1 Supplementary table 1. Pulmonary function tests before allo-HCT and at BOS- 2 diagnosis. Individual pulmonary function tests are displayed before allo-HCT and at the time 3 of diagnosis of BOS. *Pulmonary function tests performed shortly after allo-HCT 4 transplantation is shown for this patient. FEV1, forced expiratory volume in 1 s.; FVC, forced 5 volume capacity; RV, residual volume; TLC total lung capacity; DLCOc SB, diffusion 6 capacity of the lung for carbon monoxide corrected to haemoglobin (single-breath); Allo- 7 HCT, allogeneic hematopoietic transplantation; BOS, bronchiolitis obliterans syndrome; n.d., 8 not done. 9 10 Supplementary table 2. Univariate analysis of clinical factors for developing BOS after 11 reduced-intensity conditioning. Hazard ratios and confidence intervals for clinical factors 12 were estimated by Cox proportional hazards regression model. Last follow-up and death were 13 used as censored observation. 1GvHD prophylaxis with in vivo T-cell depletion includes 14 patients who received CyA/ATG or CyA/alemtuzumab before allo-HCT. 2Controlled disease 15 included complete remission (CR), partial remission (PR), stable disease (SD) and chronic 16 phase of CML (CP). 3Patients with acute GvHD grad II-IV were included. 4cGvHD besides 17 BOS was analysed as a time-dependent covariate. Patients with both limited and extensive 18 cGvHD were included. Allo-HCT, allogeneic hematopoietic cell transplantation; GvHD, 19 graft-versus-host disease; CMV, cytomegalovirus; ATG, anti T-cell globulin; BOS, 20 bronchiolitis obliterans syndrome; HR, hazard ratio. 21 22 Supplementary table 3. Extension and severity of GvHD in patients with BOS. Organs 23 affected and clinical grade of GvHD are shown for patients with BOS. 24 aGvHD, which lasted beyond 100th day of allo-HCT. 2BOS developed in this patient after 25 early cyclosporine withdrawal due to disease progression. 3Patient received interferon alpha 26 due to mixed chimerism before BOS. 4Patient received DLIs due to relapse before BOS. BOS, 27 bronchiolitis obliterans syndrome; DLI, donor lymphocyte infusion. 1 Patient developed 28 29 Supplementary table 4. Univariate analysis of risk factors for developing cGvHD besides 30 BOS after reduced-intensity conditioning. Hazard ratios and confidence intervals were 31 estimated by Cox proportional hazards regression model. 1Patients who did not receive 32 CyA/ATG or CyA/alemtuzumab before allo-HCT were included in this group. 33 disease included complete remission (CR), partial remission (PR), stable disease (SD) and 34 chronic phase of CML (CP). 3Patients with acute GvHD grad II-IV were included. Allo-HCT, 35 allogeneic hematopoietic cell transplantation; GvHD, graft-versus-host disease; cGvHD, 1 2 Controlled 1 chronic graft-versus-host disease; CMV, cytomegalovirus; ATG, anti-T cell globulin; BOS, 2 bronchiolitis obliterans syndrome; HR, hazard ratio. 3 4 Supplementary table 5. Multivariate analysis of risk factors for cGvHD besides BOS 5 after reduced-intensity conditioning. Hazard ratios and confidence intervals were estimated 6 by Cox proportional hazards regression model. Clinical characteristics with a p-value <0.1 in 7 univariate analysis were included in multivariate analysis. 