A translational program that suppresses metabolism to shield the genome

Inhibition of protein translation under matrix-deprivation stress in breast cancer cells

Matrix-deprivation stress leads to cell-death by anoikis, whereas overcoming anoikis is critical for cancer metastasis. Work from our lab and others has identified a crucial role for the cellular energy sensor AMPK in anoikis-resistance, highlighting a key role for metabolic reprogramming in stress survival. Protein synthesis is a major energy-consuming process that is tightly regulated under stress. Although an increase in protein synthesis in AMPK-depleted experimentally-transformed MEFs has been associated with anoikis, the status and regulation of protein translation in epithelial-origin cancer cells facing matrix-detachment remains largely unknown. Our study shows that protein translation is mechanistically abrogated at both initiation and elongation stages by the activation of the unfolded protein response (UPR) pathway and inactivation of elongation factor eEF2, respectively. Additionally, we show inhibition of the mTORC1 pathway known for regulation of canonical protein synthesis. We further functionally assay this inhibition using SUnSET assay, which demonstrates repression of global protein synthesis in MDA-MB-231 and MCF7 breast cancer cells when subjected to matrix-deprivation. In order to gauge the translational status of matrix-deprived cancer cells, we undertook polysome profiling. Our data revealed reduced but continuous mRNA translation under matrix-deprivation stress. An integrated analysis of transcriptomic and proteomic data further identifies novel targets that may aid cellular adaptations to matrix-deprivation stress and can be explored for therapeutic intervention.

MATRIX platform to analyze translation machinery remodeling in glioblastoma cells

Here, we present a protocol using MATRIX (mass spectrometry analysis of active translation factors using ribosome density fractionation and isotopic labeling experiments) platform to investigate changes of the protein synthesis machinery in U87MG glioblastoma cells in response to the rocaglate silvestrol. This protocol describes steps to perform SILAC (stable isotope labeling by amino acids in cell culture), ribosome density fractionation, protein isolation, and mass spectrometry analysis. This approach can be applied to study any adaptive remodeling of protein synthesis machineries. For complete details on the use and execution of this protocol, please refer to Ho et al. (2021).¹.

Global analyses of mRNA expression in human sensory neurons reveal eIF5A as a conserved target for inflammatory pain

Nociceptors are a type of sensory neuron that are integral to most forms of pain. Targeted disruption of nociceptor sensitization affords unique opportunities to prevent pain. An emerging model for nociceptors are sensory neurons derived from human stem cells. Here, we subjected five groups to high-throughput sequencing: human induced pluripotent stem cells (hiPSCs) prior to differentiation, mature hiPSC-derived sensory neurons, mature co-cultures containing hiPSC-derived astrocytes and sensory neurons, mouse dorsal root ganglion (DRG) tissues, and mouse DRG cultures. Co-culture of nociceptors and astrocytes promotes expression of transcripts enriched in DRG tissues. Comparisons of the hiPSC models to tissue samples reveal that many key transcripts linked to pain are present. Markers indicative of a range of neuronal subtypes present in the DRG were detected in mature hiPSCs. Intriguingly, translation factors were maintained at consistently high expression levels across species and culture systems. As a proof of concept for the utility of this resource, we validated expression of eukaryotic initiation factor 5A (eIF5A) in DRG tissues and hiPSC samples. eIF5A is subject to a unique posttranslational hypusine modification required for its activity. Inhibition of hypusine biosynthesis prevented hyperalgesic priming by inflammatory mediators in vivo and diminished hiPSC activity in vitro. Collectively, our results illuminate the transcriptomes of hiPSC sensory neuron models. We provide a demonstration for this resource through our investigation of eIF5A. Our findings reveal hypusine as a potential target for inflammation associated pain in males.

Difluoromethylornithine (DFMO) Enhances the Cytotoxicity of PARP Inhibition in Ovarian Cancer Cells

Ovarian cancer accounts for 3% of the total cancers in women, yet it is the fifth leading cause of cancer deaths among women. The BRCA1/2 germline and somatic mutations confer a deficiency of the homologous recombination (HR) repair pathway. Inhibitors of poly (ADP-ribose) polymerase (PARP), another important component of DNA damage repair, are somewhat effective in BRCA1/2 mutant tumors. However, ovarian cancers often reacquire functional BRCA and develop resistance to PARP inhibitors. Polyamines have been reported to facilitate the DNA damage repair functions of PARP. Given the elevated levels of polyamines in tumors, we hypothesized that treatment with the polyamine synthesis inhibitor, α-difluoromethylornithine (DFMO), may enhance ovarian tumor sensitivity to the PARP inhibitor, rucaparib. In HR-competent ovarian cancer cell lines with varying sensitivities to rucaparib, we show that co-treatment with DFMO increases the sensitivity of ovarian cancer cells to rucaparib. Immunofluorescence assays demonstrated that, in the presence of hydrogen peroxide-induced DNA damage, DFMO strongly inhibits PARylation, increases DNA damage accumulation, and reduces cell viability in both HR-competent and deficient cell lines. In vitro viability assays show that DFMO and rucaparib cotreatment significantly enhances the cytotoxicity of the chemotherapeutic agent, cisplatin. These results suggest that DFMO may be a useful adjunct chemotherapeutic to improve the anti-tumor efficacy of PARP inhibitors in treating ovarian cancer.

