This phase I trial studies how well biomarker-guided ruxolitinib works for the prevention of chronic graft versus host disease (GVHD) in patients that have undergone allogeneic hematopoietic cell transplant (HCT). Allogeneic HCT is the most effective therapy for patients with high-risk blood and bone marrow malignancies. GVHD is a disease caused when cells from a donated stem cell graft attack the normal tissue of the transplant patient. Symptoms include jaundice, skin rash or blisters, a dry mouth, or dry eyes. In chronic GVHD (cGVHD), symptoms occur more than three months after transplantation. Despite significant advances in how allogeneic HCTs are conducted, cGHVD remains a major limitation to the long-term success of the transplant and can impact patients' quality of life post-transplant. Checking GVHD biomarkers in patients' blood after allogeneic HCT may help doctors predict how likely the patient is to develop cGVHD. This information can be used to help guide patients with high levels to receive cGVHD preventative therapy with ruxolitinib. Ruxolitinib works by blocking some of the enzymes that are needed for the development of cGVHD, which may be an effective way to prevent cGVHD in patients with high levels of GVHD biomarkers.

PRIMARY OBJECTIVES:

I. To assess the safety and feasibility of ruxolitinib administration in patients with elevated levels of chronic GVHD biomarkers at day +100 after allogeneic hematopoietic cell transplantation (HCT). (Safety lead-in) II. Evaluate the efficacy of ruxolitinib in preventing chronic GVHD by assessing 1-year moderate-to-severe cGVHD-free survival (CGFS) defined as first occurrence of moderate to severe chronic GVHD or death, whichever occurs first, after the first dose of ruxolitinib. (Expansion cohort)

SECONDARY OBJECTIVES:

I. Assess the overall survival (OS) at 1 and 2 years from enrollment and immunosuppression-free survival at 1-year from enrollment.

II. Estimate cumulative incidence of relapse and non-relapse mortality (NRM) at 1 and 2 years from enrollment.

III. Cumulative incidence and grading of chronic GVHD of all grades and moderate-to severe at 1 and 2 years from enrollment.

IV. Preliminary estimate of chronic GVHD-free and relapse-free (CRFS) at 1-year post-enrollment.

V. Cumulative incidence of severe infections requiring hospitalization at 1 and 2 years from enrollment.

VI. Quality of life assessment using Patient-Reported Outcomes Measurement Information System Functional Assessment of Cancer Therapy-Bone Marrow Transplant (FACT-BMT).

VII. Further evaluation of safety of ruxolitinib for chronic GVHD prophylaxis. (Patients in the expansion cohort who are taking ruxolitinib only)

EXPLORATORY OBJECTIVES:

I. Assess levels of chronic GVHD biomarkers and other inflammatory cytokines at 6 months and 1-year post-HCT and correlate elevated levels of serum/plasma biomarkers of chronic GVHD with pre-HCT risk factors for GVHD and subsequent development of GVHD.

II. Longitudinal evaluation of the presence and levels of T cells and other immune cell subsets.

III. Assess changes in microbiome from the time of screening to 3 months after enrolment and at the time of cGVHD diagnosis.

OUTLINE: Patients undergo blood sample collection and GHVD biomarker analysis on day +100 post-HCT. Patients with elevated levels of GVHD biomarkers are assigned to arm I and patients with low levels of GVHD biomarkers are assigned to arm II.

ARM I: Starting between days +105 and +130 post-HCT, patients receive ruxolitinib orally (PO) twice daily (BID) on days 1-28 of each cycle. Cycles repeat every 28 days for up to 12 cycles in the absence of disease progression or unacceptable toxicity. Patients also undergo additional blood sample collection throughout the trial.

ARM II: Starting between days +105 and +130 post-HCT, patients receive standard of care (SOC) treatment for up to 1 year in the absence of disease progression or unacceptably toxicity. Patients also undergo additional blood sample collection throughout the trial.

After completion of study treatment, patients in arm I are followed up at 30 days, months 15, 18, and 24, and at the time of cGVHD diagnosis, if applicable. Patients in arm II are followed up at months 18 and 24 and at the time of cGVHD diagnosis, if applicable.

