Single-cell RNA sequencing reveals tissue-specific transcriptomic changes induced by perfluorooctanesulfonic acid (PFOS) in larval zebrafish (Danio rerio)

Perfluorooctanesulfonic acid (PFOS) elicits adverse effects on numerous organs and developmental processes but the mechanisms underlying these effects are not well understood. Here, we use single-cell RNA-sequencing to assess tissue-specific transcriptomic changes in zebrafish (Danio rerio) larvae exposed to 16 µM PFOS or dimethylsulfoxide (0.01 %) from 3-72 h post fertilization (hpf). Data analysis was multi-pronged and included pseudo-bulk, untargeted clustering, informed pathway queries, and a cluster curated for hepatocyte biomarkers (fabp10a, and apoa2). Overall, 8.63 % (2390/27698) genes were significantly differentially expressed. Results from untargeted analysis revealed 22 distinct clusters that were manually annotated to specific tissues using a weight-of-evidence approach. The clusters with the highest number of significant differentially expressed genes (DEGs) were digestive organs, muscle, and otolith. Additionally, we assessed the distribution of pathway-specific genes known to be involved in PFOS toxicity: the PPAR pathway, β-oxidation of fatty acids, the Nfe2l2 pathway, and epigenetic modifications by DNA methylation, across clusters and identified the blood-related tissue to be the most sensitive. The curated hepatocyte cluster showed 220 significant DEGs and was enriched for the Notch signaling pathway. These findings provide insights into both established and novel sensitive target tissues and molecular mechanisms of developmental toxicity of PFOS.

Recent advances in medicinal chemistry strategies for the development of METTL3 inhibitors

N6-methyladenosine (m6A), the most abundant RNA modification in eukaryotic cells, exerts a critical influence on RNA function and gene expression. It has attracted considerable attention within the rapidly evolving field of epitranscriptomics. METTL3 is a key enzyme for m6A modification and is essential for maintaining normal m6A levels. High expression of METTL3 is closely associated with various cancers, including gastric cancer, liver cancer, and leukemia. Inhibiting METTL3 has shown potential in slowing cancer progression, thereby driving the development of METTL3 inhibitors. In this work, we summarize recent advancements in the development of METTL3 inhibitor, with a focus on medicinal chemistry strategies employed during discovery and optimization phases. We explore the application of structure-activity relationship (SAR) studies and protein-targeted degradation techniques, while addressing key challenges associated with their characterization and clinical translation. This review underscores the therapeutic potential of METTL3 inhibitors in modulating epitranscriptomic pathways and aims to offer perspectives for future research in this rapidly evolving field.

Small molecule compounds targeting G9a/GLP: Recent advances and perspectives

As an important member of the histone methyltransferase family, G9a/GLP has been shown to be closely related to the occurrence and development of various diseases, such as tumors, fibrosis, and malaria. Selective small molecule inhibitors of G9a/GLP were first reported in 2007, and over the decade since then, more than 40 different types of G9a modulators have been developed. Classification by binding site includes s-adenosylmethionine (SAM)-competitive inhibitors and substrate-competitive inhibitors. According to the mechanism of action, these compounds can be divided into reversible inhibitors, irreversible inhibitors, dual inhibitors, degraders, etc. In this paper, we systematically reviewed the discovery methods, design strategies, structural optimization processes, binding modes, biological activity data, and pharmacokinetic properties of small molecules targeting G9a/GLP. This paper analyzed the challenges and opportunities in the development of small molecule compounds targeting G9a/GLP, aiming to offer valuable insights and perspectives for pharmaceutical researchers.

Discovery of potent and selective CDK2 inhibitors with high safety and favorable bioavailability for the treatment of cancer

Targeting cyclin-dependent kinases (CDKs) to inhibit the cell proliferation is considered as a promising strategy for the treatment of cancer, and the success of selective CDK4/6 inhibitors proves this concept. CDK2 plays an important role in the cell cycle and proliferation for the CCNE1-amplifed cancers and CDK4/6 inhibitors resistant breast cancers. Therefore, selective inhibition of CDK2 become research hotspots. In our work, we achieved a potent and selective CDK2 inhibitor 46 through virtual screening and systematic structural modification. Compound 46 could arrest cell cycle, promote apoptosis, and induce senescence-related phenotypes for CCNE1-amplifed ovarian cancer OVCAR3 cell line, and also displayed potent antitumor activity against OVCAR3 xenografts. Furthermore, 46 hold promise in overcoming resistance to CDK4/6 inhibitor. More significantly, 46 exhibited great safety properties and favorable pharmacokinetic profiles in vivo. All these results demonstrated that 46 was a potential candidate of novel anticancer drugs.

OsCHR728 encodes a chromatin remodeling factor involved in seed size and grain chalkiness in rice

The Imitation Switch (ISWI)ATP-dependent chromatin remodeling factor proteins regulate various developmental processes, spanning from flowering to stress response. However, researches on the roles of ISWI subfamily genes in rice have been limited. This study investigated the expression profile of the rice chromatin remodeler OsCHR728, encoding an ISWI protein, across various tissues and developing stages. Our findings reveal that OsCHR728 is highly accumulated during early stage of the panicle development. We generated OsCHR728 knockout (KO) lines in rice using CRISPR/Cas9 technology. These mutant lines displayed smaller grain size compared to the wild type (Zhonghua 11, ZH11). Expression analysis revealed a significant downregulation of the transcript levels of five genes associated with cell cycle regulation in KO grains compared to the wild type, consistent with the reduced cell number in the mutant grains. Additionally, total free amino acid levels were higher in the KO mutant compared to the wild type, consequently enhancing the nutritional quality of the KO mutant grains. The mature endosperm of the KO mutant exhibited a reduced percentage of chalky grains and less chalkiness, suggesting an improvement in the appearance quality of the KO mutant. These results suggest that chromatin remodeling factor OsCHR728 plays a role in grain development, potentially providing a new avenue to enhance both the appearance and nutritional quality of rice cultivars.

CCSer2 gates dynein activity at the cell periphery

Cytoplasmic dynein-1 (dynein) is a microtubule-associated, minus end-directed motor that traffics hundreds of different cargos. Dynein must discriminate between cargos and traffic them at the appropriate time from the correct cellular region. How dynein's trafficking activity is regulated in time or cellular space remains poorly understood. Here, we identify CCSer2 as the first known protein to gate dynein activity in the spatial dimension. CCSer2 promotes the migration of developing zebrafish primordium cells, macrophages, and cultured human cells by facilitating the trafficking of cargos that are acted on by peripherally localized dynein. Our data suggest that CCSer2 disfavors the interaction between dynein and its regulator Ndel1 at the cell edge, resulting in localized dynein activation. These findings support a model where the spatial specificity of dynein is achieved by the localization of proteins that trigger Ndel1's release from dynein. We propose that CCSer2 defines a broader class of proteins that activate dynein in distinct microenvironments via regulating Ndel1-dynein interaction.

