Search Results (595)

Cancer vaccination addresses four distinct problems: preventing oncogenic infection, intercepting premalignant clones, clearing molecular residual disease, and treating established cancer. This hypothesis framework proposes seven sequential gates for antigen-defined, HLA-restricted T-cell vaccines: tumor specificity, natural peptide–HLA presentation, population coverage, persistence under immune selection, selective T-cell recognition, manufacturability, and randomized clinical benefit. The proposed architecture combines a pre-manufactured core of validated shared antigens with a personalized shell when shared targets do not cover the tumor or the patient’s HLA type. Current evidence supports restraint. Individualized mRNA neoantigen therapy with pembrolizumab produced a recurrence-free-survival signal in a randomized phase 2b melanoma trial, whereas a 20-antigen shared cassette produced immunodominant responses toward encoded TP53 epitopes rather than the KRAS neoantigens carried by the tumors. No quantitative coverage or persistence score is presented because the required population frequencies and persistence measurements cannot be supplied reliably from the published record. Four falsifiable predictions define the experiments needed to test presentation-first selection, antigen persistence, escape-route independence, and biomarker-directed treatment. The framework is therefore a research agenda, not a validated decision tool. Full article

Bovine leukemia virus (BLV), a major cause of B-cell lymphoma in cattle worldwide, has been linked to human breast cancer. Here, we performed comparative whole-transcriptome analysis of single clones of human epithelial 293T, breast cancer MCF7, and cervical cancer HeLa cells, stably infected with BLV, versus uninfected controls using RNA-sequencing technology. Differential expression analysis revealed 2050, 1314, and 2772 differentially expressed genes (DEGs) between BLV-infected 293T, MCF7, and HeLa cells and controls, respectively. Most DEGs were upregulated in BLV-infected 293T (76.5%) and MCF7 (69.1%) cells but downregulated in HeLa cells (62.0%). Functional enrichment analyses revealed enrichment of “Gene expression” and “Membrane Trafficking” pathways across all cell lines, and that of “Apoptosis” and “Axon guidance” pathways uniquely in 293T and MCF7 cells. Twenty genes linked to apoptosis of 293T and MCF7 cells were identified, and expression of 11 of these was confirmed using quantitative real-time PCR. The expression of EFEMP1 and LXN, which showed the greatest fold change, was validated: EFEMP1 knockdown and LXN overexpression inhibited cell proliferation, induced apoptosis, and altered growth morphology of 293T and MCF7 cells. This is the first transcriptome profiling of human cells during BLV latency, which should help understand the behavior of BLV. Full article

Cohen syndrome, caused by pathogenic variants in VPS13B, is characterized by microcephaly, developmental delay, and progressive retinal degeneration, yet the cellular mechanisms linking VPS13B dysfunction to disease pathology remain incompletely understood. Here, we used CRISPR-Cas9 to delete VPS13B exons 2–4 in Phoenix HEK293 cells, generating five independent knockout clones. In all mutant lines, VPS13B disruption caused a marked slowing of cell proliferation due to prolongation of the G1 phase. Immunocytochemistry and transmission electron microscopy revealed that VPS13B mutations causes Golgi apparatus fragmentation, loss of VPS13B Golgi localization, ER lumen dilation with rigid membrane morphology, mitochondrial damage, impaired autophagic maturation, and the appearance of cytoplasmic fibrillary inclusions located close to ER and absent from control cells. RNA-seq analysis identified 27 differentially expressed genes common to all four mutant clones, including downregulation of genes involved in transcriptional regulation, lipid metabolism, and neuronal signaling, alongside upregulation of the stress-response genes CLU and CDKN1A (p21). While our results do not support classical unfolded protein response activation, they are consistent with a model in which lipid bilayer stress and disrupted ER–Golgi trafficking may play a role in the pathophysiology of Cohen syndrome. Together, these findings demonstrate that VPS13B deficiency results in coordinated defects in organelle homeostasis, proteostasis, and cell-cycle progression, providing new dates for understanding Cohen syndrome pathogenesis. Full article

