Burcu Ayoglu

I am an enthusiast of new molecular diagnostics & imaging technologies pushing limits every day, and a passionate advocate for a more precise and accessible medicine & healthcare enabled by such technologies. Driven by this vision, my research focuses on development and use of high-parametric protein profiling and imaging tools to shed light on human diseases, immunity, and early human life. I am currently leading a team at the Division of Cellular and Clinical Proteomics at KTH-SciLifeLab, collaborating closely with Emma Lundberg's Lab at KTH-Stanford.

Throughout my research journey, I honed my expertise in high-parametric protein analysis tools: During PhD, I worked with high-parametric immunoassays for analysis of proteins and autoantibodies in blood. During postdoc, I worked with high-parametric cytometric tools for phenotyping of immune cells. And over the last few years, I have been working with high-parametric immunofluorescence microscopy to study spatial organization in tissues. By integrating these tools effectively, we can use a unique systems approach to explore immune and other cell types in tissue space, to delve into organ development in early human life, and to discover blood and tissue-based biomarkers for human diseases.

In addition to my research pursuits, I actively engage in teaching bachelor’s, master’s and doctoral level courses covering topics such as “Current Trends in Omics”. Over the past decade, I supervised over ten master’s degree projects, coached several bachelor-level student groups, and co-supervised one completed and two ongoing doctoral studies. I participated in non-profit organizations like the Palo Alto Chapter of Association for Women in Science and the Stockholm Chapter of 500 Women Scientists, dedicated to make science and academia inclusive. I also played a key role in the initiation and activities of the Early Career Researcher Committee of the international Human Proteome Organization, addressing the lack in visibility and promotion of early career scientists within the proteomics community.

Short CV:

• Since 2018: Researcher, Principal Investigator, SciLifeLab Group Leader, KTH-SciLifeLab, Div. of Cellular & Clinical Proteomics, Dept. of Protein Science, Stockholm, Sweden
• 2015 - 2018: KAW Postdoctoral Research Fellow in Immunology, Stanford Univ., Div. of Immunology & Rheumatology, Dept. of Medicine, School of Medicine, CA, USA
• 2010 - 2015: Ph.D. in Biotechnology, KTH School of Biotech., Stockholm, Sweden. Dissertation title: “Affinity arrays for profiling proteins and autoantibody repertoires”
• 2007 - 2009: M.Sc. in Medical Biotechnology, KTH School of Biotech., Stockholm, Sweden. Thesis title: “Plasma profiling with antibody suspension bead arrays for identification of multiple sclerosis biomarkers”

Research description:

Our group's research aims to characterize the immunological features of human diseases and early human life in space and time.

We develop and combine high-parametric protein profiling and imaging tools for immunophenotyping in various human specimen, ranging from diseased organ collections and rarely available embryonic tissues to systemic fluids such as blood plasma.

By identifying and characterizing immune and other cell types in tissue space, we try to describe organ development in early human life, and we try to find blood and tissue-based biomarkers for human diseases.

Research interests in keywords:

• Proteomics
• Systems immunology
• Spatial biology
• Single cell biology
• Biomarker discovery
• Immune system development

Selected on-going projects & collaborations:

• "Human Developmental Cell Atlas Project (HDCA)" 2018-present (Role: Associated PI, funded by KAW & Erling Persson Foundations)
• "Single-cell, spatial mapping of human pancreatic microenvironment to identify the role of macrophage input on islet development and pancreas topography" 2023-present (Role: Leading PI, funded by Diabetesfonden, collaboration with Mia Phillipson)
• "Mapping the cellular and molecular dynamics of human materno-fetal immune interface” 2023-present (Role: Leading PI, funded by Swedish Research Council, collaboration with HDCA, Martin Ivarsson)
• “Spatial omics for improved pathophysiology-based diagnosis of dementia subtypes” 2023-present (Role: Associated PI, funded by Swedish Research Council, collaboration with Per Andrén, Per Svenningsson, Mats Nilsson, Lukas Käll, Luke Odell)
• "Immunology Human Organ Donor Programme” 2023-present (Role: Associated PI, funded by KAW, collaboration with Marcus Buggert, Jenny Mjösberg, Petter Brodin)

Research funding:

