Allergen-induced DNA release by the airway epithelium amplifies type 2 immunity

BACKGROUND

Alternaria alternata and house dust mite exposure evokes IL-33 secretion from the airway epithelium, which functions as an alarmin to stimulate type 2 immunity. Extracellular DNA (eDNA) is also an alarmin that intensifies inflammation in cystic fibrosis, chronic obstructive pulmonary disease, and asthma.

OBJECTIVE

We investigated the mechanisms underlying allergen-evoked DNA mobilization and release from the airway epithelium and determined the role of eDNA in type 2 immunity.

METHODS

Human bronchial epithelial (hBE) cells were used to characterize allergen-induced DNA mobilization and extracellular release using comet assays to measure DNA fragmentation, Qubit double-stranded DNA assays to measure DNA release, and DNA sequencing to determine eDNA composition. Mice were used to investigate the role of eDNA in type 2 immunity.

RESULTS

Alternaria extract rapidly induces mitochondrial and nuclear DNA release from human bronchial epithelial cells, whereas house dust mite extract induces mitochondrial DNA release. Caspase-3 is responsible for nuclear DNA fragmentation and becomes activated after cleavage by furin. Analysis of secreted nuclear DNA showed disproportionally higher amounts of promotor and exon sequences and lower intron and intergenic regions compared to predictions of random DNA fragmentation. In mice, Alternaria-induced type 2 immune responses were blocked by pretreatment with a DNA scavenger. In caspase-3-deficient mice, Alternaria-induced DNA release was suppressed. Furthermore, intranasal administration of mouse genomic DNA with Alternaria amplified secretion of IL-5 and IL-13 into bronchoalveolar lavage fluid while DNA alone had no effect.

CONCLUSION

These findings highlight a novel, allergen-induced mechanism of rapid DNA release that amplifies type 2 immunity in airways.

S5.3a Unraveling the genetic determinants of virulence in Cryptococcus neoformans

S5.3 Cellular pleomorphism and fungal virulence, September 22, 2022, 3:00 PM - 4:30 PM

 

 

Cryptococcus neoformans is a human pathogenic basidiomycete yeast that can cause cryptococcal meningitis (CM), predominantly in immunocompromised individuals. The patient outcome depends on both host and pathogen-specific factors, including C. neoformans genetics. A groundbreaking 2012 study was the first to show that patient outcome is associated with genetic differences between C. neoformans isolates. Subsequent population-wide sequencing studies have revealed over 100 sequence types (ST) of C. neoformans that are associated with both geographic location and clinical outcome. All these studies have been broad, examining the severity of disease cryptococcal phenotypes in a collection of highly diverse strains. We chose a narrow focus and collected various genotypic and phenotypic data from a single ST: ST93. ST93 is a common sequence type isolated from patients globally and is the most common clinical isolate found in the sub-Saharan African country of Uganda. Previously, we performed whole genome sequencing on 38 ST93 Ugandan clinical isolates. We identified 652 unique SNPs in this ST93 population compared to the H99 reference genome. We also showed that ST93 contained two subpopulations: ST9A and ST93B. In the current study, we further characterized the genotypic, phenotypic, and virulence differences between these 38 clinical isolates. Using Illumina sequence data, we identified a pattern of linkage disequilibrium that suggested that ST93A and ST93B are evolving separately. We performed long-read sequencing on each isolate to investigate chromosomal changes and large structural variations, allowing us to identify a chromosomal translocation event wherein parts of chromosome 11 had recombined with chromosome 3. Additionally, we characterized several in vitro phenotypes for each isolate and identified three distinct phenotypic clusters based on cell wall challenge and growth experiments. Next, we infected mice with 35 isolates and observed eight different disease manifestations, including isolates that caused non-CNS infections. Overall, by working within a single sequence type, we can gain a deeper understanding of how some small genetic changes can impact strain-specific phenotypes while others have no discernable effect. Eventually, these data can be used to provide valuable information about how each clinical isolate impacts patient outcomes.

