Strategies for whole-exome sequencing analysis in a case series study of familial male infertility

Background: Infertility is one of the common health issues around the world. The prevalence of male factor infertility among infertile couples is approximately 30%- 35%, of which genetic factors account for 15%. The family-based whole-exome sequencing (WES) approach can accurately detect novel variants. However, selecting an appropriate sample for data generation using WES has proven to be challenging in familial male infertility studies. The aim of this study was to identify types of pathogenic male infertility in cases of familial asthenozoospermia. Case: Two families with multiple cases were recruited for the purpose of WES. The study population included two affected cases in pedigree I and three affected cases in pedigree II. Two different variant callers (SAMtools and GATK) with a single-sample calling strategy (SSCS) and a multiple-sample calling strategy (MSCS), were applied to identify variant sites. Conclusion: In this study, we represented the results for variant prioritization of WES data without sequencing fertile siblings in the same pedigree by applying two different pipelines (homozygosity and linkage-based strategy). Using the aforementioned strategies, we prioritized annotated variants and generated a logical shortlist of private variants for each pedigree. Key words: Male infertility, Whole-exome sequencing, GATK, SAMtools

Temporal Gene Expression and DNA Methylation during Embryonic Stem Cell Derivation

Objective Dual inhibition of mitogen-activated protein kinase (MAPK) kinase (also known as MEK) and transforming growth factor β (TGFβ) type I receptors by PD0325901 and SB431542, known as R2i has been introduced as a highly efficient approach to the generation of mouse embryonic stem cells (ESC). In the present study, we investigated the molecular mechanisms underlying ESC derivation in the R2i condition. Materials and Methods In this experimental study, zona-free whole E3.5 blastocysts were seeded on mouse embryonic fibroblast (MEF) feeder cells in both R2i and serum conventional media. The isolated inner cell mass (ICM), ESCs and the ICM-outgrowths were collected on days 3, 5 and 7 post-blastocyst culture for quantitative real time- polymerase chain reaction (qRT-PCR) analysis as well as to assess the DNA methylation status at the time points during the transition from ICM to ESC. Results qRT-PCR revealed a significantly higher expression of the pluripotency-related genes (Oct4, Nanog, Sox2, Rex1, Dppa3, Tcf3, Utf1, Nodal, Dax1, Sall4 and β-Catenin) and lower expression of early differentiation genes (Gata6, Lefty2 and Cdx2) in R2i condition compared to the serum condition. Moreover, the upstream region of Oct4 and Nanog showed a progressive increase in methylation levels in the upstream regions of the genes following in R2i or serum conditions, followed by a decrease of DNA methylation in ESCs obtained under R2i. However, the methylation level of ICM outgrowths in the serum condition was much higher than R2i, at levels that could have a repressive effect and therefore explain the absence of expression of these two genes in the serum condition. Conclusion Our investigation revealed that generation of ESCs in the ground-state of pluripotency could be achieved by inhibiting the MEK and TGF-β signaling pathways in the first 5 days of ESC derivation

DNA methylation biomarkers in colorectal cancer: Clinical applications for precision medicine

Colorectal cancer (CRC) is the second leading cause of cancer death worldwide that is attributed to gradual long-term accumulation of both genetic and epigenetic changes. To reduce the mortality rate of CRC and to improve treatment efficacy, it will be important to develop accurate noninvasive diagnostic tests for screening, acute and personalized diagnosis. Epigenetic changes such as DNA methylation play an important role in the development and progression of CRC. Over the last decade, a panel of DNA methylation markers has been reported showing a high accuracy and reproducibility in various semi-invasive or noninvasive biosamples. Research to obtain comprehensive panels of markers allowing a highly sensitive and differentiating diagnosis of CRC is ongoing. Moreover, the epigenetic alterations for cancer therapy, as a precision medicine strategy will increase their therapeutic potential over time. Here, we discuss the current state of DNA methylation-based biomarkers and their impact on CRC diagnosis. We emphasize the need to further identify and stratify methylation-biomarkers and to develop robust and effective detection methods that are applicable for a routine clinical setting of CRC diagnostics particularly at the early stage of the disease

Effects of Dexmedetomidine on Clinical Outcomes and Renal Function after CABG

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Improvement of Mouse Preantral Follicle Survival and Development following Co-Culture with Ovarian Parenchyma Cell Suspension

