Background
Methods
Study design and study populations
Clustering methodology
Initial clustering
GLMnet classification
Biologic sample acquisition and analysis
Bronchoscopic sampling and transcriptomic analysis
Induced sputum (IS) sampling and analysis
Serum sampling and analysis
Airway type-2 inflammation high and low phenotype
Phadiatop® testing
Results
The ADEPT clinical phenotypes
Variablea
| Healthy (n = 31) | Cluster A1 (n = 28) | Cluster A2 (n = 44) | Cluster A3 (n = 49) | Cluster A4 (n = 35) |
P-value |
---|---|---|---|---|---|---|
Mean [Geo.Mean] ± SD | ||||||
FEV1, pre-bd, % predicted | 106.1 ± 13.5 | 103.5 ± 11.8 | 77.4 ± 10.2 | 76.5 ± 9.8 | 66.8 ± 11.5 |
<10
−6
|
FVC, pre-bd, % predicted | 108.8 ± 13.6 | 111.1 ± 10.8 | 100.0 ± 12.0 | 88.2 ± 9.8 | 88.7 ± 12.0 |
<10
−6
|
FEV1/FVC, pre-bd | 0.84 ± 0.06 | 0.80 ± 0.08 | 0.65 ± 0.08 | 0.72 ± 0.08 | 0.64 ± 0.11 |
<10
−6
|
bd reversibility, % change FEV1 | 4.1 ± 3.6 | 10.2 ± 6.3 | 17.6 ± 7.0 | 14.8 ± 9.6 | 32.2 ± 21.9 |
<10
−6
|
ACQ7 | na | 0.5 ± 0.5 | 1.1 ± 0.5 | 1.2 ± 0.5 | 2.6 ± 0.9 |
<10
−6
|
AQLQ | na | 6.0 ± 1.0 | 6.0 ± 0.6 | 5.9 ± 0.8 | 4.1 ± 1.1 |
<10
−6
|
FENO, ppb [Geo.Mean] | na | 35.2 + 28.1/-15.6 | 43.8 + 36.7/-20.0 | 16.4 + 9.7/-6.1 | 37.7 + 47.8/-21.1 |
<10
−6
|
Blood eosinophils, ×1000/ul [Geo.Mean] | 0.112 + 0.106/-0.054 | 0.150 + 0.168/-0.079 | 0.299 + 0.234/-0.131 | 0.131 + 0.100/-0.057 | 0.237 + 0.286/-0.130 |
<10
−6
|
PC20, mg/ml [Geo.Mean] | na | 2.8 + 11.3/-2.2 | 0.3 + 1.4/-0.3 | 2.2 + 7.0/-1.7 | 0.6 + 2.8/-0.5 |
<10
−6
|
Blood neutrophils, ×1000/ul [Geo.Mean] | 3.47 + 1.50/-1.05 | 3.26 + 1.03/-0.78 | 3.83 + 1.56/-1.11 | 3.93 + 1.65/-1.16 | 3.73 + 1.29/-0.96 | 0.0999 |
Blood WBC, ×1000/ul [Geo.Mean] | 6.01 + 1.72/-1.34 | 6.01 + 1.43/-1.16 | 6.42 + 2.04/-1.55 | 6.32 + 2.12/-1.59 | 6.49 + 1.38/-1.14 | 0.6676 |
Sputum neutrophils, % of WBCb
| 53.6 ± 20.1 | 41.4 ± 33.0 | 42.2 ± 25.8 | 63.1 ± 23.8 | 55.9 ± 21.7 |
0.0053
|
Sputum eosinophils, % of WBC [Geo.Mean]b
| 0.4 + 0.8/-0.3 | 1.0 + 4.7/-0.8 | 7.1 + 18.7/-5.1 | 0.9 + 3.5/-0.7 | 3.5 + 10.5/-2.6 |
<10
−6
|
Serum IgE, RFU [Geo.Mean] | 1.0 + 2.1/-0.7 | 7.6 + 29.5/-6.0 | 12.6 + 27.5/-8.6 | 7.1 + 20.3/-5.3 | 14.4 + 33.2/-10.0 | 0.0388 |
