Regulation Of Biogenesis Research Articles

Antioxidants Rich Herbal Formula Ger-Gen-Chyn-Lian-Tang Protects Lipotoxicity and Ameliorates Inflammation Signaling through Regulation of Mitochondrial Biogenesis and Mitophagy in Nonalcoholic Fatty Liver Disease Mice.

Non-alcoholic fatty liver disease (NAFLD) has become a prevalent issue and a consequence of metabolic syndrome impact on human health. Both of anti-atherosclerosis and anti-hepatic fibrosis capabilities of herbal medicine Ger-Gen-Chyn-Lian-Tang (GGCLT) has attracted attention, but their molecular regulatory mechanisms in a NAFLD model have not been elucidated. The aim of the present study was to explore the bioactivity of db/db mice following treatment with GGCLT. NAFLD phenotype of db/db mice were treated with GGCLT and lipogenesis, mitochondria dysfunction, mitophagy, macrophage polarization and adipose tissue browning were then evaluated using qRT-PCR and/or Western blot analysis, immunofluorescence, and immunohistochemistry assays, respectively. GGCLT not only decreased serum levels of TG and free fatty acids, but glucose and insulin tolerance test in db/db mice. In parallel, GGCLT reduced lipogenesis and hypoxia-inflammation cascades in NAFLD progression. GGCLT reduced lipid accumulation and was accompanied by the enhanced mitochondria biogenesis, M2 macrophage, and decreased M1 macrophage. The latter two events contributing to the anti-inflammation are resulting from mitochondria dynamics, and the lipotoxicity lowering effect of GGCLT of NAFLD mice is mediated by promoting mitophagy in Parkin-dependent and -independent pathways, by mitochondrial fusion over fission manner. GGCLT also inactivated lipogenesis and decreased lipid accumulation in epididymal white adipose tissue with a higher M2/M1 macrophage ratio. Besides in the liver, modulating of mitochondrial biogenesis and adipose tissue browning were characterized by increased Tmem26, Tfam, and Prdm16 expression by GGCLT in EWAT also contributes to the beneficial action in NAFLD.

Identification of Pri-miRNA Stem-Loop Interacting Proteins in Plants Using a Modified Version of the Csy4 CRISPR Endonuclease.

Regulation at the RNA level by RNA-binding proteins (RBPs) and microRNAs (miRNAs) is key to coordinating eukaryotic gene expression. In plants, the importance of miRNAs is highlighted by severe developmental defects in mutants impaired in miRNA biogenesis. MiRNAs are processed from long primary-microRNAs (pri-miRNAs) with internal stem-loop structures by endonucleolytic cleavage. The highly structured stem-loops constitute the basis for the extensive regulation of miRNA biogenesis through interaction with RBPs. However, trans-acting regulators of the biogenesis of specific miRNAs are largely unknown in plants. Therefore, we exploit an RNA-centric approach based on modified versions of the conditional CRISPR nuclease Csy4* to pull down interactors of the Arabidopsis pri-miR398b stem-loop (pri-miR398b-SL) in vitro. We designed three epitope-tagged versions of the inactive Csy4* for the immobilization of the protein together with the pri-miR398b-SL bait on high affinity matrices. After incubation with nucleoplasmic extracts from Arabidopsis and extensive washing, pri-miR398b-SL, along with its specifically bound proteins, were released by re-activating the cleavage activity of the Csy4* upon the addition of imidazole. Co-purified proteins were identified via quantitative mass spectrometry and data sets were compared. In total, we identified more than 400 different proteins, of which 180 are co-purified in at least two out of three independent Csy4*-based RNA pulldowns. Among those, the glycine-rich RNA-binding protein AtRZ-1a was identified in all pulldowns. To analyze the role of AtRZ-1a in miRNA biogenesis, we determined the miR398 expression level in the atrz-1a mutant. Indeed, the absence of AtRZ-1a caused a decrease in the steady-state level of mature miR398 with a concomitant reduction in pri-miR398b levels. Overall, we show that our modified Csy4*-based RNA pulldown strategy is suitable to identify new trans-acting regulators of miRNA biogenesis and provides new insights into the post-transcriptional regulation of miRNA processing by plant RBPs.