Systemic lipolysis promotes physiological fitness in Drosophila melanogaster

Since interventions such as caloric restriction or fasting robustly promote lipid catabolism and improve aging-related phenotypical markers, we investigated the direct effect of increased lipid catabolism via overexpression of bmm (brummer, FBgn0036449), the major triglyceride hydrolase in Drosophila, on lifespan and physiological fitness. Comprehensive characterization was carried out using RNA-seq, lipidomics and metabolomics analysis. Global overexpression of bmm strongly promoted numerous markers of physiological fitness, including increased female fecundity, fertility maintenance, preserved locomotion activity, increased mitochondrial biogenesis and oxidative metabolism. Increased bmm robustly upregulated the heat shock protein 70 (Hsp70) family of proteins, which equipped the flies with higher resistance to heat, cold, and ER stress via improved proteostasis. Despite improved physiological fitness, bmm overexpression did not extend lifespan. Taken together, these data show that bmm overexpression has broad beneficial effects on physiological fitness, but these effects did not impact lifespan.

Effects of the SLICK1 mutation in PRLR on regulation of core body temperature and global gene expression in liver in cattle

The SLICK1 mutation in bovine PRLR (c.1382del; rs517047387) is a deletion mutation resulting in a protein with a truncated intracellular domain. Cattle carrying at least one allele have a phenotype characterized by a short hair coat (slick phenotype) and increased resistance to heat stress. Given the pleiotropic nature of prolactin, the mutation may affect other physiological characteristics. The liver is one organ that could potentially be affected because of the expression of PRLR. The mutation is a dominant allele, and heterozygous animals have a similar hair coat to that of animals homozygous for the mutation. Present objectives were to determine whether inheritance of the SLICK1 mutation affects liver gene expression and if animals homozygous for the SLICK1 allele differ from heterozygotes in liver gene expression and regulation of body temperature during heat stress. In one experiment, rectal and ruminal temperatures were less for Holstein heifers that were heterozygous for the SLICK1 allele compared with wildtype heifers. There were 71 differentially expressed genes in liver, with 13 upregulated and 58 downregulated in SLICK1 heterozygotes. Among the ontologies characteristic of differentially expressed genes were those related to immune function and fatty acid and amino acid metabolism. In a prospective cohort study conducted with adult Senepol cattle, body temperature and hepatic gene expression were compared between animals heterozygous or homozygous for the SLICK1 mutation. There were no differences in ruminal temperatures between genotypes, rectal temperature was higher in animals homozygous for the SLICK1 mutation, and there was only one gene in liver that was differentially expressed. It was concluded that inheritance of the SLICK1 allele can exert functional changes beyond those related to hair growth although changes in liver gene expression were not extensive. Results are also consistent with the SLICK1 allele being dominant because there were few differences in phenotype between animals inheriting one or two copies of the allele.

Whole-genome assembly and annotation of northern wild rice, Zizania palustris L., supports a whole-genome duplication in the Zizania genus

Zizania palustris L. (northern wild rice, NWR) is an aquatic grass native to North America that is notable for its nutritious grain. This is an important species with ecological, cultural and agricultural significance, specifically in the Great Lakes region of the USA. Using flow cytometry, we first estimated the NWR genome size to be 1.8 Gb. Using long- and short-range sequencing, Hi-C scaffolding and RNA-seq data from eight tissues, we generated an annotated whole-genome de novo assembly of NWR. The assembly was 1.29 Gb in length, highly repetitive (approx. 76.0%) and contained 46 421 putative protein-coding genes. The expansion of retrotransposons within the genome and a whole-genome duplication (WGD) after the Zizania-Oryza speciation event have both led to an increase in the genome size of NWR in comparison with Oryza sativa L. and Zizania latifolia. Both events depict a genome rapidly undergoing change over a short evolutionary time. Comparative analyses revealed the conservation of large syntenic blocks between NWR and O. sativa, which were used to identify putative seed-shattering genes. Estimates of divergence times revealed that the Zizania genus diverged from Oryza approximately 26-30 million years ago (26-30 MYA), whereas NWR and Z. latifolia diverged from one another approximately 6-8 MYA. Comparative genomics confirmed evidence of a WGD in the Zizania genus and provided support that the event occurred prior to the NWR-Z. latifolia speciation event. This genome assembly and annotation provides a valuable resource for comparative genomics in the Oryzeae tribe and provides an important resource for future conservation and breeding efforts of NWR.

