Druggability of neurological disease associated cell signalling
Our lab develops and adapts molecular tools we then use to identify druggable mechanisms of synaptic dysfunction implicated in neurological disease. Our current focus is on Ras-signalling related rare neurodevelopmental disorders and Alzheimer’s Disease. Together with corresponding data analytical pipelines, some tools may also be used in screening assays, either for the generation of chemical biology reagents supporting target validation, or to screen drug or diversity libraries for repurposing or drug discovery.
As cell-based models of disease become more realistic and complex, mechanistic investigations and druggability studies demand precise and selective analytical tools and approaches. Longitudinal follow-up in a live-cell imaging setting is increasingly required. Our lab applies parallelised longitudinal imaging and optical actuation of complex cell systems, paired with the use of proteome-wide and proximity analysis at bulk and single synapse levels. These approaches are supported by advanced instrumentation at the core facilities situated in our department, especially the high-throughput microscopy instrumentation and other automation platforms at the Turku Screening Unit as well as the Turku Proteomics Core
Key words:
Neurobiology, Alzheimer’s disease, Disease mechanisms, Optical Pathway Reporters, Optogenetics, Protein engineering, Image processing, Data analysis, Druggability, Drug discovery
Selected Earlier Results:
Our lab previously identified druggable sites on proteins forming a novel disease associated pathway involving nNOS and NOS1AP. We developed molecules targeting the pathway, enabling us to demonstrate in vivo POC in several disease models (1-5). To gain further insight in disease mechanisms, we developed a simple optogenetic tool design strategy that allowed temporally precise encoding of pathway inhibition (6). We also identified methods to ease the application of optogenetics, for example by reducing blue-light burden of long-term use and developing a method for real time direct monitoring of switching and relaxation to support the optimisation of actuation protocols (7).
Current Research Activities :
We design new optical reporters, optogenetic actuators, labelling strategies and data analysis pipelines to investigate synaptopathies. One particular aim is to reveal the functional deficits of missense variants of SynGAP1 known to cause the rare disease SynGAP non-syndromic intellectual disability (8-9). Assays developed using these tools may identify neomorphic properties and, in future studies, support drug repurposing screens and help clarify the impact of variants of uncertain significance (VUS). Another project aims to define phenotypic response signatures in human neuron models of a panel of rare diseases to carry out repurposing drug screens. A more basic research project examines the turnover, protein composition and function of the neuronal synapse (10) and how it is regulated by adaptor proteins like NOS1AP, and another explores the roles of temporal encoding of neuronal signalling pathways and imbalances in the synaptic proteome on regulation of connectivity and disease-associated synaptic dysfunction.
Collaborations and network:
Local collaborations include those with Assoc. Prof. Pekka Postila and Prof. Olli Pentikäinen (Institute of Biomedicine) on the structural biology of SynGAP1, with Prof. Pekka Ruusuvuori on the applications of machine learning to data analysis pipelines, and Assoc. Prof. Otto Kauko on development of single synapse proteomics methods. International collaborations include those with Dr. Florian Freudenberg (University of Frankfurt) on NOS1AP function in psychiatric disorder endophenotypes, and the EURAS consortium (www.euras-project.eu/) on neurodevelopmental rasopathies. In addition, our team is responsible for the Lab Automation site of the Turku Screening Unit, which represents Turku at the National Drug Discovery and Chemical Biology Platform of Biocenter Finland and is a partner site of the European infrastructure project EU-OPENSCREEN.
Selected publications:
- Li LL, Ginet V, Liu X, Vergun O, Tuittila M, Mathieu M, Bonny C, Puyal J, Truttmann AC, Courtney MJ. The nNOS-p38MAPK pathway is mediated by NOS1AP during neuronal death. J Neurosci. 2013 May 8;33(19):8185-201. doi: 10.1523/JNEUROSCI.4578-12.2013. PMID: 23658158; PMCID: PMC6619617.
