Ovarian granulosa cells from women with PCOS express low levels of SARS-CoV-2 receptors and co-factors.

PURPOSE: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is global pandemic with more than 5 million deaths so far. Female reproductive tract organs express coronavirus-associated receptors and factors (SCARFs), suggesting they may be susceptible to SARS-CoV-2 infection; however, the susceptibility of ovary/follicle/oocyte to the same is still elusive. Co-morbidities like obesity, type-2 diabetes mellitus, cardiovascular disease, etc. increase the risk of SARS-CoV-2 infection. These features are common in women with polycystic ovary syndrome (PCOS), warranting further scope to study SCARFs expression in ovary of these women. MATERIALS AND METHODS: SCARFs expression in ovary and ovarian tissues of women with PCOS and healthy women was explored by analyzing publically available microarray datasets. Transcript expressions of SCARFs were investigated in mural and cumulus granulosa cells (MGCs and CGCs) from control and PCOS women undergoing in vitro fertilization (IVF). RESULTS: Microarray data revealed that ovary expresses all genes necessary for SARS-CoV-2 infection. PCOS women mostly showed down-regulated/unchanged levels of SCARFs. MGCs and CGCs from PCOS women showed lower expression of receptors ACE2, BSG and DPP4 and protease CTSB than in controls. MGCs showed lower expression of protease CTSL in PCOS than in controls. Expression of TMPRSS2 was not detected in both cell types. CONCLUSION: Human ovarian follicle may be susceptible to SARS-CoV-2 infection. Lower expression of SCARFs in PCOS indicates that the risk of SARS-CoV-2 infection to the ovary may be lesser in these women than controls. This knowledge may help in safe practices at IVF settings in the current pandemic.

An integrated in silico analysis highlighted angiogenesis regulating miRNA-mRNA network in PCOS pathophysiology.

BACKGROUND: Polycystic ovary syndrome (PCOS) is a heterogeneous endocrinopathy and a leading cause of anovulatory infertility. Angiogenesis is vital for ovarian folliculogenesis. The expression of angiogenesis-associated genes/proteins is altered in the ovary of PCOS women. However, information on microRNAs (miRNAs) regulating their expression is limited. This study aims to identify dysregulated angiogenesis-related genes in the ovary of women with PCOS, to identify miRNAs regulating them, and to construct a miRNA-mRNA network associated with angiogenesis. METHODS: A comprehensive literature search and reanalysis of seven ovarian GEO microarray datasets were performed to identify differentially expressed angiogenesis-related genes in PCOS. These target genes were used to predict their regulating miRNAs by querying miRNA databases and their expression in the ovary was verified. Panther and STRING database were used for functional enrichment. Gene expression of shortlisted miRNAs was studied in granulosa cells using digital droplet PCR. RESULTS: The miRNAs expressed in the ovary and potentially targeting dysregulated angiogenesis-related genes in PCOS were identified and those enriched in angiogenesis-related pathways, like VEGF, FGF, PI3K/Akt, Notch signaling, and ECM interaction were shortlisted. Analysis showed PI3K/Akt signaling was the most enriched pathway. MiR-218-5p, miR-214-3p, miR-20a-5p, and miR-140-3p associated with the PI3K/Akt pathway were found to be up-regulated in granulosa cells of women with PCOS. CONCLUSIONS: By in silico analysis, we identified crucial dysregulated angiogenesis-related genes, the miRNA-mRNA interactions, and signaling pathways involved in impaired follicular angiogenesis in PCOS. This work provides a novel insight into the mechanism of aberrant ovarian angiogenesis contributing to PCOS pathophysiology.

Male Infertility Knowledgebase: decoding the genetic and disease landscape.

