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Patient in a petri dish: Finding the right cell line to evaluate specific gene function in disease research

Aug 15, 2016 2:56:01 PM No Comments

Which Cell line models to use?

Sourcing biological materials that will acurately represent disease biology can be a time consuming and frustrating proceedure. Here we discuss:

  • the options available
  • and the merits and disavantages of each
  • how gene editing technology can provide bespoke cell models of disease


Advances in gene sequencing and other omic technologies are providing vast amounts of data on mutations affecting disease-linked cell phenotypes. Such information not only aids predicting disease predisposition or more accurate prognoses, but also promises to better anticipate a patient’s response to therapy. This has generated the field of personalized medicine, which is empowering treating physicians to make informed choices about optimizing therapies for individual patients based on unambiguous, validated experimental data.

 Discovering how disease phenotypes are driven by genetic alterations depends on identifying the specific on-target gene mutations involved, and unravelling the role played by these altered gene product(s) at the molecular level. Knowledge about the affected molecular functions or pathways enables targeted screening for small molecule inhibitors and rational design of drugs and treatments.

 Initially, early stage research projects need to decide which disease-related gene/protein functions or signalling pathways to investigate further. Simple cellular assays can rapidly back up preliminary hypotheses to facilitate applying for funding. Once established, results need to be validated by proof of concept, not only in independent cell lines, but also by generating complementary data using different molecular tools or strategies that require reliable biological material, such as cell lines, suitable for in vitro experiments.

The currently available sources of cell lines are discussed below.

Patient derived cells

Patient derived material containing all the pre-existing mutations is obtained from patient samples, with patient consent. Such cells are obviously a relevant, direct, readily available, and cheap source of cells for identifying genes involved in disease. They are useful for carrying out genetic screens, performing non-functional studies such as RNA or DNA analyses, and localizing gene products in fixed materials. However, such cells may also be difficult or slow to culture, produce low amounts of biological material to analyze, and be genetically unstable. They usually have high genetic variability, with many non-specific mutations acquired over the years.

 Immortalized cell lines

Tissue and disease specific cell lines have the advantages of being well established, intensively studied, relatively stable and easy to culture immortalized cell lines that are cheap and really available (ATCC/ECACC). They have been used for many years in genetic screens and functional studies to identify potential disease-relevant genes. However, they may not carry the appropriate mutations, requiring vectors to transiently overexpress relevant exogenous genes, as well as other complex genetic manipulations such as RNA silencing to switch genes off.

Transformed patient-derived material

Patient-derived material transformed into pluripotent cells (IPSC) enables researchers to generate many specialized tissues from patient samples bearing the relevant genetic mutations. The disadvantages are that such cells may contain many unspecific mutations, can be highly variable, or difficult and expensive to culture, as well as require challenging differentiation conditions.

 Gene-edited cell lines

The advantages of using gene-edited cell lines are that the mutations are precisely defined. Recent advances in technologies, such as CRISPR/Cas9, have simplified and accelerated modification of any gene. Techniques such as disabling (knockout), overexpressing (knockin) or functionally modifying a gene (point mutations) are powerful approaches to understanding the cellular role of a protein. However in diploid cells, engineering cell lines is complicated by the need to modify two alleles. Many established cell lines can be polyploidy!

HAP1 is a semi-haploid human adherent cell line derived from the male chronic myelogenous leukaemia (CML) cell line KBM-7, with a single copy of almost every human chromosome. The absence of a second allele ensures that any loss of function mutation is not masked by the presence of an unedited gene. Molecular analyses are also greatly simplified in these cells, since they are both easy to culture and provide a broad platform for testing gene function. Risks that results are due to off-target effects of gene editing (CRISPR) can be mitigated by studying multiple clones, while the parental cell line provides the ideal control ensuring that findings are not due to other mutations. Rare mutations can be reconstructed, multiple mutations can be introduced, and known or novel genes can be analyzed independently of established cell lines or patient material. 


Successful transfer from bench to bedside depends on many complex factors, but initially requires robust molecular validation tools to justify further research. HAP1 cell lines represent a cost and time effective solution to confirming the role of a mutated gene function in disease, an essential step towards discovering potential molecular biomarkers or therapeutic targets.

For more examples of HAP1 cell use:

Learn more: Application of HAP1 as disease models