Stable Expression Levels Research Articles

Evaluation and Validation of the Six Housekeeping Genes for Normalizing Mrna Expression in the Ovarian Follicles and Several Tissues in Chicken

ABSTRACT Expression of housekeeping genes is relatively constant in different tissues and cells by RT-qPCR analysis. Housekeeping genes (HGs) are usually utilized as the reference to evaluate and compare mRNA expression abundances of target genes in different cells or tissues sampled. However, the expression stabilities of different HGs in diverse samples may appear divergence. Currently, there is no exact reference data of HGs in hen ovarian follicular tissues during egg-laying period available yet. In this study, we detected the expression of 18SrRNA, ACTB, HOXC8, GAPDH, alpha-A, and alpha-D mRNA in the varied-size ovarian follicles (1-8 mm in diameter and F5), hearts, livers, spleens, lungs, and breast muscles of the laying hens by RT-qPCR, to analyze the results via Ct value, geNorm, Normfinder, and Bestkeeper. The data showed that the expression levels of 18SrRNA, alpha-A, and alpha-D transcripts were more significantly stable than the other three genes for normalizing mRNA expression in the hen ovarian follicles examination. Moreover, alpha-D, 18SrRNA, and alpha-A were also most suitable for the expression normalization in the tissues of the heart, liver, spleen, lung and breast muscle. In contrast, 18SrRNA has the most stable mRNA expression levels in all tissues sampled, so it can serve as an excellent inner control for the evaluation of the transcription levels in chickens. It is a remarkable fact that HOXC8 as a candidate reference should be avoided. Our study establishes a set of stably expressed candidate inner references in the hen ovarian follicles and several tissues, it firstly provided an exact data for validation of the inner references in normalizing transcription levels of a target gene in chickens.

Evaluation of reference genes for quantitative real-time PCR in Wharton's Jelly-derived mesenchymal stem cells after lentiviral transduction and differentiation.

Quantitative real time reverse transcription PCR, qRT-PCR, is one of the most important techniques for assessing the level of gene expression. Selecting the correct reference gene to normalize the results is a key step in this method. Inaccurate data can be generated if the correct reference gene is not selected. The level of the expression of reference genes is tissue-variable, and in the case of mesenchymal stem cells (MSC), it can be different depending on the source of their origin. The aim of this study was to select the reference gene for Wharton's Jelly-derived MSC (WJ- MSC) that were undergoing transduction and differentiation. In this work, the expression of 32 genes was analyzed, of which two (RPS17 and 18SrRNA), which had the most stable expression level, were selected. A comparative analysis of the expression stability of the selected genes was then performed with the genes that are most commonly used in the literature, i.e. β-actin and GAPDH. Next, it was determined that a false picture of the expression level of the studied genes can be obtained when a reference gene with variable expression level is used for normalization. RPS17 and 18SrRNA proved to be the most stable reference genes for the WJ-MSC that had been subjected to the lentiviral transfection procedure followed by differentiation. The expression of β-actin and GAPDH was highly unstable and therefore these genes are not suitable for use as reference genes in studies involving WJ- MSC.

Exogenous DCPTA Increases the Tolerance of Maize Seedlings to PEG-Simulated Drought by Regulating Nitrogen Metabolism-Related Enzymes

