CDK12 phosphorylates 4E-BP1 to enable mTORC1-dependent translation and mitotic genome stability.

The RNA polymerase II (RNAPII) C-terminal domain kinase, CDK12, regulates genome stability, expression of DNA repair genes, and cancer cell resistance to chemotherapy and immunotherapy. In addition to its role in mRNA biosynthesis of DNA repair genes, we show here that CDK12 phosphorylates the mRNA 5' cap-binding repressor, 4E-BP1, to promote translation of mTORC1-dependent mRNAs. In particular, we found that phosphorylation of 4E-BP1 by mTORC1 (T37 and T46) facilitates subsequent CDK12 phosphorylation at two Ser-Pro sites (S65 and T70) that control the exchange of 4E-BP1 with eIF4G at the 5' cap of CHK1 and other target mRNAs. RNA immunoprecipitation coupled with deep sequencing (RIP-seq) revealed that CDK12 regulates release of 4E-BP1, and binding of eIF4G, to many mTORC1 target mRNAs, including those needed for MYC transformation. Genome-wide ribosome profiling (Ribo-seq) further identified specific CDK12 "translation-only" target mRNAs, including many mTORC1 target mRNAs as well as many subunits of mitotic and centromere/centrosome complexes. Accordingly, confocal imaging analyses revealed severe chromosome misalignment, bridging, and segregation defects in cells deprived of CDK12 or CCNK. We conclude that the nuclear RNAPII-CTD kinase CDK12 cooperates with mTORC1, and controls a specialized translation network that is essential for mitotic chromosome stability.

Comparison of software packages for detecting unannotated translated small open reading frames by Ribo-seq.

Accurate and comprehensive annotation of microprotein-coding small open reading frames (smORFs) is critical to our understanding of normal physiology and disease. Empirical identification of translated smORFs is carried out primarily using ribosome profiling (Ribo-seq). While effective, published Ribo-seq datasets can vary drastically in quality and different analysis tools are frequently employed. Here, we examine the impact of these factors on identifying translated smORFs. We compared five commonly used software tools that assess open reading frame translation from Ribo-seq (RibORFv0.1, RibORFv1.0, RiboCode, ORFquant, and Ribo-TISH) and found surprisingly low agreement across all tools. Only ~2% of smORFs were called translated by all five tools, and ~15% by three or more tools when assessing the same high-resolution Ribo-seq dataset. For larger annotated genes, the same analysis showed ~74% agreement across all five tools. We also found that some tools are strongly biased against low-resolution Ribo-seq data, while others are more tolerant. Analyzing Ribo-seq coverage revealed that smORFs detected by more than one tool tend to have higher translation levels and higher fractions of in-frame reads, consistent with what was observed for annotated genes. Together these results support employing multiple tools to identify the most confident microprotein-coding smORFs and choosing the tools based on the quality of the dataset and the planned downstream characterization experiments of the predicted smORFs.

A short ORF-encoded transcriptional regulator.

Recent technological advances have expanded the annotated protein coding content of mammalian genomes, as hundreds of previously unidentified, short open reading frame (ORF)-encoded peptides (SEPs) have now been found to be translated. Although several studies have identified important physiological roles for this emerging protein class, a general method to define their interactomes is lacking. Here, we demonstrate that genetic incorporation of the photo-crosslinking noncanonical amino acid AbK into SEP transgenes allows for the facile identification of SEP cellular interaction partners using affinity-based methods. From a survey of seven SEPs, we report the discovery of short ORF-encoded histone binding protein (SEHBP), a conserved microprotein that interacts with chromatin-associated proteins, localizes to discrete genomic loci, and induces a robust transcriptional program when overexpressed in human cells. This work affords a straightforward method to help define the physiological roles of SEPs and demonstrates its utility by identifying SEHBP as a short ORF-encoded transcription factor.

Accurate annotation of human protein-coding small open reading frames.