8 CyA/ATG or CyA/alemtuzumab before allo-HCT as GvHD prophylaxis were included in this 9 group. 2 1 Patients who did not receive Patients with acute GvHD grad II-IV were included. Allo-HCT, allogeneic 10 hematopoietic cell transplantation; GvHD, graft-versus-host disease; cGvHD, chronic graft- 11 versus-host disease; ATG, anti T-cell globulin; CyA, cyclosporine A; BOS, bronchiolitis 12 obliterans syndrome; HR, hazard ratio. 13 14 Supplementary table 6. Carbon monoxide diffusion changes after reduced intensity 15 conditioning protocol with fludarabine, carmustine and melphalan. Changes in diffusion 16 capacity of the lungs were analysed by cumulative incidence rates. Event was defined as the 17 first time to achieve hemoglobin-corrected diffusion capacity of carbon monoxide (DLCOc 18 SB) below 60% (A) and below 80 % (B) of predicted value after allo-HCT. Statistical 19 analysis by competing risk regression by Fine and Gray was used. 20 21 Supplementary table 7. Immunosuppression before and after diagnosis of BOS and 22 clinical response regarding FEV1. Patients with BOS were classified based on 23 immunosuppressive treatment at the time of diagnosis and changes in immunosuppression 24 after diagnosis. Response was assessed regarding a decline or an increase in FEV1 in the 25 following pulmonary function test. The number of patients above the total number of patients 26 in each group is shown. BOS, bronchiolitis obstructive syndrome; CyA, cyclosporine A; 27 MMF, Mycophenolate mofetil; FEV1, forced expiratory volume in 1 s. 28 29 30 31 32 33 34 2 1 Supplementary table 1. Pulmonary function tests before allo-HCT and at diagnosis of 2 BOS. Case # FEV1 (% of predicted) AlloHCT BOS FEV1/FVC Ratio (%) AlloHCT BOS RV (% of predicted) AlloHCT BOS TLC (% of predicted) AlloHCT BOS RV/TLC Ratio (%) AlloHCT BOS DLCOc SB (% of predicted) AlloHCT BOS NIH lung score 3 98 69 74 60 102 130 108 107 30 38 n.d. 49 2 5 104 33 84 66 98 160 93 71 28 60 n.d. n.d. 3 8* 85 73 71 64 139 124 106 99 38 37 n.d. 81 1 9 77 57 90 60 107 168 79 110 44 50 n.d. 76 2 13 110 41 79 51 86 154 100 92 26 50 n.d. 61 2 15 90 30 82 47 74 264 87 121 27 70 93 78 3 38 83 68 81 69 106 129 84 86 38 45 82 75 1 39 68 61 82 67 121 140 82 90 30 47 65 50 2 43 81 71 73 66 151 151 100 140 41 42 64 59 2 49 85 41 73 51 152 160 111 68 42 48 68 66 2 56 101 33 82 57 52 162 80 93 24 64 69 58 3 63 76 35 82 61 113 189 84 96 42 61 73 44 3 65 93 50 79 64 94 129 73 107 41 43 77 53 2 77 72 59 88 68 107 121 82 84 43 46 n.d. n.d. 2 87 80 74 70 68 224 135 122 90 49 41 69 67 1 89 94 48 76 59 155 230 107 111 60 62 88 50 2 118 83 47 81 61 127 186 99 113 49 64 75 66 2 127 84 52 78 69 128 151 102 96 45 56 80 56 2 130 72 59 76 60 109 136 85 90 38 45 64 59 2 149 80 46 77 58 155 187 99 95 43 54 71 43 3 164 70 65 74 67 129 121 95 85 51 46 n.d. n.d. 1 184 90 55 78 62 124 196 91 104 42 58 79 73 2 237 70 64 82 69 108 126 85 81 44 54 73 n.d. 1 243 74 60 71 67 97 158 78 112 35 50 68 n.d. 