2000 HIV Human Functional Genomics Partnership Program

Study Overview
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Brief Summary
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Background Chronic HIV infection leads to a dysregulated immune system, even when full viral suppression is achieved. HIV causes persistent immune activation, relating to an array of common non-AIDS-related diseases such as cardiovascular disease (CVD) and non-alcoholic fatty liver disease (NAFLD). On the other hand, accelerated ageing of the immune system hinders effective immunity against infectious diseases and cancer. Likewise, this derailed inflammatory balance creates a niche for persistent viral replication and reservoir, and prevents cure or functional cure. Mechanisms behind this phenomenon are poorly understood. Inclusion of a larger cohort of HIV-infected patients allows for a more precise assessment of the factors underlying the immune dysregulation. Primary Objectives Identify a set of candidate biomarkers that correlate with particular non-AIDS-related comorbidities Unravel biological processes associated with extreme HIV clinical phenotypes. Find therapeutic targets to identify novel assets 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 standard care regimens. Evaluate the contribution of age, sex, and genetics in host-immune profiles that are: distinct to HIV infection relative to controls in other cohorts; associated with non-AIDS-related comorbidities in HIV infection relative to non-HIV chronic disease. Study design 2000 HIV patients will be included in the cohort. The investigators estimate a 2-year inclusion and 2-year follow-up period and will strive for the inclusion of several clinical phenotypes and classical risk group patients. Patients will be recruited from four Dutch HIV treatment centers. At inclusion Collection of metadata using questionnaires and patient medical records Asses co-pathology (CVD and NAFLD) Blood will be drawn for genetic, epigenetic, proteomic, metabolomic, microbiome, immunological, and virological analyses After 2 years follow-up Collection of metadata using questionnaires and patient medical records Asses co-pathology (CVD and NAFLD) Blood samples will be collected for biomarker and infection/inflammation parameter analysis

