Rice genotypes differ in aluminium tolerance, with resistant landraces sustaining root growth OsSTAR1 / OsSTAR2 mediated exclusion, organic acid efflux, and antioxidant defense, whereas sensitive varieties accumulate Al³⁺ via OsNRAT1-OsALS1 mediated internal sequestration, leading to oxidative damage. This study reveals two contrasting molecular strategies of aluminium (Al) tolerance root-based exclusion and internal detoxification among indigenous rice landraces of Northeast India, a region severely affected by acidic soil-related Al toxicity. Fifty-three rice genotypes were evaluated under hydroponic Al stress (200 μM AlCl₃) through integrated morphophysiological, biochemical, and gene expression analyses. Tolerant genotypes such as Ahom Sali and Disang sustained root growth, biomass, and relative water content, whereas sensitive types such as Ranjit Sub-1 and Jolkonwari showed severe root inhibition and oxidative damage. SSR marker analysis of 33 polymorphic loci (mean PIC = 0.48) confirmed high genetic diversity, but weak correlation with phenotypic performance, indicating complex inheritance of tolerance. Biochemical profiling revealed that tolerant landraces maintained higher chlorophyll and antioxidant enzyme activities and secreted greater quantities of organic acids (citrate and malate), facilitating Al exclusion through rhizosphere chelation. Gene expression analysis revealed the upregulation of OsSTAR1, OsSTAR2, and OsFRDL4 in tolerant genotypes, promoting Al exclusion, whereas sensitive lines showed increased OsNRAT1 and OsALS1 expression, indicating a reliance on less effective internal detoxification pathways. These findings demonstrate that aluminium tolerance in traditional rice landraces from Northeast India is driven primarily by exclusion mechanisms. The identified tolerant genotype represents a valuable genetic resource for the breeding of acid soil-resilient rice cultivars, offering promising prospects for sustainable rice production and food security in Al-affected regions.

Approximately 70% of clear cell renal cell carcinoma (ccRCC) patients harbor von Hippel‒Lindau (VHL) deficiency, which drives pseudohypoxia and metabolic reprogramming. Here, we report a histone H4 lysine 12 lactylation (H4K12la)-fueled phosphoglycerate kinase 1 (PGK1)-lactate positive feedback loop that sustains glycolytic flux in VHL-deficient ccRCC and is pharmacologically disruptable by glucocorticoids. H4K12la is markedly elevated in ccRCC tissues and is associated with advanced pathological stage and unfavorable patient outcome. Integrative transcriptomic and epigenomic profiling revealed that VHL deficiency amplifies H4K12la deposition at accessible promoters, coupled to transcriptional activation of glycolytic and tumor-promoting programs, exemplified by PGK1. Through high-content drug screening, we identify glucocorticoids as effective suppressors of H4K12la, which act via glucocorticoid receptor-mediated transcriptional repression of glycolytic genes and consequent attenuation of lactate production. Strikingly, VHL-deficient ccRCC exhibits greater on-target pathway sensitivity to dexamethasone at the H4K12la-glycolysis axis, and glucocorticoid dexamethasone potentiated the antitumor efficacy of the HIF-2α inhibitor belzutifan in both orthotopic cell line-derived and patient-derived xenograft models. Collectively, our findings establish H4K12la as a metabolic‒epigenetic amplifier in VHL-deficient ccRCC, reposition glucocorticoids as epigenetically active modulators that dampen lactate-driven chromatin activation and glycolytic output, and provide a mechanistically grounded combination strategy with HIF-2α blockade to target lactate-fueled transcriptional dependence in metabolically rigid tumors.