Functional protein-coding small open reading frames (smORFs) are emerging as an important class of genes. However, the number of translated smORFs in the human genome is unclear because proteogenomic methods are not sensitive enough, and, as we show, Ribo-seq strategies require additional measures to ensure comprehensive and accurate smORF annotation. Here, we integrate de novo transcriptome assembly and Ribo-seq into an improved workflow that overcomes obstacles with previous methods, to more confidently annotate thousands of smORFs. Evolutionary conservation analyses suggest that hundreds of smORF-encoded microproteins are likely functional. Additionally, many smORFs are regulated during fundamental biological processes, such as cell stress. Peptides derived from smORFs are also detectable on human leukocyte antigen complexes, revealing smORFs as a source of antigens. Thus, by including additional validation into our smORF annotation workflow, we accurately identify thousands of unannotated translated smORFs that will provide a rich pool of unexplored, functional human genes.

Evaluation of dielectric elastomers to develop materials suitable for actuation.

Electroactive polymers based on dielectric elastomers are stretchable and compressible capacitors that can act as transducers between electrical and mechanical energies. Depending on the targeted application, soft actuators, sensors or mechanical-energy harvesters can be developed. Compared with conventional technologies, they present a promising combination of properties such as being soft, silent, light and miniaturizable. Most of the research on dielectric elastomer actuators has focused on obtaining the highest strain, either from technological solutions using commercially available materials or through the development of new materials. It is commonly accepted that a high electrical breakdown field, a low Young's modulus and a high dielectric constant are targets. However, the interdependency of these properties makes the evaluation and comparison of these materials complex. In addition, dielectric elastomers can suffer from electromechanical instability, which amplifies their complexity. The scope of this review is to tackle these difficulties. Thus, first, two physical parameters are introduced, one related to the energy converted by the dielectric elastomer and another to its electromechanical stability. These numbers are then used to compare dielectric elastomers according to a general and rational methodology considering their physicochemical and electromechanical properties. Based on this methodology, different families of commercially available dielectric elastomers are first analyzed. Then, different polymer modification methods are presented, and the resulting modified elastomers are screened. Finally, we conclude on the trends enabling the choice of the most suitable modification procedure to obtain the desired elastomer. From this review work, we would like to contribute to affording a quick identification method, including a graphic representation, to evaluate and develop the dielectric materials that are suitable for a desired actuator.

Toward a doxorubicin-loaded bioinspired bone cement for the localized treatment of osteosarcoma.

Aims: Osteosarcoma represents the second most common cause of death in children and young adults. No biomaterial allowing local drug delivery has been specifically developed. However, a biocompatible bioactive implantable material could prevent some amputations, and the local release of an antitumor agent could limit risks of relapse and metastasis. Methods: We propose a proof of concept of a self-setting paste combining amorphous calcium phosphate and doxorubicin-loaded particles of bone-like carbonated nanocrystalline apatite, as a means of local release. Results: The cement formulation and doping, first with folic acid and then with doxorubicin, was successful. Its physicochemistry was scrutinized. Preliminary in vivo data on an invasive osteosarcoma rat model suggest a limiting effect on metastatic events in the lungs without signs of toxicity.

Repression of the transcriptional activity of ERRα with sequence-specific DNA-binding polyamides.

The orphan nuclear receptors estrogen-related receptors (ERRs) bind to the estrogen-related receptor response element (ERRE) to regulate transcriptional programs in cellular metabolism and cancer cell growth. In this study, we evaluated the potential for a pyrrole-imidazole polyamide to block ERRα binding to ERREs to inhibit gene expression. We demonstrated that the ERRE-targeted polyamide 1 blocked the binding of ERRα to the consensus ERRE and reduced the transcriptional activity of ERRα in cell culture. We further showed that inhibiting ERRα transcriptional activity with polyamide 1 led to reduced mitochondrial oxygen consumption, a primary biological effect regulated by ERRα. Finally, our data demonstrated that polyamide 1 is an inhibitor for cancer cell growth.

MIEF1 Microprotein Regulates Mitochondrial Translation.

