| 1. |
- Almeida, Natália, et al.
(författare)
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Mapping the melanoma plasma proteome (MPP) using single-shot proteomics interfaced with the WiMT database
- 2021
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Ingår i: Cancers. - : MDPI AG. - 2072-6694. ; 13:24
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Tidskriftsartikel (refereegranskat)abstract
- Plasma analysis by mass spectrometry-based proteomics remains a challenge due to its large dynamic range of 10 orders in magnitude. We created a methodology for protein identification known as Wise MS Transfer (WiMT). Melanoma plasma samples from biobank archives were directly analyzed using simple sample preparation. WiMT is based on MS1 features between several MS runs together with custom protein databases for ID generation. This entails a multi-level dynamic protein database with different immunodepletion strategies by applying single-shot proteomics. The highest number of melanoma plasma proteins from undepleted and unfractionated plasma was reported, mapping >1200 proteins from >10,000 protein sequences with confirmed significance scoring. Of these, more than 660 proteins were annotated by WiMT from the resulting ~5800 protein sequences. We could verify 4000 proteins by MS1t analysis from HeLA extracts. The WiMT platform provided an output in which 12 previously well-known candidate markers were identified. We also identified low-abundant proteins with functions related to (i) cell signaling, (ii) immune system regulators, and (iii) proteins regulating folding, sorting, and degradation, as well as (iv) vesicular transport proteins. WiMT holds the potential for use in large-scale screening studies with simple sample preparation, and can lead to the discovery of novel proteins with key melanoma disease functions.
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| 2. |
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| 3. |
- Betancourt, Lazaro Hiram, et al.
(författare)
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The human melanoma proteome atlas-Defining the molecular pathology
- 2021
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Ingår i: Clinical and Translational Medicine. - : Wiley. - 2001-1326. ; 11:7, s. 1-20
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Tidskriftsartikel (refereegranskat)abstract
- The MM500 study is an initiative to map the protein levels in malignant melanoma tumor samples, focused on in-depth histopathology coupled to proteome characterization. The protein levels and localization were determined for a broad spectrum of diverse, surgically isolated melanoma tumors originating from multiple body locations. More than 15,500 proteoforms were identified by mass spectrometry, from which chromosomal and subcellular localization was annotated within both primary and metastatic melanoma. The data generated by global proteomic experiments covered 72% of the proteins identified in the recently reported high stringency blueprint of the human proteome. This study contributes to the NIH Cancer Moonshot initiative combining detailed histopathological presentation with the molecular characterization for 505 melanoma tumor samples, localized in 26 organs from 232 patients.
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| 4. |
- Betancourt, Lazaro, et al.
(författare)
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Quantitative Assessment of Urea In-Solution Lys-C/Trypsin Digestions Reveals Superior Performance at Room Temperature over Traditional Proteolysis at 37 °C.
- 2018
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Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 17:7, s. 2556-2561
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Tidskriftsartikel (refereegranskat)abstract
- Urea-containing buffer solutions are generally used in proteomic studies to aid protein denaturation and solubilization during cell and tissue lysis. It is well-known, however, that urea can lead to carbamylation of peptides and proteins and, subsequently, incomplete digestion of proteins. By the use of cells and tissues that had been lysed with urea, different solution digestion strategies were quantitatively assessed. In comparison with traditional proteolysis at 37 °C, urea in-solution digestion performed at room temperature improved peptide and protein identification and quantitation and had a minimum impact on miscleavage rates. Furthermore, the signal intensities and the number of carbamylated and pyroglutamic acid-modified peptides decreased. Overall, this led to a reduction in the negative effects often observed for such modifications. Data are available via ProteomeXchange with identifier PXD009426.
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| 5. |
- Giwercman, Aleksander, et al.
