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Genetic variations in the host dependency factors ALCAM and TPST2 impact HIV-1 disease progression

Kruize, Zitaa; Maurer, Irmaa; Boeser-Nunnink, Brigitte D.M.a; Booiman, Thijsa,b; Kootstra, Neeltje A.a

Author Information
doi: 10.1097/QAD.0000000000002540

Abstract

Introduction

The clinical course of an untreated HIV-1 infection is highly variable, with some people developing AIDS within 2 years after infection and others showing hardly any signs of disease progression for more than 10 years. Host genetics has been shown to play an important role in the variable outcome of disease progression [1–3]. Genetic polymorphisms that affect the outcome of HIV-1 infection have mostly been identified in genes involved in the HIV-1 specific immune response (HLA-B5701 and HLA-B27), innate immunity (Trim5a, Trex1, IFI16) and host dependency factors (HDFs) such as the CCR5 coreceptor [2,4–9].

HIV-1 relies on the cellular machinery and host proteins for its replication, and therefore, these so-called HDFs are promising targets for the treatment of HIV-1 infection. In addition, host-directed therapies are associated with a much higher barrier to resistance [10]. Recently, a CRISPR-based genetic screen in CD4+ T cells identified three novel HDFs that are required for HIV-1 infection but not for cellular survival and therefore could be promising therapeutic targets [11]. Amongst these HDFs are the activated leukocyte cell adhesion molecule (ALCAM) and tyrosylprotein sulfotransferase 2 (TPST2) [11].

ALCAM is a cell surface protein expressed on activated immune cells [12]. Although its precise function is not yet fully understood, it has been demonstrated to be involved in stabilizing the immunological synapse between T cells and antigen-presenting cells [13,14] and can provide costimulatory signals, thereby contributing to T-cell activation and proliferation [15–17]. In in-vitro infection models, the loss of ALCAM resulted in disruption of cell aggregation preventing cell-to-cell spread of HIV-1 [11].

TPST2 is a trans-Golgi-resident enzyme that catalyzes the O-sulfation of tyrosines of secretory and plasma membrane proteins [18], including CCR5. TPST2 catalyzes tyrosine sulfation at the N-terminus of CCR5, thereby facilitating interactions with HIV-1 gp120 [19,20]. The loss of TPST2 was shown to interfere with HIV-1 infection at the level of viral entry due to the lack of tyrosine sulfation of CCR5 [11].

Although a role of ALCAM and TPST2 in in-vitro HIV-1 infection has clearly been demonstrated, the contribution of these genes in in-vivo HIV-1 replication and the clinical course of infection are unknown. In this study, we assessed if naturally occurring genetic variation in ALCAM and TPST2 has an effect on the outcome of untreated HIV-1 infection and disease progression.

Materials and methods

Study population

The study population consists of 365 HIV-1-infected men who have sex with men (MSM) who participated in the Amsterdam cohort studies (ACS) on HIV-1 and AIDS as previously described [5]. Of the 365 participants, 131 seroconverted during the study. The remaining 234 men were positive for HIV-1 antibodies at entry between October 1984 and April 1985. The time since seroconversion of these seroprevalent cases has been estimated on the basis of the incidence of HIV-1 infection amongst homosexual participants of the ACS and was on average 1.5 years before entry into the cohort studies [21].

Most of the participants (n = 243) did not receive any treatment, 70 received zidovudine monotherapy, 10 received didanosine monotherapy and 42 received other ineffective antiretroviral therapy during follow-up. DNA from 335 participants was available for genotype analysis. Confounding effects of population stratification were corrected using available genotyping data (Eigenstrat, implemented in Eigensoft) [3], and outliers were removed from the analysis leaving 304 individuals [5].

For flow cytometry analysis, 59 participants genotyped for the SNPs with available cryopreserved peripheral blood mononuclear cells (PBMCs) obtained at one and five years after seroconversion were included. Additional preseroconversion samples were available from 32 out of the 59 participants.

Healthy controls were obtained from the Dutch national blood bank (Sanquin) in Amsterdam.

