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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.

Background and Aim: Oncolytic viruses, as novel and advanced tools in the field of treating various types of cancer, have played a very important role in medical developments. The term “oncolytic” refers to the ability of these viruses to destroy and damage cancer cells while preserving the surrounding healthy cells. Materials and Methods: To conduct this study, a total of 270 initial results were collected through searching in the PubMed, Scopus, and Google Scholar databases from 2012 to 2024. The primary researcher reviewed 68 relevant articles, extracted and summarized the contents, and finally compiled the findings. Results: The findings from this review study demonstrate that cancer cells possess distinct characteristics that differentiate them from normal cells, including continuous growth signaling, resistance to anti-growth signaling, evasion of apoptosis, increased angiogenesis, and invasion into other body parts. Oncolytic viruses utilize these distinctive features to selectively target and infect cancer cells. Most oncolytic viruses directly eliminate host tumor cells, resulting in viral replication and induction of host antiviral responses. Moreover, these viruses can destroy cancer cells through the production of specific proteins. The cytotoxic potential of oncolytic viruses depends on viral type, genetic manipulation, optimal virus dosage for injection, natural and induced viral tropism, and cancer cell sensitivity to various forms of cell death. The mechanism driving the selective replication of oncolytic viruses in cancer cells likely relates to defects in signaling pathways specific to tumor cells. Phase III clinical trials have demonstrated significant improvements in the treatment outcomes of various cancers, including head and neck cancer, melanoma, glioblastoma, and bladder cancer, through the use of H101 (Oncorine), T-Vec, ECHO-7, and Teserpaturev (Delytact) viruses. Conclusion: Oncolytic viruses are constructed from various types of viruses and are currently being evaluated in laboratory, preclinical, and clinical stages. The use of these viruses for the treatment of cancer as a new and targeted approach has been proposed, which requires further investigation and achievement of more precise mechanisms for their better performance.

Abstract Background The objective of this study was to induce the differentiation of human theca stem cells (hTSCs) into germ cell-like cells (hGCLCs) and assess their developmental progression following in vitro 3D culture with ovarian somatic cells within the follicle-like structures. To achieve this, the hTSCs were isolated from small antral follicles of three patients of varying ages and were then seeded in a differentiation medium for 40 days. The differentiated hGCLCs were subsequently aggregated with somatic ovarian cells (cumulus cells and hTSCs) in a ratio of 1:10 and cultured in a growth medium in a suspension culture dish. In addition to examining the morphologies, sizes, and viabilities of the differentiated hGCLCs, this study also analyzed the expression of DAZL and GDF9 proteins within the follicle-like structures. Results After 12 days, the hTSCs began to differentiate into hGCLCs, with their shapes changing from spindle-shaped to spherical. The sizes of hGCLCs increased during the differentiation period (from 25 μm to 50 μm). The survival rate of the hGCLCs after differentiation and in vitro development in primordial follicle-like structures was 54%. Unlike hTSCs, which did not express the DAZL protein, the hGCLCs and follicle-like structures successfully expressed DAZL protein (P-value

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.

Objective: The most severe type of male infertility is non-obstructive azoospermia (NOA), where there is no sperm in the ejaculate due to failure of spermatogenesis, affecting 10%–20% of infertile men with azoospermia. Genetic studies have identified dozens of NOA genes. The main aim of the present study is to identify a novel monogenic mutation that may cause NOA. Materials and methods: We studied the pedigree of a consanguineous family with three NOA and one fertile brother by a family-based exome-sequencing, segregation analysis, insilico protein modeling and single-cell RNA sequencing data analysis. Results: Bioinformatics analysis followed by sanger sequencing revealed that three NOA brothers were homozygous for a rare missense variant in Cyclin Dependent Kinase Regulatory Subunit Associated Protein 2 (Centrosomin) CDK5RAP2 (NM_018249:exon26:c.A4003T:p.R1335W, rs761196443). Protein modeling demonstrated that CDK5RAP2, Arg1335Trp resided nearby the Microtubule Associated Protein RP/EB Family Member 1 (EB1/MAPRE1) interaction site. As a consequence of the R1335W mutation, the positively charged Arginine was replaced by to the hydrophobic tryptophan residue, possibly leading to local instability in the structure and perturbation in the CDK5RAP2-MAPRE1 interaction. Conclusion: Our study reports a novel missense variant of CDK5RAP2 that segregates in homozygosity with male infertility and NOA in a consanguineous family. In silico structural predictions and gene expression data indicate a potential role of the CDK5RAP2 variant in causing defective centrosomic maturation during spermatogenesis.

Abstract Many factors can lead to an increase in the prevalence of metabolic syndrome (MetS) in different populations. Using an advanced structural equation model (SEM), this study is aimed to determine the most important risk factors of MetS, as a continuous latent variable, using a large number of males and females. We also aimed to evaluate the interrelations among the associated factors involved in the development of MetS. This study used data derived from the Fasa PERSIAN cohort study, a branch of the PERSIAN cohort study, for participants aged 35 to 70 years with 10,138 males and females. SEM was used to evaluate the direct and indirect effects, as well as gender effects of influencing factors. Results from the SEM showed that in females most changes in MetS are described by waist circumference (WC), followed by hypertension (HP) and triglyceride (TG), while in males most changes in MetS are described by WC, followed by TG then fasting blood glucose (FBG). Results from the SEM confirmed the gender effects of social status on MetS, mediated by sleep and controlled by age, BMI, ethnicity and physical activity. This study also shows that the integration of TG and WC within genders could be useful as a screening criterion for MetS in our study population.

Abstract The incidence of early‐onset colorectal cancer (CRC), which affects people under 50, is increasing for unknown reasons. Additionally, no underlying genetic cause is found in 20%–30% of patients suspected of having familial CRC syndrome. Whole exome sequencing (WES) has generated evidence for new genes associated with CRC susceptibility, but many patients remain undiagnosed. This study applied WES in five early‐onset CRC patients from three unrelated families to identify novel genetic variants that could be linked to rapid disease development. Furthermore, the candidate variants were validated using Sanger sequencing. Two heterozygote variations, c.1077‐2A>G and c.199G>A, were found in the MSH2 and the MLH1 genes, respectively. Sanger sequencing analysis confirmed that these (likely) pathogenic mutations segregated in all the affected families' members. In addition, we identified a rare heterozygote variant (c.175C>T) with suspected pathogenic potential in the MAP3K1 gene; formally the variant is of uncertain significance (VUS). Our findings support the hypothesis that CRC onset may be oligogenic and molecularly heterogeneous. Larger and more robust studies are needed to understand the genetic basis of early‐onset CRC development, combined with novel functional analyses and omics approaches.

