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Khan S, Conover R, Asthagiri AR, Slavov N. Dynamics of Single-Cell Protein Covariation during Epithelial-Mesenchymal Transition. J Proteome Res 2024. [PMID: 38663020 DOI: 10.1021/acs.jproteome.4c00277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Physiological processes, such as the epithelial-mesenchymal transition (EMT), are mediated by changes in protein interactions. These changes may be better reflected in protein covariation within a cellular cluster than in the temporal dynamics of cluster-average protein abundance. To explore this possibility, we quantified proteins in single human cells undergoing EMT. Covariation analysis of the data revealed that functionally coherent protein clusters dynamically changed their protein-protein correlations without concomitant changes in the cluster-average protein abundance. These dynamics of protein-protein correlations were monotonic in time and delineated protein modules functioning in actin cytoskeleton organization, energy metabolism, and protein transport. These protein modules are defined by protein covariation within the same time point and cluster and, thus, reflect biological regulation masked by the cluster-average protein dynamics. Thus, protein correlation dynamics across single cells offers a window into protein regulation during physiological transitions.
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Affiliation(s)
- Saad Khan
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
- Department of Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Rachel Conover
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Anand R Asthagiri
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
- Department of Biology, Northeastern University, Boston, Massachusetts 02115, United States
- Department of Chemical Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Nikolai Slavov
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
- Department of Biology, Northeastern University, Boston, Massachusetts 02115, United States
- Parallel Squared Technology Institute, Watertown, Massachusetts 02472, United States
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Khan S, Conover R, Asthagiri AR, Slavov N. Dynamics of single-cell protein covariation during epithelial-mesenchymal transition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.21.572913. [PMID: 38187715 PMCID: PMC10769332 DOI: 10.1101/2023.12.21.572913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Physiological processes, such as epithelial-mesenchymal transition (EMT), are mediated by changes in protein interactions. These changes may be better reflected in protein covariation within cellular cluster than in the temporal dynamics of cluster-average protein abundance. To explore this possibility, we quantified proteins in single human cells undergoing EMT. Covariation analysis of the data revealed that functionally coherent protein clusters dynamically changed their protein-protein correlations without concomitant changes in cluster-average protein abundance. These dynamics of protein-protein correlations were monotonic in time and delineated protein modules functioning in actin cytoskeleton organization, energy metabolism and protein transport. These protein modules are defined by protein covariation within the same time point and cluster and thus reflect biological regulation masked by the cluster-average protein dynamics. Thus, protein correlation dynamics across single cells offer a window into protein regulation during physiological transitions.
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Affiliation(s)
- Saad Khan
- Department of Bioengineering, Northeastern University, Boston, MA, USA
- Department of Biology, Northeastern University, Boston, MA, USA
| | - Rachel Conover
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Anand R. Asthagiri
- Department of Bioengineering, Northeastern University, Boston, MA, USA
- Department of Biology, Northeastern University, Boston, MA, USA
- Department of Chemical Engineering, Northeastern University, Boston, MA, USA
| | - Nikolai Slavov
- Department of Bioengineering, Northeastern University, Boston, MA, USA
- Department of Biology, Northeastern University, Boston, MA, USA
- Parallel Squared Technology Institute, Watertown, MA 02472, USA
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Zadeh P, Camley BA. Picking winners in cell-cell collisions: Wetting, speed, and contact. Phys Rev E 2022; 106:054413. [PMID: 36559372 DOI: 10.1103/physreve.106.054413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 09/27/2022] [Indexed: 06/17/2023]
Abstract
Groups of eukaryotic cells can coordinate their crawling motion to follow cues more effectively, stay together, or invade new areas. This collective cell migration depends on cell-cell interactions, which are often studied by colliding pairs of cells together. Can the outcome of these collisions be predicted? Recent experiments on trains of colliding epithelial cells suggest that cells with a smaller contact angle to the surface or larger speeds are more likely to maintain their direction ("win") upon collision. When should we expect shape or speed to correlate with the outcome of a collision? To investigate this question, we build a model for two-cell collisions within the phase field framework, which allows for cell shape changes. We can reproduce the observation that cells with high speed and small contact angles are more likely to win with two different assumptions for how cells interact: (1) velocity aligning, in which we hypothesize that cells sense their own velocity and align to it over a finite timescale, and (2) front-front contact repolarization, where cells polarize away from cell-cell contact, akin to contact inhibition of locomotion. Surprisingly, though we simulate collisions between cells with widely varying properties, in each case, the probability of a cell winning is completely captured by a single summary variable: its relative speed (in the velocity-aligning model) or its relative contact angle (in the contact repolarization model). Both models are currently consistent with reported experimental results, but they can be distinguished by varying cell contact angle and speed through orthogonal perturbations.
