Proteomics & Genomics

deborah penque P

Deborah Penque

Principal Investigator

Phone: +351 217 508 137
Fax: + 351 217 526 410

luis vieira P
Luís Viera

Core Lab Manager

Technology and Innovation Unit
Phone: +351 217 526 440
Fax: + 351 217 526 410


Department of Human Genetics
Avenida Padre Cruz
1649-016 Lisboa, Portugal.


The discovery, development, and application of proteomic knowledge and technologies for translational bench-to-bedside applications.
Assess and develop proteomic tools for the study of chronic diseases, including disease associated with environmental risk factors.
Enable a full appreciation of the promises and limitations of proteomics in biomedicine, ultimately providing new proteomics-based diagnostic and prognostic tools allowing clinicians to personalize their interventions.

Research areas

Proteomics in biomarker discovery and validation/verification for Chronic Lung Diseases [Chronic Obstructive Pulmonary Disease (COPD), Obstructive Sleep Apnea (OSA), CLD associated with the exposure to toxic environmental agents (e.g., second-hand tobacco smoke exposure)].


The Technology and Innovation Unit (Unidade de Tecnologia e Inovação, UTI) provides sequencing, genotyping and bioinformatics services to members of INSA, Toxomics and external entities. The UTI processes more than 35,000 samples / year.The available equipments include 3 next-generation sequencing system (MiSeq and NextSeq from Illumina and a MinION from Oxford Nanopore Technologies), a capillary sequencer (3130XL Genetic Analyzer), a real-time PCR instrument (7500 RT-PCR System), a biomolecule analyzer (Fragment Analyzer) and a Linux server. The Unit also has a variety of auxiliary equipment, including PCR machines, fluorimeter (Qubit) and microplate centrifuge. The equipment is monitored and / or calibrated on a regular basis. Each year the Unit participates in several international quality assessment programs for sequencing and genotyping.

The analysis portfolio includes:
- Sequencing of DNA by Sanger method and capillary electrophoresis (test accredited by ISO 15189);
- Genotyping by capillary electrophoresis (e.g., MLPA);
- Genome and transcriptome sequencing (short- or long-reads);
- Metagenomics barcoding (16S rRNA gene);
- Gene panel sequencing;
- Clinical exome sequencing;
- microRNA sequencing;
- Amplicon sequencing.

Bioinformatics services should be queried and discussed on an individual basis with the Lab Manager.

Research areas

Molecular pathogenesis of Wilms tumour.

Running as PI / Co-PI:

Target Specific Immunoaffinity Assay for translation of protein biomarkers into PARKinsons diagnostic. FCT-Portugal2020 (02/SAICT/2017). PI: Vukosava Milic Torres, FCUL.; Co-PI: D Penque, INSA

Environmental Tobacco Smoke Exposure at Portuguese Restaurants, Bars and nightclubs: health effects and early molecular mechanisms underlying respiratory disorders. IGC/ACSS. PI. D Penque

Obstructive sleep apnea (OSA) and associated metabolic / cardiovascular disorders: understanding mechanisms towards early diagnosis and prognosis prediction.  HMSP-ICJ/0022/2011- Junior Investigator: Senior PIs: D Penque  (basic research) & Cristina Bárbara (clinical research). Applicant: A Feliciano, HPV

Proteomics of chronic lung diseases leading to biomarkers and therapeutic target discovery. (POCTI/SAU-MMO/56163/2004). PI: D Penque

Running as Collaborator

2017-2022 – National Mass Spectrometry Networking (RNEM), a Portuguese research infrastructure (RI) of strategic interest supported by Fundação para a Ciência e a Tecnologia (FCT). D Penque is the INSA-Infrastructure Node delegate.

2017-2020 – Genome Portugal (GenomePT) consortium, a Portuguese research infrastructure (RI) of strategic interest supported by COMPETE 2020 – Operational Programme for Competitiveness and Internationalisation (POCI), Lisboa Portugal Regional Operational Programme (Lisboa2020), Algarve Portugal Regional Operational Programme (CRESC Algarve2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF), and by Fundação para a Ciência e a Tecnologia (FCT).  Luís Vieira is the INSA-Infrastructure Node delegate.

2017-2019 -  Cost ACTION – CliniMARK: good biomarker practice to increase the number of clinically validated biomarkers (CA16113). D Penque: Leader of Working Group 3.

