The serine/threonine kinase, TOR (target of rapamycin), exists in two complexes, namely TORC1 (with either Tor1 or Tor2 kinase) and TORC2 (that contains Tor2, but not Tor1), and its pharmacological inhibition by rapamycin impairs the PIC (pre-initiation complex) formation at the ribosomal protein genes (and hence transcription and ribosome biogenesis). However, TOR's involvement in such gene regulation has not been elucidated genetically at the level of Tor1, Tor2, TORC1 or TORC2. Here, we demonstrate that null mutation of and short-term depletion of its expression do not affect the PIC formation (and transcription) at the ribosomal protein genes. Likewise, PIC formation and transcription are not altered in TORC2-specific -tsA conditional mutant or following short-term depletion of expression. These results support the dispensability of TORC2 for ribosomal protein gene expression, and indicate that Tor1 and Tor2 play redundant roles via TORC1 for PIC formation, and hence transcription. In agreement, the mutant in combination with both TORC1 and TORC2-specific tsC conditional mutation impairs PIC formation at the ribosomal protein genes with consequent reduction in transcription. Collectively, our genetic analysis support redundant, yet distinct, functions of Tor1 and Tor2 via TORC1, not TORC2, in regulation of the ribosomal protein gene expression.

The telomerase RNA-protein enzyme is critical for most eukaryotes to complete genome copying by extending chromosome ends, thus solving the end-replication problem and postponing senescence. Despite the importance of the fission yeast to biomedical research, very little is known about the structure of its 1212 nt telomerase RNA. We have determined the secondary structure of this large RNA, TER1, based on phylogenetics and bioinformatic modeling, as well as genetic and biochemical analyses. We find several conserved regions of the rapidly evolving TER1 RNA are important to maintain telomeres, based on testing truncation mutants , whereas many other large regions are dispensable. This is similar to budding yeast telomerase RNA, and consistent with functioning as a flexible scaffold for the RNP. We tested if the essential three-way junction works from other locations in TER1, finding that it can, supporting that it is flexibly scaffolded. Furthermore, we find that a half-sized Mini-TER1 allele, built from the catalytic core and the three-way junction, reconstitutes catalytic activity with TERT . Overall, we provide a secondary structure model for the large fission-yeast telomerase lncRNA, based on phylogenetics and molecular-genetic testing in cells, and insight into the RNP's physical and functional organization.

Crohn's disease (CD) is an inflammatory gastrointestinal disorder marked by impaired autophagy due to inefficient bacterial uptake. We studied the effects of autophagy modulation using Tat-beclin-1 and carbamazepine (CBZ) on dendritic cells (DCs) and Paneth cell functionality in pediatric CD patients. Twenty CD children genotyped for the ATG16L1 rs2241880 polymorphism and 10 healthy controls were enrolled. DCs were incubated with fluorochrome-conjugated particles of or DQ-ovalbumin after pretreatment with CBZ or Tat-beclin-1 to evaluate antigen processing. Treated DCs were stained for P62, LAMP1, and LC3, and analyzed by confocal microscopy. Paneth cells from biopsies were pretreated with both drugs, stained for lysozyme, and analyzed by transmission electron microscopy. Antigen processing increased after Tat-beclin-1 and CBZ treatment in all groups. DCs expressed higher activation markers HLA-DR and CD86+, notably in high-risk patients, who also showed increased DQ-OVA processing. The number of lysozymes in Paneth cells from controls did not change after Tat-beclin-1 treatment, while in the CD group, it decreased significantly, suggesting increased exocytosis. CBZ treatment increased secretory granules only in CD inflamed tissue. Our results indicate that CBZ and Tat-beclin-1 enhance autophagic flux, representing a novel approach to treating pediatric CD patients.

