Purification and analysis of micronuclei from cancer cells to develop new potential cancer screening and diagnostic methods

Background: Faulty mitosis results in chromosomes failing to incorporate into daughter nuclei. These ‘lost sheep’ build their own nuclear membrane, generating micronuclei (MN). MN are hallmarks of cancer cells, and precipitate genomic rearrangements (e.g. chromothripsis), potentially driving tumourigenesis and therapy resistance. Rupture of MN can also release DNA into the cytosol, provoking an innate immune response, and increasing metastasis in breast cancer⁴. However, a host of fundamental questions regarding micronucleus biology and their utility as novel diagnostic markers in cancer remain unanswered.

Recently, with scientific and methodological input from Qiagen, we developed a rapid, kit-based method to purify micronuclei, uniquely allowing this iCASE student to:

(i) Investigate fundamental cancer micronucleus biology and genomics

(ii) Discover how to exploit cancer patients’ micronuclei to better predict, or treat cancer.

Experimental plan: Our lab is expert in innovative methods to detect and interpret patterns and types of chromosomal instability, with a view to improve diagnosis and outcomes for cancer patients^1-3. Since we occupy a rare niche, employing both cell biology and genomics, the student will gain experience in a wide range of cutting-edge methodological skills including molecular biology, cell culture, kit development (with Qiagen), microscopy, DNA sequencing and genomics analysis. The student’s findings will feed into Qiagen’s biomarker and liquid biopsy discovery program and are thus likely to produce both high impact scientific discoveries, and the opportunity to make a real impact on the health of cancer patients.

Aim 1: Fundamental characterization of cancer micronuclei

We will use a panel of ovarian cancer cell lines (extensively characterised in our laboratory³) and a new, ‘living biobank’ of patient-derived ovarian cancer samples⁵ to ask whether the frequency, characteristics and genomic content of cancer MN can infer clinically-relevant information (sensitivity to paclitaxel/carboplatin, PARP inhibitors). Analyses will include genomics, transcriptomics, proteomics and lipidomics of MN and their membranes. We will then extend this analysis to other cancer types (leukaemia, pancreatic, prostate).

Aim 2: Determine the potential of micronucleus purification and analysis as a clinically-applicable tool.

Micronuclei in peripheral blood mononuclear cells have long been considered a marker of exposure to genome damaging agents (such as nuclear radiation). However, to date, a systematic analysis of whether comprehensive micronucleus characterisation could non-invasively predict or track cancer development is lacking. The student will:

(i) Investigate MN frequency and genomic content from leukaemic and pre-leukaemic blood samples that have available matched clinical follow up data and multiple additional ‘-omics’ (part of the ongoing CRUK programme grant on AML held within GCB, BCI)

(ii) Examine the associations between MN features above with other biomarkers, such as gene transcription signatures, exosomes, CTCs (in collaboration with QIAGEN’s liquid biopsy program).

To apply for this project, please click here.