Biology subjects

Menard, P.

Publications and source records attributed to Menard, P..

4 recordsLinked to original sources

bioRxiv2026

Delineating the Transcriptional and Phenotypic Impact from Biotherapeutic Glycoengineering

Glycosylation is critical to biopharmaceutical activity, stability, and pharmacokinetics. While production cells can be engineered to produce better protein glycoforms, glycans decorate thousands of host cell proteins, and it remains unclear how glycoengineering impacts the host cell. To decipher the cell response to glycoengineering, we studied a library of 166 glycoengineered CHO-K1 cell clones representing 54 different glycosyltransferase modifications. Through integrated analysis of glycomics, RNA-Seq, and phenotypic data, we discovered that glycoengineered mutants clustered into three distinct groups (wild-type-like, Moderate, and Substantial) based on their glycosylation patterns. Different glycosyltransferase families exhibited distinct phenotypic signatures: St3gal modifications increased growth rate and cell density, B4galt knockouts affected cell size, and Mgat knockouts enhanced cell viability. Notably, we found specific cellular reprogramming associated with each glycosyltransferase family, including alterations in energy metabolism, stress responses, and DNA repair mechanisms. These findings were validated in an independent set of 30 glycoengineered CHO-S cell lines, expressing a panel of 10 recombinant proteins. Our extensive analysis reveals phenotypic changes resulting from glycoengineering, identifies their molecular bases, and provides crucial insights for controlling glycosylation during therapeutic protein production.

synthetic biology↗

bioRxiv2024

Multiplex genome editing eliminates the Warburg Effect without impacting growth rate in mammalian cells

The Warburg effect is ubiquitous in proliferative mammalian cells, including cancer cells, but poses challenges for biopharmaceutical production, as lactate accumulation inhibits cell growth and protein production. Previous efforts to eliminate lactate production via knockout have failed in mammalian bioprocessing since lactate dehydrogenase has proven essential. However, here we eliminated the Warburg effect in Chinese hamster ovary (CHO) and HEK293 cells by simultaneously knocking out lactate dehydrogenase and regulators involved in a negative feedback loop that typically inhibits pyruvate conversion to acetyl-CoA. In contrast to long-standing assumptions about the role of aerobic glycolysis, Warburg-null cells maintain wildtype growth rate while producing negligible lactate. Further characterization of Warburg-null CHO cells showed a compensatory increase in oxygen consumption, a near total reliance on oxidative metabolism, and higher cell densities in fed-batch cell culture. These cells remained amenable for production of diverse biotherapeutic proteins, reaching industrially relevant titers and maintaining product glycosylation. Thus, the ability to eliminate the Warburg effect is an important development for biotherapeutic production and provides a tool for investigating a near-universal metabolic phenomenon.

bioengineering↗

bioRxiv2023

Inferring secretory and metabolic pathway activity from omic data with secCellFie

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 pathways 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.

systems biology↗

bioRxiv2018

Combating viral contaminants in CHO cells by engineering STAT1 mediated innate immunity

Viral contamination in biopharmaceutical manufacturing can lead to shortages in the supply of critical therapeutics. To facilitate the protection of bioprocesses, we explored the basis for the susceptibility of CHO cells, the most commonly used cell line in biomanufacturing, to RNA virus infection. Upon infection with certain ssRNA and dsRNA viruses, CHO cells fail to generate a significant interferon (IFN) response. Nonetheless, the downstream machinery for generating IFN responses and its antiviral activity is intact in these cells: treatment of cells with exogenously-added type I IFN or poly I:C prior to infection limited the cytopathic effect from Vesicular stomatitis virus (VSV), Encephalomyocarditis virus (EMCV), and Reovirus-3 virus (Reo-3) in a STAT1-dependent manner. To harness the intrinsic antiviral mechanism, we used RNA-Seq to identify two upstream repressors of STAT1: Gfi1 and Trim24. By knocking out these genes, the engineered CHO cells exhibited increased resistance to the prototype RNA viruses tested. Thus, omics-guided engineering of mammalian cell culture can be deployed to increase safety in biotherapeutic protein production among many other biomedical applications.

bioengineering↗