Meta-analysis of endometrial transcriptome data reveals novel molecular targets for recurrent implantation failure

PURPOSE

Gene expression analysis of the endometrium has been shown to be a useful approach for identifying the molecular signatures and pathways involved in recurrent implantation failure (RIF). Nevertheless, individual studies have limitations in terms of study design, methodology and analysis to detect minor changes in expression levels or identify novel gene signatures associated with RIF.

METHOD

To overcome this, we conducted an in silico meta-analysis of nine studies, the systematic collection and integration of gene expression data, utilizing rigorous selection criteria and statistical techniques to ensure the robustness of our findings.

RESULTS

Our meta-analysis successfully unveiled a meta-signature of 49 genes closely associated with RIF. Of these genes, 38 were upregulated and 11 downregulated in RIF patients' endometrium and believed to participate in key processes like cell differentiation, communication, and adhesion. GADD45A, IGF2, and LIF, known for their roles in implantation, were identified, along with lesser-studied genes like OPRK1, PSIP1, SMCHD1, and SOD2 related to female infertility. Many of these genes are involved in MAPK and PI3K-Akt pathways, indicating their role in inflammation. We also investigated to look for key miRNAs regulating these 49 dysregulated mRNAs as potential diagnostic biomarkers. Along with this, we went to associate protein-protein interactions of 49 genes, and we could recognize one cluster consisting of 11 genes (consisted of 22 nodes and 11 edges) with the highest score (p = 0.001). Finally, we validated some of the genes by qRT-PCR in our samples.

CONCLUSION

In summary, the meta-signature genes hold promise for improving RIF patient identification and facilitating the development of personalized treatment strategies, illuminating the multifaceted nature of this complex condition.

Hidradenitis suppurativa associated telomere-methylome dysregulations in blood

BACKGROUND

Hidradenitis suppurativa (HS) is a chronic debilitating disease with a significant burden of both organic and psychological comorbidities. It has been shown that certain telomere-related genes (TRGs) affect a wide range of diseases, including HS and its associated comorbidities, but their exact role in HS pathogenesis is still unknown.

OBJECTIVES

To determine whether TRG methylomes can be used as biomarkers in HS.

METHODS

Using the Illumina HumanMethylation450 BeadChip array, we examined methylation variations associated with TRGs in HS cases and age-, sex- and ethnicity-matched healthy controls. The study utilized integrated bioinformatics statistical methods, such as a false discovery rate (FDR), the area under the receiver operating characteristic curve (AUC) and principal component analysis.

RESULTS

There were a total of 585 different differentially methylated CpG sites identified in 585 TRGs associated with HS (474 hypomethylated and 111 hypermethylated) (FDR p-value < 0.05). A number of these CpGs have been identified as being involved in increased pain sensitivity including EPAS1, AHR, CSNK1D, DNMT1, IKBKAP, NOS3, PLCB1 and PRDM16 genes; GABRB3 as a potential alcohol addiction marker; DDB1, NSMCE2 and HNRNPA2B1 associated with cancers. Pathway analysis identified 67 statistically significant pathways, including DNA repair, telomere maintenance, mismatch repair and cell cycle control (p < 0.001).

CONCLUSION

The disruption of TRGs leads to the shortening of telomeres, which is associated with HS progression, ageing, cellular senescence and an increased risk of various diseases, including cancer and associated comorbidities, such as metabolic syndrome, cardiovascular disease and inflammatory disorders. Further research is necessary to better understand the underlying mechanisms and establish causal links between TRGs and HS. The present study is the first effort to comprehend potential pathomechanisms of sporadic HS cases concentrating on PBMC methylome since ours.

Hidradenitis suppurativa presents a methylome dysregulation capable to explain the pro-inflammatory microenvironment: Are these DNA methylations potential therapeutic targets?

BACKGROUND

Hidradenitis suppurativa (HS) is a chronic, systemic, inflammatory skin condition with elusive pathogenesis that affects therapeutic intervention directly.

OBJECTIVE

To characterize epigenetic variations in cytokines genes contributing to HS.

METHODS

Epigenome-wide DNA methylation profiling with the Illumina Epic array was performed on blood DNA samples from 24 HS patients and 24 age- and sex-matched controls to explore DNA methylation changes in cytokine genes.

RESULTS

We identified 170 cytokine genes including 27 hypermethylated CpG sites and 143 genes with hypomethylated sites respectively. Hypermethylated genes, including LIF, HLA-DRB1, HLA-G, MTOR, FADD, TGFB3, MALAT1 and CCL28; hypomethylated genes, including NCSTN, SMAD3, IGF1R, IL1F9, NOD2, NOD1, YY1, DLL1 and BCL2 may contribute to the pathogenesis of HS. These genes were enriched in the 117 different pathways (FDR p-values ≤ 0.05), including IL-4/IL-13 pathways and Wnt/β-catenin signalling.

