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

6 May 2019 University of Basel 2

20% of patients: expansion of X4-tropic provirus

• utgrowth of single viral variant from minority population already

present before therapy initiation

Clonal expansion? Cancer?

Method: Proviral tropism testing

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17 patients (7 X4 / 10 R5): 17 PBMC samples preART 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

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data from Bader et. al., 2016

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%)

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Results: Proviral tropism testing at 3.5% FPR

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Results: ID25318 – %X4 increases

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%X4 at 3.5% FPR: A= 3.58 F= 0.91 X= 51.87 Y= 100

A: before therapy F: post4 X: post10 / Y: post10 rep

a*= 89.11 f= 72.09 x= 73.43

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Choice of FPR?

Results: ID25971 – %X4 is stable

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%X4 at 3.5% FPR: A= 0.09 a= 0.14 F= 0.14 X= 0.05

A: before therapy F: post4 X: post10

Results: ID16177 – no identical major variants

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%X4 at 3.5% FPR: A= 0.11 F= 99.90 X= 73.69

A: before therapy F: post4 X: post10

Method: Integration Site Analysis

6 May 2019 University of Basel 11 Adapted from Ciuffi et al. 2011 Gillet et al., 2015