2016-2017 – Innuendo: A cross-sectorial platform for the integration of genomics in surveillance of food-borne pathogens, GP/EFSA/AFSCO/2015/01, EFSA, University of Helsinki, Universidade de Lisboa, University of the Basque Country, University of Veterinary Medicine, National Institute for Health and Welfare, Finnish Food Safety Authority, Instituto Nacional de Saúde Doutor Ricardo Jorge, Estonian Veterinary e Food Laboratory, Institute of Food Safety, Animal Health and Environment.

Since 2016 – The European Human Biomonitoring Initiative (EHBMI) Topic identifier: SC1-PM-05-2016. Coordinator: German Environment Agency (UBA). Participate in this European project as Portugal INSA member of Work Package 14.

2016 – 2019 – ProbeCOPD. Protease activity based probes for Chronic Obstructive Pulmonary Disease diagnostics PTDC/BBBBEP/2463/2014. PI. Rui Moreira, PhD,  iMed.ULisboa.

2015-2018 – Genetic defects of mitochondrial disorders: A next-generation sequencing approach, PTDC/DTP-PIC/2220/2014, supported by Fundação para a Ciência e a Tecnologia.


The most relevant in the last 5 years:


Feliciano A, Linhas R, Marçôa R, Cysneiros A, Martinho C, Reis RP, Penque D, Pinto P, Bárbara C. Hematological evaluation in males with obstructive Sleep apnea before and after positive airway pressure. Rev Port Pneumol (2006). 2017 Mar – Apr;23(2):71-78. doi: 10.1016/j.rppnen.2016.12.001. Epub 2017 Jan 31.PubMed PMID: 28153627.

Feliciano A, Linhas R, Marçôa R, Cysneiros A, Martinho C, Reis RP, Penque D,Pinto P, Bárbara C. Hematological evaluation in males with obstructive sleep apnea before and after positive airway pressure. Rev Port Pneumol (2006). 2017 Mar – Apr;23(2):71-78.

Feliciano A, Vaz F, Valentim-Coelho C, Torres VM, Silva R, Prosinecki V,Alexandre BM, Almeida A, Almeida-Marques C, Carvalho AS, Matthiesen R, MalhotraA, Pinto P, Bárbara C, Penque D. Evening and morning alterations in Obstructive Sleep Apnea red blood cell proteome. Data Brief. 2017 Jan 16;11:103-110.

Feliciano A, Vaz F, Torres VM, Valentim-Coelho C, Silva R, Prosinecki V, Alexandre BM, Carvalho AS, Matthiesen R, Malhotra A, Pinto P, Bárbara C, Penque D (2017). Evening-morning peroxiredoxin-2 redox/oligomeric state changes in obstructive sleep apnea red blood cells: Correlation with polysomnographic and metabolic parameters. Biochimica Biophysica Acta: Molecular Basis of Disease 1863: 621–629.

Torres VM, Popovic L, Vaz F, Penque D (2016). Proteomics as tool in the assessment of chemoresistance of antineoplastic drugs. Methods in Molecular Biology 1395:281-98.

Feliciano A, Torres VM, Vaz F, Carvalho AS, Matthiesen R, Pinto P, Malhotra A, Bárbara C, Penque D (2015). Overview of proteomics studies in obstructive sleep apnea. Sleep Medicine 16(4):437-45

Pacheco SA, Torres VM, Louro H, Gomes F, Lopes C, Marçal N, Fragoso E, Martins C, Oliveira CL, Hagenfeldt M, Bugalho-Almeida A, Penque D*, Simões T* (2013). Effects of occupational exposure to tobacco smoke: is there a link between environmental exposure and disease? Journal of Toxicology and Environmental Health A 76(4-5):311-27. *both authors contributed equally to the study.

Smith LM, Kelleher NL ; Consortium for Top Down Proteomics: Linial M, Goodlett D, Langridge-Smith P, Goo YA, Safford G, Bonilla L, Kruppa G, Zubarev R, Rontree J, Chamot-Rooke J, Garavelli J, Heck A, Loo J, Penque D, Hornshaw M, Hendrickson C, Pasa-Tolic L, Borchers C, Chan D, Young N, Agar J, Masselon C, Gross M, McLafferty F, Tsybin Y, Ge Y, Sanders I, Langridge J, Whitelegge J, Marshall A (2013). Proteoform: a single term describing protein complexity. Nature Methods 10(3):186-7.