Coffee is one of the most widely consumed beverages in the world and is a rich source of caffeine, a methylxanthine. Here we show that exposure to caffeine significantly reduces ionizing radiation (IR) induced DNA breaks and resulted in no or minimal G2/M arrest within the human cell, in contrast to IR alone. At the molecular level, we demonstrate that when naked plasmid DNA or oligomeric DNA was irradiated, the number of breaks was significantly less in the presence of caffeine. The observed radioprotection was irrespective of its sequence and was due to quenching of ROS by caffeine. Besides, caffeine treatment in NOS2 knockout (KO) mice exhibited a significantly enhanced survival compared to the corresponding WT mice post-irradiation. The transcriptome analysis revealed the upregulation of the key antioxidant genes (Gpx3, Gpx7, Gpx4, Idh1, etc.) involved in playing a role in ROS homeostasis in caffeine-treated mice following exposure to IR, which was further upregulated in the NOS2 KO mice. The increase in lifespan after whole-body irradiation in mice pretreated with caffeine demonstrates the potential of caffeine-mediated radioprotection and provides compelling evidence that caffeine mitigates the detrimental effects of ionizing radiation by reducing ROS and RNS levels and enhancing the expression of antioxidant genes.

Cholesterol trafficking from the endoplasmic reticulum (ER) through the mitochondria-associated ER membrane (MAM) and finally to mitochondria is essential for mammalian survival. ER lipid raft-associated protein 2 (ERLIN2) scaffolds raft-like microdomains in the trans-Golgi network, endosomes, and plasma membrane. We found that ERLIN2 assists in rolling cholesterol trafficking-associated lipid vesicles by facilitating the intermediate folding of cholesterol trafficker steroidogenic acute regulatory protein (StAR) from the ER to MAM prior to delivery to the outer mitochondrial membrane. Each ERLIN2-StAR interaction is short. The absence of ERLIN2 ablates mitochondrial cholesterol transport. Over time, StAR association with ERLIN2 increases from the ER to MAM, thereby enhancing mitochondrial cholesterol transport. Thus, ERLIN2 is central for regulating mitochondrial cholesterol trafficking required for mitochondrial steroid metabolism.

Since its discovery several decades ago, the proteasome has been recognized as one of the most complex and highly evolved proteolytic systems. Through the selective and rapid degradation of ubiquitinated proteins, it plays a pivotal role in maintaining cellular proteostasis and governing essential biological processes such as cell cycle regulation and signal transduction. Recent advances in cryo-electron microscopy (cryo-EM), together with developments in mass spectrometry and large-scale genetic screening, have provided unprecedented insights into proteasome biology. These approaches have not only revealed the proteasome as a precisely engineered molecular machine optimized for substrate specificity and efficient degradation, but have also facilitated the identification of previously unrecognized regulatory factors and post-translational modifications that fine-tune its activity. Moreover, accumulating evidence has demonstrated that proteasome capacity is tightly regulated at multiple levels, including transcriptional control, assembly dynamics, and subcellular localization, to meet diverse cellular demands and preserve proteostasis. Importantly, dysregulation of these processes is linked to human diseases, underscoring the proteasome's central role in cellular physiology and its promise as a therapeutic target. Ongoing research is uncovering new regulatory layers and structural complexities, highlighting the proteasome's indispensable and versatile role in health and disease.

Ulcerative colitis (UC) is a clinically common idiopathic inflammatory bowel disease. The DSS-induced colitis model was induced via 5% DSS for 7 days. Rats were gavaged with QLJCN solution in different concentrations. This study measured body weight, colon length, and DAI of rats in each group. The hematoxylin-eosin staining assessed the histopathology and histological score. Western blot analysis examined the expressions of TFF3, MUC-2, JAK2/STAT3 pathway-, and TLR4/NF-κB pathway-related markers. Moreover, the contents of IL-6, TNF-α, and LPS in the colons/serum were determined by ELISA. TLR4 activator (RS09) or JAK2/STAT3 activator (colivelin) were employed for the rescue experiments. QLJCN repressed weight loss and the increase of DAI score in DSS rats. QLJCN also increased the colon length and alleviated colonic damage, and effectively repressed the levels of IL-6 and TNF-α but elevated the levels of TFF3 and MUC-2 in the colons/serum of DSS rats. Moreover, QLJCN weakened the activation of JAK2/STAT3 and TLR4/NF-κB pathways, and alleviated the intestinal inflammation. Furthermore, these ameliorative effects of QLJCN were reversed by TLR4 activator (RS09) or JAK2/STAT3 activator (colivelin). QLJCN has protective effects on DSS-induced colitis rats by restraining JAK2/STAT3 and TLR4/NF-κB pathways. This study provides new therapeutic strategies for UC.