• Swedish Research Council (2023-)
• Knut & Alice Wallenberg Foundation (2015-2019, 2023-)
• Diabetesfonden (2023-)
• Åke Wibergs Foundation (2018-2020)
• Tore Nilsons Foundation (2018-2020)

Group members:

Current:

Sanem Sariyar, MSc (PhD student)
Iva Sutevski, MSc (PhD student)

Alumni:

Mattias Hansen (MSc degree student)
Danique van Rijswijck (Erasmus student)
Sharmishtaa Kumar (MSc degree student)
Astradeni Efthymiadou (Research assistant)

Selected publications:

• Sountoulidis A.*, Salas S.M.*, Braun E., Avenel C., Bergenstråhle J., Theelke J., Vicari M., Czarnewski P., Liontos A., Abalo X., Andrusivova Z., Mirzazadeh R., Asp M., Li X., Hu L., Sariyar S., Casals A.M., Ayoglu B., Firsova A., Michaelsson J., Lundberg E., Wählby C., Sundström E., Linnarsson S., Lundeberg J., Nilsson M., Samakovlis C. (2023) A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung. Nature Cell Biology. 25(2):351-365
• Ayoglu B.*, Donato M.*, Furst D.E., Crofford L., Goldmuntz E.A., Keyes-Elstein L., James J., Macwana S., Mayes M.D., McSweeney P., Nash R.A., Sullivan K.M., Welch B., Pinckney A., Mao R., Chung L., Khatri P., Utz P.J. (2023) Characterizing the autoantibody repertoire in systemic sclerosis following myeloablative hematopoietic stem cell transplantation. Annals of Rheumatic Diseases,82(5):670-680
• Mahdessian D.*, Cesnik A.J.*, Gnann C., Danielsson F., Stenström L., Arif M., Zhang C., Schutten R., Bäckström A., Axelsson U., Thul P., Cho N.H., Carja O., Uhlén M., Mardinoglu A., Stadler C., Lindskog C., Ayoglu B., Leonetti M., Ponten F., Sullivan D., Lundberg E. (2021) Spatiotemporal dissection of the cell cycle with single-cell proteogenomics. Nature,590(7847):649-654.
• Sng J.,Ayoglu B., Chen J., Schickel J.-N., Ferre E.M., Glauzy S., Romberg N., Hoenig M., Cunningham-Rundles C., Utz P.J., Lionakis M.S., Meffre E. (2019) AIRE expression controls the peripheral selection of autoreactive B cells. Science Immunology, 4(34): eaav6778.
• Degn S.E., van der Poel C.E.*, Firl D.J.*, Ayoglu B., Al Qureshah F.A., Bajic G., Mesin L., Reynaud C.A., Weill J.C., Utz P.J., Victora G.D., Carroll M.C. (2017) Clonal evolution of autoreactive germinal centers. Cell, 170(5):913-926.e19.
• Zandian A., Forsström B., Häggmark-Månberg A., Schwenk J.M., Uhlén M., Nilsson P., Ayoglu B. (2017) Whole-proteome peptide microarrays for profiling autoantibody repertoires within multiple sclerosis and narcolepsy. Journal of Proteome Research, 16(3):1300-1314.
• Ayoglu B., Mitsios N., Kockum I., Khademi M., Zandian A., Sjöberg R., Forsström B., Bredenberg J., Lima Bomfim I., Holmgren E., Grönlund H. ,Guerreiro-Cacais A. O., Abdelmagid N., Uhlén M., Waterboer T., Alfredsson L., Mulder J., Schwenk J. M., Olsson T., Nilsson P. (2016) Anoctamin 2 identified as an autoimmune target in multiple sclerosis. PNAS,113(8):2188-2193.
• Ayoglu B., Chaouch A., Lochmüller H., Politano L., Bertini E., Spitali P., Hiller M., Niks E. H., Gualandi F., Ponten F., Bushby K., Aartsma-Rus A., Schwartz E., Le Priol Y., Straub V., Uhlén M., Cirak S., t Hoen P. A. C., Muntoni F., Ferlini A., Schwenk J. M., Nilsson P., Al-Khalili Szigyarto C. (2014). Affinity proteomics within rare diseases: a BIO-NMD study for blood biomarkers of muscular dystrophies. EMBO Molecular Medicine, 6(7):918–936.