The developmentally timed decay of an essential microRNA family is seed-sequence dependent.

SUMMARYMicroRNA (miRNA) abundance is tightly controlled by regulation of biogenesis and decay. Here, we show that the mir-35 miRNA family undergoes selective decay at the transition from embryonic to larval development in C. elegans. The seed sequence of the miRNA is necessary and largely sufficient for this regulation. Sequences outside the seed (3′ end) regulate mir-35 abundance in the embryo but are not necessary for sharp decay at the transition to larval development. Enzymatic modifications of the miRNA 3′ end are neither prevalent nor correlated with changes in decay, suggesting that miRNA 3′ end display is not a core feature of this mechanism and further supporting a seed-driven decay model. Our findings demonstrate that seed-sequence-specific decay can selectively and coherently regulate all redundant members of a miRNA seed family, a class of mechanism that has great biological and therapeutic potential for dynamic regulation of a miRNA family’s target repertoire.

A transcriptionally repressed quiescence program is associated with paused RNA polymerase II and is poised for cell cycle re-entry.

Adult stem cells persist in mammalian tissues by entering a state of reversible quiescence, referred to as G0, which is associated with low levels of transcription. Using cultured myoblasts and muscle stem cells, we report that in G0, global RNA content and synthesis are substantially repressed, correlating with decreased RNA polymerase II (RNAPII) expression and activation. Integrating RNAPII occupancy and transcriptome profiling, we identify repressed networks and a role for promoter-proximal RNAPII pausing in G0. Strikingly, RNAPII shows enhanced pausing in G0 on repressed genes encoding regulators of RNA biogenesis (such as Ncl, Rps24, Ctdp1), and release of pausing is associated with increased expression of these genes in G1. Knockdown of these transcripts in proliferating cells leads to induction of G0 markers, confirming the importance of their repression in establishment of G0. A targeted screen of RNAPII regulators revealed that knockdown of Aff4 (a positive regulator of elongation) unexpectedly enhances expression of G0-stalled genes and hastens S phase; however, the negative elongation factor (NELF) complex, a regulator of pausing, appears to be dispensable. We propose that RNAPII pausing contributes to transcriptional control of a subset of G0-repressed genes to maintain quiescence and impacts the timing of the G0-G1 transition. This article has an associated First Person interview with the first authors of the paper.

Preprint Highlight: Collagen remodeling dictates pancreatic cancer bioenergetics and outcome through DDR1 activation or degradation.

Aberrant desmoplasia (e.g., collagen deposition) is a prominent hallmark of pancreatic ductal adenocarcinoma (PDAC) pathogenesis. The mechanisms and signaling pathways impacted by the prevalent increase in collagen deposition are poorly understood. This study demonstrated opposing roles of fibrolytic stroma (cleaved type I collagen) and inert stroma (intact type I collagen) in driving PDAC tumorigenicity. Cleaved type I collagen activates discoidin domain receptor 1 (DDR1), leading to increased tumor growth and liver metastases, macropinocytosis, metabolism, mitochondrial biogenesis, and poor patient outcomes. These effects were inhibited by intact type I collagen. This study describes new roles of DDR1-mediated regulation of macropinocytosis and mitochondrial biogenesis, delineates stromal states as oncogenic drivers of PDAC, and advances our understanding of aberrant desmoplasia.

Effects of different-intensity exercise and creatine supplementation on mitochondrial biogenesis and redox status in mice.

