The dynactin subunit DCTN1 controls osteoclastogenesis via the Cdc42/PAK2 pathway

Gonadal hormone deprivation regulates response to tibolone in neurodegenerative pathways

Gonadal hormone deprivation (GHD) and decline such as menopause and bilateral oophorectomy are associated with an increased risk of neurodegeneration. Yet, hormone therapies (HTs) show varying efficacy, influenced by factors such as sex, drug type, and timing of treatment relative to hormone decline. We hypothesize that the molecular environment of the brain undergoes a transition following GHD, impacting the effectiveness of HTs. Using a GHD model in mice treated with Tibolone, we conducted proteomic analysis and identified a reprogrammed response to Tibolone, a compound that stimulates estrogenic, progestogenic, and androgenic pathways. Through a comprehensive network pharmacological workflow, we identified a reprogrammed response to Tibolone, particularly within "Pathways of Neurodegeneration", as well as interconnected pathways including "cellular respiration", "carbon metabolism", and "cellular homeostasis". Analysis revealed 23 proteins whose Tibolone response depended on GHD and/or sex, implicating critical processes like oxidative phosphorylation and calcium signalling. Our findings suggest the therapeutic efficacy of HTs may depend on these variables, suggesting a need for greater precision medicine considerations whilst highlighting the need to uncover underlying mechanisms.

Single-cell transcriptomics of the immune system in ME/CFS at baseline and following symptom provocation

Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a serious and poorly understood disease. To understand immune dysregulation in ME/CFS, we use single-cell RNA sequencing (scRNA-seq) to examine immune cells in patient and control cohorts. Postexertional malaise (PEM), an exacerbation of symptoms following strenuous exercise, is a characteristic symptom of ME/CFS. To detect changes coincident with PEM, we applied scRNA-seq on the same cohorts following exercise. At baseline, ME/CFS patients display classical monocyte dysregulation suggestive of inappropriate differentiation and migration to tissue. We identify both diseased and more normal monocytes within patients, and the fraction of diseased cells correlates with disease severity. Comparing the transcriptome at baseline and postexercise challenge, we discover patterns indicative of improper platelet activation in patients, with minimal changes elsewhere in the immune system. Taken together, these data identify immunological defects present at baseline in patients and an additional layer of dysregulation in platelets.

Mechanistic Insights into the Anti-Proliferative Action of Gut Microbial Metabolites against Breast Adenocarcinoma Cells

The gut microbiota undergoes metabolic processes to produce by-products (gut metabolites), which play a vital role in the overall maintenance of health and prevention of disease within the body. However, the use of gut metabolites as anticancer agents and their molecular mechanisms of action are largely unknown. Therefore, this study evaluated the anti-proliferative effects of three key gut microbial metabolites-sodium butyrate, inosine, and nisin, against MCF7 and MDA-MB-231 breast adenocarcinoma cell lines. To determine the potential mechanistic action of these gut metabolites, flow cytometric assessments of apoptotic potential, reactive oxygen species (ROS) production measurements and proteomics analyses were performed. Sodium butyrate exhibited promising cytotoxicity, with IC50 values of 5.23 mM and 5.06 mM against MCF7 and MDA-MB-231 cells, respectively. All three metabolites were found to induce apoptotic cell death and inhibit the production of ROS in both cell lines. Nisin and inosine indicated a potential activation of cell cycle processes. Sodium butyrate indicated the possible initiation of signal transduction processes and cellular responses to stimuli. Further investigations are necessary to ascertain the effective therapeutic dose of these metabolites, and future research on patient-derived tumour spheroids will provide insights into the potential use of these gut metabolites in cancer therapy.

Genome-wide association study revealed suggestive QTLs for production and reproduction traits in Indian Murrah buffalo

The present study was aimed to identify the genome-wide SNPs associated with production and reproduction traits in 96 Indian Murrah buffalo genotyped based on ddRAD approach using Genome-Wide Association Study (GWAS) along with phenotypes of contemporary animals using mixed linear model for production and reproduction traits. A total of 27,735 SNPs identified using ddRAD approach in 96 Indian Murrah buffaloes were used for GWAS. A total of 28 SNPs were found to be associated with production and reproductive traits. Among these, 14 SNPs were present in the intronic region of AK5, BACH2, DIRC2, ECPAS, MPZL1, MYO16, QRFPR, RASGRF1, SLC9A4, TANC1, and TRIM67 genes and one SNP in long non-coding region of LOC102414911. Out of these 28 SNPs, 9 SNPs were found to have pleiotropic effect over milk production traits and were present in chromosome number BBU 1, 2, 4, 6, 9, 10, 12, 19, and 20. SNPs in the intronic region of AK5, TRIM67 genes were found to be associated with milk production traits. Eleven and five SNPs in the intergenic region were associated with milk production and reproduction traits respectively. The above genomic information may be used for selection of Murrah animals for genetic improvement.

