Panel A. Hematoxylin and Eosin tissue sections from an MSS CIN- , ALT+, Telomerase- rectal cancer (left) and from MSS CIN+, ALT-, Telomerase + rectal cancer. Both are moderately differentiated adenocarcinomas. The gland-to-stroma ratio is higher in the ALT+/tel- case, and it has less desmoplastic stroma. Panel B. Dot/blot showing presence of C-circles. C circles, extrachromosomal telomeric DNA, are strongly associated with ALT. Assessed in tumor DNA with isothermic amplification of C-circle complementary strand and hybridization with ³²P-(CCCTAA)₃ probe by Capital Biosciences (Capital Biosciences, Maryland, U. S. A. ), a sample was called ALT+ if C-circles were detected. The presence of C-circles are illustrated by the presence of radioactive tracer in the image on the left, and the absence of radioactivity in the blot on the right indicates absence of C-circles in the ALT- tumor. Panel C. Ideograms summarizing chromosomal gains and losses across all chromosomes evaluated by aCGH. The ALT+, telomerase negative tumor on the left had <10% of BAC clones showing aberrant hybridization and is classified as a CIN- tumor. The ALT-,,telomerase positive tumor on the right had 40% of clones with aberrant hybridization and is classified as a CIN+ tumor. Panel D. aCGH results of raw data for chromosome 17 for each tumor corresponding to the ideograms in Panel C.

https://doi.org/10.1371/journal.pone.0080015.g003