The Microbiome in HIV: The Good, Bad, and Ugly of Bugs in Health

Transcription

1 The Microbiome in HIV: The Good, Bad, and Ugly of Bugs in Health Nichole R. Klatt, PhD Associate Professor University of Washington Seattle, Washington Learning Objectives After attending this presentation, learners will be able to describe: How the microbiome contributes to HIV transmission How the microbiome contributes to HIV disease What the microbiome is Slide 3 of 45 ARS Question 1 HIV-altered microbiota can increase neutrophil accumulation in the gut by what mechanism: 1. Attaching to blood neutrophils 2. Decreasing apoptosis and increasing survival 3. Binding to viruses 4. Developing a biofilm Slide 4 of 45

2 ARS Question 2 What feature of the vaginal microbiome is associated with health and decreased HIV transmission? 1. Increased diversity 2. High inflammation 3. Decreased diversity 4. Excess mucus Slide 5 of 45 Individuals must remain on ART indefinitely Increased Non-AIDS Morbidity and Mortality Life Expectancy is Reduced Despite ART HIV Reservoir (Anatomic sanctuaries, Persistent integrated provirus) Persistent Immune Activation Mucosal Dysfunction Slide 6 of 45 Inflammation (particularly associated with mucosal dysfunction) is a key predictor of morbidities and mortality Slide 7 of 45 What are the mechanisms of mucosal dysfunction in HIV Infection?

3 Overlapping mechanisms underlying increased HIV transmission risk AND increased HIV pathogenesis TRANSMISSION 1. Barrier Damage 2. Inflammation 3. Altered Microbiome PATHOGENESIS 1. Barrier Damage 2. Inflammation 3. Altered Microbiome Slide 8 of 45 Microbiome Microbiome: Microorganisms in an environment ( trillion/person) Includes bacteria, viruses, fungi, protists, archaea Includes genes, metabolites and products Dysbiosis: An imbalanced microbial community Abundance and/or functional changes Smits LP et al., Gastroenterology Slide 9 of 45 Microbial dysbiosis is associated with many diseases Oral microbiome dysbiosis: Gingivitis Periodontal Diseases HIV Pathogenesis Lung microbiome dysbiosis: Lung Cancer Asthma COPD Cystic Fibrosis Pneumonia Skin microbiome dysbiosis: Skin Cancer Altered immunity Allergies Psoriasis Dermatitis Acne Dysplasia Vaginal microbiome dysbiosis: Vaginosis STIs Yeast Infection Preterm Birth HIV Transmission Gut microbiome dysbiosis: Colorectal Cancer Diabetes Obesity Autoimmunity Inflammatory Bowel Diseases C. difficile infection Neurological Disorders Metabolic Disorders HIV Pathogenesis Slide 10 of 45

4 Dysbiosis in HIV infection Bad/Increased in HIV: Prevotella Proteobacteria Good/Decreased in HIV: Firmicutes Bacteroides Slide 11 of 45 Slide 12 of 45 Increased colorectal neutrophil frequencies in HIV+ individuals Slide 13 of 45

5 Reduced neutrophil apoptosis in treated HIV infection Homeostatic neutrophil apoptosis Neutrophil accumulation Slide 14 of 45 Associations between colonic mucosal bacteria and neutrophil survival in vivo Caspase-3 Low,CD16 High Neutrophils vs. Prevotella (genus) Caspase-3 Low,CD16 High Neutrophils vs. Lactobacillus (genus) %Caspase-3 Low, CD16 High of Total Neutrophils Prevotella (relative abundance) %Caspase-3 Low, CD16 High of Total Neutrophils Lactobacillus (genus) Slide 15 of 45 p= Pearson R 2 = p= Pearson R 2 = Conclusions I: Neutrophils and Dysbiotic Bacteria in HIV Pathogenesis Neutrophils are increased in the GI of treated HIV infection Associated with decreased neutrophil apoptosis HIV-altered mucosal bacteria differentially affect neutrophil apoptosis Decreased Lactobacillus spp. and increased Prevotella spp may prolong neutrophil lifespan in the GI in treated HIV infection. Future directions: Further understanding how neutrophils contribute to HIV pathogenesis and barrier damage may elucidate potential targets for therapeutic interventions Slide 16 of 45

