Indira Pla - Academia.edu (original) (raw)

Papers by Indira Pla

SummaryMalignant melanoma (MM) develops from the melanocytes and in its advanced stage is the mos... more SummaryMalignant melanoma (MM) develops from the melanocytes and in its advanced stage is the most aggressive type of skin cancer. Here we report a comprehensive analysis on a prospective cohort study, including non-tumor, primary and metastasis tissues (n=77) with the corresponding plasma samples (n=56) from patients with malignant melanoma. The tumors and surrounding tissues were characterized with a combination of high-throughput analyses including quantitative proteomics, phosphoproteomics, acetylomics, and whole exome sequencing (WES) combined with in-depth histopathology analysis. Melanoma cell proliferation highly correlates with dysregulation at the proteome, at the posttranslational- and at the transcriptome level. Some of the changes were also verified in the plasma proteome. The metabolic reprogramming in melanoma includes upregulation of the glycolysis and the oxidative phosphorylation, and an increase in glutamine consumption, while downregulated proteins involved in th...

Life, 2022

Polycystic ovaries (PCO) contain antral follicles that arrest growing around 3–11 mm in diameter,... more Polycystic ovaries (PCO) contain antral follicles that arrest growing around 3–11 mm in diameter, perturbing the dominant follicle’s selection and the subsequent ovulatory process. Proteomic alterations of PCO follicular fluid (FF) (i.e., microenvironment in which the oocyte develops until ovulation) have been studied from large follicles in connection with oocyte pickup during ovarian stimulation. The present study aimed to detect proteomic alterations in FF from unstimulated human small antral follicles (hSAF) obtained from PCO. After performing deep-sequencing label-free proteomics on 10 PCO and 10 non-PCO FF samples from unstimulated hSAF (4.6–9.8 mm), 1436 proteins were identified, of which 115 were dysregulated in PCO FF samples. Pathways and processes related to the immune system, inflammation, and oxidative stress appeared to be upregulated in PCO, while extracellular matrix receptors interactions, the collagens-containing extracellular matrix, and the regulation of signalin...

Supplementary Figure S1. Novel protein markers of androgen activity in humans with potential clinical value

Supplementary Figure S1. Boxplots based on the Log2 intensities of the differentially expressed p... more Supplementary Figure S1. Boxplots based on the Log2 intensities of the differentially expressed proteins (Table S5). The healthy human model (i.e. castrated men).

Supplementary tables. Novel protein markers of androgen activity in humans with potential clinical value

Supplementary tables from the paper entitled: Novel protein markers of androgen activity... more Supplementary tables from the paper entitled: Novel protein markers of androgen activity in humans with potential clinical value.

Supplementary Files and Figures: Proteome of fluid from human ovarian small antral follicles reveals insights in folliculogenesis and oocyte maturation

This file have all Supplementary Figures and two other Files with analyses:File S1. Detailed info... more This file have all Supplementary Figures and two other Files with analyses:File S1. Detailed information on the protein identification. File S2. Selection of proteins potentially more concentrated and accessible by MS in FF from hSAF.Fig S1. Study workflow Fig S2. General strategy followed for the analysis of follicular fluids Fig S3. Venn diagram of total set of identified proteins Fig S4. Venn diagram of identified proteins by strategy, in the pool sample Fig S5. Protein identification per sample Fig S6. Workflow for the selection of proteins Fig S7. IPA functional relationship networks Fig S8. Verification of proteins

Additional file 8 of Mass spectrometry-based analysis of formalin-fixed, paraffin-embedded distal cholangiocarcinoma identifies stromal thrombospondin-2 as a potential prognostic marker

Additional file 8. Distribution of clinicopathological variables in THBS2 positive and negative s... more Additional file 8. Distribution of clinicopathological variables in THBS2 positive and negative samples.

Additional file 9 of Mass spectrometry-based analysis of formalin-fixed, paraffin-embedded distal cholangiocarcinoma identifies stromal thrombospondin-2 as a potential prognostic marker

Additional file 9. Uni- and multivariable Cox proportional hazards regressions.

Additional file 7 of Mass spectrometry-based analysis of formalin-fixed, paraffin-embedded distal cholangiocarcinoma identifies stromal thrombospondin-2 as a potential prognostic marker

Additional file 7. Peptides quantified by PRM.

Additional file 6 of Mass spectrometry-based analysis of formalin-fixed, paraffin-embedded distal cholangiocarcinoma identifies stromal thrombospondin-2 as a potential prognostic marker

Additional file 6. Peptides included in the PRM spectral library.