2-(3,4-Dichlorophenoxy) triethylamine (DCPTA) regulates plant development; however, the molecular basis of this regulation is poorly understood. In this study, RNA sequencing (RNA-seq) analysis and physiological indexes of maize seedlings (three-leaf stage) treated with 15% polyethylene glycol (PEG) with/without DCPTA were investigated to explore the possible mechanism of exogenous DCPTA-improved drought tolerance. In the library pair comparisons of DCPTA vs. the control, PEG vs. the control, and PEG + DCPTA vs. PEG, totals of 19, 38 and 20 differentially expressed genes (DEGs) were classified as being involved in metabolic processes, respectively; totals of 5, 11, and 6 DEGs were enriched in the nitrogen (N) metabolic pathway, respectively. The genes encoding nicotinamide adenine dinucleotide-nitrate reductase (NADH-NR), ferredoxin-nitrite reductase (Fd-NiR), reduced ferredoxin- glutamate synthase (Fd-GOGAT), and chloroplastic glutamine synthetase (GS 2) were common in response to PEG-simulated drought stress with/without DCPTA treatment. Moreover, DCPTA maintained stable gene relative expression levels and protein abundances of NADH-NR, Fd-NiR, GS2, and Fd-GOGAT. Moreover, exogenous DCPTA partially mitigated PEG-simulated drought-induced reductions in the enzymatic activities of NR, nitrite reductase (NiR), glutamine synthase (GS), glutamine oxoglutarate aminotransferase (GOGAT), and transaminase, as well as in the contents of nitrate (NO3−), nitrite (NO2−) and soluble proteins and increases in the contents of ammonium (NH4+) and free amino acids. Together, our results indicate that exogenous DCPTA improved plant growth and drought tolerance by regulating N-mechanism enzymatic activities involved in transcription and enzymatic protein synthesis.

Comparative analysis of proso millet (Panicum miliaceum L.) leaf transcriptomes for insight into drought tolerance mechanisms

BackgroundDrought stress is a major abiotic stress that causes huge losses in agricultural production. Proso millet (Panicum miliaceum L.) can efficiently adapt to drought stress and provides important information and gene resources to improve drought tolerance. However, its complex drought-responsive mechanisms remain unclear.ResultsAmong 37 core Chinese proso millet cultivars, Jinshu 6 (JS6) was selected as the drought-sensitive test material, whereas Neimi 5 (NM5) was selected as the drought-tolerant test material under PEG-induced water stress. After sequencing, 1695 differentially expressed genes (DEGs) were observed in JS6 and NM5 without PEG-induced water stress (JS6CK and NM5CK). A total of 833 and 2166 DEGs were found in the two cultivars under simulated drought by using 20% PEG-6000 for 6 (JS6T6 and NM5T6) and 24 h (JS6T24 and NM5T24), respectively. The DEGs in JS6T6 and JS6T24 treatments were approximately 0.298- and 0.754-fold higher than those in NM5T6 and NM5T24, respectively. Compared with the respective controls, more DEGs were found in T6 treatments than in T24 treatments. A delay in the transcriptional responses of the ROS scavenging system to simulated drought treatment and relatively easy recovery of the expression of photosynthesis-associated genes were observed in NM5. Compared with JS6, different regulation strategies were observed in the jasmonic acid (JA) signal transduction pathway of NM5.ConclusionUnder PEG-induced water stress, NM5 maintained highly stable gene expression levels. Compared with drought-sensitive cultivars, the different regulation strategies in the JA signal transduction pathway in drought-tolerant cultivars may be one of the driving forces underlying drought stress tolerance.

Study on the Role of Cytc in Response to BmNPV Infection in Silkworm, Bombyx mori (Lepidoptera).

Bombyx mori nucleopolyhedrovirus (BmNPV) is one of the primary pathogens of the silkworm. Cytochrome c (cytc) showed a significant response to BmNPV infection in our previous transcriptome study. However, little is known about the role of Bombyx mori cytc (Bmcytc) in resistance to BmNPV infection. In this study, the expression levels analysis of Bmcytc showed stable expression levels in selected tissues of the resistant strain AN following BmNPV infection, while there was downregulation in the susceptible strain p50, except in the malpighian tubule. To further study the role of Bmcytc in viral infection, Bmcytc was knocked down with siRNA in vitro, resulting in significant downregulation of selected downstream genes of the mitochondrial pathway, including Bmapaf, Bmcaspase-Nc, and Bmcaspase-1; this was also confirmed by overexpression of Bmcytc using the pIZT/V5-His-mCherry insect vector, except Bmcaspase-1. Moreover, knockdown of Bmcytc significantly promoted the infection process of BmNPV in vitro, while the infection was inhibited by overexpression of Bmcytc at the early stage and subsequently increased rapidly. Based on these results, we concluded that Bmcytc plays a vital role in BmNPV infection by regulating the mitochondrial apoptosis pathway. Our work provides valuable data for the clarification of the mechanism of silkworm resistance to BmNPV infection.

