Uncovering the Genetic Basis of Female Infertility and Endometriosis
Many people have been personally affected by or know someone affected by infertility in some way. After all, this is an increasingly common problem with about 1 in 10 women in the United States ages 15-44 having fertility problems, according to the CDC’s National Survey of Family Growth. Many of these women seek fertility treatment to aid in becoming pregnant, where they also want to determine the cause of their infertility problems. Yet there are still many unanswered questions; in some cases, the cause of infertility cannot be explained. And infertility research is lagging, despite it being a largely unmet clinical need.
“As a practicing OBGYN and high-risk pregnancy specialist, I saw an alarming rate of pregnancy complications,” Kenneth Ward, the Advisor, Laboratory Director, and Medical Geneticist at Predictive Laboratories and the Founder and CEO of Juneau Biosciences, told BioSpace. “After shifting to a full-time research career, I was surprised to learn how much we didn’t know about human reproduction and how genetic testing technology has lagged behind in fertility research.”
Predictive Laboratories, a biotech company focused on genetic testing to understand human infertility and women’s health recently formed in 2017, is making an effort to speed up its research with a recently announced collaboration with Thermo Fisher Scientific, which is a major player in female infertility research. Together, they aim to uncover underlying genetic factors that contribute to female infertility.
“The goal of this work is to improve reproductive health, including infertility,” Yan Zhang, Vice President and General Manager of Reproductive Health at Thermo Fisher Scientific, told BioSpace. “Predictive will be able to leverage its clinical and research expertise by using Thermo Fisher’s ‘toolbox’ of state-of-the-art technology and testing supplies.”
The causes of infertility
Infertility can have a variety of underlying causes, including medical disorders, hormonal problems, reproductive organ problems, and lifestyle factors in one or both partners. The most common cause of infertility in women (in up to 40% of infertility cases) is the lack of regular ovulation (releasing of an egg from the ovaries) – without an egg to fertilize, a pregnancy cannot occur. Irregular ovulation (often indicated by irregular or no periods) can be caused by an underlying condition, such as polycystic ovary syndrome (PCOS), or by lifestyle habits, such as being over- or underweight or exercising too much.
Endometriosis is another common cause of female infertility, affecting almost 40 percent of women with infertility. Endometriosis is a disorder where tissue that lines the uterus (called the endometrium) grows outside of the uterus, typically in the pelvic region on the ovaries, bladder, and bowels. The endometrium is what grows, bleeds, and sheds during the menstrual cycle in response to estrogen, regardless of its location in the body. Therefore, the endometrial tissue outside of the uterus can grow and bleed just like the tissue in the uterus. Normal tissue surrounding the endometrial spots become inflamed and swollen and can eventually lead to scar tissue formation (called adhesions). The bleeding, inflammation, and adhesions are what cause chronic pain before and during menstruation (the most common symptom of endometriosis) and heavy menstrual bleeding. Endometrial spots and adhesions can also cause pain during sexual intercourse, during bowel movements (if spots are on the bowel), and during urination (if spots are on the bladder). However, some women with endometriosis have no symptoms.
Inflammation and scarring caused by endometriosis is also why endometriosis can cause infertility. Inflammation can damage the sperm or egg and scarring can impair their movement and even block the fallopian tubes, if it is severe.
While the cause of endometriosis is not currently known, possible causes are thought to be issues with retrograde menstrual flow up the fallopian tubes, family history/genetic factors, hormone regulation, and immune system problems (where the immune system may not find and destroy endometrial tissue that makes its way out of the uterus). Because a woman has a higher risk of having endometriosis if one of her family members has endometriosis, the possibility of a genetic cause is why it is promising to search for any genetic biomarkers.
Understanding the causes of endometriosis and how it impacts fertility has been a large focus of disease-linked infertility research to date.
