Advanced Microscopy Applications Unit (ADMiRA) at the National Cancer Institute of Mexico
Super-resolution imaging, a powerful tool for the analysis of chromosome topology applied to the study of treatment resistance in cancer.
Chromosomes in interphase occupy a distinct, limited space within the nucleus, called chromosome territory (CT). It has been postulated that the non-random CT’s spatial organization within the cell nucleus contributes to the emergence of chromosome translocations. The consistent appearance of t(9;22) in pluripotent hematopoietic stem cells, apart from being the etiological factor for chronic myeloid leukemia (CML), is a clear example of what is considered a non-random chromosome aberration. This rearrangement leads to the fusion of BCR and ABL1 genes giving rise to a chimeric protein with constitutive kinase activity. Tyrosine kinase inhibitors (TKI), such as Imatinib, are used as first-line treatment for CML, though approximately 40% of CML patients do not respond to Imatinib.
In order to highlight the importance of spatial proximity, and evaluate the topological CT changes caused by t(9;22), before and after TKI treatment, we performed 3D-FISH of CT9 and CT22 in stem cells from CML patients followed by super-resolution microscopy, and image 3D reconstruction.
We found that resistance to TKI treatment in CML is characterized by high levels of CT9 and CT22 structural disruption, increased CT volumes (especially for CT22), increased intermingling between CT9 and CT22, and increased occupancy of H3K9ac, an open-chromatin epigenetic mark, in CT22.
Taken together, our findings suggest that CT9 and CT22 disruption is a potential predictive marker of response or non-response to therapy in CML, our results also provide novel insights into how the genome structure associates with the response to cancer treatments, highlighting the importance of microscopy in analyzing the topological features of the genome.