LAB MEMBERS AND ALUMNI

 

Jussi Taipale, Ph.D., Principal Investigator

Herchel Smith Professor of Biochemistry, Distinguished Professor (Rådsprofessor from Vetenskapsrådet) of Medical Systems Biology, Professor and Vice-Director of the Finnish Center of Excellence in Tumor Genetics

Professor Jussi Taipale got his Ph.D. from the University of Helsinki in 1996, and continued with postdoctoral work at the University of Helsinki and at Johns Hopkins University (Baltimore, MD, USA). He has headed an independent research laboratory since 2003, focusing on systems biology of growth control and cancer. He currently holds professorships at University of Cambridge (as Herchel Smith Professor of Biochemistry), Karolinska Institutet (supported by a Distinguished Professor grant from the Swedish Research Council) and University of Helsinki, where he is also the vice director of the Finnish Center of Excellence in Tumor Genetics.

The Taipale labs consist of two co-PIs (in KI and Helsinki), as well as seven senior scientists, three postdoctoral fellows, three graduate students and supporting staff in the form of three lab managers and one personal assistant. The work of the group is supported by an advanced automated high throughput laboratory in Cambridge as well as sequencers and other equipment in all three locations.


Senior Scientists

Inderpreet Sur, PhD, Delegated Division Head (KI)

My interest is focused on the transcriptional regulation of growth control and lineage specification with emphasis on the question of how these are tweaked to generate a cancerous cell. Based on our analysis of the Myc-335 enhancer we postulate that a cancer cell might rely on cancer-specific transcriptional switches (enhancers) for its growth. A comprehensive identification and understanding of these would be useful in designing targeted therapy against cancer cells.
Towards this goal I am currently studying:
1) the contribution of enhancer elements upstream of c-MYC to cancerous growth using in vivo models, and
2) function of transcription factor Klf5 in cellular fate specifications.

   

Daniela Ungureanu, PhD, Docent, Co-PI (Helsinki)

My research interests focus on the molecular mechanisms associated with kinases signaling. Protein kinases play a key regulatory role in nearly every aspect of cell biology making protein phosphorylation the most exploited form of posttranslational modification. Protein phosphorylation can modulate enzyme activity and it can also alter other biological activities such as transcription and translation. Kinases, as well as pseudokinases, are often dysregulated in a variety of diseases, especially cancer. Beyond the basic question of how kinases/pseudokinases function in normal and pathogenic conditions, there is also a significant interest in developing approaches to inhibit them. However, the expected development of drug resistance for the majority of kinase-specific inhibitors in the treatment of neoplastic disorders requires new approaches to solve this therapeutic challenge. My focus is toward understanding of drug-resistance mechanisms and the development of new technologies such as PROTAC-chimeras for the therapeutic targeting of kinases/pseudokinases in cancer.

 

Minna Taipale, PhD

My long time interest is regulation of the cell cycle and more recently, cellular growth control. The aim is to understand how a normal cell homeostasis differs from a tumorigenic one. I have carried out high throughput siRNA screens of human and Drosophila genes to map cell cycle regulators. Currently I am working with an oncogenic Mediator-12 model to understand how the same mutation can lead to benign uterine leiomyomas (UL) or malignant uterine leiomyosarcomas (ULMS). Our exome sequencing collaboration with Prof L Aaltonen’s group has shown that Mediator-12, which is part of the transcriptional regulator Mediator complex, is mutated in high percentage of ULs.
Part of my job is to oversee that our next generation sequencers are working well. I’m also involved in the everyday tasks of running the lab at the University of Cambridge site.

Ekaterina Morgunova, PhD

Francis Crick once notably said “If you wish to understand function, study structure”, Roger D. Kornberg took this further by noting “Extension of the structure to atomic resolution will one day reveal the regulatory mechanism”.
To understand how DNA sequence controls gene expression, one must first understand the binding specificity of transcription factors (TF) to DNA and/or other TFs/proteins. Therefore, the major aim of my research is to use X-ray crystallography to study the molecular principles underlying the interactions between TF and TF/other proteins or between TF and DNA.

 

 

Norman Zielke, PhD

Norman Zielke

I am a molecular biologist using the fruit fly Drosophila melanogaster to analyze the down-stream targets of the Myc proto-oncogene. I am particularly interested in understanding how Myc drives growth and proliferation under normal and oncogenic conditions. Furthermore, I am keen on understanding why reduction of Myc levels prolongs the lifespan of flies. I am using CRISPR/Cas9-mediated gene editing to mutate Myc binding sites in the promoter regions of conserved Myc-target genes. Cutting the regulatory nodes instead of targeting the gene itself allows to directly address the requirement of specific regulatory relationships without affecting basal expression levels that might be important for viability or other cellular processes.

