Merja Heinäniemi
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Professor at University of Eastern Finland
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About
Merja Heinäniemi is a Professor at the University of Eastern Finland, specializing in the fields of cancer research and immunology. Her recent articles address critical aspects of acute lymphoblastic leukemia, including single-cell analysis techniques and combination therapies for treatment. With an emphasis on both genetic and non-genetic factors influencing leukemia and related disorders, she contributes to advancing understanding in the area of molecular subtypes and therapeutic strategies.
Recent Grants
Grant: Close
Genomics-based tools for personalized treatment of cancer
Open Date: 2019-01-01
Close Date: 2021-01-01
Grant: Close
Genomics-based tools for personalized treatment to reduce chemotherapy burden in pediatric cancer
Open Date: 2019-01-01
Close Date: 2021-01-01
Grant: Close
Translating genomics into clinical tools for pediatric leukemia
Open Date: 2019-01-01
Close Date: 2024-01-01
Grant: Close
Capturing the cell state space from genomics data into models of treatment resistance in childhood leukemia
Open Date: 2019-01-01
Close Date: 2021-01-01
Grant: Close
Semi-supervised autoencoder models for scRNA-seq
Open Date: 2018-01-01
Close Date: 2019-01-01
Articles (20)
Comparison of high-throughput single-cell RNA-seq methods for ex vivo drug screening
Functional precision medicine (FPM) aims to optimize patient-specific drug selection based on the unique characteristics of their cancer cells. Recent advancements in high throughput ex vivo drug profiling have accelerated interest in FPM. Here, we present a proof-of-concept study for an integrated experimental system that incorporates ex vivo treatment response with a single-cell gene expression output enabling barcoding of several drug conditions in one single-cell sequencing experiment. We demonstrate this through a proof-of-concept investigation focusing on the glucocorticoid-resistant acute lymphoblastic leukemia (ALL) E/R+ Reh cell line. Three different single-cell transcriptome sequencing (scRNA-seq) approaches were evaluated, each exhibiting high cell recovery and accurate tagging of distinct drug conditions. Notably, our comprehensive analysis revealed variations in library complexity, sensitivity (gene detection), and differential gene expression detection across the methods. Despite these differences, we identified a substantial transcriptional response to fludarabine, a highly relevant drug for treating high-risk ALL, which was consistently recapitulated by all three methods. These findings highlight the potential of our integrated approach for studying drug responses at the single-cell level and emphasize the importance of method selection in scRNA-seq studies. Finally, our data encompassing 27 327 cells are freely available to extend to future scRNA-seq methodological comparisons.
Year:
2024
Year:
2024
Collaborators (36)
Kim Theilgaard-Mönch
Københavns Universitet
Fatima Crispi
Associate Professor
University of Barcelona
Stephen White
Reader in Cardiovascular Biology
Newcastle University
Sofia Aakko
University of Helsinki
Piia Karisola
University of Helsinki
Laura Oksa
University of Tampere
Kimmo Porkka
University of Helsinki
Lesley Cheng
La Trobe University
Shady Adnan Awad
University of Oxford
Ursula Schwab
Professor
University of Eastern Finland
Markus Vähä-Koskela
Coordinator of the FIMM professional postdoctoral career development programme
University of Helsinki
Samuli Eldfors
University of Helsinki
Robert Mikulik
Professor
Masaryk University
Veronica Rendo
Uppsala University
Arja Harila-Saari
Professor of paediatrics
Uppsala University
Christine Klement
Technical University of Munich
Mika Kontro
University of Helsinki
Henrik Lilljebjörn
Lund University
Reeta Rintamäki
Kuopio University Hospital
Arndt Borkhardt
Prof.
Heinrich Heine University Düsseldorf
Sampsa Hautaniemi
University of Helsinki
Anna-Liisa Levonen
University of Eastern Finland
Satu Mustjoki
University of Helsinki
Atte Nikkilä
University of Tampere
Jetty Chung-Yung Lee
Research Assistant Professor
Korea University
Krister Wennerberg
Københavns Universitet
Hanna-Riikka Teppo
University of Oulu
Olli Lohi
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Jessica Nordlund
Associate Professor & Research Group Leader at Uppsala University
Uppsala University
Tanja Ruokoranta
University of Helsinki
Komal Kumar Javarappa
University of Helsinki
Juho Miettinen
University of Helsinki
Elitsa Dimova
University of Oulu
Heikki Kuusanmäki
University of Copenhagen Biotech Research and Innovation Centre
Peter Maccallum
Chief Technical Officer
ELRIG
Sadiksha Adhikari
University of Helsinki

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