CPK27 enhances cold tolerance by promoting flavonoid biosynthesis through phosphorylating HY5 in tomato

Cold stress is a major environmental challenge affecting the production of crops. Calcium-dependent protein kinases (CDPKs/CPKs) are crucial regulators relaying calcium (Ca2+) signals into cellular stress responses. However, the specific mechanisms of CPKs in regulating cold stress signaling are not well understood. In this study, through genetic, physiological and molecular biology assays, we characterized the function of CPK27 in enhancing tomato cold tolerance. We found that CPK27 stimulates flavonoid biosynthesis in a Ca2+-dependent manner, which in turn boosts the plant's tolerance. Tomato plants lacking CPK27 (cpk27) showed decreased flavonoid levels under cold stress, accompanied by the increased sensitivity to cold. Activated by cold stress, CPK27 accumulates within the nucleus, where it physically interacts and phosphorylates ELONGATED HYPOCOTYL 5 (HY5) protein at serine23 (S23) and S57 residues, contributing to the cold-induced accumulation of HY5 protein. HY5 directly binds to the promoter regions and stimulates the transcription of flavonoid biosynthesis genes. Further genetic analysis showed that CPK27 acts upstream of HY5, and the flavonoid biosynthesis pathway activated by CPK27 is HY5-dependent. Our study elucidates the regulatory mechanism whereby the CPK27-HY5 molecule integrates cold-triggered Ca2+ signals with flavonoid biosynthesis pathways to confer cold stress tolerance, thereby uncovering the key strategy for cold signal transduction.

Conserved biological processes in partial cellular reprogramming: Relevance to aging and rejuvenation

Partial or transient cellular reprogramming is defined by the limited induction of pluripotency factors without full dedifferentiation of cells to a pluripotent state. Comparing in vitro and in vivo mouse studies, and in vitro studies in humans, supported by visualizations of data interconnections, we show consistent patterns in how such reprogramming modulates key biological processes. Generally, partial reprogramming drives dynamic chromatin remodelling, involving histone modifications that regulate accessibility and facilitate pluripotency gene activation while silencing somatic identity. These changes are accompanied by modifications in stress response programs, such as inflammation, autophagy, and cellular senescence, as well as improved mitochondrial activity and dysregulation of extracellular matrix pathways. We also underscore the challenges in evaluating complex processes like aging and cellular senescence, given the variability in biomarkers used across studies. Overall, we highlight biological processes consistently influenced by reprogramming while noting that some effects are context-dependent, varying according to cell type, species, sex, recovery time, and the reprogramming method employed. These insights inform future research and potential therapeutic applications in aging and regenerative medicine.

NEK kinases in cell cycle regulation, DNA damage response, and cancer progression

The NIMA-related kinase (NEK) family of serine/threonine kinases is essential for the regulation of cell cycle progression, mitotic spindle assembly, and genomic stability. In this review, we explore the structural and functional diversity of NEK kinases, highlighting their roles in both canonical and non-canonical cellular processes. We examine recent preclinical findings on NEK inhibition, showcasing promising results for NEK-targeted therapies, particularly in cancer types characterized by high NEK expression. We discussed the therapeutic potential of targeting NEKs as modulators of cell cycle and DDR pathways, with a focus on identifying strategies to exploit NEK activity for enhanced treatment efficacy. Future research directions are proposed to further elucidate NEK-mediated mechanisms and to develop selective inhibitors that target NEK-related pathways.

Exploration of genes related to the development of cancer of unknown primary

The biological basis of the development of cancer of unknown primary (CUP) remains largely unknown, with no evidence of whether a common biological basis exists at present. Our previous multicenter clinical study predicted the primary site of CUP for site‑specific therapy. Concomitantly with the study, a microarray analysis of tumor mRNA samples obtained from 60 participants of the study with CUP was performed, and a gene expression profile specific to CUP was constructed. Several of the genes identified as being upregulated/downregulated in CUP could potentially be clinically useful common biomarkers of CUP. In the present study, to identify genes that may be more closely related to the development of CUP (characterized by its metastatic potential) among the upregulated genes, cell‑based small interfering RNA screening was performed in vitro, and two genes, protein kinase DNA‑activated catalytic subunit (PRKDC) and proteasome subunit β type‑4 (PSMB4), were identified to be possibly involved in the metastatic ability of CUP, since knockdown of these genes resulted in reduced migration of A549 cells. These genes were further knocked down in A549 cells using short hairpin RNAs (shRNAs) and the cells were implanted into the footpad of mice. Marked suppression of the metastatic ability of implanted cells from the footpad to the popliteal lymph node (LN) was observed in cells transfected with the shRNAs for PRKDC and PSMB4. In addition, bortezomib, a proteasome inhibitor, markedly reduced the ability of cells implanted into the footpad to metastasize to the LNs, as well as cell growth at the metastatic site, compared with vehicle or NU7447 (inhibitor of PRKDC). These findings indicated that proteasomal function activation augmented the metastatic ability of malignant CUP cells.

Identification of FLYWCH1 as a regulator of platinum-resistance in epithelial ovarian cancer

Platinum-based combination chemotherapy remains the backbone of first-line treatment for patients with advanced epithelial ovarian cancer (EOC). While most patients initially respond well to the treatment, patients with relapse ultimately develop platinum resistance. This study identified FLYWCH-type zinc finger-containing protein 1 (FLYWCH1) as an important regulator in the resistance development process. We showed that the loss of FLYWCH1 promotes platinum resistance in EOC cells, and the low FLYWCH1 expression is correlated with poor prognosis of EOC patients. In platinum-sensitive cells, FLYWCH1 colocalizes with H3K9me3, but this association is significantly reduced when cells acquire resistance. The suppression of FLYWCH1 induces gene expression changes resulting in the deregulation of pathways associated with resistance. In line with its connection to H3K9me3, FLYWCH1 induces gene silencing in a synthetic reporter assay and the suppression of FLYWCH1 alters H3K9me3 at promoter regions and repeat elements. The loss of FLYWCH1 leads to the derepression of LTR and Alu repeats, thereby increasing transcriptional plasticity and driving the resistance development process. Our data highlight the importance of FLYWCH1 in chromatin biology and acquisition of platinum resistance through transcriptional plasticity and propose FLYWCH1 as a potential biomarker for predicting treatment responses in EOC patients.

SLX4 and XPF are involved in cell migration and EMT in a cell-specific manner

SLX4 and XPF are two proteins involved in DNA repair, but very little is known about their potential roles in other processes of cancer cell biology. We developed original cell models with CRISPR-Cas9-mediated knock-out of SLX4 and/or XPF using five different cell lines (A549, NCI-H1703, COLO-357, HT-29 and HEK-293 T), and performed characterization with cell biology experiments including migration assays, drug sensitivity testing, cell proliferation assessment and Western blots for relevant proteins. Results showed decreased migration of all models in HT-29 cells, of XPF-deficient COLO-357 cells and of SLX4-deficient HEK-293 T cells. Modified cell models had overall increased sensitivity to cisplatin and mitomycine C, and some models showed an increased frequency of double-stranded DNA damages. One NCI-H1703 cell model showed major karyotypic modifications, and epithelial to mesenchymal transition (EMT)-related proteins were modified in several models. Finally, knocking out one or both proteins in A549 cells had not the same impact on in vivo growth in mice. These original cell models allowed us to identify new and DNA repair-unrelated cellular roles of SLX4 and XPF in cancer cell biology. Our results should be considered within work on Nucleotide Excision Repair (NER) inhibition targeting SLX, XPF or other related proteins.

Harmine hydrochloride induces G0/G1 cell cycle arrest and apoptosis in oral squamous carcinoma cells

Oral squamous cell carcinoma (OSCC) represents the most frequently occurring form of oral cancer. However, despite the availability of advanced treatment modalities, the global 5-year survival rate for patients with advanced OSCC remains at ~50-60%. Devising alternative therapeutic strategies for oral cancer has therefore become an urgent need. Harmine, a β-carboline alkaloid, has recently been shown to exhibit anticancer activity. Compared with harmine, harmine hydrochloride (HH), a derivative of harmine, has improved water solubility and stability, so can absorb into tissues more readily. Therefore, the present study aimed to investigate the anticancer activity of HH in OSCC cells. A Cell Counting Kit-8 assay was performed to assess the cytotoxic effects of HH on the OSCC cell lines, SCC-4 and SCC-25. Flow cytometric analysis was subsequently employed to examine both the cell cycle profile and the extent of apoptosis. Western blotting was used to assess the expression levels of the regulatory proteins involved in these biological activities, and treatment with a pan-caspase inhibitor (Z-VAD-FMK) confirmed the involvement of the apoptotic pathway. Furthermore, western blotting was used to investigate which signaling pathways were affected in the HH-treated cells. Taken together, the findings of the present study demonstrated that HH was cytotoxic in OSCC cells. HH treatment induced G0/G1 phase cell cycle arrest and apoptosis. Additionally, the MAPK pathway was shown to be involved in HH-induced apoptosis in SCC-4 cells. Therefore, HH exhibited anticancer activity, and may be a putative therapeutic agent for the treatment of OSCC in the future.