Inactivating mutations in BAP1 (BRCA1-associated protein 1) are prevalent in many aggressive cancers of high global concern, including cholangiocarcinoma, mesothelioma, uveal melanoma, and renal cell carcinoma. However, research on BAP1 has been predominantly focused on single cancer types, lacking comprehensive pancancer studies that could uncover universal molecular mechanisms and therapeutic vulnerabilities. Our pancancer study uses K-ε-GG ubiquitin remnant motif pulldown coupled with mass spectrometry to comprehensively map the landscape of proteins deubiquitinated by BAP1. Combined with transcriptomics and functional assays, we uncover previously unrecognized roles of BAP1 in enhancing global genome nucleotide excision repair (GG-NER) by modulating the deubiquitination dynamics of three GG-NER DNA damage recognition proteins, DDB1, RAD23B, and COPS7B. We also identify LSD1 (lysine-specific histone demethylase 1) and PARP1 [poly(ADP-ribose) polymerase 1] as synthetic lethal partners of BAP1 through high-throughput drug inhibitor screening. Integrative analysis using ChIP sequencing, ATAC sequencing, and transcriptomics demonstrates the colocalization of BAP1, LSD1, and PARP1 on chromatin loci, with LSD1 promoting chromatin relaxation to facilitate efficient transcription-coupled NER (TC-NER) in addition to GG-NER, whereas PARP1 facilitates lesion recognition of both TC-NER and GG-NER. Combined inhibition of LSD1 and PARP1, using SP2509/SP2577 and olaparib, respectively, synergistically hinders NER, induces apoptosis, reduces tumor burden, and prolongs the survival of multiple BAP1-deficient pancancer in vitro models and in vivo xenografts. In conclusion, our results provide a deubiquitination landscape of BAP1; elucidate the mechanisms of action of BAP1, LSD1, and PARP1 in pancancers; and describe a promising combination therapeutic strategy applicable across multiple cancers with BAP1 mutations.

The persistence of latent HIV-1 reservoirs remains a major barrier to achieving a cure for HIV. While latency-reversing agents (LRAs) have been extensively studied, latency-promoting agents (LPAs) offer a complementary strategy to silence viral transcription and prevent immune activation. Here, we propose that modulation of IRF7-driven transcription may represent a novel approach to control HIV-1 latency, by characterizing the role of the Janus kinase 2 inhibitor (JAK2i) pacritinib as a novel latency-promoting agent (LPA).

Neurodegenerative diseases are complex disorders characterized by the progressive loss of neuronal structure and function, involving pathological mechanisms such as oxidative stress, chronic inflammation, protein misfolding, and impaired synaptic plasticity. Recent studies have revealed that epigenetic regulation plays a critical role in the onset and progression of these diseases, including mechanisms such as DNA methylation, histone modifications, and non-coding RNA regulation. Natural polyphenolic compounds, known for their safety and multi-target properties, have emerged as promising candidates for neuroprotection and therapeutic intervention.

Plant hormones regulate a wide array of developmental and stress-response pathways by modulating gene expression through specific transcription factors (TFs). Understanding how these TFs interact with their genomic targets is essential for dissecting hormone signaling networks. Chromatin immunoprecipitation (ChIP), coupled with quantitative PCR (ChIP-qPCR) or next-generation sequencing (ChIP-seq), offers a powerful approach to study in vivo protein-DNA interactions. However, ChIP in plants poses unique technical challenges due to the presence of rigid cell walls, abundant secondary metabolites, and chromatin accessibility constraints. Here, we present a detailed and optimized protocol for performing ChIP-qPCR and ChIP-seq in Arabidopsis thaliana to investigate hormone-responsive gene regulation. The protocol includes steps for hormone treatment, tissue fixation, chromatin extraction, immunoprecipitation using specific antibodies, reverse crosslinking, DNA purification, and downstream quantification. This method enables high-resolution mapping of transcription factor occupancy at target loci and can be adapted for different hormones and plant species. Compared to indirect transcriptomic approaches, ChIP-based assays provide direct evidence of TF-DNA binding and allow identification of primary targets in signaling cascades. The protocol supports mechanistic studies of hormone action in plants and facilitates the construction of gene regulatory networks.

