CROI 2020 Abstract eBook

Abstract eBook

Poster Abstracts

Results: The polymorphisms V241I, I257V, P272K and E297K in RT and I201V in integrase, all relatively uncommon polymorphisms occurring in or adjacent to optimally-described HLA-restricted CTL epitopes, were statistically associated with the most pronounced decreases in RC, while RT polymorphisms E6K and A158S (both in CTL epitopes) were associated with modestly reduced RC. A subset of sequences (n=89) were mutated at the RT-integrase stop codon (*849Q), leading to the usage of a stop codon 17 residues downstream. These extended integrase sequences were significantly associated with reduced RC. Our mutagenesis experiments confirmed that RT mutants A158S, V241I, I257V as well as the integrase mutation *849Q significantly and negatively impact RC Conclusion: In summary, the length of integrase influences Pol RC and RT- integrase variants in vital domains of the RT palm (158S) and RT thumb (241I and 257V) represent potential vulnerable targets for an attenuation-based vaccine. The relevant RT-integrase epitopes spanning these residues could be utilised in a vaccine construct to stimulate the CD8+ T cell responses, and in the event that the virus escapes these specific responses, this is likely to be accompanied by a replicative fitness cost 272 ASSOCIATION OF HIV AND HOST GENETIC VARIANTS IN ANTIRETROVIRAL THERAPY-NAIVE PERSONS Migle Gabrielaite 1 , Adrian G. Zucco 1 , Marc Bennedbaek 1 , Christina Ekenberg 1 , Virginia L.Kan 2 , Giota Touloumi 3 , Linos Vandekerckhove 4 , Dan Turner 5 , James Neaton 6 , H. Clifford Lane 7 , Jens D. Lundgren 1 , Rasmus L.Marvig 1 , for the INSIGHT START Trial Group 1 Rigshospitalet, Copenhagen, Denmark, 2 George Washington University, Washington, DC, USA, 3 University of Athens, Athens, Greece, 4 HIV Cure Research Center, Ghent University, Ghent, Belgium, 5 Tel Aviv Sourasky Medical Center, Tel Aviv, Israel, 6 University of Minnesota, Minneapolis, MN, USA, 7 National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA Background: HIV-1 genetic diversity allows the virus to adapt and escape the host’s immune response; conversely, certain sections of the host genome affect the replicative rate of the virus. The molecular specificity of the interplay between viral genetic escape and host genomic control remains poorly defined. Here, we associated viral genetic data with recently reported host genetic data from a demographically diverse cohort of ART naïve HIV+ participants in the Strategic Timing of AntiRetroviral Treatment (START) trial. Methods: Two 3.6 kb amplicons (HIV-1 HXB2 genome regions 1,485-5,058 and 5,967-9,517) from viral genomes from plasma samples were sequenced on Illumina platform. Sequence alignment and single nucleotide polymorphism (SNP) calling were performed with BWA and Vardict software, respectively, using HXB2 genome as reference. Associations between HIV-1 SNPs and human SNPs and imputed human HLA types, respectively, were estimated with logistic regression models adjusting for age, sex and genetic structures in the viral and human population captured by principal component analysis. Bonferroni correction was used to set significance cut-offs. Results: Human and viral genetic data was combined for 2,035 trial participants. Viral populations showed large diversity across the cohort (most common subtypes were B and C). We identified 1,461 HIV-1 SNPs for association analysis against 398,349 human SNPs and observed significant human SNP associations for a total of 7 HIV-1 SNPs (p<8.6•10-11; see Figure). All 408 associated human SNPs were in the HLA gene region. While the strongest association was observed in gag (1514C → A; rs41293883; p=2.34•10-44), 4 out of 7 significant HIV-1 SNPs were in nef (Nef downregulates CD4 and MHC class I molecules). Furthermore, we identified 15 imputed HLA alleles which were significantly associated with one or more of the 7 identified HIV-1 SNPs (p<7.9•10-5) using dominant logistic regression model. Most significant associations were 1514C → A HIV-1 SNP with B*57:01 (p=9.99•10-57) and C*06:02 (p=5.42•10-26) alleles, respectively. Conclusion: These data suggest that human immunotypes impose selection on viral genotypes through viral epitope specificity. Alleles of HLA (B*57:01 and C*06:02) observed here to be associated with viral epitope selection have previously been found to be associated with viral load in the same cohort. Hence, the present finding provides independent confirmation of a genuine biological effect of variations in HLA gene region.