In recent years, oncolytic viruses have emerged as promising agents for treating various cancers. An oncolytic virus is a non-pathogenic virus that, due to genetic manipulation, tends to replicate in and cause lysis of cancerous cells while leaving healthy cells unaffected. Among these viruses, vaccinia virus is an attractive platform for use as an oncolytic platform due to its 190 Kb genome with a high capacity for encoding therapeutic payloads. Combining oncolytic VV therapy with other conventional cancer treatments has been shown to be synergistic and more effective than monotherapies. Additionally, OVV can be used as a vector to deliver therapeutic payloads, alone or in combination with other treatments, to increase overall efficacy. Here, we present a comprehensive analysis of preclinical and clinical studies that have evaluated the efficacy of oncolytic vaccinia viruses in cancer immunotherapy. We discuss the outcomes of these studies, including tumor regression rates, overall survival benefits, and long-term responses. Moreover, we provide insights into the challenges and limitations associated with oncolytic vaccinia virus- based therapies, including immune evasion mechanisms, potential toxicities, and the development of resistance.

Gastrointestinal (GI) cancers comprise a significant number of cancer cases worldwide and contribute to a high percentage of cancer-related deaths. To improve survival rates of GI cancer patients, it is important to find and implement more effective therapeutic strategies with better prognoses and fewer side effects. The development of new drugs can be a lengthy and expensive process, often involving clinical trials that may fail in the early stages. One strategy to address these challenges is drug repurposing (DR). Drug repurposing is a developmental strategy that involves using existing drugs approved for other diseases and leveraging their safety and pharmacological data to explore their potential use in treating different diseases. In this paper, we outline the existing therapeutic strategies and challenges associated with GI cancers and explore DR as a promising alternative approach. We have presented an extensive review of different DR methodologies, research efforts and examples of repurposed drugs within various GI cancer types, such as colorectal, pancreatic and liver cancers. Our aim is to provide a comprehensive overview of employing the DR approach in GI cancers to inform future research endeavors and clinical trials in this field.

Abstract Background Retained placenta (RP) is a prevalent disorder in cattle with many health-related and economic costs for the farm owners. Its etiology has not been clarified yet and there is no definite therapy for this disorder. In this study we conducted RNA-seq, hematologic and histologic experiments to survey the causes of RP development. Methods Blood samples were collected from 4 RP and 3 healthy cows during periparturtion period for hematological assessments followed by placentome sampling within 30 min after parturition. Cows were grouped as RP and control in case the placenta was retained or otherwise expelled, respectively. Total RNA was extracted from placentome samples followed by RNA-sequencing. Results We showed 240 differentially expressed genes (DEGs) between the RP and control groups. Enrichment analyzes indicated immune system and lipid metabolism as prominent over- and under-represented pathways in RP cows, respectively. Hormonal assessments showed that estradiol-17β (E2) was lower and cortisol tended to be higher in RP cows compared to controls at the day of parturition. Furthermore, histologic experiment showed that villi-crypt junctions remain tighter in RP cows compared to controls and the crypts layer seemed thicker in the placentome of RP cows. Complete blood cell (CBC) parameters were not significantly different between the two groups. Conclusion Overall, DEGs derived from expression profiling and these genes contributed to enrichment of immune and lipid metabolism pathways. We suggested that E2 could be involved in development of RP and the concentrations of P4 and CBC counts periparturition might not be a determining factor.

Background and Aim: Genome editing is an efficient and accurate method in biological and medical studies. Among the wide range of genome editing techniques, clustered regularly interspaced short palindromic repeats (CRISPR) is one of the simplest and yet promising methods. The CRISPR system consists of two key components; an endonuclease enzyme called Cas9 and guide RNA (gRNA), ensuring that Cas9 enzyme cuts at the right point in the genome. Although CRISPR genome editing is one of the useful methods to modify the genome, there are still multiple challenges in the technique steps. Materials and Methods: sgRNAs were designed and ordered accordingly on the basis of the target site and vector of interest. Cloning procedures were performed and confirmed by sequencing as a gold standard. The list of high efficient sgRNAs for the LAMP-2 gene was prepared based on the available outstanding databases by analyzing and comparing the specificity and functionality as two main characteristics. Results: In this study, we tried to evaluate the main challenges in the process of preparing CRISPR/Cas9 popular vectors (pX330/pX459). A list of high efficient sgRNAs for an autophagy gene is also prepared as an example for clarification of the sgRNA design procedures. Conclusion: This study tried to depict problems that may be encountered during sgRNA design and plasmid preparation, followed by giving appropriate recommendations.

Objective: Autologous transplantation of epidermal cells has been used increasingly to treat vitiligo patients and is a simple, safe, and relatively efficient method. However, the outcome is not always satisfactory, and some patients show less or no response to this treatment. This study was evaluated to identify genes expressed differently among responders and non-responders to cell transplantation to find potential markers that could predict 'patients' responses to this type of cell therapy.Materials and Methods: Eleven stable vitiligo patients who received autologous epidermal cell transplantation were included in this clinical trial study. Before cell transplantation, skin samples were obtained from the recipient’s vitiligo lesions. After epidermal cell transplantation, patients were followed for at least six months to assess the response to epidermal cell injection. RNA sequencing was used to determine potential gene expression profile differences between responder and non-responder vitiligo patients.Results: The RNA sequencing results showed differences in expression levels of 470 genes between the skin specimens of responder versus non-responder patients. There were 269 up-regulated genes and 201 down-regulatedgenes. Upregulated genes were involved in processes, such as Fatty Acid Omega Oxidation. Down-regulated geneswere related to PPAR signaling pathway, and estrogen signaling pathway. Among the most differentially expressed genes (DEGs) with the most altered RNA expression levels in responders versus non-responder patients, we selected three genes (up-regulated genes KRTAP10-11 and down-regulated genes IP6K2 and C9) as potential biomarkers, which are involved in associated pathways.Conclusion: Based on our findings, it is estimated that proposed genes might predict the response of vitiligo patients to cell therapy. However, further studies are required to clarify the role of these genes in pathogenesis and to characterize gene expression in a larger number of vitiligo patients in the context of epidermal cell transplantation therapy (registration number: IRCT201508201031N16).