Spatially resolved transcriptomics captures gene expression in tissue context, enabling direct mapping of defense pathways across organs and cell layers. This chapter describes a complete Stereo-seq workflow for Arabidopsis leaves treated with salicylic acid (SA), from plant growth and hormone application through cryosectioning, fixation, bright-field imaging and optional histology, on-chip permeabilization, in situ reverse transcription and library construction on STOmics V1.3 1 × 1 cm chips, sequencing on DNBSEQ platforms, and analysis using STOmics Analysis Workflow (SAW) with downstream spatial statistics and pathway enrichment. Practical parameters are given for section thickness, fixation, imaging, permeabilization optimization, sequencing configuration, and quality control. The bioinformatics analyses include binning strategies, alignment to TAIR10, normalization, clustering, spatial differential expression, pathway testing, and integration with single-cell RNA-seq references for cell-type deconvolution.

Salicylic acid (SA) and jasmonic acid (JA) coordinate plant immunity through partially antagonistic signaling pathways that differ across cell types and over time. Single-cell and single-nucleus RNA sequencing now resolve these hormone responses at cellular resolution, allowing clear separation of early primary signaling waves from secondary and downstream transcriptional programs. In the context of plant-pathogen interactions, these approaches are particularly powerful for uncovering how distinct cell populations perceive SA and JA, reprogram defense networks, and balance growth-immunity trade-offs. This chapter provides end-to-end wet-lab protocols for nuclei-based snRNA-seq tailored to SA and JA treatments, including sample preparation, nuclei isolation, and library construction. In parallel, a bioinformatics analysis workflow is described, covering quality control, ambient RNA correction, doublet removal, dataset integration, cell type mapping, differential expression analysis, and pathway and module scoring. Together, these experimental and computational pipelines enable researchers to dissect hormone-driven immune responses at single-cell resolution and to generate cell-type-resolved hypotheses that can guide downstream genetic and physiological studies.

Salicylic acid (SA) functions as a key signaling molecule in plant defense, orchestrating responses to diverse biotic and abiotic stresses. A clear understanding of SA-mediated immunity requires systematic analysis of SA-responsive transcriptional programs at both targeted and genome-wide levels. This chapter describes methodological strategies for examining SA-responsive gene expression through quantitative polymerase chain reaction (qPCR) as well as bulk transcriptome profiling using the Bio-Rad SEQuoia Complete Stranded RNA Kit. The workflow covers experimental design, sample preparation, data acquisition, and result interpretation within the framework of plant immune responses. Integrating targeted qPCR assays with SEQuoia-enabled transcriptome analysis enables robust characterization of regulatory networks underlying SA-induced immunity and supports reproducible comparisons across experiments. This combined approach provides insights into the complexity of plant defense signaling and its transcriptional control.

Multidrug-resistant Staphylococcus aureus (MRSA). This study investigated the antimicrobial efficacy of zinc oxide (ZnO) nanoparticles synthesised through a blue laser-enhanced hydrothermal method combined with the flavonoid Naringenin (NAR) against multidrug-resistant S. aureus isolates. Sixty S. aureus strains were identified using a combination of morphological, biochemical and molecular analyses (VITEK-2 and 16 S rRNA). All strains showed total resistance (100%) to oxacillin and cefoxitin and high resistance levels (60-90%) for vancomycin, erythromycin and fluoroquinolones. Characterization confirmed hexagonal ZNPs with a crystallite size of 38.78 nm. Disk diffusion assays demonstrated enhanced efficacy of ZNPs-NAR combination, achieved a 16.67 mm inhibition zone (p ≤ 0.0001). Notably, while ZNPs singly suppressed leukocidin toxin genes lukD and lukE by 90.3% and 94.9%, inhibition, and NAR reduced expression by 62.4% and 61.9%, the ZNPs-NAR combination showed lower gene suppression (59.3% and 52.8%) yet superior bactericidal activity. This discrepancy reveals that the enhanced bactericidal effect stems not from amplified transcriptional inhibition, but from complementary mechanisms: ZNPs likely disrupt bacterial membranes to facilitate NAR uptake, while NAR concurrently interferes with intracellular targets like DNA replication. The findings demonstrate that nanoparticle-phytochemical combinations can achieve superior antimicrobial effects through synergistic mechanisms, offering a promising strategy to combat multidrug-resistant infections and reduce reliance on conventional antibiotics.

