eIF3d: A driver of noncanonical cap-dependent translation of specific mRNAs and a trigger of biological/pathological processes

Single-nuclei transcriptome analysis of IgM+ cells isolated from channel catfish (Ictalurus punctatus) spleen

Catfish production is the primary aquaculture sector in the United States, and the key cultured species is channel catfish (Ictalurus punctatus). The major causes of production losses are pathogenic diseases, and the spleen, an important site of adaptive immunity, is implicated in these diseases. To examine the channel catfish immune system, single-nuclei transcriptomes of sorted and captured IgM+ cells were produced from adult channel catfish. Three channel catfish (~1 kg) were euthanized, the spleen dissected, and the tissue dissociated. The lymphocytes were isolated using a Ficoll gradient and IgM+ cells were then sorted with flow cytometry. The IgM+ cells were lysed and single-nuclei libraries generated using a Chromium Next GEM Single Cell 3' GEM Kit and the Chromium X Instrument (10x Genomics) and sequenced with the Illumina NovaSeq X Plus sequencer. The reads were aligned to the I. punctatus reference assembly (Coco_2.0) using Cell Ranger, and normalization, cluster analysis, and differential gene expression analysis were carried out with Seurat. Across the three samples, approximately 753.5 million reads were generated for 18,686 cells. After filtering, 10,637 cells remained for the cluster analysis. The cluster analysis identified 16 clusters which were classified as B cells (10,276), natural killer-like (NK-like) cells (178), T cells or natural killer cells (45), hematopoietic stem and progenitor cells (HSPC)/megakaryocytes (MK) (66), myeloid/epithelial cells (40), and plasma cells (32). The B cell clusters were further defined as different populations of mature B cells, cycling B cells, and plasma cells. The plasma cells highly expressed ighm and we demonstrated that the secreted form of the transcript was largely being expressed by these cells. This atlas provides insight into the gene expression of IgM+ immune cells in channel catfish. The atlas is publicly available and could be used garner more important information regarding the gene expression of splenic immune cells.

Signals from the niche promote distinct modes of translation initiation to control stem cell differentiation and renewal in the Drosophila testis

Stem cells have the unique ability among adult cells to give rise to cells of different identities. To do so, they must change gene expression in response to environmental signals. Much work has focused on how transcription is regulated to achieve these changes; however, in many cell types, transcripts and proteins correlate poorly, indicating that post-transcriptional regulation is important. To assess how translational control can influence stem cell fate, we use the Drosophila testis as a model. The testis niche secretes a ligand to activate the Janus kinase (JAK)/signal transducer and activator of transcription (STAT) pathway in two stem cell populations, germline stem cells (GSCs) and somatic cyst stem cells (CySCs). We find that global translation rates are high in CySCs and decrease during differentiation, and that JAK/STAT signaling regulates translation. To determine how translation was regulated, we knocked down translation initiation factors and found that the cap binding complex, eIF4F, is dispensable in differentiating cells, but is specifically required in CySCs for self-renewal, acting downstream of JAK/STAT activity. Moreover, we identify eIF3d1 as a key regulator of CySC fate, and show that two eIF3d1 residues subject to regulation by phosphorylation are critical to maintain CySC self-renewal. We further show that Casein Kinase II (CkII), which controls eIF3d1 phosphorylation, influences the binding of eIF3d and eIF4F in mammalian cells, and that CkII expression is sufficient to restore CySC function in the absence of JAK/STAT. We propose a model in which niche signals regulate a specific translation programme in which only some mRNAs are translated. The mechanism we identify allows stem cells to switch between modes of translation, adding a layer of regulation on top of transcription and providing cells with the ability to rapidly change gene expression upon receiving external stimuli.

eIF3d and eIF4G2 mediate an alternative mechanism of cap-dependent but eIF4E-independent translation initiation