Both insufficient and excessive glucocorticoid receptor-mediated signaling impair neuronal migration

Glucocorticoids (GCs) are a class of steroid hormones that regulate numerous physiological events in the human body. Clinically, glucocorticoids are used for anti-inflammatory and immunosuppressive actions via binding with glucocorticoid receptors (GRs). Emerging evidence has also indicated that inappropriate GC and GR levels are detrimental for brain development and eventually lead to severe neurological diseases. However, the roles of GC/GR signaling in brain development are not fully understood. Here, we showed that stable GR expression levels were critical for brain development, because both GR knockdown and overexpression severely impaired neuronal migration. Further studies showed that the multipolar-bipolar transition and leading process development were interrupted in GR-knockdown and GR-overexpressing neurons. To elucidate the underlying mechanism, we screened the protein levels of downstream molecules and identified RhoA as a factor negatively regulated by the GR. Restoration of the RhoA protein level partially rescued the neuronal migration defects in the GR-knockdown and GR-overexpressing neurons, indicating that RhoA played a major role in GR-mediated neuronal migration. These data suggest that an appropriate level of GC/GR signaling is essential for precise control of neuronal migration.

Preliminary study on response and its mechanism of ginsenoside biosynthesis in Panax ginseng to water regulation

The study is aimed to explore the effect of soil moisture content on ginsenoside biosynthesis and explain its mechanism from the perspectives of antioxidant enzyme system and gene expression of key enzymes in the pathway of ginsenoside synthesis. In the study,two years old Panax ginseng was used as the experimental material and three moisture gradient,40% of saturated water content( W1),60%( W2),80%( W3) were set up. The content of 11 monomeric saponins were determined by HPLC. With GAPDH as a reference gene,six key enzymes( HMGR,SS,β-AS,CYP716 A47,CYP716 A52 v2,CYP716 A53 v2) in ginseng saponin synthesis pathway expression were analyzed by fluorescent quantitative PCR and the activities of superoxide dismutase( SOD),peroxidase( POD),catalase( CAT) activity and MDA content were also determined. With the increase of soil water,the content of ginseng saponin and biomass showed an increasing trend. PPD( Rb1,Rc,Rb2,Rd,Rh2,Rb3,Rg3),PPT( Rg1,Re,Rf) ginsenoside,Ro and total ginsenoside reached the maximum value on August 30,were 9.92,5.48,0.63 mg·g-1,respectively. During the whole regulation period,the antioxidant activity of W3 was greater than that of W1,and the MDA content was less than that of W1. At W3,expression levels of β-AS,CYP716 A47 and CYP716 A53 v2 showed an increasing trend,while HMGR and SS genes showed relatively stable expression levels under various water conditions. According to the correlation analysis,HMGR and SS genes in the W3 treatment group were significantly positively correlated with PPD,PPT ginsenoside and Ro,CYP716 A52 v2 gene was significantly positively correlated with Ro,and CYP716 A47 gene was significantly positively correlated with PPD ginsenoside. There was a significant positive correlation between β-AS gene and PPD ginsenoside in W1 and W2 treatment. Therefore,W3 is the optimum moisture content,ginseng total saponins and monomer saponin content is the highest,the gene closely correlation with content of saponins and more conducive to the accumulation of ginsenosides.

Amyloidosis causes downregulation of SorLA, SorCS1 and SorCS3 expression in mice.

