Marc Friedländer

Marc Friedländer
Stockholm University

Research Interests

Area of interest: microRNA biogenesis and function at the single-cell level

The Friedländer group applies state-of-the-art computational and genomic methods to address fundamental questions in RNA biology. The focus is on quantitatively describing and functionally characterizing mammalian transcriptomes, and methods include next-generation sequencing of single and pooled cells, as well as development of source code and custom wet-lab protocols.

Of particular interest to us are microRNAs: 22 nucleotide RNAs that can regulate the expression of protein-coding genes. Since they confer regulation on the majority of human genes, it is not surprising that microRNAs are involved in numerous biological processes, including cardiovascular, immunological, neurodegenerative, and psychiatricdiseases and cancer. Even though miRNAs have been systematically studied for more than ten years, fundamental questions regarding their biogenesis and function remain unanswered.

We study microRNA function by profiling these regulators and their gene targets in the single cells where the interactions between them occur. From the measurements we infer copy-per-cell numbers for the transcripts, and we develop mathematical models to describe the kinetics of regulation. For this purpose, we apply single-cell sequencing methods and single-molecule FISH. To study microRNA biogenesis, we have developed a method to measure processing of thousands of RNA structures simultaneously in mammalian cells.

Among our collaborators are Rory Johnson (University of Bern), Claudia Kutter, Vicent Pelechano, Rickard Sandberg, Magda Bienko, Nicola Crosetto (KI) and the SciLifeLab Eukaryotic Single Cell Genomics facility. Our research is funded by SFO, by Vetenskapsrådet and an ERC starting grant.

Group members

Marc Friedländer (group leader)
Inna Biryukova (wet-lab manager)
Bastian Fromm (senior scientist)
Morteza Aslanzadeh (PhD student)
Wenjing Kang (PhD student)
Vaishnovi Sekar (PhD student)
Marcel Tarbier (PhD student)

Key publications

Kang W; Eldfjell Y; Fromm B; Estivill X; Biryukova I; Friedländer MR†, 2018.miRTrace reveals the organismal origins of microRNA sequencing data. Genome Biology19(1):213

Bonath F; Domingo-Prim J; Tarbier M; Friedländer MR†; Visa N†, 2018.Next-generation sequencing reveals two populations of damage-induced small RNAs at endogenous DNA double-strand breaks. Nucleic Acids Research.

Kang W; Bang-Berthelsen CH; Holm A; Houben AJ; Müller AH; Thymann T; Pociot F; Estivill X; Friedländer MR†, 2017. Survey of 800+ data sets from human tissue and body fluid reveals xenomiRs are likely artifacts. RNA23(4):433-445

‘t Hoen PA; Friedländer MR†; Almlöf J†; Sammeth M; Pulyakhina I; Anvar SY; Laros JF; Buermans HP; Karlberg O; Brännvall M; den Dunnen JT; van Ommen GJ; Gut IG; Guigó R; Estivill X; Syvänen AC; Dermitzakis ET; Lappalainen T, 2013. Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories.  Nat Biotechnol 31(11):1015-22

Lappalainen T; Sammeth M†; Friedländer MR†; ‘t Hoen PA†; Monlong J†; Rivas MA†; Gonzàlez-Porta M; Kurbatova N; Griebel T; Ferreira PG; Barann M; Wieland T; Greger L; van Iterson M; Almlöf J; Ribeca P; Pulyakhina I; Esser D; Giger T; Tikhonov A; Sultan M; Bertier G; MacArthur DG; Lek M; Lizano E; Buermans HP; Padioleau I; Schwarzmayr T; Karlberg O; Ongen H; Kilpinen H; Beltran S; Gut M; Kahlem K; Amstislavskiy V; Stegle O; Pirinen M; Montgomery SB; Donnelly P; McCarthy MI; Flicek P; Strom TM; Lehrach H; Schreiber S; Sudbrak R; Carracedo A; Antonarakis SE; Häsler R; Syvänen AC; van Ommen GJ; Brazma A; Meitinger T; Rosenstiel P; Guigó R; Gut IG; Estivill X; Dermitzakis ET, 2013. Transcriptome and genome sequencing uncovers functional variation in humans.  Nature 501(7468):506-11

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