IMR-90 Human Fibroblasts Research Articles

62 - H2O2 and mTOR control the senescence-associated secretory phenotype by coordinating Ca2+ transients through TRPC6 expression and activation

Cellular senescence has evolved as a protective mechanism to arrest growth of cells with oncogenic potential. While senescent cells have lost the ability to divide, they remain metabolically active and adapt a deleterious senescence associated secretory phenotype (SASP) central to the progression of several age-associated disease pathologies. The SASP is mechanistically regulated by the pro-inflammatory cytokine interleukin-1 alpha (IL-1α) whose expression and activity is responsive to the senescence associated (SA) oxidant production and the accompanying disruption of calcium (Ca2+) homeostasis. Using primary IMR-90 human fetal lung fibroblasts as a model of replicative senescence, we explored the molecular underpinnings facilitating increased Ca2+ entry in senescent cells. We establish that the redox-responsive Transient Receptor Potential TRPC6 channel is compromised due to desensitization owing to SA increases in steady state hydrogen peroxide (H2O2) production. SA dysregulation of Ca2+ is also accompanied by loss of response to H2O2-induced Ca2+ influx that can be rescued with catalase pre-treatments. Senescent cells are also insensitive to Ca2+ entry induced by hyperforin, a specific activator of TRPC6 that can be restored by catalase pre-treatments, further suggesting redox regulation of TRPC6 in senescence. Inhibition of TRPC6 channel activity restores ability of senescent cells to respond to peroxide-induced Ca2+ in addition to suppressing SASP gene expression. Furthermore, mammalian target of rapamycin (mTOR) signaling regulates SASP by means of modulating TRPC6 channel expression. Together, our findings provide compelling evidence that H2O2 and mTOR-mediated regulation of TRPC6 channel modulates SASP gene expression. As TRP channels emerge as targets of pharmacologic intervention for numerous disease pathologies, it is exciting to speculate that effect of TRP interventions may be attributed in part to inhibition of senescence and the SASP.

XIST/miR-139 axis regulates bleomycin (BLM)-induced extracellular matrix (ECM) and pulmonary fibrosis through β-catenin.

Pulmonary fibrosis (PF), characterized by the destruction of lung tissue architecture and the abnormal deposition of extracellular matrix (ECM) proteins, currently has no satisfactory treatment. In the present study, we investigated the hypothesis that XIST play a promotive role in bleomycin (BLM)-induced ECM and pulmonary fibrosis; XIST exerts its effect through miR-139 regulation. XIST expression was upregulated in lung tissues derived from BLM-induced mouse model of PF, and was positively correlated with β-catenin and ECM protein levels, respectively. LV-sh-XIST-induced XIST knockdown led to decreased PF, reduced β-catenin and ECM protein levels in lung tissues. XIST knockdown suppressed the proliferation of IMR-90 (human fibroblast) and murine lung fibroblasts (MLFCs) and ECM protein expression. Moreover, miR-139 could directly bind to XIST and the 3’UTR of β-catenin; XIST competed with β-catenin for miR-139 binding both in IMR-90 and MLFCs. In MLFCs, miR-139 inversely regulated XIST, and could partially reverse the effect of XIST on β-catenin and ECM proteins. In lung tissues of PF mice, miR-139 expression was downregulated, whereas β-catenin expression was upregulated. In conclusion, XIST exerts positive effects on BLM-induced PF through inhibiting miR-139 to promote human/mouse fibroblast proliferation and ECM proteins.

Hypoxia inducible factor-1α regulates autophagy via the p27-E2F1 signaling pathway.

Autophagy is a highly conserved process by which the cell contents are delivered to lysosomes for degradation, or are used to provide macromolecules for energy generation under conditions of nutritional starvation. It has previously been demonstrated that cancer cells in hypoxic regions, with an oxygen concentration below the normal physiological level, express hypoxia inducible factor (HIF)-1α, in order to adapt and survive. HIF-1α is important in the regulation of oxygen homeostasis and the transcription of hundreds of genes in response to conditions of hypoxia, hence maintaining energy and redox homeostasis. To determine if HIF-1α modulates autophagy and the underlying molecular mechanisms regulating this process, the human esophageal cancer EC109 and IMR90 human diploid fibroblast cell lines were exposed to normoxic or hypoxic conditions and the expression levels of various proteins subsequently examined. Small interfering RNA was used to silence p27, in order to investigate its role in the process of HIF-1α regulated autophagy. Hypoxia induced autophagy in IMR90 cells and it was revealed that immature IMR90 cells demonstrated an increased rate of autophagy compared with mature cells. HIF-1α promoted EC109 cell autophagy via positively modulating p27, whereas silencing of p27 abolished the autophagy induced by hypoxia. The present study identified the primary components of the p27-E2F1 signaling pathway by which HIF-1α regulates autophagy. A previously unidentified mechanism is here presented, via which cancer cells may generate energy, or obtain macromolecules for survival.

The peptide Phα1β, from spider venom, acts as a TRPA1 channel antagonist with antinociceptive effects in mice.