Accumulation of β-amyloid peptide (Aβ) is regarded as a primary cause of Alzheimer's disease (AD). Aβ is derived by sequential cleavage of the amyloid precursor protein (APP). Alterations in the subcellular targeting of APP are thought to affect the degree of Aβ production. Sorting receptors, such as SorLA, convey subcellular targeting of APP. Dysfunction of SorLA, and likely of the related receptors SorCS1 and SorCS3, cause AD. Nevertheless, disease progression could also provoke altered expression of the receptors. Here, we assessed if Aβ plaque formation promotes altered expression of SorLA, SorCS1 and SorCS3. We analyzed transcript levels during aging and after amyloidosis in brain areas characterized by early amyloid plaque formation in an AD mouse model (APPPS1) and wild types. We observed stable expression levels during aging (1-12 months). After plaque formation, SorCS1 and SorLA expression were markedly reduced in the frontal cerebral cortex and to a minor extent in the hippocampus, whereas SorCS3 expression was solely reduced in the frontal cerebral cortex. Our results indicate that disease progression, associated with Aβ accumulation, can negatively regulate expression of the receptors.

Hv1-deficiency protects β cells from glucotoxicity through regulation of NOX4 level

High glucose (HG)-induced oxidative stress contributes to the dysfunction of pancreatic β cells in diabetes. The voltage-gated proton channel Hv1 has been proposed to support reactive oxygen species (ROS) production during respiratory bursts. However, the effect of Hv1 on glucotoxicity in pancreatic β cells is not clear yet. In this study, we examined the protective effects of Hv1-deficiency in HG cultured β cells. Following 48 h of treatment with 30 mM high glucose, Hv1 KO β cells showed higher cell viability, lower cell apoptosis and a more stable insulin gene expression level compared to WT β cells. In both control and HG cultured β cells, deficiency of Hv1 decreased the glucose- and PMA-induced ROS production. Finally, HG incubation led to NOX4 upregulation in WT β cells, which could be inhibited by HV1 deficiency. In conclusion, Hv1-deficiency prevents the HG treatment-induced NOX4 upregulation and protects β cells from glucotoxicity.

Transcriptomic Responses to Thermal Stress and Varied Phosphorus Conditions in Fugacium kawagutii.

Coral reef-associated Symbiodiniaceae live in tropical and oligotrophic environments and are prone to heat and nutrient stress. How their metabolic pathways respond to pulses of warming and phosphorus (P) depletion is underexplored. Here, we conducted RNA-seq analysis to investigate transcriptomic responses to thermal stress, phosphate deprivation, and organic phosphorus (OP) replacement in Fugacium kawagutii. Using dual-algorithm (edgeR and NOIseq) to remedy the problem of no replicates, we conservatively found 357 differentially expressed genes (DEGs) under heat stress, potentially regulating cell wall modulation and the transport of iron, oxygen, and major nutrients. About 396 DEGs were detected under P deprivation and 671 under OP utilization, both mostly up-regulated and potentially involved in photosystem and defensome, despite different KEGG pathway enrichments. Additionally, we identified 221 genes that showed relatively stable expression levels across all conditions (likely core genes), mostly catalytic and binding proteins. This study reveals a wide range of, and in many cases previously unrecognized, molecular mechanisms in F. kawagutii to cope with heat stress and phosphorus-deficiency stress. Their quantitative expression dynamics, however, requires further verification with triplicated experiments, and the data reported here only provide clues for generating testable hypotheses about molecular mechanisms underpinning responses and adaptation in F. kawagutii to temperature and nutrient stresses.

Genome-wide identification of the essential protein-coding genes and long non-coding RNAs for human pan-cancer.