Inclusion Criteria:

• PRE-SCREENING: Documented informed consent of the participant and/or legally authorized representative

  • Assent, when appropriate, will be obtained per institutional guidelines

• PRE-SCREENING: Agreement to allow the use of archival tissue from diagnostic tumor biopsies

  • If unavailable, exceptions may be granted with study principal investigator (PI) approval

• PRE-SCREENING: Age: ≥ 18 years

• PRE-SCREENING: Karnofsky performance status ≥ 80

• PRE-SCREENING: Patients must have undergone allogeneic hematopoietic cell transplantation with peripheral blood stem cells as graft source. Note: Patients receiving manipulated graft are not included

• PRE-SCREENING: Morphologic remission per day +30 bone marrow

• PRE-SCREENING: Any conditioning regimen (myeloablative, reduce intensity/non-myeloablative conditioning) is allowed

• PRE-SCREENING: Any GVHD prophylaxis (tacrolimus-sirolimus, tacrolimus-methotrexate, or post-transplant cyclophosphamide) is allowed

• PRE-SCREENING: Life expectancy of more than 6 months

• PRE-SCREENING: Absolute neutrophil count (ANC) > 1000/mm^3 (to be performed between day +70 and +100 after HCT unless otherwise stated)

• PRE-SCREENING: Hemoglobin ≥ 8.0 gm/dL (to be performed between day +70 and +100 after HCT unless otherwise stated)

• PRE-SCREENING: Platelets ≥ 50,000/mm^3 (to be performed between day +70 and +100 after HCT unless otherwise stated)

  • Note: Patients with lower counts can enroll if infection cytomegalovirus (CMV)/human herpesvirus 6 (HHV6), etc. is being treated actively

• PRE-SCREENING: Total bilirubin ≤ 1.5 X upper limit of normal (ULN) (unless has Gilbert's disease) (to be performed between day +70 and +100 after HCT unless otherwise stated)

• PRE-SCREENING: Aspartate aminotransferase (AST) =< 3.0 x ULN (to be performed between day +70 and +100 after HCT unless otherwise stated)

• PRE-SCREENING: Alanine aminotransferase (ALT) =< 3.0 x ULN (to be performed between day +70 and +100 after HCT unless otherwise stated)

• PRE-SCREENING: Glomerular filtration rate (GFR) ≥ 50 ml/min (to be performed between day +70 and +100 after HCT unless otherwise stated)

• PRE-SCREENING: Women of childbearing potential (WOCBP): negative urine or serum pregnancy test (to be performed between day +70 and +100 after HCT unless otherwise stated)

  • If the urine test is positive or cannot be confirmed as negative, a serum pregnancy test will be required

• PRE-SCREENING: Agreement by females and males of childbearing potential to use an effective method of birth control or abstain from heterosexual activity for the course of the study through at least 3 months after the last dose of protocol therapy

  • Childbearing potential defined as not being surgically sterilized (men and women) or have not been free from menses for > 1 year (women only)

• AFTER DAY +100 TEST RESULTS PATIENTS WITH MODERATE TO HIGH-RISK cGVHD (TREATMENT ARM): Documented informed consent of the participant and/or legally authorized representative

  • Assent, when appropriate, will be obtained per institutional guidelines

• AFTER DAY +100 TEST RESULTS PATIENTS WITH MODERATE TO HIGH-RISK cGVHD (TREATMENT ARM): Elevated serum/plasma levels of ST2, CXCL9, MMP-3, and OPN as indicated by moderate or severe risk of chronic GVHD in the test results

• AFTER DAY +100 TEST RESULTS PATIENTS WITH MODERATE TO HIGH-RISK cGVHD (TREATMENT ARM): No use of ruxolitinib or other Jak inhibitors in the past 14 days

• AFTER DAY +100 TEST RESULTS PATIENTS WITH MODERATE TO HIGH-RISK cGVHD (TREATMENT ARM): Morphologic remission per day +100 bone marrow

• AFTER DAY +100 TEST RESULTS PATIENTS WITH MODERATE TO HIGH-RISK cGVHD (TREATMENT ARM): Adequate hematopoietic recovery (hemoglobin [Hgb] ≥ 8 g/dL, platelets [PLT] ≥ 50K/ mm^3)

• AFTER DAY +100 TEST RESULTS PATIENTS WITH MODERATE TO HIGH-RISK cGVHD (TREATMENT ARM): Negative serum or urine pregnancy test (female participants with childbearing potential only)