Initiation of translation for the majority of eukaryotic mRNAs is mediated by a 5' cap structure to which the eukaryotic initiation factor 4E (eIF4E) binds. Inhibition of the activity of eIF4E by 4EBP-1 does not prevent the translation of a number of cellular capped mRNAs, indicative of the existence of previously unexplored mechanisms for the translation of these capped mRNAs without the requirement of eIF4E. eIF4G2, also known as death-associated protein 5 (DAP5), a homolog of eIFGI that lacks the eIF4E binding domain, utilizes eIF3d (a subunit of eIF3) to promote the translation of a subset of these mRNAs. Using fluorescence anisotropy-based equilibrium binding studies, we provide the first quantitative evidence of the recruitment of eIF3d as well as eIF3d and eIFG2 complexes to a subset of human mRNAs. Our quantitative studies demonstrate the critical role a fully methylated 5' mRNA cap structure plays in the recognition and recruitment of eIF3d, as well as the eIF3d and eIFG2 complex. By using luciferase reporter-based in vitro translation assays, we further show that cap-recognition ability correlates with the efficiency of translation of these mRNAs. Essentially, by preferably utilizing eIF3d and eIFG2, specific mRNA subsets are still able to translate in a cap-dependent manner even when eIF4E is sequestered. Our findings offer new insight into the use of eIF3d and eIF4G2 as an alternative for growth and survival under conditions of cellular stress. This novel mechanism of translation may offer new targets for therapeutic regulation of mRNA translation.

Structures of Saccharolobus solfataricus initiation complexes with leaderless mRNAs highlight archaeal features and eukaryotic proximity

The archaeal ribosome is of the eukaryotic type. TACK and Asgard superphyla, the closest relatives of eukaryotes, have ribosomes containing eukaryotic ribosomal proteins not found in other archaea, eS25, eS26 and eS30. Here, we investigate the case of Saccharolobus solfataricus, a TACK crenarchaeon, using mainly leaderless mRNAs. We characterize the small ribosomal subunit of S. solfataricus bound to SD-leadered or leaderless mRNAs. Cryo-EM structures show eS25, eS26 and eS30 bound to the small subunit. We identify two ribosomal proteins, aS33 and aS34, and an additional domain of eS6. Leaderless mRNAs are bound to the small subunit with contribution of their 5'-triphosphate group. Archaeal eS26 binds to the mRNA exit channel wrapped around the 3' end of rRNA, as in eukaryotes. Its position is not compatible with an SD:antiSD duplex. Our results suggest a positive role of eS26 in leaderless mRNAs translation and possible evolutionary routes from archaeal to eukaryotic translation.

Design, synthesis and biological evaluation of plant-derived miliusol derivatives achieve TNBC profound regression in vivo

Triple-negative breast cancer has become a major problem in clinical treatment due to its high heterogeneity, and Plant-derived drug discovery has been the focus of attention for novel anti-tumor therapeutics. In this study, Miliusol, a natural product isolated from the rarely reported plant Miliusa tenuistipitata, was identified as the lead compound, and 25 miliusol derivatives were designed and synthesized under antiproliferative activity guidance. The results revealed that ZMF-24 was demonstrated to have potent anti-TNBC proliferation with IC50 values of 0.22 μM and 0.44 μM in BT-549 cells and MDA-MB-231 cells respectively with low cytotoxicity to MCF10A cells, and could significantly downregulate proliferation and migration markers. Through RNAseq analysis, molecular docking and CETSA experiment, we found that ZMF-24 could inhibit Eukaryotic translation initiation factor 3 subunit D (EIF3D) that further disrupted the energy supply of TNBC by inhibiting glycolysis, induced profound TNBC apoptosis by stimulating persistent ER stress. Importantly, ZMF-24 exhibited remarkable anti-proliferation and anti-metastasis potential in nude mice xenograft TNBC model without obvious toxicity. Collectively, the findings demonstrate ZMF-24 has significant potential as a potent chemotherapy agent against triple-negative breast cancer.