CONCLUSIONS

The lack of wound healing, microbiome dysbiosis and increased tumour susceptibility are all sustained by these dysfunctional methylomes, hopefully, capable to be targeted in the next future. Since methylome describes and summarizes genetic and environmental contributions, these data may represent a further step towards a feasible precision medicine also for HS patients.

An Updated Mutation Spectrum of the γ-Secretase Complex: Novel NCSTN Gene Mutation in an Indian Family with Hidradenitis Suppurativa and Acne Conglobata

Background

Hidradenitis suppurativa (HS) is a complex, chronic inflammatory skin disorder whose pathophysiology is poorly understood. Genetic studies have shown that HS is predisposed by mutations in the γ-secretase gene, but only a proportion of familial and partial sporadic cases have been shown to possess such mutations. HS has high genetic heterogeneity and is thought to be triggered by a combination of genetics and environmental factors.

Aims

The study aimed to investigate the genetic causes of HS in a large cohort of patients and to update the mutation spectrum of γ-secretase complex genes.

Methods

We conducted mutational screening of 95 sporadic HS cases and one large family with both HS and acne conglobata (AC) to identify mutations in the coding and splice junction region of γ-secretase complex genes (nicastrin (NCSTN), presenilin 1 (PSEN1), presenilin enhancer 2 (PSENEN), and aph-1 homolog B, gamma-secretase subunit (APH1B)).

Results

Our study identified a nucleotide substitution of 1876C>T in the NCSTN gene, which caused a stop codon (p.Arg626X) in the affected members of a large family with HS and AC. No pathogenic variants were detected in 95 sporadic cases of HS, indicating there is possible genetic heterogeneity.

Conclusion

We report a new family with a nonsense mutation in the NCSTN gene that supports the role of the γ-secretase complex genes in HS with AC. The updated γ-secretase mutation spectrum for HS now includes 78 mutations.

Dysfunctional regulation of pivotal and key inflammatory pathways in infertile Indian women with genital tuberculosis

PROBLEM

Diagnosis of female genital tuberculosis (FGTB) remains elusive due to the paucibacillary nature of the disease. We evaluated if analysis of inflammatory pathways of endometrial tissue could establish a better diagnosis of FGTB.

METHOD OF STUDY

One-hundred and four infertile women suspected of having GTB or having been treated for GTB in the past, underwent endometrial biopsies for diagnosis and Gene Inflammatory Pathways analysis at our center between 2018-2020. Diagnosis of FGTB was based on acid-fast bacilli culture, immunocytochemistry, nested-polymerase chain reaction, histopathological examination, TB GeneXpert, or combinations thereof. Gene expression profiles were also analyzed.

RESULTS

Based on diagnostic tests of 104 women, 44 (42%) were considered TB-positive, 35 (34%) TB-negative, and 25 (24%) TB-negative after TB treatment in the past. Inflammatory pathways were significantly upregulated in TB-positive women versus TB-negative (41% vs 6%; p = 0.0005), and in women who were TB-negative after TB treatment in the past versus TB-negative (never treated for TB in the past) (38% vs 6%; p = 0.0037). Two-hundred seventy-one genes were upregulated, and 61 genes were downregulated in TB-positive women versus those who were TB-negative. Differentially expressed genes were mapped to various interlinked inflammatory signaling pathways, including mitogen-activated protein kinase (MAPK), Natural Killer (NK) cells, nuclear factor kappa-B (NF-kB), tumor necrosis factor (TNF), and Toll-like receptors (TLR) signaling.

CONCLUSIONS

Inflammatory pathways and gene expression profiles add to the diagnostic tools to identify TB-positive women at an early stage. The results from this study are still experimental and large multi-centric studies are suggested before their recommendation in routine clinical practice. This article is protected by copyright. All rights reserved.

Methylated miRNAs may serve as potential biomarkers and therapeutic targets for hidradenitis suppurativa

BACKGROUND

Hidradenitis suppurativa (HS) is a chronic inflammatory disease influenced by genetics, non-genetic, and environmental factors that modulate miRNA expression. Currently, no miRNA data are available for HS. In this study, we profiled DNA methylation patterns of miRNA genes associated with HS susceptibility.

OBJECTIVES

Identify miRNA gene methylation profiles associated with HS susceptibility. This study examined the methylation patterns of DNAs from 24 healthy controls and 24 patients with HS using Illumina Infinium MethylationEPIC BeadChip array analysis. methylation patterns of miRNA genes were analyzed using Ingenuity Pathway Analysis (IPA) to explore the inversely correlated pathways regulated by miRNAs.

RESULTS

We identified 60 CpG sites representing 65 unique microRNA genes including 54 hypomethylated and 6 hypermethylated CpGs as potentially associated with HS. Some of these CpGs were found to be critical for skin function, such as miR-29, miR-200, miR-205, miR-548, and miR-132. The miR-192 is implicated in non-alcoholic fatty liver disease. The miR-200c gene was identified as a vital determinant in regulating skin repair after injury and may contribute to age-associated alterations in wound repair. miR-132 was significantly upregulated during the inflammation phase of wound repair, enhancing the activity of STAT3 and ERK pathways that promote keratinocyte proliferation.