This study has been conducted in accordance with the ethical principles set out in the declaration of Helsinki and was approved by the institutional review board of the Academic Medical Center (AMC) and the Ethics Advisory Body of the Sanquin Blood Supply Foundation in Amsterdam. Written informed consent was obtained from all participants.

Single nucleotide polymorphism genotyping

Data for SNPs in the ALCAM (chr. 3) (rs1165930, rs11713106, rs12498014, rs1344861, rs1503158, rs2178419, rs2654417, rs6437534, rs7620614, rs7648727, rs7651901, rs777942, rs9809062 and rs9814707) and TPST2 (chr. 22) (rs2283832, rs4149478, rs763088 and rs9613199) regions were previously generated in a GWA study using the Illumina Infinium HumanHap300 BeadChip (Illumina, San Diego, California, USA) [3]. Additional genotyping for SNPs rs1344861 in ALCAM and rs9613199 in TPST2 was performed by PCR and sequencing using primer pairs rs1344861-FW (5’-GGTTAGTGCCTAGGTGCTTTCTC-3’) and rs1344861-RV (5’-CTCTAAGCTTAAATGGTGG-3’) and rs9613199-FW (5’-CTATGTCCTCAGGTTGCTGTGAGG-3’) and rs9613199-RV (5’-GCCTACCTTATAGATACCTGTGGGC-3’). PCR amplification was performed using GoTaq Flexi DNA Polymerase (Promega, Madison, Wisconsin, USA) and the following amplification cycles: 5 min 95°C; 35 cycles of 30 s 95°C, 30 s 50°C, 1 min 72°C; 10 min 72°C. PCR products were sequenced using the ABI prism BigDye Terminator V1.1 Cycle Sequencing Kit (Applied Biosystems, Foster City, California, USA) on an ABI 3730XL DNA Analyser for analysis.

Flow cytometry

Cryopreserved PBMCs were used for flow cytometry analysis. PBMCs were stained with fluorescent labelled antibodies for 30 min at 4oC in the dark. Subsequently, PBMCs were washed with PBS supplemented with 0.5% BSA and fixed using 250 μl of BD CellFIX (BD Biosciences, Franklin Lakes, New Jersey, USA). In the HIV-1-infected individuals, CCR5 expression on peripheral blood lymphocytes was determined by flow cytometry using the following antibodies: CCR5 FITC, CD4 PerCP, CD45RO PE, CD27 APC (BD Biosciences). T-cell activation was determined by CD38/HLA-DR coexpression using the following antibodies: CD4 APC, CD8 PerCP, CD38 PE and HLA-DR FITC (BD Biosciences). In healthy donors, CCR5 and ALCAM expression was analysed on naive (CD45RA+CD27+), memory (CD45RA-CD27+) and effector memory (CD27-) CD4+ T cells, HLA-DR and CD38 expression was analysed on CD4+ T cells, ALCAM expression was determined on classical (CD14+CD16-), intermediate (CD14+CD16+) and nonclassical (CD14-CD16+) monocytes using the following antibodies: CD3 V500, CD4 FITC, CD4 PE-Cy7, CD45RA PE-Cy7, CD27 PerCP-Cy5.5, CD38 PE and HLA-DR FITC (BD Biosciences); CD14 PE-Cy7 and CD16 eFluor 450 (eBioscience, San Diego, California, USA); ALCAM (CD166) PE (Biolegend, San Diego, California, USA).

Fluorescence was measured with the FACS Canto II (BD Biosciences). The proportion of cells expressing each marker and the mean fluorescence intensity (MFI) were determined using FlowJo 7.6 (TreeStar, Ashland, Oregon, USA).

In-vitro infections

To test the effect of the SNP rs1344861 in ALCAM and rs9613199 in TPST2 on in-vitro HIV-1 replication, PBMCs were isolated from buffy coats from 32 healthy blood donors that were genotyped for the SNP. Cells were isolated by Ficoll-Isopaque density gradient centrifugation and stimulated for 3 days in Iscove's modified Dulbecco medium supplemented with 10% foetal bovine serum, penicillin (100 U/ml), streptomycin (100 U/ml), ciproxin (5 μg/ml) and recombinant interleukin (IL)-2 (20 U/ml; Chiron Benelux, Amsterdam, the Netherlands) at a cell concentration of 5 × 106/ml. The cells were infected with either HIV-1 NL4–3, NL4–3Ba-L or YU2 at a multiplicity of infection (MOI) of 0.005 and cultured for 8 days, after which Gag p24 production in the culture supernatant was analysed as a measure of viral replication by an in-house ELISA.

