Study summary
90 FFPE samples of primary, lymph node and cutaneous metastasis tumors collected from 77 patients (38 men and 39 women) diagnosed with melanoma between 2005 and 2020 (with disease stage ranging between 1 and 4). The average age ± standard deviation (range) at diagnosis of primary was 64.3 ± 10.9 (31–91) years. The disease-free survival from primary to metastasis was 1.4 ± 2.3 (0–12.0) years and overall survival was 4.3 ± 3.7 (0–17.0) years. The dominant histotypes of primary tumors were Superficial Spreading Melanoma (SSM) with vertical growth and Nodular Melanoma (NM). The cohort included 36 patients with wild type BRAF status and 38 patients with V600E mutation in the BRAF gene (1 patient had D587G mutation). Patients were treatment-naive at the time of sample collection, but multiple have received treatment afterwards, including immunotherapy, targeted therapy, and other therapies (irradiation, chemotherapy, IFN therapy and electrochemotherapy). 18 patients did not receive any treatments.
Mass spectrometer
Q-Exactive HF-X (Orbitrap analyzer)
MS data acquisition and quantification
Data Acquisition method: Data Dependent Acquisition (DDA) - Top 20
Quantification method: Label-free
Software: Proteome Discoverer 2.4
Search engine: UniProt human database (2020/05/26) and two spectral libraries such as the Proteome tools HCD 28 PD and NIST Human Orbitrap HCD
Normalization: Sample median subtraction and centering around the global median
Study summary
Lymph node metastasis samples collected from 111 patients (68 men and 43 women) diagnosed with metastatic melanoma between 1975 and 2011 (Stage 3 and 4). The average age ± standard deviation (range) at diagnosis of lymph node metastasis was 62.4 ± 13.7 (25–89) years. The time elapsed to progression from primary tumor to lymph node metastasis was 5.0 ± 5.6 (0–18.0) years and overall survival was 7.9 ± 6.8 (0.2–43.0) years. The dominant histotypes of primary tumors were Superficial Spreading Melanoma (SSN) and Nodular Melanoma (NM). The cohort included 59% of patients with wild type BRAF status and 36% of patients with V600E mutation in the BRAF gene (4% had V600A or V600K mutation).
Mass spectrometer
Q-Exactive Plus (Orbitrap analyzer)
MS data acquisition and quantification
Data Acquisition method: Data Dependent Acquisition (DDA) - Top 15
Quantification method: Label-free
Software: Proteome Discovery 2.1
Search engine: Sequest HT using UniProtKB human database (released May 2016) excluding isoforms.
Normalization: Sample median subtraction
Study summary
Cohort of 137 patients diagnosed with metastatic melanoma between the years 1975 and 2011. The average age ± standard deviation (range) at diagnosis of metastases was 62.3 ± 13.7 (25–89) years, and the cohort had a preponderance of male individuals (65%). Among patients with available overall survival (OS) information, 50% survived less than 5 years.
The samples comprised fresh frozen metastatic tissues from lymph node (126), subcutaneous (7), cutaneous (1), and visceral (3), while for five samples the origin is unknown. These samples were collected before patient’s treatment. Mutational status: 50 tumors BRAF (V600E) mutated; 36 with NRAS Q61K/R mutation, and 37 tumors had wild type variants for both mutations.
Mass spectrometer
Q Exactive HF-X (Orbitrap analyzer)
MS data acquisition and quantification
Data Acquisition method: Data Dependent Acquisition (DDA) – Top 20
Quantification method: TMT (11 plex)
Software: Proteome Discovery 2.3
Search engine: Sequest HT using UniProtKB human database (released 2018-10-01) with isoforms.
Normalization: Sample median subtraction
Study summary
74 fresh-frozen samples of distant metastases collected after death from 22 patients (15 men and 7 women) diagnosed with melanoma. The metastases originated from various tissues such as lung (14), liver (11), adrenal (6), lien (6), and kidney (5). The average age ± standard deviation (range) at diagnosis of primary was 52.6 ± 14.5 (32–78) years. The number of metastases per patient ranged between 1 and 9. The overall survival was 4.3 ± 3.2 (0.7–11.4) years. The dominant histotypes of primary tumors were SSM and NM. The cohort included 7 patients with wild type BRAF status, 14 patients with BRAF V600E, 1 patient with BRAF K601E and 2 patients with BRAF V600K. Among patients with WT BRAF, 3 patients had NRAS mutation (1 Q61K and 2 Q61R). The majority of patients were treated before sample collection, which included treatment with IFN, chemotherapy, targeted therapy (vemurafenib). 3 patients did not receive any treatments and information is not available for 4 patients.