Infertility and endometriosis research landscape
The only way to definitively diagnose endometriosis is through surgery to look for endometrial tissue outside the uterus (called laparoscopic surgery) and biopsy any tissue found, which is incredibly invasive, expensive, and a less than ideal option for diagnosis. This leads to a delay in definitive diagnosis, which not only has a significant impact on the disease progression, but also on the woman’s quality of life.
Creating a non-invasive diagnostic tool, such as a blood test, “remains high on the list of priorities of what is needed to improve the diagnosis, management, and prognosis (progression/regression) of treated endometriosis,” according to G David Adamson, the President of the World Endometriosis Research Foundation (WERF). However, identifying a robust biomarker (or biomarkers) of disease to use in a diagnostic test involves a thorough understanding of the causes and genetics of endometriosis, which are still relatively unclear. Therefore, most ongoing research has two main goals: 1) to identify endometriosis biomarkers and use them to create a reliable blood test to diagnose endometriosis, and 2) to examine the biomarkers and genetics of endometriosis to better understand the disease.
The lack of clinical validation of biomarkers can be attributed to the varied protocols and sample collection and storage methods used by each researcher and company. This makes it more difficult (if not impossible) to compare results between researchers and hinders large-scale, high-powered studies. To increase the standardization of endometriosis research, the WERF Endometriosis Phenome and Biobanking Harmonization Project (EPHect) was created in 2013. Based off of a global meeting in March 2013, a set of standardized clinical and personal data and standard operating procedures for sample collection, transportation, processing, and long-term storage were developed and published in 2014. According to the WERF EPHect website, 29 institutions in 19 countries are currently registered users.
In 2010, although over 100 possible biomarkers for endometriosis were found in the scientific literature, none of those were verified as being clinically useful. In 2012, two panels of four biomarkers (annexin V, VEGF, CA-125, and sICAM-1 or glycodelin) were able to diagnose endometriosis with 81-90 percent specificity in blood samples from women with (n = 232) and without (n = 121) surgically-confirmed endometriosis. Despite biomarker identification and the ability of some biomarkers to identify endometriosis, no clinical test had been developed as of 2018.
A meta-analysis of 17 studies involving 1,279 patients published in May identified aromatase as a potentially promising diagnostic biomarker, but mentioned the “moderate quality of the included studies and the limited sample size” limited these conclusions.
In July, data from a new multiplex cytokine array evaluating 260 potential biomarkers of endometriosis in the blood of women with (n = 70) and without (n = 52) endometriosis was published. The array was like a high-throughput ELISA, with spots on a glass slide containing antigen-specific capture antibody, just like wells in a multi-well plate would in an ELISA. The assay identified 14 serum cytokines (6Ckine, CD14, CEACAM-1, ENA-78, ERBB3, IL-7, I-TAC, LAP (TGF-β), Lipocalin-2, MCP-1, NrCAM, RAGE, TARC, and TNF-β) that were significantly different in endometriosis patients compared to healthy controls. Seven of those biomarkers (CD14, ENA-78, I-TAC, NrCAM, RAGE, TARC, and TNF-β) were selectively different only in endometriosis patients, compared with unique serum biomarkers in women with other gynecological inflammatory disorders, including PCOS (n = 5), ovarian cysts (n = 15), and pelvic adhesions (n = 6). The array correctly identified an average of 78 percent of endometriosis samples.
In January, MDNA Life Sciences reported successful detection of endometriosis in blood samples from women with (n = 150) and without (n = 32) surgery-confirmed endometriosis. They looked at the differences in mitochondrial DNA (mtDNA), the small amount of DNA found in the mitochondria, a structure within each cell that provides energy to the cell. Two deletions in the mtDNA were significantly present in the blood of women with endometriosis (of any type and any stage of disease) compared to women without endometriosis. Overall, the two deletions could be reliably detected 81.8 percent and 85.0 percent of the time. This is comparable to the 60 to 85% accuracy of the standard diagnostic means (laparoscopic surgery with tissue biopsy). These two deletions also had a negative predictive value of 97 percent, meaning that 97 percent of women in which neither deletion is detected will not have the disease – giving a very low false negative rate.