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Affiliation(s)
- Pedrom Zadeh
- William H. Miller III Department of Physics & Astronomy, Johns Hopkins University, Baltimore, Maryland 21210, USA
| | - Brian A Camley
- William H. Miller III Department of Physics & Astronomy, Johns Hopkins University, Baltimore, Maryland 21210, USA
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA
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Luo CY, Natividad RJ, Lalli ML, Asthagiri AR. Multivariate relationships among nucleus and Golgi properties during fibrillar migration are robust to and unchanged by epithelial-to-mesenchymal transition. PLoS One 2020; 15:e0239188. [PMID: 32946467 PMCID: PMC7500656 DOI: 10.1371/journal.pone.0239188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 09/01/2020] [Indexed: 11/21/2022] Open
Abstract
Epithelial-to-mesenchymal transition (EMT) and maturation of a fibrillar tumor microenvironment play important roles in breast cancer progression. A better understanding of how these events promote cancer cell migration and invasion could help identify new strategies to curb metastasis. The nucleus and Golgi affect migration in a microenvironment-dependent manner. Nucleus size and mechanics influence the ability of a cell to squeeze through confined tumor microenvironments. Golgi positioning determines front-rear polarity necessary for migration. While the roles of individual attributes of nucleus and Golgi in migration are being clarified, how their manifold features are inter-related and work together remains to be understood at a systems level. Here, to elucidate relationships among nucleus and Golgi properties, we quantified twelve morphological and positional properties of these organelles during fibrillar migration of human mammary epithelial cells. Principal component analysis (PCA) reduced the twelve-dimensional space of measured properties to three principal components that capture 75% of the variations in organelle features. Unexpectedly, nucleus and Golgi properties that co-varied in a PCA model built with data from untreated cells were largely similar to co-variations identified using data from TGFβ-treated cells. Thus, while TGFβ-mediated EMT significantly alters gene expression and motile phenotype, it did not significantly affect the relationships among nucleus size, aspect ratio and orientation with migration direction and among Golgi size and nucleus-Golgi separation distance. Indeed, in a combined PCA model incorporating data from untreated and TGFβ-treated cells, scores of individual cells occupy overlapping regions in principal component space, indicating that TGFβ-mediated EMT does not promote a unique “Golgi-nucleus phenotype” during fibrillar migration. These results suggest that migration along spatially-confined fiber-like tracks employs a conserved nucleus-Golgi arrangement that is independent of EMT state.
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Affiliation(s)
- Catherine Y. Luo
- Department of Bioengineering, Northeastern University, Boston, MA, United States of America
| | - Robert J. Natividad
- Department of Bioengineering, Northeastern University, Boston, MA, United States of America
| | - Mark L. Lalli
- Department of Chemical Engineering, Northeastern University, Boston, MA, United States of America
| | - Anand R. Asthagiri
- Department of Bioengineering, Northeastern University, Boston, MA, United States of America
- Department of Chemical Engineering, Northeastern University, Boston, MA, United States of America
- Department of Biology, Northeastern University, Boston, MA, United States of America
- * E-mail:
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Natividad RJ, Lalli ML, Muthuswamy SK, Asthagiri AR. Golgi Stabilization, Not Its Front-Rear Bias, Is Associated with EMT-Enhanced Fibrillar Migration. Biophys J 2018; 115:2067-2077. [PMID: 30366626 PMCID: PMC6343588 DOI: 10.1016/j.bpj.2018.10.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 09/24/2018] [Accepted: 10/05/2018] [Indexed: 01/06/2023] Open
Abstract
Epithelial-to-mesenchymal transition (EMT) and maturation of collagen fibrils in the tumor microenvironment play a significant role in cancer cell invasion and metastasis. Confinement along fiber-like tracks enhances cell migration. To what extent and in what manner EMT further promotes migration in a microenvironment already conducive to migration is poorly understood. Here, we show that TGFβ-mediated EMT significantly enhances migration on fiber-like micropatterned tracks of collagen, doubling migration speed and tripling persistence relative to untreated mammary epithelial cells. Thus, cell-intrinsic EMT and extrinsic fibrillar tracks have nonredundant effects on motility. To better understand EMT-enhanced fibrillar migration, we investigated the regulation of Golgi positioning, which is involved in front-rear polarization and persistent cell migration. Confinement along fiber-like tracks has been reported to favor posterior Golgi positioning, whereas anterior positioning is observed during 2-day wound healing. Although EMT also regulates cell polarity, little is known about its effect on Golgi positioning. Here, we show that EMT induces a 2:1 rearward bias in Golgi positioning; however, positional bias explains less than 2% of single-cell variability in migration speed and persistence. Meanwhile, EMT significantly stabilizes Golgi positioning. Cells that enhance migration in response to TGFβ maintain Golgi position for 2- to 4-fold longer than nonresponsive counterparts irrespective of whether the Golgi is ahead or behind the nucleus. In fact, 28% of TGFβ-responsive cells exhibit a fully committed Golgi phenotype with the organelle either in the anterior or posterior position for over 90% of the time. Furthermore, single-cell differences in Golgi stability capture up to 18% of variations in migration speed. These results suggest a hypothesis that the Golgi may be part of a core physical scaffold that affects how cell-generated forces are distributed during migration. A stable scaffold would be expected to more consistently and therefore more productively distribute forces over time, leading to efficient migration.