Background: The parallel and continued improvements in both infertility treatment and the management of malignancycases have brought to the forefront the potential for fertility preservation. Using ovarian follicular resourcescan effectively improve reproductive capacity and prevent infertility. The primary aim of this research was to try togenerate an appropriate in vivo environment for the growth of the mouse follicles. Hence, the possible effects of theovarian parenchyma cell suspension were explored on the growth and maturation of preantral follicles in vitro.Materials and Methods: In this experimental study, ovarian parenchymal cells were mechanically dissociated frompreantral follicles of 12-14 days-old NMRI mice and then divided into 5 experimental groups (G1: Control, G2: Freshfollicle with fresh parenchyma cell suspension, G3: Vitrified-warmed follicle with fresh parenchyma cell suspension,G4: Fresh follicle with frozen-thawed parenchyma cell suspension, and G5: Vitrified-warmed follicle with frozen-thawedparenchyma cell suspension). The diameter of the follicles and immature oocytes, viability, antrum formation,resumption of meiosis, in vitro fertilization (IVF), and Gdf9, Bmp6, and Bmp15 gene expression were examined ondifferent periods.Results: The diameter of the follicles and the oocytes on days 4 and 8, as well as the survival rate of the follicles upto day 12, were significantly higher in G2 and G4 compared to the Ctrl group (G1: 73.66%, G2:87.99%, G3: 82.70%,G4: 94.37%, and G5: 78.59%). Expression of growth marker genes for G3, and G5 groups was significantly higherthan other groups, which indicated the protective effects of parenchyma cell suspension on follicles damaged by vitrificationsolutions.Conclusion: The growth, survival, and maturation of preantral follicles could be enhanced by co-culturing them withovarian parenchyma cells. Further studies are needed to optimize the conditions for a successful parenchyma cellsuspension-induced in vitro maturation (IVM) to occur in infertility clinics

The construction of a testis transcriptional cell atlas from embryo to adult reveals various somatic cells and their molecular roles

Abstract Background The testis is a complex organ that undergoes extensive developmental changes from the embryonic stage to adulthood. The development of germ cells, which give rise to spermatozoa, is tightly regulated by the surrounding somatic cells. Methods To better understand the dynamics of these changes, we constructed a transcriptional cell atlas of the testis, integrating single-cell RNA sequencing data from over 26,000 cells across five developmental stages: fetal germ cells, infants, childhood, peri-puberty, and adults. We employed various analytical techniques, including clustering, cell type assignments, identification of differentially expressed genes, pseudotime analysis, weighted gene co-expression network analysis, and evaluation of paracrine cell–cell communication, to comprehensively analyze this transcriptional cell atlas of the testis. Results Our analysis revealed remarkable heterogeneity in both somatic and germ cell populations, with the highest diversity observed in Sertoli and Myoid somatic cells, as well as in spermatogonia, spermatocyte, and spermatid germ cells. We also identified key somatic cell genes, including RPL39, RPL10, RPL13A, FTH1, RPS2, and RPL18A, which were highly influential in the weighted gene co-expression network of the testis transcriptional cell atlas and have been previously implicated in male infertility. Additionally, our analysis of paracrine cell–cell communication supported specific ligand-receptor interactions involved in neuroactive, cAMP, and estrogen signaling pathways, which support the crucial role of somatic cells in regulating germ cell development. Conclusions Overall, our transcriptional atlas provides a comprehensive view of the cell-to-cell heterogeneity in the testis and identifies key somatic cell genes and pathways that play a central role in male fertility across developmental stages

Quantitative expression of developmental genes, Pou5f1 (Oct4) and Mest (Peg1), in vitrified mouse embryos

Background: Embryo cryopreservation is the process that water is removed from the cell by cryoprotectant materials, and embryos are stored at temperature below zero. This process may affect the viability and developmental potential of embryos. Objective: In this study, the effect of the vitrification cryotop method on the expression level of Oct4 and Mest developmental genes in mouse blastocysts was examined. Materials and Methods: The collected 2-cell embryos of superovulated mouse by oviduct flushing were divided into non-vitrified and vitrified groups. These embryos were cultured to the blastocyst stage directly in the non-vitrified group and in the vitrified group, these embryos were cultured to 4-8 cell embryos, vitrified with cryotop in these stages and after 2-6 months, warmed and cultured to blastocyst embryos. Quantitative expression of two developmental genes, namely Oct4 and Mest, were performed in these groups, using RNA purification and Real-time RT-PCR. Results: Quantitative PCR analysis showed that the expression level of both genes, Oct4 and Mest, was reduced significantly in the vitrified-warmed group relative to the control group (p=0.046 and p=0.001). Conclusion: This study revealed that morphologically normal embryos show a reduced amount of Oct4 and Mest transcripts which indicate that the vitrification method negatively effects the expression level of these two developmental genes

