Cilia Regulation and Disease


Susana Lopes

Principal Investigator



Campus Sant'Ana
Pólo de Investigação, NMS, UNL
Rua do Instituto Bacteriológico, nº 5
Lab 2.3
1150-082 Lisboa, Portugal

Phone: (+351) 218 803 101 (Ext. 26045)
Lab ext:  27030
E-mail: susana.lopes(at)


Main interests

Cilia length and motility regulation
Cilia are cellular organelles that protrude from almost every cell membrane. Cilia can be motile or immotile and can appear isolated or in bundles per cell. All types of cilia are thought to have signaling properties. Important signaling pathways during animal development and disease have been related to cilia, such as the Hedgehog, FGF and Notch signaling pathways. When cilia have defective length Hedgehog signaling is abnormal. On the other hand, Notch and FGF signaling defects trigger ciliary length and motility problems. We study cilia length and motility regulation in order to understand ciliopathies. We use the vertebrate zebrafish embryo because it has many ciliated organs with all cilia types and offers excellent imaging and genetic advantages.

Cilia have acquired major biomedical relevance due to the disclosure of many different diseases as ciliopathies i.e. diseases that have a ciliary origin. Ciliary protein defects underlie several human syndromes, such as Bardet-Biedl, Alstrom, Joubert, Senior-Løken, Meckel-Gruber, and Oral Facial Digit syndromes, that involve different conjugations of conditions such as polycystic kidney disease, retinal degeneration, anosmia, polydactyly, or organ situs reversal. Several of these syndromes show features not obviously related to cilia, including obesity and mental retardation. Human syndromes such as Kartagener were already identified as ciliopathies affecting motile cilia but many others such as Jeune asphyxiating thoracic dystrophy were not known as ciliopathies and have only recently been allocated to defects in primary cilia signaling. Ciliopathies affect many cell types and organs including kidney, liver, pancreas, heart, lungs, nose, ears, eyes and brain.

Research Areas

• Cilia length regulation.
• Cilia motility: beat frequency and pattern
• Cilia generated fluid flow dynamics within embryonic organs
• Ciliary mechano-sensory versus chemo-sensory signaling pathways



AWARD from Sociedade Portuguesa de Nefrologia

Project: Sphingolipid Signaling and CFTR stimulation in Autosomal Dominant Polycystic Kidney Disease

Team: Mónica Roxo-Rosa (PI), Susana Lopes, Bárbara Tavares and Joaquim Calado (ToxOmics)

Foto web SL2


LYSOCIL: Excel in Rare Diseases’ Research: Focus on LYSOsomal Disorders and CILiopathies
01/11/2018 – 30/04/2022
European Union’s Horizon Twinning project 2020 (No 811087)

LYSOCIL is a Twinning Project led by NOVA Medical School (NMS) that aims to strengthen the research and innovation capacity of the Chronic Diseases Research Center (CEDOC-NMS|FCM) in research in rare diseases, helping it to become a national and internationally-recognized centre of excellence in chronic rare diseases research and innovation. For this project, CEDOC-NMS|FCM partnered up with two internationally-leading institutions, Münster University (WWU), a German institution with a strong research profile in basic, clinical and translational medicine connected to rare diseases, and the Telethon Institute of Genetics and Medicine (TIGEM), the leading Italian research center dedicated to understanding the molecular mechanisms behind rare genetic diseases. This partnership will boost the multidisciplinary knowledge and experience, as well as research and training practices and widen the collaborative networks to step up the excellence of the research of the involved partners. Our research group is a partner in this project.

Principal Investigators: Duarte Barral and Susana Lopes

Research on left-right development
This is the main branch of my lab. We have been investigating the role of time in the left-right organizer (LRO). This ciliated embryonic organ is crucial for determining the laterality identity of the vertebrate body-plan. This organ has exciting biophysical properties that control several mechanisms of development, making it an interesting and relevant area of investigation. Namely, biophysical fluid-flow forces that will be translated into gene expression, and determine the location of the future heart on the left and the liver on the right side of the midline axis. Such fluid-flow is directional and known to be generated by motile cilia (Sampaio et al. Dev Cell. 2014). This flow starts by being mild and later becoming strong due to an increase in motile cilia number (Tavares et al. eLIFE. 2017). As a consequence, in the LRO there are two distinct time-windows underlying two fluid-flow regimes. Our current research investigates the molecular mechanisms behind these time-windows by integrating developmental biology, genetics, live-imaging, and bespoke fluid-mechanics modelling in collaboration with the University of Birmingham (Smith et al. Bioarchitecture, 2014; Montenegro-Johnson et al. J Math Biol. 2016; Pintado et al. R. Soc. open sci. 2017).

Research on Primary Ciliary Dyskinesia
The second interest of my lab, still related to left-right development, is the rare disease Primary Ciliary Dyskinesia (PCD), a disease where 50% of the patients develop situs inversus, i.e reversal of the internal organs. Like in most countries, PCD was not properly diagnosed in Portugal. Within the context of COST Beat-PCD-BM1407, my team learned and implemented some of the required techniques according to the European guidelines for PCD. We next triggered the implementation of a Lisbon PCD consortium so that, together with the Hospital Sta Maria (HSM, Lisbon) and Instituto de Medicina Molecular (IMM, Lisbon)), we can currently provide a robust multidisciplinary diagnostic according to the recent requirements for PCD. Our lab performs high-speed videomicroscopy analysis, necessary for the evaluation of cilia beat frequency and pattern (Constant et al. 2018. Acta Pediátrica Portuguesa). As a consequence of PCD diagnostics we started a new area of research in the lab. So far, we have invested on making better diagnostic software for cilia analysis in collaboration with Carla Quintão (NOVA, FCT). Additionally, we have generated zebrafish PCD genetic mutants by using CRISPR-Cas9 gene editing to mimic and better dissect mutations found in patients. The final aim is to rescue some cilia function in patients using gene therapy in collaboration with the Omran lab (WWU, Germany), with whom we have recently been funded by H2020-WIDESPREAD-2016-2017 in the format of a Twinning project, named Lysocil, to improve research on rare diseases in Portugal, including ciliopathies.

