Epitheliocystis in Greater Amberjack: Evidence of a Novel Causative Agent, Pathology, Immune Response and Epidemiological Findings

Epitheliocystis is a fish gill disease caused by a broad range of intracellular bacteria infecting freshwater and marine fish worldwide. Here we report the occurrence and progression of epitheliocystis in greater amberjack reared in Crete (Greece). The disease appears to be caused mainly by a novel Betaproteobacteria belonging to the Candidatus Ichthyocystis genus with a second agent genetically similar to Ca. Parilichlamydia carangidicola coinfecting the gills in some cases. After a first detection of the disease in 2017, we investigated epitheliocystis in the following year’s cohort of greater amberjack juveniles (cohort 2018) transferred from inland tanks to the same cage farm in the open sea where the first outbreak was detected. This cohort was monitored for over a year together with stocks of gilthead seabream and meagre co-farmed in the same area. Our observations showed that epitheliocystis could be detected in greater amberjack gills as early as a month following the transfer to sea cages, with ionocytes at the base of the gill lamellae being initially infected. Cyst formation appears to trigger a proliferative response, leading to the fusion of lamellae, impairment of gill functions and subsequently to mortality. Lesions are characterized by infiltration of immune cells, indicating activation of the innate immune response. At later stages of the outbreak, cysts were no longer found in ionocytes but were observed in mucocytes at the trailing edge of the filament. Whole cysts appeared finally to be expelled from infected mucocytes directly into the water, which might constitute a novel means of dispersion of the infectious agents. Molecular screening indicates that meagre is not affected by this disease and confirms the presence of previously described epitheliocystis agents, Ca. Ichthyocystis sparus, Ca. Ichthyocystis hellenicum and Ca. Similichlamydia spp., in gilthead seabream. Prevalence data show that the bacteria persist in both gilthead seabream and greater amberjack cohorts after first infection.

Landscapes of cellular phenotypic diversity in breast cancer xenografts and their impact on drug response

The heterogeneity of breast cancer plays a major role in drug response and resistance and has been extensively characterized at the genomic level. Here, a single-cell breast cancer mass cytometry (BCMC) panel is optimized to identify cell phenotypes and their oncogenic signalling states in a biobank of patient-derived tumour xenograft (PDTX) models representing the diversity of human breast cancer. The BCMC panel identifies 13 cellular phenotypes (11 human and 2 murine), associated with both breast cancer subtypes and specific genomic features. Pre-treatment cellular phenotypic composition is a determinant of response to anticancer therapies. Single-cell profiling also reveals drug-induced cellular phenotypic dynamics, unravelling previously unnoticed intra-tumour response diversity. The comprehensive view of the landscapes of cellular phenotypic heterogeneity in PDTXs uncovered by the BCMC panel, which is mirrored in primary human tumours, has profound implications for understanding and predicting therapy response and resistance.

Metabolic Imaging Detects Resistance to PI3Kα Inhibition Mediated by Persistent FOXM1 Expression in ER+ Breast Cancer

PIK3CA, encoding the PI3Kα isoform, is the most frequently mutated oncogene in estrogen receptor (ER)-positive breast cancer. Isoform-selective PI3K inhibitors are used clinically but intrinsic and acquired resistance limits their utility. Improved selection of patients that will benefit from these drugs requires predictive biomarkers. We show here that persistent FOXM1 expression following drug treatment is a biomarker of resistance to PI3Kα inhibition in ER+ breast cancer. FOXM1 drives expression of lactate dehydrogenase (LDH) but not hexokinase 2 (HK-II). The downstream metabolic changes can therefore be detected using MRI of LDH-catalyzed hyperpolarized 13C label exchange between pyruvate and lactate but not by positron emission tomography measurements of HK-II-mediated trapping of the glucose analog 2-deoxy-2-[18F]fluorodeoxyglucose. Rapid assessment of treatment response in breast cancer using this imaging method could help identify patients that benefit from PI3Kα inhibition and design drug combinations to counteract the emergence of resistance.

Abstract 4077: Quantitative proteomics reveals novel immunomodulatory pathways of resistance to PARP therapy

Background Pharmacological inhibition of PARP results in the specific killing of BRCA1/2 deficient tumor cells due to a synthetic lethal interaction between the concomitant impairment in homologous recombination and the DNA damage response. Despite the success of this approach, resistance to PARP inhibition has been observed in majority of patients with advanced cancer. Novel ways of interrogating PARP resistance are necessary to further elucidate the mechanisms of drug resistance and help identify ways to overcome it. To probe potential mechanisms of resistance we applied data-independent acquisition (DIA) mass spectrometry for unbiased global protein quantification in patient derived xenografts with demonstrated resistance to PARP inhibitors.