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Affiliation(s)
- Robert J Natividad
- Department of Bioengineering, Northeastern University, Boston, Massachusetts
| | - Mark L Lalli
- Department of Chemical Engineering, Northeastern University, Boston, Massachusetts
| | - Senthil K Muthuswamy
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Anand R Asthagiri
- Department of Bioengineering, Northeastern University, Boston, Massachusetts; Department of Chemical Engineering, Northeastern University, Boston, Massachusetts; Department of Biology, Northeastern University, Boston, Massachusetts.
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Jolly MK, Somarelli JA, Sheth M, Biddle A, Tripathi SC, Armstrong AJ, Hanash SM, Bapat SA, Rangarajan A, Levine H. Hybrid epithelial/mesenchymal phenotypes promote metastasis and therapy resistance across carcinomas. Pharmacol Ther 2018; 194:161-184. [PMID: 30268772 DOI: 10.1016/j.pharmthera.2018.09.007] [Citation(s) in RCA: 198] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cancer metastasis and therapy resistance are the major unsolved clinical challenges, and account for nearly all cancer-related deaths. Both metastasis and therapy resistance are fueled by epithelial plasticity, the reversible phenotypic transitions between epithelial and mesenchymal phenotypes, including epithelial-mesenchymal transition (EMT) and mesenchymal-epithelial transition (MET). EMT and MET have been largely considered as binary processes, where cells detach from the primary tumor as individual units with many, if not all, traits of a mesenchymal cell (EMT) and then convert back to being epithelial (MET). However, recent studies have demonstrated that cells can metastasize in ways alternative to traditional EMT paradigm; for example, they can detach as clusters, and/or occupy one or more stable hybrid epithelial/mesenchymal (E/M) phenotypes that can be the end point of a transition. Such hybrid E/M cells can integrate various epithelial and mesenchymal traits and markers, facilitating collective cell migration. Furthermore, these hybrid E/M cells may possess higher tumor-initiation and metastatic potential as compared to cells on either end of the EMT spectrum. Here, we review in silico, in vitro, in vivo and clinical evidence for the existence of one or more hybrid E/M phenotype(s) in multiple carcinomas, and discuss their implications in tumor-initiation, tumor relapse, therapy resistance, and metastasis. Together, these studies drive the emerging notion that cells in a hybrid E/M phenotype may occupy 'metastatic sweet spot' in multiple subtypes of carcinomas, and pathways linked to this (these) hybrid E/M state(s) may be relevant as prognostic biomarkers as well as a promising therapeutic targets.
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Affiliation(s)
- Mohit Kumar Jolly
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA.
| | - Jason A Somarelli
- Duke Cancer Institute and Department of Medicine, Duke University Medical Center, Durham, USA
| | - Maya Sheth
- Duke Cancer Institute and Department of Medicine, Duke University Medical Center, Durham, USA
| | - Adrian Biddle
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Satyendra C Tripathi
- Department of Clinical Cancer Prevention, UT MD Anderson Cancer Center, Houston, USA
| | - Andrew J Armstrong
- Duke Cancer Institute and Department of Medicine, Duke University Medical Center, Durham, USA
| | - Samir M Hanash
- Department of Clinical Cancer Prevention, UT MD Anderson Cancer Center, Houston, USA
| | - Sharmila A Bapat
- National Center for Cell Science, Savitribai Phule Pune University Campus, Ganeshkhind, Pune, India
| | - Annapoorni Rangarajan
- Department of Molecular Reproduction, Development & Genetics, Indian Institute of Science, Bangalore, India
| | - Herbert Levine
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA.
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