Noncanonical expression mechanisms in orthoflaviviruses.

Noncanonical processing by animal Microprocessor

Response of human natural killer (NK) cell populations (NKP) against tumors in the presence of viruses was evaluated as a quite variable, early adapting for the pathological signals in organism, mobile and selective combination agents. NKP act as a result of co-functioning between the receptor lectins (RL) recognizing glycopatterns (RL as triggers, initiators and basic agents for coupled activities), and Ig-like, cytotoxic and other additional communicative and effector receptors (superstructural, tuning for achievement of final effector-type NKP constructions required), and their ligands (modulators of final cell surface receptor mosaics). Such NKP created play important role in redistribution of NKP-induced antitumor/ antiviral cytokines in organism. Intercellular communicative potential of NKP also involves other innate and innate-like cells. Such extended communications of NKP provide a prospective and universal resource of human protection. NKP must be under consideration upon development of new maneuvre and relilable prophylactic and immunotherapeutic antitumor/ antiviral systems and vaccine strategies. The ways for the fine tuning (RL—KIR/ NCR/ CD/ their combinations) algorithms of RL-based creation of antitumor/ antiviral NKP are revealed. Key role is given to screening spectrum of patient NKP for development of communicative anticancer/ antiviral strategies. The status of NK compartment will characterize resistance of individuum/ contingent of individuums to viral infections of epidemiological significance, will play important role in anti-epidemic protection of regional population.

During the integrated stress response (ISR), global translation initiation is attenuated; however, noncanonical mechanisms allow for the continued translation of specific transcripts. Eukaryotic initiation factor 5B (eIF5B) has been shown to play a critical role in canonical translation as well as in noncanonical mechanisms involving internal ribosome entry site (IRES) and upstream open reading frame (uORF) elements. The uORF-mediated translation regulation of activating transcription factor 4 (ATF4) mRNA plays a pivotal role in the cellular ISR. Our recent study confirmed that eIF5B depletion removes uORF2-mediated repression of ATF4 translation, which results in the upregulation of growth arrest and DNA damage-inducible protein 34 (GADD34) transcription. Accordingly, we hypothesized that eIF5B depletion may reprogram the transcriptome profile of the cell. Here, we employed genome-wide transcriptional analysis on eIF5B-depleted cells. Further, we validate the up- and downregulation of several transcripts from our RNA-seq data using RT-qPCR. We identified upregulated pathways including cellular response to endoplasmic reticulum (ER) stress, and mucin-type O-glycan biosynthesis, as well as downregulated pathways of transcriptional misregulation in cancer and T cell receptor signaling. We also confirm that depletion of eIF5B leads to activation of the c-Jun N-terminal kinase (JNK) arm of the mitogen-activated protein kinase (MAPK) pathway. This data suggests that depletion of eIF5B reprograms the cellular transcriptome and influences critical cellular processes such as ER stress and ISR.

A variety of cellular stresses lead to global translation attenuation due to phosphorylation of the alpha subunit of eukaryotic initiation factor 2 (eIF2), which decreases the availability of the eIF2-GTP-Met-tRNAi ternary complex. However, a subset of mRNAs continues to be translated by non-canonical mechanisms under these conditions. In fact, although translation initiation of activating transcription factor 4 (ATF4) is normally repressed by an upstream open reading frame (uORF), a decreased availability of ternary complex leads to increased translation of the main ATF4-coding ORF. We show here that siRNA-mediated depletion of eIF5B—which can substitute for eIF2 in delivering Met-tRNAi—leads to increased levels of ATF4 protein in mammalian cells. This de-repression is not due to phosphorylation of eIF2α under conditions of eIF5B depletion. Although eIF5B depletion leads to a modest increase in the steady-state levels of ATF4 mRNA, we show by polysome profiling that the depletion of eIF5B enhances ATF4 expression primarily at the level of translation. Moreover, eIF5B silencing increases the expression of an ATF4-luciferase translational reporter by a mechanism requiring the repressive uORF2. Further experiments suggest that eIF5B cooperates with eIF1A and eIF5, but not eIF2A, to facilitate the uORF2-mediated repression of ATF4 translation.