Abstract Background Spalt-like transcription factor 4 (SALL4) and aldehyde dehydrogenase1 family member A1 (ALDH1A1) expressing cells have been characterized as possessing stem cell-like properties known as cancer stem cell marker in serous ovarian carcinoma (SOC). Methods The association between SALL4 and ALDH1A1 was observed based on literature review and bioinformatics tools. Therefore, this study aimed to investigate the association between the co-expression of SALL4/ALDH1A1 proteins and clinicopathological parameters and their prognostic value in SOC patients using immunohistochemical staining on tissue microarrays (TMAs). Furthermore, benign tumors and normal tissue samples were compared with the expression of the tumor tissue samples. Results Increased co-expression of SALL4/ALDH1A1 was found to be significantly associated with the advanced FIGO stage (P = 0.047), and distant metastasis (P = 0.028). The results of Kaplan–Meier survival analysis indicated significant differences between disease- specific survival (DSS; P = 0.034) or progression-free survival (PFS; P = 0.018) and the patients with high and low co-expression of SALL4/ALDH1A1, respectively. Furthermore, high level co-expression of SALL4/ALDH1A1 was a significant predictor of worse DSS and PFS in the univariate analysis. The data also indicated that the co-expression of SALL4/ALDH1A1 was an independent prognostic factor affecting PFS. Moreover, the co-expression of SALL4/ALDH1A1 added prognostic values of DSS in patients with SOC who had grade III versus grade I in multivariate analysis. Conclusions Our data demonstrated that high co-expression of SALL4/ALDH1A1 was found to be significantly associated with tumor aggressiveness and worse DSS or PFS in SOC patients. Therefore, co-expression of SALL4/ALDH1A1 may serve as a potential prognostic biomarker of cancer progression in these cases.

Gastric cancer (GC) is one of the leading causes of cancer-related deaths worldwide. The major problems of patients with GC are the lack of proper response to the treatment, drug resistance and metastasis attributed to the presence of a subpopulation of cells inside the tumour that are called cancer stem cells (CSCs). In addition, deregulation of microRNAs (miRNAs) has been reported in different stages of GC. The aim of the present study is to determine and introduce miRNAs that contribute to regulation of stemness, metastasis and drug resistance in GC. A systematic review, we conducted data mining of available datasets and a review of previous studies to select miRNAs that target stemness, epithelial-mesenchymal transition (EMT) and drug resistance. All selected miRNAs were analysed by R software to find a common miRNA target for all three processes. Then, the target prediction of miRNAs and their related signalling pathways were obtained by using bioinformatics tools, ONCO.IO and KEGG databases, respectively. We identified seven miRNAs (miR-34a, miR-23a, miR-27a, miR-30a, miR-19b, miR-107, miR-100) from our searching approach. These miRNAs regulate pathways that contribute to stemness, EMT and drug resistance in GC. Four (miR- 34a, miR-23a, miR-30a, and miR-100) had significant interactions with each other and 52 target genes among them, from which MYC, CDK6, NOTCH1, NOTCH2, SIRT1, CD44, CD24, and AXL were involved in the regulation of several biological processes. These data suggest that the three significant properties can be regulated by common miRNAs (hsa-miR-34a, hsa-miR-23a, hsa-miR-30a and hsa-miR-100). Hence, targeting selected miRNAs or their targets might be helpful to stop tumour growth and metastasis development, and increase tumour sensitivity to chemotherapy agents. This signature can also be assumed for early detection of metastasis or drug resistance. However, there should be additional experimentation to validate these results.

Background: Recurrent pregnancy loss (RPL) is a multifactorial disorder which affects up to 5% of couples around the world. Several factors are considered to be involved in RPL; but, the etiology remains unexplained in 35-60% of cases. The aim of this study was to assess the frequency of risk factors associated with RPL in a group of our clinic clients, and their pre-implantation genetic screening (PGS) outcome.Materials and Methods: We designed a retrospective descriptive study among, 602 Iranian couples referred to the Royan Reproductive Clinic (Tehran-Iran) from 2006 to 2018. Their karyotyping test and PGS outcomes were analyzed. PGS had been applied by array comparative genomic hybridization (array-CGH) on embryos from these patients. Also, karyotyping test had been performed using standard cytogenetic techniques.Results: G-banding analysis revealed a frequency of 15.61% chromosomal abnormalities in RPL couples. Also, the reciprocal translocations were more frequent (33/1204 cases) compared to the other structural abnormalities. Pregnancy rate per embryo transferred were 50% with array-CGH approach.Conclusion: Our findings could confirm a positive correlation between chromosomal abnormalities and RPL rate. Applying PGS for the RPL couples, leads to improvement of pregnancy success rate.

Abstract Background Stearoyl-coenzyme A desaturase 1 (SCD1) is required for de novo synthesis of fatty acids. Through the fatty acid acylation process, this enzyme orchestrates post-translational modifications to proteins involved in cell development and differentiation. In this study, we used biochemical methods, immunostaining, and covalent labeling to evaluate whether a small molecule modulating unsaturated fatty acids can influence the early endodermal differentiation of human-induced pluripotent stem cells (iPSCs). Methods The hiPSCs were cultured in an endoderm-inducing medium containing activin A and defined fetal bovine serum in the presence of an SCD1 inhibitor at different time points. The cell cycles and the yields of the three germ layers (endoderm, mesoderm, and ectoderm) were assessed using flow cytometry. The expression of endoderm and pluripotency markers and the expressions of Wnt signaling pathway proteins were assessed using western blotting and RT-PCR. Total protein acylation was evaluated using a click chemistry reaction. Results When SCD1 was inhibited on the first day, the population of cells with endodermal features decreased at the end of differentiation. Moreover, early SCD1 inhibition preserved the properties of hiPSCs, preventing their shift toward mesodermal or ectodermal lineage. Also, first-day-only treatment of cells with the SCD1 inhibitor decreased β-catenin gene expression and the intensity of fluorescent emission in the click chemistry assay. The cells were effectively rescued from these effects by cotreatment with oleate. Late treatment with the inhibitor in the two subsequent days of endoderm induction did not have any significant effects on endoderm-specific markers or fluorescent intensity. Reproducible results were also obtained with human embryonic stem cells. Conclusion The small molecule SCD1 inhibitor attenuates the Wnt/β-catenin signaling pathway, conferring the maintenance of hiPSCs by opposing the initiation of endoderm differentiation. The immediate requirement for SCD1 activity in the endoderm commitment of pluripotent stem cells may be of importance in disorders of endoderm-derived organs and dysregulated metabolism. The schematic representation of the study design and main results. Activin A induces endoderm features through Smad2/3/4 and increases the expression of SCD1. SCD1 can produce MUFAs and subsequently modify the Wnt molecules. MUFA acylated/activated Wnts are secreted to interact with corresponding receptors on the target cells. β-catenin accumulates in the cytoplasm and is translocated into the nucleus after the interaction of Wnt with the receptor. Then, β-catenin increases the expression of the endoderm markers Sox17 and CXCR4.