1 Median 83 56 79 63 111 153 92 96 42 50 73 59 Min. 68 30 70 47 52 121 73 68 24 37 64 43 Max. 110 74 90 69 224 264 122 140 60 70 93 81 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 3 1 2 Supplementary table 2. Univariate analysis of risk factors for BOS BOS Clinical characteristics HR 95% CI p-value Patients <55 years at allo-HCT 4.35 1.89, 9.97 0.0005 GvHD prophylaxis without invivo T-cell depletion1 3.13 1.37, 7.14 0.01 Lung disease after allo-HCT Lymphoid malignancies 5.76 2.06 1.35, 24.5 1.10, 3.86 0.02 0.02 Donor related CMV donor status positivity Donor sex (male) Patient sex (male) Disease remission status before allo-HCT (uncontrolled vs. controlled)2 2.31 2.09 2.06 1.73 2.19 1.01, 5.31 0.89, 4.88 0.90, 4.73 0.77, 3.87 0.74, 6.5 0.05 0.09 0.09 0.18 0.16 Disease remission status before allo-HCT (untreated vs. controlled)2 0.64 0.14, 2.87 0.56 Patients with prior lung disease before allo-HCT 0.64 0.27, 1.50 0.30 Current or previous smokers 1.25 0.49, 3.15 0.64 CMV patient status positivity 0.83 0.36, 1.91 0.67 CMV reactivation 0.52 0.22, 1.22 0.16 HLA (A, B, DQB1, DRB1) difference HLA C difference 0.97 0.23, 4.12 0.97 0.67 0.20, 2.27 0.52 Acute GvHD3 cGvHD besides BOS4 0.99 2.00 0.42, 2.34 0.78, 5.00 0.99 0.14 3 4 5 6 7 8 9 10 11 12 13 14 15 4 1 Supplementary table 3. Extension and severity of GvHD in patients with BOS aGvHD Case # Organs 3 - cGvHD clinical grade - Organs Skin, gut, liver, wasting, eye, DLI-induced GvHD clinical grade Organs clinical grade 3 - - musculoskeletal 51 Skin, liver, eye, 3 - - - - wasting 82 Skin, gut 2 Skin, gut, eye, sicca-syndrome 2 - - 9 - - Skin, liver, scleroderma, eye, 2 - - gut 13 Skin 1 - - - - 15 - - Gut, liver, 3 - - immunothrombopenia 38 - - Skin 2 - - 39 Skin, gut 2 Skin, liver, eye 3 - - 43 Skin 2 Skin, gut, wasting, alopecia, 3 - - 2 - - scleroderma, sicca-syndrome, eye, dyspigmentation 49 Skin, gut 4 Liver, gut, musculoskeletal, scleroderma, eye 56 Skin 2 Gut, liver, sicca-syndrome 2 - - 63 Skin 1 Skin, gut, liver 3 - - 65 Skin 1 Skin, gut, liver 2 - - 77 Skin, liver 2 Skin, eye, liver, 3 - - 3 - - musculoskeletal 87 - - Gut, eye, liver, musculoskeletal, wasting, scleroderma 89 - - Skin 3 - - 118 - - - - Skin, wasting, gut 2 127 - - Skin, gut, wasting 3 - - 130 Skin 1 Skin, gut, eye, sicca-syndrome 3 - - 149 - - - - Skin, liver, gut 3 1643 - - - - - - 184 Skin, gut 1 Skin, liver, gut 3 - - 237 - - Gut 1 Skin, gut 1 2434 Skin, liver 3 Liver 1 - - 2 3 4 5 5 1 2 Supplementary table 4. Univariate analysis of risk factors for cGvHD besides BOS. cGvHD besides BOS Clinical characteristics HR 95% CI p-value Patients <55 years at allo-HCT 1.14 0.78, 1.65 0.51 GvHD prophylaxis without invivo T-cell depletion1 Lung disease after allo-HCT 2.28 1.57, 3.31 <0.0001 1.44 0.99, 2.09 0.05 Lymphoid malignancies 1.10 0.79, 1.56 0.56 Donor related CMV donor status positivity Donor sex (male) Patient sex (male) Disease remission status before allo-HCT (uncontrolled vs. controlled)2 1.03 1.02 1.23 1.14 1.33 0.73, 1.46 0.73, 1.44 0.88, 1.73 0.81, 1.61 0.86, 2.06 0.85 0.89 0.23 0.45 0.20 Disease remission status