Objective(s):Dietary supplementation combined with exercise may potentiate the beneficial effects of exercise by reducing exercise-induced oxidative stress and improving mitochondrial quality and capacity. In this study, the effects of creatine monohydrate (CrM) supplementation with low and high-intensity exercise on mitochondrial biogenesis regulators, Nrf2 anti-oxidant signaling pathway and muscle damage levels were investigated. Materials and Methods: Balb/c male mice were divided into six experimental groups: control, control+CrM, high-intensity exercise, high-intensity exercise+CrM, low-intensity exercise, and low-intensity exercise+CrM. Mice were given CrM supplementation and at the same time, low and high-intensity exercise was applied to the groups on the treadmill at 30min/5day/8week. Then, mitochondrial biogenesis marker (PGC-1α, NRF-1, TFAM), Nrf2 and HO-1 protein expressions, total oxidant-anti-oxidant status level, and histopathological changes were investigated in serum and muscle tissue. Results:Exercise intensity and CrM supplementation were found to be effective factors in mitochondrial biogenesis induction via the PGC-1α signaling pathway. Nrf2 and HO-1 protein levels increased with exercise intensity, and this result was directly related to serum oxidative stress markers. In addition, CrM supplementation was effective in reducing exercise-induced muscle damage. Conclusion:This combination induced skeletal muscle adaptations, including mitochondrial biogenesis and enhanced anti-oxidant reserves. This synergistic effect of dietary supplementation with low-intensity exercise may be valuable as a complement to treatment, especially in diseases caused by mitochondrial dysfunction.

Protective effect of 5-heptadecylresorcinol against obesity-associated skeletal muscle dysfunction by modulating mitochondrial biogenesis via the activation of SIRT3/PGC-1α signaling pathway

Obesity-associated skeletal muscle mitochondrial dysfunction contributed to exercise capacity decline. 5-heptadecylresorcinol (AR-C17) has been proven effective against obesity and insulin resistance. However, its effects on skeletal muscle performance remains unclear. In this study, we investigate whether AR-C17 could protect against high-fat diet induced C57 BL/6J mice skeletal muscle dysfunction. The results indicated that AR-C17 intervention significantly improved skeletal muscle exercise capacity according to the strength and endurance test. AR-C17 showed no effect on skeletal muscle myofiber type conversion and myogenesis, but could significantly enhance PGC-1α mediated mitochondrial biogenesis. Moreover, AR-C17 significantly attenuated PA-induced reduction of mitochondrial DNA content in C2C12 cells and promoted mitochondrial biogenesis regulator gene PGC-1α and its downstream signaling pathway protein expression. In addition, AR-C17 increased the protein levels of SIRT3, while the protective effect was abolished by SIRT3 inhibitor (3-TYP), indicating AR-C17 ameliorated obesity induced skeletal muscle dysfunction might through SIRT3/PGC-1α signaling pathway.

Sulforaphane Increase Mitochondrial Biogenesis-Related Gene Expression in the Hippocampus and Suppresses Age-Related Cognitive Decline in Mice.

Sulforaphane (SFN) is a potent activator of the transcriptional factor, Nuclear Factor Erythroid 2 (NF-E2)-Related factor 2 (NRF2). SFN and its precursor, glucoraphanin (sulforaphane glucosinolate, SGS), have been shown to ameliorate cognitive function in clinical trials and in vivo studies. However, the effects of SGS on age-related cognitive decline in Senescence-Accelerated Mouse Prone 8 (SAMP8) is unknown. In this study, we determined the preventive potential of SGS on age-related cognitive decline. One-month old SAMP8 mice or control SAM resistance 1 (SAMR1) mice were fed an ad libitum diet with or without SGS-containing broccoli sprout powder (0.3% w/w SGS in diet) until 13 months of age. SGS significantly improved long-term memory in SAMP8 at 12 months of age. Interestingly, SGS increased hippocampal mRNA and protein levels of peroxisome proliferator-activated receptor gamma coactivator-1 alpha (PGC1α) and mitochondrial transcription factor A (TFAM), which are master regulators of mitochondrial biogenesis, both in SAMR1 and SAMP8 at 13 months of age. Furthermore, mRNAs for nuclear respiratory factor-1 (NRF-1) and mitochondrial DNA-encoded respiratory complex enzymes, but not mitochondrial DNA itself, were increased by SGS in SAMP8 mice. These results suggest that SGS prevents age-related cognitive decline by maintaining mitochondrial function in senescence-accelerated mice.

Intervention with isoleucine or valine corrects hyperinsulinemia and reduces intrahepatic diacylglycerols, liver steatosis, and inflammation in Ldlr-/-.Leiden mice with manifest obesity-associated NASH.

