Roman J. Szczęsny, PhD, DScLaboratory of RNA Biology
Our laboratory is interested in mechanisms that control the quality, quantity, and processing of RNAs that originate from expression of the mitochondrial and nuclear genomes in humans. Our main goal is to decipher molecular machinery that is responsible for RNA surveillance. We also investigate mechanisms that maintain and regulate expression of the mitochondrial genome and the ways in which they respond and adapt the cell to different stress conditions.
Main Scientific Achievements
- We uncovered an RNA surveillance pathway that is responsible for the degradation of G4-containing non-coding RNA in human mitochondria.
- We discovered that mitochondria are a source of double-stranded RNA that can be released into the cytoplasm and trigger the interferon response.
- We identified a protein (MTRES1), the upregulation of which counteracts mitochondrial transcription arrest.
- MITOCHONDRIAL RNA EXPRESSION AND SURVEILLANCE
Mitochondria are unique organelles in human cells because their function depends on crosstalk between two genomes: nuclear and mitochondrial. Human mitochondrial DNA (mtDNA) contains only a few genes, but all of them are essential. mtDNA exists in multiple copies per cell, and the expression of mitochondrial genes can be regulated by controlling the gene copy number.
Although the human mitochondrial genome was one of the first to be sequenced, the way it functions is still not entirely understood. Our studies focus on unraveling mitochondrial gene expression mechanisms. To date, we have been mainly interested in post-transcriptional mechanisms, but our ongoing and future studies concern the mechanisms that regulate mitochondrial gene copy number. We also intend to investigate the processing of individual mitochondrial transcripts and the ways in which mitochondrial nucleic acid metabolism responds to stresses (e.g., viral infection). We also plan to explore the recent discovery that mtDNA expression leads to the formation of double-stranded RNA.
- RNA decay and surveillance
The regulation of human mitochondrial gene expression at the initiation of mtDNA transcription appears to be limited. Thus, post-transcriptional processes, including RNA decay, are critical for shaping the mitochondrial transcriptome. We contributed significantly to the identification of an RNA-degrading complex in human mitochondria (1). This complex—the mitochondrial degradosome—consists of RNA helicase SUV3 and the ribonuclease PNPase. We showed that the degradosome is essential for the surveillance and decay of human mtRNAs, particularly antisense transcripts (1). Our recent studies revealed that short mtRNAs that are generated by mtRNA processing and decay machinery are removed by REXO2 oligoribonuclease, proving that REXO2 controls short mtRNAs (2).
- Mitochondrial RNA binding proteins
RNA molecules can form different structures, many of which involve non-canonical base pairing, such as the case of G-quadruplexes (G4s). Mitochondrial genomes of vertebrates exhibit extraordinary GC skews (i.e., high guanine content on one strand). Therefore, the transcription of human mtDNA results in the synthesis of G-rich RNAs that are prone to form G4s. Such mtRNAs, mostly antisense RNAs, are transcribed at high rates, but their steady-state levels are extremely low. We described a mechanism by which G4-containing antisense mtRNAs are efficiently degraded in humans (3, 4). We showed that the RNA-binding protein GRSF1 melts G4s in mtRNAs, facilitating degradosome-mediated decay. Based on phylogenetic analyses, we proposed that GRSF1 appears in mitochondria when genomes undergo a G4-poor to G4-rich transition. This evolutionary adaptation enabled the control of G4 mtRNA levels.
- Double-stranded RNA in mitochondrial biology
The importance of degradosome-dependent mtRNA surveillance was underscored by our studies that were performed in collaboration with the Proudfoot laboratory (Oxford University, UK) and others, showing that SUV3 and PNPase are major regulators of mitochondrial dsRNA (mt-dsRNA) (5). We revealed that mtDNA transcription is a significant source of dsRNA in humans. We showed that the depletion of SUV3 or PNPase leads to the accumulation of mt-dsRNA, and in the case of PNPase, to the release of these species into the cytosol. Remarkably, once in the cytosol, mt-dsRNA triggers an innate immune response through induction of the interferon pathway (5). Our work identified a new mechanism by which mitochondria contribute to cell fate and human health. Currently, we are investigating the role of other proteins in the regulation of mt-dsRNA levels.
- Mitochondrial genome expression in stress
The maintenance of mitochondrial gene expression is crucial for cell homeostasis. Stress conditions may lead to a temporary reduction of mtDNA copy number, raising the risk of the insufficient expression of mtDNA-encoded genes. We applied a quantitative proteomic screen to search for proteins that sustain mtDNA expression under stress conditions. We found that the novel mtRNA-binding protein MTRES1 is elevated in cells with perturbances in mtDNA expression. Our study showed that MTRES1 prevented mtRNA depletion during transcription arrest (6).