Structural characterization and inhibition of the interaction between ch-TOG and TACC3

The mitotic spindle is a bipolar array of microtubules, radiating from the poles which each contain a centrosome, embedded in pericentriolar material. Two proteins, ch-TOG and TACC3, have multiple functions at the mitotic spindle due to operating either alone, together, or in complex with other proteins. To distinguish these activities, we need new molecular tools to dissect their function. Here, we present the structure of the α-helical bundle domain of ch-TOG that mediates its interaction with TACC3 and a structural model describing the interaction, supported by biophysical and biochemical data. We have isolated Affimer tools to precisely target the ch-TOG-binding site on TACC3 in live cells, which displace ch-TOG without affecting the spindle localization of other protein complex components. Inhibition of the TACC3-ch-TOG interaction led unexpectedly to fragmentation of the pericentriolar material in metaphase cells and delayed mitotic progression, uncovering a novel role of TACC3-ch-TOG in maintaining pericentriolar material integrity during mitosis to ensure timely cell division.

Tumor cell heterogeneity drives spatial organization of the intratumoral immune response

Intratumoral heterogeneity (ITH)-defined as genetic and cellular diversity within a tumor-is linked to failure of immunotherapy and an inferior anti-tumor immune response. We modeled heterogeneous tumors comprised of "hot" and "cold" tumor populations (giving rise to T cell-rich and T cell-poor tumors, respectively) and introduced fluorescent labels to enable precise spatial tracking. We found the cold tumor cell population exerted a "dominant cold" effect in mixed tumors. Strikingly, spatial analysis revealed that the tumor cells themselves created distinct local microenvironments within heterogeneous tumors: regions occupied by cold tumor cells showed pronounced immunosuppression, harboring increased CD206Hi macrophages and diminished local T cell function. This inferior T cell activity in cold regions persisted even after immunotherapy and mechanistically was mediated by CX3CL1 produced by the cold tumor cells. An immune cold tumor population within a heterogeneous tumor thus impairs tumor immunity on both a tumor-wide and a highly localized spatial scale.

Breast cancer gene-1 (BRCA1) potentiates maladaptive repair after kidney injury

Maladaptive repair following kidney tubular injury leads to the development of interstitial fibrosis, a pathology common to chronic kidney diseases (CKD). Dysfunctional DNA damage response plays an important role in the progression of CKD. We found that BRCA1 expression was increased in the kidneys of patients with CKD and fibrotic kidneys of mice. Exon 11 deletion of Brca1 in proximal tubule cells (PTCs) of mice subjected to ischemic or nephrotoxic (aristolochic acid) injury resulted in a reduced number of senescent cells, as assessed by a decrease in phospho-histone H3, p16INK4a, RAD51 recruitment, G2/M cell cycle phase cells, GATA4, and senescence-associated β-galactosidase. There was less production of inflammatory profibrotic mediators and reduced kidney fibrosis. After cisplatin exposure in vitro, human PTCs with reduced BRCA1 had increased apoptosis, decreased RAD51 nuclear foci, and fewer cells in the G2/M cell cycle phase, with reduced IL-6 and sonic hedgehog production. Thus, BRCA1 regulates nonmalignant tissue responses to kidney injury, a role hitherto unrecognized.

Leukemogenic Kras mutation reprograms multipotent progenitors to facilitate its spread through the hematopoietic system

Leukemia-driving mutations are thought to arise in hematopoietic stem cells (HSC), yet the natural history of their spread is poorly understood. We genetically induced mutations within endogenous murine HSC and traced them in unmanipulated animals. In contrast to mutations associated with clonal hematopoiesis (such as Tet2 deletion), the leukemogenic KrasG12D mutation dramatically accelerated HSC contribution to all hematopoietic lineages. The acceleration was mediated by KrasG12D-expressing multipotent progenitors (MPP) that lacked self-renewal but showed increased proliferation and aberrant transcriptome. The deletion of osteopontin, a secreted negative regulator of stem/progenitor cells, delayed the early expansion of mutant progenitors. KrasG12D-carrying cells showed increased CXCR4-driven motility in the bone marrow, and the blockade of CXCR4 reduced the expansion of MPP in vivo. Finally, therapeutic blockade of KRASG12D spared mutant HSC but reduced the expansion of mutant MPP and their mature progeny. Thus, transforming mutations facilitate their own spread from stem cells by reprogramming MPP, creating a preleukemic state via a two-component stem/progenitor circuit.

Anillin mediates unilateral furrowing during cytokinesis by limiting RhoA binding to its effectors

During unilateral furrow ingression, one side of the cytokinetic ring (leading edge) ingresses before the opposite side (lagging edge). Anillin mediates unilateral furrowing during cytokinesis in the one-cell C. elegans zygote by limiting myosin II accumulation in the ring. Here, we address the role of anillin in this process and show that anillin inhibits not only the accumulation of myosin II but also of other RhoA effectors by binding and blocking the RhoA effector site. The interaction between the anillin's RhoA-binding domain (RBD) and active RhoA is enhanced by the disordered linker region and differentially regulated at the leading and lagging edge, which together results in asymmetric RhoA signaling and accumulation of myosin II. In summary, we discover a RhoA GEF- and GAP-independent mechanism, where RhoA activity is limited by anillin binding to the RhoA effector site. Spatial fine-tuning of anillin's inhibitory role on RhoA signaling enables unilateral furrow ingression and contributes to animal development.

The Abelson kinase and the Nedd4 family E3 ligases co-regulate Notch trafficking to limit signaling

Precise output from the conserved Notch signaling pathway governs a plethora of cellular processes and developmental transitions. Unlike other pathways that use a cytoplasmic relay, the Notch cell surface receptor transduces signaling directly to the nucleus, with endocytic trafficking providing critical regulatory nodes. Here we report that the cytoplasmic tyrosine kinase Abelson (Abl) facilitates Notch internalization into late endosomes/multivesicular bodies (LEs), thereby limiting signaling output in both ligand-dependent and -independent contexts. Abl phosphorylates the PPxY motif within Notch, a molecular target for its degradation via Nedd4 family ubiquitin ligases. We show that Su(dx), a family member, mediates the Abl-directed LE regulation of Notch via the PPxY, while another family member, Nedd4Lo, contributes to Notch internalization into LEs through both PPxY-dependent and -independent mechanisms. Our findings demonstrate how a network of posttranslational modifiers converging at LEs cooperatively modulates Notch signaling to ensure the precision and robustness of its cellular and developmental functions.