Viruses are obligate, intracellular parasites that co-opt host cell machineries for propagation. Critical among these machineries are those that translate RNA into protein and their mechanisms of control. Most regulatory mechanisms effectuate their activity by targeting sequence or structural features at the RNA termini, i.e., at the 5′ or 3′ ends, including the untranslated regions (UTRs). Translation of most eukaryotic mRNAs is initiated by 5′ cap-dependent scanning. In contrast, many viruses initiate translation at internal RNA regions at internal ribosome entry sites (IRESs). Eukaryotic mRNAs often contain upstream open reading frames (uORFs) that permit condition-dependent control of downstream major ORFs. To offset genome compression and increase coding capacity, some viruses take advantage of out-of-frame overlapping uORFs (oORFs). Lacking the essential machinery of protein synthesis, for example, ribosomes and other translation factors, all viruses utilize the host apparatus to generate virus protein. In addition, some viruses exhibit RNA elements that bind host regulatory factors that are not essential components of the translation machinery. SARS-CoV-2 is a paradigm example of a virus taking advantage of multiple features of eukaryotic host translation control: the virus mimics the established human GAIT regulatory element and co-opts four host aminoacyl tRNA synthetases to form a stimulatory binding complex. Utilizing discontinuous transcription, the elements are present and identical in all SARS-CoV-2 subgenomic RNAs (and the genomic RNA). Thus, the virus exhibits a post-transcriptional regulon that improves upon analogous eukaryotic regulons, in which a family of functionally related mRNA targets contain elements that are structurally similar but lacking sequence identity. This “thrifty” virus strategy can be exploited against the virus since targeting the element can suppress the expression of all subgenomic RNAs as well as the genomic RNA. Other 3′ end viral elements include 3′-cap-independent translation elements (3′-CITEs) and 3′-tRNA-like structures. Elucidation of virus translation control elements, their binding proteins, and their mechanisms can lead to novel therapeutic approaches to reduce virus replication and pathogenicity.

In retroviruses and the double-stranded RNA totiviruses, the efficiency of programmed -1 ribosomal frameshifting is critical for ensuring the proper ratios of upstream-encoded capsid proteins to downstream-encoded replicase enzymes. The genomic organizations of many other frameshifting viruses, including the coronaviruses, are very different, in that their upstream open reading frames encode nonstructural proteins, the frameshift-dependent downstream open reading frames encode enzymes involved in transcription and replication, and their structural proteins are encoded by subgenomic mRNAs. The biological significance of frameshifting efficiency and how the relative ratios of proteins encoded by the upstream and downstream open reading frames affect virus propagation has not been explored before. Here, three different strategies were employed to test the hypothesis that the -1 PRF signals of coronaviruses have evolved to produce the correct ratios of upstream- to downstream-encoded proteins. Specifically, infectious clones of the severe acute respiratory syndrome (SARS)-associated coronavirus harboring mutations that lower frameshift efficiency decreased infectivity by >4 orders of magnitude. Second, a series of frameshift-promoting mRNA pseudoknot mutants was employed to demonstrate that the frameshift signals of the SARS-associated coronavirus and mouse hepatitis virus have evolved to promote optimal frameshift efficiencies. Finally, we show that a previously described frameshift attenuator element does not actually affect frameshifting per se but rather serves to limit the fraction of ribosomes available for frameshifting. The findings of these analyses all support a "golden mean" model in which viruses use both programmed ribosomal frameshifting and translational attenuation to control the relative ratios of their encoded proteins.

Dosage compensation equalizes gene expression in a single male X chromosome with that in the pairs of autosomes and female X chromosomes. In the fruit fly Drosophila, canonical dosage compensation is implemented by the male-specific lethal (MSL) complex functioning in all male somatic cells. This complex contains acetyl transferase males absent on the first (MOF), which performs H4K16 hyperacetylation specifically in the male X chromosome, thus facilitating transcription of the X-linked genes. However, accumulating evidence points to an existence of additional, non-canonical dosage compensation mechanisms operating in somatic and germline cells. In this review, we discuss current advances in the understanding of both canonical and non-canonical mechanisms of dosage compensation in Drosophila.

