Janne Lehtiö

Karolinska Institutet

DDLS Precision Medicine Area Lead

Keywords
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Key Publications

Sissala N, Babačić H, Leo IR, Cao X, Forshed J, Eriksson LE, Lehtiö J, Fredolini C, Åberg M, Pernemalm M. Comparative evaluation of Olink Explore 3072 and mass spectrometry with peptide fractionation for plasma proteomics. Commun Chem. 2025 Nov 4;8(1):327.
doi: 10.1038/s42004-025-01753-2.

Leo IR, Kunold E, Audrey A, Tampere M, Eirich J, Lehtiö J, Jafari R. Functional proteoform group deconvolution reveals a broader spectrum of ibrutinib off-targets. Nat Commun. 2025 Feb 25;16(1):1948.
doi: 10.1038/s41467-024-54654-8.

Pan Y, Berkovska O, Marathe S, Mermelekas G, Gudoityte G, Wolide AD, Arslan T, Seashore-Ludlow B, Lehtiö J, Orre LM. Functional-proteomics-based investigation of the cellular response to farnesyltransferase inhibition in lung cancer. iScience. 2025 Jan 21;28(2):111864.
doi: 10.1016/j.isci.2025.111864.

Tamborero D, Dienstmann R, Rachid M.J, Boekel J, Lopez-Fernandez A, Jonsson M, Razzak A, Braña I, De Petris L, Yachnin J, Baird RD, Loriot Y, Massard C, Martin-Romano P, Opdam F, Schlenk RF, Vernieri C, Masucci M, Villalobos X, Chavarria E, Cancer Core Europe consortium, Balmaña J, Apolone G, Caldas C, Bergh J, Ernberg I, Fröhling S, Garralda E, Karlsson C, Tabernero J, Voest E, Rodon J, Lehtiö J. The Molecular Tumor Board Portal supports clinical decisions and automated reporting for precision oncology. Nature Cancer 2022, Feb;3(2):251-261.
https://doi.org/10.1038/s43018-022-00332-x

Lehtiö J*, Arslan T, Siavelis I, Pan Y, Socciarelli F, Berkovska O, Umer HM, Mermelekas G, Pirmoradian M, Jönsson M, Brunnström H, Brustugun OT, Pinganksha Purohit K , Cunningham R, Foroughi H, Isaksson S, Arbajian E, Aine M, Karlsson A, Kotevska M, Hansen CG, Drageset Haakensen V, Helland Å, Tamborero D, Johansson HJ, Branca RMM, Planck M, Staaf J, Orre LM. Proteogenomics of non-small cell lung cancer reveals molecular subtypes associated with specific therapeutic targets and immune evasion mechanisms. Nature Cancer, 2021Nov;2(11):1224-1242. (*corresponding author)
https://doi.org/10.1038/s43018-021-00259-9

Johansson HJ, Socciarelli F, Vacanti NM, Haugen MH, Zhu Y, Siavelis I, Fernandez A, Aure MR, Sennblad B, Vesterlund M, Branca RM, Orre LM, Huss M, Fredlund E, Beraki E, Garred Ø, Boekel J, Sauer T, Zhao W, Nord S, Höglander EK, Jans CD, Brismar H, Haukaas TH, Bathen TF, Schlichting E, Naume B, OSBREAC, Luders T, Borgen E, Kristensen VN, Russnes HG, Lingjærde OC, Mills GB, Sahlberg KK, Børresen-Dale A.L, Lehtiö J., Breast cancer quantitative proteome and proteogenomic landscape. Nature Comm, 10 Apr, 2019. https://doi.org/10.1038/s41467-019-09018-y

SciLifeLab / Contact / Janne Lehtiö

Janne Lehtiö

Professor, Karolinska Institutet
DDLS Precision Medicine Area Lead, SciLifeLab
Platform Scientific Director, Proteomics, SciLifeLab

Research interests

Proteomics is a collective name of several techniques and methods for global/systemic analysis of proteins. Mass spectrometry (MS) based proteomics is an important research field that drives proteome systems biology and generates phenotypic information at the molecular level.

Our Cancer Proteomics Mass Spectrometry group, headed by Professor Janne Lehtiö, is continuously developing mass spectrometry and bioinformatics methods for proteome and systems biology analysis to understand and improve cancer therapy. We develop methods to increased proteome coverage on clinical samples, including increased peptide coverage/protein to study protein variants. This can be illustrated by our developed high resolution isoelectric focusing (HiRIEF) method, which improves the analytical depth in proteomics substantially and allows for search space reduction to enable human proteogenomics. Proteogenomics is an emerging exciting field in MS-based proteomics that combines sample specific information from genomic sequencing, transcriptomics and MS-based proteomics. We use proteogenomics to gain knowledge on how genome changes in cancer influence the proteome level. We have pioneered in developing proteogenomics methods and applied them for cancer proteomics by demonstrating that the method can be used to discover new protein coding loci, such as new gene variants, expressed pseudogenes and long non-coding RNA proteins. This opens up completely new opportunities to develop and improve cancer therapy e.g. immunotherapy.

Our main application focus using proteomics is within the field of breast cancer, lung cancer and leukemia. In summary, we aim to use the proteome information to develop predictive analytical tools and new molecular biomarkers to enable selection of the most effective therapy for each cancer patient.

Group members

Group leader

Janne Lehtiö, Professor, PI, Karolinska Institutet

Principal Researchers

Jenny Forshed, PhD
Rozbeh Jafari, PhD
Henrik Johansson, PhD
Lukas Orre, PhD
David Tamborero, PhD

Senior Researcher

Rui Branca, PhD

Senior Research Specialist

Yanbo Pan, PhD

Researcher

Barbara Mahler, PhD

Postdoctoral researchers

Alberto Arenas, PhD
Alexandra Argyriou, PhD
Haris Babacic, MD, PhD
Akram Emdadi, PhD
Quentin Glaziou, PhD
Soumitra Marathe, PhD
Xuekang Qi, PhD
Ioannis Siavelis, MD, PhD
Amare Wolide, PhD

PhD students

Olena Berkovska
George Field
Luca Finn Gaessler
Yaroslav Kaminskiy
Igor Schliemann
Justin Seby
Noora Sissala
Irene Villanueva Sanz

Research assistant

Kovi Govindarajan

Master students

Fatima Abdul Sattar

Research Infrastructure Specialists

Eduardo Araújo, PhD
Xiaofang Cao, PhD
Nazlı Ezgi Özkan, PhD
Georgios Mermelekas, PhD
Krishnatej Nishtala, PhD
Mahshid Zarrineh, PhD

Research engineers

Mahnaz Nikpour, PhD
Rita Hutyra-gram

Bioinformatician

Luay Assad, PhD
Felix Manske, PhD

Software developers

Jorrit Boekel, PhD
Laura Gheorghe
Markus Jonsson
Ali Razzak
Dmitrii Rudakovskii

Affiliated to research

Santeri Kiviluoto, PhD

Hospital laboratory coordinator

Ghazaleh Assadi, PhD

Senior Laboratory manager

Laura Levi, PhD

Research coordinators

Helena Bäckvall, PhD
Xenia Villalobos Alberú, PhDAdministrator

Simon Rapple

Contact

janne.lehtio@scilifelab.se

simon.rapple@ki.se

Last updated: 2026-02-26

Content Responsible: admin(website@scilifelab.se)