Chronic hepatitis C virus (HCV) infection is an established risk factor for B-cell lymphoproliferative disorders and represents a paradigmatic model of infection-driven lymphomagenesis. Although direct-acting antivirals have markedly reduced the burden of HCV-related disease, HCV-associated lymphomas continue to occur. Moreover, HCV screening remains incomplete in some geographical areas and healthcare settings, leaving a substantial proportion of infected individuals unaware of their status. This narrative review integrates current evidence on the mechanisms linking chronic HCV infection to mixed cryoglobulinemia and overt B-cell non-Hodgkin lymphoma. HCV lymphotropism and persistent antigenic stimulation could initially promote the selection and expansion of autoreactive B-cell clones, while mixed cryoglobulinemia represents the most informative pre-lymphomatous risk condition. Cytokine-mediated survival signals, particularly those involving B-cell activating factor, reinforce clonal persistence and cooperate with host genetic susceptibility, impaired apoptotic control, and activation-induced cytidine deaminase-mediated genomic instability. The progressive acquisition of somatic driver mutations, copy-number alterations, and epigenetic and transcriptomic changes may enable selected clones to escape functional anergy and become increasingly independent of the original viral stimulus that, in turn, represents an initial trigger of the lymphoproliferative process. Recurrent abnormalities converge on NF-κB, NOTCH, chromatin-regulatory, apoptotic, and cell-cycle pathways, although HCV-associated lymphomas remain molecularly heterogeneous. Emerging microRNA profiles further contribute to the molecular characterization of the transition from chronic infection and cryoglobulinemia to lymphoma. Despite the availability of highly effective antiviral therapies, HCV-associated lymphomagenesis remains clinically relevant and continues to provide an especially informative model for understanding how chronic viral infection can drive human cancer development. Full article

Philadelphia-negative (Ph-negative) myeloproliferative neoplasms (MPNs) include polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF), which are clonal hematopoietic disorders caused by somatic gene mutations in the JAK2, CALR, or MPL genes. Mutations activate the JAK–STAT pathway and disrupt NF-κB signaling, leading to a chronic inflammatory state caused by pro-inflammatory cytokines and reactive oxygen species (ROS). This altered microenvironment causes serious clinical features of the disease, such as bone marrow fibrosis, splenomegaly, vascular niche remodeling, and a greater probability of thrombosis or secondary leukemic transformation. Concurrently, MPNs cause both severe immune dysregulation and tumor evasion, as evidenced by progressive lymphopenia, T and B cell exhaustion, Natural Killer cell maturation arrest, and the accumulation of myeloid-derived suppressor cells. Although FDA-approved JAK1/JAK2 inhibitors ruxolitinib, fedratinib pacritinib and momelotinib effectively reduce splenomegaly and symptom burden and have demonstrated survival benefits in clinical trials, their ability to eliminate malignant clones or induce durable disease modification remains limited, and disease progression continues to occur in most patients. Finally, this review assesses the complex immunological dysfunction and chronic inflammatory dysregulation that characterize Ph-negative MPNs, as well as emerging therapeutic strategies, emphasizing the importance of fully understanding these intricate microenvironmental mechanisms for the identification and development of novel precision treatment targets. Full article

