Submitted by: Dr Waqasuddin Khan, Dr Javairia Khalid, Dr M. Imran Nisar, and Dr Fyezah Jehan
Advances in RNA-sequencing techniques have led to the discovery of thousands of non-coding transcripts with unknown functions. Only one to two percent of the human genome codes for proteins, dividing the RNA world into two kinds:
- RNAs that have coding potential
- RNAs without coding potential, referred to as non-coding RNAs (ncRNAs)
Although mRNAs have been studied extensively, it is ncRNAs that account for the majority of RNAs. In the past, ncRNAs were considered “evolutionary junk,” but increasingly evidence suggests that they have a huge impact on several molecular mechanisms. These regulatory molecules have critical cellular functions, including control of gene expression at transcriptional and translational mechanisms. Both short and long classes of ncRNAs can modulate epigenetic processes, chromatin remodeling, histone modification, DNA methylation, and gene silencing.
MicroRNAs (miRNAs) are short ncRNA sequences of less than 30 nucleotides that typically function by binding target mRNA to induce degradation or prevent protein translation. Long non-coding RNAs (lncRNAs) are greater than 200 nucleotides and have more varied functions than miRNAs, that is, commonly coupled with chromatin proteins to influence transcription. Both miRNAs and lncRNAs have been implicated in myriad disease states, including tumorigenesis and inflammatory conditions, such as autoimmune disorders, infections, and cardiovascular diseases. Non-coding RNAs may function as biomarkers for adverse pregnancy outcomes (APOs), including spontaneous abortion, preeclampsia, fetal growth restriction, and preterm birth (PTB).
Infants born early are at higher risk for multiple morbidities than infants born at term. While many epidemiologic reports have explored risk factors for PTB, including bacterial vaginosis, short mid-pregnancy cervical length, prior spontaneous PTB, and smoking, the molecular mechanisms underlying PTB are yet to be fully unveiled. Inflammation has sustained concern in the pathophysiology of PTB, but how it causes premature rupture of membranes, preterm labor, and cervical remodeling, all of which can lead to spontaneous PTB, remains unknown. Characterizing pregnancy-associated changes in local expression of ncRNAs within the reproductive tissues, that is, vagina, cervix, uterus, etc., is essential as these regulatory molecules are dynamic throughout the gestation period, and most likely vulnerable to environmental factors that may drive pathological events in pregnancy. Thus, it is imperative to collect samples from the tissues relevant to the physiological processes of interest. Let’s take the example of a cervix; a well-studied tissue as a clinical predictor of PTB, though the biology underlying normal parturition remains poorly understood.
Given the dynamic nature of the cervix and the cervical remodeling process, new multi-omics research has great potential to detect adverse pregnancies and the facilitation of early recognition of pathological processes implicated in adverse perinatal outcomes. Some examples of these technologies are genomics, transcriptomics, proteomics, and metabolomics, which involve the investigation of DNA, RNA, proteins, and metabolites respectively. Multi-omics offers the opportunity to understand the in-vivo and in-vitro study of molecular phenotypes through unraveling the mechanisms involved in biological processes and molecular functions, interaction, and cellular fate. Emerging precision medicine can further progress through multi-omics in the areas of predictive and prognostic biomarkers and potentially repurposed and novel drugs. Applied multi-omics involves a sound understanding of the genotypic and phenotypic relationship to help enhance diagnosis yield, prognosis, and better health consequences.
The Aga Khan University is a member of the Multi-omics for Mothers and Infants (MOMI) consortium that directly addresses APOs and their related critical issues by predicting new genetic and biological markers for PTB, preeclampsia, stillbirth, and IUGR in low-and-middle-income countries (LMICs). A recent collaborative effort led by Jehan et al, 2020 (PMCID: PMC7749442), involved a diagnostic/prognostic multi-omics study of pregnant samples from five biorepository cohorts, including the AMANHI biorepository Pakistan site. Performed in 2019, it was followed by transcriptomics, proteomics, and metabolomics at one of the MOMI partner labs, Stanford University. The study revealed that in high PTB settings and within LMICs, there were shared biological pathways associated with PTB across these five different groups of pregnant women that could be detected by utilizing data science models, e.g., robust machine learning algorithms. The researchers could develop a single test to predict early births for women from all five sites in the study. The performed study is a proof-of-concept that the multi-omics approach has the potential to improve and identify low-cost predictive surrogates in accessible biological samples for LMICs.
Focusing on the missed power of small-RNA sequencing, to compare ncRNAs expression in the cervix among pregnant and non-pregnant women, or term and preterm labor combined with other multi-omics data may shed light on whether ncRNAs are dysregulated in pregnancies complicated by adverse outcomes. Human observational studies, as well as mechanistic in-vitro and in-vivo studies, will be necessary to determine whether dysregulation of these small molecules is involved in the pathogenesis of spontaneous PTB. MOMI Pakistan group at the AKU site is also performing systematic identification and differential expression profiling of PTB-associated plasma ncRNAs (secondary analysis of cell-free transcriptomics data of PMCID: PMC7749442) and validating the predicting discoveries in a cohort of Pakistan AMANHI biorepository samples. If so, these sequences may be targets of future potential therapeutics, such as antagomirs, to disrupt the cascade of events that lead to premature cervical remodeling and PTB, or interventional therapeutic drugs. Recently, the group has received funding as part of MOMI Ideas Fund 2021 to collect cervicovaginal fluid (CVF) of 500 pregnant women from local communities to explore the proteome repertoire and its role in understanding pregnancy-related genes.
Many pregnant women around the world do not have access to the most basic prenatal ultrasound scans. Medical practitioners need effective methods to predict and prevent PTB and having simple, inexpensive tests would greatly improve prenatal care. Studies to expand MOMI analysis to a broader omics platform are already underway; these datasets along with state-of-the-art machine learning partnerships will be crucial in developing effective predictive tests that can help to overcome the long-term clinical challenge of preventing PTB.
For more info: https://www.aku.edu/mcpk/research/Pages/biorepository-and-omics.aspx