This research study is a Pilot Study. Pilot studies are conducted to see if it is practical to do this type of research ona larger scale in the future. The pilot part of the study is to assess the possibility of using pencil beam proton radiation to treat your type of cancer. Proton radiation is used for many other types of malignancies, but its use for the treatment of anal cancer has been limited. The treatment is still being studied as research doctors are trying to find out more about its use in the treatment of anal cancer. Proton beam radiation therapy is an FDA approved radiation delivery system.

You are being asked to participate in this study because you have cancer in the anal canal. Conventional radiation therapy with photons in combination with 5-FU and mitomycin-C is used as standard treatment for many patients with anal cancer.

In this research study we are looking at another type of radiation called proton radiation, which is known to spare surrounding tissue and organs from radiation. Proton radiation delivers radiation to the area requiring radiation but delivers no dose beyond the region requiring treatment. There are several techniques that can be used to deliver proton radiation therapy. One of the newer techniques, called pencil beam scanning, allows for more accurate delivery of radiation to your tumor and further reduces the amount of normal tissue exposed to radiation. Most proton patients are treated with a number of beams that study doctors conform to the shape of your tumor. Pencil beam scanning delivers radiation with a single, narrow proton beam that is swept over the area of your tumor. This may reduce side effects that patients would normally experience with conventional radiation therapy or other means of delivering proton radiation therapy, and also minimizes treatment time.

In this research study, we are evaluating the effectiveness of using pencil beam proton radiation delivered to reduce side effects associated with radiation treatment.

If you agree to participate in this study, you will be asked to undergo some screening tests or procedures to confirm that you are eligible. Many of these tests and procedures are likely to be part of regular cancer care and may be done even if it turns out that you do not take part in the research study. If you have had some of these tests or procedures recently, they may or may not have to be repeated. The screening will include the following: a medical history, physical examination, biopsy of your tumor, anal and groin exam, archival tumor tissue, CT or PET-CT, MRI, blood tests and a serum pregnancy test. If these tests show that you are eligible to participate in the research study, you will begin the study treatment. If you do not meet the eligibility criteria, you will not be able to participate in this research study.

Proton Radiation will be delivered daily for 5-6 weeks, depending on the dose prescribed by your physician. Treatment is delivered (Monday-Friday) for 5 days (no weekends or holidays). Each treatment will require that you lie on a table for 25-30 minutes.

You will receive radiation therapy as an outpatient at the Massachusetts General Hospital.

You will start receiving chemotherapy within 5 days of starting radiation treatment. The day you start chemotherapy will be considered Day 1.

You will receive Mitomycin-C on Days 1 and 29 of chemotherapy. Mitomycin-C will be delivered via IV infusion over a period of 10-30 minutes.

You will receive 5-fluorouracil on Day 1 and 29 of chemotherapy. You will be fitted with an ambulatory infusion pump that will administer 5-FU via IV infusion continuously over a period of 96 hours. The infusion pump will be about the size of a paperback book that can fit into a front-pack or "fanny-pack" around your waist. This pump will be connected to your body. The nurses in the infusion room will start the pump and disconnect it after 4 days.

At your 6 and 12 week follow up visits, a physical examination and the tests and procedures you receive will tell your study doctor whether your disease has gotten better, worse or stayed the same.

If your cancer has gotten better, you will continue to be monitored at your follow up visits.

If your cancer is suspected to have gotten worse, you will need to have a biopsy to confirm. If the biopsy is negative, you will need to come back for re-evaluation at 16 weeks (about 4 months) after completing radiation therapy.

If the biopsy confirms that your cancer has gotten worse, your doctor will recommend that you have surgery for the removal of your tumor.

If your cancer has stayed the same, your doctor will recommend that you have additional procedures done to develop a plan for treatment.

After you complete radiation therapy, you will be followed for up to 5 years.

Inclusion Criteria:

• Histologically or cytologically confirmed invasive primary squamous, basaloid or cloacogenic carcinoma of the anal canal
• Life expectancy of at least 3 months

Exclusion Criteria:

• Prior abdominopelvic radiotherapy
• Prior systemic therapy for anal cancer
• Pregnant or breastfeeding
• Receiving other investigational agents
• History of allergic reactions attributed to compounds of similar chemical or biologic composition to mitomycin-C or 5-fluorouracil
• Prior surgery for cancer of the anus that removed all macroscopic anal cancer
• Uncontrolled intercurrent illness
• AIDS based on current CDC definition
• Other immunocompromised status
• Individuals with a history of a different malignancy are ineligible except for the following circumstances: disease-free for at least 5 years or at low risk for recurrence or cervical cancer in situ, and basal cell or squamous cell carcinoma of the skin