Single-cell proteomics, Ribosome-mediated translational regulation, quantitative systems biology, mass-spectrometry
Nikolai Slavov received his undergraduate education from the Massachusetts Institute of Technology (MIT) in 2004. He pursued doctoral research in the Botstein laboratory at Princeton University, aiming to understand how cells coordinate their growth, gene expression, and metabolism. He discovered a simple mechanism that can account for the growth-rate dependent transcriptional responses across a wide range of growth conditions and growth rates (Slavov and Botstein, 2011, Slavov et al., 2011). After defending his dissertation in 2010, Nikolai Slavov began a postdoctoral project in the van Oudenaarden laboratory at MIT, aiming to understand the Warburg effect, a hallmark of cancer cells characterized by the fermentation of glucose in the presence of enough oxygen to support respiration. This work demonstrated that aerobic glycolysis can reduce the energy demands associated with respiratory metabolism and stress survival and that, contrary to expectations and decades-long assumptions, exponential growth at a constant rate can represent not a single metabolic/physiological state but a continuum of changing states characterized by different metabolic fluxes (Slavov et al., 2014). Following a lead from these experiments, Nikolai Slavov obtained direct evidence for differential stoichiometry among core ribosomal proteins in unperturbed wild-type cells (Slavov et al., 2015). His findings support the existence of ribosomes with distinct protein composition and physiological function that represent an explored layer of regulating gene expression. Most recently, the Slavov laboratory developed methods for high-throughput Single Cell ProtEomics by Mass Spectrometry (SCoPE-MS and SCoPE2) and used them to quantify proteome heterogeneity during cell differentiation.
- PhD (2010), Botstein Laboratory, Princeton University
- BS (2004), Biology, Massachusetts Institute of Technology
Honors & Awards
- NIH Director’s New Innovator Award
- SPARC Award from the Broad Institute of MIT and Harvard
- Princeton University Dean’s Award
- IRCSET Postgraduate Research Fellowship
- Finalist in the Young European Entrepreneur Competition
- Princeton Graduate Fellowship
- MIT Undergraduate Fellowship
- Eureka Fellowship for Academic Excellence
- Bronze Medal in the 31st International Chemistry Olympiad
- National Diploma for Exceptional Achievements in Chemistry
- Single-Cell Proteomics Center
- Barnett Institute of Chemical and Biological Analysis
- Broad Institute of MIT & Harvard
- American Society for Mass Spectrometry (ASMS)
- American Society for Cell Biology (ASCB)
- Genetics Society of America (GSA)
Single-cell proteomics, Ribosome-mediated translational regulation, quantitative systems biology, mass-spectrometry
Ribosome-mediated translational regulation
All living cells must coordinate their metabolism, growth, division, and differentiation with their gene expression. Gene expression is regulated at multiple layers, from histone modifications (histone code) through RNA processing to protein degradation. While most layers are extensively studied, the regulatory role of specialized ribosomes (ribosome code) is largely unexplored. Such specialization has been suggested by the differential transcription of ribosomal proteins (RPs) and by the observation that mutations of RPs have highly specific phenotypes; particular RP mutations can cause diseases, known as ribosomopathies, and affect selectively the synthesis of some proteins but not of others. This selectivity and the differential RP transcription raise the hypothesis that cells may build specialized ribosomes with different stoichiometries among RPs as a means of regulating protein synthesis.
While the existence of specialized ribosomes has been hypothesized for decades, experimental and analytical roadblocks (such as the need for accurate quantification of homologous proteins and their modifications) have limited the evidence to only a few examples, e.g., the phosphorylation of RP S6. We developed methods to clear these roadblocks and obtained direct evidence for differential stoichiometry among core RPs in unperturbed yeast and mammalian stem cells and its fitness phenotypes. We aim to characterize ribosome specialization and its coordination with gene regulation, metabolism, and cell growth and differentiation. We want to understand quantitatively, conceptually, and mechanistically this coordination with emphasis on direct precision measurements of metabolic fluxes, protein synthesis and degradation rates in absolute units, molecules per cell per hour.