before allo-HCT (untreated vs. controlled)2 1.09 0.66, 1.81 0.72 Patients with prior lung disease before allo-HCT 1.45 1.03, 2.04 0.03 Current or previous smokers 1.12 0.76, 1.66 0.55 CMV patient status positivity 0.81 0.57, 1.16 0.25 CMV reactivation 0.95 0.68, 1.34 0.79 HLA (A, B, DQB1, DRB1) difference HLA C difference 1.27 0.75, 2.14 0.37 1.35 0.90, 2.03 0.15 Acute GvHD3 2.00 1.41, 2.82 <0.0001 3 4 5 6 7 8 9 10 11 12 13 14 15 16 6 1 2 3 Supplementary table 5. Multivariate analysis of risk factors for cGvHD besides BOS after reduced-intensity conditioning and allo-HCT. cGvHD besides BOS Clinical characteristics HR 95% CI p-value GvHD prophylaxis without invivo T-cell depletion1 Acute GvHD2 1.89 1.23, 2.82 0.002 1.65 1.13, 2.41 0.009 Patients with prior lung disease before allo-HCT 1.56 1.10, 2.20 0.01 Lung disease after allo-HCT 1.38 0.95, 2.01 0.09 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 7 1 2 3 4 5 Supplementary table 6. Carbon monoxide diffusion changes after reduced intensity conditioning protocol with fludarabine, carmustine and melphalan. A. Cumulative incidence rates of DLCOc SB < 60 % of predicted values after allo-HCT ≥ 55 years < 55 years 6 7 8 9 10 11 Time after allo-HCT Cumulative incidence rate 95% CI Cumulative incidence rate 95% CI 1 year 40.1 % 30.0, 53.8 % 18.5 % 13.7, 24.9 % 5 year 41.7 % 31.4, 55.4 % 21.8 % 16.6, 28.6 % 10 year 41.7 % 31.4, 55.4 % 23.8 % 17.8, 31.9 % B. Cumulative incidence rates of DLCOc SB < 80 % of predicted after allo-HCT ≥ 55 years < 55 years Time after allo-HCT 1 year Cumulative incidence rate 53.2 % 3 year 5 year 95% CI 42.2, 66.9 % Cumulative incidence rate 41.1 % 95% CI 34.5, 48.9 % 59.9 % 48.5, 73.9 % 50.3 % 43.2, 58.4 % 64.2 % 51.8 79.6 % 51.4 % 44.2, 59.8 % 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 8 1 2 3 Supplementary table 7. Impact of immunosuppression before and after diagnosis of BOS on clinical response regarding FEV1. n/total Patients without immunosuppression before BOS 9/24 No change of immunosuppression after BOS 6/9 Decline of FEV1 > 10% Stabilization Improvement of FEV1 > 10% Increase of immunosuppression after BOS Decline of FEV1 > 10% Stabilization Improvement of FEV1 > 10% 3/9 1 0 2 15/24 Reduction in immunosuppression after BOS 5/15 Decline of FEV1 > 10% Stabilization 1 2 Improvement of FEV1 > 10% 2 Inhalative beta-agonists Oral steroids Inhalative steroids Oral steroids, CyA Oral steroids, CyA Oral steroids, CyA and MMF Oral steroids, CyA Oral steroids, MMF 4/15 Decline of FEV1 > 10% 2 Stabilization Improvement of FEV1 > 10% 1 1 Increase in immunosuppression after BOS Treatment employed/increased after BOS 1 3 2 Patients with immunosuppression before BOS No change in immunosuppression after BOS Treatment before BOS Oral steroids Oral steroids, CyA and MMF CyA CyA 6/15 Decline of FEV1 > 10% Stabilization 1 2 Improvement of FEV1 > 10% 3 Oral steroids and CyA Oral steroids and CyA Oral steroids and CyA Oral steroids and CyA Oral steroids and CyA Oral steroids Oral steroids Oral steroids Oral steroids Oral steroids Oral steroids Oral steroids and CyA 4 5 6 9