Recent technological advances led to the discovery of hundreds to thousands of peptides and small proteins (microproteins) encoded by small open reading frames (smORFs). Characterization of new microproteins demonstrates their role in fundamental biological processes and highlights the value in discovering and characterizing more microproteins. The elucidation of microprotein-protein interactions (MPIs) is useful for determining the biochemical and cellular roles of microproteins. In this study, we characterize the protein interaction partners of mitochondrial elongation factor 1 microprotein (MIEF1-MP) using a proximity labeling strategy that relies on APEX2. MIEF1-MP localizes to the mitochondrial matrix where it interacts with the mitochondrial ribosome (mitoribosome). Functional studies demonstrate that MIEF1-MP regulates mitochondrial translation via its binding to the mitoribosome. Loss of MIEF1-MP decreases the mitochondrial translation rate, while an elevated level of MIEF1-MP increases the translation rate. The identification of MIEF1-MP reveals a new gene involved in this process.

Replication stress by Py-Im polyamides induces a non-canonical ATR-dependent checkpoint response.

Pyrrole-imidazole polyamides targeted to the androgen response element were cytotoxic in multiple cell lines, independent of intact androgen receptor signaling. Polyamide treatment induced accumulation of S-phase cells and of PCNA replication/repair foci. Activation of a cell cycle checkpoint response was evidenced by autophosphorylation of ATR, the S-phase checkpoint kinase, and by recruitment of ATR and the ATR activators RPA, 9-1-1, and Rad17 to chromatin. Surprisingly, ATR activation was accompanied by only a slight increase in single-stranded DNA, and the ATR targets RPA2 and Chk1, a cell cycle checkpoint kinase, were not phosphorylated. However, ATR activation resulted in phosphorylation of the replicative helicase subunit MCM2, an ATR effector. Polyamide treatment also induced accumulation of monoubiquitinated FANCD2, which is recruited to stalled replication forks and interacts transiently with phospho-MCM2. This suggests that polyamides induce replication stress that ATR can counteract independently of Chk1 and that the FA/BRCA pathway may also be involved in the response to polyamides. In biochemical assays, polyamides inhibit DNA helicases, providing a plausible mechanism for S-phase inhibition.

The landscape of fetus metabolism in maternal hyperglycemia.

Maternal hyperglycemia contributes to abnormal fetal development; yet, how it affects fetal metabolism is poorly understood. Perez-Ramirez and colleagues recently provided a comprehensive metabolic atlas of fetal organs isolated from normal and diabetic pregnant mice, identifying novel metabolites and alterations in tissue glucose utilization throughout mid-to-late gestation by maternal hyperglycemia.

Dielectric Elastomer Actuator-Based Valveless Impedance-Driven Pumping for Meso- and Macroscale Applications.

Impedance pumps are simple designs that allow the generation or amplification of flow. They are fluid-filled systems based on flexible tubing connected to tubing with different impedances. A periodic off-center compression of the flexible tubing causes the fluid to move and generate flow. Wave reflection at the impedance mismatch is the primary driving mechanism of the flow. In addition to their straightforward design, impedance pumps are bladeless, valveless, and pulsatile. These properties are highly sought after by demanding and challenging applications, such as the biomedical field, as they present less risk of damage, disruption, and obstruction when handling viscous and delicate fluids/matter. In this study, we propose a high-performance impedance-driven pumping concept with embedded actuation based on a multilayered tubular dielectric elastomer. This pumping system is made of three parts, a dielectric elastomer actuator tube, a passive tube, and a rigid ring that binds and decouples the two subsystems. The system is able to generate net fluid flow rates up to 1.35 L/min with an internal pressure of 125 mmHg. The soft simplistic design, self-contained concept, and high performances of these pumping systems could make them disruptive in many challenging meso- and macroscale applications in general and in the biomedical field in particular.

Dielectric elastomer actuator-based valveless pump as Fontan failure assist device: introduction and preliminary study.