Plasticity of mitotic cyclins in promoting the G2-M transition

Cyclins and cyclin-dependent kinases (CDKs) orchestrate key events in the cell cycle. However, the uniqueness of individual mitotic cyclins has been a long-standing puzzle. By rapidly removing cyclins in G2 human cells, we found that deficiency of B-type cyclins attenuates mitotic onset and uncouples the G2-M kinase network from mitosis, resulting in sustained activation of PLK1 and cyclin A-CDK1. This culminates in mitotic slippage without completing nuclear envelope breakdown. Remarkably, elevating cyclin A several-fold above its endogenous level is adequate to restore mitosis, allowing cells to survive without B-type cyclins. In contrast, cyclin A is rate-limiting but not essential for G2-M due to compensation by endogenous cyclin B1-CDK2, a non-canonical pair. These findings challenge the traditional indispensable roles of different cyclins and highlight their plasticity. Due to the high malleability of the A- and B-type cyclins, cancer cells may be able to place different weights on different cyclins, while maintaining sufficient CDK activities for successful mitosis.

Extracellular vesicles adhere to cells primarily by interactions of integrins and GM1 with laminin

Tumor-derived extracellular vesicles (EVs) have attracted significant attention, yet the molecular mechanisms that govern their specific binding to recipient cells remain elusive. Our in vitro study utilizing single-particle tracking demonstrated that integrin heterodimers comprising α6β4 and α6β1 and ganglioside, GM1, are responsible for the binding of small EV (sEV) subtypes to laminin. EVs derived from four distinct tumor cell lines, regardless of size, exhibited high binding affinities for laminin but not for fibronectin, although fibronectin receptors are abundant in EVs and have functional roles in EV-secreting cells. Our findings revealed that integrins in EVs bind to laminin via the conventional molecular interface, facilitated by CD151 rather than by inside-out signaling of talin-1 and kindlin-2. Super-resolution movie observation revealed that sEV integrins bind only to laminin on living recipient cells. Furthermore, sEVs bound to HUVEC and induced cell branching morphogenesis in a laminin-dependent manner. Thus, we demonstrated that EVs predominantly bind to laminin on recipient cells, which is indispensable for cell responses.

Fully haplotyped genome assemblies of healthy individuals reveal variability in 5'ss strength and support by splicing regulatory proteins

This work presents a comprehensive investigation of sequence variations at human 5' splice sites (5'ss), exploring their impact on 5'ss strength and predicted splicing regulatory protein (SRP) binding. Leveraging 44 high-quality genomes, with fully haplotyped assemblies, we were able to fully assess homozygous and heterozygous sequence variations around and within 5'ss. Variations showed differing tolerance levels in protein-coding and non-coding transcripts. Around half of 5'ss variations did not alter 5'ss strength (measured by the HBond score, that estimates binding of the 11 nucleotides at the free U1 spliceosomal RNA 5' end). Heterozygous variations resulted in stronger 5'ss strength reductions and less compensatory effects of multiple sequence variations at the same 5'ss, compared to homozygous variations. Additionally, we observed a slight balance between changes in 5'ss strength and predicted SRP binding. Strong 5'ss (HBond score >18.8) showed strength variations in both directions, as theoretically expected for random distributions, whereas weaker 5'ss consistently showed lower strength reductions than expected or achievable. Variations at 5'ss of essential genes were less frequent than in other genes and showed a higher amount of variations that did not alter 5'ss strength. Acceptable changes in predicted SRP binding sites were highly dependent on their respective 5'ss strength.

Synergistic interaction of AaMYC2 and AaMYC2-LIKE enhances artemisinin production in Artemisia annua L

Artemisinin-based combination therapies recommended by WHO marks Artemisia annua as the only natural source of artemisinin fighting deadly disease, Malaria. In this study, we isolated two transcription factors, AaMYC2 and AaMYC2-LIKE, from A. annua and investigated their role in regulating artemisinin biosynthetic pathway. Our findings depict that both AaMYC2 and AaMYC2-LIKE are transcriptionally active and, when co-transformed in yeast cells, significantly enhance β-galactosidase activity in transactivation assays as compared to their individual transformations. Furthermore, Yeast two-hybrid (Y2H) and Biomolecular fluorescence complementation assays revealed AaMYC2 physically interacts with AaMYC2-LIKE in yeast cells and in the nucleus of onion epidermal cells respectively. Generation of transient transgenic over expression and co-expression lines of AaMYC2 and AaMYC2-LIKE resulted in elevated expression of artemisinin biosynthetic genes and trichome development genes in co-expression lines as compared to individual transgenic lines and wildtype. Importantly, the glandular trichome density and artemisinin content was also significantly higher in co-transformed transgenic lines compared to individual AaMYC2 and AMYC2-LIKE transgenic lines. Conversely, artemisinin content was markedly reduced in AaMYC2-RNAi lines, underscoring the critical role of functional AaMYC2 in synergistic regulation with AaMYC2-LIKE. Altogether the above studies provide valuable insights into the regulatory networks of MYC type bHLH transcription factors in controlling economically and medically important pathway in A. annua.

Micro-RNAs targeting the estrogen receptor alpha involved in endocrine therapy resistance in breast cancer

Endocrine therapy resistance (ETR) in breast cancer (BC) is a multicausal phenomenon with diverse alterations in the tumor cell interactome. Within these alterations, non-coding RNAs (ncRNAs) such as micro-RNAs (miRNAs) modulate the expression of tumor suppressor genes and proto-oncogenes, such as the ESR1 gene encoding estrogen receptor alpha (ERα). This work aims to review the effects of miRNAs targeting ERα mRNA and their mechanisms related to ETR in BC. A thorough review of the literature and an in silico study were carried out to elucidate the involvement of each miRNA, thus contributing to the understanding of ETR in BC.

The transcription factor Capicua maintains the oocyte polarity in the panoistic ovary of the German cockroach

The establishment of the symmetry axis is crucial for the development of all organisms. In insects, this process begins early in oogenesis with the correct distribution of the mRNAs and proteins in the oocyte. One protein that plays a role in organizing this distribution is the transcription factor Capicua (Cic). Cic has been studied in the context of oogenesis and embryonic development in Drosophila melanogaster. It is maternally expressed, begins essential for establishing the dorsoventral axis, and functions as a transcriptional repressor. Although the Cic sequences are conserved across species, their function in other types of insect ovaries is still little known. We wondered whether the function of Cic in insects has been maintained through evolution despite the ovary type or if it has been modified in parallel to the ovary evolution. To address this, we studied the Cic function in a phylogenetically basal insect, the cockroach Blattella germanica, a species with panoistic ovaries. Our findings show that B. germanica Cic is essential for oocyte development and the maturation of ovarian follicles. A loss of Cic function leads to disrupted cytoskeletal organization, defects in anterior-posterior polarity, and compromised follicle integrity. The conservation and functional divergence of Cic across different species suggest evolutionary adaptations in the mechanisms of insect oogenesis.