In a randomised controlled trial (RCT), we compared the effects of treatment with furosemide + small volumes of hypertonic saline solution (HSS) with those of furosemide alone in patients with decompensated heart failure (HF), and their effects on inflammatory and remodelling markers and epigenetic signatures.

Triple-negative breast cancer (TNBC) is an aggressive and heterogeneous subtype of breast cancer, with limited treatment options due to the absence of estrogen receptors, progesterone receptors, and human epidermal growth factor receptor 2 (HER2) expression. This characteristic renders TNBC resistant to hormone-based and HER2-targeted therapies, leaving cytotoxic chemotherapy as the predominant strategy and highlighting the urgency for novel interventions. In this study, we investigated the mechanism of action of GL24, a potent 4-(phenylsulfonyl)morpholine-based small molecule with selective tumor suppression effects on metastatic TNBC cells, while being ineffective against TNBC cells derived from the primary tumor site, using gene co-expression analysis. By considering the distinct phenotypic responses induced by GL24, we tailored our co-expression analysis approach, selecting gene pairs that exhibited differential co-expression in effective cells while excluding gene pairs that also showed differential patterns in non-effective cells. Constructing a co-expression network from these differential pairs, followed by enrichment analysis and functional annotation, revealed specific gene interactions and molecular pathways associated with GL24-mediated TNBC inhibition. These insights supported the previously established findings that showed convergence on apoptosis based on differentially expressed genes, while also providing complementary information by highlighting pathways involved in metabolic alterations, proliferation, and migration or invasion. This expanded understanding advances the knowledge of the mechanisms of GL24 in combating TNBC.

Exposure to immune stress or lipopolysaccharide (LPS) during critical developmental stages like puberty may lead to gut microbiome dysbiosis and epigenetic dysregulation in mammary glands, affecting gene expression and potentially elevating breast cancer susceptibility in adulthood. Although LPS's adverse impacts on intestinal and brain functions are well-documented, its effects on mammary glands remain underexplored. Using an immunocompetent BALB/c mouse model, we administered an acute LPS dose (1.5 mg/kg body weight) during puberty. The study evaluated the long-term consequences of LPS exposure alone and combined with AHCC (Lentinula edodes cultured extract, 2 g/kg body weight/day) on DNA methylation patterns, cytokine profiles, and microRNA expression in mammary glands at 9 weeks of age. Analyses included DNA methylation sequencing, multiplex immunoassays, quantitative PCR, and image processing. Pubertal LPS exposure produced persistent molecular dysregulation in mammary glands, including differential DNA methylation (> 5% change vs. control; FDR-adjusted p < 0.05), elevated inflammatory mediators, and altered microRNA expression. Differentially methylated regions were enriched in regulatory features, with decreased methylation at transcription start sites, promoters, and 5' UTRs of genes implicated in mammary development and oncogenic signaling (including Vav3, Pdgfa, Pdgfc, Jag2, Hras, Ksr1, Il2rb, Il17b, and Il17rb) in the LPS group, whereas the AHCC + LPS group exhibited a shift toward hypermethylation at these loci (approximately 5%-10% decrease). Inflammatory profiling showed increased IL-17A/F (∼2-fold vs. control; p < 0.05), while microRNA analyses indicated reduced let-7a/c (∼30% vs. control; p < 0.05). Notably, miR-130a and miR-34a increased ∼1.5-fold across all treatment groups relative to control. Pubertal LPS exposure induces enduring epigenetic and inflammatory changes in mammary glands that may heighten breast cancer risk. AHCC's mitigating role indicates potential for dietary interventions to counteract these effects.

