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Janne Lehtiö

Janne Lehtiö
Cancer Proteomics Mass Spectrometry
Karolinska Institutet

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
Scientific Director, Science for Life Laboratory

Research Coordinator
Helena Bäckvall, PhD

Rui Branca, PhD
Jenny Forshed, PhD
Henrik Johansson, PhD
Lukas Orre, PhD
David Tamborero, PhD

Assistant Professors
Rozbeh Jafari, PhD
Maria Pernemalm, PhD

Post docs
Jürgen Eirich, PhD
Elena Kunold, PhD
Yanbo Pan, PhD
Maan Rachid, PhD
Matthias Stahl, PhD
Husen Umer, PhD
Mattias Vesterlund, PhD

PhD students
Taner Arslan, MSc
Ioannis Siavelis, MD
Fabio Sociarelli, MD
Yan Zhou, MSc
Haris Babacic, MD

Research engineers
Hillevi Andersson-Sand, MSc
Ghazaleh Assadi, PhD
Xiaofang Cao, PhD
Georgios Mermelekas, PhD
Lingjie Tao, MSc

Scientific Programmer/Bioinformatician
Jorrit Boekel, PhD
Annsofi Sandberg, PhD

Master students
Saad Alhajri

Adrian Levitsky, Postdoc
Eduardo Ferraeira Araujo, PhD student
Mohammad Tanvir Ahamed, PhD student
Rubin Joshi, PhD student

Key publications

  • Zhu Y, Orre LM, Johansson HJ, Huss M, Boekel J, Vesterlund M, Fernandez-Woodbridge A, Branca RMM, Lehtiö J. Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow. Nature Commun. 2018 Mar 2;9(1):903.
  • Panizza E, Branca RMM, Oliviusson P, Orre LM, Lehtiö J. Isoelectric point-based fractionation by HiRIEF coupled to LC-MS allows for in-depth quantitative analysis of the phosphoproteome. Sci Rep. 2017 Jul 3;7(1):4513. doi: 10.1038/s41598-017-04798-z.
  • Zhu Y, Engström PG, Tellgren-Roth C, Baudo CD, Kennell JC, Sun S, Billmyre RB, Schröder MS, Andersson A, Holm T, Sigurgeirsson B, Wu G, Sankaranarayanan SR, Siddharthan R, Sanyal K, Lundeberg J, Nystedt B, Boekhout T, Dawson TL Jr, Heitman J, Scheynius A, Lehtiö J. Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis. Nucleic Acids Res. 2017 Jan 18
  • Boekel J, Chilton J, Cooke I, Horvatovich P, Jagtap P, Käll L, et al. Multi-omic data analysis using Galaxy. Biotechnol. 2015 Feb;33(2):137-9
  • Zhu Y, Hultin-Rosenberg L, Forshed J, Branca R, Orre L, Lehtiö J. SpliceVista, a tool for splice variant identification and visualization in shotgun proteomics data Mol. Cell Proteomics 2014 Jun;13(6):1552-62
  • Branca R.M., OrreL.M., JohanssonH.J., Granholm V., HussM., Pérez-BercoffÅ., ForshedJ., KällL., LehtiöJ. HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics. Nature Methods2014Jan;11(1):59-62.
  • Johansson H.J, Sanchez B.C., Mundt F., Forshed J., Lundgren B., Martens U., Kovacs A., Máthé G., Yakhini Z., Helou K., Einbeigi Z., Krawiec K., Kanter L., Hjerpe A., Stål O., Linderholm B.K., Lehtiö J. Retinoic acid receptor alpha has potential predictive value in tamoxifen treated breast cancer patients. Nature Commun. 2013. Jul 19;4:2175.
  • Sandberg A, Lindell G, Nordstrom-Källström B, Branca RM, Gemzell Danielsson K, Dahlberg M, Larson B, Forshed J, Lehtiö J. Tumo proteomics by multivariate analysis on individual pathway data for characterization of vulvar cancer phenotypes. Mol Cell Proteomics. 2012Jul;11(7)

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