Ferroptosis as a therapeutic vulnerability in MDM2 inhibition in dedifferentiated liposarcoma

Ferroptosis is a form of necrotic cell death characterized by phospholipid oxidation. The cystine-glutamate antiporter (xCT), composed of solute carrier family 7 member 11 (SLC7A11) and SLC3A2, imports cystine for glutathione synthesis. Glutathione peroxidase 4 (GPX4) requires glutathione to counteract lipid peroxidation and prevent ferroptosis. Erastin, an xCT inhibitor, and Ras-selective lethal small molecule 3 (RSL3), a GPX4 inhibitor, suppress GPX4 function and induce ferroptosis. Tumor protein p53 (TP53) has a paradoxical role in ferroptosis regulation. Mouse double minute 2 homolog (MDM2), a negative regulator of TP53, is a key oncogene in well-differentiated liposarcoma (WDLPS) and dedifferentiated liposarcoma (DDLPS). Therefore, the present study explored the role of ferroptosis in DDLPS treatment response and resistance. Publicly available expression profiles of WDLPS, DDLPS and adipose tissue were analyzed, and the differential expression of ferroptosis-related genes regulated by the MDM2-TP53 pathway was identified in WDLPS and DDLPS. In vitro experiments were performed to assess the effects of erastin and RSL3 on the viability, lipid peroxidation and apoptosis of DDLPS cell lines. The results revealed that erastin and RSL3 induced lipid peroxidation and apoptosis, thereby exerting cytotoxic effects. In addition, nutlin-3, an MDM2 inhibitor, was demonstrated to increase lipid peroxidation and cytotoxicity when applied prior to erastin treatment. Notably, nutlin-3 also upregulated SLC3A2 expression in DDLPS cell lines, thereby enhancing cystine uptake. This increase in cystine uptake was suppressed by erastin. In addition, nutlin-3-induced SLC3A2 upregulation was abolished by TP53 knockdown. Nutlin-3 combined with erastin or RSL3 reduced absolute p-4EBP-1 levels in NDDLS-1 cells and p-p70S6 levels in both cell lines, with no significant impact on the p-4EBP-1/4EBP-1 and p-p70S6/p70S6 ratios. These results indicate that ferroptosis is a therapeutic vulnerability in the response to MDM2 inhibition in DDLPS. Furthermore, combining MDM2 inhibitors with ferroptosis-inducing agents may provide a potential therapeutic strategy for DDLPS and the role of mTOR in the pro-apoptotic effect of these combinations deserve further investigation.

Unexpected Richness of the Bacterial Small RNA World

I stumbled onto a small RNA (sRNA) induced by oxidative stress when I did the "wrong" northern blot experiment as a second-year graduate student. I was so intrigued by the very strong induction of the 109 nt OxyS RNA that I kept working to elucidate its function while carrying out other projects. Over a decade after developing the first OxyS northern, I was able to document that the RNA acts as a regulator. This finding together with concurrent observations about the 91 nt DsrA RNA by Susan Gottesman's group led to the realization that regulatory sRNAs were far more prevalent in bacteria than initially imagined. I do not think we could have anticipated how integral sRNAs are to regulatory networks in bacteria and how much we would learn about the mechanisms by which these sRNAs regulate gene expression, most commonly through limited base pairing with target mRNAs, chaperoned by the Hfq protein. Our work was greatly facilitated by the collegiality in the bacterial sRNA field and the regular discussions and collaborations between my group and the Gottesman group. Susan and I are both writing overviews but have agreed to emphasize different aspects of the investigation into bacterial sRNAs with the intent that our articles are read in parallel.

Ginsenoside Rc maintains sleep rhythm homeostasis by alleviating oxidative stress

BACKGROUND

Sleep disorders significantly impact physical health and quality of life. However, the current treatment strategies have several limitations. Panax ginseng has been traditionally employed to calm the mind, but its active components and their mechanisms remain elusive.

PURPOSE

This study aimed to elucidate the sleep-improving actions of Panax ginseng active component, ginseng Rc, and its potential mechanisms.

METHODS

Sleep duration and rhythm of Drosophila were assessed via a behavior analysis system. Furthermore, the potential addictive side effects of ginsenoside Rc were assessed through capillary ingestion. Changes in mRNA levels of core clock genes and stress response-related genes were determined via RT-qPCR. In addition, the potential mechanisms underlying the efficacy of ginsenoside Rc were evaluated by transcriptomic methodologies. A molecular operating environment (MOE)-Dock simulation was conducted to predict the binding affinity between Pink1 and ginsenoside Rc and verified by surface plasmon resonance. Lastly, Western blotting was carried out to assess Sir2 expression and acetylation of brain proteins.

RESULTS

It was observed that ginsenoside Rc improved sleep duration, latency, fragmentation, and amplitude. Furthermore, it upregulated the expression of the clock gene and was not addictive or dependency-inducing. Moreover, it increased antioxidant-related gene expression and reduced stress-related gene expression. In addition, transcriptomic analysis demonstrated that ginsenoside Rc also upregulated autophagy-related genes. Mechanistic studies showed that it improves sleep homeostasis by activating the Pink1/Sir2 signaling pathway, reducing oxidative stress, and modulating protein acetylation levels.

CONCLUSION

This study identified ginsenoside Rc, a novel compound from ginseng, and revealed that it can maintain sleep homeostasis. Mechanistically, ginsenoside Rc alleviated oxidative stress by targeting Pink1 and Sir2. These findings provide evidence for the potential clinical application of ginsenoside Rc for treating sleep disorders.

Except for Robust Outliers, Rapamycin Increases Lesion Burden in a Murine Model of Cerebral Cavernous Malformations

Cerebral cavernous malformation (CCM) is a hemorrhagic cerebrovascular disease where lesions develop in the setting of endothelial mutations of CCM genes, with many cases also harboring somatic PIK3CA gain of function (GOF) mutations. Rapamycin, an mTORC1 inhibitor, inhibited progression of murine CCM lesions driven by Ccm gene loss and Pik3ca GOF, but it remains unknown if rapamycin is beneficial in the absence of induction of Pik3ca GOF. We investigated the effect of rapamycin at three clinically relevant doses on lesion development in the Ccm3-/-PDGFb-icreERPositive murine model of familial CCM disease, without induction of Pik3ca GOF. Lesion burden, attrition, and acute and chronic hemorrhaging were compared between placebo and rapamycin-treated mice. Plasma miRNome was compared to identify potential biomarkers of rapamycin response. Outlier, exceptionally large CCM lesions (> 2 SD above the mean lesion burden) were exclusively observed in the placebo group. Rapamycin, across all dosages, may have prevented the emergence of large outlier lesions. Yet rapamycin also appeared to exacerbate mean lesion burden of surviving mice when outliers were excluded, increased attrition, and did not alter hemorrhage. miR-30c-2-3p, decreased in rapamycin-treated mouse plasma, has gene targets in PI3K/AKT and mTOR signaling. Progression of outlier lesions in a familial CCM model may have been halted by rapamycin treatment, at the potential expense of increased mean lesion burden and increased attrition. If confirmed, this can have implications for potential rapamycin treatment of familial CCM disease, where lesion development may not be driven by PIK3CA GOF. Further studies are necessary to determine specific pathways that mediate potential beneficial and detrimental effects of rapamycin treatment, and whether somatic PIK3CA mutations drive particularly aggressive lesions.

Upregulated TCF1+ Treg Cells With Stronger Function in Systemic Lupus Erythematosus Through Activation of the Wnt-β-Catenin

The role of T-cell factor 1 (TCF1) in human regulatory T cells (Treg) and its clinical significance in systemic lupus erythematosus (SLE) remain unclear. Through bioinformatics analysis and flow cytometry, the Tcf7 gene and TCF1 protein were found to be highly expressed in Treg cells. TCF1+ Treg cells exhibited increased expression of CTLA4 and LAG3 and higher IL-10 secretion than TCF1- Treg cells. Circulating TCF1+ Treg cells were elevated and displayed increased inhibitory markers in SLE patients. The Wnt-β-catenin pathway was activated in TCF1+ Treg cells in SLE patients. The addition of XAV939 impaired the function of TCF1+ Treg cells. Clinically, TCF1+ Treg cells were not only related to CRP, ESR and IL-2, but also could differentiate SLE patients from healthy controls, primary Sjögren's syndrome patients and rheumatoid arthritis patients. In conclusion, the increased TCF1+ Treg cells in SLE patients indicate a stronger suppressive function for the activated Wnt-β-catenin pathway and help screening and assisting in the diagnosis of SLE patients.