Connecting the dots: Involvement of methyltransferase-like 3, N6-methyladenosine modification, and ferroptosis in the pathogenesis of intracerebral hemorrhage pathogenesis

Intracerebral hemorrhage is a profoundly detrimental acute cerebrovascular condition with a low overall survival rate and a high post-onset disability rate. Secondary brain injury that ensues post-ICH is the primary contributor to fatality and disability. Hence, the mitigation of brain injury during intracerebral hemorrhage progression has emerged as a crucial aspect of clinical management. N6-methyladenosine is the most pervasive, abundant, and conserved internal co-transcriptional modification of eukaryotic ribonucleic acid and is predominantly expressed in the nervous system. Methyltransferase-like 3 is a key regulatory protein that is strongly associated with the development of the nervous system and numerous neurological diseases. Ferroptosis, a form of iron-associated cell death, is a typical manifestation of neuronal apoptosis in neurological diseases and plays an important role in secondary brain damage following intracerebral hemorrhage. Therefore, this review aimed to elucidate the connection between m6A modification (particularly methyltransferase-like 3) and ferroptosis in the context of intracerebral hemorrhage to provide new insights for future intracerebral hemorrhage management approaches.

The Interplay Between the MYC Oncogene and Ribosomal Proteins in Osteosarcoma Onset and Progression: Potential Mechanisms and Indication of Candidate Therapeutic Targets

High-grade osteosarcoma (OS) is the most common primary bone tumor mainly affecting children and young adults. First-line treatment consists of neo-adjuvant chemotherapy with doxorubicin, cisplatin, and methotrexate and surgery. The mean long-term survival rate for localized disease at diagnosis is 65-70%, dropping down to 20% when metastases are present at diagnosis. Therefore, curing OS is a clinical challenge, particularly for patients that do not respond to standard treatments. MYC has frequently been reported to be involved in the pathogenesis of OS and its high expression may be associated with drug resistance and patients' worse prognosis. Moreover, MYC is a master regulator of ribosomal proteins (RPs) synthesis and ribosome biogenesis (RiBi), which is often up-regulated in human tumors. In recent years, RPs have been recognized not only for their traditional role in ribosome assembly but also for their extra-ribosomal functions, many of which are linked to the onset and progression of cancer. In this review we focus on the role and possible interplay of MYC and RPs expression in association with drug resistance and worse prognosis in OS and discuss therapeutic options that target de-regulated MYC, RiBi, or RPs, which are already clinically available or under evaluation in clinical trials.

Harnessing natural inhibitors of protein synthesis for cancer therapy: A comprehensive review

Cancer treatment remains a formidable challenge in modern medicine, necessitating a nuanced understanding of its molecular underpinnings and the identification of novel therapeutic modalities. Among the intricate web of cellular pathways implicated in oncogenesis, protein synthesis has emerged as a fundamental process warranting meticulous investigation. This review elucidates the multifaceted role of protein synthesis pathways in tumor initiation and progression, highlighting the potential of targeting key nodes within these pathways as viable therapeutic strategies. Natural products have long served as a source of bioactive compounds with therapeutic potential owing to their structural diversity and evolutionary honing. Within this framework, we provide a thorough examination of natural inhibitors of protein synthesis as promising candidates for cancer therapy, drawing upon recent advancements and mechanistic insights. By synthesizing current evidence and elucidating key challenges and opportunities, this review aims to galvanize further research into the development of natural product-based anticancer therapeutics, thereby advancing the clinical armamentarium against malignancies.

Non-canonical mRNA translation initiation in cell stress and cancer

The now well described canonical mRNA translation initiation mechanism of m7G 'cap' recognition by cap-binding protein eIF4E and assembly of the canonical pre-initiation complex consisting of scaffolding protein eIF4G and RNA helicase eIF4A has historically been thought to describe all cellular mRNA translation. However, the past decade has seen the discovery of alternative mechanisms to canonical eIF4E mediated mRNA translation initiation. Studies have shown that non-canonical alternate mechanisms of cellular mRNA translation initiation, whether cap-dependent or independent, serve to provide selective translation of mRNAs under cell physiological and pathological stress conditions. These conditions typically involve the global downregulation of canonical eIF4E1/cap-mediated mRNA translation, and selective translational reprogramming of the cell proteome, as occurs in tumor development and malignant progression. Cancer cells must be able to maintain physiological plasticity to acquire a migratory phenotype, invade tissues, metastasize, survive and adapt to severe microenvironmental stress conditions that involve inhibition of canonical mRNA translation initiation. In this review we describe the emerging, important role of non-canonical, alternate mechanisms of mRNA translation initiation in cancer, particularly in adaptation to stresses and the phenotypic cell fate changes involved in malignant progression and metastasis. These alternate translation initiation mechanisms provide new targets for oncology therapeutics development.

