Peritoneal inclusion cyst presenting as an umbilical hernia: case report and systematic review of the literature

Peritoneal inclusion cysts (PICs) are a rare and benign condition of uncertain pathogenesis. The fluid-filled, mesothelial-lined cysts manifest within the abdominopelvic cavity. This case report details an unusual occurrence of a 97 mm PIC- presenting as an umbilical hernia- in a 26-year-old male patient with no prior surgical history. Following pre-operative cross-sectional imaging, this was managed through open excision without complication. A systematic review of the literature highlighted 30 previous cases [26F, 4M] with a mean age of 34 years (std ±15.4) and a median diameter of 93 mm [IQR, 109 mm]. A total of 53% (n = 16) of cases had a history of previous abdominal surgery. Surgical excision is safe and laparoscopic modality should be considered (<1% recurrence). Accepting the limited evidence base, image guided drainage should be avoided (50% recurrence, n = 2).

NCBI GEO: archive for gene expression and epigenomics data sets: 23-year update

The Gene Expression Omnibus (GEO) is an international public repository that archives gene expression and epigenomics data sets generated by next-generation sequencing and microarray technologies. Data are typically submitted to GEO by researchers in compliance with widespread journal and funder mandates to make generated data publicly accessible. The resource handles raw data files, processed data files and descriptive metadata for over 200 000 studies and 6.5 million samples, all of which are indexed, searchable and downloadable. Additionally, GEO offers web-based tools that facilitate analysis and visualization of differential gene expression. This article presents the current status and recent advancements in GEO, including the generation of consistently computed gene expression count matrices for thousands of RNA-seq studies, and new interactive graphical plots in GEO2R that help users identify differentially expressed genes and assess data set quality. The GEO repository is built and maintained by the National Center for Biotechnology Information (NCBI), a division of the National Library of Medicine (NLM), and is publicly accessible at https://www.ncbi.nlm.nih.gov/geo/.

Targeting Replication Stress for Glioma Stem Cell Specific Cytotoxicity

AIMS

Glioma stem cells (GSC) show high levels of DNA replication stress and exhibit abnormal S phase in comparison to differentiated, non GSC tumour cells. We investigated the DNA replication phenotypes of GSC and mechanism of GSC specific cytotoxicity following DNA replication stress response inhibition with combined ATR/PARP inhibition (CAiPi).

METHOD

Paired GSC enriched (‘GSC’) and GSC deplete differentiated (‘bulk’) populations were cultured from resected GBM specimens and maintained in neurobasal media with growth factors or serum containing media respectively. Cell viability, neurosphere and clonogenic assays were used to assess cytotoxicity whilst DNA replication was interrogated utilising immunofluorescent repair foci, flow cytometry and DNA fibre assay. CAiPi consisted of VE821 (ATRi) with Olaparib (PARPi).

RESULTS

GSC show reduced DNA replication rates and alterations in cell cycle profile and demonstrate extreme sensitivity to CAiPi. CAiPi resulted in significantly elevated levels of 53BP1 nuclear bodies in GSC indicating genomic under- replication, however did not preferentially reduce fork speed compared to non-GSC. Analysis of replication fork structures revealed an increase in new origin firing in GSC dependent upon PARP trapping. GSC cytotoxicity was reduced by roscovitine induced inhibition of origin firing, suggesting an important role of dysregulated origin firing in CAiPi response. CAiPi is also potently radiosensitising by clonogenic assay.

CONCLUSION

Taken together these data suggest that GSC are vulnerable to dysregulation of origin firing which results in under-replication of their genome and reliance upon G1 cell cycle resolution of DNA damage. We propose that CAiPi is an attractive therapeutic strategy for translation to the clinic.

