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Masson HO, Samoudi M, Robinson CM, Kuo CC, Weiss L, Shams Ud Doha K, Campos A, Tejwani V, Dahodwala H, Menard P, Voldborg BG, Robasky B, Sharfstein ST, Lewis NE. Inferring secretory and metabolic pathway activity from omic data with secCellFie. Metab Eng 2024; 81:273-285. [PMID: 38145748 PMCID: PMC11177574 DOI: 10.1016/j.ymben.2023.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 11/29/2023] [Accepted: 12/14/2023] [Indexed: 12/27/2023]
Abstract
Understanding protein secretion has considerable importance in biotechnology and important implications in a broad range of normal and pathological conditions including development, immunology, and tissue function. While great progress has been made in studying individual proteins in the secretory pathway, measuring and quantifying mechanistic changes in the pathway's activity remains challenging due to the complexity of the biomolecular systems involved. Systems biology has begun to address this issue with the development of algorithmic tools for analyzing biological pathways; however most of these tools remain accessible only to experts in systems biology with extensive computational experience. Here, we expand upon the user-friendly CellFie tool which quantifies metabolic activity from omic data to include secretory pathway functions, allowing any scientist to infer properties of protein secretion from omic data. We demonstrate how the secretory expansion of CellFie (secCellFie) can help predict metabolic and secretory functions across diverse immune cells, hepatokine secretion in a cell model of NAFLD, and antibody production in Chinese Hamster Ovary cells.
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Affiliation(s)
- Helen O Masson
- Department of Bioengineering, UC San Diego, La Jolla, CA, USA
| | | | | | - Chih-Chung Kuo
- Department of Bioengineering, UC San Diego, La Jolla, CA, USA
| | - Linus Weiss
- Department of Biochemistry, Eberhard Karls University of Tübingen, Germany
| | - Km Shams Ud Doha
- Proteomics Core, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Alex Campos
- Proteomics Core, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Vijay Tejwani
- College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, NY, USA
| | - Hussain Dahodwala
- College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, NY, USA
| | - Patrice Menard
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Bjorn G Voldborg
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark; National Biologics Facility, Technical University of Denmark, Lyngby, Denmark
| | | | - Susan T Sharfstein
- College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, NY, USA
| | - Nathan E Lewis
- Department of Bioengineering, UC San Diego, La Jolla, CA, USA; Department of Pediatrics, UC San Diego, La Jolla, CA, USA.
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Masson HO, Samoudi M, Robinson CM, Kuo CC, Weiss L, Doha KSU, Campos A, Tejwani V, Dahodwala H, Menard P, Voldborg BG, Sharfstein ST, Lewis NE. Inferring secretory and metabolic pathway activity from omic data with secCellFie. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.04.539316. [PMID: 37205389 PMCID: PMC10187314 DOI: 10.1101/2023.05.04.539316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Understanding protein secretion has considerable importance in the biotechnology industry and important implications in a broad range of normal and pathological conditions including development, immunology, and tissue function. While great progress has been made in studying individual proteins in the secretory pathway, measuring and quantifying mechanistic changes in the pathway's activity remains challenging due to the complexity of the biomolecular systems involved. Systems biology has begun to address this issue with the development of algorithmic tools for analyzing biological pathways; however most of these tools remain accessible only to experts in systems biology with extensive computational experience. Here, we expand upon the user-friendly CellFie tool which quantifies metabolic activity from omic data to include secretory pathway functions, allowing any scientist to infer protein secretion capabilities from omic data. We demonstrate how the secretory expansion of CellFie (secCellFie) can be used to predict metabolic and secretory functions across diverse immune cells, hepatokine secretion in a cell model of NAFLD, and antibody production in Chinese Hamster Ovary cells.
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Affiliation(s)
- Helen O. Masson
- Department of Bioengineering, UC San Diego, La Jolla, CA, USA
| | | | | | - Chih-Chung Kuo
- Department of Bioengineering, UC San Diego, La Jolla, CA, USA
| | - Linus Weiss
- Department of Biochemistry, Eberhard Karls University of Tübingen, Germany
| | - Km Shams Ud Doha
- Proteomics Core, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Alex Campos
- Proteomics Core, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Vijay Tejwani
- College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, NY, USA
| | - Hussain Dahodwala
- College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, NY, USA
- Present address: National Institute for Innovation in Manufacturing Biopharmaceuticals, Newark, Delaware, USA
| | - Patrice Menard
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Bjorn G. Voldborg
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
- National Biologics Facility, Technical University of Denmark, Lyngby, Denmark
| | - Susan T. Sharfstein
- College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, NY, USA
| | - Nathan E. Lewis
- Department of Bioengineering, UC San Diego, La Jolla, CA, USA
- Department of Pediatrics, UC San Diego, La Jolla, CA, USA
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