Methods Patient-derived tumor xenografts (PDTXs) were generated from breast cancer patient tumor material implanted in severely immuno-compromised NOD-scid IL2rgnull (NSG) mice. PDTXs, developed as part of the CRUK Cambridge Institute biobank of PDTXs, have previously undergone extensive molecular profiling. PDTXs and short-term cultured PDTX cells (or PDTCs) capture most of originating patient's sample features, including heterogeneity, and consequently, the PDTX/PDTC platform is a robust intermediate in oncogenic drug development. Resistance to the PARP inhibitors AZD-2281 (olaparib) and BMN-673 (talazoparib) was tested ex vivo in PDTCs from 6 sensitive and 11 resistant PDTXs. Deep quantitative proteome profiling of PDTXs samples was conducted by applying an LC-MS/MS setup operated in DIA mode. Data was extracted using Spectronaut™ (Biognosys) with a sample specific spectral library. Pathway analysis was conducted to highlight dysregulated biological functions and pathways and the proteomics data was correlated with transcriptomics readouts.

Results LC-MS/MS profiling allowed the identification of more than 11'000 proteins with more than 8'700 proteins quantified across the samples. 448 human and 430 murine proteins were significantly changed between PARP inhibitor resistant and sensitive PDTX models. Resistant models were characterized by increased expression of DNA damage response proteins including ATR and FANCD2, downregulation of TP53, TP53BP1, POLB and H2AFX, and upregulated EGFR, BRAF, ERBB2, STAT3, MLLT4 and CDKN2A. Most interestingly, we observed upregulation of human CD47/SIRPa immunomodulatory signals and upregulation of mouse Ly6G, CSF1R and SHP-1 suggesting the infiltration of immunosuppressive neutrophils and monocytes in the tumor microenvironment in the models resistant to PARP inhibition.

Conclusions To our knowledge, this is the first report aiming at interrogating PARP inhibitor resistance with unbiased quantitative proteomics. The proteomics data confirmed prior observations of resistance mechanisms to PARP and elucidated potential novel mechanisms involving modulation of the immune response in resistant tumors.

Citation Format: Jakob Vowinckel, Yuehan Feng, Dimitra Georgopoulou, Alejandra Bruna, Tobias Treiber, Abigail Shea, Giulia Lerda, Martin O'Reilly, Kristina Beeler, Carlos Caldas. Quantitative proteomics reveals novel immunomodulatory pathways of resistance to PARP therapy [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4077.

Enhancer accessibility and CTCF occupancy underlie asymmetric TAD architecture and cell type specific genome topology

Cohesin and CTCF are master regulators of genome topology. How these ubiquitous proteins contribute to cell-type specific genome structure is poorly understood. Here, we explore quantitative aspects of topologically associated domains (TAD) between pluripotent embryonic stem cells (ESC) and lineage-committed cells. ESCs exhibit permissive topological configurations which manifest themselves as increased inter- TAD interactions, weaker intra-TAD interactions, and a unique intra-TAD connectivity whereby one border makes pervasive interactions throughout the domain. Such 'stripe' domains are associated with both poised and active chromatin landscapes and transcription is not a key determinant of their structure. By tracking the developmental dynamics of stripe domains, we show that stripe formation is linked to the functional state of the cell through cohesin loading at lineage-specific enhancers and developmental control of CTCF binding site occupancy. We propose that the unique topological configuration of stripe domains represents a permissive landscape facilitating both productive and opportunistic gene regulation and is important for cellular identity.

Cohesin-mediated interactions organize chromosomal domain architecture

To ensure proper gene regulation within constrained nuclear space, chromosomes facilitate access to transcribed regions, while compactly packaging all other information. Recent studies revealed that chromosomes are organized into megabase-scale domains that demarcate active and inactive genetic elements, suggesting that compartmentalization is important for genome function. Here, we show that very specific long-range interactions are anchored by cohesin/CTCF sites, but not cohesin-only or CTCF-only sites, to form a hierarchy of chromosomal loops. These loops demarcate topological domains and form intricate internal structures within them. Post-mitotic nuclei deficient for functional cohesin exhibit global architectural changes associated with loss of cohesin/CTCF contacts and relaxation of topological domains. Transcriptional analysis shows that this cohesin-dependent perturbation of domain organization leads to widespread gene deregulation of both cohesin-bound and non-bound genes. Our data thereby support a role for cohesin in the global organization of domain structure and suggest that domains function to stabilize the transcriptional programmes within them.

Epigenomic enhancer annotation reveals a key role for NFIX in neural stem cell quiescence

The majority of neural stem cells (NSCs) in the adult brain are quiescent, and this fraction increases with aging. Although signaling pathways that promote NSC quiescence have been identified, the transcriptional mechanisms involved are mostly unknown, largely due to lack of a cell culture model. In this study, we first demonstrate that NSC cultures (NS cells) exposed to BMP4 acquire cellular and transcriptional characteristics of quiescent cells. We then use epigenomic profiling to identify enhancers associated with the quiescent NS cell state. Motif enrichment analysis of these enhancers predicts a major role for the nuclear factor one (NFI) family in the gene regulatory network controlling NS cell quiescence. Interestingly, we found that the family member NFIX is robustly induced when NS cells enter quiescence. Using genome-wide location analysis and overexpression and silencing experiments, we demonstrate that NFIX has a major role in the induction of quiescence in cultured NSCs. Transcript profiling of NS cells overexpressing or silenced for Nfix and the phenotypic analysis of the hippocampus of Nfix mutant mice suggest that NFIX controls the quiescent state by regulating the interactions of NSCs with their microenvironment.