Abstract Spermatogenesis is a complex process of cellular division and differentiation that begins with spermatogonia stem cells and leads to functional spermatozoa production. However, many of the molecular mechanisms underlying this process remain unclear. Single-cell RNA sequencing (scRNA-seq) is used to sequence the entire transcriptome at the single-cell level to assess cell-to-cell variability. In this study, more than 33,000 testicular cells from different scRNA-seq datasets with normal spermatogenesis were integrated to identify single-cell heterogeneity on a more comprehensive scale. Clustering, cell type assignments, differential expressed genes and pseudotime analysis characterized 5 spermatogonia, 4 spermatocyte, and 4 spermatid cell types during the spermatogenesis process. The UTF1 and ID4 genes were introduced as the most specific markers that can differentiate two undifferentiated spermatogonia stem cell sub-cellules. The C7orf61 and TNP can differentiate two round spermatid sub-cellules. The topological analysis of the weighted gene co-expression network along with the integrated scRNA-seq data revealed some bridge genes between spermatogenesis’s main stages such as DNAJC5B, C1orf194, HSP90AB1, BST2, EEF1A1, CRISP2, PTMS, NFKBIA, CDKN3, and HLA-DRA. The importance of these key genes is confirmed by their role in male infertility in previous studies. It can be stated that, this integrated scRNA-seq of spermatogenic cells offers novel insights into cell-to-cell heterogeneity and suggests a list of key players with a pivotal role in male infertility from the fertile spermatogenesis datasets. These key functional genes can be introduced as candidates for filtering and prioritizing genotype-to-phenotype association in male infertility.

Abstract Carcinoma of Unknown Primary (CUP) is a heterogeneous and metastatic disease where the primary site of origin is undetectable. Currently, chemotherapy is the only state-of-art treatment option for CUP patients. The molecular profiling of the tumour, particularly mutation detection, offers a new treatment approach for CUP in a personalized fashion using targeted agents. We analyzed the mutation and copy number alterations profile of 1709 CUP samples deposited in the AACR Project Genomics Evidence Neoplasia Information Exchange (GENIE) cohort and explored potentially druggable mutations. We identified 52 significant mutated genes (SMGs) among CUP samples, in which 13 (25%) of SMGs were potentially targetable with either drugs are approved for the know primary tumour or undergoing clinical trials. The most variants detected were TP53 (43%), KRAS (19.90%), KMT2D (12.60%), and CDKN2A (10.30%). Additionally, using pan-cancer analysis, we found similar variants of TERT promoter in CUP and NSCLC samples, suggesting that these mutations may serve as a diagnostic marker for identifying the primary tumour in CUP. Taken together, the mutation profiling analysis of the CUP tumours may open a new way of identifying druggable targets and consequently administrating appropriate treatment in a personalized manner.

Analysis of circulating tumor DNA (ctDNA) can be used to characterize and monitor cancers. Recently, non-invasive prenatal testing (NIPT) as a new next-generation sequencing (NGS)-based approach has been applied for detecting ctDNA. This study aimed to investigate the copy number variations (CNVs) utilizing the non-invasive prenatal testing in plasma ctDNA from ovarian cancer (OC) patients who were treated with neoadjuvant chemotherapy (NAC). The plasma samples of six patients, including stages II–IV, were collected during the pre- and post-NAC treatment that were divided into NAC-sensitive and NAC-resistant groups during the follow-up time. CNV analysis was performed using the NIPT via two methods “an open-source algorithm WISECONDORX and NextGENe software.” Results of these methods were compared in pre- and post-NAC of OC patients. Finally, bioinformatics tools were used for data mining from The Cancer Genome Atlas (TCGA) to investigate CNVs in OC patients. WISECONDORX analysis indicated fewer CNV changes on chromosomes before treatment in the NAC-sensitive rather than NAC-resistant patients. NextGENe data indicated that CNVs are not only observed in the coding genes but also in non-coding genes. CNVs in six genes were identified, including HSF1, TMEM249, MROH1, GSTT2B, ABR, and NOMO2, only in NAC-resistant patients. The comparison of these six genes in NAC-resistant patients with The Cancer Genome Atlas data illustrated that the total alteration frequency is amplification, and the highest incidence of the CNVs (≥35% based on TCGA data) is found in MROH1, TMEM249, and HSF1 genes on the chromosome (Chr) 8. Based on TCGA data, survival analysis showed a significant reduction in the overall survival among chemotherapy-resistant patients as well as a high expression level of these three genes compared to that of sensitive samples (all, p < 0.0001). The continued Chr8 study using WISECONDORX revealed CNV modifications in NAC-resistant patients prior to NAC therapy, but no CNV changes were observed in NAC-sensitive individuals. Our findings showed that low coverage whole-genome sequencing analysis used for NIPT could identify CNVs in ctDNA of OC patients before and after chemotherapy. These CNVs are different in NAC-sensitive and -resistant patients highlighting the potential application of this approach in cancer patient management.

Introduction: Semaphorin 3A (Sema 3A) is a secreted protein, which plays an integral part in developing the nervous system. It has collapse activity on the growth cone of dorsal root ganglia. After the development of the nervous system, Sema 3A expression decreases. Neuropilin 1 is a membrane receptor of Sema 3A. When semaphorin binds to neuropilin 1, the recruitment of oligodendrocyte precursor cells to the demyelinated site decreases. In Multiple Sclerosis (MS), Sema 3A expression increases and inhibits oligodendrocyte precursor cell differentiation. Therefore, the remyelination of axons gets impaired. We hypothesized that the function of Sema 3A could be inhibited by neutralizing its binding to membrane NRP1. Methods: we cloned a soluble form of mouse Neuropilin 1 (msNRP1) in a lentiviral vector and expressed the recombinant protein in HEK293T cells. Then, the conditioned medium of the transduced cells was used to evaluate the effects of the msNRP1 on the inhibition of Sema 3A-induced growth cone collapse activity. Dorsal root ganglion explants of timed pregnant (E13) mice were prepared. Then, the growth cone collapse activity of Sema 3A was assessed in the presence and absence of msNRP1-containing conditioned media of transduced and non-transduced HEK293T cells. Comparisons between groups were performed by 1-way ANOVA and post hoc Tukey tests. Results: msNRP1 was successfully cloned and transduced in HEK293T cells. The supernatant of transduced cells was concentrated and evaluated for the production of msNRP1. ELISA results indicated that transduced cells secreted msNRP1. Growth cone collapse assay showed that Sema 3A activity was significantly reduced in the presence of the conditioned medium of msNRP1-transduced HEK293T cells. Conversely, a conditioned medium of non-transduced HEK293T cells could not effectively prevent Sema 3A growth cone collapse activity. Conclusion: Our results indicated that msNRP1 was successfully produced in HEK293T cells. The secreted msNRP1 effectively prevented Sema 3A collapse activity. Therefore, msNRP1 can increase remyelination in MS lesions, although more studies using animal models are required.