OBJECTIVES: Fontan failure refers to a condition in which the Fontan circulation, a surgical procedure used to treat certain congenital heart defects, becomes insufficient, leading to compromised cardiac function and potential complications. This in vitro study therefore investigates the feasibility of bladeless impedance-driven cavopulmonary assist device via dielectric elastomer actuator (DEA) as a means to address Fontan failure. METHODS: A cavopulmonary assist device, constructed using DEA technologies and employing the impedance pump concept, is subjected to in vitro testing within a closed-loop setup. This study aims to assess the device's functionality and performance under controlled conditions, providing valuable insights into its potential application as a cavopulmonary assistive technology. RESULTS: The DEA-based pump, measuring 50 mm in length and 30 mm in diameter, is capable of achieving substantial flow rates within a closed-loop setup, reaching up to 1.20 l/min at an activation frequency of 4 Hz. It also provides a broad range of working internal pressures (<10 to >20 mmHg). Lastly, the properties of the flow (direction, magnitude, etc.) can be controlled by adjusting the input signal parameters (frequency, amplitude, etc.). CONCLUSIONS: In summary, the results suggest that the valveless impedance-driven pump utilizing DEA technology is promising in the context of cavopulmonary assist devices. Further research and development in this area may lead to innovative and potentially more effective solutions for assisting the right heart, ultimately benefiting patients with heart-related health issues overall, with a particular focus on those experiencing Fontan failure.

Novel para-aortic cardiac assistance using a pre-stretched dielectric elastomer actuator.

OBJECTIVES: We propose an evolution of a dielectric elastomer actuator-based cardiac assist device that acts as a counterpulsation system. We introduce a new pre-stretched actuator and implant the device in a graft bypass between the ascending and descending aorta to redirect all blood through the device (ascending aorta clamped). The objective was to evaluate the influence of these changes on the assistance provided to the heart. METHODS: The novel para-aortic device and the new implantation technique were tested in vivo in 5 pigs. We monitored the pressure and flow in the aorta as well as the pressure-volume characteristics of the left ventricle. Different activation timings were tested to identify the optimal device actuation. RESULTS: The proposed device helps reducing the end-diastolic pressure in the aorta by up to 13 ± 4.0% as well as the peak systolic pressure by up to 16 ± 3.6%. The early diastolic pressure was also increased up to 10 ± 3.5%. With different activation, we also showed that the device could increase or decrease the stroke volume. CONCLUSIONS: The new setup and the novel para-aortic device presented here helped improve cardiac assistance compared to previous studies. Moreover, we revealed a new way to assist the heart by actuating the device at different starting time to modify the left ventricular stroke volume and stroke work.

Recent Advances in the Therapeutic Potential of Carotenoids in Preventing and Managing Metabolic Disorders.

Carotenoids constitute compounds of significant biological interest due to their multiple biological activities, such as antimicrobial, anticancer, antiadipogenic, antidiabetic, and antioxidant properties. Metabolic syndrome (MetS) comprehends a series of metabolic abnormalities (e.g., hypertension, obesity, and atherogenic dyslipidemia) that can affect children, adolescents, and the elderly. The treatment of MetS involves numerous medications, which, despite their efficacy, pose challenges due to prolonged use, high costs, and various side effects. Carotenoids and their derivatives have been proposed as alternative treatments to MetS because they reduce serum triglyceride concentrations, promote insulin response, inhibit adipogenesis, and downregulate angiotensin-converting enzyme activity. However, carotenoids are notably sensitive to pH, light exposure, and temperature. This review addresses the activity of carotenoids such as lycopene, lutein, fucoxanthin, astaxanthin, crocin, and ß-carotene towards MetS. It includes a discussion of sources, extraction methods, and characterization techniques for analyzing carotenoids. Encapsulation approaches are critically reviewed as alternatives to prevent degradation and improve the biological performance of carotenoids. A brief overview of the physiopathology and epidemiology of the diseases, including MetS, is also provided.

Pathogen-associated molecular pattern-triggered immunity and resistance to the root pathogen Phytophthora parasitica in Arabidopsis.

