ESR2: Alan Foley

Individual Project

Identification of mitochondrial DNA mutations in single cells for biopharmaceutical manufacturing

STACCATO Research

DNA is commonly thought to be contained within the nucleus of an animal cell. However, there is a small 16,00bp circular chromosome in mitochondria – the powerhouse of the cell. Recently, the Chinese Hamster Ovary (CHO) mitochondrial genome was sequenced by ultra-deep next-generation sequencing. Mutations were revealed at various sites and often unique to individual CHO cell lines.
This information is powerful as it informs on how to make a CHO cell culture more homogenous. However, this study analysed genetics by taking an average from many CHO cells. Thus, the subtle genetic nuances of single cells within a community is lost. For mitochondria this distinction is perhaps even more pertinent as its DNA makeup can exist in a state known as “heteroplasmy”; where mutated DNA molecules co-exist with wild-type DNA within the same mitochondria.
In this project, single cells will be analysed. The impact of mutations will be more specifically linked to phenotypic traits – such as recombinant protein production. This can inform on genetic engineering strategies to improve CHO cell culture performance. Additionally, since 99% of mitochondrial genes are nuclear bound, nuclear genes will be considered in tandem.

Scientific Background

Alan has a BSc and MSc degree from UK universities. His laboratory background has focussed on inducing a HEXA mutation in neuroblastoma cells to simulate Tay-Sachs Disease – a genetic disorder affecting young children.

Publications

Three publications are being prepared for submission to peer-reviewed journals in 2023.

Conferences

• Oral presentation: European Society for Animal Cell Culture Technology (ESACT), Lisbon, Portugal, 26. – 29.06.2022.
  Single CHO cell mtDNA-seq
• Poster presentation: ESACT Frontiers, Vienna, Austria, 26.10.2022.
  Single Cell Sequencing of CHO mitochondrial DNA reveals extensive heteroplasmy.
• Poster presentation: European Society for Animal Cell Culture Technology (ESACT), Lisbon, Portugal, 26. – 29.06.2022.
  Single Cell Sequencing of CHO mitochondrial DNA reveals extensive heteroplasmy.
• Youtube: A. Foley (ESR2) presenting his poster: “Single Cell Sequencing of CHO mitochondrial DNA reveals extensive heteroplasmy”