Ignacio Ortea

• PhD Proteomics
• Senior Researcher at Spanish National Research Council

Background Hepatocellular carcinoma (HCC) genetic/transcriptomic signatures have been widely described. However, its proteomic characterization is incomplete. We performed non-targeted quantitative proteomics of HCC samples and explored its clinical, functional, and molecular consequences. Methods Non-targeted quantitative proteomics were performe...

Cysteamine, an aminothiol, is the only available treatment for cystinosis, an incurable metabolic recessive disease characterized by detrimental symptoms at the renal, ocular, and muscular levels. Cystinosis is due to mutations in the CTNS gene encoding for the lysosomal symporter cystinosine. Cysteamine treatment only delays the symptoms, presents...

Aging involves the deterioration of organismal function, leading to the emergence of multiple pathologies. Environmental stimuli, including lifestyle, can influence the trajectory of this process and may be used as tools in the pursuit of healthy aging. To evaluate the role of epigenetic mechanisms in this context, we have generated bulk tissue and...

Therapy with anti-tumor necrosis factor (TNF) has dramatically changed the natural history of Crohn’s disease (CD). However, these drugs are not without adverse events, and up to 40% of patients could lose efficacy in the long term. We aimed to identify reliable markers of response to anti-TNF drugs in patients with CD. A consecutive cohort of 113...

Citation: Farabegoli, F.; Santaclara, F.J.; Costas, D.; Alonso, M.; Abril, A.G.; Espiñeira, M.; Ortea, I.; Costas, C. Exploring the Anti-Inflammatory Effect of Inulin by Integrating Transcriptomic and Proteomic Analyses in a Murine Macrophage Cell Model. Nutrients 2023, 15, 859. Abstract: Inulin is a natural polysaccharide classified as a soluble...

The relationship between the functionality and composition of high-density lipoproteins (HDL) is yet not fully studied, and little is known about the influence of the diet in HDL proteome. Therefore, the aim of this research was to elucidate the HDL proteome associated to postprandial hyperlipidemia. Male volunteers were recruited for an interventi...

The high mortality, the presence of an initial asymptomatic stage and the fact that diagnosis in early stages reduces mortality justify the implementation of screening programs in the populations at risk of lung cancer. It is imperative to develop less aggressive methods that can complement existing diagnosis technologies. In this study, we aimed t...

This review illustrates how the use of the latest omics technologies is being applied to investigate the effect of diets, foods or food components on health/disease status. Bioactive food components alter gene expression and protein levels and functions, leading to various beneficial effects on human health. Gene variants and expression, epigenetic...

The common octopus is the most demanded cephalopod species for human consumption. Despite important advances realized recently, the main bottleneck for commercial production of the common octopus, Octopus vulgaris, is the mass mortality of paralarvae in the first 15–20 days post-hatching (dph), with the main responsible factors still unknown. Thus,...

Data-independent acquisition (DIA) methods have gained great popularity in bottom-up quantitative proteomics, as they overcome the irreproducibility and under-sampling limitations of data-dependent acquisition (DDA). diaPASEF, recently developed for the timsTOF Pro mass spectrometers, has brought improvements to DIA, providing additional ion separa...

Classical and culture-based methods for the identification and characterization of the biochemical properties of microorganisms are slow and labor-intensive. Liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) has been used for the analysis of bacterial pathogen strain-specific diagnostic peptides allowing the char...

α-Linolenic acid (ALA, 18:3n-3) and γ-gamma linolenic acid (GLA, 18:3n-6) are polyunsaturated fatty acids (PUFA) that improve the human health. The present study focused on testing the in vitro antitumor actions of pure ALA and GLA on the HT-29 human colorectal cancer cell line. Cell viability was checked by MTT ((3-(4,5-Dimethylthiazol-2-yl)-2,5-d...

Coronavirus disease 2019 (COVID-19), caused by an outbreak of the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) in Wuhan, China, has led to an unprecedented health and economic crisis worldwide. To develop treatments that can stop or lessen the symptoms and severity of SARS-CoV-2 infection, it is critical to understand how the virus...

The disease known as coronavirus disease 19 (COVID-19), potentially caused by an outbreak of the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) in Wuhan, China, has hit the world hard, and has led to an unprecedent health and economic crisis. In order to develop treatment options able to stop or ameliorate SARS-CoV-2 effects, we need...

Colorectal cancer (CRC) is one of the most common and mortal types of cancer. There is increasing evidence that some polyunsaturated fatty acids (PUFAs) exercise specific inhibitory actions on cancer cells through different mechanisms, as a previous study on CRC cells demonstrated for two very long-chain PUFA. These were docosahexaenoic acid (DHA,...