- Li LL, Melero-Fernandez de Mera RM, Chen J, Ba W, Kasri NN, Zhang M, Courtney MJ. Unexpected Heterodivalent Recruitment of NOS1AP to nNOS Reveals Multiple Sites for Pharmacological Intervention in Neuronal Disease Models. J Neurosci. 2015 May 13;35(19):7349-64. doi: 10.1523/JNEUROSCI.0037-15.2015. PMID: 25972165; PMCID: PMC6705433.
- Lee WH, Carey LM, Li LL, Xu Z, Lai YY, Courtney MJ, Hohmann AG. ZLc002, a putative small-molecule inhibitor of nNOS interaction with NOS1AP, suppresses inflammatory nociception and chemotherapy-induced neuropathic pain and synergizes with paclitaxel to reduce tumor cell viability. Mol Pain. 2018 Jan-Dec;14:1744806918801224. doi: 10.1177/1744806918801224. Epub 2018 Aug 29. PMID: 30157705; PMCID: PMC6144507.
- Lee WH, Carey LM, Li LL, Xu Z, Lai YY, Courtney MJ, Hohmann AG. ZLc002, a putative small-molecule inhibitor of nNOS interaction with NOS1AP, suppresses inflammatory nociception and chemotherapy-induced neuropathic pain and synergizes with paclitaxel to reduce tumor cell viability. Mol Pain. 2018 Jan-Dec;14:1744806918801224. doi: 10.1177/1744806918801224. Epub 2018 Aug 29. PMID: 30157705; PMCID: PMC6144507.
- Esen-Sehir D, Li L, Reif A, Courtney MJ, Freudenberg F (2020) P.504 Targeting nitric oxide synthase 1 adaptor protein interactions as a possible treatment for schizophrenia: an initial proof-of-concept study in mice, European Neuropsychopharmacology, Volume 40, Supplement 1, 2020, Pages S283, ISSN 0924-977X, https://doi.org/10.1016/j.euroneuro.2020.09.368 (https://www.sciencedirect.com/science/article/pii/S0924977X20306416)
- Melero-Fernandez de Mera RM, Li LL, Popinigis A, Cisek K, Tuittila M, Yadav L, Serva A, Courtney MJ. A simple optogenetic MAPK inhibitor design reveals resonance between transcription-regulating circuitry and temporally-encoded inputs. Nat Commun. 2017 May 12;8:15017. doi: 10.1038/ncomms15017. PMID: 28497795; PMCID: PMC5437309.
- Li LL, Klein FM, Li Greci L, Popinigis A, Freudenberg F, Courtney MJ. Resonance energy transfer sensitises and monitors in situ switching of LOV2-based optogenetic actuators. Nat Commun. 2020 Oct 9;11(1):5107. doi: 10.1038/s41467-020-18816-8. PMID: 33037199; PMCID: PMC7547724.
- Courtney MJ et al. 2021, Webinar “Investigating the functional single cell biology of SynGAP1 pathways”, SynGAP research fund, USA (virtual) webinar https://www.syngapresearchfund.org/webinars/investigating-the-functional-single-cell-biology-of-syngap1-pathways
- Yotova AY, Li LL, O'Leary A, Tegeder I, Reif A, Courtney MJ, Slattery DA, Freudenberg F. Embryonic and adult synaptic proteome perturbations after maternal immune activation: Identification of persistent changes relevant for early intervention. Res Sq [Preprint]. 2023 Jul 3:rs.3.rs-3100753. doi: 10.21203/rs.3.rs-3100753/v1. PMID: 37461513; PMCID: PMC10350178.
Michael Courtney
Group Leader
Exploring the role of SHANK3 in the vasculature and the development of vascular anomalies
Our earlier discoveries in neurons, epithelial and cancer cells place SHANK3, a scaffolding protein previously linked to autism, at the nexus of complex cell signalling pathways. More recently, our preliminary data, supported by publicly available datasets, demonstrates high SHANK3 expression in endothelial cells (blood and lymphatic vasculature) where its function is unknown. In addition, SHANK3 is highly expressed in brain arteriovenous malformations (bAVMs), vascular anomalies that can trigger haemorrhagic stroke, permanent disability and death in children and young adults.
We aim to investigate the link between SHANK3 and bAVM development by first unravelling the role of SHANK3 within the normal endothelium. We will then apply the unprecedented knowledge gained from this investigation to bAVMs in mouse models and patient samples.