STEM-22. TARGETING REPLICATION STRESS RESPONSE FOR GLIOMA STEM CELL SPECIFIC CYTOTOXICITY

BACKGROUND

Evidence suggests treatment resistant glioma stem cells (GSCs) drive glioblastoma (GBM) recurrence. Current treatments fail to eradicate GSC and novel GSC targeting therapies are a priority. GSC exhibit elevated DNA replication stress (RS) versus non GSC tumour cells driving constitutive DNA damage response (DDR) activation and efficient DNA repair. We previously demonstrated that targeting RS response with combined ATR and PARP inhibition (CAiPi) (VE821 and Olaparib) provides potent GSC specific cytotoxicity. In this study we investigated the underlying DDR phenotype which determines this vulnerability.

RESULTS

Paired GSC enriched (‘GSC’) and GSC depleted, differentiated (‘bulk’) populations were cultured from GBM specimens in neurobasal media with growth factors or serum containing media respectively. GSC exhibited reduced survival following exposure to CAiPi versus bulk. CAiPi significantly increased 53BP1 G1 phase nuclear bodies (53BP1NBs) in GSC, which are known to shield under-replicated DNA in actively transcribed genes. Mapping the genomic distribution of endogenously occurring replication dependent DNA double strand breaks via Breaks Ligation In Situ Sequencing (BLISS), revealed reduced intragenic DSB in long actively transcribed genes in GSC versus bulk at baseline, suggesting a reliance upon transcription coupled DSB repair in GSC. RNA seq demonstrated CAiPi-induced transcriptomic alterations in GSC including replication regulation and initiation. DNA fibre assay showed that CAiPi increased GSC new origin firing which correlated with PARP trapping. GSCs were rescued from CAiPi by roscovitine induced inhibition of excess origin firing. CAiPi is potently radiosensitizing by clonogenic assay and we demonstrated murine blood brain barrier penetration of CAiPi utilising VE822 and pamiparib in vivo.

CONCLUSION

Dysregulation of origin firing by CAiPi exposes a GSC specific vulnerability which results in DNA under-replication and abrogation of proficient DNA repair seen at long actively transcribed genes and has potential to be clinically translated as a GSC specific cytotoxic therapy.

Excessive new origin firing underlies selective glioma stem cell cytotoxicity induced by replication stress response inhibition

Aims

Glioblastoma (GBM) is a treatment refractory cancer of extreme unmet need which exhibits treatment resistance due to a subpopulation of GBM cancer stem cells which have constitutive DNA damage response activation driven by elevated replication stress (RS). RS response inhibition is potently cytotoxic to GSC, however mechanistic understanding will be key to biomarker discovery and successful clinical translation.

We investigated response to combined ATR and PARP inhibition (CAiPi) to gain mechanistic insight and inform biomarker development.

Method

A panel of patient-derived GBM cell lines were cultured as stem enriched (GSCs) or stem depleted (bulk), to characterise response to combined ATR inhibition (VE821 5μM) and PARP inhibition (Olaparib 1μM), by CellTiter-Glo viability assay.

Mechanistic investigations included immunofluorescence of 53BP1 nuclear bodies and DNA fibre analysis. Studies into the importance of PARP trapping included another PARPi Veliparib (1μM), and investigations into inhibition of origin firing used the CDK inhibitor Roscovitine.

Results

Responses to CAiPi in a panel of primary paired GBM GSCs vs differentiated progeny were heterogenous. CAiPi is selectively GSC cytotoxic in a subpopulation of tumours. DNA fibre analysis identified increased new origin firing with PARPi, which was correlated with increased PARP trapping. Inhibition of origin firing by exposure to roscovitine rescued the CAiPi cytotoxic phenotype, suggesting origin firing has an important role in selective GSC cytotoxicity.

A population of treatment-sensitive GSCs with increased numbers of 53BP1 nuclear bodies in G1 phase with CAiPi were identified, indicative of under-replication of DNA in S phase.

Conclusion

Selective GSC cytotoxicity is induced by CAiPi via dysregulation of replication, by both DNA under-replication resulting in DNA lesions, and the novel finding of increased new origin firing in GSC due to PARPi.

