Mammalian cells, especially the Chinese hamster ovary cell line (CHO), are the most important production vehicle for making recombinant human proteins, such as cytokines and antibodies, for human therapeutic use. Improving the efficiency of production of complex biotherapeutics will be critical in controlling costs to healthcare systems as more of these drugs come to market. This field represents an important opportunity for future development of the pharmaceutical industry and a significant area for employment of scientists in Ireland. Understanding of the basic biology underpinning the CHO production system is lacking – the field has developed on a pragmatic basis without a high level of understanding of the cellular molecular biology involved. In collaboration with a number of leading international biopharmaceutical companies and academic collaborators, NICB scientists are applying state-of-the-art technologies in proteomics to profile protein expression patterns associated with desirable production phenotypes. We are also investigating the role of candidate pathways using functional genomics approaches to improve the efficiency of biotherapeutic production.

Research Area

Principal Investigators

Dr. Paula Meleady

Very little is known about the cellular and molecular mechanisms that govern the production of complex proteins by engineered mammalian cells. The majority of the work to date has largely concentrated on optimisation of cell culture conditions (e.g. media formulation), bioreactor design, and improvements in the design of expression vectors. We are undertaking proteomic studies on CHO cells and other industrially relevant cell lines, in order to understand the molecular and cellular mechanisms involved in growth and productivity in mammalian cells used for biopharmaceutical production. Protein profiles generated from both intracellular and extracellular samples from bioreactors may give insights for genetic intervention to possibly create better host cell lines, or even to provide clues to more rational strategies for process development (e.g. media design).

In CHO production cell cultures, the expression of high levels of recombinant biopharmaceuticals is linked to inducing endoplasmic reticulum (ER) stress, causing enhanced unfolded protein response (UPR) levels to maintain cell viability and productivity. ER stress mechanisms are poorly understood in CHO cells, and are a major bottleneck in improving the efficiency of production of high cost recombinant biopharmaceuticals. Advanced high-resolution state-of-the-art mass spectrometry are being used to identify proteomic changes and site-specific post translational modifications on cellular proteins as a result of changes to productivity of CHO cells. This will lead to the identification of engineering targets to improve CHO cell productivity that is of significant relevance to the Biopharmaceutical industry.


  1. Bryan L, Henry M, Kelly RM, Lloyd M, Frye CC, Osborne MD, Clynes M, Meleady P. Global phosphoproteomic study of high/low specific productivity industrially relevant mAb producing recombinant CHO cell lines. Curr Res in Biotechnol. 2021, 3:49-56.
  2. Bryan L, Clynes M, Meleady P. The emerging role of cellular post-translational modifications in modulating growth and productivity of recombinant Chinese hamster ovary cells. Biotechnol Adv. 2021 Jul-Aug;49:107757. doi: 10.1016/j.biotechadv.2021.107757.
  3. Coleman O, Suda S, Meiller J, Henry M, Riedl M, Barron N, Clynes M, Meleady P. Increased growth rate and productivity following stable depletion of miR-7 in a mAb producing CHO cell line causes an increase in proteins associated with the Akt pathway and ribosome biogenesis. J Proteomics. 2019 Mar 20;195:23-32. doi: 10.1016/j.jprot.2019.01.003.
  4. Kaushik P, Henry M, Clynes M, Meleady P. The Expression Pattern of the Phosphoproteome Is Significantly Changed During the Growth Phases of Recombinant CHO Cell Culture. Biotechnol J. 2018 Oct;13(10):e1700221. doi: 10.1002/biot.201700221.
  5. Henry M, Gallagher C, Kelly RM, Frye CC, Osborne MD, Brady CP, Barron N, Clynes M, Meleady P. Clonal variation in productivity and proteolytic clipping of an Fc-fusion protein in CHO cells: Proteomic analysis suggests a role for defective protein folding and the UPR. J Biotechnol. 2018 Sep 10;281:21-30. doi: 10.1016/j.jbiotec.2018.05.018.
Research Group Members

Dr. Esen Efeoglu (postdoctoral researcher)

Funder: SFI Frontiers for the Future Award

Esen’s research involves high resolution protein mass spectrometry analysis of Chinese hamster ovary cells to identify cellular post-translational modifications involved in bioprocessing relevant phenotypes related to biotherapeutic productivity.

David Ryan (postgraduate student)

Funder: SFI Frontiers for the Future Award

David’s research involves the proteomic analysis of recombinant CHO cells with high and low productivity (Qp) phenotypes in different bioprocess-relevant culture conditions.

Christiana Sideri (Postgraduate Student)

Funder: SFI Frontiers for the Future Award

Christiana’s research involves the proteomic analysis of recombinant CHO cells following the induction of cellular stress in different bioprocess-relevant culture conditions

Laura Bryan (Postgraduate Student)

Funder: Irish Research Council Enterprise Partnership Scheme

Laura’s research investigates the phenotype variability between industrially relevant Chinese hamster ovary clonally derived cell lines using proteomic, phosphoproteomic and miRNA approaches.

Principal Investigators

Associate Prof Ciaran Fagan
+353 (0) 700 5288

Dr. Ciarán Fagan seeks to improve the stability of enzymes. Enzymes are ideal “green” catalysts: they can enable newer processes that are less hazardous and less costly than traditional methods, while producing less waste.

Enzymes’ many industrial applications range from detergents to the food and (bio)pharma industries. Unfortunately, enzymes may become unstable and lose their catalytic abilities under the demands of process conditions, or upon prolonged use or extended storage. Dr. Fagan uses two main strategies to increase the stability of enzymes, namely protein engineering and chemical modification. He has prepared enzymes that are more tolerant of heat, organic solvents or oxidizing conditions, or that give improved biosensor performance.

Although he has worked on numerous enzymes, his special focus is on plant peroxidases (which are used for a variety of purposes). These, together with a “resurrected” ancient plant peroxidase, an evolutionary precursor of the modern-day enzymes, provide opportunities for postgraduate research.


  1. Hui Ma, Ciarán Ó’Fágáin, Richard O’Kennedy (2019) ‘Unravelling enhancement of antibody fragment stability – role of format structure and cysteine modification’. Journal of Immunological Methods, 464: 57-63.
  2. Ó’Fágáin, Ciarán; Colliton, Keith. (2017) ‘Storage and Lyophilization of Pure Proteins’ In: Walls, Dermot, Loughran, Sinead (eds). Protein Chromatography Methods and Protocols 2nd ed. NY: Humana Press-Springer Nature. 159-190.
  3. Loughran NB, O’Connell MJ, O’Connor B, Ó’Fágáin C. (2014) ‘Stability properties of an ancient plant peroxidase’. BIOCHIMIE, 104: 156-159.
  4. Loughran, NB; Hinde, S; McCormick-Hill, S; Leidal, KG; Bloomberg, S; Loughran, ST; O’Connor, B; Ó´Fágáin, C; Nauseef WJ; O’Connell, MJ. (2012) ‘Functional Consequence of Positive Selection Revealed Through Rational Mutagenesis of Human Myeloperoxidase’. MOLECULAR BIOLOGY AND EVOLUTION, 29: 2039-2046.
  5. McEntee G, Minguzzi S, O’Brien K, Ben Larbi N, Loscher C, Ó’Fágáin C, & Parle-McDermott A. (2011) ‘The former annotated human pseudogene dihydrofolate reductase-like 1 (DHFRL1) is expressed and functional’. NATIONAL ACADEMY OF SCIENCES. PROCEEDINGS (PRINT), 108: 15157-15162.