Statistical analysis

Kaplan–Meier and Cox proportional-hazard analyses were performed to study the relation between polymorphisms in the ALCAM and TPST2 gene regions and disease progression. The following endpoints were considered for analysis: AIDS-defining events according to the 1987 Centers for Disease Control (CDC) definition, AIDS-defining events including CD4+ T-cell counts below 200 cells/μl according to the 1993 CDC definition and AIDS-related death. Individuals who started effective cART or who were lost to follow-up were censored. Student's t-test was used to compare the expression of membrane proteins as analysed by flowcytometry between the groups. Differences in in-vitro HIV-1 viral replication were analysed by Student's t-test. Bonferroni correction for multiple testing was used where indicated. Linear regression was used to determine the slope. Statistical analyses were performed using IBM SPSS Statistics for Windows v.25 (IBM, Armonk, New York, USA).

Results

Frequencies of single nucleotide polymorphisms in the ALCAM and TPST2 gene regions

The frequency of 14 SNPs in the ALCAM gene region (rs1165930, rs11713106, rs12498014, rs1344861, rs1503158, rs2178419, rs2654417, rs6437534, rs7620614, rs7648727, rs7651901, rs777942, rs9809062 and rs9814707) and four SNPs in the TPST2 region (rs2283832, rs4149478, rs763088 and rs9613199) were studied in 304 HIV-1-infected MSM who participate in the ACS on HIV-1 infection and AIDS (ACS) (Table 1). The frequency of the minor allele of each SNP analysed in HIV-1-infected individuals was similar to the frequencies reported for European by the Genome Aggregation Database (gnomAD) and the 1000 Genomes Project [22] and no deviation from the Hardy–Weinberg equilibrium was observed.

Table 1
Table 1:
Single nucleotide polymorphisms in the gene regions coding for ALCAM and TPST2.

Effect of single nucleotide polymorphisms in the ALCAM gene regions on the clinical course of untreated HIV-1 infection

The effect of SNPs in the ALCAM gene region on HIV-1 disease progression was analysed using Cox proportional-hazard survival analysis with AIDS according to the 1987 CDC definition, the 1993 CDC definition and AIDS-related death as endpoints. A recessive model was used to determine the effect of the minor allele on disease progression. SNPs with a homozygous minor allele frequency larger than 5% were included in the analysis (rs1165930, rs12498014, rs1344861, rs1503158, rs2654417, rs7620614, rs7648727). SNP rs1165930, rs12498014, rs1503158 and rs2654417 in the ALCAM gene region had no effect on disease outcome, while two SNPs in ALCAM (rs7620614 and rs7648727) were associated with progression to AIDS (CDC 1987) and AIDS-related death (Table 2). Interestingly, an accelerated disease progression towards AIDS (CDC 1987 and CDC 1993 definition) and AIDS-related death was observed for the minor allele of rs1344861 in ALCAM with a relative hazard of 1.9 [95% confidence interval (95% CI) 1.19–3.13], 1.9 (95% CI 1.22–2.88) and 2.2 (95% CI 1.41–3.43,) respectively (Table 2). Multivariate analysis demonstrated that the minor allele of rs1344861 in ALCAM was associated with an accelerated disease progression (P = 0.004, relative hazard 2.0, 95% CI 1.25–3.16 for AIDS and P = 0.004, relative hazard 2.3, 95% CI 1.44–3.57 for AIDS-related death), this effect was independent of age at seroconversion, temporary use of ineffective monotherapy and HBV/HCV coinfection. Kaplan–Meier survival analysis showed that the 50% survival rate of the group homozygous for the minor allele of rs1344861 in ALCAM was reached for the endpoints AIDS (CDC1987), AIDS (CDC 1993) or AIDS-related death 38, 22 or 34 months earlier, respectively (Fig. 1a). The accelerated disease progression associated with the minor allele of rs1344861 was independent of the CCR5Δ32 genotype and HLA-B57 (supplementary Table 1, https://links.lww.com/QAD/B712). Moreover, a significant increase in viral load at set point was observed in individuals carrying the minor allele (P = 0.0022) (Fig. 1c).

