PURPOSE:This study was designed to determine whether loss of heterozygosity and/or microsatellite instability correlate with HIV infection and tumor recurrence after chemoradiation therapy in patients with squamous‐cell carcinoma of the anus.BACKGROUND:The molecular mechanisms leading to the progression of HIV‐related squamous‐cell carcinoma of the anus are poorly understood. In particular, genetic alterations responsible for resistance to chemoradiation have important clinical and functional implications.METHODS:In a case‐control study, we analyzed normal and tumor DNA samples of four patients with squamous‐cell carcinoma of the anus who were successfully treated with chemoradiotherapy and four patients with radio‐resistant squamous‐cell carcinoma of the anus who required abdominoperineal resection for local recurrence. To determine the presence of microsatellite instability, we used the reference panel of five pairs of microsatellite primers recommended for colorectal cancer specimens. These include the microsatellite markers BAT25, BAT26, D5S346 (APC), D2S123 (hMSH2), and D17S250 (P53). In addition, we used microsatellite markers for loss of heterozygosity analyses that were tightly linked to tumor suppressor genes. These included D3S1611 (hMLH1), D17S513 (P53), D18S46 and 18qTA (DCC/SMAD4), D5S107 (APC), and CA5 (hMSH2).RESULTS:There were two HIV‐positive and two HIV‐negative patients in each group. Three HIV‐positive patients (one in the chemoradiotherapy group and two in the nonchemoradiotherapy group) demonstrated loss of heterozygosity. In the chemoradiotherapy group, one HIV‐positive patient demonstrated loss of heterozygosity at the hMLH1 locus. In the nonchemoradiotherapy group, two HIV‐positive patients exhibited a total of four instances of loss of heterozygosity. One tumor had loss of heterozygosity at hMSH2 and DCC/SMAD4; another tumor demonstrated loss of heterozygosity at hMSH2 and APC. Microsatellite instability‐low was found in two HIV‐positive patients. No instances of loss of heterozygosity and microsatellite instability were detected in HIV‐negative patients.CONCLUSION:Loss of heterozygosity and microsatellite instability, which reflect inactivation of tumor‐suppressor genes and genomic instability, occur with increased frequency in HIV‐associated squamous‐cell carcinoma. These data demonstrate for the first time evidence of loss of heterozygosity at the APC and DCC/SMAD4 gene loci in anal carcinoma. Although the findings presented here need to be expanded in a larger study, the recurrent loss of heterozygosity at D2S123, which was demonstrated in HIV‐positive patients with radio‐resistant squamous‐cell carcinoma of the anus, is notable.