Additional file 5 of Mass spectrometry-based analysis of formalin-fixed, paraffin-embedded distal cholangiocarcinoma identifies stromal thrombospondin-2 as a potential prognostic marker

Additional file 5. Detailed enrichment analysis.

Additional file 3 of Mass spectrometry-based analysis of formalin-fixed, paraffin-embedded distal cholangiocarcinoma identifies stromal thrombospondin-2 as a potential prognostic marker

Additional file 3. Total proteins identified by discovery LC-MS/MS.

Additional file 2 of Mass spectrometry-based analysis of formalin-fixed, paraffin-embedded distal cholangiocarcinoma identifies stromal thrombospondin-2 as a potential prognostic marker

Additional file 2. Clinicopathological data of analyzed samples.

Cancers, 2021

Plasma analysis by mass spectrometry-based proteomics remains a challenge due to its large dynami... more 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-kno...

Translational Research, 2019

resectable pancreatic cancer from healthy controls. Combining AGP1 with CA 19-9 enhanced the diag... more resectable pancreatic cancer from healthy controls. Combining AGP1 with CA 19-9 enhanced the diagnostic performance, with an AUC of 0.963. This study suggests that AGP1 is a novel prognostic biomarker in pancreatic cancer tissue. Serum AGP1 levels may be useful as part of a biomarker panel for early detection of pancreatic cancer but further studies are needed.

Neurobiology of Disease, 2019

Background: Alzheimer's disease (AD) is the most common neurodegenerative disorder. Depositions o... more Background: Alzheimer's disease (AD) is the most common neurodegenerative disorder. Depositions of amyloid β peptide (Aβ) and tau protein are among the major pathological hallmarks of AD. Aβ and tau burden follows predictable spatial patterns during the progression of AD. Nevertheless, it remains obscure why certain brain regions are more vulnerable than others; to investigate this and dysregulated pathways during AD progression, a mass spectrometry-based proteomics study was performed. Methods: In total 103 tissue samples from regions early (entorhinal and parahippocampal cortices-medial temporal lobe (MTL)) and late affected (temporal and frontal cortices-neocortex) by tau pathology were subjected to label-free quantitative proteomics analysis. Results: Considering dysregulated proteins during AD progression, the majority (625 out of 737 proteins) was region specific, while some proteins were shared between regions (101 proteins altered in two areas and 11 proteins altered in three areas). Analogously, many dysregulated pathways during disease progression were exclusive to certain regions, but a few pathways altered in two or more areas. Changes in protein expression indicate that synapse loss occurred in all analyzed regions, while translation dysregulation was preponderant in entorhinal, parahippocampal and frontal cortices. Oxidative phosphorylation impairment was prominent in MTL. Differential proteomic analysis of brain areas in health state (controls) showed higher metabolism and increased expression of AD-related proteins in the MTL compared to the neocortex. In addition, several proteins that differentiate brain regions in control tissue were dysregulated in AD. Conclusions: This work provides the comparison of proteomic changes in brain regions affected by tau pathology at different stages of AD. Although we identified commonly regulated proteins and pathways during disease advancement, we found that the dysregulated processes are predominantly region specific. In addition, a distinct proteomic signature was found between MTL and neocortex in healthy subjects that might be related to AD

EBioMedicine, 2019

Background: Pancreatic cancer is a heterogenous disease with a poor prognosis. This study aimed t... more Background: Pancreatic cancer is a heterogenous disease with a poor prognosis. This study aimed to discover and validate prognostic tissue biomarkers in pancreatic cancer using a mass spectrometry (MS) based proteomics approach. Methods: Global protein sequencing of fresh frozen pancreatic cancer and healthy pancreas tissue samples was conducted by MS to discover potential protein biomarkers. Selected candidate proteins were further verified by targeted proteomics using parallel reaction monitoring (PRM). The expression of biomarker candidates was validated by immunohistochemistry in a large tissue microarray (TMA) cohort of 141 patients with resectable pancreatic cancer. Kaplan-Meier and Cox proportional hazard modelling was used to investigate the prognostic utility of candidate protein markers. Findings: In the initial MS-discovery phase, 165 proteins were identified as potential biomarkers. In the subsequent MS-verification phase, a panel of 45 candidate proteins was verified by the development of a PRM assay. Brain acid soluble protein 1 (BASP1) was identified as a new biomarker candidate for pancreatic cancer possessing largely unknown biological and clinical functions and was selected for further analysis. Importantly, bioinformatic analysis indicated that BASP1 interacts with Wilms tumour protein (WT1) in pancreatic cancer. TMA-based immunohistochemistry analysis showed that BASP1 was an independent predictor of prolonged survival (HR 0.468, 95% CI 0.257-0.852, p = .013) and predicted favourable response to adjuvant chemotherapy, whereas WT1 indicated a worsened survival (HR 1.636, 95% CI 1.083-2.473, p = .019) and resistance to chemotherapy. Interaction analysis showed that patients with negative BASP1 and high WT1 expression had the poorest outcome (HR 3.536, 95% CI 1.336-9.362, p = .011). Interpretation: We here describe an MS-based proteomics platform for developing biomarkers for pancreatic cancer. Bioinformatic analysis and clinical data from our study suggest that BASP1 and its putative interaction partner WT1 can be used as biomarkers for predicting outcomes in pancreatic cancer patients.

