Defining cell types and lineage in the Drosophila midgut using single cell transcriptomics

A single-cell atlas of the Culex tarsalis midgut during West Nile virus infection

The mosquito midgut functions as a key interface between pathogen and vector. However, studies of midgut physiology and associated virus infection dynamics are scarce, and in Culex tarsalis - an extremely efficient vector of West Nile virus (WNV) - nonexistent. We performed single-cell RNA sequencing on Cx. tarsalis midguts, defined multiple cell types, and determined whether specific cell types are more permissive to WNV infection. We identified 20 cell states comprised of 8 distinct cell types, consistent with existing descriptions of Drosophila and Aedes aegypti midgut physiology. Most midgut cell populations were permissive to WNV infection. However, there were higher levels of WNV RNA (vRNA) in enteroendocrine cells and cells enriched for mitochondrial genes, suggesting enhanced replication in these populations. In contrast, proliferating intestinal stem cell (ISC) populations had the lowest levels of vRNA, a finding consistent with studies suggesting ISC proliferation in the midgut is involved in viral control. Notably, we did not detect significant WNV-infection induced upregulation of canonical mosquito antiviral immune genes (e.g., AGO2, R2D2, etc.) at the whole-midgut level. Rather, we observed a significant positive correlation between immune gene expression levels and vRNA in individual cells, suggesting that within midgut cells, high levels of vRNA may trigger antiviral responses. Our findings establish a Cx. tarsalis midgut cell atlas, and provide insight into midgut infection dynamics of WNV by characterizing cell-type specific enhancement/restriction of, and immune response to, infection at the single-cell level.

The septate junction component bark beetle is required for Drosophila intestinal barrier function and homeostasis

Age-related loss of intestinal barrier function has been documented across species, but the causes remain unknown. The intestinal barrier is maintained by tight junctions (TJs) in mammals and septate junctions (SJs) in insects. Specialized TJs/SJs, called tricellular junctions (TCJs), are located at the nexus of three adjacent cells, and we have shown that aging results in changes to TCJs in intestines of adult Drosophila melanogaster. We now demonstrate that localization of the TCJ protein bark beetle (Bark) decreases in aged flies. Depletion of bark from enterocytes in young flies led to hallmarks of intestinal aging and shortened lifespan, whereas depletion of bark in progenitor cells reduced Notch activity, biasing differentiation toward the secretory lineage. Our data implicate Bark in EC maturation and maintenance of intestinal barrier integrity. Understanding the assembly and maintenance of TCJs to ensure barrier integrity may lead to strategies to improve tissue integrity when function is compromised.

Comparative transcriptome analysis reveals regional specialization of gene expression in larval silkworm (Bombyx mori) midgut

Insect midgut plays a central role in food digestion and nutrition absorption. Larval silkworm midgut could be divided into 3 distinct regions based on their morphological colors. However, it remains rudimentary of regional gene expression and physiological function in larval silkworm midgut. Through transcriptome sequencing of 3 midgut compartments, a comprehensive analysis of gene expression atlas along the anterior-posterior axis was conducted. Posterior midgut was found transcriptionally divergent from anterior and middle midgut. Differentially expressed gene analysis revealed the regional specialization of digestive enzyme production, transmembrane transport, chitin metabolism, and hormone regulation in different midgut regions. In addition, gene subsets of pan-midgut and region-specific transcription factors (TFs) along the length of midgut were also identified. The results suggested that homeobox TFs might play an essential role in transcriptional variations across the midgut. Altogether, our study provided the first fundamental resource to investigate physiological function and regulation mechanism in larval midgut compartmentalization.

Ursolic Acid Protects Sodium Dodecyl Sulfate-Induced Drosophila Ulcerative Colitis Model by Inhibiting the JNK Signaling

Ursolic acid (UA) is a bioactive molecule widely distributed in various fruits and vegetables, which was reported to play a therapeutic role in ulcerative colitis (UC) induced by toxic chemicals. However, the underlying mechanism has not been well clarified in vivo. Here, using a Drosophila UC model induced by sodium dodecyl sulfate (SDS), we investigated the defensive effect of UA on intestinal damage. The results showed that UA could significantly protect Drosophila from the damage caused by SDS exposure. Further, UA alleviated the accumulation of reactive oxygen species (ROS) and malondialdehyde (MDA) induced by SDS and upregulated the activities of total superoxide dismutase (T-SOD) and catalase (CAT). Moreover, the proliferation and differentiation of intestine stem cells (ISCs) as well as the excessive activation of the c-Jun N-terminal kinase (JNK)-dependent JAK/STAT signaling pathway induced by SDS were restored by UA. In conclusion, UA prevents intestine injury from toxic compounds by reducing the JNK/JAK/STAT signaling pathway. UA may provide a theoretical basis for functional food or natural medicine development.

Genetics of metallothioneins in Drosophilamelanogaster

Metallothioneins (MTs) are ubiquitous metal-chelating proteins involved in cellular metal homeostasis. MTs were found to be related with almost all the biological processes and their malfunctioning is responsible for a lot of important human diseases. Invertebrate MTs were also used broadly as biomarkers of metal contamination due to their inducible expression by metal exposure. MT system plays a significant role in maintaining human health and ecological stability. Drosophila melanogaster, the vinegar fly, is a perfect model for studying insect MT systems. Six MTs were identified in D. melanogaster, and were designated MtnA to F. All the MTs are considered as Cu-thioneins except for MtnF, which is putatively a Zn-thionein. Expression of all the MTs are regulated by MTF-1/MRE system, thus being able to be induced by heavy metal exposure. The expression pattern and function of separated MTs are partially overlapped and partially distinct. In this work, we made a summary of all the studies on D. melanogaster MTs. From this review, we noted that, compared with studies on mammalian MTs, the understanding of the MT system of D. melanogaster and other invertebrates, especially the regulation mechanism for MT expression and protein-protein interaction with them, is still in a low level.

FlyPhoneDB: an integrated web-based resource for cell-cell communication prediction in Drosophila

Multicellular organisms rely on cell-cell communication to exchange information necessary for developmental processes and metabolic homeostasis. Cell-cell communication pathways can be inferred from transcriptomic datasets based on ligand-receptor expression. Recently, data generated from single-cell RNA sequencing have enabled ligand-receptor interaction predictions at an unprecedented resolution. While computational methods are available to infer cell-cell communication in vertebrates such a tool does not yet exist for Drosophila. Here, we generated a high-confidence list of ligand-receptor pairs for the major fly signaling pathways and developed FlyPhoneDB, a quantification algorithm that calculates interaction scores to predict ligand-receptor interactions between cells. At the FlyPhoneDB user interface, results are presented in a variety of tabular and graphical formats to facilitate biological interpretation. To illustrate that FlyPhoneDB can effectively identify active ligands and receptors to uncover cell-cell communication events, we applied FlyPhoneDB to Drosophila single-cell RNA sequencing data sets from adult midgut, abdomen, and blood, and demonstrate that FlyPhoneDB can readily identify previously characterized cell-cell communication pathways. Altogether, FlyPhoneDB is an easy-to-use framework that can be used to predict cell-cell communication between cell types from single-cell RNA sequencing data in Drosophila.