Microalgae are a rich source of bioactive metabolites, including unsaturated fatty acids, chlorophylls, carotenoids, and phenolic compounds with antioxidant and nutraceutical potential. Salicylic acid (SA) and its volatile ester, methyl salicylate (MS), are well-known elicitors of secondary metabolism in higher plants, yet their mechanisms of action in green microalgae, particularly the effects of MS, remain poorly understood. Therefore, we evaluated how salicylates applied at concentrations of 0.1, 1, and 10 µM affect the growth and accumulation of bioactive compounds in a high-productivity clone of Planktochlorella nurekis, combining gas chromatography coupled mass spectrometry (GC-MS) fatty acid profiling with spectrophotometric determination of pigment levels, total phenols, and L-phenylalanine ammonia-lyase (PAL) activity. SA increased cell number and size, whereas 0.1 µM MS resulted in a six-fold gain in cell number. Accordingly, 10 µM MS raised chlorophyll b levels—nearly three-fold (from 76 to 211 µg per g D.W.)—and total carotenoids—roughly four-fold (129 to 520 µg per g D.W.)—while both elicitors significantly increased the monounsaturated fatty acid fraction (from 29% to about 40%). Notably, 10 µM SA lowered the levels of saturated fatty acids. Moreover, 10 µM MS doubled the PAL activity and increased the total phenols by 17% compared to the control. Thus, SA and MS act as effective elicitors of high-value metabolites in P. nurekis. Full article

Spike density is an important component of wheat spike architecture and is determined by the combined effects of spike-axis elongation and spikelet number. In this study, we characterized an ethyl methanesulfonate (EMS)-induced recessive dense-spike mutant, ds, which was obtained from EMS mutagenesis of the wheat cultivar YN21 in 2013 and displays a field-visible compact spike architecture associated with a shortened spike axis, reduced spike internode spacing, and increased spikelet number. Genetic analysis showed that all F₁ plants exhibited normal spikes and that segregation in the F₂ population fitted a 3:1 ratio, supporting control by a single recessive nuclear gene. Through genome-wide marker-based linkage screening, enlarged-population validation, and fine mapping, ds was delimited to an approximately 864.819 kb interval between ID2B2796 and ID2B7615 on chromosome 2B. This interval contains 11 high-confidence annotated genes, including F-box protein, actin, ubiquitin-conjugating enzyme, ribosomal protein L16, RecX, plant cysteine oxidase, PI4KIIγ, and two adjacent GA3OX-family-related genes. Integrated RNA-seq and RT-qPCR analyses showed that the two adjacent GA3OX-family-related genes were expressed in young spikes and exhibited reduced expression in ds-sib relative to WT-sib. These expression data support their retention as plausible, non-exclusive candidates but do not establish causality. Transcriptome analysis further revealed changes in hormone-related pathways, cell-wall organization, carbohydrate metabolism, and transcription-factor regulation. These results provide a reliable genetic basis for further molecular cloning of ds and suggest that altered hormone- and growth-related transcriptional responses may be associated with dense-spike formation in wheat. Full article

Parvovirus infection causes severe diseases in both feline and canine species. It primarily affects adult cats and dogs but poses a higher risk to kittens and puppies. This virus is highly contagious and is easily transmitted through contaminated food, shared shelter environments, as well as the hands and clothing of people. The recovered species may continue to shed parvovirus in their feces for an extended period, leading to severe environmental contamination. There is no universal vaccine available that protects dogs and cats against parvovirus infections. The main goal of this study is to design a pan-parvovirus multiepitope-based vaccine that could be administered to dogs and cats. We utilized AI-machine learning-incorporated server tools such as IEDB and NetMHCpan to predict B-cell and T-cell epitopes. VaxiJen and ToxinPred were used to analyze immune characteristic features and docking with feline alleles using the HADDOCK server. Following this, the immune response and stability of the vaccine construct were confirmed with disulfide engineering, normal mode analysis, and molecular docking performed with toll-like receptors of both feline and canine (TLR4 and TLR5), and molecular dynamics simulation was performed for 10 ns. The triggered immune response was determined with immuno-simulation (ImmSim), and their activity in a biological environment was reinforced with in silico cloning. The B-cell epitopes (NS1-9, NS2-4, VP1-12 and VP2-9) predicted with the IEDB database were subjected to antigenicity prediction. MHC class I and IFN prediction and MHC class II and IL-4 prediction were performed with IEDB and NetMHCpan. The T-cell epitopes showed high binding affinities with the feline alleles. The final vaccine was designed by combining the top-ranked B-cell epitopes and T-cell epitopes, filtered for high antigenicity, non-allergic, non-toxic, and good solubility, and with the better binding affinity score of the structural and non-structural proteins (NS1, NS2, VP1, and VP2) of feline and canine parvoviruses through linkers and adjuvants. The disulfide bond prediction and normal mode analysis showed that our vaccine construct is stable and flexible. The molecular docking analysis was performed between the designed vaccine epitopes and the TLRs (TLR4–feline and TLR5–canine) with Biovia Discovery Studio using Zdock; it showed better binding interactions with a value of 22.26 (Zdock score), −47.409 (Zrank score) for feline and 16.54 (Zdock score), −134.295 (Zrank score) for canine. A pan-multi-epitope-based vaccine based on the two structural and non-structural proteins (NS1, NS2, VP1, and VP2) was designed and constructed to provide dual protection against parvovirus in both feline and canine species. The molecular docking and molecular dynamics simulation analysis showed higher binding affinities and stable conformations with canine (TLR5) and feline (TLR4) toll-like receptors. Although computational analysis supports the prediction of top-ranked epitopes and their immunogenic properties with greater precision, further experimental validation is required before they can be used against these viruses. Full article