CONCLUSIONS

Epigenetically altered microRNA genes are implicated in wound healing, inflammation, keratinocyte proliferation, and wound modulation. This is the first study to analyze methylation profiles of miRNA genes in the HS population, highlighting the unique role that miRNAs might play in diagnosing and treating HS.

Protective Effects of Melatonin Against 2,4-Dichlorophenoxyacetic Acid Induced Altered Haematological Variables in Mice: An <i>In Vivo</i> and <i>In Silico</i> Approach

2,4-Dichlorophenoxyacetic acid (2,4-D) is a systemic phenoxy herbicide that induces oxidative stress. In contrast, melatonin is a secretory product of the pineal gland with antioxidant properties. In the present study, the ameliorative potential of melatonin (10 mg/kg body weight) was investigated against 2,4-D (low, mid, and high dose-16.5, 33.0, and 66.0 mg/kg body weight) induced altered haematological variables using in vivo and in silico models. Doses of 2,4-D and melatonin were administered orally for 28 days. The evaluated haematological indices in the present study were Haemoglobin (Hb), Red Blood Corpuscles (RBC), Haematocrit (HCT), Mean Corpuscular Volume (MCV), Mean Corpuscular Haemoglobin (MCH), Mean Corpuscular Haemoglobin Concentration (MCHC), White Blood Corpuscles (WBC), Lymphocytes, Monocytes, Granulocytes, Platelet Count (PT), Mean Platelet Volume (MPV), Plateletcrit (PCT), and Erythrocyte Sedimentation Rate (ESR). The statistical significant value was considered at p<0.05. Molecular docking study was performed for interaction of 2,4-D and melatonin with haemoglobin. In vivo results revealed that 2,4-D treatment showed a significant dose-dependent alteration in above all studied haematological indices. No significant auto reversal effects were observed in the withdrawal study, on the contrarily, the altered haematological indices were normalized and comparable to control when melatonin was given alone and in combination with 2,4-D. In silico results also demonstrated that 2,4-D and melatonin showed competitive bindings with haemoglobin. In nutshell, these in vivo and in silico findings depicted those haematological indices were altered by 2,4-D toxicity and can be abridged by melatonin attributed to its ameliorative potential as also evidenced by molecular docking.

Melatonin Ameliorates 2,4-Dichlorophenoxyacetic Acid Induced Testicular Steroidogenesis Upset in Mice: An <i>In Vivo</i> and <i>In Silico</i> Study

2,4-Dichlorophenoxyacetic acid (2,4-D) is used as a selective herbicide and associated with a variety of toxicities in mammals. In contrast, melatonin is an antioxidant that promotes the elimination of free radicals. In the present study, the protective effects of melatonin (10 mg/kg body weight) against 2,4- D (low, mid, and high dose-16.5, 33.0, and 66.0 mg/kg body weight) induced testicular steroidogenesis alteration were examined using in vivo and in silico models. Doses of 2,4-D and melatonin were administered orally for 28 days. The evaluated parameters were body weight, total protein, markers for male reproductive function, and steroidogenesis i.e. testis weight, total lipid, cholesterol, testosterone, 3 beta-hydroxysteroid dehydrogenase, 17 betahydroxysteroid dehydrogenase, total sperm count, sperm motility, and sperm viability along with the histopathology of the testis. The statistical significant value was considered at p<0.05. Molecular docking study was performed for interaction of 2,4-D and melatonin with steroid binding proteins. In vivo results revealed that 2,4-D treatment showed a significant dose-dependent alteration in above all studied parameters. No significant auto-recovery was observed in the withdrawal study, on the contrarily, the altered parameters were normalized and comparable to control when melatonin was given alone and in combination with 2,4-D. In silico results also demonstrated that the binding affinity of melatonin with steroid binding proteins is higher than 2,4-D. Collectively, these in vivo and in silico findings indicated that 2,4-D induced testicular toxicity accompanied by steroidogenesis upset and can be reduced by melatonin significantly by interacting directly and strongly with studied molecular markers.

Spiders (Arachnida: Araneae) of Gujarat University Campus, Ahmedabad, India with additional description of Eilica tikaderi (Platnick, 1976)

We report a checklist of spiders based on a survey made from August 2013 to July 2014 in Gujarat University Campus, an urban area located in the middle of Ahmadabad City, Gujarat State. A total of 77 species of spiders belonging to 53 genera and 20 families of spiders were recorded from the study area represented by 31.74% of the total 63 families reported from India. Salticidae was found to be the most dominant family with 18 species from 14 genera. Guild structure analysis revealed six feeding guilds, namely stalkers, orb-web builders, space-web builders, ambushers, foliage hunters and ground runners. Stalkers and orb-web builders were the most dominant feeding guilds representing 28.58% and 20.78% respectively among all studied guilds. Species Eilica tikaderi (Platnick, 1976) is reported for the first time from Gujarat with additional description and detailed genitalic illustrations.