Loss of aryl hydrocarbon receptor reduces pancreatic tumor growth by increasing immune cell infiltration

Pancreatic ductal adenocarcinoma (PDAC) is a devastating disease which remains poorly understood. Increasing evidence suggests that the aryl hydrocarbon receptor (AHR) plays a role in the pathogenesis of several cancers; however, its role in PDAC is unclear because AHR exhibits both pro- and anti-tumor activities. Here we evaluated the role of AHR in CR705 and K8484 murine PDAC cells in vitro and CR705 cells in vivo. Loss of Ahr did not affect cell proliferation compared with Cas9 control cells and no differences in tumor development between CR705Cas9 and CR705AhrKO cells were observed in immunocompromised mice. Conversely, tumors from CR705AhrKO cells grew more slowly than tumors from CR705Cas9 cells in immune competent mice. RNA sequencing identified 1279 genes upregulated and 586 genes downregulated in CR705AhrKO tumors compared with CR705Cas9 tumors. Pathway analysis identified immunoregulatory interactions, interferon signaling, and chemokine signaling among the top upregulated pathways. Increased infiltration of CD45+ cells and higher numbers of CD8+ T cells and F4/80+ cells were observed in CR705AhrKO tumors. Ahr deficiency in macrophages (LysMCre) or lymphocytes (RorcCre) did not alter tumor development of CR705Cas9 cells compared with Ahrfl/fl mice. CR705AhrKO tumors in RorcCre mice, but not in LysMCre mice had significantly lower tumor weights normalized to body weights compared with CR705AhrKO tumors in WT mice. These findings show that Ahr loss in CR705 pancreatic cancer cells is sufficient to induce proinflammatory gene responses that contribute to increased immune cell infiltration and reduced tumor growth.

Understanding the genetics of sex determination in insects and its relevance to genetic pest management

Sex determination pathways regulate male and female-specific development and differentiation and offer potential targets for genetic pest management methods. Insect sex determination pathways are comprised of primary signals, relay genes and terminal genes. Primary signals of coleopteran, dipteran, hymenopteran and lepidopteran species are highly diverse and regulate the sex-specific splicing of relay genes based on the primary signal dosage, amino acid composition or the interaction with paternally inherited genes. In coleopterans, hymenopterans and some dipterans, relay genes are Transformer orthologs from the serine-arginine protein family that regulate sex-specific splicing of the terminal genes. Alternative genes regulate the splicing of the terminal genes in dipterans that lack Transformer orthologs and lepidopterans. Doublesex and Fruitless orthologs are the terminal genes. Doublesex and Fruitless orthologs are highly conserved zinc-finger proteins that regulate the expression of downstream proteins influencing physical traits and courtship behaviours in a sex-specific manner. Genetic pest management methods can use different mechanisms to exploit or disrupt female-specific regions of different sex determination genes. Female-specific regions of sex determination genes can be exploited to produce a lethal gene only in females or disrupted to impede female development or fertility. Reducing the number of fertile females in pest populations creates a male-biased sex ratio and eventually leads to the local elimination of the pest population. Knowledge on the genetic basis of sex determination is important to enable these sex determination pathways to be exploited for genetic pest management.

Meta-Analysis of Transcriptomic Studies of Blood and Six Brain Regions Identifies a Consensus of 15 Cross-Tissue Mechanisms in Alzheimer's Disease and Suggests an Origin of Cross-Study Heterogeneity

The comprehensive genome-wide nature of transcriptome studies in Alzheimer's disease (AD) should provide a reliable description of disease molecular states. However, the genes and molecular systems nominated by transcriptomic studies do not always overlap. Even when results do align, it is not clear if those observations represent true consensus across many studies. A couple of sources of variation have been proposed to explain this variability, including tissue-of-origin and cohort type, but its basis remains uncertain. To address this variability and extract reliable results, we utilized all publicly available blood or brain transcriptomic datasets of AD, comprised of 24 brain studies with 4007 samples from six different brain regions, and eight blood studies with 1566 samples. We identified a consensus of AD-associated genes across brain regions and AD-associated gene-sets across blood and brain, generalizable machine learning and linear scoring classifiers, and significant contributors to biological diversity in AD datasets. While AD-associated genes did not significantly overlap between blood and brain, our findings highlighted 15 dysregulated processes shared across blood and brain in AD. The top five most significantly dysregulated processes were DNA replication, metabolism of proteins, protein localization, cell cycle, and programmed cell death. Conversely, addressing the discord across studies, we found that large-scale gene co-regulation patterns can account for a significant fraction of variability in AD datasets. Overall, this study ranked and characterized a compilation of genes and molecular systems consistently identified across a large assembly of AD transcriptome studies in blood and brain, providing potential candidate biomarkers and therapeutic targets.

From Function to Mechanism: Unveiling the Role of Small Nucleolar Ribonucleic Acids in Digestive Tumours

Small nucleolar ribonucleic acids (snoRNAs) have emerged as crucial regulators in various biological processes and have garnered significant attention for their potential roles in cancer. These noncoding ribonucleic acids (RNAs) primarily guide ribosomal RNA (rRNA) pseudouridylation and 2'-O-methylation modifications and exhibit stable expression in the serum, making them promising biomarkers and therapeutic targets. Digestive tract cancer poses a severe global health threat due to its high mortality rate and difficulty in early detection. Understanding the molecular mechanisms underlying tumor development is critical for improving diagnostic and therapeutic strategies. Small nucleolar RNAs, with their diverse functions and stable presence in biological fluids, offer a unique opportunity to address these challenges. Small nucleolar RNAs are a class of small noncoding RNAs mainly located in the nucleolus of eukaryotic cells. They play essential roles in the maturation and modification of rRNAs, transfer RNAs, and small nuclear RNAs. They also participate in alternative splicing regulation and exhibit microRNA-like functions, influencing various cellular processes. Abnormal expression of snoRNAs has been closely linked to the development, invasion, and metastasis of digestive system tumors. Given their stable expression in serum and the ability to function independently of host genes, snoRNAs hold great potential as biomarkers for early screening, prognosis prediction, and therapeutic targets in digestive system tumors. Their involvement in key signaling pathways and molecular mechanisms provides a foundation for developing targeted therapies and improving patient outcomes. This review highlights the significance of snoRNAs in digestive system tumors, their biological roles, connections to cancer progression, and potential clinical applications. Further exploration of snoRNAs is expected to provide new insights into the diagnosis and treatment of digestive system tumors.

Cardiac enhancers: Gateway to the regulatory mechanisms of heart regeneration

The adult mammalian heart has limited regenerative capacity. Cardiac injury, such as a myocardial infarction (MI), leads to permanent scarring and impaired heart function. In contrast, neonatal mice and zebrafish possess the ability to repair injured hearts. Cardiac regeneration is driven by profound transcriptional changes, which are controlled by gene regulatory elements, such as tissue regeneration enhancer elements (TREEs). Here, we review recent studies on cardiac injury/regeneration enhancers across species. We further explore regulatory mechanisms governing TREE activities and their associated binding regulators. We also discuss the potential of TREE engineering and how these enhancers can be utilized for heart repair. Decoding the regulatory logic of cardiac regeneration enhancers presents a promising avenue for understanding heart regeneration and advancing therapeutic strategies for heart failure.

Impact of diet and exercise on mitochondrial quality and mitophagy in Alzheimer's disease

Alzheimer's disease (AD) is a devastating neurodegenerative disorder that affects millions of people worldwide. It is characterized by the accumulation of beta-amyloid and phosphorylated tau, synaptic damage, and mitochondrial abnormalities in the brain, leading to the progressive loss of cognitive function and memory. In AD, emerging research suggests that lifestyle factors such as a healthy diet and regular exercise may play a significant role in delaying the onset and progression of the disease. Mitochondria are often referred to as the powerhouse of the cell, as they are responsible for producing the energy to cells, including neurons to maintain cognitive function. Our article elaborates on how mitochondrial quality and function decline with age and AD, leading to an increase in oxidative stress and a decrease in ATP production. Decline in mitochondrial quality can impair cellular functions contributing to the development and progression of disease with the loss of neuronal functions in AD. This article also covered mitophagy, the process by which damaged or dysfunctional mitochondria are selectively removed from the cell to maintain cellular homeostasis. Impaired mitophagy has been implicated in the progression and pathogenesis of AD. We also discussed the impact of impaired mitophagy implicated in AD, as the accumulation of damaged mitochondria can lead to increased oxidative stress. We expounded how dietary interventions and exercise can help to improve mitochondrial quality, and mitochondrial function and enhance mitophagy in AD. A diet rich in antioxidants, polyphenols, and mitochondria-targeted small molecules has been shown to enhance mitochondrial function and protect against oxidative stress, particularly in neurons with aged and mild cognitively impaired subjects and AD patients. Promoting a healthy lifestyle, mainly balanced diet and regular exercise that support mitochondrial health, in an individual can potentially delay the onset and progression of AD. In conclusion, a healthy diet and regular exercise play a crucial role in maintaining mitochondrial quality and mitochondrial function, in turn, enhancing mitophagy and synaptic activities that delay AD in the elderly populations.

Necrostatin-1 attenuates oral squamous cell carcinoma by modulating tumour immune response in mice

BACKGROUND

Necroptosis has been shown to play an important role in various pathologies, including pancreatic cancer (PDAC). However, its role in the progression of oral cancer (OSCC) remains unclear.

OBJECTIVES

To determine the expression of key necroptosis pathway markers in an OSCC mouse model and evaluate the therapeutic effect of a necroptosis inhibitor on the progression of OSCC.