Newly emerged proteomic methodologies, particularly data‐independent acquisition (DIA) analysis–related approaches, would improve current gene expression–based classifications of colorectal cancer (CRC). Therefore, this study was aimed to identify protein expression signatures using SWATH‐MS DIA and targeted data extraction, to aid in the classific...

Adulteration and mislabeling of food products and the commercial fraud derived, either intentionally or not, is a global source of economic fraud to consumers but also to all stakeholders involved in food production and distribution. Legislation has been enforced all over the world aimed at guaranteeing the authenticity of the food products all alo...

Background Therapy with anti-TNF has improved notably the management of Crohn's disease (CD).¹ However, 25–40% of patients treated with these drugs lose response long-term.² In addition, these treatments are expensive and not without risk of adverse events. Therefore, it is essential to identify reliable markers that will select those patients who...

Food adulteration, mislabeling and fraud, either unintentional or deliberate, is a worldwide and growing concern. Current challenges associated with food authentication comprise many topics: geographic origin, breed/variety identification, production method, feeding regime, technological processing, undeclared components, detection of genetically m...

Galiellalactone (GL) is a fungal metabolite that presents antitumor and antiinflammatory activities in vitro and in vivo. Previous studies have shown that GL targets NF-κB and STAT3 pathways and induces G2/M cell cycle arrest in androgen-insensitive prostate cancer cells. In this study, we show that GL-induced cell cycle arrest is independent of th...

Aberrant DNA hypermethylation is a hallmark of cancer although the underlying molecular mechanisms are still poorly understood. To study the possible role of 5-hydroxymethylcytosine (5hmC) in this process we analyzed the global and locus-specific genome-wide levels of 5hmC and 5mC in human primary samples from 12 non-tumoral brains and 53 gliomas....

Two PUFAs, DHA and ARA, as well as derivatives such as eicosanoids, regulate different activities, affecting transcription factors and therefore DNA transcription, being a critical step for the functioning of FA-derived signalling. This work has attempted to determine the in vitro anticancer activities of these molecules linked to the gene transcri...

Significance: Currently there is no single biochemical parameter available for the accurate diagnosis of growth hormone (GH) deficiency (GHD) in children. Simple GH measurements are not an option: because GH is released in a pulsatile action, its blood levels fluctuate throughout the day and remain nearly undetectable for most of that time. This m...

Food components are regularly adulterated, either deliberately or unintentionally, and this may lead to substitutions of a species by a similar but lower-quality counterpart, mislabeling of products, and therefore to commercial fraud. The authentication of food products is a request from consumers and industry, and accordingly global food regulatio...

Aberrant DNA hypermethylation is a hallmark of cancer although the underlying molecular mechanisms are still poorly understood. To study the possible role of 5-hydroxymethylcytosine (5hmC) in this process we analyzed the global and locus-specific genome-wide levels of 5hmC in primary samples from 54 gliomas and 72 colorectal cancer patients. Levels...

The need for complete and truthful information about the food products we eat is a primary request from consumers. In the last years many regulations have appeared in order to avoid food adulteration, mislabelling and fraud. For these reasons, the authentication of food products must be guaranteed, and therefore accurate and reliable analytical met...

Currently, food allergies are an important health concern worldwide. The presence of undeclared allergenic ingredients or the presence of traces of allergens due to contamination during food processing poses a great health risk to sensitized individuals. Therefore, reliable analytical methods are required to detect and identify allergenic ingredien...

Unlabelled: Consumers have the right to know what is in the food they are eating. Accordingly, European and global food regulations require that the provenance of the food can be guaranteed from farm to fork. Many different instrumental techniques have been proposed for food authentication. Although traditional methods are still being used, new ap...

Response to treatment of rheumatoid arthritis shows large inter-individual variability. This heterogeneity is observed with all the anti-rheumatic drugs, including the commonly used TNF inhibitors. It seems that drug-specific and target-specific factors lead individual patients to respond or not to a given drug, although this point has been challen...

Significance: Bronchoalveolar lavage fluid (BALF) analysis can contribute to clinical practice with more sensitive biomarkers, thus complementing cytohistological studies in order to aid in the diagnosis, prognosis, and subtyping of lung cancer, as well as the monitoring of treatment response. Here we report a panel of candidate protein biomarkers...

DNA methylation is an epigenetic mechanism regulating gene expression that has been insufficiently studied in the blood of rheumatoid arthritis (RA) patients, as only T cells and total peripheral blood mononuclear cells (PBMCs) from patients with established RA have been studied and with conflicting results. Five major blood cell subpopulations: T,...

Authentication of food products has demanded great attention by consumers and the food industry in recent years. Food components may be adulterated, leading to mislabeling and commercial fraud, especially in fish and shellfish products, where the substitution of high quality species by lower quality ones is frequent. Many regulations have appeared...