Non-alcoholic steatohepatitis (NASH) is associated with a disturbed metabolism in liver, insulin resistance, and excessive accumulation of ectopic fat. Branched-chain amino acids (BCAAs) may beneficially modulate hepatic lipids, however, it remains unclear whether individual BCAAs can attenuate already established NASH and associated oxidative-inflammatory stress. After a 26 weeks run-in on fast food diet (FFD), obese Ldlr-/-.Leiden mice were treated for another 12 weeks with either valine or isoleucine (3% of FFD) and then compared to FFD controls. Valine and isoleucine did not affect obesity, dyslipidemia, gut permeability, or fecal fatty acid excretion, but significantly reduced hyperinsulinemia. Valine and isoleucine reduced ALT, CK18-M30, and liver steatosis with a particularly pronounced suppression of the microvesicular component (-61% by valine and -71% by isoleucine). Both BCAAs decreased intrahepatic diacylglycerols and 4-hydroxynonenal immunoreactivity, a marker for oxidative stress-induced lipid peroxidation. Functional genomics analysis demonstrated that valine and isoleucine affected BCAA metabolism genes, deactivated master regulators of anabolic pathways related to steatosis (e.g., SREBPF1), and activated master regulators of mitochondrial biogenesis (e.g., PPARGC1A) and lipid catabolism (e.g., ACOX1, AMPK). This correction of critical metabolic pathways on gene expression level was accompanied by a significant decrease in histological liver inflammation, and suppression of FFD-stimulated cytokine and chemokine proteins KC/CXCL1, MCP-1/CCL2, and MIP-2/CXCL2 and their pathways. In conclusion, dietary intervention with either valine or isoleucine corrected liver diacylglycerols, gene expression of multiple metabolic processes, and reduced NASH histology with profound hepatoprotective effects on oxidative stress and inflammatory proteins.

G Protein-Coupled Receptors-Receptors With New Tricks Up Their Sleeves.

G Protein-Coupled Receptors-Receptors With New Tricks Up Their Sleeves.

Ophiopogonin D′-induced mitophagy and mitochondrial damage are associated with dysregulation of the PINK1/Parkin signaling pathway in AC16 cells

Shenmai injection (SMI) is a patented traditional Chinese medicine that is extracted from Panax ginseng and Ophiopogon japonicus and is commonly used to treat cardiovascular diseases and tumors. The O. japonicus extract Ophiopogonin D′ (OPD') is highly cardiotoxic. Mitochondria are central to OPD'-induced cardiotoxicity, although the precise mechanisms remain unclear. Excessive mitophagy activation and mitochondrial dysfunction lead to apoptosis, and the PTEN-induced kinase 1(PINK1)/Parkin pathway is critical in regulating mitophagy and mitochondrial function. We investigated the role of the PINK1/Parkin pathway in OPD'-induced mitochondrial damage and cardiotoxicity in AC16 cells. Concentrations of 2 μM OPD' and above inhibited cardiomyocyte viability and increased lactate dehydrogenase (LDH) release in a concentration- and time-dependent manner. OPD' was toxic to cells and mitochondria and increased the rate of apoptosis, triggering pyknosis, decreasing mitochondrial membrane potential (MMP), and decreasing the protein expression of the biogenesis regulator peroxisome proliferator-activated receptor γ coactivator-1 alpha (PGC-1α). The increased ratio of microtubule-associated proteins 1 A/1B light chain 3B (LC3-II/LC3-I) in mitochondria indicated that OPD' induced mitophagy. OPD' significantly induced oxidative stress and apoptosis, including increased reactive oxygen species (ROS) generation and decreased nuclear factor erythroid-2 related factor 2 (Nrf2), heme oxygenase-1(HO-1), and B-cell lymphoma 2 (Bcl-2) protein expression. OPD' activated the PINK1/Parkin pathway and promoted PINK1/Parkin translocation to mitochondria. Inhibiting mitophagy attenuated OPD'-induced PINK1/Parkin pathway activation and preserved mitochondrial biogenesis, consequently mitigating OPD'-induced mitochondrial dysfunction and apoptosis. These findings suggest that OPD'-induced cardiomyocyte mitophagy and mitochondrial damage are at least partially mediated by dysregulation of the PINK1/Parkin pathway.