Peptides from venomous animals have long been important for understanding pain mechanisms and for the discovery of pain treatments. Here, we hypothesized that Phα1β, a peptide from the venom of the armed spider Phoneutria nigriventer, produces analgesia by blocking the TRPA1 channel. Cultured rat dorsal root ganglion (DRG) neurons, human fetal lung fibroblasts (IMR90) or HEK293 cells expressing the human TRPA1 (hTRPA1-HEK293), human TRPV1 (hTRPV1-HEK293) or human TRPV4 channels (hTRPV4-HEK293), were used for calcium imaging and electrophysiology. Nociceptive responses induced by TRPA1, TRPV1 or TRPV4 agonists or by bortezomib were investigated in mice. Phα1β selectively inhibited calcium responses and currents evoked by the TRPA1 agonist, allyl isothiocyanate (AITC), on hTRPA1-HEK293, IMR90 fibroblasts and DRG neurons. Phα1β did not affect calcium responses evoked by selective TRPV1 (capsaicin) or TRPV4 (GSK 1016790A) agonists on the various cell types. Intrathecal (i.t.) and intraplantar (i.pl.) administration of low doses of Phα1β (up to 300pmol per paw) attenuated acute nociception and mechanical and cold hyperalgesia evoked by AITC (i.t. or i.pl.), without affecting responses produced by capsaicin or hypotonic solution. Notably, Phα1β abated the TRPA1-dependent neuropathic pain-like responses induced by bortezomib. In vitro and in vivo inhibition of TRPA1 by Phα1β was reproduced by a recombinant form of the peptide, CTK 01512-2. Phα1β and CTK 01512-2 selectively target TRPA1, but not other TRP channels. This specific action underlines the potential of Phα1β and CTK 01512-2 for pain treatment.

161 - Redox-Dependent Calcium-Mediated Signaling Networks That Control the Senescence-Associated Secretory Phenotype

Cellular senescence has evolved as one of the protective mechanisms to arrest the growth of cells with oncogenic potential. While senescent cells lose the ability to divide, they remain metabolically active and adapt a senescence-associated secretory phenotype (SASP). The SASP is central to the progression of several age-associated disease pathologies perpetuated by inflammation. A key modulator of SASP is the pro-inflammatory cytokine interleukin-1 alpha (IL-1α) whose expression and activity is responsive to the senescence-associated (SA) oxidant production and the accompanying disruption of calcium (Ca2+) homeostasis. Members of the Transient Receptor Potential (TRP) channel family control cellular Ca2+ and are sensitive to activation by steady state hydrogen peroxide (ss-H2O2). This study aims at determining the molecular identity of the Ca2+ channel(s) that control the activity of the SASP regulator IL-1α. Using primary IMR-90 human fetal lung fibroblasts as a cellular senescence model, we have begun to explore the likely channel responsible for increased Ca2+ entry in senescent cells. We establish the idea that the redox-responsive TRPM2/TRPC5 channel activity is compromised during senescence due to desensitization by increased ss-H2O2 and TRPC6 channel activity is elevated to compensate for this loss of H2O2-responsive channel activity, thereby modulating SA dysregulation of Ca2+. We hypothesize that modification of this Ca2+ channel in the senescent cells can limit the downstream processing and regulation of IL-1α thereby reversing the SASP. This can establish a new paradigm of communication between the mitochondrial reactive oxygen species (ROS), cytosolic Ca2+ and nuclear IL-1α in senescence. Also, IL-1 α and TRPC6 have been shown to be independently regulated by mechanistic target of rapamycin (mTOR) signaling, a nutrient sensing pathway involved in regulation of aging processes. Overall, these studies identifying the TRPC6-mediated IL1α regulatory loop in senescence have the potential to identify new therapeutic approaches that limit the disease promoting properties of senescent cells without impairing their ability to defend against oncogenic insult.

Biocompatible nano-gallium/hydroxyapatite nanocomposite with antimicrobial activity.

Intensive research in the area of medical nanotechnology, especially to cope with the bacterial resistance against conventional antibiotics, has shown strong antimicrobial action of metallic and metal-oxide nanomaterials towards a wide variety of bacteria. However, the important remaining problem is that nanomaterials with highest antibacterial activity generally express also a high level of cytotoxicity for mammalian cells. Here we present gallium nanoparticles as a new solution to this problem. We developed a nanocomposite from bioactive hydroxyapatite nanorods (84 wt %) and antibacterial nanospheres of elemental gallium (16 wt %) with mode diameter of 22 ± 11 nm. In direct comparison, such nanocomposite with gallium nanoparticles exhibited better antibacterial properties against Pseudomonas aeruginosa and lower in-vitro cytotoxicity for human lung fibroblasts IMR-90 and mouse fibroblasts L929 (efficient antibacterial action and low toxicity from 0.1 to 1 g/L) than the nanocomposite of hydroxyapatite and silver nanoparticles (efficient antibacterial action and low toxicity from 0.2 to 0.25 g/L). This is the first report of a biomaterial composite with gallium nanoparticles. The observed strong antibacterial properties and low cytotoxicity make the investigated material promising for the prevention of implantation-induced infections that are frequently caused by P. aeruginosa.

