Lysosomes and Disease

Lysosomes, acidic, hydrolase-rich cellular organelles, are the final destination of endocytic and autophagic pathways. Cell homeostasis is vitally linked to lysosomal function; malfunction being associated with several chronic pathologies including atherosclerosis, the main cause of cardiovascular diseases. Lysosomes are involved in almost the whole process of atherosclerosis. We aim to contribute to the better understanding of these pivotal organelles in the biology/physiology and pathophysiology of atherosclerosis.


We expect to:

  • Identify the molecular mechanisms of lysosome malfunction
  • Understand how lysosome dysfunction affects cell homeostasis and contributes to the pathogenesis of atherosclerosis;
  • Translate our findings into clinical practices.

Our research currently applies some state-of-the-art techniques including Live-Cell Imaging, EM, Shotgun Lipidomics, Biochemical, Biophysical, and Pharmacological approaches applied to primary human cells, animal models and human tissues.

Graphical Abstract


  • Project on Cholesteryl Hemiesters and Dysfunctional Lysosomes in Atherosclerosis

Atherosclerosis, a chronic systemic inflammatory disease that leads to myocardial infarction, stroke, and lower limb ischemia, is the major cause of cardiovascular disease (CVD)-related death globally. It results from constitutive uptake by macrophages and smooth muscle cells of modified Low Density Lipoproteins (LDL), trapped in the arterial intima that, with time, start to accumulate irreversibly in lysosomes, contributing to chronic inflammation, cell death etc.

One of the modifications that LDL undergoes is lipid oxidation, which leads to the formation of oxidized lipid species that, with time, will be detected in the blood. Based on this reasoning, we determined the lipidome of the blood plasma of CVD patients. The results showed that while total cholesterol concentrations were only slightly different, the concentrations of a family of previously not investigated oxidized-lipids, cholesteryl hemiesters (ChE), was significantly higher in CVD patients than in normal donors.

Lysosomal dysfunction is a common and early contributing factor in the onset of several chronic diseases but it has been almost neglected in the pathobiology of atherosclerosis.

Thus, the goal of this project is to characterize the novel family of oxidized lipids as new risk factors in atherosclerosis and as inducers of lysosome dysfunction as well as to understand the molecular mechanisms behind lysosomal dysfunction in ChE-treated macrophages, smooth muscle cells and in zebrafish larvae.

We are using cutting-edge techniques such as shotgun lipidomics alongside complementary molecular cell biology methods. We are confident that this proposal will uncover important new CVD risk factors and concepts underlying the pathogenesis of atherosclerosis that may guide the development of new drugs with therapeutic activity towards CVD.