Three factors defining the traceability of a food product are production method (wild or farmed), geographical origin and biological species, which have to be checked and guaranteed, not only in order to avoid mislabelling and commercial fraud, but also to address food safety issues and to comply with legal regulations. The aim of this study was to...

Background Biological therapies have been a great advance in Rheumatoid Arthritis (RA) treatment. However, up to a third of the RA patients do not respond to a given biologic and a method to predict response is not yet available. Therefore, the only approach to select effective biological drugs is by trial and error. In addition, assessment of resp...

This review is a critical overview of advances in proteomics applied in food technology, which may be classified into two main topics: (i) authentication of food components as a tool to comply with foodlabeling regulations and policies; and, (ii) food-technology research, mainly for the development of fast, reliable methods to detect and to identif...

Background Epigenetic regulation influences gene expression and can affect disease course and treatment response. Global DNA methylation of T cells from patients with RA is decreased1. This hypomethylation could favour inflammation and tissue destruction through aberrant gene expression. However, little is known about this process and whether other...

The close relationship between nutrition and health has led to changes in the habits of consumers, who are demanding products that meet their dietary and nutritional preferences. In light of this demand, both academia and food industries face a new challenge: the need for developing strategies and products that are not only safe, but also contribut...

Biologics such as TNF antagonists are a new class of drugs that have greatly improved Rheumatoid Arthritis (RA) treatment.However, for unknown reasons, individual patientswith RA respond to one of these drugs but not to others even those targeting the same molecule. Methods to predict response are sorely needed because these drugs are currently sel...

Although seafood species identification has traditionally relied on morphological analysis, sometimes this is difficult to apply for the differentiation among penaeid shrimps owing to their phenotypic similarities and to the frequent removal of external carapace during processing. The objective of this review is to provide an updated and extensive...

Genomic and proteomic techniques for species identification of meat and seafood products are being widely used. In this study, a genomic approach was used to differentiate Pandalus borealis (the Northern shrimp), which belongs to the superfamily Pandaloidea, from 30 crustaceans consisting of 19 commercially relevant prawns/shrimps species that belo...

Selected tandem mass spectrometry (MS/MS) ion monitoring (SMIM) is the most suitable scanning mode to detect known peptides in complex samples when an ion-trap mass spectrometer is the instrument used for the analysis. In this mode, the MS detector is programmed to perform continuous MS/MS scans on one or more selected precursors, either during a s...

Polymerase chain reaction-based methodologies have been developed for the identification of three commercially-relevant penaeid shrimp species, these were: Litopenaeus vannamei, Penaeus monodon and Fenneropenaeus indicus in food products. Such three species represent more than 80% of the whole farmed shrimp production worldwide and may be fraudulen...

Native isoelectric focusing (IEF) of water-soluble sarcoplasmic proteins was applied to the identification of 14 shrimp species of food interest belonging to the order Decapoda. These species have different commercial values, but due to their phenotypic similarities and carapace removal in their industrial processing, incorrect food labelling and d...

The effect of a previous hydrostatic highpressure (HHP) treatment on hydrolysis, breakdown and aggregation events in chemical constituents of chilled farmed coho salmon (Oncorhynchus kisutch) was studied. Three different HHP conditions were applied (135 MPa- 30 s; 170 MPa-30 s; 200 MPa-30 s; treatments T-1, T-2 and T-3, respectively) and compared t...

The identification of commercial shrimp species is a relevant issue to ensure correct labeling, maintain consumer confidence and enhance the knowledge of the captured species, benefiting both, fisheries and manufacturers. A proteomic approach, based on 2DE, tryptic in-gel digestion, MALDI-TOF MS, and ESI-MS/MS analyses, is proposed for the identifi...

A proteomic approach aimed at species identification and taxonomic analysis of shrimp species of commercial interest is presented. Six different species belonging to the order Decapoda were considered. Preliminary, two-dimensional gel electrophoresis (2-DE) analysis of the sarcoplasmic proteome revealed interspecific variability in the isoelectric...

The suitability of a proteomic approach was explored to establish phylogenetic relationships among closely-related species. Decapoda penaeid shrimps were chosen as case study because these species have been widely studied and their phylogenetic relationships have been inferred by extensively validated methods, among which mitochondrial DNA-based PC...

Tiger prawn, Penaeus monodon, and banana white prawn, Fenneropenaeus indicus—two of the most important commercial shrimp species—share world distribution, habitat, and similar morphometric characters. Because of commercial regulations about labeling and traceability requirements, species authentication methods are of great interest to fisheries and...

3 Food engineering department, universidad de bío-bío, Chillán, Chile; 4 Food engineering department Abstract: Coho salmon (Oncorhynchus kisutch) has recently attracted a great interest as a farmed product. This research focuses on its commercialisation as a chilled product. Thus, the effect of a previous hydrostatic high pressure (HHP) treatment o...