Schizophrenia is a severe psychiatric illness affecting almost 25 million people worldwide and is conceptualized as a disorder of synaptic plasticity and brain connectivity. Antipsychotics are the primary pharmacological treatment after more than sixty years after their introduction in therapy. Two findings hold true for all presently available antipsychotics. First, all antipsychotics occupy the dopamine D2 receptor (D2R) as an antagonist or partial agonist, even if with different affinity; second, D2R occupancy is the necessary and probably the sufficient mechanism for antipsychotic effect despite the complexity of antipsychotics' receptor profile. D2R occupancy is followed by coincident or divergent intracellular mechanisms, implying the contribution of cAMP regulation, β-arrestin recruitment, and phospholipase A activation, to quote some of the mechanisms considered canonical. However, in recent years, novel mechanisms related to dopamine function beyond or together with D2R occupancy have emerged. Among these potentially non-canonical mechanisms, the role of Na2+ channels at the dopamine at the presynaptic site, dopamine transporter (DAT) involvement as the main regulator of dopamine concentration at synaptic clefts, and the putative role of antipsychotics as chaperones for intracellular D2R sequestration, should be included. These mechanisms expand the fundamental role of dopamine in schizophrenia therapy and may have relevance to considering putatively new strategies for treatment-resistant schizophrenia (TRS), an extremely severe condition epidemiologically relevant and affecting almost 30% of schizophrenia patients. Here, we performed a critical evaluation of the role of antipsychotics in synaptic plasticity, focusing on their canonical and non-canonical mechanisms of action relevant to the treatment of schizophrenia and their subsequent implication for the pathophysiology and potential therapy of TRS.

The chicken TH1 response: Potential therapeutic applications of ChIFN-γ

The eukaryotic initiation factor 4G2 (eIF4G2, DAP5, Nat1, p97) was discovered in 1997. Over the past two decades, dozens of papers have presented contradictory data on eIF4G2 function. Since its identification, eIF4G2 has been assumed to participate in noncanonical translation initiation mechanisms, but recent results indicate that it can be involved in scanning as well. In particular, eIF4G2 provides leaky scanning through some upstream open reading frames (uORFs), which are typical for long 5' UTRs of mRNAs from higher eukaryotes. It is likely the protein can also help the ribosome overcome other impediments during scanning of the 5' UTRs of animal mRNAs. This may explain the need for eIF4G2 in higher eukaryotes, as many mRNAs that encode regulatory proteins have rather long and highly structured 5' UTRs. Additionally, they often bind to various proteins, which also hamper the movement of scanning ribosomes. This review discusses the suggested mechanisms of eIF4G2 action, denotes obscure or inconsistent results, and proposes ways to uncover other fundamental mechanisms in which this important protein factor may be involved in higher eukaryotes.

Simian immunodeficiency virus from Rhesus macaques (SIVmac) is a primate lentivirus that exhibits extensive similarities with human immunodeficiency viruses (HIVs) in morphology, genome organization and biological properties. Like HIV, SIV is dependent on the host cellular machinery for transcription, translation and protein production. Alternative RNA splicing generates many mRNAs that allow the expression of all viral proteins. Consistent with the idea that translation occurs predominantly via a cap-dependent scanning mechanism, one usually does not find AUGs upstream of the open reading frames (ORFs) in HIV and SIV. In SIVmac239, the envelope (Env) glycoprotein is translated from a 4 kb mRNA that also contains the upstream ORF (uORF) for Rev. It is currently accepted that the level of Env expression is dependent on leaky scanning due to suboptimal translation initiation at the upstream Rev AUG. Interestingly, another potential start codon is present immediately upstream of the Rev-AUG. We also identified an alternative Rev-Env mRNA that has in fact four upstream AUGs, raising questions about the regulation of Rev and Env translation. We constructed subgenomic Rev-Env reporter mRNAs to analyze how the different upstream AUGs affect protein expression. Our results indicate that the virus uses these unique upstream AUG codons to modulate the level of translation of the Rev and Env proteins.

