Key Publications

(2024) High-parametric protein maps reveal the spatial organization in early-developing human lung
Sariyar S., Sountoulidis A., Hansen J.N., Marco Salas S., Mardamshina M., Martinez Casals A., Ballllosera Navarro F., Andrusivova Z., Li X., Czarnewski P., Lundeberg J., Linnarsson S., Nilsson M., Sundström E., Samakovlis C., Lundberg E.*, Ayoglu B.*.
Nature Communications. 15(1):9381

(2023) A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung
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.
Nature Cell Biology. 25(2):351-365

(2023) Characterizing the autoantibody repertoire in systemic sclerosis following myeloablative hematopoietic stem cell transplantation
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.
Annals of Rheumatic Diseases. 82(5):670-680

(2021) Spatiotemporal dissection of the cell cycle with single-cell proteogenomics
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.
Nature, 590(7847):649-654

(2019) AIRE expression controls the peripheral selection of autoreactive B cells
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.
Science Immunology, 4(34): eaav6778

(2017) Clonal evolution of autoreactive germinal centers
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.
Cell, 170(5):913-926.e19

(2016) Anoctamin 2 identified as an autoimmune target in multiple sclerosis
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.
PNAS, 113(8):2188-2193

We are interested in how molecular and cellular immune features manifest in the spatial context of human tissues in both health and disease. We study non-diseased lymphoid and visceral tissues across life stages to define the baseline organization of immune cells in health. In parallel, we investigate how inflammation structurally and functionally reshapes tissue architecture in relation to key biological processes such as organ development, autoimmunity, or neurodegeneration.

We are also interested in understanding how local, tissue-resident immune activity relates to systemic immune features. Determining how immune dynamics within tissues correspond to, or diverge from, what is detected in circulation is essential for translating spatial insights into clinically meaningful outcomes.

To address these questions, we primarily use multiplexed, antibody-based proteomics, including custom-designed, high-dimensional immunofluorescence microscopy assays that generate single-cell resolved protein maps of tissues. We are increasingly integrating our in-house developed spatial proteomics assays with other omics readouts to build a multi-dimensional view of tissue organization and immune activity.

Through this work, we aim to improve how the human immune system is understood, not only as a circulating system observed in blood, but as a spatially organized, tissue-embedded network that plays a central role in human development, homeostasis, and disease.

Funding

  • Swedish Brain Foundation, Hjärnfonden (2026-2027)
  • KI StratNeuro (2026-2028)
  • Swedish Research Council, VR Starting Grant (2023-2027)
  • Swedish Research Council, VR Research Environment Grant (2023-2028)
  • Knut & Alice Wallenberg Foundation Project Grant (2023-2028)
  • Diabetesfonden (2022-2023)
  • SciLifeLab Technology Development Grant (2028-2020)
  • Åke Wibergs Foundation (2018-2020)
  • Tore Nilsons Foundation (2018-2019)
  • Knut & Alice Wallenberg Foundation Repatriation Fellowship (2018-2020)

Group Members

Current:

Iva Sutevski, MSc (PhD student)

Past:

Sanem Sariyar, PhD student
Rafael Marques, Research engineer
Astradeni Efthymiadou, Research assistant

Supervised MSc thesis students:

Natthaphong Kaewkam (2025)
Mahima Sharma (2025)
Bruno Stojcic (2024)
Mattias Hansen (2022)
Nardin Saad (2021)
Danique van Rijswijck (2020)
Sharmishtaa Kumar (2019)

Last updated: 2025-09-17

Content Responsible: David Gotthold(david.gotthold@scilifelab.se)