METHODS AND RESULTS

4-NQO-induced OSCC in mice resembles very closely to human OSCC. The expression of RIPK-1, RIPK-3, MLKL and their respective phosphorylation was increased in OSCC tissues of cancer-bearing mice. In the analysis of the necroptosis pathway in human OSCC with the TCGA database, we found similar overexpression of RIPK-1 in human cancer, which correlated with the severity of cancer in terms of different cancer grades and stages. Pharmacological blockade of necroptosis with necrostatin-1 (NEC-1) reduced the progression and development of OSCC, characterized by reduced number and severity of tumour lesions, improved histology with reduced hyperplasia, dysplasia and invasive carcinoma. Immune profiling of blood, spleen and tumour tissues demonstrated suppressed expression of MDSCs (CD11b+Gr-1+) and M2-macrophages (CD11b+F4/80+CD206+), while M1-macrophages (CD11b+F4/80+MHCII+) were elevated in the treatment group. The ratio of M2/M1 was reduced in the treated group, suggesting the promotion of anti-tumour immune response. Expression of Arg-1, YM1/2, IL-10 and TGF-β was reduced in tumour tissues in the treated group.

CONCLUSION

In summary, blocking the necroptosis pathway alters the tumour microenvironment (TME) and inhibits the progression of OSCC. Targeting necroptosis could be an effective therapy for treating OSCC in a clinical setup.

Role of antidiarrheal agents nifuroxazide in antitumor multi‑target anticancer, multi‑mechanism anticancer drug (Review)

Nifuroxazide (NFZ) is an antimicrobial drug, which has been found to be a promising antitumor agent in recent years. In addition to being a classic STAT3 inhibitor, NFZ can also act on IL-6 and exert an anti-tumor role through inflammatory factor pathways. It can also bind to target proteins of aldehyde dehydrogenase 1, one of the families of E-twenty-six transcription factors and ubiquitin-specific protease 21 to play an anti-tumor role in different pathways. NFZ is able to act on the tumor cell microenvironment to inhibit tumor angiogenesis and tumor cell migration, enhance tumor immune cells, increase the cytotoxicity of tumor cells and enhance the anti-tumor effect of other drugs. Furthermore, it has high safety with few toxic side effects. The anti-tumor mechanisms of NFZ were described in the current review, aiming to provide insight and a reference for future studies promoting the implementation of NFZ as an anti-tumor drug in the clinic.

The immunomodulation of outer membrane vesicles from Vibrio parahaemolyticus causing acute hepatopancreatic necrosis disease in Pacific white shrimp Litopenaeus vannamei

Vibrio parahaemolyticus causing acute hepatopancreatic necrosis disease (VpAHPND) is a significant bacterial pathogen to Litopenaeus vannamei aquaculture with a substantial economic burden. Outer membrane vesicles (OMVs) released by Gram-negative pathogenic bacteria play complex roles in the modulation on host's immune response. To elucidate the potential roles of VpAHPND-OMVs on L. vannamei innate immune responses, this study investigated the immune responses and molecular mechanisms induced by VpAHPND-OMVs in hepatopancreas using transcriptomic and proteomic analysis. Shrimps were fed diets supplemented with 30 μg kg-1 (T1 group) or 60 μg kg-1VpAHPND-OMVs (T2 group), and the control group was fed a normal diet (CK group). Neither growth rate and hepatopancreas histological structure were affected by VpAHPND-OMVs. The most pronounced changes in the activities of immune-related enzymes, including lysozyme, superoxide dismutase, alkaline phosphatase and glutathione S-transferase, were observed at 7 and 14 days of the experiment, which suggested that VpAHPND-OMVs can rapidly and significantly enhance the activity of immune enzymes within a short period. The transcription levels of genes associated with immune and pathogen defense were significantly downregulated in the T1 and T2 groups including heat shock 70 kDa protein cognate 4-like (HSP70), beta-1,3-glucan-binding protein-like (GNBP1), C-type mannose receptor 2-like (MRC2), penaeidin-3a-like (PEN-3), and chitinase 10 (Cht10). Several key proteins were also significantly downregulated in the proteomics analysis, including alkaline phosphatase, integrin, cathepsin, C-type lectin 2, ras-related protein Rab-11A, and ferritin. Furthermore, the KEGG enrichment analysis revealed that the differentially expressed genes and differentially expressed proteins were associated with innate immune signaling pathways like apoptosis (ko04210), phagosome (ko04145) and lysosome (ko04142). All these results suggest that VpAHPND-OMVs may have a dual regulatory effect on shrimp, initially activating the immune system but potentially leading to an immunosuppressive with prolonged exposure. This study enhanced our understanding on shrimp immune regulation.

ATXN2L primarily interacts with NUFIP2, the absence of ATXN2L results in NUFIP2 depletion, and the ATXN2-polyQ expansion triggers NUFIP2 accumulation

The cytoplasmic Ataxin-2 (ATXN2) protein associates with TDP-43 in stress granules (SG) where RNA quality control occurs. Mutations in this pathway underlie Spinocerebellar Ataxia type 2 (SCA2) and Amyotrophic Lateral Sclerosis. In contrast, Ataxin-2-like (ATXN2L) is predominantly perinuclear, more abundant, and essential for embryonic life. Its sequestration into ATXN2 aggregates may contribute to disease. In this study, we utilized two approaches to clarify the roles of ATXN2L. First, we identified interactors through co-immunoprecipitation in both wild-type and ATXN2L-null murine embryonic fibroblasts. Second, we assessed the proteome profile effects using mass spectrometry in these cells. Additionally, we examined the accumulation of ATXN2L interactors in the SCA2 mouse model, Atxn2-CAG100-KnockIn (KIN). We observed that RNA-binding proteins, including PABPN1, NUFIP2, MCRIP2, RBMS1, LARP1, PTBP1, FMR1, RPS20, FUBP3, MBNL2, ZMAT3, SFPQ, CSDE1, HNRNPK, and HNRNPDL, exhibit a stronger association with ATXN2L compared to established interactors like ATXN2, PABPC1, LSM12, and G3BP2. Additionally, ATXN2L interacted with components of the actin complex, such as SYNE2, LMOD1, ACTA2, FYB, and GOLGA3. We noted that oxidative stress increased HNRNPK but decreased SYNE2 association, which likely reflects the relocalization of SG. Proteome profiling revealed that NUFIP2 and SYNE2 are depleted in ATXN2L-null fibroblasts. Furthermore, NUFIP2 homodimers and SYNE1 accumulate during the ATXN2 aggregation process in KIN 14-month-old spinal cord tissues. The functions of ATXN2L and its interactors are therefore critical in RNA granule trafficking and surveillance, particularly for the maintenance of differentiated neurons.

Matrix metalloproteinase 9 implication during colorectal carcinogenesis. Effect of doxycycline

BACKGROUND

Matrix metalloproteinases (MMPs), including MMP9, play a significant role in colorectal cancer (CRC) progression, mainly by extracellular matrix remodeling. However, little is known about MMP9 role in aberrant crypt foci (ACF) cluster formation, the earliest colon preneoplastic lesions.

AIMS AND METHODS

We conducted a bioinformatics analysis of MMPs expression in CRC using Gene Expression Profiling Interactive Analysis2 (GEPIA2). Subsequently, we investigated MMP9 expression during the early stage of colon carcinogenesis in mice and assessed the effect of doxycycline (DOX), a global inhibitor of MMPs, on ACF cluster formation. Thus, NMRI mice received two weekly injections of 1,2-Dimethylhydrazine (DMH, 20 mg/kg, subcutaneously), followed or not by DOX (100 mg/kg, orally, from the 4th to the 6th week).

RESULTS

GEPIA2 analysis indicated that among the 28 identified MMPs with collagenase and doxycycline-sensitive activities, MMPs 1, 3, 7, 9, and 13 were overexpressed in CRC tissues. Moreover, only MMP1 and MMP9 correlated well with collagen expression in colorectal tumors. In vivo, methylene blue-stained DMH-treated colons revealed multiple ACF clusters at week 6, associated with mucosa remodeling and sustained nitrosative stress as attested by enhanced collagen fibers, malondialdehyde level, and nitrotyrosine deposits. Pyrosequencing showed increased methylation at the tenth CpG site of the MMP9 promoter, which was associated with increased MMP9 expression. Interestingly, DOX attenuated the number and size of ACF clusters and mucosa remodeling without rebalancing nitrosative stress.

CONCLUSION

Overexpression of MMP9 occurs early during colorectal carcinogenesis, and doxycycline may control the pathological remodeling of colon mucosa into ACF clusters by attenuating MMP9 activity.

Mai-wei-yang-fei decoction protects against pulmonary fibrosis by reducing telomere shortening and inhibiting AECII senescence via FBW7/TPP1 regulation

BACKGROUND

Pulmonary fibrosis (PF) is a fatal disease associated with ageing. The senescence of alveolar epithelial type II cells (AECIIs) can drive PF. Therefore, reducing AECII senescence is a promising treatment to prevent PF. Mai-wei-yang-fei decoction (MWYF) has shown significant clinical efficacy in the treatment of patients with PF. However, its mechanism of action remains unclear.

PURPOSE

To investigate the role and underlying mechanism of MWYF in protecting against PF.