Genome-scale CRISPR/Cas9 system has been a democratized gene editing technique and widely used to investigate gene functions in some biological processes and diseases especially cancers. Aiming to characterize gene aberrations and assess their effects on cancer, we designed a pipeline to identify the essential genes for pan-cancer. CRISPR screening data were used to identify the essential genes that were collected from published data and integrated by Robust Rank Aggregation algorithm. Then, hypergeometrics test and random walks with restart (RWR) were used to predict additional essential genes on broader scale. Finally, the expression status and potential roles of these genes were explored based on TCGA portal and regulatory network analysis. We collected 926 samples from 10 CRISPR-based screening studies involving 33 different types of cancer to identify cancer-essential genes, which consists of 799 protein-coding genes (PCGs) and 97 long non-coding RNAs (lncRNAs). Then, we constructed a 'bi-colored' network with both PCGs and lncRNAs and applied it to predict additional essential genes including 495 PCGs and 280 lncRNAs on a broader scale using hypergeometrics test and RWR. After obtaining all essential genes, we further investigated their potential roles in cancer and found that essential genes have higher and more stable expression levels, and are associated with multiple cancer-associated biological processes and survival time. The regulatory network analysis detected two intriguing modules of essential genes participating in the regulation of cell cycle and ribosome biogenesis in cancer. . Supplementary data are available at Bioinformatics online.

Optogenetic Stimulation of the Axons of Visual Cortex and Hippocampus Pyramidal Neurons in Living Brain Slices

Widening and deepening our understanding of how the brain works requires constant improvements not only in methods of recording neuron activity, but also improvements in experimental approaches to activating individual cells and their compartments. Optogenetic stimulation methods using finely focused light to trigger the opening of the light-activated depolarizing cation channel rhodopsin-2 (ChR2) have become widely used in recent years. Current molecular biological methods provide for the genetic expression of ChR2 in different cell types, which, along with the ability to carry out electrophysiological experiments with reproducible patterns of activation and stable levels of ChR2 expression, have developed optogenetics into an effective method for gathering physiological data previously unavailable to conventional methods. We report here the use of local activation of axons using an optogenetic stimulation method. Experiments were performed in combination with recording the electrical activity of neurons using the patch-clamp method, as well as laser scanning confocal microscopy. Experiments used the transgenic mouse strain Thy1-ChR2-YFP, in which ChR2 is expressed in only a small proportion of pyramidal cells. Direct studies of the effects of functional activity in the proximal branches of pyramidal neuron axons in layer 5 of the visual cortex and hippocampal field CA1 on the shape and generation of action potentials were carried out. We also describe methodological advances and means of solving problems encountered in the optogenetic stimulation of the axons of pyramidal neurons in the central nervous system of mammals.

Acute Drug Effects on the Human Placental Tissue: The Development of a Placental Murine Xenograft Model.

A pilot study was conducted to establish a human placental xenograft, which could serve as a model to evaluate the effect of toxic exposures during pregnancy. The protocol consisted of engraftment of third-trimester human placental tissue in immunocompromised mice, after induction of a pseudo-pregnancy state by ovariectomy and progesterone supplementation. To validate the model, the placental tissue before and after engraftment was examined by immunohistochemistry, fluorescence-activated cell sorting (FACS), single-nucleotide polymorphism (SNP) genotyping, and whole transcriptome sequencing (WTSS). The human chorion gonadotropin (hCG) production in serum and urine was examined by enzyme-linked immunosorbent assay. Microscopic evaluation of the placental tissue before and after engraftment revealed a stable morphology and preserved histological structure of the human tissue. Viable trophoblast was present after engraftment and remained stable over time. Vascularization and hormonal secretion (hCG) were present till 3 weeks after engraftment. Thirty-one SNPs were equally present, and there was a stable expression level for 56 451 genes evaluated by whole transcriptome sequencing. Although this human placental xenograft model cannot copy the unique uterine environment in which the placenta develops and interacts between the mother and the fetus, it could be a suitable tool to evaluate the acute impact and adaptive processes of the placental tissue to environmental changes.