Key words:
SHANK3, Scaffold protein, Actin cytoskeleton, Cytoskeletal reorganisation, Cell adhesion, Integrin signalling, KRAS, Vascular anomaly, bAVM, Stroke, Brain health
Main points of the research topic:
- SHANK3 is highly expressed in normal human vasculature and in bAVM, where its role is unknown
- SHANK3 is at the nexus of several key signalling pathways, including KRAS signalling, Rap1-mediated integrin activation and actin cytoskeletal reorganisation – these pathways regulate cell adhesion, morphology and migration
- In cancer models, targeting SHANK3 is effective against KRAS-driven cancers in in vitro and in vivo models.
- In more than 50% of bAVM cases, a causative mutation in the oncogenic RAS-RAF-MEK-ERK pathway has been observed.
- We will combine this expertise to understand the role of SHANK3 in the endothelium and as a potential target in bAVM.
Methodology:
- endothelial cell culture
- microfluidics
- KRAS signalling readouts
- protein-protein interaction
- proteomic analyses
- Immunofluorescence and immunohistochemistry
- analysis of patient samples
Suitable background experience :
- PhD degree and proven expertise (A publication within the research topic) related to the research theme (e.g. vascular biology, cell signalling, SHANK3 biology, KRAS signalling, animal models of endothelial barriers)
- Excellent communication skills in both spoken and written English.
Selected publications:
- J. Lilja, J. Kaivola, J. R. W. Conway, J. Vuorio, H. Parkkola, P. Roivas, T. Varila, G. Jacquemet, E. Peuhu, E. Wang, U. Pentikäinen, I. M. D. Posada, H. Hamidi, A. K. Najumudeen, O. J. Sansom, I. L. Barsukov, D. Abankwa, I. Vattulainen, M. Salmi, J. Ivaska, Targeting a broad spectrum of KRAS-mutant cancers by hyperactivation-induced cell death. BioRxiv (2022), p. 2022.09.21.508660, doi:10.1101/2022.09.21.508660.
- S. I. Salomaa, M. Miihkinen, E. Kremneva, I. Paatero, J. Lilja, G. Jacquemet, J. Vuorio, L. Antenucci, K. Kogan, F. Hassani Nia, P. Hollos, A. Isomursu, I. Vattulainen, E. T. Coffey, H.-J. Kreienkamp, P. Lappalainen, J. Ivaska, SHANK3 conformation regulates direct actin binding and crosstalk with Rap1 signaling. Curr Biol. 31, 4956-4970.e9 (2021).
- J. Lilja, J. Ivaska, Integrin activity in neuronal connectivity. J Cell Sci. 131, jcs212803 (2018).
- J. Lilja, T. Zacharchenko, M. Georgiadou, G. Jacquemet, N. De Franceschi, E. Peuhu, H. Hamidi, J. Pouwels, V. Martens, F. H. Nia, M. Beifuss, T. Boeckers, H.-J. Kreienkamp, I. L. Barsukov, J. Ivaska, SHANK proteins limit integrin activation by directly interacting with Rap1 and R-Ras. Nat Cell Biol. 19, 292–305 (2017).
Professor Johanna Ivaska
Principal Investigator
Dr Hellyeh Hamidi
Research Support Coordinator
Single-cell analyses of immune responses in cardiovascular disease
T cells and other inflammatory cells are crucial in the growth and instability of atherosclerotic plaques. Recent single-cell analyses have shown that the T cells accumulating in the atherosclerotic aorta are phenotypically distinct from those in circulation, underscoring the significance of regulatory events within the aortic tissue microenvironment.
Our laboratory is dedicated to understanding the interaction between immune and stromal cells in atherosclerosis and autoimmune disorders, utilizing single-cell transcriptomics, immune receptor sequencing, and spatial omics. We are particularly focused on obesity-associated remodeling of perivascular adipose tissue and its impact on immune cell migration and plaque formation. Our research integrates data from both mouse models and patient samples, employing multidisciplinary wet lab and bioinformatics approaches. Our ultimate aim is to identify novel peripheral biomarkers and potential therapeutic targets.