Age, years | 31.5 ± 9.1 | 32.5 ± 14.3 | 42.4 ± 12.0 | 43.0 ± 11.8 | 46.8 ± 13.3 |
0.0002
|
Age of onset, years | na | 15.4 ± 13.9 | 21.0 ± 14.0 | 22.7 ± 15.2 | 23.7 ± 18.6 | 0.1537 |
Body Mass Index (kg/m2) | 24.7 ± 3.3 | 25.2 ± 3.2 | 25.7 ± 3.6 | 26.9 ± 3.7 | 26.6 ± 4.1 | 0.1622 |
Percent of clinical cluster | ||||||
Mild, no ICS (%) | na | 93% | 16% | 27% | 11% | |
Moderate, low-medium ICS (%) | na | 7% | 52% | 43% | 26% |
<10
−6
|
Severe, high ICS (%) | na | 0% | 32% | 31% | 63% | |
Male (%) | 65% | 46% | 48% | 43% | 43% | 0.9500 |
Atopic, Phadiatop positive (%) | 0% | 79% | 91% | 69% | 71% |
0.0670
|
Serum IgE-high, >95th %ile of controls (%) | 0% | 71% | 86% | 69% | 83% |
0.1692
|
Sputum Pauci (Eos < %3, PMN < 60%) (%)b
| 45% | 48% | 16% | 36% | 21% | |
Sputum Neutr. (Eos < 3, PMN > =60%) (%)b
| 50% | 30% | 13% | 43% | 17% |
0.0012
|
Sputum Mix (Eos ≥ 3%, PMN > =60%) (%)b
| 0% | 0% | 13% | 14% | 29% | |
Sputum Eos. (Eos ≥ 3%, PMN < 60%) (%)b
| 5% | 22% | 59% | 7% | 33% | |
FENO ≥ 35 ppb (%) | na | 50% | 61% | 4% | 44% |
<10
−6
|
Blood eosinophils ≥ 300/ul (%) | 6% | 21% | 50% | 6% | 34% |
2.9 x10
−5
|
FENO ≥ 35 ppb OR Blood eos. ≥ 300/ul (%) | na | 57% | 84% | 10% | 57% |
<10
−6
|
Biopsy CCL26-high (%)c
| 0% | 56% | 42% | 16% | 31% | 0.0515 |
Variablea
| Phenotype A2 (n = 37) | Phenotype A3 (n = 36) | Phenotype A4 (n = 31) |
P-value |
---|---|---|---|---|
Mean [Geo.Mean] ± SD | ||||
FEV1, pre-bd, % predicted | 74.6 ± 8.2 | 73.8 ± 9.8 | 65.5 ± 11.5 |
3.0 x10
−4
|
FVC, pre-bd, % predicted | 97.4 ± 9.8 | 87.4 ± 10.2 | 88.6 ± 12.2 |
2.0 x10
−4
|
FEV1/FVC, pre-bd | 0.64 ± 0.08 | 0.70 ± 0.07 | 0.62 ± 0.10 |
9.0 x10
−4
|
bd reversibility, % change FEV1 | 17.3 ± 6.6 | 16.5 ± 10.5 | 32.0 ± 21.5 |
1.1 x10
−5
|
ACQ-7 | 1.1 ± 0.4 | 1.3 ± 0.6 | 2.6 ± 0.9 |
<10
−6
|
AQLQ | 6.0 ± 0.6 | 5.8 ± 0.9 | 4.1 ± 1.2 |
<10
−6
|
FENO, ppb [Geo.Mean] | 42.0 + 35.9/-20.9 | 15.6 + 8.8/-7.9 | 37.1 + 47.9/-17.8 |
<10
−6
|
Blood eosinophils, ×1000/ul [Geo.Mean] | 0.317 + 0.244/-0.134 | 0.124 + 0.094/-0.037 | 0.235 + 0.285/-0.151 |
<10
−6
|
PC20, mg/ml [Geo.Mean] | 0.5 + 1.8/-0.5 | 2.2 + 8.8/-2.2 | 0.4 + 1.4/-0.4 |
1.0 x10
