Project description:Total RNA were extracted from 5 primary melanoma and 5 nevus tissues, all of which were formalin-fixed and parrffin-embedded tissues.
Project description:Total RNA were extracted from 5 primary melanoma and 4 nevus tissues, all of which were formalin-fixed and parrffin-embedded tissues.
Project description:A substantial part of cutaneous malignant melanomas develops from benign nevi. However, the precise molecular events driving the transformation from benign to malignant melanoma are not well understood. We used laser microdissection and mass spectrometry to analyze the proteomes of melanoma subtypes, including superficial spreading melanomas (SSM, n=17), nodular melanomas (NM, n=17), and acral melanomas (AM, n=15). Furthermore, we compared the proteomes of nevi cells and melanoma cells within the same specimens (nevus-associated melanoma (NAM, n=14)). In total, we quantified 7,935 proteins. Despite the genomic and clinical differences of the melanoma subtypes, our analysis revealed relatively similar proteomes, except for the upregulation of proteins involved in immune activation in NM vs AM. Examining NAM versus nevi, we found 1,725 differentially expressed proteins. Among these proteins were 140 that overlapped with cancer hallmarks, tumor suppressors, and regulators of metabolism and cell cycle. Pathway analysis indicated aberrant activation of the RAS/MAPK and PI3K-AKT-mTOR pathways, as well as the Hippo-YAP pathway. Using a classifier, we identified six proteins capable of distinguishing melanoma from nevi samples. Our study represents the first comprehensive comparative analysis of the proteome in melanoma subtypes and associated nevi, offering new insights into the biological behavior of these distinct entities.
Project description:To explore the role of long non-coding RNAs (lncRNAs) in melanoma progression, we performed lncRNAs microarray to identify differentially expressed lncRNAs between primary melanoma and nevus.
Project description:The aim of this study was to decode the gene expression program characterizing odontogenic keratocyst (OKC) development, by performing a comprehensive transcriptomics analysis applied on whole OKC tissue derived from sporadic and Basal Cell Nevus Syndrome (BCNS)-associated OKCs, and control samples of pericoronal tissues of impacted teeth (dental follicles, DFs) derived from healthy individuals.
Project description:To predict differentially expressed miRNAs between monosomy 3 and disomy 3, and to associate these miRNAs with the clinico-pathological parameters in South Asian Indian population with uveal melanoma (UM). The study consists of six uveal melanoma primary tumour tissues of South Asian-Indian population. These six tumours have been screened for chromosome 3 aberration using Chromogenic in-situ hybridisation (CISH). Thus, sample under the study includes, three each of monosomy 3 and disomy 3. The miRNA profiling was carried out from the tumor sections of formalin-fixed paraffin embedded eyeball samples. miRNA expression profile was obtained in monosomy 3 and disomy 3 samples, analysed by unsupervised analysis (Principal Component Analysis) and supervised analysis (Significance analysis of microarray). The select up-regulated and candidate miRNAs associated with monosomy 3 uveal melanoma tumors were validated further with qRT-PCR (n=86). Thus, this study indicates the role of miRNAs in UM tumor progression and their implication in predetermining the liver metastasis. The study consists of six uveal melanoma primary tumour tissues of South Asian-Indian population. These six tumours have been screened for chromosome 3 abberation using chromogenic in-situ hybridisation (CISH). Thus, samples under the study includes three each of monosomy 3 and disomy 3. The miRNA profiling were carried out from the tumor sections of formalin-fixed paraffin embedded eyeball samples. The up-regulated miRNAs associated with monosomy 3 uveal melanoma tumors were short listed and the candidate miRNAs were validated further with qRT-PCR. Agilent one-color experiment, Organism: Homo sapiens, Agilent Human miRNA 8x15k Arrays AMADID: 021827 [Agilent miRNA labeling reagent and Hybridization Kit Cat # 5190-0408]
Project description:To investigate the differences in miRNA profiles specially related to lymph node metastasis in cervical cancer, six primary cervical cancer tissues derived from stage І-ІІ patients with (n=3) or without (n=3) lymph node metastasis were collected. The differential expression of seven representative miRNAs (top seven miRNAs included: miR-135-5p, miR-221-3p, miR-25-3p, miR-96-5p, miR-182-5p, miR-183-5p, and miR-144-3p) was verified using qRT-PCR in the same tissues used for microarray analysis.
Project description:This project analyzes peripheral blood profiles of melanoma cancer patients. Since miRNAs are known to be valuable diagnostic markers we asked whether respective patterns of melanoma patients can be detected in peripheral blood samples rather than in biopsies. The project aimed at an improved understanding of complex profiles rather than single markers. Thus, a high-throughput technique was necessary, profiling all known miRNAs integratively. Top markers have been validated by using qPCR. n = 22 normal controls and n = 35 melanoma cancer samples have been screened for the complete miRNA repertoire. The melanoma samples have been collected by two clinicians using the same procedure. Please note that each miRNA has been measured in seven replicates and the median of the replica has been computed.