TFAM downregulation promotes autophagy and ESCC survival through mtDNA stress-mediated STING pathway.

The dynamics of mitochondrial biogenesis regulation is critical in maintaining cellular homeostasis for immune regulation and tumor prevention. Here, we report that mitochondrial biogenesis disruption through TFAM reduction significantly impairs mitochondrial function, induces autophagy, and promotes esophageal squamous cell carcinoma (ESCC) growth. We found that TFAM protein reduction promotes mitochondrial DNA (mtDNA) release into the cytosol, induces cytosolic mtDNA stress, subsequently activates the cGAS-STING signaling pathway, thereby stimulating autophagy and ESCC growth. STING depletion or mtDNA degradation by DNase I abrogates mtDNA stress response, attenuates autophagy, and decreases the growth of TFAM depleted cells. In addition, autophagy inhibitor also ameliorates mitochondrial dysfunction-induced activation of the cGAS-STING signaling pathway and ESCC growth. In conclusion, our results indicate that mtDNA stress induced by mitochondria biogenesis perturbation activates the cGAS-STING pathway and autophagy to promote ESCC growth, revealing an underappreciated therapeutic strategy for ESCC.

Light-emitting diode photomodulation of uterine adenocarcinoma cells inhibited angiogenesis capacity via the regulation of exosome biogenesis.

This study was conducted to investigate the inhibitory effects of light-emitting diodes (LEDs) on exosome biogenesis and angiogenesis capacity in Ishikawa endometrial cancer cells. To this end, cells were exposed to different energy densities (fluences) of 4, 8, 16, 32, and 64J/cm2 for 5days (once every 24h), and cell viability was determined using an MTT assay. Based on data from the MTT panel, cells were exposed to 4 and 16J/cm2 for subsequent analyses. Exosome biogenesis was also monitored via monitoring the expression of CD63, ALIX, and Rab27a and b. The size and morphology of exosomes in the supernatant were measured using scanning electron microscopy (SEM), and dynamic light scattering (DLS). Using Transwell insert, the migration capacity of these cells was studied. The angiogenic effects of irradiated Ishikawa cell secretome at different fluences were monitored on human endothelial cells using in vitro tubulogenesis. Results indicated LED can reduce the viability of Ishikawa cells in a dose-dependent manner. According to our data, 4 and 64J/cm2 groups exhibited minimum and maximum cytotoxic effects compared to the control cells. Data revealed a close proportional relationship between the power of laser and exosome average size compared to the non-treated control cells (p < 0.05). Real-time PCR analysis showed the suppression of Rab27b and up-regulation of Rab27a in irradiated cells exposed to 4 and 16J/cm2 (p < 0.05). These effects were evident in the 16J/cm2 group. Likewise, LED can inhibit the migration of Ishikawa cells in a dose-dependent manner (p < 0.05). Tubulogenesis activity of endothelial cells was suppressed after incubation with the secretome of irradiated Ishikawa cells (p < 0.05). These data showed tumoricidal properties of LED irradiation on human adenocarcinoma Ishikawa cells via the inhibition of exosome biogenesis and suppression of angiogenesis capacity.

Lost in Translation: Exploring microRNA Biogenesis and Messenger RNA Fate in Anoxia-Tolerant Turtles

