Integration of HIV-1 as contributor to altered cellular regulation? - PowerPoint PPT Presentation

Integration of HIV-1 as contributor to altered cellular regulation? Nina Marty, 03.05.2019

Background of the project 20% of patients: expansion of X4-tropic provirus outgrowth of single viral variant from minority population already present before therapy initiation  Clonal expansion?  Cancer? 6 May 2019 University of Basel 2

Method: Proviral tropism testing 17 patients (7 X4 / 10 R5): 17 PBMC samples preART } data from Bader et. al., 2016 17 PBMC samples post4 17 PBMC samples post10 (if available) Extraction of gDNA (by Maxwell) Nested PCR: amplification of V3 region Sequencing MiSeq Illumina Tropism analysis: Geno2pheno[454] Viral phylogenetic changes and sequence evolution: MEGA 6.0, iTOL 2.0 Geneious 11.1.5 6 May 2019 University of Basel 3

Results: Proviral tropism testing at 3.5% FPR R5 patients: %X4 stays stable at a low level • • 1 R5 patient (ID25318) with increasing %X4 (3.58%  0.99%  53.87%) • X4 patients: %X4 fluctuates - increasing level post4, decreasing level post10 • 1 X4 patient (ID16579) with increasing %X4 (0.06%  80.65%  99.84%) • 6 May 2019 University of Basel 4

Results: Proviral tropism testing at 3.5% FPR 6 May 2019 University of Basel 5

? Results: ID25318 – %X4 increases %X4 at 3.5% FPR: A= 3.58 a*= 89.11 F= 0.91 f= 72.09 X= 51.87 Y= 100 x= 73.43 Choice of FPR? A: before therapy F: post4 X: post10 / Y: post10 rep 6 May 2019 University of Basel 7

Results: ID25971 – %X4 is stable %X4 at 3.5% FPR: A= 0.09 a= 0.14 F= 0.14 X= 0.05 A: before therapy F: post4 X: post10 6 May 2019 University of Basel 8

Results: ID16177 – no identical major variants %X4 at 3.5% FPR: A= 0.11 F= 99.90 X= 73.69 A: before therapy F: post4 X: post10 6 May 2019 University of Basel 9

Method: Integration Site Analysis Gillet et al., 2015 Adapted from Ciuffi et al. 2011 6 May 2019 University of Basel 11