Abstract 1410: Chemotherapy resistance pathways identified in ovarian cancer patients treated with neoadjuvant chemotherapy using single cell RNA sequencing of matched tumor biopsies

Background: Women with ovarian cancer suffer from a high rate of mortality due to the development of chemotherapy resistance. To better understand the mechanisms of chemotherapy resistance we initiated a prospective study of women with ovarian cancer, which we refer to as the Ovarian Cancer Precision Medicine Initiative (OCPMI) where we collect tumor biopsies and perform comprehensive molecular analyses. Our goal is to use the molecular data from these specimens to understand the mechanisms of chemo-resistance and use that information to improve therapeutic approaches.

Methods: In this study, we report our analysis of pairs of matched tumor specimens taken from seven ovarian cancer patients enrolled in OCPMI who were treated using neoadjuvant chemotherapy (NACT). The first tumor specimen was taken at time of initial diagnostic biopsy (pre-NACT), while the matched second tumor biopsy was taken after NACT administration (post-NACT), during interval debulking surgery. All fourteen tumor biopsies were subjected to single cell RNA sequencing to generate gene expression data on 54,827 pre-NACT cells and 30,661 post-NACT cells. Bioinformatic techniques were used to compare the post-NACT tumor cells that had experienced chemotherapy to the chemo-naïve pre-NACT tumor cells. Gene/pathway enrichment tests were performed to identify genes and pathways that correlated with the chemo resistance phenotype.

Results: In all matched biopsies we found that the majority of cells in the chemo-experienced post-NACT samples could be mapped to a subset of the cells in the chemo-naïve, pre-NACT samples based on gene expression patterns. We hypothesize that this subset of pre-NACT cells are the precursor cells that are able to withstand chemotherapy and could be the cause of recurrence. Analysis of the genes and signaling pathways that were upregulated in the chemo-resistant subset of pre-NACT cells identified potential novel therapeutic targets including TNFa signaling, JAK-STAT signaling, interferon signaling, TGFb signaling, and STK33 kinase activation.

Conclusions: Single cell RNA sequencing combined with sequential biopsies provides an unprecedented ability to understand mechanisms of response to chemotherapy. This type of analysis can be used to identify novel therapeutic approaches targeting the chemo-resistance phenotype.

Citation Format: Timothy K. Starr, Shobhana Talukdar, Zenas Chang, Jason Cepela, Christopher Tastad, Mihir Shetty, Isaac Schneider, Jun Woo, Marissa Macchietto, Christine Henzler, Ying Zhang, Joshua Baller, Constantin Aiferis, Sarah Munro, Andrew C. Nelson, Jinhua Wang, Boris J. Winterhoff. Chemotherapy resistance pathways identified in ovarian cancer patients treated with neoadjuvant chemotherapy using single cell RNA sequencing of matched tumor biopsies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1410.