Red-eared slider turtles face natural changes in oxygen availability throughout the year. This includes long-term anoxic brumation where they reduce their metabolic rate by ~90% for months at a time, which they survive without apparent tissue damage. This metabolic rate depression (MRD) is underlaid by various regulatory mechanisms, including messenger RNA (mRNA) silencing via microRNA (miRNA), leading to mRNA decay or translational inhibition in processing bodies (P-bodies) and stress granules. Regulation of miRNA biogenesis was assessed in red-eared slider turtle liver and skeletal muscle via immunoblotting. Hepatic miRNA biogenesis was downregulated in early processing steps, while later steps were upregulated. These contradictory findings indicate either overall decreased miRNA biogenesis, or increased biogenesis if sufficient pre-miRNA stores were produced in early anoxia. Conversely, muscle showed clear upregulation of multiple biogenesis steps indicating increased miRNA production. Additionally, immunoblotting indicated that P-bodies may be favoured by the liver for mRNA storage/decay during reoxygenation with a strong suppression of stress granule proteins in anoxia and reoxygenation. Muscle however showed downregulation of P-bodies during anoxia and reoxygenation, and upregulation of stress granules for mRNA storage during reoxygenation. This study advances our understanding of how these champion anaerobes regulate miRNA biogenesis to alter miRNA expression and mRNA fate during prolonged anoxia.

Transcriptome profile in the skeletal muscle of cattle progeny as a function of maternal protein supplementation during mid-gestation

This study aimed to evaluate the differentially expressed genes (DEG), their biological functions, and the main predictor genes in skeletal muscle of the offspring resulting from dams supplemented or not with protein during mid-gestation. From 100 to 200 days of gestation, 10 Tabapuã cows pregnant of males were assigned to one of two treatments: Control [(CON) - supply of basal diet achieving 5.5% of crude protein (CP); n = 6]; or Supplemented [(SUP) - basal diet plus a supplement with 40% of CP provided at the level of 3.5 g/kg of body weight; n = 4]. Muscle samples were collected from the progeny at 260d of postnatal age to RNA-seq, Gene Ontology (GO) enrichment, and Random Forest (RF) analyses. A total of 310 DEG (q-value < 0.05) were identified for the effect of diet, being 187 and 123 genes down-regulated and up-regulated in the SUP diet, respectively. Within the SUP up-regulated genes, were genes related to insulin receptor signaling pathway (LOC107131843) and apoptosis regulation (KRT18, KRT8 and KRT19). While the enriched GOs terms are implicated in mitochondrial metabolism through the overrepresentation of the GO terms microtubule polymerization or depolymerization (GO:0031109, GO:0046785) and positive regulation of cellular component biogenesis (GO:0044089). Moreover, RF analysis revealed predictor genes related to the skeletal muscle development, including genes that participates in the PI3K/Akt pathways (PITPNA), myoblast proliferation (ALKBH1) and differentiation (CDK5R1 and miR-206). In conclusion, maternal protein supplementation during mid-gestation positively affected the energy metabolism and favored the hypertrophic processes of the skeletal muscle of the offspring.

Abstract 4109: Covalent JNK inhibitor, JNK-IN-8, suppresses tumor growth in triple-negative breast cancer in part by activating lysosome biogenesis and autophagy via TFEB and TFE3