Mass spectrometer
Q-Exactive HF-X (Orbitrap analyzer)
MS data acquisition and quantification
Data Acquisition method: Data Independent Acquisition (DIA)
Quantification method: Label-free
Software:
Search engine:
Normalization: Sample median subtraction and centering around the global median
Manuscript is currently under preparation
Study summary:
The Cuarto cohort of samples relates to a prospective study on melanoma, which involved obtaining a total of 77 surgically resected tissue samples from 47 melanoma patients. The samples were categorized based on their source, such as non-tumor (NT) samples (n=11), tumor microenvironment (TM) samples (n=6), primary tumor (PT) samples (n=16), local recurrences (LR) samples (n=7), cutaneous metastases (CM) samples (n=9), regional lymph node metastases (LN) samples (n=23), and distant metastases (DM) samples (n=5), originating from various parts of the body, such as the gallbladder, brain, liver, spleen, and breast. The patients included in the study had an average age of 65 years at diagnosis, and 27 of them were male, accounting for 57% of the total.
The samples were stored as fresh-frozen and prepared for quantitative proteomics using a method previously described [1,2]. Mass spectrometry data was obtained using Q-exactive HF-X, following a high-resolution DIA-MS approach. A customized spectral library was used to search for proteins in the samples, with the Spectronaut search engine. A total of 9040 proteins were confidently identified and quantified using a label-free approach. The data was normalized and standardized by log2 transformation and subtraction by the median.
This dataset provides a suitable basis for studying proteins involved in the development and progression of melanoma, as well as the tumor proliferation status, BRAF biology, and sample origin.
Mass spectrometer
Q-Exactive HF-X (Orbitrap)
MS data acquisition and quantification
Data Acquisition method: Data Independent Acquisition (DIA) – High resolution DIA-MS variable window
Quantification method: Label-free
Software: Spectronaut 11
Search engine: Spectronaut using customized spectral library
Normalization and standardization: Log2 transformation, subtraction by the median
References:
1. Gil, J.; Ramírez-Torres, A.; Chiappe, D.; Luna-Penãloza, J.; Fernandez-Reyes, F.C.; Arcos-Encarnación, B.; Contreras, S.; Encarnación-Guevara, S. Lysine Acetylation Stoichiometry and Proteomics Analyses Reveal Pathways Regulated by Sirtuin 1 in Human Cells. J. Biol. Chem. 2017, 292, 18129–18144, doi:10.1074/jbc.M117.784546.
2. Gil, J.; Kim, Y.; Szeitz, B.; Doma, V.; Çakır, U.; Almeida, N.P. de; Hagemeijer, Y.P.; Guryev, V.; Johansson, J.G.; Sharma, Y.; et al. Proteogenomics Reveals How Metastatic Melanoma Modulates the Immune System to Allow Immune Evasion. bioRxiv 2021, 2021.04.10.439245, doi:10.1101/2021.04.10.439245.
This page presents a summary of all clinical variables and includes explanations for each abbreviation.
SampleType: Can vary between cutaneous metastasis (CM), distant metastasis (DM),lymph node metastasis (LN),local recurrence (LR), non-tumor (NT), primary tumor (PT), tumor microenvironment (TM)
Age: Refers to the age of the patient at the time of diagnosis
Sex: Refers to the sex of the patient
AJCC8_stage: Tumor stage based on American Joint Committee on Cancer (AJCC) staging
MelanomaSubType: Refers to the histological subtype of melanoma: superficial spreading melanoma (SSM), nodular melanoma (NM), and acral lentiginous melanoma (ALM)
Clark_level: The Clark Level is a classification system used to describe the depth of melanoma infiltration within the layers of the skin. Varies between L1 and L5
BRAFstatus: BRAF mutation status
Breslow_stage: Staging based on Breslow thickness
Tumor_content: The percentage of tumor cells observed on the slide by the pathologist
PFS(months): Progression-free survival
OS(months): Overall survival
Breslow_thickness: The Breslow thickness measures the vertical thickness of a melanoma lesion.
stage: Staging based on TNM classification
NRAS: NRAS mutation status
DistMetLocation: Distant metastasis location
OS_DAYS: Overall survival in days
cKIT: cKIT mutation status
Origin: Origin of metastatic site in the Tercero study
OS.months: Overall survival in months
Primary_localization: Localization of the primary tumor