After visiting the Keystone conference I was wondering if genetic factors of the hostess could be related to her vaginal microbiome. Janneke van de Wijgert pointed me towards the HELIUS study, that has both SNP data and vaginal microbiome available for a few hundred participants. I wrote a proposal to compare these datasets. I hope we will be able to perform this study this year. If you are working on something comparable, let me know and perhaps we can join forces! If you have any other proposals of promising SNP’s that we should take into account in the analysis, I would be very interested to hear about this.
Summary Evidence is accumulating that glycogen released by endometrium and the cervicovaginal epithelium functions as an important carbohydrate for vaginal bacteria. Luminal glycogen is found to vary both with hormonal status and with the bacterial make-up of the reproductive tract. Here we propose to study whether host genetic factors that are involved in glycogen metabolism regulation show correlation with vaginal microbial signatures.
The multi-ethnic HELIUS cohort of Amsterdam is uniquely positioned for this analysis . The vaginal microbiome of several participants was characterized previously , showing a variation in Lactobacillus-dominated microbiota and Lactobacillus-depleted dysbiotic states. This latter microbial state is associated with an increased risk of preterm labor and acquisition of sexually transmitted infection. Of a subset of these women (346 in total) genome wide SNP data will become available this year. We propose to analyze whether women with Lactobacillus-dominated vaginal microbiota are significantly more likely to carry certain alleles in the most prominent SNP’s of the TCF7L2 gene that are associated with type 2 diabetes. This preliminary analysis data could inform novel studies within this same HELIUS cohort to study the correlations between host vaginal glycogen synthesis, lactate concentration and vaginal microbiome.
Hypothesis: Glycogen functions as a carbon source for Lactobacillus species colonizing and acidifying the human vagina. We hypothesize that genetic changes in the glycogen synthesis pathway and its regulatory factors can affect the ability of Lactobacillus species to acidify the vagina and prevent changing to a bacterial vaginosis microbial state. Moreover, unpublished experiments have shown that bacterial members of this dysbiotic state such as Gardnerella and Prevotella also benefit from glycogen to grow to high numbers, produce biogenic amines (odor), cause inflammation (recruiting target cells for HIV to the mucosal surfaces), desialylation of the mucosa and exfoliation of the vaginal epithelium (discharge). Lower glycogen stores may partially explain why certain women with this microbial state have less symptoms, such as odor, discharge and inflammation, than other women.
Background During reproductive years glycogen is synthesized by the tissues of the reproductive tract [3, 4] and is essential for early embryo implantation and development. Glycogen shed into the vaginal lumen functions as a carbon source for vaginal lactobacilli such as Lactobacillus crispatus [5, 6] and iners but also for Gardnerella vaginalis and Prevotella bivia (unpublished data). Glycogen levels are reduced in women who have Lactobacillus-depleted microbial states  which could be explained by the interplay between host factors (glycogen synthesis) and bacterial factors (glycogen breakdown) .
It has been well-established that ethnicity is an important factor determining the odds of a woman to have bacterial vaginosis. Women of African descent are found to have more Lactobacillus iners than Lactobacillus crispatus and are more often colonized by a Lactobacillus-depleted community [9-11]. These women often have symptoms such as discharge and odor, and are at higher risk of acquiring sexually transmitted infection [12, 13], are more likely to have persistent HPV colonization [14, 15] and are more likely to give birth prematurely [15-17].
There has been considerable effort to understand the variation of health outcomes and symptoms amongst women with comparable vaginal microbiota. Most studies were directed at understanding this variation from a bacterial perspective, for instance by looking at genetic variation amongst bacterial isolates of Gardnerella vaginalis [18, 19] and Lactobacillus crispatus [6, 20]. We believe that the dataset we propose to analyze provides a unique opportunity to also take host factors into consideration.
Variations in glycogen metabolism due to host genetic factors may affect both hepatic glycogen accumulation as well as endometrial and vaginal glycogen accumulation. For a long time it was thought that progesterone was the main controlling hormone for glycogen synthesis in the endometrium [21, 22]. A recent study has now found that the progesterone/glycogen link is only indirect. Insulin is the hormone that inactivates glycogen synthase kinase 3β thereby activating glycogen synthase, similarly in liver tissue as well as in endometrial cells .
These commonalities lead to our hypothesis that there may be a genetic relationship between bacterial vaginosis and type 2 diabetes. In genome-wide association studies into genetic risk factors for type 2 diabetes several SNP’s have been identified. The most robust and consistent SNP’s are found in the TCF7L2 gene. Certain SNP’s in this transcription factor (elsewhere referred to as a TCF/LEF or TCF7) confer up to twofold increased risk of developing type 2 diabetes . TCF7L2 knockout mice had reduced glycogen stores in the liver . People carrying the risk allele synthesized less insulin in response to a glucose challenge test [26, 27]. This lower insulin production may have consequences for glycogen accumulation in the reproductive tract. Less glycogen synthesized means less carbohydrate for vaginal Lactobacillus species to acidify and Gardnerella to cause symptoms, odor and discharge. As of yet the ethnic differences in type 2 diabetes (where African ethnicity are at higher risk) were not able to be traced back to any SNP’s. The link between one specific TCF7L2 SNP’s (rs7903146) and type 2 diabetes was found in various regions of the world.
This would be the first study into host genetic factors and vaginal colonization.. The strength that this analysis offers is that it does not only include people from European heritage but includes a variety of groups with Asian, African and European roots. Clues from this study may inform bigger studies where we could look at the influence of genetic factors on lactate and glycogen taking into account the different ethnic groups and vaginal colonization patterns. If glycogen metabolic commonalities are found between diabetes and BV, this opens up a wide range of new treatment options for BV and related conditions, and possibly novel applications for established diabetes drugs including amylase inhibitors, insulin and metformin.
To study the SNP’s of the TCF7L2 gene and their relationship to vaginal microbiome. The HELIUS cohort will this year have both datasets available for 346 women. The vaginal microbiome of these women was previopusly studied and the authors are willing to share these data too. We propose to look at three SNP’s of the TCF7L2 gene, specifically rs7903146, rs 4506565 and rs12255372 and study whether their relationship with having a Lactobacillus-deplete (case) or Lactobacillus-dominated (control) microbiome. In case the study cohorts permit (and the odds ratio), we could differentiate further into ethnicity. In case we find a strong signal that would warrant further study, we could look at glycogen concentration, lactate concentration, vaginal microbiome and ethnicity. There are many more vaginal swabs available and SNP data for 12,000 participants in total.
Collaboration and transparency This is an Open Kitchen Science project, meaning that the aim is to maximize collaboration and transparency. All data files, methods and results, either positive or negative, will be released and published prior to peer review (either on a preprint-server or on blog). Regular information about proceedings will be shared (including this proposal, without financial details) on blogs.
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