Drosophila grainyhead gene and its neural stem cell specific enhancers show epigenetic synchrony in the cells of the central nervous system

Enhancers are the epicentres of tissue-specific gene regulation. In this study, we have used the central nervous system (CNS) specific expression of the Drosophila grainyhead (grh) gene to make a case for deleting the enhancers in a sensitised background of other enhancer deletion, to functionally validate their role in tissue-specific gene regulation. We identified novel enhancers for grh and subsequently deleted two of them, to establish their collective importance in regulating grh expression in CNS. This showed that grh relies on multiple enhancers for its robust expression in neural stem cells (NSCs), with different combinations of enhancers playing a critical role in regulating its expression in various subset of these cells. We also found that these enhancers and the grh gene show epigenetic synchrony across the three cell types (NSCs, intermediate progenitors and neurons) of the developing CNS; and grh is not transcribed in intermediate progenitor cells, which inherits the Grh protein from the NSCs. We propose that this could be a general mechanism for regulating the expression of cell fate determinant protein in intermediate progenitor cells. Lastly, our results underline that enhancer redundancy results in phenotypic robustness in grh gene expression, which seems to be a consequence of the cumulative activity of multiple enhancers.

Repurposing tavaborole to combat resistant bacterial infections through competitive inhibition of KPC-2 and metabolic disruption

The rise of carbapenem-resistant Enterobacteriaceae (CRE) strains has emerged as an increasing threat to global public health. The development of antibiotic adjuvants presents an economical and promising approach to address this crisis. Through a high-throughput screen of the FDA-approved compound library, we identified tavaborole (AN2690) as a broad-spectrum β-lactamase inhibitor. The mechanistic study revealed that tavaborole formed a reversible binding with the active serine of KPC-2, showing effective competitive inhibition. Its electron-deficient boron atom formed a borate ester bond with hydroxyl group of the serine residue at the active site of KPC-2, transitioning to an sp3-hybridized state that mimicked the tetrahedral intermediate during KPC-2 catalytic. Moreover, transcriptomic analysis and bacterial metabolism assays further unveiled tavaborole addition can inhibit tricarboxylic acid (TCA) cycle, coupled with downregulation of intracellular ATP levels, indicating that tavaborole compromised the bacterial metabolic homeostasis and exerted synergistic antibacterial activity. Notably, the combination treatment further suppressed the development of meropenem resistance. In mouse intraperitoneal infection models, tavaborole effectively restored the efficacy of meropenem against CRE bacteria. These findings elucidate the synergistic mechanisms of tavaborole, expand its potential applications in anti-infection therapeutics, and provide a promising strategy for addressing CRE infections.

New insights into Gremlin-1: A tumour microenvironment landscape re-engineer and potential therapeutic target

Gremlin-1 (GREM1), a well-known bone morphogenetic protein (BMP) antagonist, is highly expressed in various malignant tumours. However, the specific role of GREM1 in tumours remains controversial and may be attributed to the heterogeneity and complexity of the tumour microenvironment (TME). It is currently believed that GREM1 regulates the complex landscape of the TME, primarily by antagonising BMP signalling or BMP-independent pathways. Both GREM1 and BMP play dual roles in tumour progression. Therefore, the mutual crosstalk between tumour cells and tumour-associated fibroblasts and the regulation of various secreted factors in the TME affect the secretion level of GREM1, which in turn regulates the amplitude balance between GREM1 and BMP, affecting tumour progression. The inhibition of GREM1 activity in the TME can disrupt this amplitude balance and prevent the formation of a tumour-supportive microenvironment, demonstrating that GREM1 is a potential therapeutic target. In this study, we reviewed the specific signalling pathways via which GREM1 in the TME regulates epithelial-mesenchymal transition, construction of the tumour immune microenvironment, and maintenance of tumour cell stemness via BMP-dependent and BMP-independent regulation, and also summarised the latest clinical progress of GREM1.

Circadian rhythms and gastrointestinal hormone-related appetite regulation

PURPOSE OF REVIEW

Circadian biology influences the gastrointestinal system as exemplified by hormonal patterns that modulate appetite. Indeed, people tend to get hungrier towards the later parts of the day. How misalignment of our circadian biology with behavioral factors (i.e. diet, exercise, sleep, etc.) influences obesity related disease has been an area of intense recent investigation.

RECENT FINDINGS

The gastrointestinal hormones (e.g. ghrelin, glucagon-like polypeptide-1, glucose dependent insulinotrophic peptide, peptide tyrosine-tyrosine, and insulin) play unique roles across the 24-h cycle in fostering anticipatory responses that promote desires to eat while concurrently responding to environmental stimuli. A persons chronotype has emerged as a target area since it provides a metric of circadian biology interacting with environmental factors and affects all people. In fact, later chronotypes tend to be at higher risk for obesity, due to in part, alterations in gastrointestinal hormones (e.g. GIP, insulin) that align with behavioral observations of greater food intake and desires to eat fatty/sweet foods later in the day.

SUMMARY

Changes in gastrointestinal hormones across the 24-h cycle impact obesity risk when misalignment of our circadian biology occurs with behavioral cycles. Better understanding how chronotype modulates appetite may enable personalized prescription of exercise, diet and/or medication to foster reduced chronic disease risk.

Epigenetic regulation of ferroptosis in gastrointestinal cancers (Review)

Ferroptosis is a type of iron‑dependent cell death characterized by excessive lipid peroxidation and may serve as a potential therapeutic target in cancer treatment. While the mechanisms governing ferroptosis continue to be explored and elucidated, an increasing body of research highlights the significant impact of epigenetic modifications on the sensitivity of cancer cells to ferroptosis. Epigenetic processes, such as DNA methylation, histone modifications and non‑coding RNAs, have been identified as key regulators that modulate the expression of ferroptosis‑related genes. These alterations can either enhance or inhibit the sensitivity of gastrointestinal cancer (GIC) cells to ferroptosis, thereby affecting the fate of GICs. Drugs that target epigenetic markers for advanced‑stage cancer have shown promising results in enhancing ferroptosis and inhibiting tumor growth. This review explores the intricate relationship between epigenetic regulation and ferroptosis in GICs. Additionally, the potential of leveraging epigenetic modifications to trigger ferroptosis in GICs is investigated. This review highlights the importance of further research to elucidate the specific mechanisms underlying epigenetic control of ferroptosis and to advance the development of novel therapeutic approaches.

Functional Analyses of SATB2 Variants Reveal Pathogenicity Mechanisms Linked With SATB2-Associated Syndrome

SATB2-associated syndrome (SAS) is characterized by intellectual disability, neurodevelopmental disorders, cleft palate, and dental abnormalities. SAS is caused by variants in the special AT-rich sequence-binding protein 2 (SATB2), which encodes a transcription factor containing two CUT domains and a homeobox (HOX) domain. Here, we report the case of a 16-year-old male diagnosed with SAS using exome sequencing and investigate the functional consequences of previously reported SATB2 variants, including those in this case. The patient carried a heterozygous missense variant (c.1147G>C, p.A383P) in SATB2, which was predicted to be pathogenic in silico but was absent from public databases. Immunofluorescence assays demonstrated that SATB2 proteins with variants in the CUT2 domain predominantly localized to the cytoplasm. Functional analysis further revealed that wild-type SATB2 increased the activity of the Msx1 promoter, which is involved in palatogenesis and tooth development, whereas variants in the CUT1 domain disrupted this transcriptional activation. These findings suggest that the nuclear localization signal of SATB2 resides in the CUT2 domain and that Msx1 promoter impairment owing to SATB2 variants may contribute to the pathogenesis of cleft palate and tooth agenesis in SAS. This research highlights a novel pathogenic variant and the functional implications for understanding SAS.