Sepsis induced myocardial injury (SIMI) remains a life threatening complication with mortality rates exceeding 40% to 50%, yet effective therapies are lacking. This study investigates the cardioprotective effects of eupatilin (EUP), a bioactive flavonoid derived from Artemisia argyi, and reveals a previously unrecognized mechanism involving selective modulation of KAT5 mediated histone H3K27 lactylation (H3K27la). Using an LPS induced murine model and TNF-α stimulated human AC16 cardiomyocytes, we evaluated cardiac function, inflammatory responses, and apoptotic pathways through dose response analyses. Multi omics approaches including RNA seq, metabolomics, ChIP seq, and molecular docking were integrated to dissect the pharmacodynamic profile of EUP. EUP conferred concentration dependent cardioprotection with optimal effects at 25 μM. Compared with conventional glucocorticoid therapy, EUP showed enhanced target selectivity, markedly reducing pro inflammatory cytokines such as TNF-α, IL-1β, and IL-6 while improving cardiac function parameters including ejection fraction and fractional shortening. Mechanistically, EUP bound KAT5 with high affinity, suppressed its lactylation activity, and reduced H3K27la enrichment at the promoters of inflammatory genes. Metabolic flux analysis further indicated that EUP inhibited glycolytic lactate production and restored oxidative phosphorylation. Together, these findings identify EUP as a natural modulator of the KAT5-H3K27la axis, addressing both metabolic dysregulation and epigenetic reprogramming in SIMI. With a favorable pharmacokinetic profile and superior target specificity relative to standard immunosuppressive regimens, EUP holds promise for clinical translation in sepsis associated cardiac dysfunction.

Mitochondria are central to cellular homeostasis and play a critical role in aging and age-related disorders, making them promising therapeutical targets. Here, we identify terbinafine and miglustat as novel mitochondrial stress inducers that extend lifespan and improve healthspan in Caenorhabditis elegans. Through a two-step screening, we found that both compounds activate the mitochondrial stress response (MSR) and exhibit distinct mechanisms of action. Terbinafine and miglustat robustly activated the mitochondrial unfolded protein response (UPRmt) mediator ATFS-1, upregulated MSR pathways, and modulated mitochondrial function across species, similarly to doxycycline. Interestingly, both compounds also engaged the insulin/IGF-1 signaling (IIS) pathway in C. elegans, revealing an integrated stress response involving coordinated action of ATFS-1 and the FOXO transcription factor DAF-16, distinct from canonical IIS activation. Experiments in human HEK293T cells confirmed the translational potential, with both compounds inducing mitochondrial stress and modulating mitochondrial function in mammalian systems. This study highlights the potential of harnessing the MSR to promote longevity and mitigate age-related functional decline. The identification of terbinafine and miglustat as mitochondrial stressors paves the way for novel anti-aging therapies.

Triple-negative breast cancer (TNBC) is known for its more aggressive clinical behavior, poor prognosis, and distinctive patterns of metastasis. Neoadjuvant chemotherapy (NAC) can influence both tumor cells and the tumor microenvironment. Emerging evidence highlights the critical role of actin cytoskeletal dynamics in cancer progression.

Heart failure (HF) represents the terminal stage of various cardiovascular diseases, and its prevalence continues to rise while current therapeutic approaches remain insufficient to reverse disease progression. Epigenetic regulation, with a particular focus on histone methylation, has gained increasing attention for its involvement in the initiation and advancement of HF. Histone methylation is a reversible post-translational modification controlled by histone methyltransferases and demethylases, and it participates in essential biological processes such as gene expression regulation, cell cycle, apoptosis, and metabolic reprogramming. This review systematically summarizes the multifaceted roles of histone methylation in HF, including the specific functions in cardiac regeneration, hypertrophy, fibrosis, apoptosis, metabolic remodeling, and inflammation. The review also highlights the promising effects of inhibitors that target histone methylation enzymes in animal studies, including anti-hypertrophic, anti-fibrotic, and cardioprotective properties, suggesting significant potential for clinical translation.

