Table 1.: Expression of Viral Genes and Cellular Targets was Analyzed in 6 Cell Lines, 3 Normal Cervix and 10 Clinical Samples in Relation to HPV DNA Status

HPV16-Samples E2-E4 E2N E6-E7 Ratio E2N/E6-E7 Ratio E2E4/E6-E7 CyclinB1 E2 IHC P16INK4 HPV DNA
Caski 11000 2500 8500 0.3 1.3 4600 - ND Int
Caski+E2 340 200 300 0.6 1.1 390 - ND Int
SiHa 4 360 1930 0.18 - 3900 - ND Int
IC3 5 1960 4900 0.4 - 2300 - ND Int
C33 4 5 2 - - 3300 - ND No
N-TERT 5 7 4 - - 2700 - ND No
2Ncervix 5 9 2 - - 130 - - No
4Ncervix 5 10 6 - - 110 - - No
8Ncervix 4 4 3 - - 60 - - No
2CIN2 15800 1520 570 2.6 27 290 +++ ++ Rep ++
3CIN2 21500 4000 3100 1.3 7 1060 +++ ++ Rep ++
4CIN2 33000 3900 2300 1.7 14 870 +++ + Rep +++
2CIN3 3600 520 1130 0.5 3 460 - +++ Rep+/- Int?
12CIN3 136 29 70 0.4 2 200 +/- + Rep+/- Int?
18CIN3 81 38 38 1 2 190 - +++ Rep+/- Int?
2SCC 3090 860 1680 0.5 1.8 600 + ++ Int + rep?
6SCC 73600 37000 31500 1.17 2.3 3200 - +++ Int
7SCC 11600 1500 5330 0.28 2.2 2000 +/- ++ Int+ rep?
8SCC 15200 2200 7800 0.28 1.9 1600 - +++ Int

Transcription of the viral and cellular genes was measured by digital quantification using the NanoString technology. For each probe, the table shows the actual number of RNA molecules to which the probe has been bound, after standardization with 3 housekeeping genes: RPL27, RPS13 and ACTB. Coefficients of variation are typically < 7% for values above 10. Protein expression of E2 and p16INK4 was determined by immunohistochemistry (IHC) and HPV DNA status was assessed by in situ hybridization (ISH). RNA extraction, ISH and IHC were performed on serial sections of the same samples. Staining was summarized as +++ when at least half, ++ one third and + less than 1/3 of the cells of the samples were stained. For ISH, the 2 types of signals are indicated as replication (Rep) for uniform staining of the nuclei or integrated (Int) for homogenous punctate staining as shown in Fig. (3B). ND: Not Determined.