Abstract Background Intrauterine Insemination (IUI) outcome prediction is a challenging issue which the assisted reproductive technology (ART) practitioners are dealing with. Predicting the success or failure of IUI based on the couples' features can assist the physicians to make the appropriate decision for suggesting IUI to the couples or not and/or continuing the treatment or not for them. Many previous studies have been focused on predicting the in vitro fertilization (IVF) and intracytoplasmic sperm injection (ICSI) outcome using machine learning algorithms. But, to the best of our knowledge, a few studies have been focused on predicting the outcome of IUI. The main aim of this study is to propose an automatic classification and feature scoring method to predict intrauterine insemination (IUI) outcome and ranking the most significant features. Methods For this purpose, a novel approach combining complex network-based feature engineering and stacked ensemble (CNFE-SE) is proposed. Three complex networks are extracted considering the patients' data similarities. The feature engineering step is performed on the complex networks. The original feature set and/or the features engineered are fed to the proposed stacked ensemble to classify and predict IUI outcome for couples per IUI treatment cycle. Our study is a retrospective study of a 5-year couples' data undergoing IUI. Data is collected from Reproductive Biomedicine Research Center, Royan Institute describing 11,255 IUI treatment cycles for 8,360 couples. Our dataset includes the couples' demographic characteristics, historical data about the patients' diseases, the clinical diagnosis, the treatment plans and the prescribed drugs during the cycles, semen quality, laboratory tests and the clinical pregnancy outcome. Results Experimental results show that the proposed method outperforms the compared methods with Area under receiver operating characteristics curve (AUC) of 0.84 ± 0.01, sensitivity of 0.79 ± 0.01, specificity of 0.91 ± 0.01, and accuracy of 0.85 ± 0.01 for the prediction of IUI outcome. Conclusions The most important predictors for predicting IUI outcome are semen parameters (sperm motility and concentration) as well as female body mass index (BMI).

Objective: In vitro fertilization (IVF) is one of the most efficient approaches within the context of assisted reproductive technology (ART) to treat infertility. High pregnancy rates have become the major index of successful IVF in clinical studies. It is not clear yet which factors are certainly responsible for IVF success, as various outcomes were obtained in different IVF centers with different settings. In this study, we aimed to address controversies in the interpretation of promising results of IVF with respect to preimplantation genetic screening (PGS). Materials and Methods: In this retrospective case series study, we built a dataset containing data from 213 IVF patient candidates for PGS (654 embryos) with blastomere biopsy at day 3 and trophectoderm biopsy in day 5, referred to Royan Institute, Tehran, Iran from 2015 to 2018. Next, the data were analyzed to find influential factors affecting success rate of ART cycles. Results: Data analyses showed that regardless of PGS indications (ART failures, recurrent miscarriage, chromosomal abnormalities, etc.), the pregnancy rate is influenced by maternal and embryonic factors such as the age of mother as well as quantity and quality of transferred embryos. Furthermore, genotyping of embryos using array comparative genomic hybridization (aCGH) depicted the highest rate of chromosomal aberrations for chromosomes 1, 16 and 19 while the lowest frequency for chromosomes 11 and 17. Similarly, we detected 463 genetically abnormal embryos by aCGH, among which only 41.9% could be detected by classical fluorescent in situ hybridization (FISH) method. Conclusion: This study not only highlighted the advantages of aCGH over the FISH method in detection of chromosomal abnormalities, but also emphasized the importance of genetic abnormality as an indication for determination of IVF success rate.

Cardiomyopathies are a group of common heart disorders that affect numerous people worldwide. Left ventricular non-compaction (LVNC) is a structural disorder of the ventricular wall, categorized as a type of cardiomyopathy that mostly caused by genetic disorders. Genetic variations are underlying causes of developmental deformation of the heart wall and the resultant contractile insufficiency. Here, we investigated a family with several affected members exhibiting LVNC phenotype. By whole-exome sequencing (WES) of three affected members, we identified a novel heterozygous missense variant (c.1963C>A:p.Leu655Met) in the gene encoding myosin heavy chain 7 (MYH7). This gene is evolutionary conserved among different organisms. We identified MYH7 as a highly enriched myosin, compared to other types of myosin heavy chains, in skeletal and cardiac muscles. Furthermore, MYH7 was among a few classes of MYH in mouse heart that highly expresses from early embryonic to adult stages. In silico predictions showed an altered actin-myosin binding, resulting in weaker binding energy that can cause LVNC. Moreover, CRISPR/Cas9 mediated MYH7 knockout in zebrafish caused impaired cardiovascular development. Altogether, these findings provide the first evidence for involvement of p.Leu655Met missense variant in the incidence of LVNC, most probably through actin-myosin binding defects during ventricular wall morphogenesis.

Abstract Ovarian cancer is the eighth most commonly occurring cancer in women. Clinically, the limitation of conventional screening and monitoring approaches inhibits high throughput analysis of the tumor molecular markers toward prediction of treatment response. Recently, analysis of liquid biopsies including circulating tumor DNA (ctDNA) open new way toward cancer diagnosis and treatment in a personalized manner in various types of solid tumors. In the case of ovarian carcinoma, growing pre-clinical and clinical studies underscored promising application of ctDNA in diagnosis, prognosis, and prediction of treatment response. In this review, we accumulate and highlight recent molecular findings of ctDNA analysis and its associations with treatment response and patient outcome. Additionally, we discussed the potential application of ctDNA in the personalized treatment of ovarian carcinoma. Graphical abstract ctDNA-monitoring usage during the ovarian cancer treatments procedures.