Pancreatic ductal adenocarcinoma (PDAC) remains largely refractory to therapy, due in part to the complex interplay between tumor cells and their microenvironment. Human antigen R (HuR/ELAVL1), a ubiquitously expressed RNA-binding protein, is emerging as an important regulator both of tumor-intrinsic and tumor-extrinsic pathways that govern PDAC progression. While the role of HuR in promoting cancer cell survival under stress is well established, recent studies reveal its broader role in shaping the tumor microenvironment (TME), including metabolic rewiring, stromal activation, angiogenesis, and immune modulation. In this review, we examine how tumor-intrinsic HuR drives epithelial-mesenchymal transition, stabilizes key transcripts involved in metabolic adaptation, and alters the tumor secretome to influence extracellular matrix deposition and fibroblast behavior. We further explore the role of HuR in regulating immune cell function and the immune landscape of PDAC. Notably, HuR-driven TME remodeling reinforces environmental stressors that further activate HuR, establishing a feed-forward loop that drives disease progression. These findings underscore HuR as a central regulator of the PDAC TME and therapeutic resistance, and thus, highlight its potential as a target in PDAC.

Mitochondria rely on the coordinated function of over 1000 proteins, most of which are nuclear-encoded, synthesized in the cytosol, and imported into distinct mitochondrial sub-compartments. Thirteen additional proteins are synthesized within the organelle itself, forming core components of the oxidative phosphorylation (OXPHOS) system. Once inside, mitochondrial precursors undergo precise maturation, folding, and assembly, supported by specialized factors that ensure their function. These processes are safeguarded by an intricate network of chaperones, proteases, and disaggregases that maintain proteome integrity. Protein biogenesis and quality control are deeply interconnected, operating continuously to preserve mitochondrial function. Disruption at any stage, whether in import, folding, assembly, or degradation, can lead to proteotoxic stress and mitochondrial dysfunction, underlying a wide spectrum of mitochondrial diseases. Despite progress in characterizing many of these pathways in human cells, large gaps in knowledge remain. A complete understanding of protein biogenesis and surveillance mechanisms is essential to uncover how their dysregulation drives disease. This knowledge will be foundational for interpreting pathogenic mutations, predicting disease mechanisms, and ultimately guiding therapeutic strategies aimed at restoring mitochondrial proteostasis and health.

p53 is a key tumor suppressor, and mutations in the p53 gene occur in more than half of all human cancers. p53, which is under tight and complex regulation in cells, functions primarily as a transcription factor regulating genes involved in many cellular processes, including cell cycle arrest, apoptosis, senescence, ferroptosis, and metabolism, thereby maintaining genomic integrity and preventing tumorigenesis. While the cell-intrinsic functions of p53, which contribute to its tumor-suppressive activity, have been extensively studied, it is now clear that p53 also plays an important role in immune regulation, a connection first observed when p53 was identified as a cellular protein interacting with viral antigens. Growing evidence shows that p53 modulates both innate and adaptive immunity by regulating cytokine production, antigen presentation, and the functions of immune cells, thereby contributing to host defense against infections, inflammatory responses, and antitumor immunity. In this review, we summarize and discuss the multifaceted roles of p53 and its signaling in regulating immune functions and their implications in human diseases, particularly cancer. A better understanding of the immune-related functions of p53 is crucial for advancing cancer treatment and broadening insights into immunity and disease.