6 Overlapping mechanisms underlying increased HIV transmission risk AND increased HIV pathogenesis TRANSMISSION 1. Barrier Damage 2. Inflammation 3. Altered Microbiome PATHOGENESIS 1. Barrier Damage 2. Inflammation 3. Altered Microbiome Slide 17 of 45 Every minute, two women are infected with HIV What are the biological mechanisms leading to HIV acquisition in women? Slide 18 of 45 Women tend to get infected at a younger age Sub-Saharan Africa has 2x women ages than men with HIV infection Pregnancy / mother-tochild transmission Sexual violence, lack of condom/sexual protection negotiation rights Slide 19 of 45 (Burgener, McGowan, Klatt; Curr Opinion Immunol 2015)

7 Vaginal microbiome can be broken into distinct community type (CT) structures Grosmann; Kwon et al., Immunity 2017 Slide 20 of 45 Bacterial Vaginosis (BV) is typically clinical diagnosis of microbiome dysbiosis Most common cause of vaginitis Inflammation, discharge, discomfort Loss of Lactobacillus spp. and increased diversity of vaginal microbiome Clinically diagnosed by Nugent score (0-10) and/or Amsel s criteria Wet mount, clue cells, morphology Typical antibiotic treatment is not effective, with frequent recurrence ph < 4.7 Nugent = 0 ph > 4.7 Nugent 7-10 Amsel s + Slide 21 of 45 Clinical Bacterial Vaginosis testing by Nugent score does not accurately predict vaginal dysbiosis Slide 22 of 45 (CVLs from Miami WIHS Cohort)

8 Tenofovir Placebo Tenofovir Tenofovir Placebo Placebo Vaginal dysbiosis and BV increase HIV infection risk Grosmann; Kwon et al., Immunity 2017 Slide 23 of 45 Effectiveness of pre-exposure prophylaxis (PrEP) is highly variable in women Study TDF2 daily Tenovofir-Emtricitabine (Women & Men - Botswana)# Effect size (CI) 75%* (24; 94) Partners PrEP daily oral Tenofovir (Discordant couples Kenya, Uganda) 71%* (37; 87) Oral PrEP Partners PrEP daily Tenovofir-Emtricitabine (Discordant couples Kenya, Uganda) 66%* (28; 84) FEMPrEP daily Tenovofir-Emtricitabine (Women Kenya, South Africa, Tanzania) 6% (-52; 41) MTN003/VOICE daily Tenovofir-Emtricitabine (Women South Africa, Uganda, Zimbabwe) -4% (-49; 27) MTN003/VOICE daily Tenofovir (Women - South Africa, Uganda, Zimbabwe) -49% (-129; 3) Topical PrEP CAPRISA 004 coital Tenofovir gel (Women South Africa) 39% (6; 60) MTN003/VOICE daily Tenofovir gel (Women South Africa, Uganda, Zimbabwe) 15% (-21; 40) FACTS 001 coital Tenofovir gel (Women South Africa) 0% (-40, 30) #(Study population and countries where the study was conducted) *Effect size calculated from the incidence rate ratio for women only Effectiveness (%) Varying outcomes from PrEP trials - attributed to adherence What biological factors affect PrEP? Slide 24 of 45 Vaginal microbial groups in CAPRISA 004 alter efficacy G. vaginalis dominant Lactobacillus dominant Probability of HIV infection 0.40 A. Lactobacillus dominant Efficacy, 61% 95% CI, 11 to 84% P=0.013 Probability of HIV infection Ef HR = 0.39 (95% CI: 0.20; 0.83) Years in Study Lactobacillus dominant women at risk (Cumulative number of infections) A. Lactobacillus dominant Tenofovir 0.40 B. Non-Lactobacillus dominant 205 (0) 204 (1) 183 (3) 129 (7) 46 (9) 0 (9) Placebo (0) 196 (4) 173 (12) 123 (19) 51 (22) 0 (22) Non-Lactobacillus domin Tenofovir 140 (0) Placebo 141 (0) Probability of HIV infection <50% 0.10 Lactobacillus 0.05 Efficacy, 61% 95% CI, 11 to 84% >50% Lactobacillus P=0.013 Probability of HIV infection 0.30 Efficacy, 18% 95% CI, -77 to 63% P=0.644 Slide 25 of 45 HR = 0.39 (95% CI: 0.20; 0.83) HR = 0.82 (95% CI: 0.40; 1.65) Years in Study Klatt et al., Science 2017 Years in Study Lactobacillus dominant women at risk (Cumulative number of infections) Non-Lactobacillus dominant women at risk (Cumulative number of infections)