Single-cell proteomics by mass-spectrometry
Cellular heterogeneity is important to biological processes, including cancer and development. However, proteome heterogeneity is largely unexplored because of the limitations of existing methods for quantifying protein levels in single cells. To alleviate these limitations, our laboratory developed Single Cell ProtEomics by Mass Spectrometry (SCoPE-MS), and validated its ability to identify distinct human cancer cell types based on their proteomes. To further advance single-cell protein analysis, we developed SCoPE2.
SCoPE2 introduced automated and miniaturized sample preparation that substantially lowers cost and hands-on time. It uses data-driven analytics to optimize instrument parameters for sampling more ion copies per protein, thus supporting quantification with improved count statistics. Furthermore, SCoPE2 uses peptide identification enhanced by incorporating retention time information within a principled framework, DART-ID.
SCoPE2 enables scalable, robust and affordable quantification of about 1,000 proteins per single cell, and about 3,000 proteins across many cells. This coverage is achieved with 90 min of analysis time per SCoPE2 set (about 6 min / cell), which allowed us to analyze hundreds of cells on a single instrument in a couple of days. Importantly, SCoPE2 succeeded in delivering and quantifying hundreds of ion copies from most detected proteins. This observation strongly supports the feasibility of single-cell LC-MS/MS protein quantification without amplification.
We aim to understand the rules governing emergent systems-level behavior and to use these rules to rationally engineer biological systems. We make quantitative measurements, often at the single-cell level, to test different conceptual frameworks and discriminate among different classes of models.
Selected Research Projects
Research Centers and Institutes
Department Research Areas
- Slavov N.✉ (2020) Single-cell protein analysis by mass-spectrometry, Current Opinion in Chemical Biology, 60, 1-9 PDF
- Slavov N.✉ (2020) Unpicking the proteome in single cells, Science, 367 (6477) :512–513
- Slavov N.✉ et al. (2019) Voices in methods development: Single-cell proteomics Nature Methods, PDF
- Specht H, Emmott E, Koller T, Slavov N.✉ (2019) High-throughput single-cell proteomics quantifies the emergence of macrophage heterogeneity
bioRxiv DOI: 10.1101/665307 PDF | Data | SCP2019 talk | SCoPE2 Web
- Chen A, Franks A, Slavov N.✉ (2019) DART-ID increases single-cell proteome coverage, PLoS Computational Biology, DOI: 10.1371/journal.pcbi.1007082 | PDF | RAW Data @ MassIVE | GitHub | DART-ID web
- Huffman RG, Specht H, Chen AT, Slavov N. (2019) DO-MS: Data-Driven Optimization of Mass Spectrometry Methods, J. of Proteome Res., DOI: 10.1021/acs.jproteome.9b00039 | DO-MS web | DO-MS @ GitHub
- Budnik B., Levy E., Harmonage G., Slavov N. (2018) SCoPE-MS: mass spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation, Genome Biology, DOI: 10.1186/s13059-018-1547-5 | Data Web | SCoPE-MS blog | Highlight by Proteomics News | Highlight by Front Line Genomics
- Emmott EP, Jovanovic M, Slavov N.✉ (2018) Ribosome stoichiometry: from form to function, Trends in Biomedical Sciences, DOI: 10.1016/j.tibs.2018.10.009 PDF
- Malioutov D., Chen T., Jaffe J., Airoldi E., Budnik B., Slavov N. ✉ (2018) Quantifying homologous proteins and proteoforms, Molecular & Cellular Proteomics, DOI: 10.1101/168765 | PDF | HIquant server
- Specht H, Harmange G, Perlman DH, Emmott E, Niziolek Z, Budnik B, Slavov N.✉Automated sample preparation for high-throughput single-cell proteomics, bioRxiv, DOI: 10.1101/399774 PDF | RAW Data @ MassIVE | SCP2018 Talk
- Specht H. & Slavov N. (2018) Transformative opportunities for single cell proteomics J. of Proteome Res., 17 (8), 2565 – 2571
- Berg P., Budnik B., Slavov N., Semrau S. (2017) Dynamic post-transcriptional regulation during embryonic stem cell differentiation, bioRxiv, DOI: 10.1101/123497
- Franks A., Airoldi E.M., Slavov N. (2017) Post-transcriptional regulation across human tissues, PLoS Computational Biology, 13(5): e1005535, DOI: 10.1101/020206 | Highlight by The Scientist
- Slavov N. (2015) Making the most of peer review, eLife, 4:e12708
- Slavov N., Semrau S., Airoldi E., Budnik B., van Oudenaarden A., (2015) Differential Stoichiometry among Core Ribosomal Proteins, Cell Reports, 13(5), 865-873. (TiBS Spotlight)
- Malioutov D., Slavov N. (2014) Convex Total Least Squares, Journal of Machine Learning Research, W&CP, 32(1), 109-117.
