Jukka Alinikula
PhD, Adjunct professor, Director of education for ImmuDocs
juilal@utu.fi +358 29 450 4577 +358 50 516 7449 Kiinamyllynkatu 10 Turku Office: 7th floor ORCID identifier: https://orcid.org/0000-0001-9926-6439 |
Immunology; B cells; Antibodies; Somatic hypermutation; Infection immunity; Lymphoma; Cancer genomics; Adaptive immunity; Immunopharmacology
InFLAMES Flagship
I completed my PhD with Prof. Olli Lassila at the University of Turku, where I studied the transcriptional regulation of B-cell and plasma-cell development. During my postdoctoral training with Prof. David G. Schatz at Yale University (2012–2015), I investigated the mechanisms that target somatic hypermutation to immunoglobulin genes.
I established my research group at the Institute of Biomedicine, University of Turku, shortly thereafter. Our work focuses on understanding how B cells generate protective antibody responses and how the mutational mechanisms that optimize antibody function can also contribute to cancer development.
In addition to leading an independent research team, I serve as University Lecturer in Immunology and Drug Development. My research combines molecular immunology, genomics, genome engineering and single-cell approaches to study antibody diversification, infection immunity and lymphomagenesis.
Protective immunity depends on germinal center B cells that generate high-affinity, class-switched antibodies during infection and in response to vaccination. We investigate the molecular mechanisms that enable these antibody responses and establish long-term humoral immunity.
A major focus of our research is somatic hypermutation (SHM), a specialized mutational process that diversifies immunoglobulin genes and drives antibody affinity maturation. While most cells minimize mutations to preserve genome stability, germinal center B cells deliberately mutate their antibody genes to improve antigen recognition. We aim to understand how SHM is targeted with high specificity to immunoglobulin genes and how this process is regulated across the genome.
Our work seeks to uncover the molecular rules that determine why some genomic regions are highly mutable while others remain protected. We are particularly interested in the roles of transcription, gene regulation and genome organization in directing SHM activity. These studies provide insight into fundamental mechanisms underlying antibody diversification and adaptive immunity.
Because SHM relies on DNA mutagenesis, errors in targeting can have severe consequences for genome integrity. Off-target mutations contribute to the development of lymphoma and other malignancies, making SHM both a key mechanism of protective immunity and an important source of cancer-associated mutations. We therefore also investigate how mutational processes become mis-targeted to proto-oncogenes, other genomic loci and viral genomes.
To address these questions, we combine molecular immunology, functional genomics, genome engineering, reporter systems, high-throughput sequencing and single-cell technologies to uncover the principles that govern antibody diversification, mutation targeting and disease.
My teaching focuses on immunology and immunopharmacology across Bachelor's, Master's, MD, and doctoral programmes in both English and Finnish.
I employ a range of teaching methods, including lectures, case-based learning, journal clubs, laboratory courses, mentoring, thesis supervision, and online learning. My teaching covers innate and adaptive immunity, immunomodulatory drugs, therapeutic antibodies, and protein-based therapeutics.
I have completed university pedagogy studies and actively supervise doctoral researchers. In addition, I serve on the follow-up committees of PhD students and contribute to the development of undergraduate, postgraduate, and doctoral education.
- Super-Enhancer Transcription Converges on AID (2014)
- Cell
(A2 Refereed review article in a scientific journal ) - Targeting of Somatic Hypermutation by immunoglobulin Enhancer and Enhancer-Like Sequences (2014)
- PLoS Biology
(A1 Refereed original research article in a scientific journal) - A Critical Context-Dependent Role for E Boxes in the Targeting of Somatic Hypermutation (2013)
- Journal of Immunology
(A1 Refereed original research article in a scientific journal) - Alternate pathways for Bcl6-mediated regulation of B cell to plasma cell differentiation (2011)
- European Journal of Immunology
(A1 Refereed original research article in a scientific journal) - Gene interaction network regulates plasma cell differentiation (2011)
- Scandinavian Journal of Immunology
(A1 Refereed original research article in a scientific journal) - Bursa of Fabricius (2010)
- Encyclopedia of Life Sciences
(D2 Article in a professional compilation book) - Concerted action of Helios and Ikaros controls the expression of the inositol 5-phosphatase SHIP (2010)
- European Journal of Immunology
(A1 Refereed original research article in a scientific journal) - Regulation of B Cell Gene Expression and Function by Ikaros, Helios and Bcl6 (2010) Jukka Alinikula
(G5 Article dissertation ) - Spontaneous acquisition of plasma cell phenotype in DT40 B cells with inactivation of Bcl-6 (2007)
- Scandinavian Journal of Immunology
(D3 Article in a professional conference publication) - DT40 mutants: a model to study transcriptional regulation of B cell development and function (2006) Alinikula Jukka, Lassila Olli, Nera Kalle-Pekka
(A2 Refereed review article in a scientific journal )



