Autologous Stem Cell Transplantation in Patients With Systemic Sclerosis

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 \<35%, determined by pulmonary function tests for those able to complete spirometry adequately (per investigator's determination) 2. O2 sat \<92% at rest in room air 3. Estimated CrCl \<40 mL/min,using Cockcroft-Gault formula based on actual body weight. 4. Active, untreated SSc renal crisis at the time of consent. 5. ALT \> 4x upper limit of normal. 6. Active, uncontrolled infection that would be a contraindication to safe use of high-dose immunosuppressive therapy or cyclophosphamide. 7. 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. 8. 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. 9. Past or current medical problems or findings from medical history, 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. Cohort 2 for Adults 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 ≥ 16 years of age who are developmentally able, assent or affirmation will be obtained. 2. Age 1618-705560, inclusive, at time of consent. Patients up to age 24, diagnosed with SSc at age ≤ 19, will be included in Cohort 1 and evaluated according to the Pediatric and Young Adult criteria listed in sections 3.1.1 and 3.1.2. 3. Diagnosed with Systemic Sclerosis (SSc), according to the 2013 ACR/EULAR criteria (van den Hoogen et al., 2013). 4. All patients must meet either the following skin or ILD criteria. Disease duration is defined as time from first non-Raynaud symptom. Skin Criteria: Diffuse SSc, defined by presence of proximal skin thickening and: A. If disease duration is of \<2 years, patients must have a calculated mortality risk prediction score which places them in the intermediate or high- risk category (Domsic et al., 2016). Refer to Appendix 5 for calculation criteria. B. If disease duration is of \>2 years, patients must have evidence of active cutaneous disease based upon 1) a worsening Modified Rodnan Skin Score (MRSS) in the preceding three months or 2) the presence of palpable tendon friction rubs. ILD Criteria: A. The presence of recognized fibrosis on imaging of \<2 years AND either \> 10% of lung involvement by CT scan or FVC% pred \<80% or B. Fibrosis on imaging of any duration with a decline in FVC% pred of ≥10% over the preceding 12-18 months. 5. Negative for human immunodeficiency virus (HIV), hepatitis B virus and hepatitis C virus, all confirmed by PCR testing. 6. Negative pregnancy test for females. 7. 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 Criteria Individuals who meet any of these criteria are not eligible for this study. 1. Moderate to severe cardiac involvement defined by any of the following: 1. New York Heart Association classification of heart failure ≥3. 2. Left ventricular ejection fraction (LVEF) \<50% as determined by cardiac MRI. 3. Significant pulmonary hypertension, for subjects ≥ 18 years of age, defined as mean PASP ≥30 mmHg determined by right heart catheterization, or for subjects ≤ 17 years of age, defined as mean PASP \>45 mmHg, determined by echocardiogram. 4. Atrial tachycardia, atrial fibrillation or atrial flutter of ≥1-minute duration, determined by electrocardiogram (EKG) or, cardiac event monitor and/or im