Teemu Kivioja, PhD

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I am a computer scientist applying and developing efficient computational methods needed in the lab. As the experiments in the lab can generate very large and complex data sets, both the design and analysis of the experiments create many interesting computational challenges, especially when the assay is new and thus standard approaches do not exist.
I have worked on many sequencing-based assays but lately I have concentrated on design and analysis of CRISPR-cas9 and STARR-seq experiments.

 

 
 

Kimmo Palin, PhD

I am a senior staff scientist working in Taipale and Aaltonen groups at the University of Helsinki.
My research is Bioinformatics and Computational Biology from genetics and functional regulatory genomics perspective.
I’m involved especially with genetic epidemiology and biobank research related projects and have special interest in functional genomics, gene regulation and functional understanding of non-coding genetic variation.

 

Päivi Pihlajamaa, PhD

I am interested in the regulation of cellular processes by transcription factors, and especially, how aberrant transcriptional pathways promote tumorigenesis.

My main project focuses on studying the transcriptional targets of the MYC oncogene and their role in regulating cell growth and proliferation.To this end, I am using modern experimental methods in mammalian cells, such as CRISPR/Cas9-based precision genome editing and genome-wide screening approaches, to study the functional relationship between transcription factor binding, gene expression, and cell proliferation.

 


Postdoctoral fellows

Yin Lin, PhD

I joined Taipale group in Cambridge on Jun 2018 with a background in synthetic biology.
My current research interest is regulatory characterisation of high-grade serous ovarian cancer (HGS-OvCA) cell lines to understand the molecular mechanisms behind ovarian cancer. I have utilized different technologies to achieve this goal, such as ATI/EMSA-seq (to reveal the main transcriptional regulators of HGS-OvCA), CRISPR/Cas9 screening (to identify a set of transcription factors that are necessary for the growth of the ovarian cancer cell lines) and CUT&RUN (characterise the TFs which are main transcriptional regulators or relevant to chemoresistance of HGS-OvCA).

 

 

Otto Kauko, MD, PhD

Growth signals are transmitted by diverse and redundant mechanisms. This redundancy is needed for tissue specific regulation of cell growth, but also makes it challenging to block growth signalling in cancer cells. 

Although signal transduction has been studied a lot, it is inadequately understood how the growth signal pathways interface with conserved processes of cell growth.

My aim is to identify and characterize common dependencies of proliferating cancer cells. To achieve this, I am manipulating proliferation and pathway usage in different cancer cell types, and collecting data using phosphoproteomics, thermal proteome profiling, single-cell RNAseq, and targeted genome editing based dropout screens.

Eevi Kaasinen, PhD, part time post-doc

My particular role in the Center of Excellence in Tumor genetics lies in processing and integration of DNA methylation, ChIP-seq, ATAC-seq, HiChIP and MNase-seq functional high-throughput sequencing data. I’m interested in deciphering epigenetic and chromatin alterations in diseases.


PhD students

Jilin Zhang, PhD

I joined Taipale lab in December 2014 at Karolinska Institutet and defended my Ph.D. thesis in May 2020.

Gene expression is a complex dynamic process regulated by many distinct regulatory molecules, including DNA, RNA and proteins. To date, our understanding regarding the mechanism of gene regulation is limited due to insufficient knowledge of regulatory elements, even though sequencing technology has greatly broadened our horizons concerning the gene expression pattern alternation. My interest is to decipher the functional role of non-coding regions (or their products) in the gene regulation process, especially those regulatory elements associated with human diseases. To elucidate their roles may help to explain, at least partly, the mechanism by which gene expression is precisely controlled.

Tuomo Hartonen

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I am a final year PhD student working on computational modeling and analysis of large scale genomics experiments. I have mainly been working with data from experiments like STARR-seq, ChIP-exo/nexus/seq, ATAC-seq, ATI-seq and HT-SELEX. Lately my focus has been on applying machine learning, especially deep learning, to understand the important features controlling gene expression in human promoters and enhancers.

Tuomo in LinkedIn >>

Tuomo in Twitter >>


Lab managers

John Davies, Cambridge

I graduated from the University of London and undertook a PhD at St. Bartholomew’s Hospital on Integrin expression in Osteoclasts.  Since graduation I have worked in academic laboratories in the USA and UK, focusing mostly on factors determining cell fate and differentiation – during development or disease.  I moved to Cambridge in 1996 to work on research projects at the Addenbrooke’s Hospital Biomedical Campus.  The University has provided opportunities to conduct fundamental and more clinically based research.  Topics of study at Addenbrooke’s have ranged from using ScFv technology to identify antibodies causing autoimmune thrombocytopaenia to the analysis of patient mutations associated with Disorders of Sex Development.  After leaving Anna Philpott’s group investigating post-translational modifications of bHLH transcription factors in 2019, I began working as a Senior Research Technician with Jussi Taipale in the Department of Biochemistry.  The laboratory is located downtown in the heart of the university research campus, an exciting place to work and carryout ground breaking research.