1334 Improving Patient Flow Through the Hand Trauma Pathway

Aim

A full-cycle audit was conducted at our plastic surgery unit, assessing adherence to hand trauma standards by the British Society for Surgery of the Hand. These stipulate that time from referral to clinic for open injuries and closed fractures should be within 24 hours and 72 hours respectively and time to theatre from date of injury (DOI) within 4 and 7 days, respectively.

Method

Data for the initial audit was collected from Nov 2019-Feb 2020 and for the re-audit from Aug-Dec 2020. Lists were generated of 50 patients with open injuries including flexor tendon, extensor tendon and nerve injuries and 50 hand fractures in both cycles. Data was collected on DOI, date of referral, clinic review and surgery.

Results

The initial audit results showed poor DOI documentation (open injuries 30%, fractures 54%). For open injuries, 44% met standards for clinical review within 24 hours and 94% for time to theatre. For fractures, 94% met the standard for time to clinic and 90% for time to theatre. The interventions included adding the standards to the clinic booking form and creating a mandatory DOI field on the referral system. The re-audit showed improvement of DOI documentation (open injuries 95%, fractures 100%) and the proportion of open injuries seen within 24 hours to 60%.

Conclusions

The interventions had a positive impact on our hand trauma pathway. Areas for improvement include reducing the number of patient visits to the service and encouraging early decision-making, particularly for patients reviewed in the emergency department.

Jupyter notebook-based tools for building structured datasets from the Sequence Read Archive

The Sequence Read Archive (SRA) is a large public repository that stores raw next-generation sequencing data from thousands of diverse scientific investigations.  Despite its promise, reuse and re-analysis of SRA data has been challenged by the heterogeneity and poor quality of the metadata that describe its biological samples. Recently, the MetaSRA project standardized these metadata by annotating each sample with terms from biomedical ontologies. In this work, we present a pair of Jupyter notebook-based tools that utilize the MetaSRA for building structured datasets from the SRA in order to facilitate secondary analyses of the SRA’s human RNA-seq data. The first tool, called the Case-Control Finder, finds suitable case and control samples for a given disease or condition where the cases and controls are matched by tissue or cell type.  The second tool, called the Series Finder, finds ordered sets of samples for the purpose of addressing biological questions pertaining to changes over a numerical property such as time. These tools were the result of a three-day-long NCBI Codeathon in March 2019 held at the University of North Carolina at Chapel Hill.

Comparative validation of the D. melanogaster modENCODE transcriptome annotation

Accurate gene model annotation of reference genomes is critical for making them useful. The modENCODE project has improved the D. melanogaster genome annotation by using deep and diverse high-throughput data. Since transcriptional activity that has been evolutionarily conserved is likely to have an advantageous function, we have performed large-scale interspecific comparisons to increase confidence in predicted annotations. To support comparative genomics, we filled in divergence gaps in the Drosophila phylogeny by generating draft genomes for eight new species. For comparative transcriptome analysis, we generated mRNA expression profiles on 81 samples from multiple tissues and developmental stages of 15 Drosophila species, and we performed cap analysis of gene expression in D. melanogaster and D. pseudoobscura. We also describe conservation of four distinct core promoter structures composed of combinations of elements at three positions. Overall, each type of genomic feature shows a characteristic divergence rate relative to neutral models, highlighting the value of multispecies alignment in annotating a target genome that should prove useful in the annotation of other high priority genomes, especially human and other mammalian genomes that are rich in noncoding sequences. We report that the vast majority of elements in the annotation are evolutionarily conserved, indicating that the annotation will be an important springboard for functional genetic testing by the Drosophila community.