To initiate or not to initiate: A critical assessment of eIF2A, eIF2D, and MCT-1·DENR to deliver initiator tRNA to ribosomes

Selection of the correct start codon is critical for high-fidelity protein synthesis. In eukaryotes, this is typically governed by a multitude of initiation factors (eIFs), including eIF2·GTP that directly delivers the initiator tRNA (Met-tRNAi Met ) to the P site of the ribosome. However, numerous reports, some dating back to the early 1970s, have described other initiation factors having high affinity for the initiator tRNA and the ability of delivering it to the ribosome, which has provided a foundation for further work demonstrating non-canonical initiation mechanisms using alternative initiation factors. Here we provide a critical analysis of current understanding of eIF2A, eIF2D, and the MCT-1·DENR dimer, the evidence surrounding their ability to initiate translation, their implications in human disease, and lay out important key questions for the field. This article is categorized under: RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes Translation > Mechanisms Translation > Regulation.

Protein translation: biological processes and therapeutic strategies for human diseases

Protein translation is a tightly regulated cellular process that is essential for gene expression and protein synthesis. The deregulation of this process is increasingly recognized as a critical factor in the pathogenesis of various human diseases. In this review, we discuss how deregulated translation can lead to aberrant protein synthesis, altered cellular functions, and disease progression. We explore the key mechanisms contributing to the deregulation of protein translation, including functional alterations in translation factors, tRNA, mRNA, and ribosome function. Deregulated translation leads to abnormal protein expression, disrupted cellular signaling, and perturbed cellular functions- all of which contribute to disease pathogenesis. The development of ribosome profiling techniques along with mass spectrometry-based proteomics, mRNA sequencing and single-cell approaches have opened new avenues for detecting diseases related to translation errors. Importantly, we highlight recent advances in therapies targeting translation-related disorders and their potential applications in neurodegenerative diseases, cancer, infectious diseases, and cardiovascular diseases. Moreover, the growing interest lies in targeted therapies aimed at restoring precise control over translation in diseased cells is discussed. In conclusion, this comprehensive review underscores the critical role of protein translation in disease and its potential as a therapeutic target. Advancements in understanding the molecular mechanisms of protein translation deregulation, coupled with the development of targeted therapies, offer promising avenues for improving disease outcomes in various human diseases. Additionally, it will unlock doors to the possibility of precision medicine by offering personalized therapies and a deeper understanding of the molecular underpinnings of diseases in the future.

eIF3d controls the persistent integrated stress response

Cells respond to intrinsic and extrinsic stresses by reducing global protein synthesis and activating gene programs necessary for survival. Here, we show that the integrated stress response (ISR) is driven by the non-canonical cap-binding protein eIF3d that acts as a critical effector to control core stress response orchestrators, the translation factor eIF2α and the transcription factor ATF4. We find that during persistent stress, eIF3d activates the translation of the kinase GCN2, inducing eIF2α phosphorylation and inhibiting general protein synthesis. In parallel, eIF3d upregulates the m6A demethylase ALKBH5 to drive 5' UTR-specific demethylation of stress response genes, including ATF4. Ultimately, this cascade converges on ATF4 expression by increasing mRNA engagement of translation machinery and enhancing ribosome bypass of upstream open reading frames (uORFs). Our results reveal that eIF3d acts in a life-or-death decision point during chronic stress and uncover a synergistic signaling mechanism in which translational cascades complement transcriptional amplification to control essential cellular processes.