• AFTER DAY +100 TEST RESULTS PATIENTS WITH MODERATE TO HIGH-RISK cGVHD (TREATMENT ARM): Absence of active infection not responding to antibiotics

• AFTER DAY +100 TEST RESULTS PATIENTS WITH MODERATE TO HIGH-RISK cGVHD (TREATMENT ARM): Absence of progressive acute GVHD. Note: prednisone administration (flat dose of < 0.25 mg/kg) is allowed. Patients receiving any other medication to control active/progressive GVHD will be excluded

• AFTER DAY +100 TEST RESULTS PATIENTS WITH MODERATE TO HIGH-RISK cGVHD (TREATMENT ARM): Absence of any clinically significant uncontrolled sickness

• AFTER DAY +100 TEST RESULTS PATIENTS WITH LOW-RISK cGVHD (CONTROL ARM): Documented informed consent of the participant and/or legally authorized representative

  • Assent, when appropriate, will be obtained per institutional guidelines

• AFTER DAY +100 TEST RESULTS PATIENTS WITH LOW-RISK cGVHD (CONTROL ARM): Low serum/plasma levels of ST2, CXCL9, MMP-3, and OPN as indicated by low risk of chronic GVHD in the test results

• AFTER DAY +100 TEST RESULTS PATIENTS WITH LOW-RISK cGVHD (CONTROL ARM): No use of ruxolitinib or other Jak inhibitors in the past 14 days

• AFTER DAY +100 TEST RESULTS PATIENTS WITH LOW-RISK cGVHD (CONTROL ARM): Morphologic remission per day +100 bone marrow

• AFTER DAY +100 TEST RESULTS PATIENTS WITH LOW-RISK cGVHD (CONTROL ARM): Adequate hematopoietic recovery (Hgb ≥ 8 g/dL, PLT ≥ 50K/ mm^3)

• AFTER DAY +100 TEST RESULTS PATIENTS WITH LOW-RISK cGVHD (CONTROL ARM): Negative serum or urine pregnancy test (female participants with childbearing potential only)

• AFTER DAY +100 TEST RESULTS PATIENTS WITH LOW-RISK cGVHD (CONTROL ARM): Absence of active infection not responding to antibiotics

• AFTER DAY +100 TEST RESULTS PATIENTS WITH LOW-RISK cGVHD (CONTROL ARM): Absence of progressive acute GVHD. Note: prednisone administration (flat dose of < 0.25 mg/kg) is allowed. Patients receiving any other medication to control active/progressive GVHD will be excluded

• AFTER DAY +100 TEST RESULTS PATIENTS WITH LOW-RISK cGVHD (CONTROL ARM): Absence of any clinically significant uncontrolled sickness

Exclusion Criteria:

• PRE-SCREENING: Prior chemotherapy < 14 days prior to study biospecimen collection on day +100 post-HCT
• PRE-SCREENING: Previous use of ruxolitinib or other JAK-inhibitors is allowed but administration should be stopped for at least 14 days prior to enrollment. Note: Previous use of Jak inhibitors before enrollment (including the pre-HCT period) should be recorded
• PRE-SCREENING: History of allergic reactions attributed to compounds of similar chemical or biologic composition to study agent
• PRE-SCREENING: Active/progressive acute GVHD at the time of screening. Prednisone administration (flat dose of < 0.25 mg/kg) is allowed. Patients receiving any other medication to control active/progressive GVHD will be excluded
• PRE-SCREENING: Patients with history of major adverse cardiovascular event (MACE)/other thrombosis (myocardial infarction [MI]/stroke and pulmonary embolism [PE]/deep vein thrombosis [DVT]) in the past 6 months
• PRE-SCREENING: Patients with a history of tuberculosis
• PRE-SCREENING: Clinically significant uncontrolled illness
• PRE-SCREENING: Active infection not responding to antibiotics
• PRE-SCREENING: Other active malignancy. Patients with a prior or concurrent malignancy whose natural history or treatment does not have the potential to interfere with the safety or efficacy assessment of the investigational regimen are eligible for this trial
• PRE-SCREENING: Females only: Pregnant or breastfeeding
• PRE-SCREENING: Any other condition that would, in the investigator's judgment, contraindicate the patient's participation in the clinical study due to safety concerns with clinical study procedures
• PRE-SCREENING: Prospective participants who, in the opinion of the investigator, may not be able to comply with all study procedures (including compliance issues related to feasibility/logistics)