Multiple sclerosis (MS)-Epstein-Barr virus (EBV) relation is similar to doing a complicated puzzle: it consists of many pieces that become more and more clear as the issue is viewed from different sides. Based on the research findings, there is powerful evidence that EBV and MS have a strong relation where high levels of EBV DNA are able to be shown in all the spinal cord and the blood of the MS patients, but these are shown during disease relapses, and this implies a role in these illnesses. It kind of narrows the choices that you have to look for, just like how gathering evidence can lead to finding the missing person. In the analysis, new ways of EBV participation in MS progression are expected to be installed, and even new therapeutics are expected to be made. A comprehensive literature search of PubMed was conducted until November 2023 to identify studies investigating the association between Epstein-Barr virus (EBV) infection and multiple sclerosis (MS). Only articles that met stringent criteria, including validation of EBV infection through laboratory testing, were included in the analysis. A total of 16 articles were identified as applicable for the background review, and this conformed with the discovery that the initiation of EBV/IM was consistent across various studies, namely, retrospective, cross-sectional, or prospective. The statistics reveal a glimpse into the need for prolonged research in studying the pattern of this link between EBV and MS. Novel treatment approaches targeting EBV, including adoptive T-cell therapy and gene-based immunotherapy, show promise in mitigating MS progression by targeting EBV-infected cells. Clinical trials investigating antiviral therapies and vaccination strategies are underway, aiming to translate these findings into effective treatments for MS. Despite promising advances, challenges remain in developing EBV-targeted therapies for MS, including safety concerns and the multifactorial nature of MS pathogenesis. Advance treatment options that focus on EBV, such as adoptive T-cell therapy and gene-based immunotherapy, are shown to be effective in the improvement of MS management that targets the viral-infected cell. The clinical trials for antiviral drugs and vaccination tactics are going on to benefit from these findings and eventually to invent effective therapeutics for MS. While these new therapeutic directions may offer great promise, challenges remain in these approaches as safety concerns and complex factors that underlie MS pathology need to be taken care of. The ethical aspects linked to picking the patients and giving informed consent make the progress of EBV-related treatments are even more difficult. Future research is recommended so that the primary mechanisms through which EBV contributes to MS development will be elucidated; in addition, the main MS subtype sources must be addressed. Longitudinal studies and other advanced research technologies will provide hope because they can solve the complicated problems of MS due to viruses and look for new therapeutic targets. The review brings up EBV/IM disease as a vital aspect of MS susceptibility, encouraging research in the field of longitudinal studies. Although we have made advances, we are still far from clear on the labyrinthine pairing between EBV and MS and the development of therapeutic strategies to attack EBV infection in MS patients.