METHODS

The main chemical components of MWYF were identified using UPLC-MS. The mouse and in vitro cell models of PF were established using BLM. Micro-CT, H&E, and Masson staining were used to observe the protective effect of MWYF on mice with PF. Immunohistochemistry, β-galactosidase staining, and IF-FISH were used to observe the inhibitory effect of MWYF on senescence and telomere shortening in mouse lung tissue or A549 cells. The Transwell assay and cell co-culture method were used to observe the effect of MWYF on the migration and activation of lung fibroblasts by inhibiting AECII senescence. Finally, lentiviral vector was used to overexpress FBW7 gene in A549 cells in vitro to observe the mechanism pathway of MWYF inhibiting AECII senescence and telomere shortening.

RESULTS

MWYF was effective in protecting against bleomycin (BLM)-induced PF. Furthermore, MWYF alleviated cellular senescence by reducing the DNA damage response (DDR) and shortening of the telomere in AECⅡs in mouse lung tissues. Mechanistically, genes related to telomere disorders were detected in BLM-induced PF mouse models using q-PCR. MWYF mainly inhibited telomere shortening by regulating FBW7 and reducing the degradation of TPP1. In vitro, MWYF reduced BLM-induced senescence in A549 cells, as well as proliferation and migration of MRC5 cells, by inhibiting DDR and telomere shortening via regulation of the FBW7/TPP1 axis.

CONCLUSION

MWYF is a potential therapeutic agent against PF, as it inhibits telomere shortening and reduces AECII senescence by regulating FBW7/TPP1.

2-(Diarylalkyl)aminobenzothiazole derivatives induce autophagy and apoptotic death through SIRT inhibition and P53 activation In MCF7 breast cancer cells

Sirtuins (SIRTs) are multifunctional proteins that exhibit a wide range of substrate preferences and cellular localizations. They are reliant on NAD+ and are essential for the regulation of several cellular functions. The SIRT proteins play important role towards tumor survival and resistance mechanisms in tumor cells. Therefore, molecules targeting SIRT proteins gained significant recognition in cancer research. In this work, we explored the anticancer property, potential and mode of action of 2-(diarylalkyl)aminobenzothiazole derivatives on MCF7 human breast cancer cells. Our studies established that 2-(diarylalkyl)aminobenzothiazole derivatives 1-((6-chlorobenzo[d]thiazol-2-ylamino)(3,4-dichlorophenyl)methyl)naphthalen-2-ol (7ab) and 1-((6-chlorobenzo[d]thiazol-2-ylamino)(4-bromophenyl)methyl)naphthalen-2-ol (7ba) treatment in a dose dependent manner drastically lowered the cell proliferation in MCF7 cells and the IC50 values of 7ab and 7ba was found to be 11.4 µM and 9.6 µM at 24 hr in these cells. Docking and molecular dynamic simulation studies further revealed that 7ab and 7ba show significant binding with SIRT1 protein. Consistently, treatment with 7ab and 7ba reduced the expression levels of SIRT1 protein while increasing acetylation of p53, a known SIRT protein target in MCF-7 cells. We observed that SIRT1inhibition was associated with activation of p53, an essential protein for apoptotic cell death, in MCF-7 cell lines. Furthermore, 7ab and 7ba treatment induced LC3-II expression and vacuole formation in the cytoplasm leading to autophagic cell death. Our findings together reveal the plausible cellular targets and specificity of these new small molecules as SIRT inhibitors, which increase p53 acetylation and suppress the proliferation of MCF-7 human breast cancer cells by triggering autophagic and apoptotic cell death.

Autophagy and endoplasmic reticulum stress-related protein homeostasis links palmitic acid to hepatic lipotoxicity in zebrafish (Danio rerio), counteracted by linoleic acid

Saturated fatty acids (SFAs) are the primary contributors to hepatic lipotoxic injuries accompanied by the accumulation of hepatic insoluble protein inclusions that are composed of ubiquitinated proteins and p62, but the role of these inclusions in the SFA-induced hepatic lipotoxic injuries and their regulatory mechanisms are incompletely understood. In this study, we demonstrated that palmitic acid (PA), a dietary SFA, induced aberrant accumulation of hepatic insoluble protein inclusions, leading to hepatic lipotoxic injuries in zebrafish. Mechanistically, the accumulation of hepatic insoluble protein inclusions and the subsequent lipotoxic injuries induced by PA were attributed to reduced autophagy activity and increased endoplasmic reticulum (ER) stress. In addition, the upregulation of p62 by the ER stress response factor XBP1s and ATF4 further exacerbated PA-induced accumulation of hepatic insoluble protein inclusions and subsequent lipotoxic injuries. Importantly, the ω-6 PUFA linoleic acid (LA) attenuated PA-induced accumulation of hepatic insoluble protein inclusions and subsequent lipotoxic injuries by improving defective autophagy and reducing ER stress induced by PA. Overall, the present study provides new mechanisms by which SFAs and ω-6 PUFA influence hepatic lipotoxic injuries. These findings not only advance the understanding of hepatic lipotoxic injuries induced by SFAs, but also provide new insights for optimizing the rational substitution of fish oil by vegetable oils in aquaculture and the balance of fatty acid intake in human diets.

Toxic effects and transcriptome analysis of the early life stages of Larimichthys crocea exposed to the bloom-forming dinoflagellate Alexandrium tamarense

This study investigated the effects of the bloom-forming dinoflagellate Alexandrium tamarense and its potentially associated paralytic shellfish toxins on the early life stages of Larimichthys crocea (large yellow croaker) by integrating physiological effects with transcriptomic analysis to explore the molecular mechanisms underlying these harmful impacts. The results showed that 48-h acute exposure to A. tamarense culture and cell-free filtrate significantly reduced the heart rate in embryos and increased mortality rates in both embryos and larvae. Transcriptome sequencing of the filtrate-exposed group identified 130 differentially expressed genes in the embryo group and 884 in the juvenile group. Further analysis revealed that algal exposure triggered the activation of innate immunity in embryos, as evidenced by the significant upregulation of immune-related cytokines such as CCL20, IL11, and ILRA10. These genes were enriched in the cytokine-cytokine receptor interaction pathway and may induce immune responses through their respective downstream pathways. Additionally, the downregulation of the RNA polymerase and ribosome pathways suggests that protein synthesis was affected during the embryo stress response induced by A. tamarense. In juveniles, genes related to cardiac function, particularly those associated with myocardial contraction and calcium ion regulation, were downregulated after exposure to algal filtrate, further suggesting that A. tamarense, possibly through paralytic shellfish toxins, inhibits the heart function of L. crocea. The findings of this study elucidate the toxicological mechanisms of A. tamarense on the early life stages of L. crocea, providing scientific evidence for the impact of harmful algal blooms on marine life health and offering valuable insights for management strategies in aquaculture.

CmCYC2d is a Regulator of Leaf Abaxial Curling in Chrysanthemum morifolium

Leaf morphology is crucial for plant photosynthesis and stress adaptation. While CIN-like TCP transcription factors are well-known for their roles in leaf curling and morphogenesis, the function of CYC-like TCPs in leaf development remains largely unexplored. This study identifies CmCYC2d as a key regulator of abaxial leaf curling in Chrysanthemum morifolium. Phenotypic analysis revealed that the downward curling observed in OX-CmCYC2d transgenic lines was primarily due to the enlargement of adaxial epidermal cells. Furthermore, a reduction in epidermal cell number was identified as a significant contributor to the smaller leaf area in these plants. Transcriptome and WGCNA analyses highlighted CmSAUR55 as a potential downstream target of CmCYC2d. ChIP-qPCR, EMSA, and LUC assays confirmed that CmCYC2d directly bound to the CmSAUR55 promoter. Additionally, transcriptome data revealed that the reduced cell number in OX-CmCYC2d transgenic lines may be mediated by auxin-related pathways and key genes such as CNR7. The CmCYC2d-CmSAUR55 module was also closely linked to the development of enlarged adaxial epidermal cells in the leaf sinus, emphasising its role in this developmental process. This study highlights the regulatory role of CmCYC2d in leaf development and sheds light on the molecular mechanisms underlying leaf curling in chrysanthemum.

Cognitive frailty: A comprehensive clinical paradigm beyond cognitive decline

Cognitive frailty is an emerging concept in research and clinical practice that incorporates both physical frailty and mild cognitive impairment (MCI) or subjective cognitive decline (SCD). Unlike traditional approaches that separate physical frailty and dementia, cognitive frailty treats these domains as interrelated and coexisting, with significant implications for clinical outcomes and predicting cognitive decline. Despite growing recognition of this interrelationship, a dualistic view of physical and cognitive processes persists. The paradigm of cognitive frailty holds promise as a biomarker- like amyloid plaques or neurofibrillary tangles- but with the advantage of identifying risk at a prefrail stage, before clinical signs of MCI or dementia emerge. This review examines the pathophysiological and clinical dimensions of cognitive frailty and promotes for its integration into routine assessments in memory clinics.