Objective: Health-related studies have been recently at the heart attention of the media. Social media, such as Twitter, has become a valuable online tool to describe the early detection of various adverse drug reactions (ADRs). Different medications have adverse effects on various cells and tissues, sometimes more than one cell population would be adversely affected. These types of side effect are occasionally associated with the direct or indirect influence of prescribed drugs but do not have general unfavorable mutagenic consequences on patients. This study aimed to demonstrate a quick and accurate method to collect and classify information based on the distribution of approved data on Twitter. Materials and Methods: In this classification method, we selected "ask a patient" dataset and combination of Twitter "Ask a Patient" datasets that comprised of 6,623, 26,934, and 11,623 reviews. We used deep learning methods with the word2vec to classify ADR comments posted by the users and present an architecture by HAN, FastText, and CNN. Results: Natural language processing (NLP) deep learning is able to address more advanced peculiarity in learning information compared to other types of machine learning. Moreover, the current study highlighted the advantage of incorporating various semantic features, including topics and concepts. Conclusion: Our approach predicts drug safety with the accuracy of 93% (the combination of Twitter and "Ask a Patient" datasets) in a binary manner. Despite the apparent benefit of various conventional classifiers, deep learningbased text classification methods seem to be precise and influential tools to detect ADR.

The novel coronavirus has been spreading since December 2019. It was initially reported in Wuhan, Hubei province of China. Coronavirus disease 2019 (COVID-19) has currently become a pandemic affecting over seven million people worldwide, and the number is still rising. Wenzhou, as the first hit city out of Hubei Province, achieved a remarkable success in effectively containing the disease. A great record was also observed in Wenzhou for the clinical management of COVID-19 patients, leading to one of the lowest death rates in China. Researchers and clinical specialists proposed and formulated combined approaches such as computerized tomography (CT)- scans and molecular assays, as well as using both allopathic and traditional medications to mitigate its effects. Iranian and Chinese specialists and scientists had a communication in clinical, molecular and pharmaceutical aspects of COVID-19. A proper guideline was prepared according to the experiences of Chinese clinicians in managing the full spectrum of COVID-19 patients, from relatively mild to highly complex cases. The purpose of this guideline is to serve a reference in the hospital for specialists so that they may better diagnose cases and provide effective therapies and proposed antiviral and anti-inflammatory drugs for patients.

Background and purpose: The optimization of an effective non-viral gene delivery method for genetic manipulation of primary human T cells has been a major challenge in immunotherapy researches. Due to the poor transfection efficiency of conventional methods in T cells, there has been an effort to increase the transfection rate in these cells. Protamine is an FDA-approved compound with a documented safety profile that enhances DNA condensation for gene delivery. Experimental approach: In this study, the effect of protamine sulfate on the transfection efficiency of standard transfection reagents, was evaluated to transfect primary human T cells. In this regard, pre-condensation of DNA was applied using protamine, and the value of the zeta potential of DNA/protamine/cargo complexes was determined. T cells were transfected with DNA/protamine/cargo complexes. The transfection efficiency rate was evaluated by flow cytometry. Also, the green fluorescent protein expression level and cytotoxicity of each complex were identified using real-time polymerase chain reaction and MTT assay, respectively. Findings/Results: Our results demonstrated that protamine efficiently increases the positive charge of DNA/cargo complex without any cytotoxic effect on the primary human T cells. We observed that the transfection efficiency in DNA/protamine/ Lipofectamine® 2000 and DNA/protamine/TurboFect™ was 87.2% and 78.9%, respectively, while transfection of T cells by Lipofectamine® 2000 and TurboFect™ would not result in sufficient transfection. Conclusion and implications: Protamine sulfate enhanced the transfection rate of T cells; and could be a promising non-viral gene delivery method to achieve a safe, rapid, cost-effective, and efficient system which will be further applied in gene therapy and T cells manipulation methods.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a new emerging respiratory virus, caused evolving pneumonia outbreak around the world. In SARS-Cov-2 infected patients, diabetes mellitus (DM) and obesity are two metabolic diseases associated with higher severity of SARS-CoV-2 related complications, characterized by acute lung injury requiring assisted ventilation as well as fibrosis development in surviving patients. Different factors are potentially responsible for this exacerbated response to SARS-CoV-2 infection. In patients with DM, base-line increase in inflammation and oxidative stress represent preexisting risk factors for virus-induced damages. Such factors are also likely to be found in obese patients. In addition, it has been proposed that massive injury to the alveolar epithelial type 2 (AT2) cells, which express the SARS-CoV-2 receptor angiotensin-converting enzyme 2 (ACE2), leads to the activation of their stromal niches represented by the Lipofibroblasts (LIF). LIF are instrumental in maintaining the self-renewal of AT2 stem cells. LIF have been proposed to transdifferentiate into Myofibroblast (MYF) following injury to AT2 cells, thereby contributing to fibrosis. We hypothesized that LIF’s activity could be impacted by DM or obesity in an age- and gender-dependent manner, rendering them more prone to transition toward the profibrotic MYF status in the context of severe COVID-19 pneumonia. Understanding the cumulative effects of DM and/or obesity in the context of SARS-CoV-2 infection at the cellular level will be crucial for efficient therapeutic solutions.

The etiologic agent SARS-CoV-2 has caused the outbreak of COVID-19 which is spread widely around the world. It is vital to uncover and investigate the full genome sequence of SARS-CoV-2 throughout the world to track changes in this virus. To this purpose, SARS-CoV-2 full genome sequence profiling of 20 patients in Iran and different countries that already had a travel history to Iran or contacts with Iranian cases were provided from the GISAID database. The bioinformatics analysis showed 44 different nucleotide mutations that caused 26 nonsynonymous mutations in protein sequences with regard to the reference full genome of the SARS-CoV-2 sequence (NC_045512.2). R207C, V378I, M2796I, L3606F, and A6407V in ORF1ab were common mutations in these sequences. Also, some of the detected mutations only were found in Iranian data in comparison with all the available sequences of SARS-CoV-2. The position of S protein mutations showed they were far from the binding site of this protein with angiotensin-converting enzyme-2 (ACE2) as the host cell receptor. These results can be helpful to design specific diagnostic tests, trace the SARS-CoV-2 sequence changes in Iran, and explore therapeutic drugs and vaccines.