Abstract The heterogeneity and aggressiveness of Triple-Negative Breast Cancer (TNBC) contribute to its early recurrence and metastasis. Despite substantial research to identify effective molecular targets for therapy, TNBC remains particularly elusive in terms of improving patient outcomes for advanced disease. Here, we report that a covalent JNK inhibitor, JNK-IN-8, suppresses TNBC growth in cell lines and patient-derived organoids in vitro and patient-derived xenograft tumors in vivo. JNK-IN-8 reduced colony formation in TNBC cell lines and cell viability in both cell lines and patient-derived organoids in a concentration-dependent manner. Further, the compound significantly slowed tumor growth compared to vehicle in a patient-derived xenograft model in vivo. Cells treated with JNK-IN-8 exhibited large, cytoplasmic vacuoles with lysosomal markers. To examine the molecular mechanism of this phenotype, we looked at the master regulators of lysosome biogenesis and autophagy TFEB and TFE3. JNK-IN-8 inhibited TFEB phosphorylation and induced nuclear translocation of both TFEB and TFE3. This was accompanied by an upregulation of TFEB/TFE3 target genes associated with lysosome biogenesis and autophagy. Depletion of both TFEB and TFE3 diminished the JNK-IN-8-driven reduction of colony formation and the upregulation of lysosome biogenesis and autophagy markers. JNK-IN-8 also reduced the phosphorylation of other mTOR targets in a concentration-dependent manner. Ectopic expression of RagC (S75L) rescued mTOR signaling and restored TFEB phosphorylation and cytoplasmic localization. In contrast, knockout of JNK1 and/or JNK2 had no impact on TFEB/TFE3 activation or mTOR inhibition by JNK-IN-8, but did inhibit colony formation. Similarly, re-expression of either wildtype or drug-nonbinding JNK (C116S) in JNK knockout cells did not reverse JNK-IN-8-induced TFEB dephosphorylation. In summary, JNK-IN-8 induced lysosome biogenesis and autophagy by activating TFEB and TFE3 via mTOR inhibition independently of JNK. Together, these findings demonstrate the in vitro and in vivo efficacy of JNK-IN-8 as a targeted therapy for TNBC and reveal its novel lysosome- and autophagy-mediated mechanism of action. Citation Format: Milad Soleimani, Tamer Kaoud, Alex Somma, Jorge Bustamante, Dennis C. Wylie, Nisha Holay, Agnieszka Looney, Uma Giri, Todd Triplett, Jeanne Kowalski-Muegge, Kevin N. Dalby, S. Gail Eckhardt, Carla Van Den Berg. Covalent JNK inhibitor, JNK-IN-8, suppresses tumor growth in triple-negative breast cancer in part by activating lysosome biogenesis and autophagy via TFEB and TFE3 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 4109.

Requirement and functional redundancy of two large ribonucleotide reductase subunit genes for cell cycle, chloroplast biogenesis and photosynthesis in tomato.

Ribonucleotide reductase (RNR), functioning in the de novo synthesis of deoxyribonucleoside triphosphates (dNTPs), is crucial for DNA replication and cell cycle progression. In most plants, the large subunits of RNR have more than one homologous gene. However, the different functions of these homologous genes in plant development remain unknown. In this study, we obtained the mutants of two large subunits of RNR in tomato and studied their functions. The mutant ylc1 was obtained by ethyl methyl sulfonate (EMS) treatment. Through map-based cloning, complementation and knock-out experiments, it was confirmed that YLC1 encodes a large subunit of RNR (SlRNRL1). The expression level of the genes related to cell cycle progression, chloroplast biogenesis and photosynthesis was assessed by RNA-sequencing. In addition, we knocked out SlRNRL2 (a SlRNRL1 homologue) using CRISPR-Cas9 technology in the tomato genome, and we down-regulated SlRNRL2 expression in the genetic background of slrnrl1-1 using a tobacco rattle virus-induced gene silencing (VIGS) system. The mutant slrnrl1 exhibited dwarf stature, chlorotic young leaves and smaller fruits. Physiological and transcriptomic analyses indicated that SlRNRL1 plays a crucial role in the regulation of cell cycle progression, chloroplast biogenesis and photosynthesis in tomato. The slrnrl2 mutant did not exhibit any visible phenotype. SlRNRL2 has a redundant function with SlRNRL1, and the double mutant slrnrl1slrnrl2 is lethal. SlRNRL1 is essential for cell cycle progression, chloroplast biogenesis and photosynthesis. In addition, SlRNRL1 and SlRNRL2 possess redundant functions and at least one of these RNRLs is required for tomato survival, growth and development.

Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq

SUMMARYA central goal of genetics is to define the relationships between genotypes and phenotypes. High-content phenotypic screens such as Perturb-seq (CRISPR-based screens with single-cell RNA-sequencing readouts) enable massively parallel functional genomic mapping but, to date, have been used at limited scales. Here, we perform genome-scale Perturb-seq targeting all expressed genes with CRISPR interference (CRISPRi) across >2.5 million human cells. We use transcriptional phenotypes to predict the function of poorly characterized genes, uncovering new regulators of ribosome biogenesis (including CCDC86, ZNF236, and SPATA5L1), transcription (C7orf26), and mitochondrial respiration (TMEM242). In addition to assigning gene function, single-cell transcriptional phenotypes allow for in-depth dissection of complex cellular phenomena—from RNA processing to differentiation. We leverage this ability to systematically identify genetic drivers and consequences of aneuploidy and to discover an unanticipated layer of stress-specific regulation of the mitochondrial genome. Our information-rich genotype-phenotype map reveals a multidimensional portrait of gene and cellular function.