DNA origami-based protein manipulation systems: From function regulation to biological application

Proteins directly participate in tremendous physiological processes and mediate a variety of cellular functions. However, precise manipulation of proteins with predefined relative position and stoichiometry for understanding protein-protein interactions and guiding cellular behaviors are still challenging. With superior programmability of DNA molecules, DNA origami technology is able to construct arbitrary nanostructures that can accurately control the arrangement of proteins with various functionalities to solve these problems. Herein, starting from the classification of DNA origami nanostructures and the category of assembled proteins, we summarize the existing DNA origami-based protein manipulation systems (PMSs), review the advances on the regulation of their functions, and discuss their applications in cellular behavior modulation and disease therapy. Moreover, the limitations and potential directions of DNA origami-based PMSs are also presented, which may offer guidance for rational construction and ingenious application.

Localization and Functional Roles of Components of the Translation Apparatus in the Eukaryotic Cell Nucleus

Components of the translation apparatus, including ribosomal proteins, have been found in cell nuclei in various organisms. Components of the translation apparatus are involved in various nuclear processes, particularly those associated with genome integrity control and the nuclear stages of gene expression, such as transcription, mRNA processing, and mRNA export. Components of the translation apparatus control intranuclear trafficking; the nuclear import and export of RNA and proteins; and regulate the activity, stability, and functional recruitment of nuclear proteins. The nuclear translocation of these components is often involved in the cell response to stimulation and stress, in addition to playing critical roles in oncogenesis and viral infection. Many components of the translation apparatus are moonlighting proteins, involved in integral cell stress response and coupling of gene expression subprocesses. Thus, this phenomenon represents a significant interest for both basic and applied molecular biology. Here, we provide an overview of the current data regarding the molecular functions of translation factors and ribosomal proteins in the cell nucleus.

Proteomics reveal cap-dependent translation inhibitors remodel the translation machinery and translatome

Tactical disruption of protein synthesis is an attractive therapeutic strategy, with the first-in-class eIF4A-targeting compound zotatifin in clinical evaluation for cancer and COVID-19. The full cellular impact and mechanisms of these potent molecules are undefined at a proteomic level. Here, we report mass spectrometry analysis of translational reprogramming by rocaglates, cap-dependent initiation disruptors that include zotatifin. We find effects to be far more complex than simple “translational inhibition” as currently defined. Translatome analysis by TMT-pSILAC (tandem mass tag-pulse stable isotope labeling with amino acids in cell culture mass spectrometry) reveals myriad upregulated proteins that drive hitherto unrecognized cytotoxic mechanisms, including GEF-H1-mediated anti-survival RHOA/JNK activation. Surprisingly, these responses are not replicated by eIF4A silencing, indicating a broader translational adaptation than currently understood. Translation machinery analysis by MATRIX (mass spectrometry analysis of active translation factors using ribosome density fractionation and isotopic labeling experiments) identifies rocaglate-specific dependence on specific translation factors including eEF1ε1 that drive translatome remodeling. Our proteome-level interrogation reveals that the complete cellular response to these historical “translation inhibitors” is mediated by comprehensive translational landscape remodeling.

Tactical protein synthesis inhibition is actively pursued as a cancer therapy that bypasses signaling redundancies limiting current strategies. Ho et al. show that rocaglates, first identified as inhibitors of eIF4A activity, globally reprogram cellular translation at both protein synthesis machinery and translatome levels, inducing cytotoxicity through anti-survival GEF-H1/RHOA/JNK signaling.

Different continuous exercise training intensities induced effect on sertoli-germ cells metabolic interaction; implication on GLUT-1, GLUT-3 and MCT-4 transporting proteins expression level

Despite other tissues, the effect of different exercise training protocols (ETPs) on the expression levels of metabolic substrates transmembrane transporters in the testicular tissue, remains completely unexplored. Thus, the effects of low, moderate and high-intensity ETPs on the SCs and germ cells potentials in GLUT-1, GLUT-3 and MCT-4 expression levels was investigated in this study. The animals were assigned into 4 groups, including sedentary control, low-intensity continuous (LICT), moderate-intensity (MICT) and high-intensity (HICT) ETPs-induced groups (n = 6/group). The GLUT-1, GLUT-3 and MCT-4 expressions, cytoplasmic carbohydrate storages of SCs and germ cells, the SCs survival and the spermatogenesis and spermiogenesis rates were assessed. The LICT and MICT did not significantly alter the protein expression levels of GLUT-3 and MCT-4 in the SCs and germ cells, while decreased the GLUT-1 protein content versus the sedentary control animals. In contrast, the HICT remarkably suppressed the GLUT-1 and MCT-4 in both SCs, and germ cells and diminished GLUT-3 in SCs and increased in the germ cells. No significant changes were revealed in the cytoplasmic carbohydrate storage in the LICT and MICT groups, while significantly diminished in the HICT group. The HICT group showed a failed spermatogenesis and spermiogenesis, which were not demonstrated in the sedentary control, LICT and MICT groups. In conclusion, the HICT, by reducing the GLUT-1, GLUT-3 and MCT-4 protein contents in the SCs and reducing the SCs survival, can suppress the glucose transmembrane transport and inhibit the lactate export from SCs, which in turn, ends with failed spermatogenesis and spermiogenesis.