Male infertility is a multifactorial condition that contributes to around one-third of cases of infertility worldwide. Several chromosomal aberrations, single-gene and polygenic associations with male factor defects have been reported. These defects manifest as sperm number or sperm quality defects leading to infertility. However, in almost 40% of cases, the genetic etiology of male infertility remains unexplained. Understanding the causal genetic factors is crucial for effective patient management and counseling. Integrating the vast amount of available omics data on male infertility is a first step towards understanding, delineating and prioritizing genes associated with the different male reproductive disorders. The Male Infertility Knowledgebase (MIK) is a manually curated repository developed to boost research on the elusive genetic etiology of male infertility. It integrates information on ∼17 000 genes, their associated pathways, gene ontology, diseases and gene and sequence-based analysis tools. In addition, it also incorporates information on reported chromosomal aberrations and syndromic associations with male infertility. Disease enrichment of genes in MIK indicate a shared genetic etiology between cancer, male and female infertility disorders. While the genes involved in cancer pathways were found to be common causal factors for sperm number and sperm quality defects, the interleukin pathways were found to be shared and enriched between male factor defects and non-reproductive conditions like cardiovascular diseases, metabolic diseases, etc. Disease information in MIK can be explored further to identify high-risk conditions associated with male infertility and delineate shared genetic etiology. Utility of the knowledgebase in predicting novel genes is illustrated by identification of 149 novel candidates for cryptorchidism using gene prioritization and network analysis. MIK will serve as a platform for review of genetic information on male infertility, identification pleiotropic genes, prediction of novel candidate genes for the different male infertility diseases and for portending future high-risk diseases associated with male infertility. Database URL: http://mik.bicnirrh.res.in/.

From cell surface to signalling and back: the life of the mammalian FSH receptor.

Follicle-stimulating hormone receptor (FSHR) is a class A G protein-coupled receptor that belongs to the subfamily of glycoprotein hormone receptors (GPHRs). The interaction of FSH with FSHR triggers downstream signaling pathways that play a central role in mammalian reproduction, such as folliculogenesis in females and the maintenance of spermatogenesis in males. This warrants a detailed investigation into FSHR, from its genesis, to the post-translational modifications that enable it to become functionally competent, followed by its trafficking to the cell membrane. Subsequently, FSH-stimulated Gs uncoupling and transduction of G protein-mediated signaling pathways takes place, after which the receptor undergoes ß-arrestin-mediated internalization and may trigger other noncanonical signaling pathways. The majority of the FSH-FSHR complexes are recycled back to the cell surface and only a small proportion are routed to lysosomal degradation pathways, thus completing the lifecycle of the FSH receptor. Information about important epitopes and aspects of FSH receptor function has been gleaned from a number of sources, including structure-function studies on both naturally occurring and induced mutations, single nucleotide polymorphisms, peptides and antipeptide antibodies corresponding to predicted functional residues, X-ray crystallography analysis and high resolution imaging studies, in addition to the information available for the other GPHRs. In this review, we have traversed through the life cycle of the FSH receptor and discuss the reproductive pathophysiologies that could result from an impairment in receptor function, as may arise from defects during its journey from its birth to its degradation. Moreover, the unresolved questions and challenges that require exploration have been highlighted.

Proteolytic cleavage of Trop2 at Arg87 is mediated by matriptase and regulated by Val194.

Proteolytic processing is an important post-translational modification affecting protein activity and stability. In the current study, we investigate the N-terminal cleavage of Trop2, a protein which is overexpressed in many cancers. We demonstrate that Trop2 is cleaved at Arg87 by a transmembrane serine protease, matriptase. Homology modeling and site-directed mutagenesis of amino acids in close proximity to the matriptase cleavage site reveal the importance of Val194 in regulating Trop2 cleavage. Co-immunoprecipitation studies confirm that amino acid substitutions at Arg87, Thr88, Lys189, Val194, and His195 do not affect Trop2 dimerization. However, cleavage of wild-type Trop2 by matriptase is inhibited when it is allowed to dimerize with a V194 A mutant monomer, further confirming the role of Val194 in matriptase-mediated N-terminal cleavage.

Endometriosis Knowledgebase: a gene-based resource on endometriosis.