Gastric mucosa-associated lymphoid tissue (MALT) lymphoma, also known clinically as gastric MALT lymphoma (GML) or MALToma, is an indolent B-cell neoplasm strongly associated with chronic Helicobacter pylori (H. pylori) infection. While early-stage disease is based on persistent antigenic stimulation and chronic inflammation, the metabolic and molecular transitions that drive monoclonal B-cell autonomy remain poorly understood. Importantly, H. pylori maintain this long-term colonization by defusing the host’s innate immunity; specifically, its lipid A portion features unique elongated acyl chains, composed of 16–18 carbon atoms, that fail to bind to and activate host TLR4/MD2 receptors, resulting in exceptionally weak endotoxic potency. Persistent colonization relies on key oncoproteins, particularly cytotoxin-associated gene A (CagA) and vacuolar cytotoxin A (VacA), which orchestrate early inflammatory infiltration (neutrophils, Th1, Th2 and Th17 cells) before shifting the microenvironment toward a suppressive regulatory T cell (Treg) phenotype. In this study, we propose a new critical step in the oncogenesis of gastric metastasis: chronic mitochondrial and immunometabolic adaptation within the gastric microenvironment. We claim that H. pylori act not only as a trigger for infection but also as a chronic driver of mitochondrial adaptation to oxidative stress and hypoxia, which subsequently results in defective mitophagy. CagA- and VacA-mediated mitochondrial damage induces reactive oxygen species (ROS) and functional hypoxia, stabilizing HIF-1α to force a glycolytic metabolic shift, while incomplete mitophagy rescues metabolically altered, apoptosis-resistant clones to drive monoclonal B-cell expansion. Within this ecological-microenvironmental framework, the predominantly cytoplasmic sequestration of BCL10 and the NF-κB subunit p65 observed in GML is reinterpreted not as evidence of signaling inactivity, but as a dynamically regulated adaptive state. This configuration is orchestrated by mitochondrial stress responses that enable adaptation to the chronic microenvironmental pressures imposed by H. pylori, acting in concert with the metabolic programs governed by MYC, NRF2, and BCL2. Overall, this review outlines the multi-step pathogenesis of H. pylori-mediated GML, highlighting how mitochondrial dysfunction and metabolic remodeling drive the transition from chronic infection to malignant transformation. Full article