Phenolic extract from olive mill wastewater sustains mitochondrial bioenergetics upon oxidative insult

In the last few years, many efforts have been devoted to the recovery and valorization of olive oil by-products because of their potentially high biological value. The olive mill wastewater (OMWW), a dark-green brown colored liquid that mainly consists of olive fruit vegetation water, is particularly exploited in this regard for its great content in phenolic compounds with strong antioxidant properties. In our previous work, we produced different OMWW fractions enriched in hydroxytyrosol- and hydroxytyrosol/oleuropein (i.e. C and OPE extracts, respectively) that exhibited considerable anti-microbial and radical-scavenging activities in vitro. Based on these findings, the present study aimed to assess the impact of C and OPE samples on mitochondrial function and oxidative stress response in mouse fibroblast-like cells (NCTC). Accordingly, OMWW phenolic extracts proved to enhance mitochondrial biogenesis and to reduce cellular sensitivity to hydrogen peroxide. Moreover, high-resolution respirometry experiments first time revealed the efficiency of OMWW phenols recovered by selective resin extraction in preventing mitochondrial respiration failure upon oxidative insult. Collected data definitely demonstrate the bioactivity of our phenolic-rich fractions, supporting the advantages of reusing the olive mill wastewater to generate, at low-cost, high added value molecules that could be useful for the improvement of health and nutrition products.

Non-coding RNA-mediated granulosa cell dysfunction during ovarian aging: From mechanisms to potential interventions

As the earliest aging organ in the reproductive system, the ovary has both reproductive and endocrine functions, which are closely related to overall female health. The exact pathogenesis of ovarian aging (OA) remains incompletely understood, with granulosa cells (GCs) dysfunction playing a significant role in this process. Recent advancements in research and biotechnology have highlighted the importance of non-coding RNAs (ncRNAs), including micro RNAs, long non-coding RNAs, and circular RNAs, in regulating the biological functions of GCs through gene expression modulation. This paper provides a comprehensive overview of the role of ncRNAs in various cellular functions such as apoptosis, autophagy, proliferation, and steroid synthesis in GCs, and explores the underlying regulatory mechanisms. Additionally, the therapeutic potential of ncRNAs, particularly those carried by exosomes derived from mesenchymal stem cells, in delaying OA is discussed. Understanding the regulatory mechanisms of ncRNAs in GC function and the current progress in this field is crucial for identifying effective biomarkers and therapeutic targets, ultimately aiding in the early diagnosis, prognostic assessment, and individualized treatment of OA.

Plourde M, Joly DL, Germain H. Comprehensive mapping of Arabidopsis alternative splicing landscape reveals key insights into plant development and immunity

The different steps of alternative splicing (AS) in plants and its regulatory mechanisms have already been studied extensively. Its broader impact on cell identity, plant immunity-related genes, and their study as a whole remains to be investigated. Using transgenic plants, we sorted 11 different Arabidopsis thaliana cell types ranging from root to aerial organs using fluorescence-activated cell sorting. RNA-seq data were analyzed with vast-tools and enabled us to generate a high-resolution AS landscape across multiple cell types, all collected through the same experimental procedure. The analysis of cell type-specific gene expression and alternative splicing events highlights the importance of AS on transcription and AS regulation itself. AS is also shown to be tightly linked to cell identity. By using closely related cell types, we captured alternative splicing events involved in specific stages of plant development. The columella cells, among others, show intensified AS regulation and an interesting splicing profile, especially regarding immunity-related genes. Overall, our analysis brings a valuable tool in the study of cell type identity, plant immunity, and AS.

The INO80 Chromatin Remodeling Complex Regulates Histone H2A.Z Mobility and the G1-S Transition in Oligodendrocyte Precursors

Chromatin remodeling complexes (CRCs) participate in oligodendrocyte (OL) differentiation, survival, and maintenance. We asked whether CRCs also control the proliferation of OL precursors (OPs)-focusing on the INO80 complex, which is known to regulate the proliferation of a variety of other cell types during development and disease. CRISPR/Cas9-mediated inactivation of Ino80 in vitro, or Cre-mediated deletion in vivo, slowed the OP cell cycle substantially by prolonging G1. RNAseq analysis revealed that E2F target genes were dysregulated in OPs from INO80-deficient mice, but correlated RNAseq and ATAC-seq uncovered no general correlation between gene expression and altered nucleosome positioning at transcription start sites. Fluorescence photobleaching experiments in cultured OPs demonstrated that histone H2A.Z mobility increased following the loss of INO80, suggesting that INO80 regulates the cell cycle machinery in OPs through H2A.Z/H2A exchange. We also present evidence that INO80 associates with OLIG2, a master regulator of OL development.

A potential therapeutic molecule target: lncRNA AK023507 inhibits the metastasis of breast cancer by regulating the WNT/DOCK4/β-catenin axis

PURPOSE

Breast cancer (BC) has become the most common malignant tumor in women worldwide. This study was carried out to find and validate a novel molecular therapeutic target for BC.

METHODS

Long non-coding RNA (lncRNA) AK023507 was selected as the study objects through microarray analysis. The function of lncRNA AK023507 was verified by various cell function experiments in vitro, subcutaneous tumorigenesis experiments, and lung metastasis model experiments in vivo. The RNA pull-down experiment and Western blot experiment were used to confirm the mechanism regulation pathway and the recovery experiment was used to verify it. TCGA datasets were used for clinical and immune function prediction analysis.

RESULTS

In vitro cell function tests and in vivo experiments suggested that overexpression of lncRNA AK023507 inhibited the proliferation and metastasis of BC cells. The RNA pull-down experiment and Western blot analysis validated that lncRNA AK023507 interacted with the dedicator of cytokinesis 4 (DOCK4) protein. Analysis of public databases predicted that DOCK4 is a potential prognostic risk factor associated with epithelial-mesenchymal transition (EMT) and central memory T cell (TCM) cellular immune infiltration.

CONCLUSIONS

LncRNA AK023507 inhibits the proliferation and metastasis of BC by regulating the DOCK4/β-catenin axis. This discovery will provide new potential therapeutic targets for BC.

Fabrication of GDNF-Gel/HA-Mg nerve conduit and its role in repairing peripheral nerve defects

Background

Magnesium (Mg) and its alloys are receiving increasing attention in peripheral nerve regeneration, but they were limited due to the low corrosion resistance and rapid degradation. In this study, GDNF-Gel/HA-Mg was prepared and its value in peripheral nerve defects repairment was explored both in vitro and in vivo.

Methods

A hydroxyapatite (HA) coating was first applied to the pure Mg surface, followed by the formation of gelatin methacrylate (GelMA) loaded with glial cell-derived neurotrophic factor (GDNF) on the HA-coated Mg surface. GDNF-Gel/HA-Mg corrosion resistance was explored. The effect of GDNF-Gel/HA-Mg conduit on Schwann cell proliferation and migration abilities were investigated. And sciatic nerve defects models were established to explored the role of GDNF-Gel/HA-Mg conduit in peripheral nerve defects repairment.

Findings

The electrochemical, immersion, and hydrogen evolution experiments indicated that the corrosion resistance in phosphate buffer saline (PBS) of pure Mg was significantly improved by the GDNF-Gel/HA coating. Cell cycle, Cell Count Kit-8 (CCK-8), and clone formation assays indicated that GDNF-Gel/HA-Mg promoted the proliferation of Schwann cells. Scratch and Transwell assay results demonstrated that GDNF-Gel/HA-Mg promoted Schwann cell migration ability dose-dependently. GDNF-Gel/HA-Mg was found to enhance the secretion of nerve growth factor (NGF) and the expression of p75NTR. Flow cytometry results showed that GDNF-Gel/HA-Mg could reduce H2O2-induced oxidative stress and Schwann cell apoptosis. GDNF-Gel/HA-Mg inhibited M1 macrophage polarization while facilitated M2 macrophage polarization in a concentration-dependent manner. The in vivo studies demonstrated that GDNF-Gel/HA-Mg conduit could significantly promote the regeneration and myelination of sciatic nerve, as well as the recovery of denervated gastrocnemius atrophy.

Interpretation

The GDNF-Gel/HA-Mg conduit prepared in this study exhibited good hydrophilicity and corrosion resistance and greatly enhanced the proliferation, migration, and invasion abilities of Schwann cells, as well as peripheral nerve regeneration.

The role of recurrent somatic mutations that alter conserved m6A motifs in human cancer

N6-methyladenosine (m6A) is the most abundant internal RNA modification in eukaryotes and plays a key role in cellular growth and development. Global changes in cellular methylated RNA and m6A-mediated transcript regulation significantly impact oncogenesis. Here, we investigate how recurrent synonymous and non-synonymous somatic mutations abolishing individual canonical methylated m6A motifs affect transcript levels and survival of patients with cancer. Moreover, we explore the effect of these mutations on creating de novo m6A motifs. To this end, we compared publicly available data on m6A sites with mutations reported in The Cancer Genome Atlas (TCGA). We find that mutations disrupting or creating m6A motifs display a low recurrence and have a negligible impact on RNA abundance. Patients with the highest number of disrupted m6A sites or newly generated m6A motifs did not generally exhibit alterations in mortality risk or outcomes. Hence, our data suggest that mutational alterations in the m6A motif landscape are unlikely to be a primary mechanism for regulating gene function across most cancer types. This may be attributed to the fact that mutations typically affect individual m6A sites, which is likely insufficient to significantly impact gene expression.