Table 2
Table 2:
Effect of single nucleotide variation in the gene region coding for ALCAM and TPST2 on HIV-1 disease progression.
Fig. 1
Fig. 1:
The effect of single nucleotide polymorphisms in ALCAM and TPST2 on HIV-1 disease progression, viral load and CD4+ T-cell count at set point.

In-vitro infection of PBMC with the CXCR4-using NL-4–3 HIV-1 variant and the CCR5-using HIV-1 variants YU2 and NL4–3 Ba-L demonstrated that HIV-1 replication in PBMCs homozygous for minor allele of rs1344861 in ALCAM was comparable to PBMCs heterozygous/homozygous for the major allele of rs1344861 in ALCAM (Fig. 2a). Moreover, we observed no significant differences in the ALCAM expression levels on CD4+ T-cell subsets as well as monocytes (Fig. 2b), indicating the SNP rs1344861 minor allele did not have a clear effect on in-vitro viral replication and ALCAM expression.

Fig. 2
Fig. 2:
The effect of single nucleotide polymorphism rs1344861 on HIV-1 replication, ALCAM expression and CD4+ T-cell activation.

T-cell activation measured by the percentage of HLA-DR+/CD38+ cells within the CD4+ T-cell population in HIV-1-infected individuals has previously been shown to be associated with disease progression [23]. In individuals homozygous for the minor allele of rs1344861 (CC), an accelerated increase in T-cell activation levels over time (from preseroconversion until 5 years after seroconversion; slope 0.8620, P = 0.05) was observed; however, this was not significantly different from the increase observed in individuals carrying the major allele (slope 0.6892, P < 0.0001) (Fig. 2c).

ALCAM has also been implicated to play an important role in monocyte migration over the blood–brain barrier (BBB) and thereby contribute to the development HIV-1 associated neurocognitive disorders [24]. No association between SNP rs1344861 and AIDS dementia development in our cohort was observed (data not shown).

Effect of single nucleotide polymorphisms in the TPST2 gene regions on the clinical course of untreated HIV-1 infection

Cox proportional-hazard survival analysis with AIDS according to 1987 CDC definition, the 1993 CDC definition and AIDS-related death as endpoints was used to determine the effect of SNPs in the TPST2 gene region on the clinical course of untreated HIV-1 infection. A recessive model was used to determine the effect of the minor allele of the SNPs rs2283832, rs4149478, rs763088, rs9613199. No effect of SNP rs4149478, rs763088 in the TPST2 region on disease outcome was observed. However, the minor alleles of rs2283832 and rs9613199 in TPST2 were associated with a delayed progression to disease outcome [Table 2; relative hazard of 0.5 (95% CI 0.32–0.76) for AIDS (CDC1987), relative hazard of 0.5 (95% CI 0.36–0.73] for AIDS (CDC1993) and relative hazard 0.5 (95% CI 0.34–0.78) for AIDS-related death for rs9613199 and relative hazard of 0.6 (95% CI 0.46–0.89) for AIDS (CDC1987), relative hazard of 0.7 (95% CI 0.52–0.91) for AIDS (CDC1993) and relative hazard 0.7 [(95% CI 0.48–0.91) for AIDS-related death) for rs2283832]. Multivariate cox regression analysis showed that the minor allele of rs9613199 in TPST2, and not rs2283832, was associated with the observed protective effect (P = 0.008, relative hazard 0.6, 95% CI 0.40–0.87 for AIDS and P = 0.008, relative hazard 0.6, 95% CI 0.37–0.86 for AIDS-related death); this effect was independent of age at seroconversion, temporary use of ineffective monotherapy and HBV/HCV infection. In the group homozygous for the minor allele of rs9613199 in TPST2, the 50% survival rate was prolonged by 35, 47 and 42 months for the endpoints AIDS (CDC1987), AIDS (CDC1993) and AIDS-related death, respectively (Fig. 1b). The protective effect of the minor allele of rs9613199 in TPST2 was independent of the CCR5Δ32 genotype and HLA-B57 (supplementary Table 1, https://links.lww.com/QAD/B712). However, no differences in viral load and CD4+ T-cell counts at set point between individuals carrying the major or minor allele were observed (Fig. 1c), indicating that the effect of the SNP was not evident during early phases of infection.