Margareta Kling Pilström, Stockholm

I joined the KI lab in February 2018, in time to move the lab into our current premises in Biomedicum in Solna.

Today I work with various molecular biology assays, including sample purification, gel analysis, PCR, immunohistochemistry etc. helping the researchers in the lab with various tasks.

I also take care of the day-to-day operation of the lab such as ordering of supplies, maintenance of instruments, handling inventories of instruments and chemicals etc., along with administrative tasks such as handling invoices and travels amongst other things.

Katariina Sarin, Helsinki

katariina_sarin_image

I Joined Taipale lab in July 2019. My daily routines include taking care of the lab equipment, orders, shipments, and assisting in research projects, especially the drosophila related ones. I also take care of our extensive drosophila stock and help with analysis.

My personal interests are in the regulation of growth and aging, and identifying new drug targets.

Katariina in LinkedIn >>


Administration

Jane Arnold, Cambridge

My role as PA for Professor Taipale is a varied and busy one.

I assist Professor Taipale by managing the diary and reviewing emails to identify immediate daily priorities and future correspondence.

I work with team members to set up meetings and carry out all follow up actions. My role also involves organizing travel, coordinating grant applications and monitoring expenditure.

I work with members of all three labs to ensure the smooth running of the administration. I also work closely with departmental and wider University administration in Cambridge regarding employment contracts, recruitment, finance, expenses and invoicing for the Taipale research group.


Alumni

Former post docs

Gonghong Wei, PhD, Professor at Department of Biochemistry and Molecular Biology, Shanghai Medical College, Fudan University, China

Emma Haapaniemi, PhD, PI Precision pediatrics and gene editing group,
Centre for Molecular Medicine, Norway.

Yimeng Yin, PhD, PI, School of Medicine at Tongji University, China

Anna Vähärautio, PhD, Academy Research Fellow, PI, University of Helsinki, Finland
Single-cell transcriptomics of cancer lab

Martin Enge, PhD, Assistant Professor at the Department of Oncology and Pathology at Karolinska Institutet and Karolinska universitetssjukhuset Solna, Sweden, https://ki.se/en/onkpat/research-team-martin-enge

Bernhard Schmierer, PhD, Director and Head of Facility, High Throughput Genome Engineering, Karolinska Genome Engineering, SciLifeLab, Dept. of Medical Biochemistry and Biophysics, Karolinska Institutet, Sweden

Biswajyoti Sahu, PhD, PI, Docent in Molecular Genetics, Applied Tumor Genomics Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Finland

Mikael Björklund, PhD, Associate Professor and Principal Investigator, Zhejiang University – University of Edinburgh Institute, China

Kazuhiro Nitta, PhD, Lecturer, Juntendo University, Graduate School of Medicine Diagnostics and Therapeutics of Intractable Diseases Intractable Disease Research, Japan

Song-Ping Li, PhD, Senior Researcher, Institute of Biomedicine, University of Turku, Finland

Sandeep Botla, PhD, Senior Scientist, Discovery Sciences, AstraZeneca, Sweden

Kashyap Dave, PhD, Senior Research Scientist at iCellate Medical AB,  Sweden

Fan Zhong, PhD, Associate Researcher in Bioinformatics at the Laboratory of Systems Biology, Institute of Biomedical Sciences, Fudan University.

Ning (Nina) Wang, PhD

Alexander Minidis, PhD

Fangjie Zhu, PhD

 

Former graduate students

Jian Yan, PhD, Assistant Professor at City University of Hong Kong https://www.cityu.edu.hk/bms/profile/jianyan.htm

Markku Varjosalo, PhD, PI Systems Biology/Pathology Research Group, University of Helsinki, Finland

Arttu Jolma Sidhu, PhD, Postdoc in the Laboratory of Timothy R. Hughes, University of Toronto, Toronto, Ontario, Canada.

Outi Hallikas, PhD, Post-doctoral fellow in Jukka Jernvall group at University of Helsinki, Finland

Mikko Turunen, PhD, Associate Research Scientist, Department of Systems Biology, Columbia University, USA

Bei Wei, PhD, Post-doctoral researcher in William Greenleaf lab, Stanford University, School of Medicine, USA

 

Former Karolinska High Throughput Center (KHTC) members

Anders Eriksson, PhD, Manager of Karolinska High Throughput Center.

Jianping Liu, PhD, Manager of Karolinska High Throughput Center.

Natalia Nekhotiaeva, PhD, Research Engineer of Karolinska High Throughput Center.

 

Former members

Emma Inns, former PA to professor Taipale

Åsa Kolterud, PhD, Previously coordinated Syscol EU projects within the group. Currently Research coordinator with Prof Lauri Aaltonen at KI.

Sini Miettinen, B.Ls., lab manager

Sandra Augsten, lab manager

Maria Hoh, lab manager

Lijuan Hu, PhD, lab manager

Anna Zetterlund, lab manager

Estefania Mondragon, visiting graduate student

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