Docosapentaenoic (22:5 n-6) and docosahexaenoic (22:6 n-3) acids exhibit highly lipogenic properties in rainbow trout preadipocytes

Dietary polyunsaturated fatty acids are essential for fish health. Adipose tissue is the major tissue for fatty acid storage in rainbow trout (Oncorhynchus mykiss), and its development and function can be impacted by the fatty acids themselves. In the present study, the effects of seven fatty acids, oleic (OA, 18:1 n-9), α-linolenic (ALA, 18:3 n-3), eicosapentaenoic (EPA, 20:5 n-3), docosahexaenoic (DHA, 22:6 n-3), linoleic (LA, 18:2 n-6), arachidonic (AA, 20:4 n-6), and docosapentaenoic (DPA, 22:5 n-6) acids, on adipogenesis were investigated in primary cultures of rainbow trout preadipocytes. In terms of lipid accumulation, DPA and DHA appeared to be the most lipogenic fatty acids, while all treatments modified the fatty acid composition of the cellular phospholipids and neutral lipids. The fatty acid of interest added to the culture medium was the most abundant in preadipocytes, while the first bioconversion products were detected in lower amounts. In terms of transcriptional effects, DPA increased the expression of the early transcription factor CCAAT/enhancer binding protein δ, while DHA upregulated the expression of genes involved in neutral lipid synthesis, notably lipoprotein lipase, fatty acid transport protein 1 and glycerol-3-phosphate dehydrogenase. Both fatty acids decreased the expression of fatty acid synthase. These results highlight that DPA and DHA exert a significant effect on lipid deposition in rainbow trout preadipocytes, potentially through different pathways, and confirm that fatty acids have major impacts on preadipocyte lipid metabolism and adipogenesis.

Neural crest cells are sensitive to radiation-induced DNA damage

Radiation-induced DNA damage introduces mutations that have various deleterious effects, which may lead to apoptosis and carcinogenesis. Different tissues and cell types exhibit varying degrees of sensitivity to radiation-induced DNA damage, which is often attributed to the frequency of cell division. In this study, we showed that irradiation affects early zebrafish embryos in a manner that is not explained by direct DNA damage and repair nor by the frequency of cell division. Zebrafish embryos irradiated at 2 h post fertilization showed drastic apoptosis, mainly in the head region, during organogenesis. Herein, we show that these apoptotic cells did not show aneuploidy or micronuclei, and that not all descendants of the same cells with the same DNA damage were necessarily apoptotic. Finally, we demonstrate that apoptotic cells have various origins and that neural crest cells have a sensitive cell fate. Our results suggest the existence of a radiation damage response mechanism other than those previously described, the elucidation of which may inform strategies for greater protection against radiation injury.

AI-powered precision medicine: utilizing genetic risk factor optimization to revolutionize healthcare

The convergence of artificial intelligence (AI) and biomedical data is transforming precision medicine by enabling the use of genetic risk factors (GRFs) for customized healthcare services based on individual needs. Although GRFs play an essential role in disease susceptibility, progression, and therapeutic outcomes, a gap exists in exploring their contribution to AI-powered precision medicine. This paper addresses this need by investigating the significance and potential of utilizing GRFs with AI in the medical field. We examine their applications, particularly emphasizing their impact on disease prediction, treatment personalization, and overall healthcare improvement. This review explores the application of AI algorithms to optimize the use of GRFs, aiming to advance precision medicine in disease screening, patient stratification, drug discovery, and understanding disease mechanisms. Through a variety of case studies and examples, we demonstrate the potential of incorporating GRFs facilitated by AI into medical practice, resulting in more precise diagnoses, targeted therapies, and improved patient outcomes. This review underscores the potential of GRFs, empowered by AI, to enhance precision medicine by improving diagnostic accuracy, treatment precision, and individualized healthcare solutions.

Characterization of wheat oligo-tiller mutant ot2 and fine mapping of the mutant gene Taot2

Tiller number is a crucial determinant of grain yield in wheat (Triticum aestivum L.), and identifying functional alleles can enhance our understanding of wheat tiller development. Here, we describe the ot2 wheat mutant, which exhibits a 91% reduction in tiller number compared to the wild type and displays inhibited tiller bud differentiation from the 2-3 leaf stage. Bulked segregant analysis combined with exon sequencing mapped the Taot2 gene to chromosome 1BL. Fourteen kompetitive allele-specific PCR markers were developed and utilized to narrow down the region containing Taot2 to a 2.22 Mb interval. This region encompasses 39 high-confidence genes. Through transcriptomic analysis and functional gene investigation, TraesCS1B03G1126300 was identified as the candidate gene, encoding an auxin-responsive protein of the auxin/indole-3-acetic acid family. Our findings provide the foundation for map-based cloning of Taot2, a novel wheat tiller gene, and offer valuable insights into wheat tiller bud initiation.

The dual role of chaperone-mediated autophagy in the response and resistance to cancer immunotherapy

Cancer immunotherapy has become a revolutionary strategy in oncology, utilizing the host immune system to fight malignancies. Notwithstanding major progress, obstacles such as immune evasion by tumors and the development of resistance still remain. This manuscript examines the function of chaperone-mediated autophagy (CMA) in cancer biology, focusing on its effects on tumor immunotherapy response and resistance. CMA is a selective degradation mechanism for cytosolic proteins, which is crucial for sustaining cellular homeostasis and regulating immune responses. By degrading specific proteins, CMA can either facilitate tumor progression in stressful conditions, or promote tumor suppression by removing oncogenic factors. This double-edged sword highlights the complexity of CMA in cancer progression and its possible effect on treatment results. Here we clarify the molecular mechanisms by which CMA can regulate the immune response and its possible role as a therapeutic target for improving the effectiveness of cancer immunotherapy.