- NUCLEAR-ENCODED RNA SURVEILLANCE AND PROCESSING
- Regulation of double-stranded RNA in the nucleus
Transcription of the nuclear genome has the potential to produce long dsRNA species. However, under normal conditions, such RNAs are hardly detectable, suggesting their tight control. To identify proteins that are involved in this regulation, we performed a loss-of-function screen. This screen indicated a pathway, the inhibition of which led to the upregulation of nuclear dsRNA. The molecular mechanism that underlies dsRNA accumulation is the subject of our ongoing studies.
- Borowski et al. Nucleic Acids Res. 2013. doi: 10.1093/ar/gks1130
- Szewczyk et al. Nucleic Acids Res. 2020. doi: 10.1093/nar/gkaa302
- Pietras et al. Nat Commun. 2018. doi: 10.1038/s41467-018-05007-9
- Pietras et al. Mol Cell Oncol. 2018. doi: 10.1080/23723556.2018.1516452
- Dhir et al. Nature. 2018. doi: 10.1038/s41586-018-0363-0
- Kotrys et al. Nucleic Acids Res. 2019. doi: 10.1093/nar/gkz542
- Szczesny et al. PLoS One. 2018. doi: 10.1371/journal.pone.0194887
- We combine a range of molecular biology, biochemical, and cellular biology methods to achieve our research goals.
- We perform high-throughput genome-wide siRNA screens. We are equipped with necessary instruments and human siRNAs libraries (genome-wide and targeted).
- We conduct siRNA and DNA plasmid transfections, immunofluorescence staining, and other cell culture experiments in high-throughput compatible 384-well formats.
- We use our Attune NxT flow cytometer to apply a range of cell biology assays.
- We apply confocal and high-content fluorescent microscopy (thanks to a collaboration with IGiB UW).
- We create human cellular models for functional studies (gene silencing and overexpression). We co-developed a straightforward method for DNA cloning into more than 50 vectors that is dedicated to mammalian cell-based studies (7).
- We use various biochemical assays to study the activity of proteins that act on nucleic acids (e.g., degradation, binding, and polymerization).
- We use next-generation sequencing-based approaches, proteomics, and cryo-electron microscopy in collaboration with other laboratories.
- Dedicated surveillance mechanism controls G-quadruplex forming non-coding RNAs in human mitochondria. Pietras Z, Wojcik MA, Borowski LS, Szewczyk M, Kulinski TM, Cysewski D, Stepien PP, Dziembowski A*, Szczesny RJ*. Nat Commun. 2018. doi: 10.1038/s41467-018-05007-9.
- Mitochondrial double-stranded RNA triggers antiviral signalling in humans. Dhir A*, Dhir S, Borowski LS, Jimenez L, Teitell M, Rötig A, Crow YJ, Rice GI, Duffy D, Tamby C, Nojima T, Munnich A, Schiff M, de Almeida CR, Rehwinkel J, Dziembowski A, Szczesny RJ*, Proudfoot NJ*. Nature. 2018. doi: 10.1038/s41586-018-0363-0.
- Human REXO2 controls short mitochondrial RNAs generated by mtRNA processing and decay machinery to prevent accumulation of double-stranded RNA. Szewczyk M, Malik D, Borowski LS, Czarnomska SD, Kotrys AV, Klosowska-Kosicka K, Nowotny M, Szczesny RJ*. Nucleic Acids Res. 2020. doi: 10.1093/nar/gkaa302.
- Quantitative proteomics revealed C6orf203/MTRES1 as a factor preventing stress-induced transcription deficiency in human mitochondria. Kotrys AV, Cysewski D, Czarnomska SD, Pietras Z, Borowski LS, Dziembowski A, Szczesny RJ*. Nucleic Acids Res. 2019. doi: 10.1093/nar/gkz542.
- Marcin Nowotny, Laboratory of Protein Structure, International Institute of Molecular and Cell Biology in Warsaw, Poland, www.iimcb.gov.pl/en/research/laboratories/6-laboratory-of-protein-structure-nowotny-laboratory.
- Michał Szymański, Structural Biology Laboratory, University of Gdańsk, Poland. https://mrslab.ug.edu.pl/
Prizes and Awards
- Roman Szczęsny. Prime Minister Award for Habilitation. 2020. Prime Minister, Poland.
- Anna Kotrys. START Fellowship. 2020. Foundation for Polish Science, Poland.
- Roman Szczęsny. NCN Award. 2019. National Science Centre, Poland.
- Roman Szczęsny. Minister Award for Scientific Achievements. 2019. Minister of Science and Higher Education, Poland.
- Roman Szczęsny and others. Jan Karol Parnas Award for the best Polish biochemical publication. 2019. The Polish Biochemical Society, Poland.