Refractory celiac disease (RCeD) is a rare but severe complication of celiac disease characterized by persistent or recurrent malabsorptive symptoms and villous atrophy despite a strict gluten-free diet, after exclusion of ongoing gluten exposure, alternative enteropathies, and overt lymphoma. RCeD comprises two biologically distinct entities. RCeD-I is associated with phenotypically normal, polyclonal intraepithelial lymphocytes and generally reflects persistent gluten-independent mucosal inflammation with a relatively favorable prognosis. RCeD-II is defined by expansion of aberrant clonal intraepithelial lymphocytes lacking normal surface T-cell markers and is increasingly regarded as a low-grade intraepithelial lymphoma or in situ lymphomatous disorder, with substantial risk of progression to enteropathy-associated T-cell lymphoma (EATL). Mechanistic studies identify epithelial stress, IL-15-driven IEL survival, stromal and innate immune amplification, and cytotoxic epithelial injury as central drivers of refractory mucosal damage. In RCeD-II, aberrant IELs acquire a hybrid T/NK-like phenotype, persist through anti-apoptotic IL-15/JAK–STAT signaling, and induce enterocyte killing, while molecular alterations involving JAK1, STAT3, JAK/STAT regulators, NF-κB signaling, epigenetic regulators, and chromosomal abnormalities support stepwise lymphomagenesis. Recent single-cell multiomic studies further reveal genetically altered intestinal lymphocyte clones and intratumoral heterogeneity across the RCeD-II–EATL continuum. From a nutritional immunology perspective, RCeD illustrates a setting in which removal of the initiating dietary antigen is insufficient to restore mucosal immune homeostasis. This review summarizes the pathogenic processes that distinguish RCeD-I from RCeD-II and link failed mucosal recovery after gluten withdrawal to persistent immune-mediated epithelial injury, aberrant IEL expansion, clonal evolution, and lymphoma progression. Full article

Multiple myeloma (MM) is a genetically and clinically heterogeneous plasma cell malignancy characterised by clonal expansion of differentiated B cells within the bone marrow (BM). Patients start with monoclonal gammopathy of undetermined significance (MGUS) and progress to an intermediate stage called smouldering multiple myeloma (SMM), characterised by several genetic alterations that represent the genomic backbone of the malignant clone. Immune checkpoint pathways play a central role in shaping an immunosuppressive BM niche, contributing to T-cell dysfunction, immune evasion, and therapeutic resistance. Key inhibitory receptors such as PD-1, CTLA-4, TIM-3, LAG-3, and CD47 are frequently dysregulated, promoting T-cell exhaustion, anergy, and senescence. Emerging evidence highlights extracellular vesicles (EVs) as critical mediators of intercellular communication in MM. MM-derived EVs carry bioactive cargo, including proteins and miRNAs, that reprogram immune and stromal cells, enhancing tumour progression and immune escape. Notably, EV-associated immune checkpoint molecules contribute to the establishment of a permissive microenvironment. This review provides an integrated overview of immune checkpoint dysregulation and EV-mediated immunomodulation in MM, emphasising their role in disease pathogenesis and progression. Furthermore, we discuss the therapeutic potential of targeting immune checkpoints and exploiting EVs as novel biomarkers and drug delivery systems, highlighting their promise for improving precision medicine approaches in MM. Full article

Resistance to combined BRAF and MEK inhibition remains a major barrier to durable disease control in BRAF-mutant melanoma. Acyclic retinoid (ACR; peretinoin) is a clinically studied retinoid, but its activity in MAPK inhibitor-resistant melanoma remains incompletely defined. Here, we established A375P-derived dabrafenib plus trametinib-resistant clones and evaluated ACR mainly in the A375PDTR-D clone as an in vitro proof-of-concept model. Resistant clones retained higher viability and failed to suppress ERK phosphorylation under dabrafenib plus trametinib treatment. In A375PDTR-D cells, ACR reduced short-term viability and clonogenic growth and was associated with decreased STAT3 Tyr705 phosphorylation, reduced EGFR, Cyclin D1, and Cyclin B1 expression, and increased p27KIP1. ACR did not detectably suppress AKT, MEK/ERK, or basal JNK phosphorylation under the tested conditions. These findings support further investigation of ACR as a candidate non-MAPK adjunct strategy; however, generalizability to broader melanoma models, formal drug-interaction status, direct cell-cycle/apoptosis effects, clinically achievable exposure, and in vivo efficacy remain to be established. Full article

