Abstract
Original language | English |
---|---|
Journal | Oxidative Medicine and Cellular Longevity |
Volume | 2018 |
DOIs | |
Publication status | Published - 2018 |
Keywords
- atg9a protein
- autophagy related protein
- bag1 protein
- capn2 protein
- chmp2b protein
- gnai3 protein
- itgb4 protein
- kiaa0226 protein
- pex3 protein
- tumor marker
- unclassified drug
- wipi1 protein
- BCL2-associated athanogene 1 protein
- DNA binding protein
- lipoprotein
- membrane protein
- peroxin
- Pex3 protein, human
- transcription factor
- WIPI-1 protein, human
- Article
- autophagy
- cancer prognosis
- cancer survival
- computer model
- esophagus cancer
- gene ontology
- gene overexpression
- human
- human tissue
- kidney cancer
- lymphoma
- major clinical study
- melanoma
- metastatic melanoma
- nevus
- oropharynx cancer
- sensitivity and specificity
- skin biopsy
- tissue section
- tumor biopsy
- biosynthesis
- gene expression
- genetic database
- genetics
- metabolism
- pathology
- prognosis
- Autophagy
- Autophagy-Related Proteins
- Databases, Genetic
- DNA-Binding Proteins
- Gene Expression
- Humans
- Lipoproteins
- Melanoma
- Membrane Proteins
- Peroxins
- Prognosis
- Transcription Factors
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WIPI1, BAG1, and PEX3 autophagy-related genes are relevant melanoma markers. / D'Arcangelo, D.; Giampietri, C.; Muscio, M.; Scatozza, F.; Facchiano, F.; Facchiano, A.
In: Oxidative Medicine and Cellular Longevity, Vol. 2018, 2018.Research output: Contribution to journal › Article › peer-review
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TY - JOUR
T1 - WIPI1, BAG1, and PEX3 autophagy-related genes are relevant melanoma markers
AU - D'Arcangelo, D.
AU - Giampietri, C.
AU - Muscio, M.
AU - Scatozza, F.
AU - Facchiano, F.
AU - Facchiano, A.
N1 - Export Date: 11 April 2019 Correspondence Address: Facchiano, A.; Istituto Dermopatico dell'Immacolata, IDI-IRCCS, Via Monti di Creta 104, Italy; email: a.facchiano@idi.it Chemicals/CAS: peroxin, 210099-21-1; Autophagy-Related Proteins; BCL2-associated athanogene 1 protein; DNA-Binding Proteins; Lipoproteins; Membrane Proteins; Peroxins; Pex3 protein, human; Transcription Factors; WIPI-1 protein, human Funding details: RC3.4-2017 Funding text 1: This study has been supported in part by a grant from the Italian Ministry of Health, RC3.4-2017 to AF. References: Kunz, M., Hölzel, M., The impact of melanoma genetics on treatment response and resistance in clinical and experimental studies (2017) Cancer Metastasis Reviews, 36 (1), pp. 53-75; Zhang, X.-Y., Zhang, P.-Y., Genetics and epigenetics of melanoma (2016) Oncology Letters, 12 (5), pp. 3041-3044; Ribero, S., Longo, C., Glass, D., Nathan, P., Bataille, V., What is new in melanoma genetics and treatment? 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PY - 2018
Y1 - 2018
N2 - ROS and oxidative stress may promote autophagy; on the other hand, autophagy may help reduce oxidative damages. According to the known interplay of ROS, autophagy, and melanoma onset, we hypothesized that autophagy-related genes (ARGs) may represent useful melanoma biomarkers. We therefore analyzed the gene and protein expression of 222 ARGs in human melanoma samples, from 5 independent expression databases (overall 572 patients). Gene expression was first evaluated in the GEO database. Forty-two genes showed extremely high ability to discriminate melanoma from nevi (63 samples) according to ROC (AUC ≥ 0.85) and Mann-Whitney (p <0.0001) analyses. The 9 genes never related to melanoma before were then in silico validated in the IST online database. BAG1, CHMP2B, PEX3, and WIPI1 confirmed a strong differential gene expression, in 355 samples. A second-round validation performed on the Human Protein Atlas database showed strong differential protein expression for BAG1, PEX3, and WIPI1 in melanoma vs control samples, according to the image analysis of 80 human histological sections. WIPI1 gene expression also showed a significant prognostic value (p <0.0001) according to 102 melanoma patients' survival data. We finally addressed in Oncomine database whether WIPI1 overexpression is melanoma-specific. Within more than 20 cancer types, the most relevant WIPI1 expression change (p = 0.00002; fold change = 3.1) was observed in melanoma. Molecular/functional relationships of the investigated molecules with melanoma and their molecular/functional network were analyzed via Chilibot software, STRING analysis, and gene ontology enrichment analysis. We conclude that WIPI1 (AUC = 0.99), BAG1 (AUC=1), and PEX3 (AUC = 0.93) are relevant novel melanoma markers at both gene and protein levels. Copyright © 2018 Daniela D'Arcangelo et al.