Scientific Reports, 2019

Metastatic melanoma is one of the most common deadly cancers, and robust biomarkers are still nee... more Metastatic melanoma is one of the most common deadly cancers, and robust biomarkers are still needed, e.g. to predict survival and treatment efficiency. Here, protein expression analysis of one hundred eleven melanoma lymph node metastases using high resolution mass spectrometry is coupled with in-depth histopathology analysis, clinical data and genomics profiles. This broad view of protein expression allowed to identify novel candidate protein markers that improved prediction of survival in melanoma patients. Some of the prognostic proteins have not been reported in the context of melanoma before, and few of them exhibit unexpected relationship to survival, which likely reflects the limitations of current knowledge on melanoma and shows the potential of proteomics in clinical cancer research. The incidence of malignant melanoma is increasing worldwide, particularly in Western countries, and survival does not seem to improve substantially 1. Primary surgery is curative in most patients but around 10-15% of tumors are showing progression. Thus, it is important to early identify those patients who carry a skin tumor with progressive pathobiology. Currently, Breslow thickness is the most accurate tool for predicting the disease outcome of primary melanoma 2. To improve the prediction of disease outcome, more fine-tuned molecular profiling and data integration tools and efforts are needed to search for alternative biomarkers 3. Metastatic melanoma (MM) still remains a tumor with poor outcome 4,5 despite interventions with targeted therapy and antibody-driven modulation of the immune response 6-11. Recent technological developments utilizing both genomic and proteomic analysis provide the opportunity to identify better predictive markers of melanomas 12-16. It is possible to monitor the expression of certain genes and also gain understanding how these genes are expressed and regulated as functional proteins. Accordingly, detailed, personalized information on gene and protein expression and regulation, as well as data on specific mutations that may guide the treatment, can be monitored. Another cornerstone of prognostic predictions is

Journal of Proteome Research, 2018

Quantitative assessment of urea in-solution Lys-C/trypsin digestions reveals superior performance... more Quantitative assessment of urea in-solution Lys-C/trypsin digestions reveals superior performance at room temperature over traditional proteolysis at 37°C.

Analytical biochemistry, Jan 15, 2018

Cell line-based proteomics studies are susceptible to intrinsic biological variation that contrib... more Cell line-based proteomics studies are susceptible to intrinsic biological variation that contributes to increasing false positive claims; most of the methods that follow these changes offer a limited understanding of the biological system. We applied a quantitative proteomic strategy (iTRAQ) to detect intrinsic protein variation across SH-SY5Y cell culture replicates. More than 95% of the quantified proteins presented a coefficient of variation (CV) < 20% between biological replicates and the variable proteins, which included cytoskeleton, cytoplasmic and housekeeping proteins, are widely reported in proteomic studies. We recommend this approach as an additional quality control before starting any proteomic experiment.

Molecular and Cellular Endocrinology, 2019

Follicular fluid (FF) acts as a vehicle for paracrine signalling between somatic cells of the fol... more Follicular fluid (FF) acts as a vehicle for paracrine signalling between somatic cells of the follicle and the oocyte. To investigate changes in the protein composition of FF during ovulation, we conducted a prospective cohort study including 25 women undergoing fertility treatment. Follicular fluid was aspirated either before or 12, 17, 32 or 36 hours after induction of ovulation (five patients per time point). Liquid chromatography-mass spectrometry was used to identify and quantify FF proteins. In total, 400 proteins were identified and the levels of 40 proteins changed significantly across ovulation evaluated by analysis of covariance (adjusted p<0.05) and on-off expression patterns. The majority peaked after 12 to 17 hours, e.g., AREG (p<0.0001), TNFAIP6 (p<0.0001), and LDHB (p=0.0316), while some increased to peak after 36 hours e.g., ACPP (p<0.0001), TIMP1 (p<0.0001) and SERPINE1 (p=0.0002). Collectively, this study highlights proteins and pathways of importance for ovulation and oocyte competence in humans.