2000 HIV Human Functional Genomics Partnership Program

Chronic HIV infection leads to a deregulated immune system, even if viral
suppression is achieved by combination AntiRetroviral Therapy (cART). On the
one hand, HIV causes persistent immune activation, which is related to an array
of common non-AIDS related diseases such as cardiovascular disease (CVD) or
non-alcoholic fatty liver disease (NAFLD). On the other hand, accelerated
aging/depletion (senescence) of the immune system hinders effective immunity
against infectious diseases and cancer. Likewise, this derailed inflammatory
balance creates a niche for persisting viral replication and reservoir, and
prevents cure or functional cure. Mechanisms behind this phenomenon are poorly
understood. Restoring this balance has proven to be challenging and new targets
for effectively restoring it are lacking. An integrative view on the
functionality of different traits of the immune system is therefore warranted.
Studies within the Human Functional Genomics Project (HFGP) have shown such
integrative view in healthy subjects and certain disease cohorts. Also a
limited HFGP study in 200 HIV patients provided first insights in immune
dysregulation in these patients. Inclusion of a larger cohort of HIV infected
patients in the discovery cohort, also with more extreme clinical phenotypes
allows us a more precise assessment of the factors underlying the immune
dysregulation, findings that need to be confirmed in a confirmation cohort.
These studies may eventually result in new targeted treatments restoring the
balance in immunity, reducing subsequent morbidity and mortality, and pave the
way for effective strategies on viral elimination.

Primary Objectives
• Employ a systems biology approach to identify a set of candidate biomarkers
(BM) in circulation and/or pathways & mechanisms that correlate with particular
non-AIDS defining comorbidities (ie NASH, CVD) in HIV+ individuals relative to
healthy controls and well matched non-HIV chronic disease phenotypes; candidate
BMs may be single or algorithm-based multi-parameter BM profile.
• Integrate diverse *omics* data to delineate biological processes (biomarkers,
pathways, and/or mechanisms) associated with extreme HIV+ clinical phenotypes
such as elite controllers, post-treatment controllers, immunological
non-responders and rapid progressors.
• Prioritize therapeutic host targets of interest either for drug discovery to
identify novel assets (ie screening and/or lead optimization) or for
repurposing of clinical phase assets from other disease areas for HIV.

Secondary Objectives
• Evaluate potential relationship of host/immune profiles on efficacy, safety,
and tolerability of different standard of care regimens.
• Evaluate the contribution of aging, female gender, and genetic background in
host-immune profiles that are:
- distinct to HIV infection relative to well-matched healthy controls;
- associated with non-AIDS defining comorbidities in HIV infection
relative to non-HIV chronic disease.

A multicenter study will performed, to build two cohorts with a total of 2000
HIV patients within the HFGP, consisting of a discovery cohort (n=1200) and
confirmation cohort (n=800). We estimate a 2-year inclusion and 2-year
follow-up period. We will strive for the inclusion of several clinical
phenotypes such as long-term non-progressors (~2-3%), immunologic
non-responders (~3%), and rapid progressors (~4-5%) and classical risk group
patients such as men who have sex with men (MSM), females and subjects from Sub
Sahara Africa. The samples size and patient selection will provide sufficient
statistical power as well as representation of ethnic/genetic diversity to
properly analyse patients with different HIV clinical outcomes as well as
compare the data with well characterized cohorts of Healthy Controls and
individuals with other disease(s).

We will use several approaches to characterize our study population:

At inclusion
1. Metadata will be collected from all the participants using
questionnaires on lifestyle, health and clinical symptoms, including
neuropsychiatric symptoms. Relevant data will also be collected from
the patients records and the HIV Monitoring Foundation.
2. Co-pathology will be assesed:
- Cardiovascular risk scores (D:A:D risk score and Framingham CVD
score) will be collected as well as intima-media thickness (IMT) in minimal
300 included patients.
- Non-Alcoholic Fatty Liver Disease (NAFLD) assessment through specific
ultrasound and fibroscan will be performed in minimal 600 included
patients.
3. Blood will be drawn (89 ml):
- DNA will be isolated for genetic analysis.
- The function of the immune system will be analysed at several levels
using circulating cells from venous blood: immunophenotyping will be done
using FCM analysis, circulating factors will be measured in plasma or
serum, in-vitro stimulations of cells and analysis of mRNA and cytokine
responses.
- Metabolism will be analysed by metabolome analysis.
- Virological analysis, characterizing the HIV reservoir, HIV resistance
and viral sequences in circulating DNA and RNA
4. Microbiome analysis will be performed on stool and saliva.
5. Urine sample will be collected for metabolomics.

After 2 years (20-26 months) follow-up
1. Clinical data from last 2 years will be retrieved from electronic patient
files.
2. Co-pathology will be assessed:
- Cardiovascular risk scores (Framingham CVD score) will be collected.
- Non-alcoholic fatty liver disease (NAFLD) assessment through specific
ultrasound and fibroscan will be done in those subjects in whom a first
assessment was performed 2 years before.
4. Blood samples (10ml) will be collected for biomarker and
infection/inflammation parameter analysis. 6. For a subset of participants, we
collect an additional 40 mL blood for extra in-depth analysis of virology and
additional in-depth immunological analyses.This subset is defined as follows:
• The 2000HIV participants who have been registered to have the elite control
clinical phenotype (n*70);
• And the 2000HIV participants identified as *normal progressors* who have also
participated in the 2000HIV-trained substudy (NL76999.091.21/2021-7495, n*30).

No risks other than local hematoma related to a single venous puncture.
The burden for the patients consists mainly of time investment. Filling in the
questionnaire will take approximately 30-40 minutes. The collection of feces,
urine en swabs wil together take approximately 10 minutes. Patients also get
two appointments with someone of the research team to perform non-invasive
measurements and to draw blood. We will try to plan these appointments on the
same day as their regular checkup in the hospital. Each visit for the study
will take approximately 60 minutes.