Importantly, presence of the smaller deletion was not influenced by hormonal status or where the women were in their menstrual cycle, both of which typically plague endometriosis biomarker detection by causing variability in biomarker expression. The second larger deletion was significantly affected by menstrual cycle, but given the smaller patient size of this study, a larger study is needed to confirm that correlation, as well as the overall correlation of these two mtDNA deletions with the presence of endometriosis. So far, the role that the genes in the two deletions play in endometriosis is unknown.
In April, MDNA Life Sciences announced their plans to launch a blood test for endometriosis biomarker detection based on detecting the two mtDNA deletions from blood samples. A kit is being created with the intentions of it being used by clinical laboratories to test patient samples. The test kit was estimated to be launched in early 2020.
Juneau Biosciences is examining the genetic factors involved in endometriosis by conducting a clinical study, called End to Endo. They have already studied tens of thousands of women, but in order to extend, refine, and replicate their discoveries, they continue to look for women who have had “gynecological surgery due to pelvic pain or infertility” who either have or do not have endometriosis. (If you are interested in joining, you can submit your information here.) They used genome-wide association studies (GWAS), copy number analyses, and next generation sequencing to analyze data collected from their clinical study and identify reliable biomarkers for endometriosis.
“Understanding the genetics of endometriosis will not only replace the need for surgical diagnosis with a non-invasive blood test, but it will tease out the biomarkers associated with increased risk of certain cancers, autoimmune disease, and other conditions seen at a higher incidence in women with endometriosis,” Ward said. “The goal of a blood test for endometriosis should be to diagnose, subclassify the disease (as endometriosis is likely a spectrum of conditions, not just one disease), and understand the risks associated with each woman’s endometriosis.”
Juneau, in partnership with Predictive, now offers the “first, non-invasive, integrated test for endometriosis and genetic causes of infertility,” called ARTguide. ARTguide is a blood test that looks for thousands of gene variants associated with endometriosis and 12 genes associated with fertility. It can tell a woman her probability of having endometriosis based on how many risk factors she has and if she has any genetic mutations that may impact her fertility. This test is designed for women who plan to use assisted reproductive technologies (ART), like in vitro fertilization (IVF). ARTguide was designed to better inform a woman and her doctor while undergoing ART by providing otherwise unknown fertility information and personalized treatment plans based on that information. This will hopefully reduce the number of fertility cycles needed to achieve a successful pregnancy.
Thermo Fisher, Predictive partnership to advance infertility research
The ARTguide tests are also a part of the Predictive, Thermo Fisher research as the tests will be run using Thermo Fisher’s AmpliSeq technology. All testing is currently done in Predictive’s CLIA-regulated laboratory; however, Predictive is also developing kits that can be sent to other labs for testing elsewhere. So far, these kits have been rolled out at a few sites and they hope that they will be available nationwide by the end of the year. In the future, Predictive also wants to develop kits formatted especially for other parts of the world, including language translations, analysis of different genetic variations (accounting for the genetic variations seen in different populations), and culturally appropriate representation of information.
Although Predictive and Thermo Fisher plan to examine multiple causes of female infertility, they will focus on endometriosis first, as it is the most well-studied with the most data to date. Using Thermo Fisher’s assays and next-generation sequencers, Predictive is leveraging its DNA sample library, databases, and records to investigate the genetic basis of endometriosis via whole exome sequencing (sequencing of the portions of the genome that encode for proteins, called the exome).
In addition to the partnership, Predictive recently presented their latest data on the genetics of endometriosis at the European Society of Human Reproduction and Embryology (ESHRE) in June. They identified four mutated genes (ZNF586, LUZP4, POP4 and UNC5CL) identified in blood or saliva samples from women with surgery-confirmed endometriosis (n = 2,596). While only eight percent of the population carries these mutations, 25 percent of women with endometriosis had one of these mutations. This is the first time these genes have been implied in endometriosis. Unfortunately, none of the proteins that these genes code for have any known role in endometriosis.