N6-methyladenosine (m6A), the most prevalent modification in mRNAs, influences mRNA stability, splicing, and translation. Dysregulation of m6A patterns has been linked to various diseases, including cancer, highlighting its significance in cellular homeostasis. However, accurate detection and precise quantification of m6A sites within individual transcripts remains challenging. In this study, we employed nanopore sequencing to achieve transcriptome-wide, base-resolution map of the m6A methylome in human breast cancer cells. By investigating m6A distribution across breast cancer cell lines and implementing a CRISPR/Cas9-based knockout of the major m6A eraser ALKBH5, we provide insights into the differential methylation levels and motif-specific characteristics of m6A transcriptomic sites. We elucidated the m6A epitranscriptome in five well-established breast cancer cell lines derived from distinct molecular subtypes of the disease and confirmed a DRACH-dependent activity of ALKBH5. Comparative methylation analysis with the non-cancerous MCF-10A cell line revealed that MCF-7 and BT-474 breast cancer cells are primarily hypomethylated, while BT-20, MDA-MB-231 and SK-BR-3 cells show widespread hypermethylation. These cell line-based patterns highlight the potential regulatory role of m6A in breast cancer heterogeneity. Overall, our findings enhance the understanding of m6A dynamics in breast cancer.

The concentration of cellular labile pool of copper must be strictly regulated because disruption in copper homeostasis results in diseases. In , elevated levels of labile copper impair cell viability by inhibiting Sec61-mediated protein translocation into the endoplasmic reticulum. We investigated how metabolic pathways, specifically mitochondrial respiration and autophagy, contribute to copper homeostasis and the translocation of secretory proteins. We show that copper selectively inhibits protein translocation in yeast cells grown in minimal medium but not in a rich medium, highlighting a critical role of nutrients in modulating copper toxicity. Supplementation of specific amino acids suppresses the copper-induced defects in protein translocation and cell death, identifying amino acids as suppressors of the copper toxicity. Using a panel of gene deletion mutants affecting mitochondrial functions, autophagy, peroxisomes, and lipid droplets, we demonstrate that metabolic pathways regulate subcellular concentration of copper and translocation of secretory proteins. Further, disruption of redox and pH homeostasis, and pharmacological inhibition of respiration, reveals that correct subcellular concentration of copper is essential to prevent inhibitory effects on protein translocation. Together, our findings provide mechanistic insights into how metabolic status influences cellular copper homeostasis and the secretory pathway of proteins, with broader implications for understanding diseases of copper metabolism.

Over the past few decades, liver disease has emerged as one of the leading causes of death worldwide. Liver injury is frequently associated with infections, alcohol consumption, or obesity, which trigger hepatic inflammation and ultimately lead to progressive fibrosis and carcinoma. Although various cell populations contribute to inflammatory and fibrogenic processes in the liver, macrophages serve as a pivotal mediator. Hepatic macrophages exhibit substantial heterogeneity and perform diverse functions that depend on the pathological microenvironment. The immune response gene 1 (IRG1), a critical metabolic regulatory gene, encodes the mitochondrial enzyme aconitate decarboxylase 1 (ACOD1), which influences macrophage functional polarization by promoting the synthesis of itaconate, a metabolite produced via a side pathway of the tricarboxylic acid (TCA) cycle. Increasing evidence indicates that itaconate and its derivatives exert immunomodulatory effects in processes such as oxidative stress, viral infection, inflammation, tumorigenesis, and wound healing, thereby demonstrating significant potential for treating liver disorders. In this review, we summarize the roles of itaconate and its derivatives in liver diseases and their underlying mechanisms, thereby providing insights into the therapeutic potential of targeting macrophages.

Topoisomerase I (Top1) alleviates DNA supercoiling during replication and transcription, but its catalytic cycle can be hijacked by chemotherapeutic agents such as camptothecin (CPT), stabilizing Top1-DNA covalent complexes (Top1cc) that threaten genome integrity. Efficient resolution of these trapped intermediates is crucial to prevent replication stress, DNA breaks, and cell death. Poly (ADP-ribose) polymerase 1 (PARP1) is a key sensor of Top1cc, facilitating repair by recruiting tyrosyl-DNA phosphodiesterase 1 (TDP1) and modifying chromatin to promote lesion accessibility. Beyond this canonical pathway, emerging evidence highlights PARP1-independent mechanisms such as endo nucleolytic cleavage, proteolytic degradation of Top1 and replication-associated processing. Intriguingly, PARP1 appears to act as a molecular switch between TDP1 and the endonuclease pathway for the repair of Top1cc. This review highlights mechanisms of PARP1-dependent and -independent Top1cc repair pathways, their interplay and redundancy, and how their targeting can enhance Top1-based cancer therapies and overcome resistance.