Health economics in decision making for influenza management

Estrogen receptor positive (ER+) breast cancer (BC) represents nearly 50% of all BC brain metastasis (BCBM) but remains understudied. Most ER+ BCBMs occur in postmenopausal women due to age or prior endocrine therapies, yet most in vivo ER+ BC models are estrogen (E2)-dependent and studied in young hosts. Thus, the mechanisms underlying metastatic progression in the aged/E2-depleted brain tumor microenvironment (TME) remain unknown. FGFR1-amplification (amp), a well-known driver of ER+ BC endocrine therapy resistance, was the only genomic alteration associated with increased risk of late recurrence in post-menopausal women with ER+ early BC on aromatase inhibitors, and FGFR aberrations are significantly higher in BCBM patients compared to non-BM in metastatic BC. While FGFRamp is often associated with auto-activation, TME-dependent activation of FGFR1 has emerged as an important mechanism modulating its activity. Here, we tested the hypothesis that canonical and non-canonical activation of FGFR1 by astrocytes and neurons promotes FGFR1-dependent ER+ BCBM in E2-high/young and E2-low/aged hosts. Intracardiac injection of ER+ PDX-derived cell lines showed higher BM incidence in FGFR1amp lines, and brain colonization was E2-dependent in young mice and E2-independent in aged hosts. FGFR1 knockdown (KD) did not alter 2D proliferation but decreased their growth in organotypic brain slices and their ability to colonize the brain in E2-high/young and E2-low/aged mice. Spatial transcriptomics of ER+ BCBMs and surrounding glial cells showed that while late-stage ER+ BCBMs are transcriptionally similar, aging and E2-depletion reduced FGF2 expression and FGF/FGFR signaling in surrounding glial cells, suggesting that TME-mediated paracrine activation of FGFR1 may be distinct in young and aged hosts. Since astrocytes were the main FGF2 source in the brain, we tested how changes in their FGF2 levels impact ER+ BC growth. Young astrocytes more effectively activated FGFR1 in ER+ BC cells than aged astrocytes and promoted FGFR1-dependent proliferation and mammosphere initiation of ER+ cells, suggesting that paracrine FGF2-driven FGFR1 activation contributes to ER+ BCBM growth in young hosts, but less in aged hosts. In the absence of FGF2, NCAM1, a cell adhesion molecule expressed in the surface of neurons and astrocytes, activates FGFR1 and contributes to neural development and synaptic plasticity. We found that like neurons, NCAM1 activated FGFR1 kinase activity and downstream signaling in ER+ BC, and induced differential expression of neuronal gene signatures including neural cell adhesion. FGFR1 KD decreased ER+ BC cell migration along neurites in co-culture with primary neurons and decreased the formation of synaptic puncta. NCAM1 KD in neuron-like SH-SY5Y neuroblastoma cells decreased migration of FGFR1amp ER+ BC cells, suggesting that FGFR1/NCAM1 facilitates interaction of ER+ BC cells with neurons and contributes to early BCBM colonization. Surprisingly, FGFR1 phosphorylation was higher in young versus aged mice at early stages of brain colonization but absent in all late-stage ER+ BCBMs, suggesting that paracrine activation of FGFR1 and interactions with neurons and astrocytes are critical for early BM colonization. Consistently, an FDA-approved FGFR inhibitor blocked ER+ BCBM when administered from early stages of BM colonization in young mice but did not block metastatic progression at late stages or in aged mice, suggesting limited efficacy of FGFR inhibitors to block non-kinase-dependent FGFR1 functions in vivo. Together, these studies suggest a novel mechanism whereby canonical and non-canonical activation of FGFR1 promote brain metastatic colonization of ER+ BC in young and aged/E2-depleted hosts, and caution that FGFR1 inhibition may only be effective to prevent but not to treat BMs. Citation Format: M. S. Fox, J. A. Jaramillo-Gómez, R. Marquez Ortiz, K. Alvarez-Eraso, M. J. Contreras-Zárate, S. Koliavas, P. Kabos, N. J. Serkova, C. A. Sartorius, E. A. Wellberg, D. M. Cittelly. Fgfr1 promotes brain metastases of er+ breast cancer through canonical and non-canonical mechanisms in young and aged hosts [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2025; 2025 Dec 9-12; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2026;32(4 Suppl):Abstract nr PS1-11-25.

The emergence of the COVID-19 JN.1 variant has raised global health concerns as it gains prevalence in several regions worldwide. First identified in August 2023, JN.1 evolved from the Omicron lineage's BA.2.86 subvariant. Patients infected with JN.1 commonly exhibit symptoms such as sore throat, fever, dry cough, nausea, and vomiting. While the World Health Organization has labeled JN.1 a Variant of Interest, it currently presents a low global health risk. However, its increased transmissibility, particularly in cold, dry climates, is concerning. This review provides a comprehensive overview of JN.1's biological characteristics, epidemiology, transmissibility, immune evasion, and the efficacy of existing antiviral treatments and vaccination strategies. A literature search across key databases targeted studies from January 2023 to August 2024, emphasizing recent insights into JN.1's spread and clinical impact. Findings reveal that JN.1 exhibits higher infectivity and immune evasion than previous variants, largely due to the L4555 mutation. From November 2023 to March 2024, JN.1 showed an increasing trend in transmission. Previously approved antivirals, including Paxlovid, Veklury, and Lagevrio, demonstrate effectiveness against JN.1, and current vaccines still protect against severe illness from this variant. However, vaccination rates remain low. Monitoring efforts include genomic assessments, wastewater surveillance, and digital tracking to contain the variant's spread. It is essential to encourage the public to maintain vaccination and preventive measures to reduce JN.1's impact. Continued research is critical for understanding and managing the evolving landscape of COVID-19 and its emerging variants.