We collaborate closely with the single-cell omics core facility at Turku Bioscience Centre, ensuring access to cutting-edge precision genomics and immunoprofiling techniques. Additionally, we are part of the InFLAMES research flagship, a prestigious immunological R&D cluster. Our team is international and interdisciplinary, with a robust network of collaborators in immunology, genomics, bioinformatics, and cardiovascular health. We are committed to fostering equality, diversity, and a healthy work-life balance.
We are seeking a highly qualified PhD-level scientist with a degree in life sciences, bioinformatics, or a related field. Experience in immunology, cardiovascular diseases, genomics, or proficiency with command-line tools is an asset. Proficiency in English, both oral and written, is required as it is our working language. We also value strong interpersonal skills and the ability to collaborate with individuals from diverse backgrounds.
Key words:
Atherosclerosis, Adipose, Obesity, Immunity, Single-cell, Omics, Transcriptomics, Bioinformatics
Selected Earlier Results:
We have previously used single-cell transcriptomics and epigenomics to characterise the cellular landscape in atherosclerosis in both human (1, 2) and in hyperlipidaemic mouse model (3). These studies have identified disease-associated cell states and explored their relationships with known genetic risk loci. In a complementary line of studies, we have used functional assays and single-cell sequencing to measure the immunoregulatory functions of adipose tissue-derived stem cells in lean and obese individuals, and how these functions are modified by metabolic syndrome (4).
Collaborations and network:
We collaborate locally with the teams of Prof. Pekka Ruusuvuori (imaging-based bioinformatics), Prof. Anne Roivainen (PET), and Prof. Laura Elo (single-cell bioinformatics). We have extensive long-term collaboration with teams of Prof. Minna Kaikkonen-Määttä and Merja Heinäniemi at the University of Eastern Finland, who are both experts in cardiovascular diseases and genomics methods. In addition, we have an ongoing collaboration with group of Prof. Anders Woetmann Andersen at the University of Copenhagen, Denmark. We are also part of the InFLAMES research flagship, funded by the Research Council of Finland, which provides excellent collaborative network including connections to local pharma and biotech companies.
Selected publications:
- Depuydt MAC, Prange KHM, Slenders L, Örd T, Elbersen D, Boltjes A, de Jager SCA, Asselbergs FW, de Borst GJ, Aavik E, Lönnberg T, Lutgens E, Glass CK, Kaikkonen MU, Bot I, Slütter B, van der Laan SW, Yla-Herttuala S, Mokry M, Kuiper J, de Winther MPJ & Pasterkamp G: Microanatomy of the human atherosclerotic plaque by single-cell transcriptomics. Circulation Research 2020 127(11):1437-1455. PMID: 32981416
- Örd T, Õunap K, Stolze LK, Aherrahrou R, Nurminen V, Toropainen A, Selvarajan I, Lönnberg T, Aavik E, Ylä-Herttuala S, Civelek M, Romanoski CE, Kaikkonen MU: Single-Cell Epigenomics and Functional Fine-Mapping of Atherosclerosis GWAS Loci. Circulation Research 2021 129(2):240-258. PMID: 34024118
- Örd T, Lönnberg T, Nurminen V, Ravindran A, Niskanen H, Kiema M, Öunap K, Maria M, Moreau PR, Mishra PP, Palani S, Virta J, Liljenbäck H, Aavik E, Roivainen A, Ylä-Herttuala S, Laakkonen JP, Lehtimäki T & Kaikkonen MU: Dissecting the polygenic basis of atherosclerosis via disease-associated cell state signatures. The American Journal of Human Genetics 2023 110:1-19. PMID: 37060905
- Oliva-Olivera W, Castellano-Castillo D, von Meyenn F, Cardona F, Lönnberg T & Tinahones FJ: Human adipose tissue-derived stem cell paracrine networks vary according metabolic risk and after TNFα-induced death: an analysis at the single-cell level. Metabolism 2021; 116:154466. PMID: 33333081
Tapio Lönnberg
Principal Investigator, Docent
Systems-biology based target discovery for new disease-modifying heart failure treatments
We are looking for a motivated postdoctoral fellow to help us discover new ways to treat heart diseases. Our research aims to elucidate molecular mechanisms mediating cardiac regeneration and remodelling, to identify and validate new therapeutic targets, and eventually to develop new pharmacological treatments that stop or reverse the progression of heart failure.