AB - ROS and oxidative stress may promote autophagy; on the other hand, autophagy may help reduce oxidative damages. According to the known interplay of ROS, autophagy, and melanoma onset, we hypothesized that autophagy-related genes (ARGs) may represent useful melanoma biomarkers. We therefore analyzed the gene and protein expression of 222 ARGs in human melanoma samples, from 5 independent expression databases (overall 572 patients). Gene expression was first evaluated in the GEO database. Forty-two genes showed extremely high ability to discriminate melanoma from nevi (63 samples) according to ROC (AUC ≥ 0.85) and Mann-Whitney (p <0.0001) analyses. The 9 genes never related to melanoma before were then in silico validated in the IST online database. BAG1, CHMP2B, PEX3, and WIPI1 confirmed a strong differential gene expression, in 355 samples. A second-round validation performed on the Human Protein Atlas database showed strong differential protein expression for BAG1, PEX3, and WIPI1 in melanoma vs control samples, according to the image analysis of 80 human histological sections. WIPI1 gene expression also showed a significant prognostic value (p <0.0001) according to 102 melanoma patients' survival data. We finally addressed in Oncomine database whether WIPI1 overexpression is melanoma-specific. Within more than 20 cancer types, the most relevant WIPI1 expression change (p = 0.00002; fold change = 3.1) was observed in melanoma. Molecular/functional relationships of the investigated molecules with melanoma and their molecular/functional network were analyzed via Chilibot software, STRING analysis, and gene ontology enrichment analysis. We conclude that WIPI1 (AUC = 0.99), BAG1 (AUC=1), and PEX3 (AUC = 0.93) are relevant novel melanoma markers at both gene and protein levels. Copyright © 2018 Daniela D'Arcangelo et al.
KW - atg9a protein
KW - autophagy related protein
KW - bag1 protein
KW - capn2 protein
KW - chmp2b protein
KW - gnai3 protein
KW - itgb4 protein
KW - kiaa0226 protein
KW - pex3 protein
KW - tumor marker
KW - unclassified drug
KW - wipi1 protein
KW - BCL2-associated athanogene 1 protein
KW - DNA binding protein
KW - lipoprotein
KW - membrane protein
KW - peroxin
KW - Pex3 protein, human
KW - transcription factor
KW - WIPI-1 protein, human
KW - Article
KW - autophagy
KW - cancer prognosis
KW - cancer survival
KW - computer model
KW - esophagus cancer
KW - gene ontology
KW - gene overexpression
KW - human
KW - human tissue
KW - kidney cancer
KW - lymphoma
KW - major clinical study
KW - melanoma
KW - metastatic melanoma
KW - nevus
KW - oropharynx cancer
KW - sensitivity and specificity
KW - skin biopsy
KW - tissue section
KW - tumor biopsy
KW - biosynthesis
KW - gene expression
KW - genetic database
KW - genetics
KW - metabolism
KW - pathology
KW - prognosis
KW - Autophagy
KW - Autophagy-Related Proteins
KW - Databases, Genetic
KW - DNA-Binding Proteins
KW - Gene Expression
KW - Humans
KW - Lipoproteins
KW - Melanoma
KW - Membrane Proteins
KW - Peroxins
KW - Prognosis
KW - Transcription Factors
U2 - 10.1155/2018/1471682
DO - 10.1155/2018/1471682
M3 - Article
VL - 2018
JO - Oxidative Medicine and Cellular Longevity
JF - Oxidative Medicine and Cellular Longevity
SN - 1942-0900
ER -