of AD. COL18A1+ fibroblasts express COL6A5, COL4A1, TNC, and CCL19 and interact with CCR7 positive LAMP3+ dendritic cells and T cells. CCL13+ and CCL18+ M2 macrophages show an interaction with T cells by MRC1‐PTPRC and CD14‐ITGB1/2. The serum level of TNC and CCL18 shows a positive correlation with AD severity. Abbreviations: AD, atopic dermatitis; CCL, C–C motif chemokine ligand; CCR, C–C motif chemokine receptor; COL, collagen; ITGB, integrin beta; LAMP3, lysosome‐associated membrane glycoprotein 3; MRC, mannose receptor C; PTPRC, protein tyrosine phosphatase receptor; TNC, Tenascin C
The intestinal epithelium is a highly structured tissue composed of repeating crypt-villus units. Enterocytes perform the diverse tasks of absorbing a wide range of nutrients while protecting the ...body from the harsh bacterium-rich environment. It is unknown whether these tasks are spatially zonated along the villus axis. Here, we extracted a large panel of landmark genes characterized by transcriptomics of laser capture microdissected villus segments and utilized it for single-cell spatial reconstruction, uncovering broad zonation of enterocyte function along the villus. We found that enterocytes at villus bottoms express an anti-bacterial gene program in a microbiome-dependent manner. They next shift to sequential expression of carbohydrates, peptides, and fat absorption machineries in distinct villus compartments. Finally, they induce a Cd73 immune-modulatory program at the villus tips. Our approach can be used to uncover zonation patterns in other organs when prior knowledge of landmark genes is lacking.
Display omitted
•Laser capture microdissection reveals a large panel of enterocyte landmark genes•These genes are used to spatially localize single RNA-sequenced enterocytes•Enterocyte function is broadly zonated along the villus axis•Enterocytes traverse a series of cell states during their migration along the villus
A broadly applicable single-cell spatial transcriptomics approach reveals broad regional and functional heterogeneity of small intestinal enterocytes.
The process of cardiac morphogenesis in humans is incompletely understood. Its full characterization requires a deep exploration of the organ-wide orchestration of gene expression with a single-cell ...spatial resolution. Here, we present a molecular approach that reveals the comprehensive transcriptional landscape of cell types populating the embryonic heart at three developmental stages and that maps cell-type-specific gene expression to specific anatomical domains. Spatial transcriptomics identified unique gene profiles that correspond to distinct anatomical regions in each developmental stage. Human embryonic cardiac cell types identified by single-cell RNA sequencing confirmed and enriched the spatial annotation of embryonic cardiac gene expression. In situ sequencing was then used to refine these results and create a spatial subcellular map for the three developmental phases. Finally, we generated a publicly available web resource of the human developing heart to facilitate future studies on human cardiogenesis.
Display omitted
•Profiled spatiotemporal gene expression patterns in human cardiogenesis•Mapped cell-type distribution and spatial organization in the human embryonic heart•Thoroughly analyzed roles of diverse cell types in cardiac development•A publicly available web resource of the human embryonic heart
The gene expression landscape of human heart development is explored at single-cell resolution with spatial transcriptomic approaches to construct a 3D organ-wide atlas.
PDF
