Natural probiotics improve heritable sterility

Disrupting the small RNA pathway and chromatin-modifying enzymes in C. elegans often leads to a mortal germline (Mrt) phenotype, characterized by progressive sterility observed over multiple generations at elevated temperature. This phenotype arises from the inheritance of aberrant epigenetic memory across generations. In this issue of EMBO Reports, Frézal and colleagues reported that, while in standard laboratory environment C. elegans wild isolates exhibit the Mrt phenotype, sterility does not occur when the worms are exposed to naturally associated bacteria and microsporidia. Excitingly, diet-induced epigenetic memory may persist for multiple generations. This suggests intriguing diet-gene interactions in modulating nongenetic inheritance, potentially shaping the evolutionary trajectory of the animals.

Deoxyhypusine hydroxylase: A novel therapeutic target differentially expressed in short-term vs long-term survivors of glioblastoma

Glioblastoma (GB) is the most aggressive neoplasm of the brain. Poor prognosis is mainly attributed to tumor heterogeneity, invasiveness and drug resistance. Only a small fraction of GB patients survives longer than 24 months from the time of diagnosis (ie, long-term survivors [LTS]). In our study, we aimed to identify molecular markers associated with favorable GB prognosis as a basis to develop therapeutic applications to improve patients' outcome. We have recently assembled a proteogenomic dataset of 87 GB clinical samples of varying survival rates. Following RNA-seq and mass spectrometry (MS)-based proteomics analysis, we identified several differentially expressed genes and proteins, including some known cancer-related pathways and some less established that showed higher expression in short-term (<6 months) survivors (STS) compared to LTS. One such target found was deoxyhypusine hydroxylase (DOHH), which is known to be involved in the biosynthesis of hypusine, an unusual amino acid essential for the function of the eukaryotic translation initiation factor 5A (eIF5A), which promotes tumor growth. We consequently validated DOHH overexpression in STS samples by quantitative polymerase chain reaction (qPCR) and immunohistochemistry. We further showed robust inhibition of proliferation, migration and invasion of GB cells following silencing of DOHH with short hairpin RNA (shRNA) or inhibition of its activity with small molecules, ciclopirox and deferiprone. Moreover, DOHH silencing led to significant inhibition of tumor progression and prolonged survival in GB mouse models. Searching for a potential mechanism by which DOHH promotes tumor aggressiveness, we found that it supports the transition of GB cells to a more invasive phenotype via epithelial-mesenchymal transition (EMT)-related pathways.

RNAlysis: analyze your RNA sequencing data without writing a single line of code

BACKGROUND

Among the major challenges in next-generation sequencing experiments are exploratory data analysis, interpreting trends, identifying potential targets/candidates, and visualizing the results clearly and intuitively. These hurdles are further heightened for researchers who are not experienced in writing computer code since most available analysis tools require programming skills. Even for proficient computational biologists, an efficient and replicable system is warranted to generate standardized results.

RESULTS

We have developed RNAlysis, a modular Python-based analysis software for RNA sequencing data. RNAlysis allows users to build customized analysis pipelines suiting their specific research questions, going all the way from raw FASTQ files (adapter trimming, alignment, and feature counting), through exploratory data analysis and data visualization, clustering analysis, and gene set enrichment analysis. RNAlysis provides a friendly graphical user interface, allowing researchers to analyze data without writing code. We demonstrate the use of RNAlysis by analyzing RNA sequencing data from different studies using C. elegans nematodes. We note that the software applies equally to data obtained from any organism with an existing reference genome.

CONCLUSIONS

RNAlysis is suitable for investigating various biological questions, allowing researchers to more accurately and reproducibly run comprehensive bioinformatic analyses. It functions as a gateway into RNA sequencing analysis for less computer-savvy researchers, but can also help experienced bioinformaticians make their analyses more robust and efficient, as it offers diverse tools, scalability, automation, and standardization between analyses.

Dual suppression of follicle activation pathways completely prevents the cyclophosphamide-induced loss of ovarian reserve

STUDY QUESTION

To what extent and how does combined administration of the follicle activation pathway suppressive agents temsirolimus (Tem) and c-terminus recombinant anti-Müllerian hormone (rAMH) protect against chemotherapy-induced ovarian reserve loss?

SUMMARY ANSWER

Combined administration of Tem and rAMH completely prevents cyclophosphamide (Cy)-induced follicle depletion and protects the ovarian reserve in mice, primarily via primordial follicle (PMF) suppression of activation and to a lesser degree by reducing apoptosis.