Background: Asthenozoospermia, as the most prevalent cause of male infertility, is defined as low percentage of progressively motile spermatozoa per ejaculate. It occurs in both non-syndromic and syndromic forms and later it manifests as a part of primary ciliary dyskinesia. In the last decade, with the advent of Next-generation sequencing technologies numerous genes have been introduced in the pathogenesis of different diseases. Here, we review the genes implicated in asthenozoospermia by genetic studies. Materials and Methods: Strategies employed by infertility genetics studies in original research articles extracted from PubMed database are critically reviewed. Afterwards, genes implicated in asthenozoospermia and primary ciliary dyskinesia are discussed. Results: Until today, pathogenic variants in DNAH1, SEPT12, SLC26A8, CATSPER1, CATSPER2 and ADCY10 have been reported to cause non-syndromic asthenozoospermia. Moreover, DNAI1, DNAH5, DNAAF2, CCDC39, DYC1X1 and LRRC6 have been implicated in primary ciliary dyskinesia and syndromic asthenozoospermia. Conclusion: Next-generation sequencing technologies and especially whole-exome sequencing in families with multiple asthenozoospermic patients showed considerable success in introduction of genes involved in asthenozoospermia leading to a more comprehensive knowledge on genetics of infertility.

Background and Aim: There is increasing evidence that cancer cells in addition to multiple genetic mutations, also acquire epigenetic abnormalities during development, maintenance, and progression. By utilizing the reprogramming technology as a tool to introduce the ‘pressure’ to alter epigenetic regulations, we might be able to clarify the epigenetic behavior that is unique to cancer cells. So far, iPSCs have been generated from normal primary cells, but it is unclear whether human primary cancer cell can be reprogrammed. We investigated the production of the iPS cells from the pancreatic adenocarcinoma cells using defined transcription factors. Materials and Methods: We sought to reprogram patient derived xenograft from human PDAC, by introducing lentiviral mediated induction of Yamanaka Factors (OSKM) and characterized of induced cells by Alkaline Phosphatase staining, Real-Time PCR and immunostaining. Ethical Considerations: This study with research ethics code EC/93/1025 has been approved by research ethics committee at Royan Institute. Findings: Alkaline Phosphatase staining, Real-Time PCR and immunostaining showed that induction with the OSKM results in generating iPS cell line from fibroblast cells but not from PDAC PDX cells .We showed that, PDAC cells could not fully reprogrammed by the expression of 4 transcription factors. Conclusion: This study demonstrated that the PDAC-PDX cancer cells were distinct from PDAC induced cells with regard to their epigenetic modifier genes expression pattern, although the expression of pluripotency genes did not increased significantly in the induced PDAC cells.

Objective Cadherin-1 (CDH1) plays an important role in the metastasis, while expression of this protein is under control of epigenetic changes on its gene promoter. Therefore we evaluated both DNA methylation (DNAmet) and histone modification marks of CDH1 in prostate cancer stem like cells (PCSLCs). Materials And Methods In this experimental study, we isolated PCSLCs using cell surface marker and prostaspheroid formation, respectively. The cells isolated from both methods were characterized and then the levels of H3K4me2, H3K27me3, H3K9me2/3 and H3K9ac as well as DNAmet were assessed in CDH1 promoter of the isolated cells. Results The CD44+ CD49hi cells were not validated as PCSLCs. However, prostaspheres overexpressed stemness related genes and had higher ability of invasion potential, associated with reduction in CDH1 expression. Epigenetic status analysis showed that CDH1 promoter was hypo-methylated. Histone modifications of H3K9ac and H3K4me3 were significantly reduced, in parallel with an increased level of H3K27me3. Conclusion Our results suggest that slight decrease of DNAmet of the CpG island in CDH1 promoter does not significantly contribute to the change of CDH1 expression. Therefore, histone modifications are responsible in repressing CDH1 in PCSLCs.

After lifting the COVID-19 lockdown restrictions and opening businesses, screening is essential to prevent the spread of the virus. Group testing could be a promising candidate for screening to save time and resources. However, due to the high false-negative rate (FNR) of the RT-PCR diagnostic test, we should be cautious about using group testing because a group's false-negative result identifies all the individuals in a group as uninfected. Repeating the test is the best solution to reduce the FNR, and repeats should be integrated with the group-testing method to increase the sensitivity of the test. The simplest way is to replicate the test twice for each group (the 2Rgt method). In this paper, we present a new method for group testing (the groupMix method), which integrates two repeats in the test. Then we introduce the 2-stage sequential version of both the groupMix and the 2Rgt methods. We compare these methods analytically regarding the sensitivity and the average number of tests. The tradeoff between the sensitivity and the average number of tests should be considered when choosing the best method for the screening strategy. We applied the groupMix method to screening 263 people and identified 2 infected individuals by performing 98 tests. This method achieved a 63% saving in the number of tests compared to individual testing. Our experimental results show that in COVID-19 screening, the viral load can be low, and the group size should not be more than 6; otherwise, the FNR increases significantly. A web interface of the groupMix method is publicly available for laboratories to implement this method.

Objective In this study, we have examined human theca stem cells (hTSCs) in vitro differentiation capacity into human oocyte like cells (hOLCs). Materials And Methods In this interventional experiment study, hTSCs were isolated from the theca layer of small antral follicles (3-5 mm in size). Isolated hTSCs were expanded and cultured in differentiation medium, containing 5% human follicular fluid, for 50 days. Gene expressions of PRDM1, PRDM14, VASA, DAZL, OCT4, ZP1, 2, 3 GDF9, SCP3 and DMC1 were evaluated by quantitative reverse transcription polymerase chain reaction (qRT-PCR) on days 0, 18, and 25 after monoculture as well as one week after co-culture with human granulosa cells (hGCs). In addition, GDF9, OCT4, DAZL, VASA, and ZP3 proteins were immune-localized in oocyte-like structures. Results After 16-18 days, the color of the medium became acidic. After 25 days, the cells started to differentiate into round-shaped cells (20-25 µm diameter). One week after co-culturing with hGCs, the size of the round cells increased 60 to70 µm and convert to hOLCs. However, these growing cells expressed some primordial germ cell (PGC)- and germ cell genes (PRDM1, PRDM14, VASA, DAZL, and OCT4) as well as oocyte specific genes (ZP1, 2, 3 and GDF9), and meiotic-specific markers (SCP3 and DMC1). In addition, GDF9, OCT4, DAZL, VASA, and ZP3 proteins were present in hOLCs. Conclusion To sum up, hTSCs have the ability to differentiate into hOLCs. This introduced model paved the way for further in vitro studies of the exact mechanisms behind germ cell formation and differentiation. However, the functionality of hOLCs needs further investigation.