SRSF2 overexpression induces transcription-/replication-dependent DNA double-strand breaks and interferes with DNA repair pathways to promote lung tumor progression

SRSF2 (serine/arginine-rich splicing factor 2) is a critical regulator of pre-messenger RNA splicing, which also plays noncanonical functions in transcription initiation and elongation. Although elevated levels of SRSF2 are associated with advanced stages of lung adenocarcinoma (LUAD), the mechanisms connecting SRSF2 to lung tumor progression remain unknown. We show that SRSF2 overexpression increases global transcription and replicative stress in LUAD cells, which correlates with the production of DNA damage, notably double-strand breaks (DSBs), likely resulting from conflicts between transcription and replication. Moreover, SRSF2 regulates DNA repair pathways by promoting homologous recombination and inhibiting nonhomologous end joining. Mechanistically, SRSF2 interacts with and enhances MRE11 (meiotic recombination 11) recruitment to chromatin, while downregulating 53BP1 messenger RNA and protein levels. Both events are likely contributing to SRSF2-mediated DNA repair process rerouting. Lastly, we show that SRSF2 and MRE11 expression is commonly elevated in LUAD and predicts poor outcome of patients. Altogether, our results identify a mechanism by which SRSF2 overexpression promotes lung cancer progression through a fine control of both DSB production and repair. Finally, we show that SRSF2 knockdown impairs late repair of ionizing radiation-induced DSBs, suggesting a more global function of SRSF2 in DSB repair by homologous recombination.

Resveratrol attenuates pressure overload-induced myocardial remodeling in ovariectomized rats by rescuing the adaptive angiogenic response

BACKGROUND

Resveratrol (RES), a polyphenol with putative estrogen (E2) -like effects, is believed to counteract left ventricular hypertrophy (LVH). However, how RES exerts its protection is not well understood, particularly when prominent risk factors, such as E2 depletion and pressure overload (PO), coexist. Here, we evaluated the impact of RES and E2 on angiogenesis and LVH in rats subjected to ovariectomy (OVX) and PO.

METHODS

Three weeks after bilateral OVX induction, abdominal aortic banding was performed on Wistar female rats to trigger PO. The animals were treated with either RES or E2 for six weeks. Finally, the heart-to-body weight ratio (HW/BW), cell size, fibrosis, and atrial natriuretic peptide (ANP) mRNA expression were assessed. Angiogenesis was determined by evaluating vascular endothelial growth factor (VEGF) mRNA and protein expression and by CD31 immunostaining. Serum E2 levels were also measured.

RESULTS

OVX + PO caused more severe myocardial hypertrophy (HW/BW) and fibrosis compared with PO alone, but did not aggravate cell size and ANP mRNA expression. OVX blunted the angiogenic response to PO, with reduced VEGF expression. RES increased VEGF expression and CD31, and abrogated LVH and fibrosis. E2 treatment improved VEGF expression and fibrosis, but not to the same extent as RES. RES improved serum levels of E2 in OVX + PO rats.

CONCLUSION

Our findings suggest that RES limits OVX-induced exacerbation of LVH and fibrosis in a PO model, and targets systemic E2 levels and myocardial angiogenesis as underpinning protective mechanisms. Thus, RES may provide cardioprotection for post-menopausal women.

Divergent Plasmodium kinases drive MTOC, kinetochore and axoneme organisation in male gametogenesis

Sexual development and male gamete formation of the malaria parasite in the mosquito midgut are initiated by rapid endomitosis in the activated male gametocyte. This process is highly regulated by protein phosphorylation, specifically by three divergent male-specific protein kinases (PKs): CDPK4, SRPK1, and MAP2. Here, we localise each PK during male gamete formation using live-cell imaging, identify their putative interacting partners by immunoprecipitation, and determine the morphological consequences of their absence using ultrastructure expansion and transmission electron microscopy. Each PK has a distinct location in either the nuclear or the cytoplasmic compartment. Protein interaction studies revealed that CDPK4 and MAP2 interact with key drivers of rapid DNA replication, whereas SRPK1 is involved in RNA translation. The absence of each PK results in severe defects in either microtubule-organising centre organisation, kinetochore segregation, or axoneme formation. This study reveals the crucial role of these PKs during endomitosis in formation of the flagellated male gamete and uncovers some of their interacting partners that may drive this process.

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.

Integration of BrfS into the biofilm-controlling cascade promotes sessile Salmonella growth at low temperatures

Biofilm formation is stimulated by different stress-related physiological and environmental conditions. In Salmonella and Escherichia coli, curli fibers and phosphoethanolamine-cellulose are the major extracellular components of biofilms. The production of both is under the control of CsgD, a transcriptional regulator whose expression is modulated by a number of factors responding to different signals. The atypical MerR-like regulator MlrA is key in the activation of csgD transcription in both Salmonella and E. coli. Recently, MlrB, a SPI-2-encoded MlrA-like regulator that counteracts MlrA by repressing csgD transcription and biofilm formation inside macrophages was identified. Here, we characterize STM1266, a Salmonella-specific MlrA-like regulator, recently renamed BrfS. In contrast to mlrA, brfS transcription increases in minimal growth media and at 20 °C, a temperature not commonly tested in laboratories. Under these conditions, as well as in salt-limited rich medium, deletion or overexpression of brfS affects extracellular matrix production. Using transcriptomics, we uncovered genes under BrfS control relevant for biofilm formation such as csgB and bapA. Transcriptional analysis of these genes in mutants lacking brfS, csgD or both, indicates that BrfS controls curli biosynthesis both in a CsgD-dependent and independent manner. By contrast, at low temperatures, bapA transcription depends only on BrfS, and neither deletion of csgD nor of mlrA modify its expression. Based on these results, we propose that BrfS contributes to Salmonella persistence in the environment, where the pathogen encounters low temperatures and nutrient limitation.

Suppression of global protein synthesis and hepatocellular carcinoma cell growth by Benzimidazoisoquinoline, 4,11-Dichloro-BBQ

The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor best known for mediating biological responses to a wide range of xenobiotics, such as dioxins and polycyclic aromatic hydrocarbons. Recently, AhR has emerged as an important player in cancer biology, with the potential for therapeutic applications through targeted modulation of its activity in specific cancer types. In this study, we report that 4,11-dichloro-BBQ (DiCl-BBQ), a benzimidazoisoquinoline, exhibits AhR-mediated antiproliferative activity in HepG2 hepatocellular carcinoma cells. DiCl-BBQ was found to decrease cell growth at nanomolar concentrations, and this antiproliferative effect persisted even after the compound's removal. Using inducible shRNA expression system, we demonstrated that the inhibitory effect of DiCl-BBQ was significantly reduced following AhR knockdown. Flow cytometric analysis revealed that DiCl-BBQ halted cell division and induced G1 cell cycle arrest in an AhR-dependent manner. Proteomic profiling identified the top four enriched pathways following DiCl-BBQ exposure: metabolism of RNA, translation, ribonucleoprotein complex biogenesis, and carboxylic acid metabolic processes. Notably, DiCl-BBQ caused a dramatic downregulation of translation-associated proteins, with this response diminished in AhR-depleted cells. Consistently, global protein synthesis was significantly repressed in DiCl-BBQ-treated cells. Together, these results indicate that DiCl-BBQ effectively inhibits HepG2 cells growth by inducing G1 cell cycle arrest and downregulating the protein translation machinery in an AhR-dependent manner.