Prostate cancer (PCa) is the most common cancer and the second leading cause of cancer death in American men. Most patients with metastatic disease respond initially to androgen deprivation therapy (ADT) but almost inevitably progress to castration-resistant prostate cancer (CRPC). Identification of markers and drivers of Metastatic CRPC (mCRPC) that (a) represent a progenitor-type cancer cell population, (b) persist in castration-resistant disease, (c) are actionable targets expressed on the cell surface, and (d) are induced by hypoxia is required to facilitate the development of novel targeted therapies. We identified prostatic acid phosphatase (PAP), particularly the transmembrane form (TMPAP), as one such potential target. PAP is both a phosphatase and a 5′ectonucleotidase that generates adenosine. PAP is a human tumor marker first described in 1936 and is still used as an important prognostic marker for advanced metastatic prostate cancer. Our group recently reported that the transmembrane form of the protein (TMPAP) is expressed in CRPC and can serve as a potential therapeutic target. We identified a lead human anti-TMPAP antibody clone 3D8 (3D8-Ab). 3D8-ADCs (Antibody Drug Conjugates) and 3D8-Ab were tested for their ability to reduce tumor size/volume in a xenograft model. The human PAP-expressing PCa cell line VCaP, originally derived from a vertebral metastasis from a patient with CRPC, was inoculated subcutaneously into SCID mice. Treatment with either 3D8-Ab or 3D8-ADC significantly reduced tumor size and increased animal survival. These data indicate that targeting PAP with monoclonal antibodies either alone or conjugated to toxins has the potential to treat CRPC. Full article

The inherent genomic plasticity of RNA viruses, particularly influenza viruses and SARS-CoV-2, poses a major obstacle to the establishment of durable herd immunity. This challenge is further compounded by immune imprinting, whereby prior antigenic exposures bias subsequent responses toward previously encountered epitopes at the expense of effective recognition of antigenically drifted variants. In this review, we delineate the mechanistic basis of immune imprinting, with emphasis on the competitive dominance of cross-reactive memory B cells (MBCs). We discuss how the rapid “back-boosting” of these pre-existing clones can limit de novo priming of naïve B cells—through epitope masking and competition for antigen and T follicular helper cell support—thereby diverting germinal center selection and affinity maturation away from variant-specific de novo epitopes and promoting viral immune escape. To address this challenge, this article further reviews the characteristics of immune imprinting responses in influenza viruses, coronaviruses, and dengue virus, as well as corresponding countermeasures, providing a theoretical basis and new avenues for intervention to address immune imprinting induced by rapidly mutating RNA viruses. Full article

Interferon (IFN)-resistant cell clones 3Cl8 and 3γR8, isolated from wild-type Friend erythroleukemia cells 745A were characterized to identify the resistance defect. The 3Cl8 cell clone is resistant to type I IFNs and sensitive to type II IFN, whereas 3γR8, derived from 3Cl8, is resistant to both type I and II IFNs. Here, we report that no activation of the JAK-STAT pathway is detected after IFN treatment of resistant cells. Interestingly, the absence of major transcripts of the IFNAR2 receptor chain has been observed in type I IFN-resistant cells, and a point mutation relative to the IFNGR2 receptor chain (β chain) has been identified in type II IFN-resistant cells, inducing a frameshift leading to premature termination of translation. In addition, we have identified a new polymorphism of the murine IFNAR1 chain and possibly the presence of a murine IFNAR2b transmembrane, non-transducing chain in 745A cells, similar to that observed in humans and differing from previous reports on other murine systems. Full article