Detailed Description
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Study population A cohort with a total of 2000 HIV patients will be built, consisting of a discovery cohort (n=1200) and confirmation cohort (n=800). The investigators estimate a 2-year inclusion and 2-year follow-up period and 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. Patients will be recruited from the following Dutch HIV Treatment Centers: Radboudumc (Nijmegen), Erasmus MC (Rotterdam), OLVG (Amsterdam), Elisabeth Twee-Steden Ziekenhuis (Tilburg). A sample size calculation cannot be provided due to the variable frequencies of the various traits in genome-microbiome interaction, and their effect on cytokine production. Because of the explorative nature of this study, the size calculation will be variable depending on the type of polymorphism analyzed. The frequencies of the various microorganism classes in the colonizing microbiome is not known in our study population, and therefore power calculations are impossible to be performed. Earlier studies in the Human Functional Genomics Project have assessed microbiome traits in 250-500 individuals. An earlier HFGP study included a uniform cohort of 200 HIV-infected individuals (all MSM). The present study will also include HIV-infected patients with a more extreme phenotype, females and subjects originating from Sub-Sahara Africa. Because of this, the investigators decided to increase the number of individuals tested to 2000, consisting of a discovery cohort of 1200 subjects, and a confirmation cohort of 800 participants. Study visits and procedures At inclusion The investigators will collect metadata using questionnaires on lifestyle, health and clinical symptoms, including neuropsychiatric symptoms. Relevant data will also be collected from the patients records in the medical centers and the HIV Monitoring Foundation. Co-pathology will be assesed: Cardiovascular risk scores (D:A:D risk score and Framingham CVD score) will be collected as well as ECG and intima-media thickness (IMT) measurements. Non-Alcoholic Fatty Liver Disease (NAFLD) assessment through liver ultrasound and FibroScan. Blood will be drawn (90 ml): DNA will be isolated for genetic and epigenetic analysis. The function of the immune system will be analyzed at several levels using circulating white blood cells from venous blood. Metabolism and proteomics will be analyzed Virological analysis, characterizing the HIV reservoir, HIV resistance and viral sequences in circulating DNA and RNA. Microbiome analysis will be performed on stool and saliva samples. Urine sample will be collected for creatinine measurements and microbiome. After 2 years follow-up The investigators will collect metadata using questionnaires on lifestyle, health and clinical symptoms, including neuropsychiatric symptoms. Relevant data will also be collected from the patients records in the medical centers and the HIV Monitoring Foundation. Co-pathology will be assesed: Cardiovascular risk scores (D:A:D risk score and Framingham CVD score) will be collected as well as ECG. Non-Alcoholic Fatty Liver Disease (NAFLD) assessment through liver ultrasound and FibroScan. Blood samples (10ml) will be collected for biomarker and infection/inflammation parameter analysis. Patient informed consent procedure Patients will always be approached first by a treating physician or specialized nurse. They will be provided with information and will be asked if a physician-researcher may contact the patient. If there is oral consent for this, the researcher contacts the patient in one week to ask if they are interested in participating in the study. the physician-researcher will answer any questions the patient may have and plan the first visit. The informed consent procedure will be conducted during the patient's first visit. Patient registry procedures All patient data will be recorded only in coded form in a secure database with audit and edit trail (CASTOR EDC). During the informed consent procedure, the patient is given a study code. The identifying patient data and study code is kept in a password-protected key file, only accessible to the local research team. No patient-identifying data will leave the local medical center. In the questionnaires and eCRFs in CASTOR, the investigators will enter as many data checks as possible Biomaterials All biomaterial (blood, stool, urine, saliva) will be transported to and processed in the laboratory of Experimental Internal Medicine of the Radboudumc in Nijmegen. Here, all the biomaterial will also be stored collectively. All materials will be handled and stored only under the patient's study code. Monitoring Monitoring will be performed by an independent monitor according to the latest guidelines of the The Netherlands Federation of University Medical Centers. An initiation and close-out visit will be planned in plenary form with all the centers in Radboudumc. There will be one extra visit per center. During these visits informed consents will be checked, as well as inclusion and exclusion criteria and source data verification in a small subset of total participants. Data collection for patient registry Baseline data collected from electronic patient files or the HIV Monitoring Foundation during inclusion visit: Medical history: Inclusion date Length and weight Last known blood pressure (and date measured) Seroconversion date (if known) Date first HIV-positive test Date start cART HIV transmission risk behavior: MSM Heterosexual Injecting drug use Contaminated blood products Unknown First CD4 count CD4 nadir CD4/CD8 ratio pre-cART HIV stadium at start cART according to CDC criteria Pre-cART HIV RNA zenith Opportunistic conditions before start cART None MTB Fungal infections Parasitic infections, Bacterial infections Malignancies before start cART None If yes, specify what kind, when and treatment Other known medical problems before start cART, which require long-term treatment None If yes, specify what kind, when and treatment Response cART: Period between start cART and viral load < 500 (months) Viral loads: Undetectable after 24 weeks: yes/no Number/frequency of residual viremia (positive test with signal <50 copies): last year and last 5 years Number of viral blips (50-200): last year and last 5 years Number of viremia: 200-1000: last year and last 5 years Number of failing cART (>1000): last year and last 5 years Resistance associated mutations pre-cART and following failure CD4 reconstitution CD4/CD8 ratio and normalization >1 yes/no after cART initiation IRIS, yes/no Opportunistic conditions after start cART (if known) None MTB Fungal infections Parasitic infections, Bacterial infections Malignancies after start cART (if known) None If yes, specify what kind, when and treatment Vascular diseases after start cART: None Stroke/ TIA Angina pectoris Myocardial infarction Claudicatio intermittens Venous thrombo-embolism Other … SOAs None HAV: yes/no, if yes: treatment and how often HBV: Infected: active infection (PCR+) or non-active infection Vaccination: No/Yes Once with anti-HBs> 100 Two times vaccination leading to anti-HBs> 100 anti-HBs< 100 No infection HCV: yes/no, if yes: treatment and how often Lues: yes/ no: if yes: treatment and how often Chlamydia/Go: yes/ no: if yes: treatment and how often HPV COVID-19 infection before or after start cART: Was a COVID-19 test done and if so type of test if known (PCR or antigen test), date of test and result of laboratory test for COVID-19 (positive or negative) COVID-19 Serology results Register COVID-19-related hospital admissions COVID-19 vaccination: type and date(s) Side effects of COVID-19 vaccination: Mild: overall malaise, fatigue, muscle ache, pain at injection site, shivers, headache. Moderate: mild symptoms to the extend (self)medication/pain relief is required. Severe: fever >38.5 degrees Celsius and/or one or more days bedridden cART regimes Reasons for switching Prescribed co-medication Full current medication list Physical examination Signs of Kaposi sarcoma Lymphadenopathy For determination of medication levels: when was the last date and time HIV-medication was taken? Other abnormalities: … Cardiovascular risk profile: D:A:D (R) and Framingham scores ECG Laboratory results of date closest to inclusion date (standard care at least once a year according to Dutch guidelines): Full blood count Liver enzymes (ALAT, AF, bilirubin) Creatinine HIV-RNA CD4 and CD8 counts Glucose Lipid profile TPHA/VDRL HCV serology (for all at risk, such as MSM and i.v. drug users) If positive, HCV PCR HPV diagnostics in females (PAP, PCR) Urine diagnostics (if available): α1-microglobulin, protein, albumin, phosphate, creatinin Baseline data collected from electronic patient files or the HIV Monitoring Foundation during 2-year follow-up visit: Medical history last 2 years: Date of 2 year follow-up visit Weight Last known blood pressure (and date measured) Response cART last 2 years Number of residual viremia: last 2 years Number of viral blips (20-200): last 2 years Number of viremia (200-1000): last 2 years Number of failing cART (>1000): last 2 years CD4 count CD4/CD8 ratio (if known) Opportunistic conditions last 2 years None MTB Fungal infections Parasitic infections, Bacterial infections Malignancies in the last 2 years None If yes, specify what kind, when and treatment Signs/symptoms of cardiovascular diseases in the last 2 years: None Stroke/ TIA Angina pectoris Myocardial infarction Claudicatio intermittens Venous thrombo-embolism Other … New SOAs in the last 2 years HAV: yes/no, if yes: treatment and how often HBV: Infected: active infection (PCR+), non-active infection, Vaccination: No/Yes Once with anti-HBs> 100 Two times vaccination leading to anti-HBs> 100 anti-HBs< 100 No infection HCV: yes/no, if yes: treatment and how often Lues: yes/ no: if yes: treatment and how often Chlamydia/Go: yes/ no: if yes: treatment and how often COVID-19 infection before or after start cART: Was a COVID-19 test done and if so type of test if known (PCR or antigen test), date of test and result of laboratory test for COVID-19 (positive or negative) COVID-19 Serology results Register COVID-19-related hospital admissions COVID-19 vaccination: type and date(s) Side effects of COVID-19 vaccination: Mild: overall malaise, fatigue, muscle ache, pain at injection site, shivers, headache. Moderate: mild symptoms to the extend (self)medication/pain relief is required. Severe: fever >38.5 degrees Celsius and/or one or more days bedridden cART regimes in the last 2 years Reasons for switching available from 'Stichting HIV Monitoring' Prescribed co-medication Full current medication list Physical examination Signs of Kaposi sarcoma Lymphadenopathy For determination of medication levels: when was the last date and time HIV-medication was taken? Other abnormalities: … Cardiovascular risk profile: D:A:D (R) and Framingham scores ECG Laboratory results of date closest to follow-up visit date: Full blood count Liver enzymes (ALAT, AF, bilirubin) Creatinine HIV-RNA CD4 and CD8 counts Glucose Lipid profile TPHA/VDRL HCV serology o If positive, HCV PCR HPV diagnostics in females (PAP, PCR) Urine diagnostics