The effect of dietary supplementation of low crude protein on intestinal morphology in pigs

To explore the effects of reducing the Cp levels on intestinal barrier function, low Cp (LP) and NRC standard Cp (NP) diets were fed to pigs from 45 to 160 days, and in vitro experiments were performed using monolayers of IPEC-J2 cells. The number of goblet cells, expression of proteins related to cell junction, amino acid transport, glucose transport, transepithelial electrical resistance (TEER), dextran permeability, and IL-6 secretion level were detected in pigs. The results demonstrated that a moderate reduction of Cp levels did not affect intestinal morphology, as demonstrated by a normal villi height, crypt depth and normal numbers of goblet cells. The maintenance of the intestinal structure obtained with LP was also confirmed by stable mRNA expression levels of muc2 and E-cadherin in the jejunum. We also found that LP did not affect the protein expression of cationic amino acid transporter 1 (CAT-1) and alanine serine cysteine transporter 1 (ASCT1) from 45 to 160 days. Moreover, the excitatory amino acid transporter 3 (EAAT3), sodium-glucose cotransporter 1 (SGLT1) and glucose transporter (GLUT2) protein expression levels in the jejunum were significantly increased at a certain age during the rearing period. Furthermore, we also demonstrated that a reduction in protein concentration up to 15% in the cultural medium of IPEC-J2 cells did not impact the mucosal barrier function. This study demonstrated that a moderate reduction of the protein level did not affect intestinal mucosal barrier function and morphology in the jejunum.

Abstract 16713: Defining the Tbx5-Dependent miRNA Regulatory Networks of Atrial Fibrillation

Atrial fibrillation (AF) is the most commonly diagnosed arrhythmic disorder, characterized by random electrical activity in the heart. Complications of AF include stroke and heart failure, which makes understanding the molecular mechanism underlying this conduction defect imperative. The Tbx5 locus has been implicated by genome wide association studies (GWAS) to have an increased risk for AF. Our lab has previously demonstrated the absence of this transcription factor leads to spontaneous and sustained AF, which corroborates the importance of Tbx5 in the maintenance of cardiac rhythm. While Tbx5 is known to drive the network for cardiac rhythm, the downstream regulatory components need to be further characterized, including the downstream miRNAs. The components involved in cardiac rhythm are dose sensitive, therefore small perturbations in gene expression can lead to arrhythmias. Maintaining stable levels of gene expression can be regulated with miRNAs, which provide a negative feedback in dose sensitive pathways. Tbx5 -deficient mice developed spontaneous, sustained AF; in order to further interrogate the TBX5-dependent pathway that led to AF, we transcriptionally profiled small RNAs from the left atrium of Tbx5 -deficient mice. The most downregulated TBX5-dependent miRNA was miR10b. In concordance with previous publications, our miR10b mimic and inhibitor experiments in HL-1 cardiomyocytes demonstrate that miR10b negatively regulates Tbx5 expression. Therefore, we hypothesized that miR10b was crucial in the maintenance of atrial rhythm. Cellular electrophysiology studies with the overexpression of miR10b in HL-1 cardiomyocytes led to the elongation of atrial action potentials, similar to the phenotype we saw in the Tbx5 -deficient atrial tissue. Using whole mouse electrophysiology, we found that the mir10b removal in the hearts leads to increased AF susceptibility. Thus, providing evidence that mirR10b is crucial for the maintenance of normal cardiac conduction. In order to identify other miRNAs essential for cardiac conduction, we examined the other TBX5-dependent miRNAs in a high-throughput calcium screen. Further defining the miRNAs can provide a better understanding of the regulatory mechanisms crucial for cardiac conduction.

Prss56 expression in the rodent hypothalamus: Inverse correlation with pro-opiomelanocortin suggests oscillatory gene expression in adult rat tanycytes.

We recently reported that the number of hypothalamic tanycytes expressing pro-opiomelanocortin (Pomc) is highly variable among brains of adult rats. While its cause and significance remain unknown, identifying other variably expressed genes in tanycytes may help understand this curious phenomenon. In this in situ hybridization study, we report that the Prss56 gene, which encodes a trypsin-like serine protease and is expressed in neural stem/progenitor cells, shows a similarly variable mRNA expression in tanycytes of adult rats and correlates inversely with tanycyte Pomc mRNA. Prss56 was expressed in α1, β1, subsets of α2, and some median eminence γ tanycytes, but virtually absent from β2 tanycytes. Prss56 was also expressed in vimentin positive tanycyte-like cells in the parenchyma of the ventromedial and arcuate nuclei, and in thyrotropin beta subunit-expressing cells of the pars tuberalis of the pituitary. In contrast to adults, Prss56 expression was uniformly high in tanycytes in adolescent rats. In mice, Prss56-expressing tanycytes and parenchymal cells were also observed but fewer in number and without significant variations. The results identify Prss56 as a second gene that is expressed variably in tanycytes of adult rats. We propose that the variable, inversely correlating expression of Prss56 and Pomc reflect periodically oscillating gene expression in tanycytes rather than stable expression levels that vary between individual rats. A possible functional link between Prss56 and POMC, and Prss56 as a potential marker for migrating tanycytes are discussed.

