Nikolai Slavov
Associate Professor, Bioengineering
Allen Distinguished Investigator, Allen Frontiers Group
Director, Single-Cell Proteomics Center
Affiliated Faculty, Biology
Faculty Fellow , Barnett Institute
Office
- Mugar Life Sciences, Office 334
Related Links
Research Focus
Single-cell proteomics, Ribosome-mediated translational regulation, quantitative systems biology, mass-spectrometry
About
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.
Education
- PhD (2010), Botstein Laboratory, Princeton University
- BS (2004), Biology, Massachusetts Institute of Technology
Honors & Awards
- Allen Distinguished Investigator Award
- 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
Teaching Interests
Leadership Positions
Established the annual Single-cell Proteomics conference: single-cell.net/
Co-organized Learning Meaningful Representations of Life workshop at NeurIPS
Professional Affiliations
- 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)
Research Overview
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.
Slavov Laboratory
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
Selected Publications
- Petelski A, Emmott E, Leduc A, Huffman RG, Specht H, Perlman D, Slavov N.✉ (2021) Multiplexed single-cell proteomics using SCoPE2 Nature Protocols preprint | OA | PDF | Data web | Video Tutorials
- Slavov N.✉ (2021) Driving Single Cell Proteomics Forward with Innovation, J. of Proteome Res., doi: 10.1021/acs.jproteome.1c00639 | PDF
- Slavov N.✉ (2021) Increasing proteomics throughput, Nature Biotechnology PDF
- Slavov N.✉ et al. (2021) Voices of biotech research: Single-cell proteomics, Nature Biotechnology, 39, 281–286 PDF
- Specht H, Emmott E, Petelski A, Huffman RG, Perlman D, Serra M, Kharchenko P, Koller A. Slavov N.✉ (2021) Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity using SCoPE2 Genome Biology preprint | PDF | Data | SCP2019 talk | SCoPE2 Web
- Specht H, Slavov N.✉ (2020) Optimizing accuracy and depth of protein quantification in experiments using isobaric carriers, J. of Proteome Res. Preprint | PDF | WebSite | SCP2020 talk | Code
- Petelski AA, Slavov N.✉ (2020) Analyzing ribosome remodeling in health and disease, Proteomics preprint PDF
- 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
Nov 02, 2021
Research from the Slavov Laboratory published in Nature Protocols
Research from the laboratory of BioE Associate Professor and Allen Distinguished Investigator Nikolai Slavov has been published as “Multiplexed single-cell proteomics using SCoPE2” in Nature Protocols.
Nov 02, 2021
Slavov Research Featured on Cover of C&EN
BioE Associate Professor and Allen Distinguished Investigator Nikolai Slavov’s research on “Individual cells’ proteins vary. Single-cell proteomics can now show how” was featured on the cover of the C&EN journal. In Brief Measurements of cell mixtures can hide differences between cells that might be important in biology or disease studies. Researchers have long had tools […]
Sep 28, 2021
Identifying Novel Markers of Senescence Cells
BioE Associate Professor Nikolai Slavov, in collaboration with Massachusetts General Hospital, was awarded a $588K NIH grant from the National Cancer Institute for “Single-Cell Proteomic Identification of Novel Markers of Senescence.”
Sep 21, 2021
Single-cell Proteomics takes Centre Stage
BioE Associate Professor and Allen Distinguished Investigator Nikolai Slavov was featured in the Nature technology feature “Single-cell proteomics takes centre stage” which highlights single-cell proteomics technology developed by the Slavov Laboratory.
Aug 05, 2021
Towards resolving proteomes in single cells
BioE Associate Professor Nikolai Slavovo was featured in the Nature Methods article “Towards resolving proteomes in single cells” which highlights single-cell proteomics methods (SCoPE-MS and SCoPE2) developed by the Slavov Laboratory, and their application to characterising the emergence of molecular diversity in a type of innate immune cells, macrophages.
May 11, 2021
Just What the Doctor Ordered
Human beings are some of the most complex systems in the world, and responses to illness, disease, and impairments manifest in countless different ways. When it comes to making sure that your system stays up and running, healthcare professionals typically have their own deep well of knowledge—but the addition of artificial intelligence tools offers unprecedented […]
Mar 29, 2021
Nature Biotechnology Perspective on Increasing proteomics throughput
BioE Assistant Professor and Allen Distinguished Investigator Nikolai Slavov published a perspective article in Nature Biotechnology “Increasing proteomics throughput” highlighting new mass-spectrometry technologies transcending limitations in the throughput of proteomics and opening the stage for many exciting applications.
Mar 16, 2021
Voices of biotech research
As part of the 25th anniversary of Nature Biotechnology, BioE Assistant Professor and Allen Distinguished Investigator Nikolai Slavov published his future vision in the article “Voices of biotech research” about what he thinks are the most exciting and essential biotechnology opportunities.
Oct 08, 2020
Slavov Named Paul G. Allen Distinguished Investigator for Pioneering Single Cell Proteomics Research
Bioengineering Assistant Professor Nikolai Slavov was recently named a prestigious Allen Distinguished Investigator and was awarded a $1.5 million three-year grant to further his novel research on single cell proteomics. The Paul G. Allen Frontiers Group supports early-stage research with the potential to reinvent entire fields. Slavov is the first from Northeastern to receive the award.
Feb 12, 2020
The single cell proteomics revolution
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.