- Slavov N., Budnik B., Schwab D., Airoldi E., van Oudenaarden A. (2014) Constant Growth Rate Can Be Supported by Decreasing Energy Flux and Increasing Aerobic Glycolysis, Cell Reports 7(3), 705-714.
- Slavov N., Carey, J., Linse, S. (2013) Calmodulin transduces Ca+2 oscillations into differential regulation of its target proteins, ACS Chemical Neuroscience, 4, 601-612.
- Slavov N., Botstein D. (2013) Decoupling Nutrient Signaling from Growth Rate Causes Aerobic Glycolysis and Deregulation of Cell Size and Gene Expression, Molecular Biology of the Cell, 24(2), 157-168,
- Slavov N., van Oudenaarden A. (2012) How to Regulate a Gene: To Repress or to Activate?, Molecular Cell, 46(5), 551-552.
- Slavov N., Airoldi E.M., van Oudenaarden A., Botstein D. (2012) A Conserved Cell Growth Cycle Can Account for the Environmental Stress Responses of Divergent Eukaryotes, Mol. Biol. Cell, vol. 23, no. 10
- Slavov N., Macinskas J., Caudy A., Botstein D. (2011) Metabolic Cycling without Cell Division Cycling in Respiring Yeast, PNAS, vol. 108, 19090-19095
- Slavov N., Botstein D. (2011) Coupling among Growth Rate Response, Metabolic Cycle and Cell Division Cycle in Yeast, Mol. Biol. Cell, vol. 22
- Slavov N. (2010) Inference of Sparse Networks with Unobserved Variables. Application to Gene Regulatory Networks, JMLR, W&CP vol. 9
- Slavov, N., Dawson, K. (2009) Correlation Signature of the Macroscopic States of the Gene Regulatory Network in Cancer, PNAS, vol. 106, no. 11 PDF
Feb 12, 2020
An editorial in BioanalysisZone highlights research from the Slavov Lab that has led to the rapidly advancing field of single-cell protein analysis by mass-spec.
Jan 31, 2020
BioE Assistant Professor Nikolai Slavov’s research into using single-cell mass-spectrometry methods for high-throughput analysis of proteins is featured in the Science article “Unpicking the proteome in single cells.”
Sep 30, 2019
As part of the 15th anniversary of Nature Methods, BioE Assistant Professor Nikolai Slavov was featured in the article “Voices in methods development” about what he thinks are the most exciting and essential methodological biology challenges that are poised to be tackled in the near future.
Aug 14, 2019
BioE Assistant Professor Nikolai Slavov Lab was highlighted in the Nature Methods article A Dream of Single-Cell Proteomics highlighting their research in single-cell proteomics.
Jul 10, 2019
Bioengineering Assistant Professor Nikolai Slavov has developed a breakthrough method of identifying more than a thousand proteins per cell which could help map the functions of them throughout the body.
Feb 01, 2019
BioE Assistant Professors Ambika Bajpayee and Nikolai Slavov were each recipients of a $125K Sanofi iAward, which were created to promote scientific breakthroughs by tapping into the world’s greatest minds through close collaboration with renowned academic institutions.
Nov 09, 2018
The NIH Director’s office highlighted game-changing research on “Pinpointing Plenty of Proteins – in a Single Cell” conducted by BioE Assistant Professor Nikolai Slavov and his team.
Oct 22, 2018
BioE Assistant Professor Nikolai Slavov has devised a method to identify more than a thousand proteins in an individual cell and estimate their abundance.
Oct 17, 2018
Research from BioE Assistant Professor Nikolai Slavov’s lab was featured in Technology Network’s article “Through the Looking Glass of Single Cell Proteomics“
Aug 03, 2018
The article “Transformative Opportunities for Single-Cell Proteomics”, which is research from BioE Assistant Professor Nikolai Slavov’s Laboratory, is featured on the cover of the Journal of Proteome Research.