−4
|
Blood neutrophils, ×1000/ul [Geo.Mean] | 3.80 + 1.64/-3.80 | 3.95 + 1.78/-3.95 | 3.67 + 1.33/-3.67 | 0.6916 |
Blood WBC, ×1000/ul [Geo.Mean] | 6.34 + 2.10/-0.35 | 6.35 + 2.28/-0.29 | 6.44 + 1.39/-0.44 | 0.9687 |
Sputum neutrophils, % of WBCb
| 43.1 ± 26.6 | 61.6 ± 25.1 | 56.2 ± 22.1 |
0.0239
|
Sputum eosinophils, % of WBC [Geo.Mean]b
| 7.8 + 20.7/-0.6 | 0.7 + 2.7/0.0 | 3.1 + 8.5/-0.2 |
<10
−6
|
Age, years | 43.0 ± 12.3 | 45.6 ± 10.7 | 47.9 ± 12.3 | 0.2340 |
Age of onset, years | 20.9 ± 14.2 | 23.4 ± 15.5 | 26.1 ± 18.3 | 0.4040 |
Body Mass Index (kg/m2) | 25.7 ± 3.6 | 27.3 ± 3.7 | 26.8 ± 4.2 | 0.2308 |
Percent of clinical cluster group | ||||
Mild, no ICS (%) | na | na | na | |
Moderate, low-medium ICS (%) | 62% | 58% | 29% |
0.0135
|
Severe, high ICS (%) | 38% | 42% | 71% | |
Male (%) | 49% | 44% | 48% | 0.9240 |
Atopic, Phadiatop positive (%) | 92% | 72% | 71% | 0.0530 |
Sputum Pauci (Eos < %3, PMN < 60%) (%)b
| 10% | 38% | 22% | |
Sputum Neutr. (Eos < 3, PMN > =60%) (%)b
| 14% | 46% | 17% |
0.0003
|
Sputum Mix (Eos > =3%, PMN > =60%) (%)b
| 14% | 8% | 30% | |
Sputum Eos. (Eos > =3%, PMN < 60%) (%)b
| 62% | 8% | 30% | |
FENO ≥ 35 ppb (%) | 59% | 3% | 43% |
1.8 x10
−6
|
Blood eosinophils ≥ 300/ul (%) | 54% | 6% | 32% |
4.1 x10
−5
|
FENO ≥ 35 ppb OR Blood eos. ≥ 300/ul (%) | 81% | 8% | 55% |
<10
−6
|
Biopsy CCL26-high (%)c
| 33% | 11% | 29% | 0.2179 |
The ADEPT phenotypes resist perturbation
The ADEPT phenotypes are stable longitudinally
The ADEPT matched U-BIOPRED sub-population also optimally partitions into 4 phenotypes
Variablea
| Healthy (n = 101) | Cluster US1 (n = 25) | Cluster US2 (n = 32) | Cluster US3 (n = 17) | Cluster US4 (n = 8) |
P-value |
---|---|---|---|---|---|---|
Mean [Geo.Mean] ± SD | ||||||
FEV1, % predicted (pre-bd) | 101.8 ± 12.9 | 73.7 ± 7.3 | 66.6 ± 9.0 | 67.6 ± 9.9 | 57.0 ± 8.5 |
8.8 x10
−5
|
FVC, % predicted (pre-bd) | 107.8 ± 13.4 | 90.9 ± 12.4 | 91.5 ± 12.6 | 72.9 ± 11.5 | 81.2 ± 10.5 |
6.1 x10
−6
|
FEV1/FVC (pre-bd) | 0.79 ± 0.06 | 0.68 ± 0.08 | 0.62 ± 0.09 | 0.79 ± 0.09 | 0.60 ± 0.06 |
<10
−6
|
bd reversibility, % change FEV1 | na | 13.7 ± 16.7 | 17.9 ± 9.3 | 12.9 ± 12.5 | 45.6 ± 24.5 |