Chromatin remodelers are important for maintaining chromatin structure and regulating gene expression. In this study, we investigated the roles of histone acetyltransferases (HATs) Gcn5 and Esa1 in regulating RSC and histone occupancy on chromatin, as well as their impact on transcription across the genome. Our findings reveal distinct effects of HATs on RSC occupancy in promoters and ORFs. The lack of HATs leads to the accumulation of RSC, and it was greater in nucleosome-depleted regions (NDRs) containing fragile nucleosomes (FNs), relative to other NDRs. The increased RSC NDR-binding was greater in Esa1-deficient cells than in those lacking Gcn5. The increased RSC binding was not seen in cells lacking the H3 or H4 tails. The mutants also led to significant increases in histone occupancies around the NDRs genome-wide. Overall, the data suggest that hypoacetylated tails may recruit RSC to NDRs, especially to FN-containing NDRs, and that subsequent histone acetylation enhances histone eviction. The HAT mutants also exhibited reduced recruitment of TBP and Pol II. In contrast to the promoters, RSC occupancies were significantly reduced in transcribed ORFs in the HAT mutants. Thus, our data implicate HATs and RSC in maintaining NDRs, regulating chromatin structure, and promoting transcription.

DNA methylation inhibitors are widely used in treating myeloid malignancies, yet their precise effects on chromatin organization and nuclear architecture remain incompletely understood. Here, the integrated molecular, cellular, and biophysical approaches to investigate the impact of azacitidine (AZA) and decitabine (DEC) on chromatin structure and nuclear mechanics in AML-007 leukemia cells are presented. Confocal microscopy revealed drug-induced alterations in nuclear morphology and actin cytoskeleton organization, with DEC inducing significant nuclear enlargement and disorganization at lower concentrations (1.0 µM) compared to AZA (5.0 µM). Chromatin condensation assays demonstrated that DEC increased chromatin accessibility in a concentration-dependent manner, while AZA produced subtler effects. Optical tweezers measurements showed both agents reduced nuclear stiffness, with DEC exerting a greater impact. Spectroscopic analysis confirmed differential drug incorporation into DNA, with higher methylation loss and structural changes observed following DEC treatment. Refractive index mapping revealed chromatin decompaction, aligning with increased accessibility and nuclear softening. These findings demonstrate that DNA hypomethylating agents exert distinct, concentration-dependent effects on nuclear organization and chromatin structure, which can be quantified through molecular and biophysical readouts. This study underscores the value of integrative methods for revealing epigenetic drug effects on chromatin architecture in leukemia cells.

Mammalian cell membranes contain ether lipids, which include an alkyl chain derived from a fatty alcohol that is produced by fatty acyl-CoA reductases (FARs). There are two mammalian FAR genes, and , and mutations in cause the peroxisomal fatty acyl-CoA reductase 1 disorder (PFCRD), which is accompanied by various symptoms, including neurological disorders. To date, the contributions of and to brain ether lipid production and the molecular mechanism of PFCRD have remained unknown. To investigate these, we analyzed knockout (KO) mice of and . In the brain, the expression levels of were higher than those of , and was widely expressed. Lipidomic analyses showed that the quantity of ether lipids ethanolamine-plasmalogens was reduced in KO mice, with a complementary increase in diacyl-type phosphatidylethanolamines, but not in KO mice. Electron microscope analysis of the corpus callosum revealed reductions in the percentage of myelinated axons and myelin thickness in KO mice relative to WT mice. In conclusion, FAR1 is the major FAR isozyme involved in ether lipid synthesis in the brain, and its deficiency causes hypomyelination. We speculate that this hypomyelination is one of the causes of the neurological symptoms of PFCRD.