Therapeutic targets in the Wnt signaling pathway: Treating cancer with specificity

The Wnt signaling pathway is a critical regulatory mechanism that governs cell cycle progression, apoptosis, epithelial-mesenchymal transition (EMT), angiogenesis, stemness, and the tumor immune microenvironment, while also maintaining tissue homeostasis. Dysregulated activation of this pathway is implicated in various cancers, closely linked to tumor initiation, progression, and metastasis. The Wnt/β-catenin axis plays a central role in the pathogenesis of common cancers, including colorectal cancer (CRC), breast cancer (BC), liver cancer, and lung cancer. Unlike traditional chemotherapy, targeted therapy offers a more precise approach to cancer treatment. As a key regulator of oncogenesis, the Wnt pathway represents a promising target for clinical interventions. This review provides a comprehensive analysis of the Wnt signaling pathway, exploring its roles in tumor biology and its implications in human malignancies. It further examines the molecular mechanisms and modes of action across different cancers, detailing how the Wnt pathway contributes to tumor progression through mechanisms such as metastasis promotion, immune modulation, drug resistance, and enhanced cellular proliferation. Finally, therapeutic strategies targeting Wnt pathway components are discussed, including inhibitors targeting extracellular members, as well as those within the cell membrane, cytoplasm, and nucleus. The potential of these targets in the development of novel therapeutic agents underscores the critical importance of intervening in the Wnt signaling pathway for effective cancer treatment.

E3 ubiquitin ligases and their therapeutic potential in disease Management

Ubiquitination is a vital post-translational modification that regulates protein stability and various cellular processes through the addition of ubiquitin molecules. Central to this process are E3 ubiquitin ligases, which determine the specificity of ubiquitination by coordinating the attachment of ubiquitin to target proteins, influencing their degradation, localization, and activity. E3 ubiquitin ligases are involved in numerous cellular pathways, including DNA repair, cell proliferation, and immune responses. Dysregulation of E3 ubiquitin ligases is often associated with cancer, contributing to tumor progression and resistance to therapies. The development of targeted protein degraders, such as proteolysis-targeting chimeras (PROTACs), represents a significant advancement in drug discovery, leveraging the specificity of E3 ubiquitin ligases to selectively eliminate pathogenic proteins. However, challenges remain in translating this knowledge into effective therapies, including issues related to tissue-specific targeting and off-target effects. The limitations also include a limited understanding of ligase-substrate interactions that includes both the identification of novel E3 ligases and their substrates, as well as understanding the dynamic, context-dependent nature of these interactions, which can vary across tissue types or disease states This review emphasizes the therapeutic potential of E3 ubiquitin ligases, exploring their diverse roles in disease, their contribution to targeted degradation strategies while highlighting the need for further research to overcome current limitations and enhance therapeutic efficacy.

Mechanism by which Rab5 promotes regeneration and functional recovery of zebrafish Mauthner axons

JOURNAL/nrgr/04.03/01300535-202506000-00031/figure1/v/2024-08-05T133530Z/r/image-tiff Rab5 is a GTPase protein that is involved in intracellular membrane trafficking. It functions by binding to various effector proteins and regulating cellular responses, including the formation of transport vesicles and their fusion with the cellular membrane. Rab5 has been reported to play an important role in the development of the zebrafish embryo; however, its role in axonal regeneration in the central nervous system remains unclear. In this study, we established a zebrafish Mauthner cell model of axonal injury using single-cell electroporation and two-photon axotomy techniques. We found that overexpression of Rab5 in single Mauthner cells promoted marked axonal regeneration and increased the number of intra-axonal transport vesicles. In contrast, treatment of zebrafish larvae with the Rab kinase inhibitor CID-1067700 markedly inhibited axonal regeneration in Mauthner cells. We also found that Rab5 activated phosphatidylinositol 3-kinase (PI3K) during axonal repair of Mauthner cells and promoted the recovery of zebrafish locomotor function. Additionally, rapamycin, an inhibitor of the mechanistic target of rapamycin downstream of PI3K, markedly hindered axonal regeneration. These findings suggest that Rab5 promotes the axonal regeneration of injured zebrafish Mauthner cells by activating the PI3K signaling pathway.

Autophagy: The convergence point of aging and cancer

Autophagy, a dynamic intracellular degradation system, is critical for cellular renovation and maintaining equilibrium. By eliminating damaged components and recycling essential molecules, autophagy safeguards cellular integrity and function. The versatility of the autophagy process across various biological functions enable cells to adapt and maintain homeostasis under unfavourable conditions. Disruptions in autophagy can shift a cell from a healthy state to a disease state or, conversely, support a return to health. This review delves into the multifaceted role of autophagy during aging and age-related diseases such as cancer, highlighting its significance as a unifying target with promising therapeutic implications. Cancer development is a dynamic process characterized by the acquisition of diverse survival capabilities for proliferating at different stages. This progression unfolds over time, with cancer cells exploiting autophagy to overcome encountered stress conditions during tumor development. Notably, there are several common pathways that utilize the autophagy process during aging and cancer development. This highlights the importance of autophagy as a crucial therapeutic target, holding the potential to not only impede the growth of tumor but also enhance the patient's longevity. This review aims to simplify the intricate relationship between cancer and aging, with a particular focus on the role of autophagy.

Tanshinone IIA promotes ferroptosis in cutaneous melanoma via STAT1-mediated upregulation of PTGS2 expression

BACKGROUND

Melanoma is highly aggressive, metastatic with a poor prognosis. Despite significant advances in targeted therapies and immunotherapies, their efficiency limited by drug resistance. Tanshinone IIA (Tan IIA), a bioactive compound derived from Traditional Chinese plant, exhibits significant anticancer potential, which still needs more research in its complex regulatory mechanisms.

PURPOSE

This study aimed to elucidate the putative targets and regulatory mechanisms of Tan IIA in anti-melanoma, with a focus on its role in inducing ferroptosis.

STUDY DESIGN

We designed the experiment to explore the effects of Tan IIA on melanoma through both in vitro and in vivo experiments and to investigate the underlying mechanisms through transcriptomics combining network pharmacology analysis.

METHOD

Ferroptosis monitored by Malondialdehyde (MDA), Fe2+, reactive oxygen species (ROS) and glutathione (GSH) in vivo and in vitro. RNA sequence was performed to explore the key regulatory pathways involved in Tan IIA-induced ferroptosis. Chromatin immunoprecipitation (ChIP) and Luciferase assays were used to validate transcription factor responsible for prostaglandin-endoperoxide synthase 2 (PTGS2) regulation. Additionally, RT-qPCR, western blot, IF, IHC were aimed to evaluate the expression of target gene.