TPST2 catalyzes tyrosine sulfation, a posttranslation protein modification that plays an important role in protein–protein interactions. Tyrosine sulfation of the HIV-1 coreceptors CCR5 and CXCR4 has been demonstrated to support interactions with HIV-1 gp120 [19,20,25,26]. To test whether the SNP rs9613199 affected CCR5 and CXCR4 sulfation and subsequent viral entry, we analysed in-vitro HIV-1 infection in PBMCs from 32 healthy donors that were genotyped for the SNP. No differences were observed in the infection efficiency of the CXCR4-using NL-4–3 HIV-1 variant as well as the CCR5-using HIV-1 variants YU2 and NL4–3 Ba-L, in PBMCs homozygous for the TPST2 SNP rs9613199 minor allele compared to PBMCs heterozygous/homozygous for the TPST2 SNP rs9613199 major allele (Fig. 3a). This indicated that the SNP rs9613199 minor allele was not associated with susceptibility of cells to in-vitro HIV-1 infection. Moreover, no differences in T-cell activation levels (HLA-DR/CD38 expression; Fig. 3b) and CCR5 expression (Fig. 3c) were observed in the PBMC of these healthy donors irrespective of the rs9613199 genotype.

Fig. 3
Fig. 3:
The effect of SNP rs9613199 on HIV-1 replication and on CD4+ T-cell activation.

In addition, we analysed the level of T-cell activation by the percentage of HLA-DR+/CD38+ cells within the CD4+ T-cell population in HIV-1-infected individuals at 1 year and 5 years after seroconversion and prior to seroconversion. We observed a significant increase in T-cell activation over time (from preseroconversion until 5 years after seroconversion; slope 0.8882, P < 0.0001) (Fig. 3d) in individuals carrying the major allele of SNP rs9613199 (CC or CT), but not in HIV-1-infected individuals homozygous for the minor allele of rs9613199 (TT) (slope 0.3386, P = ns) (Fig. 3d). In agreement, a significant increase in percentage of CCR5 expressing CD4+ memory T cells was observed in individuals carrying the major allele of SNP rs9613199 (CC or CT) over time [slope 1.059, P = 0.009, whereas no significant increase of CCR5 expressing cells was observed in HIV-1-infected individuals homozygous for the minor allele of rs9613199 (TT) (slope 0.4657, P = ns)] (Fig. 3e).

Discussion

Recently, ALCAM and TPST2 have been identified as important HIV-1 dependency factors that are indispensable for HIV-1 replication in vitro[11]. Here, we determined whether naturally occurring variations in these genes could impact the clinical course of untreated HIV-1 infection, through the alteration of the function or expression levels of ALCAM and TPST2.

We identified SNP rs1344861 located in the ALCAM gene region to be associated with a higher viral load at set point and an accelerated disease progression towards AIDS and AIDS-related death. ALCAM is known to stimulate the antigen-specific immune response through homophilic (ALCAM-ALCAM) or heterophilic interaction with CD6 (ALCAM-CD6). High ALCAM expression levels on antigen-presenting cells (monocytes, dendritic cells) and low-level expression on resting T cells indicate that the induction of the antigen-specific immune response is mainly controlled by the ALCAM-CD6 interaction between antigen-presenting cells and T cells [16,17]. Whereas ALCAM–ALCAM interactions are essential to maintain cell proliferation of activated T cells in which ALCAM expression is high. SNP rs1344861 may alter the ALCAM expression levels, thereby increasing immune activation and cell proliferation thus supporting HIV-1 replication and cell-to-cell spread of the virus eventually resulting in accelerated disease progression.

ALCAM, as an adhesion molecule, has also been implicated to play an important role in monocyte migration over the BBB and thereby contributing to the development of HIV-1 associated neuroinflammation and neurocognitive disorders [24]. However, no association between the SNP rs1344861 in ALCAM and development of HAD was observed in our cohort.