9 Assessing biodegradation of PrEP drugs from primary cervicovaginal lavage (CVL) samples CVL (WIHS) (29) BV - (15) BV + Tenofovir (TFV) Drug Metabolism Microbiome communities Slide 26 of 45 Dysbiotic bacteria metabolize Tenofovir (TFV) Intracellular TFV-DP (TFV) - Lactobacillus 1.5 TFV-DP (ug/ml) **** 0.0 >50% <50% Slide 27 of 45 Dysbiotic bacteria metabolize Dapivirine (DPV) Bacteria Relative Abundance α-diversity Shannon Index BV Status by Nugent Score Positive Negative DPV (ug/ml) Intracellular DPV - Lactobacillus >50% **** <50% Dapivirine Degradation Rate

10 Bacteria do not metabolize Tenofovir Alafenamide (TAF) Intracellular TFV-DP (TAF) - Lactobacillus 1.5 TFV-DP (ug/ml) >50% <50% ARV drug metabolism Inflammation Barrier damage Slide 30 of 45 (Burgener, McGowan, Klatt; Curr Opinion Immunol 2015) Conclusions Dysbiosis of vaginal bacteria is a key factor in vaginal inflammation, epithelial barrier integrity and HIV acquisition Dysbiotic bacteria can metabolize Tenofovir Potentially contributes to decreased PrEP efficacy Understanding the vaginal microbiome and how to increase Lactobacillus communities and prevent BV/dysbiosis recurrence will be essential in improving efficacy Slide 31 of 45

11 Potential therapeutics Better assessments of and interventions for vaginal dysbiosis are critically needed Current standard of care is antibiotics (Metronidazole/Flagyl, Clindamycin) Limited efficacy, frequent recurrences Probiotics/Prebiotics/Live Biotherapeutics Lactin V Microbiome material transplant Phage Therapy Gene targeting/editing Slide 32 of 45 ARS Question 1 HIV-altered microbiota may increase neutrophil accumulation in the gut by what mechanism: 1. Attaching to blood neutrophils 2. Decreasing apoptosis and increasing survival 3. Binding to viruses 4. Developing a biofilm Slide 33 of 45 ARS Question 2 What feature of the vaginal microbiome is associated with health and decreased HIV transmission? 1. Increased diversity 2. High inflammation 3. Decreased diversity 4. Excess mucus Slide 34 of 45

12 UW/WaNPRC/Pharmaceutics CAPRISA University of Miami Dept. of Pediatrics Salim Abdool Karim Klatt Lab Quarraisha Abdool Karim Ryan Cheu Lyle McKinnon Andrew Gustin Anneke Grobler Jennifer Manuzak Tiffany Hensley-McBain UW Harborview Hospital Alex Zevin Ann Collier Charlene Miller Michalina Montano Connor Driscoll Lindsay Legg Oliver Appelbe UCSF SCOPE Debbie Bratt Peter Hunt Ernesto Coronado Ma Somsouk De Neka Gary Montha Pao Courtney Broedlow Monika Deswal Jake Modesitt Rebecca Hoh Alex Roederer Acknowledgements University of Miami Maria Alcaide University of Manitoba/ National Microbiology Laboratory Adam Burgener Kenzie Birse Laura Romas Michelle Perner Slide 35 of 45 Slide 44 of 45 Northwestern University Tom Hope Mike McRaven NIH/NIAID 1K22AI NIH/NIAID 1R01AI NIH/NIDDK RO1DK NIH/NIDA 1DP13A UW CFAR CIHR Mucosal Team Grant (Burgener)