Table 1. Clinical Cohort of PWH versus HIV Uninfected Controls for Interferome Profiling.
| Patient | Blood | Colon | Plasma | Colon | Plasma | Plasma | Colon | Colon | Colon | ||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Code | Sex | Age | CD4a | CD4a | Viral Loadb | HIV RNAb | IL-6c | LPSc | IFNαd | IFNβd | RNAseqe |
| H124 | M | 48 | 400 | 17.21 | 8400 | 96367 | 4.00 | 17.92 | 1.42 | 0.49 | 26582093 |
| H132 | M | 25 | 532 | 23.35 | 26000 | 9766703 | 1.39 | 19.87 | 2.33 | 0.83 | 40017132 |
| H154 | F | 58 | 400 | 10.65 | 22000 | 33674734 | 5.09 | 14.49 | 1.27 | 1.08 | 36371772 |
| H88 | M | 44 | 836 | 13.60 | 133000 | 7711893 | 1.22 | - | 0.70 | 0.32 | 37883074 |
| H217 | M | 22 | 744 | 11.35 | 25200 | 877550 | 0.56 | 12.63 | 1.40 | 0.53 | 28424144 |
| H286 | F | 52 | 693 | 12.34 | 3850 | 5146 | 1.19 | 14.26 | 1.25 | 0.89 | 15826112 |
| H307 | M | 34 | 624 | 9.36 | 9180 | 58572835 | 1.16 | 15.06 | 1.74 | 0.75 | 36680004 |
| H323 | M | 54 | 429 | 15.14 | 9440 | 2638399 | 1.02 | 11.25 | 2.62 | 1.46 | 32581853 |
| H391 | F | 29 | 238 | 5.63 | 196000 | 63106379 | 1.52 | 27.02 | 1.60 | 0.91 | 22519787 |
| H428 | M | 28 | 460 | 13.66 | 25100 | 82064684 | 1.78 | 20.29 | 1.16 | 1.09 | 14458796 |
| H594 | M | 46 | 338 | 7.46 | 88600 | 17181454 | 1.55 | - | 1.63 | 0.85 | 114526468 |
| H622 | M | 33 | 340 | 12.36 | 112000 | 98345366 | 1.96 | 16.85 | 1.30 | 0.88 | 27481534 |
| H648 | M | 31 | 420 | 13.39 | 2880 | 235737 | 0.52 | 11.84 | 2.08 | 0.58 | 40795690 |
| H683 | M | 25 | 504 | 12.43 | 59500 | 228774501 | 0.43 | 19.34 | 1.32 | 0.57 | 14796014 |
| H819 | M | 27 | 527 | 14.50 | 4670 | 42395309 | 0.98 | 15.90 | 1.50 | 0.81 | 27989141 |
| H825 | M | 34 | 364 | 8.81 | 43200 | 2238746 | 0.60 | 16.48 | - | - | 19068317 |
| H839 | F | 39 | 250 | 8.34 | 64900 | 453116 | 3.98 | 19.04 | 1.25 | 0.98 | 27398968 |
| H965 | F | 26 | 221 | 5.21 | 155000 | 17123 | 1.43 | 16.70 | - | - | 7814434 |
| H998 | F | 25 | 782 | 12.77 | 119000 | 163678357 | 0.87 | 8.29 | 1.52 | 0.92 | 158592070 |
| C138 | M | 29 | 728 | 35.48 | - | - | 2.16 | 9.52 | 2.26 | 0.17 | 13485914 |
| C178 | M | 33 | 736 | 35.74 | - | - | 0.51 | 9.80 | 2.15 | 0.22 | 12991623 |
| C255 | M | 34 | 588 | 34.27 | - | - | 0.69 | 14.48 | 3.95 | 0.33 | 36937567 |
| C278 | M | 23 | 532 | 27.52 | - | - | 0.73 | 7.45 | 3.23 | 0.27 | 42178568 |
| C361 | F | 33 | 720 | 34.68 | - | - | 0.19 | 8.68 | 7.80 | 0.26 | 43047608 |
| C404 | F | 29 | 1071 | 27.14 | - | - | 1.35 | 9.70 | 8.92 | 1.03 | 63291613 |
| C493 | F | 28 | 672 | 37.26 | - | - | 0.19 | 5.99 | 2.99 | 0.45 | 24871985 |
| C582 | M | 54 | 976 | 49.89 | - | - | 0.7 | 8.13 | 2.23 | 0.42 | 54886951 |
| C708 | M | 47 | 468 | 32.03 | - | - | 0.27 | 14.11 | 8.96 | 0.47 | 34241151 |
| C716 | M | 27 | 1035 | 26.52 | - | - | 0.47 | 11.78 | 3.90 | 0.30 | 107139307 |
| C914 | F | 43 | 690 | 20.44 | - | - | 1.21 | 8.78 | 4.77 | 0.29 | 62956103 |
| C947 | M | 25 | 480 | 25.18 | - | - | 0.78 | 7.66 | - | - | 21578149 |
| C972 | F | 51 | 1035 | 22.12 | - | - | 0.48 | 11.93 | 1.98 | 0.19 | 71620117 |
a CD4 counts were based on number per μl for the blood, and as a percentage of CD45+ cells in the colon.
b Plasma viral loads were based on copies/ml, whereas colon HIV RNA levels were based on copies per CD4 T cell [40]
c Plasma levels of IL6 and LPS were based on pg/ml.
d Colon IFNα and IFNβ mRNA levels (copies per 104 x GAPDH) were quantified by qPCR as described [33]
e Illumina Sequence Read Counts for each colon biopsy sample following quality control (this study)