Tyrosylprotein sulfotransferases, of which TPST2 is one of the isoforms, is an enzyme that catalyzes the sulfation reaction of protein tyrosines, a posttranslational modification of proteins. The HIV-1 coreceptors, CCR5 and CXCR4, undergo this modification which is critical for high affinity interactions with the HIV-1 envelope glycoprotein gp120 in complex with CD4 [19,20,25,26]. Therefore, naturally occurring variations in the TPST2 gene that alter the expression levels or the functionality of the protein could also impact the clinical course of untreated HIV-1 infection. Here, we identified SNP rs9613199 in the TPST2 gene region to be associated with a strong delay in disease progression towards AIDS and AIDS-related death. An effect of SNP rs9613199 on the TPST2 sulfation reaction of CCR5 or CXCR4 and thereby the affinity of the coreceptor for the HIV-1 gp120 envelop glycoprotein, could not be demonstrated in in-vitro HIV-1 infections assays and efficient infection of CCR5 as well as CXCR4-using HIV-1 variants was observed irrespective of the SNP rs9613199 genotype.

We did observe that the levels of immune activation, as demonstrated by an increase of HLA-DR+/CD38+ CD4+ T cells and CCR5-expressing CD4+ memory T cells, were less pronounced in HIV-1-infected individuals homozygous for the rs9613199 minor allele. Indeed, slower HIV-1 disease progression has been associated with lower levels of immune activation, and this is consistent with lower levels of CCR5 expressing HIV-1 target cells and lower viral replication [23,27–30].

TPST2 has also been demonstrated to be involved in tyrosine sulfation of the HIV-1 envelope protein gp120, which affects protein stability, modulates sensitivity to neutralizing antibodies and induction of neutralizing antibodies [31], furthermore tyrosine sulfation of antibodies modulates their functionality [32]. Although we were unable to demonstrate an effect of the SNP rs9613199 on the neutralizing antibody titres [33], a combination of minor changes associated with the SNP in coreceptor binding, sensitivity of the virus to neutralizing antibodies and antibody functionality may contribute to the prolonged survival of individuals homozygous for the minor allele.

A limitation of this study is that our cohort is of moderate size and a causal relation between the SNP and disease progression could not be determined. The SNP in ALCAM and TPST2 identified in this study have not been associated with any change in functionality or disease, which indicates that the effect of the SNP on expression and function of the encoded protein is most likely minor. This is in agreement with our in-vitro experiments in which we observed that the SNPs have no effect on HIV-1 infectivity and replication, indicating that the expression and function of CCR5 and ALCAM was not affected by rs9613199 and rs1344861 respectively. In this study, we analysed the effect of tagging SNPs on HIV-1 disease progression, and the causative polymorphism has yet to be established in future studies. Nevertheless, the effect of SNPs in the gene regions of ALCAM and TPST2 demonstrates that these genes indeed play an important role in HIV-1 infection either by a direct effect on viral replication as demonstrated previously [11] or indirectly via for instance the immune response (neutralizing antibodies, antigen presentation). Our present study also demonstrates that naturally occurring genetic variations that do not have severe functional implications can have a major effect on the outcome of HIV-1 infection, and therefore, these HDFs might be attractive and effective target for new HIV-1 treatment strategies.

Acknowledgements

The ACS on HIV infection and AIDS, a collaboration between the Public Health Service Amsterdam, the Amsterdam UMC of the University of Amsterdam, Sanquin Blood Supply Foundation, Medical Center Jan van Goyen and the HIV Focus Center of the DC-Clinics, are part of the Netherlands HIV Monitoring Foundation and financially supported by the Center for Infectious Disease Control of the Netherlands National Institute for Public Health and the Environment (http://www.amsterdamcohortstudies.org/).

Z.K. designed the study and the experiments, interpreted data and wrote the manuscript. I.M. and B.B.N. performed experiments. T.B. helped with study design and data analysis. N.A.K. designed the study and the experiments, interpreted data and wrote the manuscript.

Conflicts of interest

All the authors declare that there are no potential conflicts of interest related to this manuscript.