The most common causes of heart failure are myocardial infarction (MI) caused by coronary artery disease and hypertension. In adult mammals, cell loss during and after an MI results in formation of a fibrotic scar and remodelling of the surrounding cardiac muscle, and often leads to heart failure. Remarkably, some lower vertebrates and neonatal mammals can fully regenerate their hearts after an injury. This capacity is however lost soon after birth due to cardiomyocyte cell cycle exit. The exact molecular mechanisms regulating cardiac regeneration and the postnatal loss or regenerative capacity are however not known, which hinders the development of regenerative therapies. Furthermore, hypertension and MI increase cardiac workload and thereby cause structural and functional changes in the myocardium, including cardiomyocyte hypertrophy and fibrosis, which eventually lead to contractile dysfunction and heart failure. Current pharmacological treatments cannot effectively stop or reverse the progression of pathological remodelling and heart failure, and thus there is an urgent need for the development of therapies that would promote cardiac regeneration or stop and reverse cardiac remodelling.
Methods:
Our research is mainly based on hPSC-based cardiac in vitro models, including co-cultures and 3D microtissues consisting of two to three cardiac cell types: cardiomyocytes, endothelial cells, and cardiac fibroblasts. In addition to standard lab techniques, we utilise omics technologies (transcriptomics, proteomics, metabolomics) and phenotypic screening techniques such as high content imaging and cell painting.
Requirements:
Successful candidates should have a PhD degree and proven expertise related to the research theme (e.g. hPSC-based cardiac in vitro models, bioinformatics, cell signalling, molecular biology), excellent communication skills in both spoken and written English, and ability to work as a team in a dynamic multicultural research environment.
Selected publications:
- Majid QA, Ghimire BR, Merkely B, Randi AM, Harding SE, Talman V*, Földes G*: Generation and characterisation of scalable and stable human pluripotent stem-cell derived microvascular-like endothelial cells for cardiac applications. Angiogenesis 2024; 27: 561-582. https://doi.org/10.1007/s10456-024-09929-5 *Co-senior authors
- Pohjolainen L, Kinnunen SM, Auno S, Kiriazis A, Pohjavaara S, Kari-Koskinen J, Zore M, Jumppanen M, Yli-Kauhaluoma J, Talman V, Ruskoaho H, Välimäki M: Switching hypertrophic signalling towards enhanced cardiomyocyte maturity by GATA4-targeted compound. Stem Cell Res Ther 2024; 15:5. https://doi.org/10.1186/s13287-023-03623-x
- Chaudhari U, Pohjolainen L, Ruskoaho H, Talman V: Genome-wide profiling of miRNA-gene regulatory networks in mouse postnatal heart development - implications for cardiac regeneration. Front Cardiovasc Med 2023; 10:1148618. https://doi.org/10.3389/fcvm.2023.1148618
- Pohjolainen L, Ruskoaho H, Talman V: Transcriptomics reveal stretched human pluripotent stem cell-derived cardiomyocytes as an advantageous hypertrophy model. J Mol Cell Cardiol Plus 2022, 2:100020. https://doi.org/10.1016/j.jmccpl.2022.100020
- Karhu ST, Ruskoaho H, Talman V: Distinct regulation of cardiac fibroblast proliferation and transdifferentiation by classical and novel protein kinase C isoforms: possible implications for new antifibrotic therapies. Mol Pharmacol 2021; 99:104-113. https://doi.org/10.1124/molpharm.120.000094
- Talman V, Teppo J, Pöhö P, Movahedi P, Vaikkinen A, Karhu ST, Trošt K, Suvitaival T, Heikkonen J, Pahikkala T, Kotiaho T, Kostiainen R, Varjosalo M, Ruskoaho H: Molecular atlas of postnatal heart development. J Am Heart Assoc 2018; 7:e010378. https://doi.org/10.1161/JAHA.118.010378