Lactate, historically considered a metabolic byproduct, has emerged as a key regulator of muscle physiology and metabolism. This study explores its potential as an exercise mimetic to counteract disuse muscle atrophy (DMA) in aging skeletal muscle using a hindlimb suspension model in senescence-accelerated prone 8 (SAMP8) mice. The mice were divided into four groups: Control, lactate-treated control, hindlimb suspension, and hindlimb suspension with lactate intervention. Lactate administration preserved gastrocnemius muscle mass, restored muscle strength, and attenuated oxidative fiber atrophy. Electrophoretic and histological analyses showed increased MyHC I expression, indicating protection of oxidative fibers. Functional assessments revealed improved muscle endurance and contractile force, while metabolomic profiling identified changes in energy metabolism, amino acid metabolism, and protein synthesis pathways. Specifically, lactate improved impaired branched-chain amino acid metabolism, suggesting enhanced protein synthesis. In addition, lactate boosted Cori cycle activity, upregulated hepatic lactate transporters, and increased lactate dehydrogenase B activity, facilitating efficient lactate metabolism and gluconeogenesis. These results provide new insights into the role of lactate as a metabolic regulator and highlight its potential as a therapeutic intervention to combat exercise-induced muscle wasting and preserve muscle function in aging and immobilized individuals.

CTCF is a multifunctional protein that mediates long-range -DNA interactions in mammalian genomes. Chromatin architecture governs spatial and functional interactions of gene regulatory elements at various loci and is impacted by the ability of CTCF to restrict cohesin complex dependent chromatin extrusion. In addition, at antigen receptor loci, long-range interactions facilitate spatial proximity of gene segments for VDJ recombination that generates functional genes encoding immunoglobulins and T-cell receptors in developing lymphocytes. To investigate the role of CTCF in VDJ recombination, we mutated CTCF binding sites (CBS) of murine locus. Our analysis revealed that CBS interspersed in the domain encompassing variable gene segments (Vb) are not redundant. They exhibit independent but additive effects on dynamic chromatin organization leading to distinct VDJ recombination profiles in CBS mutants depending on positions of mutated CBS relative to Vb segments. Further, inversion of a single CBS drastically altered the chromatin loop organization and VDJ recombination profile. Our results demonstrate the critical importance of chromatin extrusion for generation of chromatin loops for VDJ recombination and underscore its dynamic impediment by CTCF binding at specific points within Vb segment domain to be essential to diversify the usage of Vb segments for VDJ recombination at locus.

COPD is characterized by airway epithelial barrier dysfunction. We hypothesized that downregulation of E-cadherin results in abnormal responses to cigarette smoke extract (CSE) with impaired repair and increased pro-inflammatory activity. We used CRISPR-Cas9-engineered 16HBE cells with 1-2 copies of the gene encoding E-cadherin ( or ) to study effects on tight junctional protein zonula occludens (ZO-1), CSE-induced epithelial barrier dysfunction using electric cell-substrate impedance sensing and pro-inflammatory cytokine production. In airway epithelial cells (AECs) from nine COPD stage IV transplant lungs and tracheobronchial tissue of nine non-COPD donors, we assessed E-cadherin, ZO-1 and pro-inflammatory cytokines. Lower electrical resistance in 16HBE cells was accompanied by ZO-1 delocalization. CSE exposure induced transient barrier dysfunction, from which cells recovered more slowly than cells. Similarly, cells showed a delayed repair response upon wounding, while gene expression and secretion of pro-inflammatory cytokines were higher in unexposed cells (CXCL8, IL-1α) and/or showed a stronger CSE-induced increase (IL-1α, GM-CSF). AECs from COPD patients displayed lower E-cadherin and TJP1 levels and higher CSE-induced expression compared to control. Downregulation of E-cadherin resulted in disrupted ZO-1 expression, aggravated CSE-induced barrier dysfunction, impaired recovery from injury and a more pro-inflammatory epithelial phenotype in 16HBE cells.