Genomic Landscape of Methylation Islands in Hymenopteran Insects.

Recent genome-wide DNA methylation analyses of insect genomes accentuate an intriguing contrast compared with those in mammals. In mammals, most CpGs are heavily methylated, with the exceptions of clusters of hypomethylated sites referred to as CpG islands. In contrast, DNA methylation in insects is localized to a small number of CpG sites. Here, we refer to clusters of methylated CpGs as “methylation islands (MIs),” and investigate their characteristics in seven hymenopteran insects with high-quality bisulfite sequencing data. Methylation islands were primarily located within gene bodies. They were significantly overrepresented in exon–intron boundaries, indicating their potential roles in splicing. Methylated CpGs within MIs exhibited stronger evolutionary conservation compared with those outside of MIs. Additionally, genes harboring MIs exhibited higher and more stable levels of gene expression compared with those that do not harbor MIs. The effects of MIs on evolutionary conservation and gene expression are independent and stronger than the effect of DNA methylation alone. These results indicate that MIs may be useful to gain additional insights into understanding the role of DNA methylation in gene expression and evolutionary conservation in invertebrate genomes.

A Three-Dimensional Collagen-Elastin Scaffold for Heart Valve Tissue Engineering.

Since most of the body’s extracellular matrix (ECM) is composed of collagen and elastin, we believe the choice of these materials is key for the future and promise of tissue engineering. Once it is known how elastin content of ECM guides cellular behavior (in 2D or 3D), one will be able to harness the power of collagen-elastin microenvironments to design and engineer stimuli-responsive tissues. Moreover, the implementation of such matrices to promote endothelial-mesenchymal transition of primary endothelial cells constitutes a powerful tool to engineer 3D tissues. Here, we design a 3D collagen-elastin scaffold to mimic the native ECM of heart valves, by providing the strength of collagen layers, as well as elasticity. Valve interstitial cells (VICs) were encapsulated in the collagen-elastin hydrogels and valve endothelial cells (VECs) cultured onto the surface to create an in vitro 3D VEC-VIC co-culture. Over a seven-day period, VICs had stable expression levels of integrin β1 and F-actin and continuously proliferated, while cell morphology changed to more elongated. VECs maintained endothelial phenotype up to day five, as indicated by low expression of F-actin and integrin β1, while transformed VECs accounted for less than 7% of the total VECs in culture. On day seven, over 20% VECs were transformed to mesenchymal phenotype, indicated by increased actin filaments and higher expression of integrin β1. These findings demonstrate that our 3D collagen-elastin scaffolds provided a novel tool to study cell-cell or cell-matrix interactions in vitro, promoting advances in the current knowledge of valvular endothelial cell mesenchymal transition.

Rare targetable drivers (RTDs) in non-small cell lung cancer (NSCLC): Outcomes with immune check-point inhibitors (ICPi)