Malignant melanoma is the most aggressive and lethal type of skin cancer associated with increased mortality rates. Moreover, beyond the genetic background, the altered epigenetic landscape (e.g., abnormal patterns of DNA methylation, aberrant histone modifications and de-regulated expression levels of ncRNAs) further contributes to the pathophysiology of the disease. In addition, despite the improvement of current anti-melanoma strategies and the development of new therapeutic approaches, the 5-year survival among melanoma patients is still high, mainly due to acquired-drug resistance. On the other hand, phytochemicals have been associated with various health-promoting properties through pleiotropic mechanisms including acting as potent epigenetic regulators restoring back a normal phenotype in various experimental cancer models. In this review article, we discuss the general characteristics of malignant melanoma and current therapeutic approaches while we report the epigenetic basis of the disease along with the main compounds capable of restoring a normal epigenetic landscape. Finally, we describe the role of various phytochemicals in targeting the epigenome of malignant melanoma thereby potentially acting as an alternative therapeutic approach.

Nanoparticles offer promising applications in agriculture due to their unique physicochemical properties. This study investigated selenium nanoparticles (SeNPs) as a rooting agent to improve rice tolerance to low phosphate stress. IR64 rice was grown in media with varying SeNP concentrations (0-25 ppm), and plants were analyzed at 2 and 6 weeks for phenotypic traits, histology, biochemistry, and gene expression. At 2 weeks, 25 ppm SeNPs led to a threefold increase in root length versus untreated controls. Histological analysis revealed increased root perimeter and diameter, along with reduced aerenchyma perimeter. After 6 weeks under phosphate starvation, SeNP-treated plants showed higher phosphate and selenium content in roots and shoots, increased shoot length and weight, and reduced root length, weight, and phenolic content. Gene expression analysis showed that SeNPs upregulated key phosphate deficiency response genes, including OsPAP21, OsPT9, OsSPX, and OsPHR2. The most dramatic change was observed in OsSPX expression, which increased nearly 250-fold in shoots under full phosphate conditions. This is the first study to demonstrate that SeNPs promote root growth, enhance phosphate uptake, and regulate gene expression, suggesting SeNPs may serve as a sustainable strategy to boost phosphate use efficiency in rice cultivation.

Constitutive defense profiles underlie potato resistance to PVX ROTH1 and P. infestans. Treatment with aqueous rosemary extract (ARE) primes susceptible cultivars, enhancing their defense and offering a sustainable strategy to boosts resilience against these major foliar pathogens. Potato (Solanum tuberosum L.) is a major global food crop increasingly threatened by viral and oomycete pathogens, such as potato virus X (PVX) and Phytophthora infestans, whose impact is exacerbated under changing environmental conditions. Although priming strategies offer a sustainable approach to enhance disease resistance, it remains unclear how cultivar-specific metabolic states influence priming efficiency. Infection responses to PVX (strain ROTH1) and a P. infestans isolate were evaluated in four commercial cultivars. Cultivar-dependent differences were observed: Innovator exhibited higher resistance, Kennebec and Spunta greater susceptibility, and Frital-INTA was resistant to PVX ROTH1 but susceptible to P. infestans. 1H NMR metabolomics combined with defense gene expression analysis under non-inoculated conditions revealed distinct cultivar-specific signatures. Resistant and susceptible cultivars segregated into separate clusters, identifying metabolites associated with constitutive defense states. These results indicate that basal metabolic configuration contributes to differential pathogen susceptibility and may influence responsiveness to priming. Spunta, due to its broad cultivation and susceptibility, was selected to assess aqueous rosemary extract (ARE)-mediated priming. ARE treatment reduced PVX ROTH1 accumulation by ~ 70% and decreased P. infestans lesion size by ~ 30%, demonstrating that it enhances potato immunity by integrating both constitutive and inducible defense mechanisms.