  • FCT project (PTDC/MED-PAT/29395/2017), Exocytosis of Dysfunctional Lysosomes as a New Paradigm Shift in the Pathogenesis of Atherosclerosis.
    (2018-2022): Principal Investigator
  •  FCT project (PTDC/BIA/MIC/31561/2017), Development and Evaluation of a Surfactant-hydrogel for Preventing Direct Contact Transmitted Infections.
    (2018-2022): Co-Principal Investigator
  • European Union’s Horizon Twinning project 2020 (No 811087)-LYSOCIL - Excel in Rare Diseases’ Research: Focus on LYSOsomal Disorders and CILiopathies. (2018-2022: Partner
  • FCT project (03/SAICT/2015), NEw Targets in DIAstolic heart failure: from coMOrbidities to persoNalizeD medicine. (2016 – 2021): Partner
  • iNOVA4health project , The role of cholesteryl hemiesters in the etiology, development and instability of atheromata. (2015 – 2017): Principal Investigator
  • FCT Investigator, Understanding the molecular etiology and cellular mechanisms involved in atherogenic irreversible lipid accumulation in macrophages and its consequences for atherogenesis. (2014 – 2017): Principal Investigator
  • FCT project, Harvard Medical School Program (HMSP-ICT/0024/2010) “A New Approach to Fight Tuberculosis” (2012 – 2015): Principal Investigator
  • Prémio Arrisca C 2011- Prémio ACIC – Concurso de ideias de negócio. Projecto. “Synthesis and assessment of new microbicides for topical use in sexually transmitted infections”. 2012: Principal Investigator
  • FCT project (PTDC/BIA-BCM/112138/2009), Role of RabGTPases On Phagocytosis And Phagosomal Maturation Of IgG-Opsonized Heat-killed and Mycobacterium tuberculosis”. (2011 – 2014): Principal Investigator
  • Bolsa de Ignição da Universidade de Coimbra, Surfactants in the Prophylaxis of Sexually Transmitted Infections. 2011: Principal Investigator
  • FCT project (PTDC/SAU-MII/66285/2006), Role and Molecular Mechanisms Underlying CD36-Mediated Phagocytosis of Apoptotic Cells: Implications for Atherosclerosis. (2007 – 2010): Principal Investigator
  • Elizeth Lopes; Gisela Machado de Oliveira; Catarina Guerreiro Simões; Inês Ferreira; Cristiano Manuel Colaço Ramos; José Ramalho; Maria I. L. Soares, Teresa M. V. D. Pinho e Melo, Rosa Puertollano, André R. A. Marques, Otília V. Vieira 1. Cholesteryl hemiazelate present in cardiovascular disease patients causes lysosome dysfunction in murine fibroblasts. Cells 2023, 12(24), 2826; DOI.10.3390/cells12242826 
  • N. Domingues, J. Gaifém, A.R.A. Marques, R. Matthiesen, D. Saraiva, L. Bento, M.I.L. Soares, J. Sampaio, C. Klose, M.A. Surma, M.S. Almeida, G. Rodrigues, P.A. Gonçalves, J. Ferreira, R. Gouveia e Melo, L. M. Pedro, K. Simons, T.M.V.D. Pinho e Melo, G. Cabral, A. Jacinto, R. Silvestre, W. Vaz, O. V. Vieira1. Inflammatory Profile of human immune cells and zebrafish larvae exposed to a New Lipid Identified in Cardiovascular Disease Patients. J Lipid Res. (2023) 21:100419. DOI: 10.1016/j.jlr.2023.100419.
  • Domingues N, Marques ARA, Calado RDA, Ferreira IS, Ramos C, Ramalho J, Soares MIL, Pereira T, Oliveira L, Vicente JR, Wong LH, Simões ICM, Pinho E Melo TMVD, Peden A, Almeida CG, Futter CE, Puertollano R, Vaz WLC, Vieira OV. Oxidized cholesteryl ester induces exocytosis of dysfunctional lysosomes in lipidotic macrophages. Traffic. 2023 Jul;24(7):284-307. doi: 10.1111/tra.12888. Epub 2023 May 2. PMID: 37129279.
  • Alves LS, Marques ARA, Padrão N, Carvalho FA, Ramalho J, Lopes CS, Soares MIL, Futter CE, Pinho E Melo TMVD, Santos NC, Vieira OV. Cholesteryl hemiazelate causes lysosome dysfunction impacting vascular smooth muscle cell homeostasis. J Cell Sci. 2022 Mar 1;135(5):jcs254631. doi: 10.1242/jcs.254631. 
  • Matthiesen R, Lauber C, Sampaio JL, Domingues N, Alves L, Gerl MJ, Almeida MS, Rodrigues G, Araújo Gonçalves P, Ferreira J, Borbinha C, Pedro Marto J, Neves M, Batista F, Viana-Baptista M, Alves J, Simons K, Vaz WLC, Vieira OV*. Shotgun mass spectrometry-based lipid profiling identifies and distinguishes between chronic inflammatory diseases. EBioMedicine. 2021 Jul 23;70:103504. doi: 10.1016/j.ebiom.2021.103504. *Commentary in EBioMedicine 70:103526, DOI:
  • Marques, ARA; Ramos, C; Machado-Oliveira, G; Vieira, OV. Lysosome (Dys)function in Atherosclerosis—A Big Weight on the Shoulders of a Small Organelle. Frontiers in Cell and Developmental Biology Vol. 9, 29 March 2021. doi: 10.3389/fcell.2021.658995.
  • Oliveira GM, Ramos C, Marques ARA, Vieira OV. Cell Senescence, Multiple Organelle Dysfunction and Atherosclerosis. Cells, 2020 Sep 23;9(10):2146. doi: 10.3390/cells9102146.
  • Gerl MJ, Vaz WLC, Domingues N, Klose C, Surma MA, Sampaio JL, Almeida MS, Rodrigues G, Araújo-Gonçalves P, Ferreira J, Borbinha C, Marto JP, Viana-Baptista M, Simons K, Vieira OV. Cholesterol is Inefficiently Converted to Cholesteryl Esters in the Blood of Cardiovascular Disease Patients. Sci Rep. 2018 Oct 3;8(1):14764. doi: 10.1038/s41598-018-33116-4.
  • Gibson MS, Domingues N, Vieira OV. Lipid and Non-lipid Factors Affecting Macrophage Dysfunction and Inflammation in Atherosclerosis. Front Physiol. 2018 Jun 26;9:654. doi: 10.3389/fphys.2018.00654.
  • Santarino IB, Viegas MS, Domingues NS, Ribeiro AM, Soares MP, Vieira OV. Involvement of the p62/NRF2 signal transduction pathway on erythrophagocytosis. Sci Rep. 2017 Jul 19;7(1):5812. doi: 10.1038/s41598-017-05687-1
  • N. Domingues, L. Estronca, J. Silva, M. Encarnação, R. Mateus, D. Silva, I. Santarino, M. Saraiva, M. Soares, T. Pinho e Melo, A. Jacinto, W. Vaz and O.V. Vieira. Cholesteryl hemiesters alter lysosome structure and function and induce proinflammatory cytokine production in macrophages. BBA - Molecular and Cell Biology of Lipids. February 2017 1862; 2: 210–220. doi: 10.1016/j.bbalip.2016.10.009
  • M. Encarnação, L. Espada, C. Escrevente, D. Mateus, J. Ramalho, X. Michelet, I. Santarino, V. W. Hsu, M. B. Brenner, D. Barral and O. V. Vieira. (2016).* Encarnação M, Espada L, Escrevente C, Mateus D, Ramalho J, Michelet X, Santarino I, Hsu VW, Brenner MB, Barral D, Vieira OV. A Rab3a-dependent complex essential for lysosome positioning and plasma membrane repair. J Cell Biol. 2016 Jun 20;213(6):631-40. doi: 10.1083/jcb.201511093. J. Cell Biol. 2016 213:631-640.
    * Spotlight in J. Cell Biol. 2016 213:613-615. Recommended in F1000Prime.
  • Â. Inácio, A. Nunes, C. Milho C, L. J. Mota, M. J. Borrego, J. P. Gomes, W. L. C. Vaz and O. V. Vieira. In vitro activity of quaternary ammonium surfactants against streptococcal, chlamydial, and gonococcal infective agents. Antimicrob Agents Chemother. 2016 23;60(6):3323-32. doi: 10.1128/AAC.00166-16
  • Â. Inácio, N. S. Domingues, A. Nunes, P. T. Martins, M. J. Moreno, L. M. Estronca, R. Fernandes, A. J. M. Moreno, M. J. Borrego, J. P. Gomes, W. L. C. Vaz and O. V. Vieira. Quaternary ammonium surfactant structure determines selective toxicity towards bacteria: mechanisms of action and clinical implications in antibacterial prophylaxis. J Antimicrob Chemother 2016; 71(3):641-54. doi: 10.1093/jac/dkv405
  • L.M.B.B. Estronca, J. Silva, J. Sampaio, A. Shevchenko, P. Verkade, W.L.C. Vaz and O.V. Vieira. Molecular Etiology of Atherogenesis - In Vitro Induction of Lipidosis in Macrophages with a New LDL Model. PLoS One. 2012;7(4):e34822. doi: 10.1371/journal.pone.003482
  • C.M. Cardoso, L. Jordão and O.V. Vieira. Rab10 is required for phagosome maturation and its overexpression can change the fate of Mycobacterium-containing phagosomes. Traffic. 2010 11(2):221-35. doi: 10.1111/j.1600-0854.2009.01013.x.
  • World’s Top 2% Scientists list, 2021, (Winchil Vaz)
  • FCT Investigator (“consolidator level”), 2014 (Otilia Vieira)
  • Prémio Arrisca C 2011- Prémio ACIC – Concurso de ideias de negócio, com o trabalho intitulado “Síntese de novos surfactantes e sua avaliação como microbicidas para uso tópico em doenças sexualmente transmissíveis”, 2012 (Otilia Vieira)
  • Bolsa de Ignição da Universidade de Coimbra com o título “Surfactants in the Prophylaxis of Sexually Transmitted Infections”, 2011 (Otilia Vieira)
  • Bolsa de Pós-doutoramento da Sociedade Max-Planck (Max-Planck-Gesellschaft), Alemanha, 2004 (Otilia Vieira).
  • Bolsa de Pós-doutoramento da Comissão da União Europeia (Bolsa Marie-Curie), 2002 (Otilia Vieira).
  • Bolsa da European Molecular Biology Organization (EMBO) de Pós-doutoramento, 2002 (Otilia Vieira).
2 PhD Research Opportunities @ Lysosomes and Disease Lab
Collaboration between multiple NMS labs leads to joint publication