WHAT IS KNOWN ALREADY

There is conflicting evidence regarding the contributory roles of apoptosis and follicle activation in chemotherapy-induced PMF loss. Tem, a mammalian target of rapamycin (mTOR) inhibitor, reduces activity of the phosphoinositide 3-kinases-phosphatase and tensin homolog (PI3K-PTEN) pathway which provides intrinsic regulation of PMF activation. Anti-Müllerian hormone (AMH), secreted by early growing follicles, is an extrinsic regulator of PMF activation.

STUDY DESIGN, SIZE, DURATION

Whole ovaries of 12-day-old mice were cultured ex vivo for 7 days in the presence of Cy ± rAMH or Tem. Eight-week-old mice were randomized into eight treatment groups: vehicle control/rAMH/Tem/Cy/Tem + rAMH/Cy + Tem/Cy + rAMH/Cy + Tem + rAMH. Twelve hours after treatment, ovaries were removed for DNA damage analysis, and 24 h after treatment either for analysis of PI3K pathway proteins or to be fixed and immunostained for analyses of proliferation and apoptosis. Three or 21 days following treatment, ovaries were fixed and sectioned for follicle counting.

PARTICIPANTS/MATERIALS, SETTING, METHODS

Hematoxylin and eosin staining was used for differential follicle counts of primordial, primary, and secondary follicles in ex vivo (n = 16-18 ovaries per group) and in vivo ovaries (n = 8 mice per group). Histological analyses were carried out to measure proliferation by quantifying Ki-67-positive granulosa cells in primary follicles (n = 4 mice per group). DNA damage and apoptosis were measured by quantification of phosphorylated form of histone 2AX (γH2AX) and cleaved poly (ADP-ribose) polymerase (cPARP)-positive PMF oocytes, respectively (n = 8 mice per group). Protein extracts from whole ovaries were analyzed by western blotting.

MAIN RESULTS AND THE ROLE OF CHANCE

In vivo experiments show that treatment with Cy alone caused significant loss of PMF reserve (32 ± 2.12 versus 144 ± 2.8 in control, P < 0.001), and this was significantly attenuated by treatment with either Tem (P < 0.001) or rAMH (P < 0.001). Combined cotreatment with Cy + Tem + rAMH provided complete protection of the PMF reserve, with no significant difference in numbers of PMF versus untreated animals. Similar results were demonstrated in the ex vivo experiments. Proliferation marker Ki-67 staining was significantly reduced in granulosa cells of primary follicles in the Cy + Tem + rAMH group compared with Cy alone group (after 24 h in vivo administration of Cy, 16% versus 65%, respectively; P < 0.001). Protein analysis demonstrated not significant increased phosphorylation of follicle activation proteins rpS6 and mTOR with in vivo administration of Cy alone (1.9 and 1.4 times the control ovaries, respectively), and this was reduced to below control levels in the Cy + Tem + rAMH group (P < 0.01). The Cy + Tem + rAMH combined cotreatment protected the follicle reservoir via inhibition of Cy-induced upregulation of the PI3K signaling pathway, together with replacement of AMH suppression of PMF activation with rAMH, implying a complementary effect of the two inhibitors. The DNA damage marker γH2AX was highly positive in PMF oocytes from Cy-treated ovaries 12 h after treatment, compared with controls (94% versus 59%, respectively, P < 0.001) and was significantly reduced to (69%) in Cy + Tem + rAMH cotreated ovaries (P < 0.001). However, only 22% of PMF oocytes of the Cy group showed apoptosis at 24 h, and this was significantly reduced (12%) in ovaries after treatment with Cy + Tem + rAMH (P < 0.01). This suggests that it is not possible to equate DNA damage with oocyte death, and also indicates that less than one-third of the total PMF loss can be attributed to apoptosis, implying that most of the PMF depletion results from PMF activation but that both mechanisms play a significant role.

LARGE SCALE DATA

N/A.

LIMITATIONS, REASONS FOR CAUTION

The experimental design was limited by the selection of one time point for analysis of PMF activation and apoptosis (i.e. 24 h after Cy administration), although DNA damage was measured at 12 h after Cy administration and any impact on short-term follicle dynamics at 3 days after treatment. Protein analysis was conducted on whole ovary lysates therefore the protein changes identified cannot be localized to specific cells within the ovary. However, this complementary assay showed that there was activation in the ovary through massive reduction in the phosphorylation of key proteins in the PI3K cascade (rpS6 and mTOR), which is consistent with the sequence of events after Cy administration.

WIDER IMPLICATIONS OF THE FINDINGS

Understanding the complementary nature of different follicle activation pathways and the impact of their suppression in prevention of chemotherapy-induced ovotoxic damage, as well as their involvement in DNA damage inhibition, provides an interesting direction for future research, and the potential for noninvasive pharmacological fertility preservation.

STUDY FUNDING/COMPETING INTEREST(S)

This work was supported by a grant from the Morris Kahn Foundation. The authors declare no conflicts of interest.