Endometriosis is a complex, benign, estrogen-dependent gynecological disorder with an incidence of ~10% women in reproductive age. The implantation and growth of endometrial cells outside the uterus leads to the development of endometriosis. Endometriosis is also associated with comorbid conditions like cardiovascular and autoimmune diseases. The absence of non-invasive diagnostic markers, delayed diagnosis, high risk of recurrence of the disease on surgical removal of the tissue and absence of a definitive cure for endometriosis makes it imperative to gain insights into the complex etiology of endometriosis. A plethora of genes identified from blood and endometrial biopsies, involved in different pathways like steroid metabolism, angiogenesis, inflammation, etc. have been associated with endometriosis. However, the exact mechanism and genetic etiology of endometriosis still remain unclear. The polygenic nature of the disease, incongruent phenotypic manifestations in different ethnic populations and information scattered in literature makes it difficult to delineate the sub-network of genes that will aid in disease diagnosis and effective treatment. Endometriosis Knowledgebase is a manually curated database with information on genes associated with endometriosis. It holds information on 831 genes, their associated polymorphisms, gene ontologys, pathways and diseases. Genes in the database are enriched in pathways important for cell signaling, immune regulation and reproduction. A genetic overlap is seen between endometriosis and cancers, endocrine/reproductive, nervous system, immune and metabolic diseases. Network analysis of genes in the Endometriosis Knowledgebase helped predict 13 new candidate genes for endometriosis. These genes were found to be enriched in biological processes associated with endometriosis. The Endometriosis Knowledgebase and incorporated tools for gene and sequence-based analysis will benefit both researchers and clinicians working in the realm of reproductive biology.

Designing Antibacterial Peptides with Enhanced Killing Kinetics.

Antimicrobial peptides (AMPs) are gaining attention as substitutes for antibiotics in order to combat the risk posed by multi-drug resistant pathogens. Several research groups are engaged in design of potent anti-infective agents using natural AMPs as templates. In this study, a library of peptides with high sequence similarity to Myeloid Antimicrobial Peptide (MAP) family were screened using popular online prediction algorithms. These peptide variants were designed in a manner to retain the conserved residues within the MAP family. The prediction algorithms were found to effectively classify peptides based on their antimicrobial nature. In order to improve the activity of the identified peptides, molecular dynamics (MD) simulations, using bilayer and micellar systems could be used to design and predict effect of residue substitution on membranes of microbial and mammalian cells. The inference from MD simulation studies well corroborated with the wet-lab observations indicating that MD-guided rational design could lead to discovery of potent AMPs. The effect of the residue substitution on membrane activity was studied in greater detail using killing kinetic analysis. Killing kinetics studies on Gram-positive, negative and human erythrocytes indicated that a single residue change has a drastic effect on the potency of AMPs. An interesting outcome was a switch from monophasic to biphasic death rate constant of Staphylococcus aureus due to a single residue mutation in the peptide.

Functional characterization of two naturally occurring mutations V221G and T449N in the follicle stimulating hormone receptor.

Naturally occurring mutations in follicle stimulating hormone receptor (FSHR) affect the receptor function. Here, we characterized two such previously reported mutations, V221G and T449N, in the extracellular domain and transmembrane helix 3, of FSHR, respectively. Functional studies with the V221G mutant demonstrated an impairment in FSH binding and signaling. Validation of X-ray crystallography data indicating the contribution of FSHR specific residues in the vicinity of V221 to contribute to FSH-FSHR interaction was carried out. In vitro mutational studies showed that these residues are determinants of both FSH binding and FSH induced signaling. Analysis of the T449N mutation revealed that it results in an increase in FSH binding and high cAMP response at lower doses of FSH. A marginal hCG induced and no TSH induced cAMP production was also observed. These findings corroborated with the clinical manifestations of primary amenorrhea (V221G) and spontaneous ovarian hyperstimulation syndrome (T449N) in women harbouring these mutations.

Comparison of marmoset and human FSH using synthetic peptides of the ß-subunit L2 loop region and anti-peptide antibodies.

