Autologous Stem Cell Transplantation in Patients With Systemic Sclerosis

The purpose of this study is to determine whether a regimen of high-dose immunoablative therapy will demonstrate safety that is consistent or improved with other published regimens in SSc patients, while maintaining a treatment effect.

Cohort 1: Children, Adolescents and Young Adults (Cohort 1) Inclusion: Individuals must meet all the following criteria to be eligible for this study. 1. Patient, parent, or legal guardian must have given written informed consent. For patients ≥ 168 years of age who are developmentally able, assent or affirmation will be obtained. 2. Age 8-24, inclusive, at time of consent. 3. Diagnosed with Systemic Sclerosis (SSc) at the age of ≤19. 4. Failure to respond, specifically no improvement or progression of disease, to at least 2 disease-modifying antirheumatic drugs (DMARDS) within 12 months of consent with any of the following conditions: 1. Progression of skin thickening over the past 6 months or Modified Rodnan skin score (mRSS) ≥ 20 2. Progression of ILD within 18 months prior to consent. Progression to be determined by either of the following: * CT scan showing increased ground glass opacities or reticulations OR * Pulmonary function testing (PFTs) showing a decrease in FVC% or DLCO% predicted value of ≥10%. 3. Myositis - CPK \> 2x upper limit of normal or MRI consistent with myositis 4. Childhood Myositis Assessment Score \< 30 5. Arthritis 6. Digital tip ulcerations 5. Cardiology clearance to undergo stem cell transplantation (documented in subject's medical chart) 6. Negative for human immunodeficiency virus (HIV), hepatitis B virus and hepatitis C virus, all confirmed by PCR testing. 7. Negative pregnancy test for females. who have reached menarche. 87\. All females of childbearing potential and sexually active males must agree to use an FDA approved method of birth control for up to 24 months after BMT or for as long as they are taking any medication that may harm a pregnancy, an unborn child or may cause a birth defect. Exclusion: Individuals who meet any of these criteria are not eligible for this study. 1. FVC \2x upper limit of normal. 10. Evidence of moderate to severe periportal fibrosis, determined by liver biopsy, if applicable. 11. Active, uncontrolled infection that would be a contraindication to safe use of high-dose immunosuppressive therapy or cyclophosphamide. 12. Hematologic abnormalities as defined by any of the following peripheral blood counts: 1. ANC \< 1500 cell/µL. 2. Platelets \< 100,000 cells/ µL. 3. Hemoglobin \< 9.0 g/dL. 13. Evidence of myelodysplasia (MDS), confirmed by bone marrow aspirate, if applicable. 14. Malignancy within 2 years prior to enrollment, excluding adequately treated squamous cell cancer, basal cell carcinoma or carcinoma in situ. Treatment should have been completed with cure/remission status documented for at least 2 years, with the exception of hormonal therapy for breast cancer. 15. Females who are pregnant or who are lactating. 16. Tobacco use, by subject admission, within previous 4 weeks of time of consent. 17. History of sensitivity to murine proteins or E. coli proteins. 18. Known history of substance abuse, determined by medical record or subject admission, within 6 months of time of consent. 19. Patient with systemic reaction to anti-thymocyte globulin or any other equine gamma globulin preparation 20. Past or current medical problems or findings from physical examination or laboratory testing that are not listed above, which, in the opinion of the investigator, may pose additional risks from participation in the study, may interfere with the participant's ability to comply with study requirements or that may impact the quality or interpretation of the data obtained from the study.