Research carried out by several of our laboratories is supported by the LYSOCIL project and has been published in Traffic magazine.

LYSOCIL project on rare diseases has its final conference

The final conference of the LYSOCIL project took place on the 8th and 9th of April at the Hotel Vila Galé in Cascais. It featured presentations from the various project partners and collaborators worldwide, including Italy and Germany.

  • Prof. Teresa Pinho e Melo and Dr. Isabel Soares, Department of Chemistry, University of Coimbra, Portugal.
  • Prof. Kai Simons, Lipotype, Dresden, Germany.
  • Dr. João Paulo Gomes, Dr. Alexandra Nunes and Dr. Maria José Borrego, Instituto Nacional de Saúde “Ricardo Jorge” (INSA), Lisbon, Portugal.
  • Prof. Clare Futter, Department of Cell Biology, University College London Institute of Ophthalmology, London, United Kingdom.
  • Prof. Anthony H. Futerman, Department of Biomolecular Sciences, Weizmann Insitute, Israel.
  • Dr. Jorge Ferreira, Dr. Manuel Almeida and Prof. Pedro Gonçalves, Hospital Santa Cruz, Carnaxide, Lisbon, Portugal.
  • Dr. Miguel Viana Baptista, Hospital Egas Moniz, Lisbon, Portugal.
  • Prof. Nuno Santos, IMM and Faculdade de Medicina, Universidade de Lisboa.
  • Prof. Rosa Puertollano, NIH, Maryland, USA.
  • Prof. Luís Mendes Pedro and Dr. Ryan Gouveia e Melo, Hospital de Santa Maria/ Centro Hospitalar Universitario Lisboa Norte, Portugal.
  • Prof. João Conde, CEDOC, NOVA MEDICAL SCHOOL, Lisbon, Portugal.
  • Dr. Claudia Santos, CEDOC, NOVA MEDICAL SCHOOL, Lisbon, Portugal.
  • Dr. Rune Matthiesen, CEDOC, NOVA MEDICAL SCHOOL, Lisbon, Portugal.

Principal Investigator

Otilia V. Vieira
Principal Investigator


Winchil Vaz
Senior Scientist
André Marques
Junior Researcher FCT Scientific Employment Stimulus
Elizeth Lopes
PhD student
Inês Ferreira
PhD student
Catarina Guerreiro Simões
Research Fellow
Quélia Ribeiro
Research Fellow