Research on Delta-Notch signalling
This signaling pathway is important for ciliary length regulation as well as for deciding the number of motile cilia. We investigated how is DeltaD linked to ciliogenesis and its impact on left-right development (Lopes et al. Development. 2010). This project carried on and we have now identified many interesting genes that are differentially expressed in zebrafish wild-type embryos and deltaD homozygous mutants. Our aim is to understand what are the genes downstream of the Delta-Notch signaling that can rescue cilia length and motility. A recent article from our lab summarizes this branch of our research: ‘Notch/Her12 signalling modulates motile/immotile cilia ratio downstream of Foxj1a in zebrafish left-right organizer’ (Tavares et al. eLIFE. 2017). We will continue searching for Her12 effector genes involved in this fate process.

Research on Pkd2 signalling
This cation channel is thought to partner with Pkd1l1 and sense ‘nodal flow’, an important feature in left-right development. We ask if having no flow has the same impact as having no Pkd2-mediated sensing. We realized this question is much harder to answer then we thought and we are generating new methods to tackle this question. Most interesting, this question led us to another perhaps more fascinating problem which is, how does the embryo try to rescue a defective ‘nodal flow’ during early left-right development?

Selected Publications
  • C. Constant, R. Sousa, A. Pinto, J.F. Moura Nunes, P. Sampaio, SS. Lopes, T. Bandeira and L. Pereira (2017) New era in Primary Ciliary Dyskinesia diagnosis. Accepted on the 16th November 2017
  • Smith Dj, Montenegro-Johnson T, Lopes S.S. (2014) Organized chaos in Kupffer's vesicle: How a heterogeneous structure achieves consistent left-right patterning. May-Jun;4(3):119-25. Bioarchitecture doi: 10.4161/19490992.2014.956593.
  • Cristina Casalou, Cecília Seixas, Ana Portelinha, Petra Pintado, Mafalda Barros, José S Ramalho, Susana S Lopes, Duarte C Barral (2014) Arl13b and the non-muscle myosin heavy chain IIA are required for circular dorsal ruffle formation and cell migration. Journal of cell science, jcs. 143446
  • Tavares B, Santos Lopes S. (2013) The Importance of Zebrafish in Biomedical Research. Acta Med Port., 26(5):583-592. Epub 2013 Oct 31.
  • Lourenço R, Lopes SS, Saúde L. Left-right function of dmrt2 genes is not conserved between zebrafish and mouse. PLoS One. 2010 Dec 28;5(12):e14438. PMID:21203428
  • Lopes SS, Lourenço R, Pacheco L, Moreno N, Kreiling J, Saúde L. Notch signalling regulates left-right asymmetry through ciliary length control. Development. 2010 Nov;137(21):3625-32. Epub 2010 Sep 28. PMID: 20876649
  • Rocha SF, Lopes SS, Gossler A, Henrique D. Dll1 and Dll4 function sequentially in the retina and pV2 domain of the spinal cord to regulate neurogenesis and create cell diversity. Dev Biol. 2009 Apr 1;328(1):54-65. Epub 2009 Jan 14. PMID: 19389377
  • Lopes SS, Yang X, Müller J, Carney TJ, McAdow AR, Rauch GJ, Jacoby AS, Hurst LD, Delfino-Machín M, Haffter P, Geisler R, Johnson SL, Ward A, Kelsh RN. Leukocyte tyrosine kinase functions in pigment cell development. PLoS Genet. 2008 Mar 7;4(3):e1000026. PMID:18369445
  • Dutton KA, Pauliny A, Lopes SS, Elworthy S, Carney TJ, Rauch J, Geisler R, Haffter P, Kelsh RN. Zebrafish colourless encodes sox10 and specifies non-ectomesenchymal neural crest fates. Development. 2001 Nov;128(21):4113-25. PMID: 11684650
  • Parichy DM, Mellgren EM, Rawls JF, Lopes SS, Kelsh RN, Johnson SL. Mutational analysis of endothelin receptor b1 (rose) during neural crest and pigment pattern development in the zebrafish Danio rerio. Dev Biol. 2000 Nov 15;227(2):294-306. PMID: 11071756


Ongoing collaborations

Ras LT C detail_SL3
- Ivo Telley - Micromanipulations and fluidics. Instituto Gulbenkian Ciência, Oeiras
- Adan Guerrero - 3D flow Imaging. Instituto Gulbenkian de Ciência, Oeiras
- Thomas Johnson-Montenegro - Simulations for cilia beating and flow. School of Mathematics, U. of Birmingham, UK
- Christopher Westlake - Primary cilium assembly. NCI-Frederick National Laboratory, USA
- David Smith - Simulations fluid flow. School of Mathematics, U. of Birmingham, UK
- Carla Quintão - Software. Department of Physics from FCT-NOVA, Portugal
- Duarte Barral - Cellular Traffic. CEDOC. NOVA Medical School. Portugal
- Paulo Pereira - Exosome biology. CEDOC. NOVA Medical School. Portugal


Team photos

lab day out Sintra1

1st retreat Algarve

CEDO IGC  12-6-2013 -7483-1



We welcome spontaneous Applications from posdocs with strong experience in
molecular biology.
Contact: susana.lopes(at)