The cellulose binding elicitor lectin (CBEL) of the genus Phytophthora induces necrosis and immune responses in several plant species, including Arabidopsis thaliana. However, the role of CBEL-induced responses in the outcome of the interaction is still unclear. This study shows that some of CBEL-induced defence responses, but not necrosis, required the receptor-like kinase BAK1, a general regulator of basal immunity in Arabidopsis, and the production of a reactive oxygen burst mediated by respiratory burst oxidases homologues (RBOH). Screening of a core collection of 48 Arabidopsis ecotypes using CBEL uncovered a large variability in CBEL-induced necrotic responses. Analysis of non-responsive CBEL lines Ws-4, Oy-0, and Bla-1 revealed that Ws-4 and Oy-0 were also impaired in the production of the oxidative burst and expression of defence genes, whereas Bla-1 was partially affected in these responses. Infection tests using two Phytophthora parasitica strains, Pp310 and Ppn0, virulent and avirulent, respectively, on the Col-0 line showed that BAK1 and RBOH mutants were susceptible to Ppn0, suggesting that some immune responses controlled by these genes, but not CBEL-induced cell death, are required for Phytophthora parasitica resistance. However, Ws-4, Oy-0, and Bla-1 lines were not affected in Ppn0 resistance, showing that natural variability in CBEL responsiveness is not correlated to Phytophthora susceptibility. Overall, the results uncover a BAK1- and RBOH-dependent CBEL-triggered immunity essential for Phytophthora resistance and suggest that natural quantitative variation of basal immunity triggered by conserved general elicitors such as CBEL does not correlate to Phytophthora susceptibility.

Comparison of software packages for detecting unannotated translated small open reading frames by Ribo-seq.

Accurate and comprehensive annotation of microprotein-coding small open reading frames (smORFs) is critical to our understanding of normal physiology and disease. Empirical identification of translated smORFs is carried out primarily using ribosome profiling (Ribo-seq). While effective, published Ribo-seq datasets can vary drastically in quality and different analysis tools are frequently employed. Here, we examine the impact of these factors on identifying translated smORFs. We compared five commonly used software tools that assess ORF translation from Ribo-seq (RibORFv0.1, RibORFv1.0, RiboCode, ORFquant, and Ribo-TISH), and found surprisingly low agreement across all tools. Only ~2% of smORFs were called translated by all five tools and ~15% by three or more tools when assessing the same high-resolution Ribo-seq dataset. For larger annotated genes, the same analysis showed ~72% agreement across all five tools. We also found that some tools are strongly biased against low-resolution Ribo-seq data, while others are more tolerant. Analyzing Ribo-seq coverage as a proxy for translation levels revealed that highly translated smORFs are more likely to be detected by more than one tool. Together these results support employing multiple tools to identify the most confident microprotein-coding smORFs, and choosing the tools based on the quality of the dataset and planned downstream characterization experiments of predicted smORFs.

Integrated workflow for discovery of microprotein-coding small open reading frames.

Small open reading frame (smORF)-encoded microproteins, proteins containing less than 100-150 amino acids, are an emerging class of functional biomolecules. Here, we present a protocol for identifying translated smORFs in mammalian systems genome wide. We describe steps for generation of ribosome profiling (Ribo-seq) data, in silico translation of a transcriptome assembly to create an ORF database, and computational analysis of Ribo-seq to score individual smORFs for translation. Identification of translated smORFs is the first step to studying the functions of microproteins. For complete details on the use and execution of this protocol, please refer to Martinez et al.1.

Hemodynamic effects of a dielectric elastomer augmented aorta on aortic wave intensity: An in-vivo study.

Dielectric elastomer actuator augmented aorta (DEA) represents a novel approach with high potential for assisting a failing heart. The soft tubular device replaces a section of the aorta and increases its diameter when activated. The hemodynamic interaction between the DEA and the left ventricle (LV) has not been investigated with wave intensity (WI) analysis before. The objective of this study is to investigate the hemodynamic effects of the DEA on the aortic WI pattern. WI was calculated from aortic pressure and flow measured in-vivo in the descending aorta of two pigs implanted with DEAs. The DEAs were tested for different actuation phase shifts (PS). The DEA generated two decompression waves (traveling upstream and downstream of the device) at activation followed by two compression waves at deactivation. Depending on the PS, the end-diastolic pressure (EDP) decreased by 7% (or increased by 5-6%). The average early diastolic pressure augmentation (Pdia¯) increased by 2% (or decreased by 2-3%). The hydraulic work (WH) measured in the aorta decreased by 2% (or increased by 5%). The DEA-generated waves interfered with the LV-generated waves, and the timing of the waves affected the hemodynamic effect of the device. For the best actuation timing the upstream decompression wave arrived just before aortic valve opening and the upstream compression wave arrived just before aortic valve closure leading to a decreased EDP, an increased Pdia¯ and a reduced.WH.