273 CXCR5 EXPRESSION ON HUMAN CD8+ T CELLS IS TIGHTLY REGULATED BY EPIGENETIC MECHANISMS Funsho Ogunshola 1 , Werner Smidt 2 , Veron Ramsuran 2 , Thumbi Ndungú 2 , Bruce D. Walker 3 , Tulio de Oliveira 2 , Zaza Ndhlovu 3 1 Africa Health Research Institute, Mtubatuba, South Africa, 2 University of KwaZulu- Natal, Durban, South Africa, 3 Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA Background: CD8+ T cells located in B cell follicles play an important role in viral and tumor control. However, only a small subset of CD8+ T cells called follicular CD8+ T cells express CXCR5, the chemokine receptor required for cell migration into B cell follicles. We investigated why most LN CD8+ T cells lack CXCR5 expression, and why there is reduced CXCR5 expression on CXCR5+CD8 T cells (fCD8s) relative to GCTfh. Methods: We FACS-sorted CXCR5+CD8+ (fCD8s), CXCR5-CD8+ (non-fCD8s), naïve CD8+ T cells and GCTfh from lymph nodes of HIV-1 infected individuals and performed RNA-sequencing (RNA-Seq). DNA methylation was used to profile methylation pattern of the CXCR5 gene and the Assay for Transposase-Accessible Chromatin using Sequencing (ATAC-Seq) was used to quantify accessible genes and to identify epigenetic modules governing CXCR5 expression. Results: RNA-seq data analysis of fCD8 and non-fCD8s identified 43 gene among the most differentially expressed genes (FDR<0.01) that are associated with epigenetic gene regulation. DNA bisulfite treatment and sequencing showed that 70% of CpG islands in CXCR5 gene were methylated whereas fCD8 had less than 7%methylation levels at equivalent sites. ATAC-Seq analysis revealed a closed chromatin conformation at the CXCR5 TSS in non-fCD8s whereas fCD8s had open chromatin at equivalent sites. Furthermore, analysis of nucleosomal footprinting around the CXCR5 TSS revealed greater nucleosomal occupancy in fCD8s compared to GCTfh, computational simulation indicated that the presence of nucleosomes at the TSS interfered with transcription efficiency resulting in attenuated expression of the CXCR5 gene. Conclusion: We show that DNA methylation coupled with chromatin compaction at TSS prevent CXCR5 gene expression in non-fCD8s and greater nucleosomal occupancy down-modulate CXCR5 expression levels in fCD8s. Together, these data provide insights into both the underlying molecular mechanisms that repress CXCR5 in non-fCD8s and the molecular mechanisms responsible for the low CXCR5 expression in fCD8s, with implications for HIV cure strategy or eradication of B cell-derived tumors. 274 ADDITIVE DETRIMENTAL EFFECT OF B*35/39 TYPES IN A LARGE MEXICO/ CENTRAL AMERICA COHORT Humberto Valenzuela Ponce 1 , Maribel Soto-Nava 1 , Ingrid Y. Escobar-Urias 2 , Rodolfo Pinzón-Meza 2 , Juan Miguel Pascale 3 , Yamitzel Zaldivar 3 , Guillermo Porras-Cortés 4 , Carlos Quant-Durán 5 , Rita Isabel Meza Martínez 6 , Elsa Y. Palou 7 , Marvin Manzanero 8 , Rolando A. Cedillos 9 , Santiago Avila-Rios 1 , Gustavo Reyes- Terán 1 , for the Mesoamerican HIV Project Group 1 National Institute of Respiratory Diseases, Mexico City, Mexico, 2 Roosevelt Hospital, Guatemala City, Guatemala, 3 Instituto Conmemorativo Gorgas de Estudios de la Salud, Panama City, Panama, 4 Hospital Metropolitano Vivian Pellas, Managua, Nicaragua, 5 Hospital Roberto Calderón, Managua, Nicaragua, 6 Honduras HIV National Laboratory, Tegucigalpa, Honduras, 7 Hospital Escuela Universitario,

Poster Abstracts

93

CROI 2020