Electrocardiographic Changes in Mitral Valve Prolapse Syndrome

Background- Mitral valve prolapse syndrome (MVP) is most common valvular abnormality in young and is correlated with increased frequency of cardiac dysrhythmias and sudden death. The aim of this study was to compare frequency of "early repolarization" in electrocardiogram (ECG) between MVP patients and healthy adults. Methods- In this cross-sectional study, we compared ECG presentations of early repolarization including notch in descending arm of QRS and J-point and/or ST segment changes in 100 patients with MVP with 100 healthy individuals. MVP patients were referred to cardiology clinic with symptoms of palpitation, chest pain or anxiety. Results-The mean age in patients with MVP was significantly less than healthy subjects (29.5 ± 9.3 years versus 31.0 ± 6.9 years in control group, p=0.1967). We detected an early repolarization as a prevalent sign in ECG of patients, which was a notch in descending arm of QRS and/or ST segment or J-point elevation seen in 74% of patients ( 51% in inferior leads and 23% in I and aVL leads) , whilst the same findings was seen in 8 men (8%) in control group (p=0.0001). Conclusion- Early repolarization in ECG presented as a notch in descending arm of QRS and/or ST segment or J-point elevation is more frequent in in young patients with MVP syndrome

The Impact of Genetic Variation and Gene Expression Level of The Follicle-Stimulating Hormone Receptor on Ovarian Reserve

Objective Ovarian reserve is defined as the capacity of the ovary to provide fertile oocytes. Diminished ovarian reserve (DOR) is a disorder in which ovaries are prone to go through early menopause. Where this loss of function occurs before the age of 40, it results in the premature ovarian failure (POF) disease. Throughout folliculogenesis, the follicle-stimulating hormone receptor (FSHR) starts a signaling cascade in the granulosa cells where its inactivation leads to the arrest of follicle maturation and therefore adversely affects ovarian reserve. The aim of this study was to investigate the association of genetic variation (polymorphisms and inactivating mutations) of FSHR with POF and DOR. Materials and Methods This case-control study comprised 84 POF, 52 DOR and 80 fertile Iranian women. To determine the presence of the 566C>T mutation and the -29G>A polymorphism in FSHR, PCR-RFLP method was used. SSCP-sequencing was used to identify any allelic variants in exon 10. The expression of human FSHR at the transcript level was also compared between DOR and fertile controls by real time-polymerase chain reaction (PCR). Results The 566C>T polymorphism was normal in all the cases. All genotypes of -29G>A and 919G>A (exon 10) polymorphisms were observed. Statistically significant differences were seen in the genotypic distribution of both polymorphisms when comparing the control group with the DOR patient group. A decrease was observed in FSHR expression of DOR patients compared with the control group but was not significant. Conclusion We conclude that the -29G>A and 919G>A polymorphisms in FSHR may be associated with DOR. Although these polymorphisms had significant differences at the genic level, no significant variation was found at the transcript level

Attitude of A Sample of Iranian Researchers toward The Future of Stem Cell Research

Objective Stem cells that have unlimited proliferation potential as well as differentiation potency are considered to be a promising future treatment method for incurable diseases. The aim of the present study is to evaluate the future trend of stem cell researches from researchers’ viewpoints. Materials and Methods This was a cross-sectional descriptive study on researchers involved in stem cell research at Royan Institute. We designed a questionnaire using a qualitative study based on expert opinion and a literature review. Content validity was performed using three rounds of the Delphi method with experts. Face validity was undertaken by a Persian literature expert and a graphics designer. The questionnaire was distributed among 150 researchers involved in stem cell studies in Royan Institute biology laboratories. Results We collected 138 completed questionnaires. The mean age of participants was 31.13 ± 5.8 years; most (60.9%) were females. Participants (76.1%) considered the budget to be the most important issue in stem cell research, 79.7% needed financial support from the government, and 77.5% felt that charities could contribute substantially to stem cell research. A total of 90.6% of participants stated that stem cells should lead to commercial usage which could support future researches (86.2%). The aim of stem cell research was stipulated as increasing health status of the society according to 92.8% of the participants. At present, among cell types, importance was attached to cord blood and adult stem cells. Researchers emphasized the importance of mesenchymal stem cells (MSCs) rather than hematopoietic stem cells (HSCs, 57.73%). The prime priorities were given to cancer so that stem cell research could be directed to sphere stem cell research whereas the least preference was given to skin research. Conclusion Regenerative medicine is considered the future of stem cell research with emphasis on application of these cells, especially in cancer treatment