References

1. Fellay J, Shianna KV, Ge D, Colombo S, Ledergerber B, Weale M, et al. A whole-genome association study of major determinants for host control of HIV-1. Science 2007; 317:944–947.
2. Pereyra F, Jia X, McLaren PJ, Telenti A, de Bakker PI, Walker BD, et al. The major genetic determinants of HIV-1 control affect HLA class I peptide presentation. Science 2010; 330:1551–1557.
3. van Manen D, Delaneau O, Kootstra NA, Boeser-Nunnink BD, Limou S, Bol SM, et al. Genome-wide association scan in HIV-1-infected individuals identifying variants influencing disease course. PLoS One 2011; 6:e22208.
4. Booiman T, Kootstra NA. Polymorphism in IFI16 affects CD4(+) T-cell counts in HIV-1 infection. Int J Immunogenet 2014; 41:518–520.
5. Booiman T, Setiawan LC, Kootstra NA. Genetic variation in Trex1 affects HIV-1 disease progression. AIDS 2014; 28:2517–2521.
6. van Manen D, Rits MA, Beugeling C, van Dort K, Schuitemaker H, Kootstra NA. The effect of Trim5 polymorphisms on the clinical course of HIV-1 infection. PLoS Pathog 2008; 4:e18.
7. de Roda Husman AM, Koot M, Cornelissen M, Keet IP, Brouwer M, Broersen SM, et al. Association between CCR5 genotype and the clinical course of HIV-1 infection. Ann Intern Med 1997; 127:882–890.
8. Dean M, Carrington M, Winkler C, Huttley GA, Smith MW, Allikmets R, et al. Genetic restriction of HIV-1 infection and progression to AIDS by a deletion allele of the CKR5 structural gene. Hemophilia Growth and Development Study, Multicenter AIDS Cohort Study, Multicenter Hemophilia Cohort Study, San Francisco City Cohort, ALIVE Study. Science 1996; 273:1856–1862.
9. Michael NL, Chang G, Louie LG, Mascola JR, Dondero D, Birx DL, et al. The role of viral phenotype and CCR-5 gene defects in HIV-1 transmission and disease progression. Nat Med 1997; 3:338–340.
10. Friedrich BM, Dziuba N, Li G, Endsley MA, Murray JL, Ferguson MR. Host factors mediating HIV-1 replication. Virus Res 2011; 161:101–114.
11. Park RJ, Wang T, Koundakjian D, Hultquist JF, Lamothe-Molina P, Monel B, et al. A genome-wide CRISPR screen identifies a restricted set of HIV host dependency factors. Nat Genet 2017; 49:193–203.
12. Bowen MA, Patel DD, Li X, Modrell B, Malacko AR, Wang WC, et al. Cloning, mapping, and characterization of activated leukocyte-cell adhesion molecule (ALCAM), a CD6 ligand. J Exp Med 1995; 181:2213–2220.
13. Dustin ML. Cell adhesion molecules and actin cytoskeleton at immune synapses and kinapses. Curr Opin Cell Biol 2007; 19:529–533.
14. Reyes R, Cardenes B, Machado-Pineda Y, Cabanas C. Tetraspanin CD9: a key regulator of cell adhesion in the immune system. Front Immunol 2018; 9:863.
15. Gimferrer I, Calvo M, Mittelbrunn M, Farnos M, Sarrias MR, Enrich C, et al. Relevance of CD6-mediated interactions in T cell activation and proliferation. J Immunol 2004; 173:2262–2270.
16. Hassan NJ, Barclay AN, Brown MH. Frontline: optimal T cell activation requires the engagement of CD6 and CD166. Eur J Immunol 2004; 34:930–940.
17. Zimmerman AW, Joosten B, Torensma R, Parnes JR, van Leeuwen FN, Figdor CG. Long-term engagement of CD6 and ALCAM is essential for T-cell proliferation induced by dendritic cells. Blood 2006; 107:3212–3220.
18. Beisswanger R, Corbeil D, Vannier C, Thiele C, Dohrmann U, Kellner R, et al. Existence of distinct tyrosylprotein sulfotransferase genes: molecular characterization of tyrosylprotein sulfotransferase-2. Proc Natl Acad Sci U S A 1998; 95:11134–11139.