Hypoxia-regulated carbonic anhydrase IX (CAIX) protein is an independent prognostic indicator in triple negative breast cancer

BackgroundThe effect of extracellular microenvironment (hypoxia and pH) has been regarded as a key hallmark in cancer progression. The study aims to investigate the effects of carbonic anhydrase IX (CAIX), a key hypoxia-inducible marker, in triple-negative breast cancer (TNBC) in correlation with clinicopathological parameters and predicting survival outcomes.MethodsA total of 323 TNBC cases diagnosed at the Department of Anatomical Pathology, Singapore General Hospital from 2003 to 2013 were used. Immunohistochemical staining (IHC) was performed using CAIX antibody and digital mRNA quantification was performed using NanoString assays. CAIX membranous expression was correlated with clinicopathological parameters using Chi-squared test or Fisher’s exact tests. Disease-free survival (DFS) and overall-survival (OS) were estimated using Kaplan–Meier analysis and compared between groups with the log-rank test.ResultsForty percent of TNBCs were observed to express CAIX protein and demonstrated significant association with larger tumour size (P = 0.002), higher histological grade (P < 0.001), and significantly worse disease-free survival (DFS) and overall survival (OS) (after adjustment: HR = 2.99, 95% CI = 1.78–5.02, P < 0.001 and HR = 2.56, 95% CI = 1.41–4.65, P = 0.002, respectively). Gene ontology enrichment analysis revealed six significantly enriched cellular functions (secretion, cellular component disassembly, regulation of protein complex assembly, glycolytic process, cellular macromolecular complex assembly, positive regulation of cellular component biogenesis) associated with genes differentially expressed (CAIX, SETX, WAS, HK2, DDIT4, TUBA4α, ARL1). Three genes (WAS, SETX and DDIT4) were related to DNA repair, indicating that DNA stability may be influenced by hypoxia in TNBC.ConclusionsOur results demonstrate that CAIX appears to be a significant hypoxia-inducible molecular marker and increased CAIX protein levels are independently associated with poor survival in TNBC. Identification of CAIX-linked seven gene-signature and its relationship with enriched cellular functions further support the implication and influence of hypoxia-mediated CAIX expression in TNBC tumour microenvironment.

A pivotal role of selective autophagy in mitochondrial quality control: Implications for zinc oxide nanoparticles induced neurotoxicity

Excessive occupational, medical, and environmental exposure of zinc oxide nanoparticles (ZnONPs) caused its accumulation in the nervous system and raised global concerns over its detrimental effects. However, very few researches had been conducted on the impact of mitochondrial quality control process on central nervous system (CNS) after ZnONPs administration, including mitochondrial fission, fusion, biogenesis, and autophagy. In present study, mitochondrial dysfunction and apoptosis were triggered in ZnONPs-exposed human neuroblastoma SH-SY5Y cells. Upregulation of mitochondrial biogenesis regulator (PGC-1α) and fission proteins (Drp1) and downregulation of fusion proteins (OPA1 and Mfn2) were observed in 3 and 6 μg/mL ZnONPs-treated cells. Meanwhile, loss of mitochondrial dynamics and biogenesis was observed in the severe impaired cells (treated with 12 μg/mL ZnONPs). More, autophagy and mitophagy were significantly activated in ZnONPs-treated cells. The increased Beclin1 and LC3 II proteins, decreases of p62 protein, and activated PINK1/Parkin signaling were quantified. The autophagy agonist (Rapamycin), inhibitor (3-MA), and mitophagy inhibitor (Cyclosporine A, CsA) were employed to verify the roles of autophagy and mitophagy in ZnONPs-treated cells. Consequently, mitochondrial dysfunction and apoptosis were aggravated by the blockage of autophagy and mitophagy. Our research could be used to evaluate the risk assessment of ZnONPs exposure in CNS neurons so as to provide a crucial guideline for their future biological applications.