(författare)
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Novel protein markers of androgen activity in humans : proteomic study of plasma from young chemically castrated men
- 2022
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Ingår i: eLife. - 2050-084X. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- Background: Reliable biomarkers of androgen activity in humans are lacking. The aim of this study was, therefore, to identify new protein markers of biological androgen activity and test their predictive value in relation to low vs normal testosterone values and some androgen deficiency linked pathologies. Methods: Blood samples from 30 healthy GnRH antagonist treated males were collected at three time points: (1) before GnRH antagonist administration; (2) 3 weeks later, just before testosterone undecanoate injection, and (3) after additional 2 weeks. Subsequently, they were analyzed by mass spectrometry to identify potential protein biomarkers of testosterone activity. Levels of proteins most significantly associated with testosterone fluctuations were further tested in a cohort of 75 hypo- and eugonadal males suffering from infertility. Associations between levels of those markers and cardiometabolic parameters, bone mineral density as well as androgen receptor (AR) CAG repeat lengths, were explored. Results: Using receiver operating characteristic analysis, 4-hydroxyphenylpyruvate dioxygenase (4HPPD), insulin-like growth factor-binding protein 6 (IGFBP6), and fructose-bisphosphate aldolase (ALDOB), as well as a Multi Marker Algorithm, based on levels of 4HPPD and IGFBP6, were shown to be best predictors of low (<8 nmol/l) vs normal (>12 nmol/l) testosterone. They were also more strongly associated with metabolic syndrome and diabetes than testosterone levels. Levels of ALDOB and 4HPPD also showed association with AR CAG repeat lengths. Conclusions: We identified potential new protein biomarkers of testosterone action. Further investigations to elucidate their clinical potential are warranted. Funding: The work was supported by ReproUnion2.0 (grant no. 20201846), which is funded by the Interreg V EU program.
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| 6. |
- Pla Parada, Indira
(författare)
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Data analysis for discovering the protein profile dynamics of the human ovarian follicular fluid and BRAF mutated metastatic melanoma tissue. : -
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Proteomics is widely utilized to understand the function of cellular processes at the molecular level. Using liquid chromatography interfaced with mass spectrometry (LC-MS)-based proteomics, thousands of proteins can be identified and quantified in a single experiment and their relationship and interactions can be analyzed. This makes the analysis of high-throughput proteomics data a cornerstone in the escalating field of translational medicine. Our group has been conducting deep mining LC-MS-based proteomics studies on two complex medical conditions that affect a high rate of the world population, female infertility and malignant melanoma (MM). To study female reproductive disorders, our group profiled the protein composition of the ovarian follicular fluid (FF) since it constitutes the microenvironment in which the oocyte develops during antral stages until follicular rupture at ovulation. In addition, it is believed that the FF mirrors what happens at the molecular level in the ovary and plasma due to pathological disorders. In the case of MM, we profiled the protein composition of metastatic tumor tissue from patients with BRAF mutation. The large amount of data generated from these experiments involves challenges related to data processing, analysis, and visualization of the results. The main challenge in complex disease pathology is the unraveling of the data from experimental outputs. In most cases the answer lies within that biological sample – the challenge is to analyze it and understand the meaning of the data.In this thesis, I performed data analyses to interrogate proteomics data (high resolution LC-MS expression data sets) from a bioinformatics and biostatistical point of view. Using different workflows, analyses and mathematical principles, I combined biological knowledge with bioinformatics and biostatistical approaches to integrate proteomics, clinical, and histopathological data in order to obtain new relevant biological insights from protein profiles of ovarian follicular fluids and MM tissues.The strategy applied in paper I, allowed us to describe progressive proteomic changes occurring in the FF during the ovulation process linked with oocyte maturation, hormone regulation and release of the oocyte. Here, we studied the most detailed temporal ovulatory interval, which included five time points. Paper II constituted the first large-scale proteomic characterization of FF extracted from small antral follicles (SAF) (6.1±0.4 mm) in their natural state. Using a multivariate approach, a signature of proteins appeared to play a role in oocyte maturation and oocyte meiotic resumption already from the early follicular stage. As a follow-up, paper III reported for the first time evidence of proteomic alterations occurring in the FF of SAF of polycystic ovaries (PCO). Alterations were associated with the dysfunction of follicular growth and subsequent oocyte competence usually observed in PCO syndrome. Furthermore, uncharacterized or poorly characterized proteins identified in the FF of unstimulated SAF were assessed and their functionality during folliculogenesis was described in paper IV (manuscript). In paper V, data analysis revealed for the first time that the high expression, in the MM tumor, of the B-raf V600E (mutated) protein could be a significant risk factor for poorer prognosis of patients with stages 3 or 4 of MM. A follow-up of this finding was performed on a larger cohort of patients with BRAF mutation, in which subgroups of patients with different mortality risks were identified and associated with the activation of different BRAF-related pathways, such as the immune response.Supported by data-driven results, this thesis characterized the protein profile dynamics of human ovarian FF during folliculogenesis (paper I-IV) and malignant melanoma tissue of patients with BRAF mutation (paper V). Findings from paper I to IV may open up new pathways for augmenting or attenuating subsequent oocyte viability in the pre-ovulatory follicle when it is ready to undergo ovulation, which may be of importance to future advances in reproductive medicine. On the other hand, findings from paper V may enable the eventual delineation of patient response therapy for MM with BRAF mutation.
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