19. Farzan M, Mirzabekov T, Kolchinsky P, Wyatt R, Cayabyab M, Gerard NP, et al. Tyrosine sulfation of the amino terminus of CCR5 facilitates HIV-1 entry. Cell 1999; 96:667–676.
20. Seibert C, Cadene M, Sanfiz A, Chait BT, Sakmar TP. Tyrosine sulfation of CCR5 N-terminal peptide by tyrosylprotein sulfotransferases 1 and 2 follows a discrete pattern and temporal sequence. Proc Natl Acad Sci U S A 2002; 99:11031–11036.
21. Geskus RB. On the inclusion of prevalent cases in HIV/AIDS natural history studies through a marker-based estimate of time since seroconversion. Stat Med 2000; 19:1753–1769.
22. Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, et al. A global reference for human genetic variation. Nature 2015; 526:68–74.
23. Hazenberg MD, Otto SA, van Benthem BH, Roos MT, Coutinho RA, Lange JM, et al. Persistent immune activation in HIV-1 infection is associated with progression to AIDS. AIDS 2003; 17:1881–1888.
24. Williams DW, Calderon TM, Lopez L, Carvallo-Torres L, Gaskill PJ, Eugenin EA, et al. Mechanisms of HIV entry into the CNS: increased sensitivity of HIV infected CD14+CD16+ monocytes to CCL2 and key roles of CCR2, JAM-A, and ALCAM in diapedesis. PLoS One 2013; 8:e69270.
25. Kajumo F, Thompson DA, Guo Y, Dragic T. Entry of R5X4 and X4 human immunodeficiency virus type 1 strains is mediated by negatively charged and tyrosine residues in the amino-terminal domain and the second extracellular loop of CXCR4. Virology 2000; 271:240–247.
26. Lin G, Baribaud F, Romano J, Doms RW, Hoxie JA. Identification of gp120 binding sites on CXCR4 by using CD4-independent human immunodeficiency virus type 2 Env proteins. J Virol 2003; 77:931–942.
27. van Rij RP, Hazenberg MD, van Benthem BH, Otto SA, Prins M, Miedema F, et al. Early viral load and CD4+ T cell count, but not percentage of CCR5+ or CXCR4+ CD4+ T cells, are associated with R5-to-X4 HIV type 1 virus evolution. AIDS Res Hum Retroviruses 2003; 19:389–398.
28. Plaeger S, Bass HZ, Nishanian P, Thomas J, Aziz N, Detels R, et al. The prognostic significance in HIV infection of immune activation represented by cell surface antigen and plasma activation marker changes. Clin Immunol 1999; 90:238–246.
29. Carbone J, Gil J, Benito JM, Navarro J, Munoz-Fernandez A, Bartolome J, et al. Increased levels of activated subsets of CD4 T cells add to the prognostic value of low CD4 T cell counts in a cohort of HIV-infected drug users. AIDS 2000; 14:2823–2829.
30. Fahey JL, Taylor JM, Detels R, Hofmann B, Melmed R, Nishanian P, et al. The prognostic value of cellular and serologic markers in infection with human immunodeficiency virus type 1. N Engl J Med 1990; 322:166–172.
31. Cimbro R, Gallant TR, Dolan MA, Guzzo C, Zhang P, Lin Y, et al. Tyrosine sulfation in the second variable loop (V2) of HIV-1 gp120 stabilizes V2-V3 interaction and modulates neutralization sensitivity. Proc Natl Acad Sci U S A 2014; 111:3152–3157.
32. Xu Z, Wise MC, Choi H, Perales-Puchalt A, Patel A, Tello-Ruiz E, et al. Synthetic DNA delivery by electroporation promotes robust in vivo sulfation of broadly neutralizing anti-HIV immunoadhesin eCD4-Ig. EBioMedicine 2018; 35:97–105.
33. Euler Z, van Gils MJ, Boeser-Nunnink BD, Schuitemaker H, van Manen D. Genome-wide association study on the development of cross-reactive neutralizing antibodies in HIV-1 infected individuals. PLoS One 2013; 8:e54684.
Keywords:

ALCAM; disease progression; genetic variation; HIV-1; host dependency factor; pathogenesis; TPST2

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