Abstract PO-013: Defining immune infiltrate heterogeneity and its role in ovarian cancer chemotherapy resistance using single cell RNA sequencing

Objectives: Immune cell infiltration is correlated with therapy response in ovarian cancer (OC), but exceptions to this correlation are numerous, which could be due to heterogeneity in the immune cell composition and functional phenotype of immune cells. To better understand the immune landscape of OC and to develop biomarkers predictive of OC response to chemotherapy we initiated a prospective study to analyze the unique molecular and histopathological characteristics of tumor samples taken during primary debulking, interval debulking and at recurrence. Methods: We have enrolled over 100 women and have completed single cell RNA sequencing (scRNAseq), multiplex immunohistochemical assays, H&E scoring for tumor infiltrating lymphocytes (TILs) and NanoString molecular subtyping in 30 women. Platinum status in the cohort was: sensitive (20), resistant (4), refractory (3), and not determined (3). ScRNAseq was performed using the 10X genomics platform and multiple bioinformatic algorithms were applied to annotate cell types present in the sample. Comparisons between cell types identified by scRNAseq and multiplex IHC were performed and statistical correlations were made between clinical characteristics such as platinum resistance and molecular phenotypes. TIL scoring was performed using Salgado scoring criteria and PDL-1/PD-1 IHC staining was assessed based on Tumor proportion score (TPS) and Combined Proportion score (CPS). Results: ScRNAseq combined with multiplex IHC revealed extensive heterogeneity both within and between patients. PD-1 and PDL-1 genes were expressed in 23/30 (76%) patients across some cell types (% expression range: 1-22%) while 20/30 (66%) showed expression both in immune and epithelial cells. Highest expression of both genes was noted in 4/30 (12%) patients. PDL-1 gene levels by ScRNAseq demonstrated robust linearity across high and low expression ranges noted on IHC assays. ScRNAseq demonstrated an added advantage of being able to detect genes on tumor samples with absent PDL-1 IHC staining. Differential expression of PD-1/PDL-1 genes among 4 molecular subtypes showed highest expression level in immunoreactive group. Interestingly, 2 patients in this group did not express these genes indicating that molecular subtyping alone might not be predictive of immunotherapy response. Stromal TILs of 50-90% and 20-40% were observed in 4/30 (13%) and 10/30 patients (33%) respectively, although no correlation was noted between TIL scoring and level of PD-1/PDL-1 genes. Conclusions: ScRNAseq identifies more patients with PD-1/PD-L1 compared to IHC assays, suggesting single biomarker analysis might not be predictive of treatment response. Our study is ongoing and we will present our analysis of molecular phenotypes and correlations with clinical features such as platinum resistance. The goal of this project is to use comprehensive molecular analyses to identify patients most likely to benefit from immunotherapy and further understand the mechanism of immune evasion in OC.

Citation Format: Shobhana Talukdar, Jason Cepela, Zenas Chang, Mihir Shetty, Ying Zhang, Marissa Macchietto, Christine Henzler, Sarah A. Munro, Christopher Tastad, Aaron Grad, Sally A. Mullany, Jun Woo, Jinhua Wang, Andrew Nelson, Boris A. Winterhoff, Timothy K. Starr. Defining immune infiltrate heterogeneity and its role in ovarian cancer chemotherapy resistance using single cell RNA sequencing [abstract]. In: Proceedings of the AACR Virtual Special Conference on Tumor Heterogeneity: From Single Cells to Clinical Impact; 2020 Sep 17-18. Philadelphia (PA): AACR; Cancer Res 2020;80(21 Suppl):Abstract nr PO-013.

Hybrid Assembly of the Genome of the Entomopathogenic Nematode Steinernema carpocapsae Identifies the X-Chromosome

Entomopathogenic nematodes from the genus Steinernema are lethal insect parasites that quickly kill their insect hosts with the help of their symbiotic bacteria. Steinernema carpocapsae is one of the most studied entomopathogens due to its broad lethality to diverse insect species and its effective commercial use as a biological control agent for insect pests, as well as a genetic model for studying parasitism, pathogenesis, and symbiosis. In this study, we used long-reads from the Pacific Biosciences platform and BioNano Genomics Irys system to assemble the most complete genome of the S. carpocapsae ALL strain to date, comprising 84.5 Mb in 16 scaffolds, with an N50 of 7.36 Mb. The largest scaffold, with 20.9 Mb, was identified as chromosome X based on sex-specific genome sequencing. The high level of contiguity allowed us to characterize gene density, repeat content, and GC content. RNA-seq data from 17 developmental stages, spanning from embryo to adult, were used to predict 30,957 gene models. Using this improved genome, we performed a macrosyntenic analysis to Caenorhabditis elegans and Pristionchus pacificus and found S. carpocapsae's chromosome X to be primarily orthologous to C. elegans' and P. pacificus' chromosome II and IV. We also investigated the expansion of protein families and gene expression differences between adult male and female stage nematodes. This new genome and more accurate set of annotations provide a foundation for additional comparative genomic and gene expression studies within the Steinernema clade and across the Nematoda phylum.