3.1 x10
−6
|
FENO, ppb [Geo.Mean] | 19.9 + 14.2/-8.3 | 20.8 + 16.0/-9.1 | 47.4 + 49.8/-24.3 | 18.1 + 15.0/-8.2 | 38.8 + 33.4/-17.9 |
1.6 x10
−6
|
ACQ7 | 0.0 ± 0.1 | 1.4 ± 0.7 | 2.0 ± 0.7 | 3.3 ± 1.2 | 4.1 ± 0.8 |
<10
−6
|
AQLQ | 7.0 ± 0.1 | 6.0 ± 0.6 | 5.1 ± 0.9 | 4.0 ± 1.1 | 3.4 ± 0.8 |
<10
−6
|
Blood eosinophils, x1000/ul [Geo.Mean] | 0.098 + 0.180/-0.063 | 0.143 + 0.155/-0.075 | 0.484 + 0.356/-0.205 | 0.161 + 0.204/-0.090 | 0.345 + 0.254/-0.146 |
<10
−6
|
Blood neutrophils, ×1000/ul [Geo.Mean] | 3.23 + 1.67/-1.10 | 3.77 + 1.58/-1.11 | 4.09 + 1.33/-1.00 | 4.57 + 2.13/-1.45 | 1.84 ± 0.49 | 0.2128 |
Blood WBC, ×1000/ul [Geo.Mean] | 5.64 + 2.04/-1.50 | 6.41 + 1.62/-1.29 | 7.39 + 1.79/-1.44 | 7.83 + 2.24/-1.74 | 2.71 ± 0.36 |
0.0236
|
Sputum neutrophils, % of WBCb
| 30.8 + 40.3/-17.4 | 42.8 ± 28.3 | 42.0 ± 23.5 | 73.9 ± 24.2 | 70.0 ± 21.3 |
0.0129
|
Sputum eosinophils, % of WBC [Geo.Mean]b
| 0.2 + 0.3/-0.1 | 0.5 + 4.7/-0.5 | 6.1 + 44.5/-5.4 | 0.7 + 4.8/-0.6 | 6.3 + 21.0/-4.9 |
0.0123
|
IgE Total (IU/ml) [Geo.Mean] | 25 + 87/-19 | 121.1 + 377.2/-91.7 | 245.0 + 1,005.0/-197.0 | 84.5 + 267.5/-64.2 | 179.6 + 295.1/-111.7 | 0.0940 |
Age | 39 ± 13 | 46 ± 15 | 49 ± 16 | 50 ± 12 | 44 ± 15 | 0.7000 |
Age of onset, years | na | 21 ± 18 | 26 ± 19 | 29 ± 19 | 14 ± 12 | 0.2028 |
Body Mass Index (kg/m2) | 25.3 ± 3.6 | 27.6 ± 5.4 | 27.6 ± 5.8 | 30.9 ± 7.8 | 27.1 ± 4.8 | 0.2408 |
Percent of clinical cluster group | ||||||
Severe / Non-severe asthma (N / N) | na | 11 / 14 | 25 / 7 | 16 / 1 | 8 / 0 |
0.0004
|
Male (%) | 61% | 36% | 34% | 29% | 25% | 0.9276 |
Atopic, Skin prick test or serum IgE-RAST (%) | 45% | 100% | 86% | 88% | 100% | 0.5816 |
Sputum Pauci (Eos < %3, PMN < 60%) (%)b
| 76% | 42% | 25% | 25% | 0% |
0.0496
|
Sputum Neutr. (Eos < 3, PMN > =60%) (%)b
| 24% | 33% | 6% | 63% | 25% | |
Sputum Mix (Eos > =3%, PMN > =60%) (%)b
| 0% | 0% | 6% | 0% | 25% | |
Sputum Eos. (Eos > =3%, PMN < 60%) (%)b
| 0% | 25% | 63% | 13% | 50% | |
FENO ≥ 35 ppb (%) | 18% | 24% | 59% | 12% | 50% |
0.0032
|
Blood eosinophils ≥ 300/ul (%) | 7% | 20% | 75% | 35% | 63% |
0.0003
|
FENO ≥ 35 ppb OR Blood eos. ≥ 300/ul (%) | 21% | 32% | 88% | 41% | 88% |
3.3 x10
−5
|