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.

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.

Abstract Background DNA methylation at promoters is largely correlated with inhibition of gene expression. However, the role of DNA methylation at enhancers is not fully understood, although a crosstalk with chromatin marks is expected. Actually, there exist contradictory reports about positive and negative correlations between DNA methylation and H3K4me1, a chromatin hallmark of enhancers. Results We investigated the relationship between DNA methylation and active chromatin marks through genome-wide correlations, and found anti-correlation between H3K4me1 and H3K4me3 enrichment at low and intermediate DNA methylation loci. We hypothesized “seesaw” dynamics between H3K4me1 and H3K4me3 in the low and intermediate DNA methylation range, in which DNA methylation discriminates between enhancers and promoters, marked by H3K4me1 and H3K4me3, respectively. Low methylated regions are H3K4me3 enriched, while those with intermediate DNA methylation levels are progressively H3K4me1 enriched. Additionally, the enrichment of H3K27ac, distinguishing active from primed enhancers, follows a plateau in the lower range of the intermediate DNA methylation level, corresponding to active enhancers, and decreases linearly in the higher range of the intermediate DNA methylation. Thus, the decrease of the DNA methylation switches smoothly the state of the enhancers from a primed to an active state. We summarize these observations into a rule of thumb of one-out-of-three methylation marks: “In each genomic region only one out of these three methylation marks {DNA methylation, H3K4me1, H3K4me3} is high. If it is the DNA methylation, the region is inactive. If it is H3K4me1, the region is an enhancer, and if it is H3K4me3, the region is a promoter”. To test our model, we used available genome-wide datasets of H3K4 methyltransferases knockouts. Our analysis suggests that CXXC proteins, as readers of non-methylated CpGs would regulate the “seesaw” mechanism that focuses H3K4me3 to unmethylated sites, while being repulsed from H3K4me1 decorated enhancers and CpG island shores. Conclusions Our results show that DNA methylation discriminates promoters from enhancers through H3K4me1-H3K4me3 seesaw mechanism, and suggest its possible function in the inheritance of chromatin marks after cell division. Our analyses suggest aberrant formation of promoter-like regions and ectopic transcription of hypomethylated regions of DNA. Such mechanism process can have important implications in biological process in where it has been reported abnormal DNA methylation status such as cancer and aging.

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.

Pluripotent cells emanate from the inner cell mass (ICM) of the blastocyst and when cultivated under optimal conditions immortalize as embryonic stem cells (ESCs). The fundamental mechanism underlying ESC derivation has, however, remained elusive. Recently, we have devised a highly efficient approach for establishing ESCs, through inhibition of the MEK and TGF-β pathways. This regimen provides a platform for dissecting the molecular mechanism of ESC derivation. Via temporal gene expression analysis, we reveal key genes involved in the ICM to ESC transition. We found that DNA methyltransferases play a pivotal role in efficient ESC generation. We further observed a tight correlation between ESCs and preimplantation epiblast cell-related genes and noticed that fundamental events such as epithelial-to-mesenchymal transition blockage play a key role in launching the ESC self-renewal program. Our study provides a time course transcriptional resource highlighting the dynamics of the gene regulatory network during the ICM to ESC transition.

Human brain development is a complex process that follows sequential orchestration of gene expression, begins at conceptual stages, and continues into adulthood. Altered profile of gene expression drives many cellular and molecular events required for development. Here, the molecular events during development of human prefrontal cortex (PFC) (as an important executive part of the brain) were investigated. First, the RNA-sequencing data of BrainSpan were used to obtain differentially expressed genes between each two developmental stages and then, the relevant biological processes and signaling pathways were deduced by gene set enrichment analysis. In addition, the changes in transcriptome landscape of PFC during development were analyzed and the potential biological processes underlie the changes were found. Comparison of the four regions of PFC based on their biological processes showed that additional to common biological processes and signaling pathways, each PFC region had its own molecular characteristics, conforming their previously reported functional roles in brain physiology. The most heterogeneity in transcriptome between the PFC regions was observed at the time of birth which was concurrent with the activity of some region-specific regulatory systems such as DNA methylation, transcription regulation, RNA splicing, and presence of different transcription factors and microRNAs. In conclusion, this study used bioinformatics to present a comprehensive molecular overview on PFC development which may explain the etiology of brain neuropsychiatric disorders originated from malfunctioning of PFC.

Objective: The purpose of this study was to evaluate the quantitative expressions ofBAG1, BAX and BCL-2 in human embryos with different fragmentation grades as derivedfrom assisted reproduction technology (ART).Materials and Methods: Fragmented and normal human 8-cell embryos were scoredaccording to the degree of fragmentation with an inverted microscope and divided intofour grades (grade І: no or minimal fragmentation (25% fragmentation and grade ІV: apoptotic inducedembryos with actinomycin D). In this study, TUNEL labeling was initially used todetect apoptosis, and then revers transcription polymerase chain reaction (RT-PCR) andquantitative PCR were used to define the quantitative expressions of experimental genesin human embryos with different fragmentation grades.Results: The results of TUNEL labeling showed that embryos with higher fragmentationhad a high number of apoptotic bodies. The results of RT-PCR and q-PCR analysesshowed a significantly decreased amount of BAGI transcript expression from group I togroup IV. The highest expression of BAX gene was observed in group II, however, thetranscript of BCL-2 gene was not observed in any of the experimental groups. The effectof actinomycin D on transcript expression amounts of experimental genes in apoptoticinduced embryos (group IV) compared to control embryos (group I) showed a significantdecrease.Conclusion: mRNA expression of BAG1 gene can be used as a good marker to detectapoptosis in human embryos. However, the transcript of BCL-2 gene does not play a rolein the detection of apoptosis in human embryos at the 8-cell stage.

Decision making at a cellular level determines different fates for isogenic cells. However, it is not yet clear how rational decisions are encoded in the genome, how they are transmitted to their offspring, and whether they evolve and become optimized throughout generations. In this paper, we use a game theoretic approach to explain how rational decisions are made in the presence of cooperators and competitors. Our results suggest the existence of an internal switch that operates as a biased coin. The biased coin is, in fact, a biochemical bistable network of interacting genes that can flip to one of its stable states in response to different environmental stimuli. We present a framework to describe how the positions of attractors in such a gene regulatory network correspond to the behavior of a rational player in a competing environment. We evaluate our model by considering lysis/lysogeny decision making of bacteriophage lambda in E. coli.