Novel automated three‐dimensional genome scanning based on the nuclear architecture of telomeres

Abstract

Telomeres, the end of chromosomes, are organized in a nonoverlapping fashion and form microterritories in nuclei of normal cells. Previous studies have shown that normal and tumor cell nuclei differ in their 3D telomeric organization. The differences include a change in the spatial organization of the telomeres, in telomere numbers and sizes and in the presence of telomeric aggregates. Previous attempts to identify the above parameters of 3D telomere organization were semi-automated. Here we describe the automation of 3D scanning for telomere signatures in interphase nuclei based on three-dimensional fluorescent in situ hybridization (3D-FISH) and, for the first time, define its sensitivity in tumor cell detection. The data were acquired with a highthroughput scanning/acquisition system that allows to measure cells and acquire 3D images of nuclei at high resolution with 403 or 603 oil and at a speed of 10,000-15,000 cells h 21 , depending on the cell density on the slides. The automated scanning, TeloScan, is suitable for large series of samples and sample sizes. We define the sensitivity of this automation for tumor cell detection. The data output includes 3D telomere positions, numbers of telomeric aggregates, telomere numbers, and telomere signal intensities. We were able to detect one aberrant cell in 1,000 normal cells. In conclusions, we are able to detect tumor cells based on 3D architectural profiles of the genome. This new tool could, in the future, assist in patient diagnosis, in the detection of minimal residual disease, in the analysis of treatment response and in treatment decisions. '

Three-Dimensional Telomere Dynamics in Follicular Thyroid Cancer

“…Our findings confirm previous reports identifying 3D telomere FISH as an effective diagnostic tool for early detection of individual cancer cells, tumor subtypes, and suitable prognostic indicator of disease progression (24,25,31,62). Recently, we developed an automated 3D telomere scanning procedure capable of rapid imaging of telomere profiles from interphase nuclei, and specific TeloScan software was shown to identify individual tumor cells in large samples (63). This novel 3D telomere technique will make it feasible to test large numbers of human thyroid tissues in clinical screening rapidly.…”

Dynamic Length Changes of Telomeres and Their Nuclear Organization in Chronic Myeloid Leukemia

“…The emergence of automated and high-resolution microscopies [28,33] would make more efficient and more accurate the study of telomeric nuclear organization and deepen our understanding on the cross talk between telomeres and nuclear structures. Further studies should be undertaking by using CML as a disease model to better understand molecular mechanisms underlying dynamic changes of individual telomere lengths and remodeling of telomeric nuclear organization during oncogenesis.…”

“…Likewise telomere shortening, the alteration of telomeric nuclear organization has been associated with genomic instability and cancer progression [28,29,30,31,32,33]. Telomeric nuclear organization is defined by: (1) the number of telomeres (telomere signals), (2) telomere length (telomere signal intensity), (3) the number of telomere aggregates (TAs) (telomere clusters, found in close proximity that cannot be further resolved as separate entities at an optical resolution limit of 200 nm), (4) telomere distribution within a nucleus, and (5) telomere positions (the distance of each telomere from the nuclear center versus the periphery) [28,32,34,35].…”

State‐of‐the‐art FISHing: Automated analysis of cytogenetic aberrations in interphase nuclei

“…While the technological and computational development continued with undiminished energy during the following years (22,35,38,41,44,46,60,61,66,(81)(82)(83)(84)(85)(86)(87)(88)(89)(90)(91)(92)(93), even more emphasis was laid on practical approaches and a broad spectrum of clinical applications appeared in the beginning of the 21st century.…”

“…Last but not least, there are some special applications of automated analysis including the quantification of telomere length and revealing their abnormal pattern (28,39,91) and scrutinizing the exact location of chromosome territories (60). These examinations are however not yet part of clinical practice.…”