Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Quantitative TMT-MS of HPV42, HPV16 or empty vector transduced keratinocytes.

ABSTRACT: The skin serves as a barrier to the environment and is constantly exposed to viral pathogens. Whether viral pathogens contribute to the oncogenesis of rare skin cancers has not been systematically explored. Here, we analyzed 18 skin cancer types by exploiting off-target reads from commonly available next-generation sequencing data. We identified human papillomavirus 42 (HPV42) in all digital papillary adenocarcinoma (DPA) cases but not in any of 11,091 tumors from common cancer types. HPV42 was previously not described as an oncogenic driver, yet we show that HPV42 recapitulates the molecular hallmarks of oncogenic HPVs. Using a machine learning approach, we identified a conserved transcriptomic fingerprint of HPV transformation common to oncogenic HPVs, including HPV42. Collectively, our results establish HPV42 as an oncogenic HPV, which has implications for the diagnosis and treatment for DPA patients.

INSTRUMENT(S): Orbitrap Exploris 480

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Keratinocyte, Skin

SUBMITTER: Richard Imre

LAB HEAD: Anna Christina Obenauf

PROVIDER: PXD031764 | Pride | 2022-10-18

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20210708_E4_LC10_Leiendecker_Obenauf_IMP_ID341_TMT_SCX_50per_fr11_15.raw	Raw
	20210708_E4_LC10_Leiendecker_Obenauf_IMP_ID341_TMT_SCX_50per_fr16_20.raw	Raw
	20210708_E4_LC10_Leiendecker_Obenauf_IMP_ID341_TMT_SCX_50per_fr1_5.raw	Raw
	20210708_E4_LC10_Leiendecker_Obenauf_IMP_ID341_TMT_SCX_50per_fr52_55.raw	Raw
	20210708_E4_LC10_Leiendecker_Obenauf_IMP_ID341_TMT_SCX_50per_fr55_60.raw	Raw

Items per page:

1 - 5 of 33

Similar Datasets

Human papillomavirus 42 is an oncogenic driver in Digital Papillary Adenocarcinoma [transductions]

Project description:The skin serves as a barrier to the environment and is constantly exposed to viral pathogens. However, whether and how viral pathogens contribute to oncogenesis of rare skin cancers has not been explored. We analyzed 18 skin cancers by exploiting sparse off-target reads from commonly available next-generation sequencing data and identify human papillomavirus 42 (HPV42) reads in digital papillary adenocarcinoma (DPA). We show that HPV42 recapitulates the molecular hallmarks of oncogenic HPVs and shares a conserved transcriptomic fingerprint of HPV-transformation. Finally, we show that HPV42 relies on established cellular targets of oncogenic HPVs for its transforming activity. The discovery of HPV42 as a novel oncogenic driver highlights the utility of next-generation sequencing data for the discovery of novel pathogen-disease associations and suggests expansion of current HPV vaccination programs to reduce the cancer burden in humans.

2022-10-10 | GSE196217 | GEO

Human papillomavirus 42 is an oncogenic driver in Digital Papillary Adenocarcinoma [full_genomes]

2022-10-10 | GSE196216 | GEO

Human papillomavirus 42 is an oncogenic driver in Digital Papillary Adenocarcinoma [tumors]

2022-10-10 | GSE196215 | GEO

Human_SAGE_cervix_normal_B_1

Project description:Uterine cervix normal SAGE, CGAP non-normalized SAGE library, bulk method , HPV negative This GEO Series was created by the GEO staff as part of a cleanup effort to ensure that all GEO Samples are included within a Series entry.

2010-12-01 | E-GEOD-25753 | biostudies-arrayexpress

Project description:HPV transcription in skin tumors

| PRJNA493709 | ENA

HPV cell lines and HPV tissue MicroRNA SOLiD sequencing

Project description:Human papillomaviruses (HPV) preferentially infect keratinocytes of mucous membranes or skin and cause numerous benign and malignant lesions at different anatomical locations. We sequenced small RNA (sRNA) libraries of two HPV 16 immortalized cell lines and ten formalin fixed paraffin embedded (FFPE) tissue samples from HPV infected cervical epithelium by SOLiD 4 technology.

2020-06-30 | GSE62239 | GEO

Expression data from HPV(-) and HPV(+) squamous cell carcinoma cell lines

Project description:Oncogenic human papillomaviruses (HPVs) are associated with nearly all carcinomas of the uterine cervix and have also become an increasingly important factor in the etiology of a subset of oropharyngeal tumors. HPV-associated head and neck cancers (HNSCCs) have a distinct risk profile and appreciate a prognostic advantage compared to HPV-negative HNSCC. We analyzed the genome-wide expression patterns in two HPV(+) and two HPV(-) squamous cell carcinoma (SCC) cell lines. The Affymetrix Human Genome U133 Plus 2.0 Array platform was used to assess genome-wide expression differences between the HPV(+) and HPV(-) cell lines utilizing the RMA normalization package available for R. Cell lines analyzed: UM-SCC-4, UM-SCC-47, UM-SCC-74A, and CaSki.

2010-12-01 | E-GEOD-24089 | biostudies-arrayexpress

Lack of human papilloma virus transcriptional activity in cutaneous squamous cell carcinoma stratified by histological grade and host immune status

Project description:Human Papilloma Virus (HPV) infection is known to contribute to mucosal (m)SCC, but its role in cutaneous (c)SCC progression remains unclear, especially in lesions determined to be at high-risk for metastasis. We hypothesized that histologically high grade cSCCs in immunosuppressed patients would display increased transcriptional activity of HPV when compared to low histologic grade lesions in otherwise healthy patients. To assess the role of viruses in cSCC pathogenesis we utilized high throughput RNA sequencing across risk-stratified lesions. Skin excisions classified as high grade in immunocompromised patients, low grade in otherwise healthy patients, and normal skin were used for detection of any non-human RNA. Reads were aligned to known viral transcriptomes using our recently developed Microbiome Coverage Profiler. While approximately two-thirds of all samples tested positive for HPV gDNA, no skin sample had detectable expression of HPV RNA.

2021-03-02 | GSE111354 | GEO

Total protein abundances upon Mcm6 knockdown in the murine CH12 cells

Project description:Chromosomal translocations result from joining of DNA double-strand breaks (DSBs) and frequently cause cancer. Yet, the steps linking DSB formation to DSB ligation remain undeciphered. We report that DNA replication timing (RT) directly regulates lymphomagenic Myc translocations during antibody maturation in B-cells downstream of DSBs and independently of DSB frequency. Depletion of minichromosome-maintenance (MCM) complexes alters replication origin activity, decreases translocations and abrogates global RT. Ablating a single origin at Myc causes an early-to-late RT switch, loss of translocations and reduced nuclear proximity with a translocation partner locus, phenotypes that were reversed by restoring early RT. Disruption of shared early RT also reduced tumorigenic translocations in human leukemic cells. Thus, RT constitutes a new, unprecedented mechanism in translocation biogenesis linking DSB formation to DSB ligation

2022-09-13 | PXD034446 | Pride

Expression data from HPV(-) and HPV(+) squamous cell carcinoma cell lines

2010-12-01 | GSE24089 | GEO