Official Title
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2000 HIV Human Functional Genomics Partnership Program

Conditions
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HIV Infections

Participation Criteria
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Eligibility Criteria
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Inclusion Criteria: HIV-infected, aged ≥18 years, on cART ≥6 months with an HIV-RNA load <200 copies/mL, *Apart from the above-mentioned subjects, elite controllers that are not on cART, are also eligible. Exclusion Criteria: No informed consent Insufficient communication because of language or other problems Active hepatitis B/C or signs of acute infections Pregnancy

Ages Eligible for Study
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Minimum Age: 18 Years

Sexes Eligible for Study
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All

Accepts Healthy Volunteers
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No

Study Plan
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How is the study designed?
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What is the study measuring?
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Primary Outcome Measures

| Outcome Measure | Measure Description | Time Frame |
| --- | --- | --- |
| Change in liver fibrosis | Change in liver fibrosis measurement by FibroScan (method by Echosens) | Change: 2-year value - baseline value | 
| Change in liver steatosis | Change in liver steatosis measurement by FibroScan (method by Echosens) and liver ultrasound (method developed by Radboudumc) | Change: 2-year value - baseline value | 
| Change in cardiovascular risk score (Framingham score) | Framingham score | Change: 2-year value - baseline value | 
| Change in cardiovascular risk score (D:A:D score) | D:A:D score | Change: 2-year value - baseline value | 
| Number and type of cardiovascular events | Recoring of cadiovascular diseases from patient file: Stroke/ TIA Angina pectoris Myocardial infarction Claudicatio intermittens Venous thrombo-embolism Other … | Number of events over 2 years between baseline and 2-year time point | 
| Genetic data | Genome-wide genotype data including >8 million SNPs per individual | At baseline only | 
| Colonizing microbiome profile | Colonizing microbiome profile will be generated from stool and saliva samples | At baseline only | 
| Transcriptomics | RNA-sequencing will be performed in PBMCs | At baseline only | 
| Quantification of a wide range of metabolites | Metabolomics analysis by multiplex immunoassays will be performed in plasma or serum | At baseline only | 
| Cytokine production of PBMCs in ex vivo stimulation experiments | Ex vivo cytokine responses of isolated PBMCs to a range of stimuli (TLR ligands, killed pathogens and viral antigen stimuli) | At baseline only | 
| Immune phenotyping | Extensive phenotyping of circulating immune cells by flow cytometry analysis | At baseline only | 
| Change in ECG | Standardized signs of myocardial infarction with MEANS ECG software, as extensively described elsewehere. In addition, we will look at the full list of ECG output measurements as described elsewhere*: in brief, MEANS reliably provides output on interpretation of the ECG rhythm and morphology. The morphological interpretation consists of separate analyses of the P wave, QRS complex, and ST-T segment. Reference: Van den Berg ME, Rijnbeek PR, Niemeijer MN, et al. Normal values of corrected heart-rate variability in 10-second electrocardiograms for all ages. Front Physiol. 2018;9:424 | ECG paramater changes between baseline and 2-year time visit | 
| Intima-media thickness | Ultrasound measurement of intima-media thickness in the carotid artery as a measure for atherosclerosis and cardiovasculr disease risk. | At baseline only | 

 Terms related to the study
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Keywords Provided by Centre Hospitalier Valida
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HIV, Non-alcoholic fatty liver disease, Cardiovascular disease, Omics data, Inflammation