Activation, interaction and intimation of Nrf2 pathway and their mutational studies causing Nrf2 associated cancer

Responses against infection trigger several signaling pathways that lead to the production of cytokines, these cytokines release ROS and RNS, damaging DNA and proteins turn into various diseases including cancer. To combat these harmful cytokines, the Nrf2 pathway is activated. The gene NFE2L2 encodes Nrf2, which is divided into seven conserved domains (Neh1-7). The DLG and ETGE motifs, conserved sequences of amino acid in the Neh2 domain of Nrf2, bind to the BTB domain of Keap1. BTB domain promotes Keap1's homodimerization resulting in Cul3 recruitment providing scaffold formation to E2 ubiquitin ligase to form ubiquitin complex. Under normal conditions, this complex regularly degrades Nrf2. However, once the cell is exposed to oxidative stress by ROS interaction with Keap1 resulting in conformational changes that stabilize the Nrf2. Nrf2 further concentrates on the nucleus where it binds with the transcriptional factor to perform the desired genes transcription for synthesizing SOD, GSH, CAT, and various other proteins which reduce the ROS levels preventing certain diseases. To prevent cells from oxidative stress, molecular hydrogen activates the Nrf2 pathway. To activate the Nrf2 pathway, molecular hydrogen oxidizes the iron porphyrin which acts as an electrophile and interacts with Keap1's cysteine residue.

A gene regulatory network for specification and morphogenesis of a Mauthner Cell homolog in non-vertebrate chordates

Transcriptional regulation of gene expression is an indispensable process in multicellular development, yet we still do not fully understand how the complex networks of transcription factors operating in neuronal precursors coordinately control the expression of effector genes that shape morphogenesis and terminal differentiation. Here we break down in greater detail a provisional regulatory circuit downstream of the transcription factor Pax3/7 operating in the descending decussating neurons (ddNs) of the tunicate Ciona robusta. The ddNs are a pair of hindbrain neurons proposed to be homologous to the Mauthner cells of anamniotes, and Pax3/7 is sufficient and necessary for their specification. We show that different transcription factors downstream of Pax3/7, namely Pou4, Lhx1/5, and Dmbx, regulate distinct "branches" of this ddN network that appear to be dedicated to different developmental tasks. Some of these network branches are shared with other neurons throughout the larva, reinforcing the idea that modularity is likely a key feature of such networks. We discuss these ideas and their evolutionary implications here, including the observation that homologs of all four transcription factors (Pax3/7, Lhx5, Pou4f3, and Dmbx1) are key for the specification of cranial neural crest in vertebrates.

Integrating cuproptosis and immunosenescence: A novel therapeutic strategy in cancer treatment

Recent advancements in our understanding of cell death mechanisms have progressed beyond traditional apoptosis to encompass various forms of regulated cell death, notably cuproptosis. This copper-dependent cell death occurs when copper interacts with lipoylated enzymes in the tricarboxylic acid cycle, leading to protein aggregation and subsequent cell death. Alongside this, immunosenescence the gradual decline in immune function due to aging has emerged as a significant factor in cancer progression and response to treatment. Innovative strategies that integrate cuproptosis and immunosenescence are showing considerable promise in cancer therapy. By leveraging the altered copper metabolism in cancer cells, cuproptosis can selectively induce cell death, effectively targeting and eliminating tumors. Simultaneously, addressing immunosenescence can rejuvenate the aging immune system, enhancing its capacity to identify and destroy cancer cells. This dual approach creates a synergistic effect, optimizing therapeutic efficacy by directly attacking tumor cells while revitalizing the immune response. Such integration bolsters the defense against cancer progression and recurrence and holds great potential for advancing cancer treatment modalities and improving patient outcomes. This paper delves into the interactions between cuproptosis and immunosenescence, emphasizing their implications for developing innovative cancer therapies.

Protein Ubiquitination Modification in Pulmonary Fibrosis

Pulmonary fibrosis (PF) is a chronic, progressive fibrotic interstitial lung disease characterized by a high incidence and mortality rate, which encompasses features, such as diffuse alveolar inflammation, invasive fibroblast activation, and uncontrolled extracellular matrix (ECM) deposition. Beyond the local pathological processes, PF can be better understood in light of interorgan communication networks that are involved in its progression. Notably, pulmonary inflammation can affect cardiovascular, renal, hepatic, and neural functions, highlighting the importance of understanding these systemic interactions. Posttranslational modifications play a crucial role in regulating protein function, localization, stability, and activity. Specifically, protein ubiquitination modifications are involved in PF induced by various stimuli, involving a range of ubiquitin-modifying enzymes and substrates. In this review, we provide an overview of how E3 ubiquitin ligases and deubiquitinating enzymes (DUBs) modulate PF through several signaling pathways, such as TGF-β, Wnt, metabolic activity, aging, ferroptosis, endoplasmic reticulum stress, and inflammatory responses. This perspective includes the role of ubiquitin-proteasome systems in interorgan communication, affecting the progression of PF and related systemic conditions. Additionally, we also summarize the currently available therapeutic compounds targeting protein ubiquitination-related enzymes or ubiquitination substrates for the treatment of PF. Understanding the interplay between ubiquitination and interorgan communication may pave the way for novel therapeutic strategies.

Dorsomorphin (DM) inhibits the ovarian development of Portunus trituberculatus by acting on the BMP signaling pathway

Bone morphogenic proteins (BMPs) regulate animal growth, cell proliferation and differentiation. The BMP signaling pathway plays an important regulatory role during ovarian follicle development in mammals. However, related studies in crustaceans are limited. The focus of this study was the key gene of the BMP signaling pathway, the BMP type I receptor. Portunus trituberculatus was injected with different concentrations of dorsomorphin (DM) and observed for one month to identify the optimal effective concentration for interference with the BMP signaling pathway. Subsequent transcriptomics, proteomics, and metabolomics measurements were performed to identify the effects of BMP signaling on ovarian development in P. trituberculatus. A preliminary mechanism of action of the BMP signaling pathway in the regulation of ovarian development was revealed through combined multiomics analysis and lipid analysis. This study provides a theoretical basis for further exploration of the molecular mechanism regulating gonadal development in crustaceans.

Nicotine-driven enhancement of tumor malignancy in triple-negative breast cancer via additive regulation of CHRNA9 and IGF1R

Cigarette smoking is a significant risk factor for cancer development with complex mechanisms. This study aims to investigate the impact of nicotine exposure on the regulation of stemness- and metastasis-related properties via cholinergic receptor nicotinic alpha 9 subunit (CHRNA9) and insulin-like growth factor-1 receptor (IGF1R) and to evaluate their therapeutic potential in triple-negative breast cancer (TNBC). We performed Kaplan-Meier survival analysis of public databases and revealed that high expression of CHRNA9, IGF1R signaling molecules, and stemness genes was significantly associated with poor recurrence-free survival (RFS) and distant metastasis-free survival (DMFS) in TNBC samples. Additionally, we examined two patient cohorts to determine the clinical associations between the expression levels of different genes (n = 67) and proteins (n = 42) and showed a strong positive correlation between the expression levels of CHRNA9, IGF1R signaling molecules, and stemness markers POU5F1/NANOG in tumor tissues. We carried out nicotine treatment and knockdown of CHRNA9 and IGF1R in TNBC cells to identify the effects on stemness-related properties in vitro. Furthermore, primary and secondary metastatic in vivo animal models were examined using micro-computed tomography (μCT) screening and in situ hybridization with a human Alu probe to detect tumor cells. Nicotine was found to upregulate the expression of CHRNA9, POU5F1, and IGF1R, influencing stemness- and metastasis-related properties. Knockdown of CHRNA9 expression attenuated nicotine-induced stemness-related properties in a TNBC cell model. Furthermore, knockdown of IGF1R expression significantly alleviated nicotine/CHRNA9-induced stemness features and cancer cell metastasis in cell cultures and lung metastatic mouse models. These results demonstrate that nicotine triggers IGF1R signaling, thereby enhancing stemness-related properties, cell migration, invasion, and tumor metastasis, resulting in a poorer prognosis for patients with TNBC. These findings highlight IGF1R as a promising therapeutic target for reducing stemness and metastasis in TNBC patients exposed to environmental nicotine. © 2025 The Pathological Society of Great Britain and Ireland.