Alexandre B, Charro N, Blonder J, Lopes C, Azevedo P, Bugalho de Almeida A, Chan KC, Prieto DA, Issaq H, Veenstra TD, Penque D (2012). Profiling the erythrocyte membrane proteome isolated from patients diagnosed with chronic obstructive pulmonary disease. Journal of Proteomics 76 Spec No:259-69.

Pacheco+, Aguiar F+, Ruivo P, Proença MC, Sekera M, Penque D*, Simões T* (2012). Occupational exposure to environmental tobacco smoke: a study in Lisbon restaurants. Journal of Toxicology and Environmental Health A 75(13-15):857-66.

Simões T, Charro N, Alexandre BM, Penque D (2012). Proteomics in Detection and Monitoring Chronic Lung Diseases: The Human Nasal Epithelium as a Molecular Model. Journal of Allergy and Therapy- -OMICS Group S7:004. Review.

Alexandre BM, Penque D (2012). Chronic Obstructive Pulmonary Disease and Proteomics: A Match for Success? Journal of Allergy and Therapy- -OMICS Group S7:003. Review.


Faria R, Silva B, Silva C, Loureiro P, Queiroz A, Fraga S, Esteves J, Mendes D, Fleming R, Vieira L, Gonçalves J, Faustino P. Next-generation sequencing of hereditary hemochromatosis-related genes: Novel likely pathogenic variants found in the Portuguese population. Blood Cells Mol Dis. 2016 Oct;61:10-5.

Pinto M, Borges V, Antelo M, Pinheiro M, Nunes A, Azevedo J, Borrego MJ, Mendonça J, Carpinteiro D, Vieira L, Gomes JP. Genome-scale analysis of the non-cultivable Treponema pallidum reveals extensive within-patient genetic variation. Nat Microbiol. 2016 Oct 17;2:16190.

Manageiro V, Clemente L, Duarte S, Vieira L, Caniça M. 2016. Draft genome sequence of an Escherichia coli strain isolated from a Gallus gallus broiler producing the novel CTX-M-166 variant. Genome Announc 4(5):e01029-16.

Jones-Dias D, Manageiro V, Ferreira E, Barreiro P, Vieira L, Moura IB, Caniça M. Architecture of Class 1, 2, and 3 Integrons from Gram Negative Bacteria Recovered among Fruits and Vegetables. Front Microbiol. 2016 Sep 13;7:1400.

Borges V, Nunes A, Sampaio DA, Vieira L, Machado J, Simões MJ, Gonçalves P, Gomes JP (2016) Legionella pneumophila strain associated with the first evidence of person-to-person transmission of legionnaires’ disease: a unique mosaic genetic backbone. Scientific Reports 6: 26261.

Correia AM, Ferreira JS, Borges V, Nunes A, Gomes B, Capucho R, Gonçalves J, Antunes DM, Almeida S, Mendes A, Guerreiro M, Sampaio DA, Vieira L, Machado J, Simões MJ, Gonçalves P, Gomes JP (2016) Probable person-to-person transmission of legionnaires’ disease. New England Journal of Medicine 374: 497-8.

Borges V, Pinheiro M, Antelo M, Sampaio DA, Vieira L, Ferreira R, Nunes A, Almeida F, Mota LJ, Borrego MJ, Gomes JP (2015). Chlamydia trachomatis in vivo to in vitro transition reveals mechanisms of phase variation and down-regulation of virulence factors. PLoS One. Jul 24; 10(7):e0133420.

Vieira L, Vaz A, Matos P, Ambrósio AP, Nogueira M, Marques B, Pereira AM, Jordan P, da Silva MG. Three-way translocation (X;20;16)(p11;q13;q23) in essential thrombocythemia implicates NFATC2 in dysregulation of CSF2 expression and megakaryocyte proliferation. Genes Chromosomes Cancer. 2012 Dec;51(12):1093-108.

• University of Lund, Sweden:
Peter James (LC/MS/MS)
Gyorgy Marko-Varga (Biobanking).

• University of Ribeirão Preto, São Paulo Brasil:
Fernando Barbosa (metabolomics)

• Centro Hospitalar Lisboa Norte
Cristina Bárbara
(Pneumologia, Hospital Sta Maria e Hospital Pulido Valente)

• Instituto Português de Oncologia de Francisco Gentil (Lisboa)
Branca Cavaco (investigadora)

• Universidade de Trás-os-Montes e Alto Douro
Gilberto Igrejas (investigador)