Dataset Information

Bronchoalveolar Lavage proteomics

ABSTRACT: Mass spectrometry based proteome analysis on an observational prospective cohort consisting of 90 suspected lung cancer cases (suspicious=7, no lung cancer suspicion=47 and lung cancer=36 as diagnosed in 2014) which were followed during two years (suspicious=2, no lung cancer suspicion= 39 and Lung cancer=49).

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Rune Matthiesen

LAB HEAD: Rune Matthiesen

PROVIDER: PXD004700 | Pride | 2017-02-13

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

Items per page:

1 - 5 of 103

Publications

Bronchoalveolar Lavage Proteomics in Patients with Suspected Lung Cancer.

Carvalho Ana Sofia AS Cuco Célia Marina CM Lavareda Carla C Miguel Francisco F Ventura Mafalda M Almeida Sónia S Pinto Paula P de Abreu Tiago Tavares TT Rodrigues Luís Vaz LV Seixas Susana S Bárbara Cristina C Azkargorta Mikel M Elortza Felix F Semedo Júlio J Field John K JK Mota Leonor L Matthiesen Rune R

Scientific reports 20170207

Lung cancer configures as one of the deadliest types of cancer. The future implementation of early screening methods such as exhaled breath condensate analysis and low dose computed tomography (CT) as an alternative to current chest imaging based screening will lead to an increased burden on bronchoscopy units. New approaches for improvement of diagnosis in bronchoscopy units, regarding patient management, are likely to have clinical impact in the future. Diagnostic approaches to address mortali ...[more]

PMID: 28169345

Similar Datasets

Project description:Alternative splicing analysis of laser micro-dissected lung dysplasia RNA samples Lung dysplasia is a precancerous condition with high risk of malignant transformation. Little is known about alternative spliced (AS) genes in dysplasia. We therefore investigated laser micro-dissected microscopic foci of non-contaminant dysplasia and/or lung adenocarcinoma of c-Raf transgenic mice and searched genome wide for AS genes using exon arrays. Notably, bioinformatics defined 34 and 36 AS genes in the comparison dysplasia versus transgenic unaltered and non-transgenic lung tissue while the comparison adenocarcinoma versus transgenic unaltered and non-transgenic lung tissue revealed 54 and 56 genes, respectively. So far only 6 of these were reported for lung cancer. Importantly, dysplasia related AS genes were also regulated in lung cancer to suggest a role in disease onset. Next to exon skipping/inclusion alternative splicing at the 3M-bM-^@M-^Y and 5M-bM-^@M-^Y was common and included genes of the splicing regulatory pathway. Disease dependent changes of variant transcripts were confirmed by RT-PCR while Western blotting identified alternative splicing to modulate protein levels of AS genes. For the AS genes Add3, Cast, Osbpl6, Nedd4l, Numb, Picalm and Slk transcript and protein level agreed well, whereas for Arhgef11, Clstn1, Dlg1, Dock9, Mbnl2, Mfge8, Npnt, Pdlim5, Ppp2r5c, Tjp1 notable differences in the abundance of variant transcripts were observed by RT-PCR and gel electrophoresis. Moreover, expression of individual variants differed between dysplasia and carcinoma to suggest their disease dependent regulation. Western blotting of IQGAP1, MYO6, PTPRM, RABGAP1L and RAD50 confirmed significant regulation of isoforms in lung cancer as compared to non-transgenic, transgenic unaltered and dysplastic lung tissue. For 46 AS genes expression of the non-variant protein was reported in human lung cancer (www.proteinatlas.org) and for 13 of these, cancer related AS events are known. Overall, new insight into lung dysplasia was obtained with 43 new cancer related AS genes to aid diagnosis and molecular intervention strategies. We analyzed and compared dysplastic (n=4) and adenocarcinoma (n=4) lesions and with transgenic but unaltered (n=4) and non-transgenic (n=5) lung tissue obtained from SPC/c-Raf transgenic mice with aid of laser micro dissection pressure catapulted (LMPC) technique. Dysplasia is a pre-neoplastic condition and developed at 5 month of age in the proposed mouse model. LMPC provides precise microscopic lesion collection without contamination. The RNA samples were analyzed using the Affymetrix Mouse Exon 1.0 ST platform. Alternative splicing was analyzed using Biotique XRAY tool. No technical replicates were performed.

			Action	DRS
	10_SQ22.RAW	Raw
	10_SQ26_N.RAW	Raw
	10_SQ52_N.RAW	Raw
	10_sQ31_NO.RAW	Raw
	11_SQ27_N.RAW	Raw