Comparative Transcriptomics of Steinernema and Caenorhabditis Single Embryos Reveals Orthologous Gene Expression Convergence during Late Embryogenesis

Cells express distinct sets of genes in a precise spatio-temporal manner during embryonic development. There is a wealth of information on the deterministic embryonic development of Caenorhabditis elegans, but much less is known about embryonic development in nematodes from other taxa, especially at the molecular level. We are interested in insect pathogenic nematodes from the genus Steinernema as models of parasitism and symbiosis as well as a satellite model for evolution in comparison to C. elegans. To explore gene expression differences across taxa, we sequenced the transcriptomes of single embryos of two Steinernema species and two Caenorhabditis species at 11 stages during embryonic development and found several interesting features. Our findings show that zygotic transcription initiates at different developmental stages in each species, with the Steinernema species initiating transcription earlier than Caenorhabditis. We found that ortholog expression conservation during development is higher at the later embryonic stages than at the earlier ones. The surprisingly higher conservation of orthologous gene expression in later embryonic stages strongly suggests a funnel-shaped model of embryonic developmental gene expression divergence in nematodes. This work provides novel insight into embryonic development across distantly related nematode species and demonstrates that the mechanisms controlling early development are more diverse than previously thought at the transcriptional level.

SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification

High-throughput sequencing of full-length transcripts using long reads has paved the way for the discovery of thousands of novel transcripts, even in well-annotated mammalian species. The advances in sequencing technology have created a need for studies and tools that can characterize these novel variants. Here, we present SQANTI, an automated pipeline for the classification of long-read transcripts that can assess the quality of data and the preprocessing pipeline using 47 unique descriptors. We apply SQANTI to a neuronal mouse transcriptome using Pacific Biosciences (PacBio) long reads and illustrate how the tool is effective in characterizing and describing the composition of the full-length transcriptome. We perform extensive evaluation of ToFU PacBio transcripts by PCR to reveal that an important number of the novel transcripts are technical artifacts of the sequencing approach and that SQANTI quality descriptors can be used to engineer a filtering strategy to remove them. Most novel transcripts in this curated transcriptome are novel combinations of existing splice sites, resulting more frequently in novel ORFs than novel UTRs, and are enriched in both general metabolic and neural-specific functions. We show that these new transcripts have a major impact in the correct quantification of transcript levels by state-of-the-art short-read-based quantification algorithms. By comparing our iso-transcriptome with public proteomics databases, we find that alternative isoforms are elusive to proteogenomics detection. SQANTI allows the user to maximize the analytical outcome of long-read technologies by providing the tools to deliver quality-evaluated and curated full-length transcriptomes.

Adapting the Smart-seq2 Protocol for Robust Single Worm RNA-seq

Most nematodes are small worms that lack enough RNA for regular RNA-seq protocols without pooling hundred to thousand of individuals. We have adapted the Smart-seq2 protocol in order to sequence the transcriptome of an individual worm. While developed for individual Steinernema carpocapsae and Caenorhabditis elegans larvae as well as embryos, the protocol should be adaptable for other nematode species and small invertebrates. In addition, we describe how to analyze the RNA-seq results using the Galaxy online environment. We expect that this method will be useful for the studying gene expression variances of individual nematodes in wild type and mutant backgrounds.