Follicle stimulating hormone (FSH) is a glycoprotein hormone required for female and male gametogenesis in vertebrates. Common marmoset (Callithrix jacchus) is a New World primate monkey, used as animal model in biomedical research. Observations like, requirement of extremely high dose of human FSH in marmosets for superovulation compared to other primates and generation of antibodies in marmoset against human FSH after repeated superovulation cycles, point towards the possibility that FSH-FSH receptor (FSHR) interaction in marmosets might be different than in the humans. In this study we attempted to understand some of these structural differences using FSH peptides and anti-peptide antibody approach. Based on sequence alignment, in silico modeling and docking studies, L2 loop of FSH ß-subunit (L2ß) was found to be different between marmoset and human. Hence, peptides corresponding to region 32-50 of marmoset and human L2ß loop were synthesized, purified and characterized. The peptides displayed dissimilarity in terms of molecular mass, predicted isoelectric point, predicted charge and in the ability to inhibit hormone-receptor interaction. Polyclonal antibodies generated against both the peptides were found to exhibit specific binding for the corresponding peptide and parent FSH in ELISA and Western blotting respectively and exhibited negligible reactivity to cross-species peptide and FSH in ELISA. The anti-peptide antibody against marmoset FSH was also able to detect native FSH in marmoset plasma samples and pituitary sections. In summary, the L2ß loop of marmoset and human FSH has distinct receptor interaction ability and immunoreactivity indicating possibility of subtle conformational and biochemical differences between the two regions which may affect the FSH-FSHR interaction in these two primates. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.

PCOSKB: A KnowledgeBase on genes, diseases, ontology terms and biochemical pathways associated with PolyCystic Ovary Syndrome.

Polycystic ovary syndrome (PCOS) is one of the major causes of female subfertility worldwide and ≈ 7-10% of women in reproductive age are affected by it. The affected individuals exhibit varying types and levels of comorbid conditions, along with the classical PCOS symptoms. Extensive studies on PCOS across diverse ethnic populations have resulted in a plethora of information on dysregulated genes, gene polymorphisms and diseases linked to PCOS. However, efforts have not been taken to collate and link these data. Our group, for the first time, has compiled PCOS-related information available through scientific literature; cross-linked it with molecular, biochemical and clinical databases and presented it as a user-friendly, web-based online knowledgebase for the benefit of the scientific and clinical community. Manually curated information on associated genes, single nucleotide polymorphisms, diseases, gene ontology terms and pathways along with supporting reference literature has been collated and included in PCOSKB (http://pcoskb.bicnirrh.res.in).

Prostate Secretory Protein of 94 amino acids (PSP94) binds to prostatic acid phosphatase (PAP) in human seminal plasma.

Prostate Secretory Protein of 94 amino acids (PSP94) is one of the major proteins present in the human seminal plasma. Though several functions have been predicted for this protein, its exact role either in sperm function or in prostate pathophysiology has not been clearly defined. Attempts to understand the mechanism of action of PSP94 has led to the search for its probable binding partners. This has resulted in the identification of PSP94 binding proteins in plasma and seminal plasma from human. During the chromatographic separation step of proteins from human seminal plasma by reversed phase HPLC, we had observed that in addition to the main fraction of PSP94, other fractions containing higher molecular weight proteins also showed the presence of detectable amounts of PSP94. This prompted us to hypothesize that PSP94 could be present in the seminal plasma complexed with other protein/s of higher molecular weight. One such fraction containing a major protein of ~47 kDa, on characterization by mass spectrometric analysis, was identified to be Prostatic Acid Phosphatase (PAP). The ability of PAP present in this fraction to bind to PSP94 was demonstrated by affinity chromatography. Co-immunoprecipitation experiments confirmed the presence of PSP94-PAP complex both in the fraction studied and in the fresh seminal plasma. In silico molecular modeling of the PSP94-PAP complex suggests that ß-strands 1 and 6 of PSP94 appear to interact with domain 2 of PAP, while ß-strands 7 and 10 with domain 1 of PAP. This is the first report which suggests that PSP94 can bind to PAP and the PAP-bound PSP94 is present in human seminal plasma.

ClassAMP: a prediction tool for classification of antimicrobial peptides.

Antimicrobial peptides (AMPs) are gaining popularity as anti-infective agents. Information on sequence features that contribute to target specificity of AMPs will aid in accelerating drug discovery programs involving them. In this study, an algorithm called ClassAMP using Random Forests (RFs) and Support Vector Machines (SVMs) has been developed to predict the propensity of a protein sequence to have antibacterial, antifungal, or antiviral activity. ClassAMP is available at http://www.bicnirrh.res.in/classamp/.