Klebsiella pneumoniae strain:PC-2022-1 | isolate:broiler anal swab
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA879870 | ENA |
REPOSITORIES: ENA
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Project description:HPV infection results in changes in host gene methylation which, in turn, are thought to contribute to the neoplastic progression of HPV-associated cancers. The objective of this study was to identify joint and disease-specific genome-wide methylation changes in anal and cervical cancer as well as changes in high-grade pre-neoplastic lesions. Formalin-fixed paraffin-embedded (FFPE) anal tissues (n=143; 99% HPV+) and fresh frozen cervical tissues (n=28; 100% HPV+) underwent microdissection, DNA extraction, HPV genotyping, bisulfite modification, DNA restoration (FFPE) and analysis by the Illumina HumanMethylation450 Array.
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Project description:Etiologically linked to HPV infection, malignancies of the anal canal have substantially increased in incidence over the last 20 years. Although most anal squamous cell carcinomas (SCC) respond well to chemoradiotherapy, for undetermined reasons, a subgroup of patients experience a poor outcome. Despite cumulative efforts for discovering independent predictors for overall survival, both nodal status and tumor size are still the only reliable factors predicting patient outcome. In the present study, we correlated both proteomic signatures and clinicopathological features of neoplastic lesions arising from two distinct portions of the anal canal: the lower part (squamous zone) and the more proximal anal transitional zone. Although microdissected cancer cells appeared indistinguishable by morphology (squamous phenotype), unsupervised clustering analysis of the whole proteome significantly highlighted the heterogeneity that exists within anal canal tumors. More importantly, two region-specific subtypes of SCC were revealed. The expression profile (sensitivity/specificity) of several selected biomarkers (keratin filaments) further confirmed the subclassification of anal (pre)cancers based on their cellular origin. Less commonly detected compared to their counterparts located in the squamous mucosa, SCC originating in the transitional zone displayed more frequently a poor or basaloid differentiation and were significantly correlated with reduced disease-free and overall survivals. Taken together, we present for the first time direct evidence that anal canal SCC comprises two distinct entities with different cells of origin, proteomic signatures and survival rates. This study forms the basis for a novel dualistic classification of anal carcinoma with implications for management, outcome expectations and possibly therapeutic approaches.
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Project description:Anal squamous cell carcinoma (ASCC) is a rare gastrointestinal malignancy that is linked to high-risk Human papillomavirus (HPV) infection. It is often preceded by precursor lesions like Low-Grade Squamous Intraepithelial Lesions (LGSIL) and High-Grade Squamous Intraepithelial Lesions (HGSIL). The incidence of ASCC varies across populations, with heightened risk in HIV-positive individuals. In a previous study, we characterized the anal microbiome in high-risk HIV-exposed MSM and TGW subjects. We revealed oncogenic viromes and pertinent bacterial species associated with anal SILs. Our current investigation aimed to delineate transcriptomic and metatranscriptomic changes during the progression from precancerous lesions to ASCC. We collected 70 anal tissue samples across various lesion stages (LGSIL, HGSIL, and ASCC). Our metatranscriptomic analysis revealed that Fusobacterium nucleatum, F. gonidiaformans, Bacteroides fragilis, Campylobacter ureolyticus, and Cribacterium bergeronii were more prevalent in ASCC than in precancerous lesions. These bacterial species contributed with gene encoding enzymes (e.g.: Acca, glyQ, eno, pgk and por) and oncoproteins (FadA and dnaK) revealing potential new markers for diagnosis or treatment approaches. Our unsupervised transcriptome analysis identified two distinct sample clusters based on histological diagnosis, immune infiltrate, HIV and HPV status, and pathway activities such as immune activation, cell cycle, and antiviral signaling that recapitulate the natural history of anal cancer progression. Mutations were observed affecting KMT2C (30%), PIK3CA (21%), EP300 (21%) and NOTCH1 (13%) cancer driver genes among ASCC but also in precancerous lesions. Our study provides insights into the molecular mechanisms governing anal cancer progression, offering valuable information that may help to stratify HGSIL cases with low- or high-risk progression to the malignant stages.
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Project description:Interventions: Brief name: anal swab
Kidney transplant recipients attending routine review appointments will be approached to participate. They will be provided a participant information and consent form (PICF) detailing the purpose, methods and risks and benefits of the study. The study will include adults willing and able to give informed consent in English. Consented participants will complete an initial coded demographic and behavioural questionnaire. Trained staff will then take an anal swab taken using a moistened Dacron swab for subsequent HPV testing. The Dacron swab will be vigorously eluded into a ThinPrep (Hologic) vial containing PreservCyt fixative medium. Any participant with either a significant cytological abnormality, or in whom high risk HPV is detected, will be referred for further investigation at a specialist clinic. A letter will be sent to participants with negative or low-risk results as well as their nominated GP.
This pilot study will evaluate the feasibility of collecting potentially sensitive behavioural data, taking anal swab specimens and performing rectal examinations, in order to identify those at high risk of serious disease.
Primary outcome(s): Prevalence of type-specific anal human papilloma virus (HPV) infection in renal transplant recipients, using PCR amplification of target DNA, and hybridization with a reverse line blot system.[ Anal swab will be performed within 14 days after completion of baseline questionnaire. Genotyping will be performed in batches, for every 20 participant samples.];Prevalence and type of anal cytological abnormalities in renal transplant recipients, using ThinPrep (Hologic) standard procedure.
[ Anal swab will be performed within 14 days after completion of baseline questionnaire. Cytology testing will be performed within 7 days of sample collection.];Feasibility of use of anal swabs as a screening tool for the detection of HPV infection and abnormal cytological abnormalities. This will be assessed through enrolment rates from all eligible approached participants and also feedback given in the baseline questionnaires.[ Feasibility will be assessed after all participants have been tested, and followed up if needed.]
Study Design: Purpose: Diagnosis; Allocation: Non-randomised trial; Masking: Open (masking not used);Assignment: Single group;Type of endpoint: Efficacy
| 2464549 | ecrin-mdr-crc