Publications (IBB PAS affiliated)
ROMAN J. SZCZĘSNY, PhD, DSc
From early in childhood, my favourite pastime was exploring the nature in my immediate vicinity. I had a lot of opportunities to interact with and explore different forms of life. During my school days, this turned into a passion for ecology and environmental biology. Then as a university student, I had the opportunity to discover the world of molecular biology, which opened up entirely new possibilities for me. Since then, experimental laboratory work has become a passion in my life. Through it, I have learned to find answers to fundamental questions that interest me. What is perhaps the most exciting for me about biological sciences, and science in general, is that every answer obtained only raises new questions. This makes it a fascinating, never-ending journey.
- AUTHOR IDENTIFIERS
- SOCIAL MEDIA
2019 – D.Sc. Institute of Biochemistry and Biophysics, Polish Academy of Sciences, (Honors), biological sciences
2009 – Ph.D. Institute of Biochemistry and Biophysics, Polish Academy of Sciences, (Honors), biochemistry
2004 – M.Sc. Faculty of Biology, University of Warsaw, (Honors), biotechnology
2002 – B.Sc. Faculty of Biology, University of Warsaw, (Honors), biotechnology
- PROFESSIONAL EMPLOYMENT/ EXPERIENCE
Since 2012 – Assistant Professor, Institute of Biochemistry and Biophysics, Polish Academy of Sciences
2009 – 2016 – Research Assistant, Faculty of Biology, University of Warsaw
- PROFESSIONAL AFFILIATIONS
2023 – present – Member of the Scientific Council of the Nencki Institute of Experimental Biology of the Polish Academy of Sciences
2022 – Expert, Committee for Science Evaluation, Ministry of Education and Science
2019 – present – Deputy Director of Science, Institute of Biochemistry and Biophysics Polish Academy of Sciences
2018 – present – Member of the Scientific Council of the Institute of Biochemistry and Biophysics of the Polish Academy of Sciences
- AWARDS AND FELLOWSHIPS
2020 – Prime Minister Award for Habilitation, Prime Minister, Poland
2019 – NCN Award for the best young scientists. National Science Centre, Poland
2019 – Minister Award for Outstanding Scientific Achievements. Minister of Science and Higher Education, Poland
2019 – Jan Karol Parnas Award for the best Polish biochemical publication. 2019. The Polish Biochemical Society, Poland
2012 – 2015 – Scholarship for outstanding young scientists from the Polish Ministry of Science and Higher Education
2010, 2011 – Scholarship START from the Foundation for Polish Science for young, most talented scientists
2010 – Scholarship from the University of Warsaw for the best young doctors
2010 – Award from the Polish Biochemical Society and Merck Sp. z o.o. for the best doctoral thesis in biochemistry in Poland in 2009
2010 – Award for outstanding doctoral thesis. Director of Institute of Biochemistry and Biophysics, PAS
- DOCTORATES DEFENDED UNDER LAB LEADER’S SUPERVISION
Łukasz Borowski (auxiliary supervision; thesis defended with distinction; Prime Minister’s Award), Maciej Szewczyk (auxiliary supervision; thesis defended with distinction), Anna Kotrys (principal supervision; thesis defended with distinction; Prime Minister’s Award)
- Roman Szczęsny, PhD, DSc, Head of Laboratory, ORCID: 0000-0002-0686-1632
- Łukasz Borowski, PhD, Employee, ORCID: 0000-0003-3766-0726
- Aneta Jurkiewicz, PhD, Employee, ORCID: 0000-0003-2123-4255
- Giulia Santonoceto, Employee
- Elżbieta Speina, PhD, DSc, Employee, ORCID: 0000-0002-0734-9390
- Przemysław Surowiecki, PhD, Employee, ORCID: 0000-0001-8308-7153
- Joanna Grochowska, PhD Student, ORCID: 0000-0002-0767-3297
- Development of novel mRNA/VLP-based vaccines against emerging zoonotic viral diseases. Roman Szczesny (co-PI) (consortium Leader: ADAMED PHARMA S.A.). RNA Technologies, Medical Research Agency, 2021-2024, direct 858 326 PLN, of total 58 494 498 PLN.
- Identification and analysis of mechanisms controlling steady-state levels and quality of mitochondrial mRNA. Roman Szczesny. SONATA BIS 11, National Science Center, 2022-2027, 4 165 600 PLN.
- Expanding the mitochondrial proteome via the non-canonical translation mechanisms. Roman Szczęsny (co-PI) (consortium Leader: Joanna Kufel, University of Warsaw). OPUS 21, National Science Center, 2022-2027, direct 1 596 000 PLN, of total 3 582 000 PLN.
- Quality Control of the Mitochondrial Gene Expression System in Health and Disease. Roman Szczesny (co-PI) (consortium Leader: University of Udine). Horizon Europe Framework Programme (HORIZON, HORIZON-MSCA-2021-DN-01), European Commission, 2022-2026, direct 226 512 EUR, of total 2 623 752 EUR.