Prior studies have identified recurrent oncogenic mutations in colorectal adenocarcinoma1 and have surveyed exons of protein-coding genes for mutations in 11 affected individuals2,3. Here we report whole-genome sequencing from nine individuals with colorectal cancer, including primary colorectal tumors and matched adjacent non-tumor tissues, at an average of 30.7× and 31.9× coverage, respectively. We identify an average of 75 somatic rearrangements per tumor, including complex networks of translocations between pairs of chromosomes. Eleven rearrangements encode predicted in-frame fusion proteins, including a fusion of VTI1A and TCF7L2 found in 3 out of 97 colorectal cancers. Although TCF7L2 encodes TCF4, which cooperates with β-catenin4 in colorectal carcinogenesis5,6, the fusion lacks the TCF4 β-catenin–binding domain. We found a colorectal carcinoma cell line harboring the fusion gene to be dependent on VTI1A-TCF7L2 for anchorage-independent growth using RNA interference-mediated knockdown. This study shows previously unidentified levels of genomic rearrangements in colorectal carcinoma that can lead to essential gene fusions and other oncogenic events.

Fanconi anemia (FA) patients have an increased risk for squamous cell carcinomas (SCCs) at sites of predilection for infection with high-risk human papillomavirus (HPV) types, including the oral cavity and the anogenital tract. We show here that activation of the FA pathway is a frequent event in cervical SCCs. We found that FA pathway activation is triggered mainly by the HPV type 16 (HPV-16) E7 oncoprotein and is associated with an enhanced formation of large FANCD2 foci and recruitment of FANCD2 as well as FANCD1/BRCA2 to chromatin. Episomal expression of HPV-16 oncoproteins was sufficient to activate the FA pathway. Importantly, the expression of HPV-16 E7 in FA-deficient cells led to accelerated chromosomal instability. Taken together, our findings establish the FA pathway as an early host cell response to high-risk HPV infection and may help to explain the greatly enhanced susceptibility of FA patients to squamous cell carcinogenesis at anatomic sites that are frequently infected by high-risk HPVs.Fanconi anemia (FA) is a rare autosomal recessive or Xlinked cancer susceptibility syndrome characterized by congenital abnormalities, progressive bone marrow failure, and cellular sensitivity to DNA cross-linking agents (10). FA patients have a greatly increased susceptibility to squamous cell carcinomas (SCCs) of the anogenital tract and the oral cavity (24), sites with a predilection for infection with high-risk human papillomaviruses (HPVs) (33). An analysis of head and neck SCCs from FA patients showed that over 80% of the tumors contained high-risk HPV DNA, in particular that of HPV type 16 (HPV-16) (13). However, these results have been challenged by a study in which HPVs were undetectable in four cell lines derived from head and neck SCCs that developed in FA patients (31). Nonetheless, there is evidence that FA genes can become epigenetically inactivated during cervical carcinogenesis in the general population (22). The reason for the increased susceptibility of FA patients to SCCs that frequently arise at sites of HPV infection and why they develop these tumors at a significantly younger age than the general population is currently unknown (16).High-risk HPV types, such as HPV-16, encode two oncoproteins, E6 and E7, which have important functions during the viral life cycle by reinitiating DNA replication in terminally growth-arrested host keratinocytes (1,15,20). The efficiency of HPV-16 oncoproteins to subvert cell cycle checkpoints in order to create an S-phase-like milieu supportive of viral DNA replication is likely to be critical for their oncogenic potential. Unscheduled entry into S phase and the deregulation of cyclin expression, characteristics of HPV-16 E7-expressing cells (17,18,25), have previously been suggested to result in perturbations of DNA replication, increased stalling of replication forks, and chromosomal instability (4,26).Previous studies have shown that the FA pathway can become activated by stalled replication forks (9). Upon activation, the core complex of FA proteins mediate...

Patients with the rare genetic disease, Fanconi anemia (FA), are highly susceptible to squamous cell carcinomas arising at multiple anatomic sites including the head and neck region. Human papillomaviruses (HPVs), particularly HPV16, are associated with $20% of head and neck squamous cell carcinomas (HNSCCs) in the general population. Some but not other investigators have reported that HNSCCs in FA patients are much more frequently positive for HPV. In addition, studies have demonstrated an interaction between the HPV16 E7 oncoprotein and the FA pathway, a DNA damage response pathway deficient in FA patients. On the basis of these studies, it was hypothesized that the FA pathway contributes to repair of DNA damage induced by HPV16 E7, providing one explanation for why FA patients are predisposed to HPV-associated HNSCCs. To determine the importance of the FA pathway in modulating the oncogenic abilities of E7, we crossed K14E7 transgenic (K14E7) and fancD2 knockout mice (FancD2À/À and K14E7/FancD2 þ/þ mice and monitored their susceptibility to HNSCC when treated with a chemical carcinogen. K14E7/FancD2 À/À mice had a significantly higher incidence of HNSCC compared with K14E7/FancD2 þ/þ mice. This difference correlated with an increased proliferative index and the increase in expression of biomarkers that are used to assess levels of DNA damage. These animal studies support the hypotheses that FA patients have increased susceptibility to HPV-associated cancer and that the FA DNA damage response pathway normally attenuates the oncogenic potential of HPV16 E7. Cancer Res; 70(23); 9959-68. Ó2010 AACR.