Activated entomopathogenic nematode infective juveniles release lethal venom proteins

Entomopathogenic nematodes (EPNs) are unique parasites due to their symbiosis with entomopathogenic bacteria and their ability to kill insect hosts quickly after infection. It is widely believed that EPNs rely on their bacterial partners for killing hosts. Here we disproved this theory by demonstrating that the in vitro activated infective juveniles (IJs) of Steinernema carpocapsae (a well-studied EPN species) release venom proteins that are lethal to several insects including Drosophila melanogaster. We confirmed that the in vitro activation is a good approximation of the in vivo process by comparing the transcriptomes of individual in vitro and in vivo activated IJs. We further analyzed the transcriptomes of non-activated and activated IJs and revealed a dramatic shift in gene expression during IJ activation. We also analyzed the venom proteome using mass spectrometry. Among the 472 venom proteins, proteases and protease inhibitors are especially abundant, and toxin-related proteins such as Shk domain-containing proteins and fatty acid- and retinol-binding proteins are also detected, which are potential candidates for suppressing the host immune system. Many of the venom proteins have conserved orthologs in vertebrate-parasitic nematodes and are differentially expressed during IJ activation, suggesting conserved functions in nematode parasitism. In summary, our findings strongly support a new model that S. carpocapsae and likely other Steinernema EPNs have a more active role in contributing to the pathogenicity of the nematode-bacterium complex than simply relying on their symbiotic bacteria. Furthermore, we propose that EPNs are a good model system for investigating vertebrate- and human-parasitic nematodes, especially regarding the function of excretory/secretory products.

Steinernema carpocapsae belongs to a special group of insect-parasitic nematodes known as entomopathogenic nematodes (EPNs). These differ from other insect parasites in at least two ways; first they kill their hosts quickly (within 2–3 days), and second they associate with bacteria to facilitate their parasitic lifestyle. The infective stage of these parasites, the infective juvenile (IJ) stage, is the only free-living stage and these IJs are developmentally arrested and only reinitiate development once they are inside a suitable host. Little is known about the early stages of parasitism and how these parasites initiate the parasitic phase of their life cycle and reinitiate development. Here we characterized the changes that occur to the nematodes' physical morphology, gene expression, and the release of protein molecules that accompany the transition from developmentally arrested IJ to active, developing parasite. We showed that contrary to long-held assumptions, the nematodes are not merely transporting pathogenic bacteria but that the nematodes contribute to parasitism by releasing toxic proteins into the host. Many of the S. carpocapsae toxins are also found in species of human-parasitic nematodes, and S. carpocapsae may serve as a valuable model for understanding the specific function of these toxins.

Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks

BACKGROUND

Parasitism is a major ecological niche for a variety of nematodes. Multiple nematode lineages have specialized as pathogens, including deadly parasites of insects that are used in biological control. We have sequenced and analyzed the draft genomes and transcriptomes of the entomopathogenic nematode Steinernema carpocapsae and four congeners (S. scapterisci, S. monticolum, S. feltiae, and S. glaseri).

RESULTS

We used these genomes to establish phylogenetic relationships, explore gene conservation across species, and identify genes uniquely expanded in insect parasites. Protein domain analysis in Steinernema revealed a striking expansion of numerous putative parasitism genes, including certain protease and protease inhibitor families, as well as fatty acid- and retinol-binding proteins. Stage-specific gene expression of some of these expanded families further supports the notion that they are involved in insect parasitism by Steinernema. We show that sets of novel conserved non-coding regulatory motifs are associated with orthologous genes in Steinernema and Caenorhabditis.

CONCLUSIONS

We have identified a set of expanded gene families that are likely to be involved in parasitism. We have also identified a set of non-coding motifs associated with groups of orthologous genes in Steinernema and Caenorhabditis involved in neurogenesis and embryonic development that are likely part of conserved protein-DNA relationships shared between these two genera.