Transcriptomic Analysis on the Effects of Altered Water Temperature Regime on the Fish Ovarian Development of Coreius guichenoti under the Impact of River Damming

Field investigation indicated that the reduction in fish spawning was associated with the alteration in water temperatures, even a 2-3 °C monthly difference due to reservoir operations. However, the physiological mechanism that influences the development of fish ovary (DFO) remains unclear. Thus, experiments of Coreius guichenoti were conducted at three different temperatures, optimal temperature (~20 °C, N) for fish spawning, lower (~17 °C, L), and higher (~23 °C, H), to reveal the effects of altered water temperature on the DFO. Comparisons were made between the L and N (LvsN) conditions and H and N (HvsN) conditions. Transcriptomic analysis differentially expressed transcripts (DETs) related to heat stress were observed only in LvsN conditions, indicating that the DFO showed a stronger response to changes in LvsN than in HvsN conditions. Upregulation of DETs of vitellogenin receptors in N temperature showed that normal temperature was conducive to vitellogenin entry into the oocytes. Other temperature-sensitive DETs, including microtubule, kinesin, dynein, and actin, were closely associated with cell division and material transport. LvsN significantly impacted cell division and nutrient accumulation in the yolk, whereas HvsN only influenced cell division. Our results highlight the impact of altered water temperature on the DFO, thereby providing insights for future reservoir operations regarding river damming and climate change and establishing fish conservation measures.

CoRe: a robustly benchmarked R package for identifying core-fitness genes in genome-wide pooled CRISPR-Cas9 screens

BACKGROUND

CRISPR-Cas9 genome-wide screens are being increasingly performed, allowing systematic explorations of cancer dependencies at unprecedented accuracy and scale. One of the major computational challenges when analysing data derived from such screens is to identify genes that are essential for cell survival invariantly across tissues, conditions, and genomic-contexts (core-fitness genes), and to distinguish them from context-specific essential genes. This is of paramount importance to assess the safety profile of candidate therapeutic targets and for elucidating mechanisms involved in tissue-specific genetic diseases.

RESULTS

We have developed CoRe: an R package implementing existing and novel methods for the identification of core-fitness genes (at two different level of stringency) from joint analyses of multiple CRISPR-Cas9 screens. We demonstrate, through a fully reproducible benchmarking pipeline, that CoRe outperforms state-of-the-art tools, yielding more reliable and biologically relevant sets of core-fitness genes.

CONCLUSIONS

CoRe offers a flexible pipeline, compatible with many pre-processing methods for the analysis of CRISPR data, which can be tailored onto different use-cases. The CoRe package can be used for the identification of high-confidence novel core-fitness genes, as well as a means to filter out potentially cytotoxic hits while analysing cancer dependency datasets for identifying and prioritising novel selective therapeutic targets.

Preventive effect of tetrahedral framework nucleic acids on bisphosphonate-related osteonecrosis of the jaw

Zoledronic acid (ZA) is a bisphosphonate (BP) drug that has been widely used in clinical treatments as a potent bone resorption inhibitor. In recent years, an increasing number of cases of bisphosphonate-associated osteonecrosis of the jaw (BRONJ) have been reported. This is a severe maxillofacial complication characterized clinically by bone exposure, necrosis, pain, and halitosis. Its pathogenesis is still not clear, and there is no effective clinical treatment known. Therefore, prevention of BRONJ is especially important. To provide a new research direction for the treatment of BRONJ, this study used a new tetrahedral framework nucleic acid (TFNA), which can antagonize the inhibitory effect of ZA on the differentiation and maturation of osteoclasts (OCs). In vivo and in vitro experiments showed that TFNAs at a specific concentration exhibited no cytotoxicity and could reverse the inhibition of ZA on OC differentiation and maturation, effectively inhibiting the formation of BRONJ.

Endogenous Mechanisms of Neuroprotection: To Boost or Not to Boost

Postmitotic cells, like neurons, must live through a lifetime. For this reason, organisms/cells have evolved with self-repair mechanisms that allow them to have a long life. The discovery workflow of neuroprotectors during the last years has focused on blocking the pathophysiological mechanisms that lead to neuronal loss in neurodegeneration. Unfortunately, only a few strategies from these studies were able to slow down or prevent neurodegeneration. There is compelling evidence demonstrating that endorsing the self-healing mechanisms that organisms/cells endogenously have, commonly referred to as cellular resilience, can arm neurons and promote their self-healing. Although enhancing these mechanisms has not yet received sufficient attention, these pathways open up new therapeutic avenues to prevent neuronal death and ameliorate neurodegeneration. Here, we highlight the main endogenous mechanisms of protection and describe their role in promoting neuron survival during neurodegeneration.