RESULT

Tan IIA markedly suppresses melanoma growth in a xenograft model. The same effect performed on inhibition melanoma cells and promotion to ferroptosis with accumulation of ROS, MDA, and Fe²⁺levels and GSH consumption. RNA sequencing and public database analysis revealed that Tan IIA regulates PTGS2, the critical marker of ferroptosis, and PTGS2-knockdown attenuates Tan IIA -induced ferroptosis in melanoma cells. Furthermore, we identified that Tan IIA stimulate signal transducer and activator of transcription 1 (STAT1), a transcription factor, promoting PTGS2 expression and localized in the cell cytoplasm. Moreover, downregulation of the transcription factor STAT1 lead to PTGS2 downregulation and also inhibit ferroptosis in melanoma.

CONCLUSION

This study, the first to link Tan IIA-induced ferroptosis to the STAT1/PTGS2 axis in melanoma, identifies STAT1 and PTGS2 as novel therapeutic targets for melanoma, which demonstrates the potential of natural compounds Tan IIA in overcoming drug resistance and integrates traditional medicine with advanced molecular techniques for mechanistic exploration.

Integrated transcriptomic and lipidomic analysis reveals that arachidonic acid mediates the allograft-induced stress response in Pinctada fucata martensii

This study investigated the protective effect of arachidonic acid (ARA) against the allograft-induced stress response in Pinctada fucata martensii by characterizing pearl production traits and changes in genes and lipids during postoperative care. Survival and pearl production traits were higher in the ARA treatment group (ARAG) than in the control group (CG). There were 1536 differentially expressed genes (DEGs) in CG-1d vs ARAG-1d and 833 DEGs in CG-3d vs ARAG-3d. DEGs in CG-1d vs ARAG-1d were mainly enriched in "NOD-like receiver signaling pathway," "Glycerolipid metabolism," and "Sphingolipid metabolism." DEGs in CG-3d vs ARAG-3d were mainly enriched in "Apoptosis" and "ARA metabolism." Lipidomics analysis revealed 36 types of lipids. The PC, LPE (22:5), and LPE (18:0) content at 3 d after implantation was lower in the ARAG than in the CG. The PS (37,1) content was significantly higher at 3 d after implantation and the content of ceramides was significantly lower at 1 and 3 d after implantation in the ARAG than in the CG. The results indicated that ARA may alter the composition of lipids, modify the unsaturation of lipids, and regulate apoptosis, immunity, and lipid metabolism in pearl oysters, which enhances pearl production traits. These findings provide theoretical and practical basis for further alleviating the inflammatory response of pearl oysters after implantation.

Current updates regarding biogenesis, functions and dysregulation of microRNAs in cancer: Innovative approaches for detection using CRISPR/Cas13‑based platforms (Review)

MicroRNAs (miRNAs) are short non‑coding RNAs, which perform a key role in cellular differentiation and development. Most human diseases, particularly cancer, are linked to miRNA functional dysregulation implicated in the expression of tumor‑suppressive or oncogenic targets. Cancer hallmarks such as continued proliferative signaling, dodging growth suppressors, invasion and metastasis, triggering angiogenesis, and avoiding cell death have all been demonstrated to be affected by dysregulated miRNAs. Thus, for the treatment of different cancer types, the detection and quantification of this type of RNA is significant. The classical and current methods of RNA detection, including northern blotting, reverse transcription‑quantitative PCR, rolling circle amplification and next‑generation sequencing, may be effective but differ in efficiency and accuracy. Furthermore, these approaches are expensive, and require special instrumentation and expertise. Thus, researchers are constantly looking for more innovative approaches for miRNA detection, which can be advantageous in all aspects. In this regard, an RNA manipulation tool known as the CRISPR and CRISPR‑associated sequence 13 (CRISPR/Cas13) system has been found to be more advantageous in miRNA detection. The Cas13‑based miRNA detection approach is cost effective and requires no special instrumentation or expertise. However, more research and validation are required to confirm the growing body of CRISPR/Cas13‑based research that has identified miRNAs as possible cancer biomarkers for diagnosis and prognosis, and as targets for treatment. In the present review, current updates regarding miRNA biogenesis, structural and functional aspects, and miRNA dysregulation during cancer are described. In addition, novel approaches using the CRISPR/Cas13 system as a next‑generation tool for miRNA detection are discussed. Furthermore, challenges and prospects of CRISPR/Cas13‑based miRNA detection approaches are described.

Synergistic enhancement of PARP inhibition via small molecule UNI66-mediated suppression of BRD4-dependent transcription of RAD51 and CtIP

Targeted therapy leveraging synthetic lethality in homologous recombination (HR)-defective tumors, particularly in BRCA-mutated tumors through poly(ADP-ribose) polymerase (PARP)-dependent repair inhibition, has shown success. However, the challenge lies in the ability of the tumors to reactivate HR via diverse mechanisms, leading to resistance against PARP-dependent repair inhibition. Addressing this issue, the down-regulation of HR activity has been explored as a potential strategy to overcome PARP inhibitor-resistant tumors. Yet, the intricate modulation of HR gene expression in mammalian cells is still not fully understood. In this study, we used a small molecule, UNI66, identified from high-throughput screening, to investigate regulatory mechanisms of HR. UNI66 was observed to induce synthetic lethality in PARP1-deficient cells and enhanced the sensitivity of multiple cancer cells to PARP inhibitors, suggesting a role in HR down-regulation. Mechanistically, UNI66 was found to interact with and inhibit BRD4 protein binding to the promoters of CtIP and RAD51 genes, resulting in the down-regulation of their transcription. This decrease in CtIP and RAD51 expression was associated with reduced HR activity, thereby increasing the sensitivity of tumors to PARP inhibitors. These findings indicate that BRD4-mediated transcriptional regulation of CtIP and RAD51 influences HR activity, which may have implications for overcoming resistance to PARP inhibitors.

A dynamin-like protein in Plasmodium falciparum plays an essential role in parasite growth, mitochondrial development and homeostasis during asexual blood stages

Malaria parasites harbour a single mitochondrion, and its proper segregation during parasite multiplication is crucial for the propagation of the parasite within the host. Mitochondrial division machinery consists of several proteins that associate with the mitochondrial membrane during segregation. Here, we have identified a dynamin-like protein in P. falciparum, PfDyn2, and deciphered its role in mitochondrial growth and homeostasis. A GFP targeting approach combined with high-resolution microscopy studies showed that the PfDyn2 associates with the mitochondrial membrane at specific sites during mitochondrial division. The C-terminal degradation tag mediated inducible knock-down (iKD) of PfDyn2 significantly inhibited parasite growth. PfDyn2-iKD hindered mitochondrial development and functioning, decreased mtDNA replication, and induced mitochondrial oxidative stress, ultimately causing parasite death. Regulated overexpression of a phosphorylation mutant of PfDyn2 (Ser-612-Ala) did not affect the recruitment of PfDyn2 on the mitochondria; normal mitochondrial division and parasite growth showed that phosphorylation/dephosphorylation of this conserved serine residue (Ser612) may not be responsible for regulating recruitment of PfDyn2 to the mitochondrion. Overall, we show the essential role of PfDyn2 in mitochondrial development and maintaining its homeostasis during the asexual cycle of the parasite.

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.

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.