ObjectivesEfficacy of immune check-point inhibitors (ICPi) in NSCLC with rare targetable drivers (RTDs) is largely unknown. Materials and MethodsConsecutive patients with NSCLC and RTDs (non-EGFR/ALK, n-82) were selected from the Davidoff Cancer Center database. ORR, PFS, OS with ICPi, OS since advanced disease diagnosis, TMB, MSI, and PD-L1 expression were analyzed; uni- and multivariate PFS and OS analyses were done. OS with ICPi was compared between the RTD cohort and the non-selected NSCLC cohort (n-278). ResultsOf 50 tumors tested, 32%, 38%, and 30% were associated with ≥50%, 1–49% and <1% PD-L1 expression, respectively. Median TMB (n-48) comprised 4 muts/Mb (0–57); TMB ≥ 10 muts/Mb was seen in 19% of tumors. Both TMB and PD-L1 expression varied across different RTDs. All the 47 tumors were MSI stable. ORR with ICPi (n-44) was 16%, median PFS was 3.2 months (95% CI, 2.6–5.0), median OS was 16.2 months (95% CI, 8.4-NR). No correlation was seen between OS with ICPi and PD-L1 expression (p > 0.4), TMB (p > 0.8), or RTD type (p > 0.3). In the multivariate analysis, ECOG PS (p-0.005), targeted agents exposure (p-0.005), and ICPi exposure (p-0.04) were the only variables which correlated with OS since advanced disease diagnosis. Median OS since advanced disease diagnosis comprised 32 months (95% CI, 19.9–44.9) and 13 months (95% CI, 6.6–15.9) for patients who were and were not exposed to ICPi, respectively (log-rank test-6.3; p-0.01). In the inter-cohort comparison, for patients matched for ECOG PS (0/1), median OS with ICPi comprised 17.5 months (95% CI, 8.1-NR) and 8.6 months (95% CI, 6.7-NR) for RTD and non-selected patients, respectively (log-rank test-2.4, p-0.1). ConclusionIn NSCLC with RTD, ICPi have favorable efficacy and independent impact on OS. NSCLC with RTD is associated with MSI stable status and variable levels of PD-L1 expression and TMB; their predictive value remains to be determined.

Anti-replicative recombinant 5S rRNA molecules can modulate the mtDNA heteroplasmy in a glucose-dependent manner.

Mutations in mitochondrial DNA are an important source of severe and incurable human diseases. The vast majority of these mutations are heteroplasmic, meaning that mutant and wild-type genomes are present simultaneously in the same cell. Only a very high proportion of mutant mitochondrial DNA (heteroplasmy level) leads to pathological consequences. We previously demonstrated that mitochondrial targeting of small RNAs designed to anneal with mutant mtDNA can decrease the heteroplasmy level by specific inhibition of mutant mtDNA replication, thus representing a potential therapy. We have also shown that 5S ribosomal RNA, partially imported into human mitochondria, can be used as a vector to deliver anti-replicative oligoribonucleotides into human mitochondria. So far, the efficiency of cellular expression of recombinant 5S rRNA molecules bearing therapeutic insertions remained very low. In the present study, we designed new versions of anti-replicative recombinant 5S rRNA targeting a large deletion in mitochondrial DNA which causes the KSS syndrome, analyzed their specific annealing to KSS mitochondrial DNA and demonstrated their import into mitochondria of cultured human cells. To obtain an increased level of the recombinant 5S rRNA stable expression, we created transmitochondrial cybrid cell line bearing a site for Flp-recombinase and used this system for the recombinase-mediated integration of genes coding for the anti-replicative recombinant 5S rRNAs into nuclear genome. We demonstrated that stable expression of anti-replicative 5S rRNA versions in human transmitochondrial cybrid cells can induce a shift in heteroplasmy level of KSS mutation in mtDNA. This shift was directly dependent on the level of the recombinant 5S rRNA expression and the sequence of the anti-replicative insertion. Quantification of mtDNA copy number in transfected cells revealed the absence of a non-specific effect on wild type mtDNA replication, indicating that the decreased proportion between mutant and wild type mtDNA molecules is not a consequence of a random repopulation of depleted pool of mtDNA genomes. The heteroplasmy change could be also modulated by cell growth conditions, namely increased by cells culturing in a carbohydrate-free medium, thus forcing them to use oxidative phosphorylation and providing a selective advantage for cells with improved respiration capacities. We discuss the advantages and limitations of this approach and propose further development of the anti-replicative strategy based on the RNA import into human mitochondria.