Epigenetic regulation of oogenesis and germ stem cell maintenance by the Drosophila histone methyltransferase Eggless/dSetDB1

The Drosophila melanogaster histone lysine methyltransferase (HKMT) Eggless (Egg/dSETDB1) catalyzes methylation of Histone H3 lysine 9 (H3K9), a signature of repressive heterochromatin. Our previous studies showed that H3K9 methylation by Egg is required for oogenesis. Here we analyze a set of EMS-induced mutations in the egg gene, identify the molecular lesions of these mutations, and compare the effects on oogenesis of both strong loss-of-function and weak hypomorphic alleles. These studies show that H3K9 methylation by Egg is required for multiple stages of oogenesis. Mosaic expression experiments show that the egg gene is not required intrinsically in the germ cells for their early differentiation, but is required in the germ cells for their survival past stage 5 of oogenesis. egg is also required in germ stem cells for their maintenance, since egg- germ stem cells initially survive but are not maintained as females age. Mosaic analysis also reveals that the early egg chamber budding defects in egg- ovaries are due to an intrinsic requirement for egg in follicle stem cells and their descendents, and that egg plays a non-autonomous role in somatic cells in the germarium to influence the differentiation of early germ cells.

Genomics of sex determination in Drosophila

Drosophilists have identified many, or perhaps most, of the key regulatory genes determining sex using classical genetics, however, regulatory genes must ultimately result in the deployment of the genome in a quantitative manner, replete with complex interactions with other regulatory pathways. In the last decade, genomics has provided a rich picture of the transcriptional profile of the sexes that underlies sexual dimorphism. The current challenge is linking transcriptional profiles with the regulatory genes. This will be a complex synthesis, but the prospects for progress are outstanding.

Near Infra-Red Chemical Species Tomography of Sprays of Volatile Hydrocarbons (Nah-Infrarot-Tomographie zur Bestimmung der Verteilung von Spraypartikeln und flüchtigen Kohlenwasserstoffen)

We report an All-Opto-Electronic tomography system that is sensitive to hydrocarbon vapour distribution, or liquid spray distribution, with temporal resolution of over 3000 frames per second. A tomography system comprising 32 channels has been built and tested. For chemical sensitivity to saturated hydrocarbons, we exploit the principle of Near Infra-Red (NIR) absorption at 1700 nm relative to a reference wavelength, using laser diode sources whose technology is based on that of the communications industry. Images are obtained from a laboratory set-up incorporating both gaseous injection and a liquid Gasoline Direct Injection (GDI) system. The performance of a prototype system on a running GDI engine is reported. The difficulty in performing concentration measurements of the gaseous fuel within the liquid spray region is shown, and means to improve this performance are discussed. However, it has been found possible to image the liquid spray cone using attenuation of the reference beam. These images correlate well with other techniques [1].

Histone methylation is required for oogenesis in Drosophila

SET domain proteins are histone lysine methyltransferases (HMTs) that play essential roles in development. Here we show for the first time that histone methylation occurs in both the germ cells and somatic cells of the Drosophila ovary, and demonstrate in vivo that an HMT, the product of the eggless (egg) gene, is required for oogenesis. Egg is a SET domain protein that is similar to the human protein SETDB1 and its mouse ortholog ESET. These proteins are members of a small family of HMTs that contain bifurcated SET domains. Because depletion of SETDB1 in tissue culture cells is cell-lethal, and an ESET mutation causes very early periimplantation embryonic arrest, the role of SETDB1/ESET in development has proven difficult to address. We show that egg is required in the Drosophilaovary for trimethylation of histone H3 at its K9 residue. In females bearing an egg allele that deletes the SET domain, oogenesis arrests at early stages. This arrest is accompanied by reduced proliferation of somatic cells required for egg chamber formation, and by apoptosis in both germ and somatic cell populations. We propose that other closely related SET domain proteins may function similarly in gametogenesis in other species.

An XXY sex-chromosome constitution in a dog with testicular hypoplasia and congenital heart disease

A sterile male German shorthair pointer with testicular hypoplasia and a ventricular septal defect was found to have a 79, XXY chromosome constitution in peripheral-blood leukocytes, bone marrow and fascia lata fibroblasts. The presence of a late-labeling X chromosome in peripheral-blood leukocytes was demonstrated by autoradiographic studies. This is the first report of the occurrence of the XXY condition in a dog.