Sustained tenascin-C expression drives neointimal hyperplasia and promotes aortocaval fistula failure

End-stage kidney disease (ESKD) impacts over 740,000 individuals in the United States, with many patients relying on arteriovenous fistulae (AVF) for hemodialysis due to superior patency and reduced infections. However, AVF patency is reduced by thrombosis and neointimal hyperplasia, yielding a 1-yr patency of only 40%-50%. We hypothesized that tenascin-C (TNC), a regulator of inflammation and immune responses after injury, also regulates venous remodeling during AVF maturation. AVF were created in wild-type (WT) and Tnc knockout (Tnc-/-) mice, and proteomic analyses were conducted to identify protein changes between sham and AVF WT tissue. Immunofluorescence and Western blot assays compared venous tissue from WT and Tnc-/- mice. In vitro studies using human umbilical vein endothelial cells and human umbilical vein smooth muscle cells examined TNC-siRNA effects on thrombomodulin (THBD) and NF-κB. Macrophages from WT and Tnc-/- mice were assessed for anti-inflammatory phenotype polarization and tissue factor expression. TNC expression was spatially and temporally regulated in WT mice with AVF, and TNC colocalized with matrix remodeling but not with THBD expression; TNC expression was downregulated in patent AVF but sustained in occluded AVF, both in WT mice and human AVF specimens. Tnc-/- mice had reduced AVF patency, less wall thickening, and increased thrombosis, with increased THBD expression. In vitro, TNC-siRNA increased THBD and reduced NF-κB activation. Macrophages from Tnc-/- mice showed increased anti-inflammatory macrophage polarization and tissue factor expression, facilitating thrombosis. Sustained TNC expression drives neointimal hyperplasia and AVF failure by promoting a prothrombotic, inflammatory microenvironment. Targeting TNC pathways may enhance AVF patency and improve dialysis outcomes.NEW & NOTEWORTHY This study identifies Tenascin-C (TNC) as a key regulator of arteriovenous fistula (AVF) patency. TNC is spatially and temporally regulated, driving neointimal hyperplasia and thrombosis by promoting a prothrombotic, inflammatory microenvironment. In Tnc-/- mice, reduced TNC expression increased thrombomodulin and anti-inflammatory macrophage polarization but impaired wall thickening and AVF patency. These findings link sustained TNC expression to AVF failure and suggest that targeting TNC pathways could enhance AVF outcomes in patients requiring hemodialysis.

The critical role of the Hippo signaling pathway in renal fibrosis

Renal fibrosis is a fundamental pathological change in the progression of various chronic kidney diseases to the end stage of renal disease. The Hippo signaling pathway is an evolutionary highly conserved signaling pathway that is involved in the regulation of organ size, tissue regeneration, and human reproduction and development. Currently, many studies have shown that it is closely associated with renal diseases, such as, renal fibrosis, diabetic nephropathy, and renal cancer. Here, we review the current researches on the effect of Hippo signaling pathway on renal fibrosis, which provides new ideas and theoretical basis for clinical therapeutics of renal fibrosis.

Regulatory differences between atypical and typical MAP kinases in Dictyostelium discoideum

Within the large family of mitogen activated protein kinases (MAPKs), one outlier group referred to as atypical MAPKs is not regulated by conventional upstream MAPK kinases (MAP2Ks). This includes the Dictyostelium discoideum atypical MAPK Erk2, a protein kinase essential for chemotactic movement and development. The regulation and functional specificity of Erk2 was investigated through phenotypic analysis of chimeric and mutant MAPKs. Chimeric MAPKs containing regions of Erk2 were created using complementary regions of the more typical MAPK Erk1, that provides very different functions in this amoeba. The chimeric MAPKs were not phosphorylated at levels observed for wild-type MAPKs and none rescued wild-type MAPK function to erk1- or erk2- cells. Endogenous Erk1 and Erk2 MAPKs were destabilized in cells expressing chimeric MAPKs containing the same carboxyl terminus. A carboxyl terminal motif conserved among atypical MAPKs was important but not essential for Erk2 regulation and function and the motif did not confer atypical MAPK regulation when present in Erk1. A kinase-dead version of Erk2 was phosphorylated in response to folate or cAMP chemotactic stimulation, suggesting Erk2 is activated in vivo by an upstream protein kinase, contrary to previous predictions of autophosphorylation. This regulation implies a protein kinase distinct from the single conventional MAP2K in Dictyostelium regulates atypical MAPK signaling. A non-activatable form of Erk2 was not capable of rescuing Erk2 function in erk2- cells. These findings suggest that the regulation of atypical and typical MAPKs is substantially different and carried out by distinct upstream protein kinases.

Application of array tomography to elucidate nuclear clustering architecture in giant-feeding cells induced by root-knot nematodes

Plant-parasitic nematodes like root-knot nematodes (RKN; Meloidogyne spp.) cause great losses in agriculture by inducing root swellings, named galls, in host roots disturbing plant growth and development. Previous two-dimensional studies using different microscopy techniques revealed the presence of numerous nuclear clusters in nematode-induced giant cells within galls. Here, we show in three dimensions (3D) that nuclear clustering occurring in giant cells is revealed to be much more complex, illustrating subclusters built of multiple nuclear lobes. These nuclear subclusters are unveiled to be interconnected and likely communicate via nucleotubes, highlighting the potential relevance of this nuclear transfer for disease. In addition, microtubules and microtubule organizing centers are profusely present between the densely packed nuclear lobes, suggesting that the cytoskeleton might be involved in anchoring nuclear clusters in giant cells. This study illustrates that it is possible to apply volume electron microscopy (EM) approaches such as array tomography (AT) to roots infected by nematodes using basic equipment found in most EM facilities. The application of AT was valuable to observe the cellular ultrastructure in 3D, revealing the remarkable nuclear architecture of giant cells in the model host Arabidopsis thaliana. The discovery of nucleotubes, as a unique component of nuclear clusters present in giant cells, can be potentially exploited as a novel strategy to develop alternative approaches for RKN control in crop species.

Interoception and aging

Interoception refers to the body's perception and regulation of internal physiological states and involves complex neural mechanisms and sensory systems. The current definition of interoception falls short of capturing the breadth of related research; here, we propose an updated definition. Homeostasis, a foundational principle of integrated physiology, is the process by which organisms dynamically maintain optimal balance across all conditions through neural, endocrine, and behavioral functions. This review examines the role of interoception in body homeostasis. Aging is a complex process influenced by multiple factors and involving multiple levels, including physical, psychological, and cognitive. However, interoceptive and aging interoceptive interactions are lacking. A new perspective on interoception and aging holds significant implications for understanding how aging regulates interoception and how interoception affects the aging process. Finally, we summarize that arachidonic acid metabolites show promise as biomarkers of interoception-aging. The aim of this study is to comprehensively analyze interoceptive-aging interactions, understand the aging mechanism from a novel perspective, and provide a theoretical basis for exploring anti-aging strategies.

Efficient identification of de novo mutations in family trios: a consensus-based informatic approach

Accurate identification of de novo variants (DNVs) remains challenging despite advances in sequencing technologies, often requiring ad hoc filters and manual inspection. Here, we explored a purely informatic, consensus-based approach for identifying DNVs in proband-parent trios using short-read genome sequencing data. We evaluated variant calls generated by three sequence analysis pipelines-GATK HaplotypeCaller, DeepTrio, and Velsera GRAF-and examined the assumption that a requirement of consensus can serve as an effective filter for high-quality DNVs. Comparison with a highly accurate DNV set, validated previously by manual inspection and Sanger sequencing, demonstrated that consensus filtering, followed by a force-calling procedure, effectively removed false-positive calls, achieving 98.0-99.4% precision. At the same time, sensitivity of the workflow based on the previously established DNVs reached 99.4%. Validation in the HG002-3-4 Genome-in-a-Bottle trio confirmed its robustness, with precision reaching 99.2% and sensitivity up to 96.6%. We believe that this consensus approach can be widely implemented as an automated bioinformatics workflow suitable for large-scale analyses without the need for manual intervention, especially when very high precision is valued over sensitivity.

Molecular and cellular mechanisms underlying peripheral nerve injury-induced cellular ecological shifts: Implications for neuroregeneration

The peripheral nervous system is a complex ecological network, and its injury triggers a series of fine-grained intercellular regulations that play a crucial role in the repair process. The peripheral nervous system is a sophisticated ecological network, and its injury initiates a cascade of intricate intercellular regulatory processes that are instrumental in the repair process. Despite the advent of sophisticated microsurgical techniques, the repair of peripheral nerve injuries frequently proves inadequate, resulting in adverse effects on patients' quality of life. Accordingly, the continued pursuit of more efficacious treatments is of paramount importance. In this paper, a review of the relevant literature from recent years was conducted to identify the key cell types involved after peripheral nerve injury. These included Schwann cells, macrophages, neutrophils, endothelial cells, and fibroblasts. The review was conducted in depth. This paper analyses the phenotypic changes of these cells after injury, the relevant factors affecting these changes, and how they coordinate with neurons and other cell types. In addition, it explores the potential mechanisms that mediate the behaviour of these cells. Understanding the interactions between these cells and their mutual regulation with neurons is of great significance for the discovery of new neuroregenerative treatments and the identification of potential therapeutic targets.

A novel human organoid model system reveals requirement of TCF4 for oligodendroglial differentiation

Heterozygous mutations of TCF4 in humans cause Pitt-Hopkins syndrome, a neurodevelopmental disease associated with intellectual disability and brain malformations. Although most studies focus on the role of TCF4 in neural stem cells and neurons, we here set out to assess the implication of TCF4 for oligodendroglial differentiation. We discovered that both monoallelic and biallelic mutations in TCF4 result in a diminished capacity to differentiate human neural progenitor cells toward myelinating oligodendrocytes through the forced expression of the transcription factors SOX10, OLIG2, and NKX6.2. Using this experimental strategy, we established a novel organoid model, which generates oligodendroglial cells within a human neurogenic tissue-like context. Also, here we found a reduced ability of TCF4 heterozygous cells to differentiate toward oligodendroglial cells. In sum, we establish a role of human TCF4 in oligodendrocyte differentiation and provide a model system, which allows to dissect the disease etiology in a human tissue-like context.