De novo deciphering three-dimensional chromatin interaction and topological domains by wavelet transformation of epigenetic profiles.

Defining chromatin interaction frequencies and topological domains is a great challenge for the annotations of genome structures. Although the chromosome conformation capture (3C) and its derivative methods have been developed for exploring the global interactome, they are limited by high experimental complexity and costs. Here we describe a novel computational method, called CITD, for de novo prediction of the chromatin interaction map by integrating histone modification data. We used the public epigenomic data from human fibroblast IMR90 cell and embryonic stem cell (H1) to develop and test CITD, which can not only successfully reconstruct the chromatin interaction frequencies discovered by the Hi-C technology, but also provide additional novel details of chromosomal organizations. We predicted the chromatin interaction frequencies, topological domains and their states (e.g. active or repressive) for 98 additional cell types from Roadmap Epigenomics and ENCODE projects. A total of 131 protein-coding genes located near 78 preserved boundaries among 100 cell types are found to be significantly enriched in functional categories of the nucleosome organization and chromatin assembly. CITD and its predicted results can be used for complementing the topological domains derived from limited Hi-C data and facilitating the understanding of spatial principles underlying the chromosomal organization.

Identification of a novel senolytic agent, navitoclax, targeting the Bcl-2 family of anti-apoptotic factors.

SummaryClearing senescent cells extends healthspan in mice. Using a hypothesis‐driven bioinformatics‐based approach, we recently identified pro‐survival pathways in human senescent cells that contribute to their resistance to apoptosis. This led to identification of dasatinib (D) and quercetin (Q) as senolytics, agents that target some of these pathways and induce apoptosis preferentially in senescent cells. Among other pro‐survival regulators identified was Bcl‐xl. Here, we tested whether the Bcl‐2 family inhibitors, navitoclax (N) and TW‐37 (T), are senolytic. Like D and Q, N is senolytic in some, but not all types of senescent cells: N reduced viability of senescent human umbilical vein epithelial cells (HUVECs), IMR90 human lung fibroblasts, and murine embryonic fibroblasts (MEFs), but not human primary preadipocytes, consistent with our previous finding that Bcl‐xl siRNA is senolytic in HUVECs, but not preadipocytes. In contrast, T had little senolytic activity. N targets Bcl‐2, Bcl‐xl, and Bcl‐w, while T targets Bcl‐2, Bcl‐xl, and Mcl‐1. The combination of Bcl‐2, Bcl‐xl, and Bcl‐w siRNAs was senolytic in HUVECs and IMR90 cells, while combination of Bcl‐2, Bcl‐xl, and Mcl‐1 siRNAs was not. Susceptibility to N correlated with patterns of Bcl‐2 family member proteins in different types of human senescent cells, as has been found in predicting response of cancers to N. Thus, N is senolytic and acts in a potentially predictable cell type‐restricted manner. The hypothesis‐driven, bioinformatics‐based approach we used to discover that dasatinib (D) and quercetin (Q) are senolytic can be extended to increase the repertoire of senolytic drugs, including additional cell type‐specific senolytic agents.

PCTAIRE1 phosphorylates p27 and regulates mitosis in cancer cells.

PCTAIRE1 is distant relative of the cyclin-dependent kinase family that has been implicated in spermatogenesis and neuronal development, but it has not been studied in cancer. Here, we report that PCTAIRE1 is expressed in prostate, breast, and cervical cancer cells, where its RNAi-mediated silencing causes growth inhibition with aberrant mitosis due to defects in centrosome dynamics. PCTAIRE1 was not similarly involved in proliferation of nontransformed cells, including diploid human IMR-90 fibroblasts. Through yeast two-hybrid screening, we identified tumor suppressor p27 as a PCTAIRE1 interactor. In vitro kinase assays showed PCTAIRE1 phosphorylates p27 at Ser10. PCTAIRE1 silencing modulated Ser10 phosphorylation on p27 and led to its accumulation in cancer cells but not in nontransformed cells. In a mouse xenograft model of PPC1 prostate cancer, conditional silencing of PCTAIRE1 restored p27 protein expression and suppressed tumor growth. Mechanistic studies in HeLa cells showed that PCTAIRE1 phosphorylates p27 during the S and M phases of the cell cycle. Notably, p27 silencing was sufficient to rescue cells from mitotic arrest caused by PCTAIRE1 silencing. Clinically, PCTAIRE1 was highly expressed in primary breast and prostate tumors compared with adjacent normal epithelial tissues. Together our findings reveal an unexpected role for PCTAIRE1 in regulating p27 stability, mitosis, and tumor growth, suggesting PCTAIRE1 as a candidate cancer therapeutic target.

Nuclear cytoplasmic trafficking of proteins is a major response of human fibroblasts to oxidative stress.

We have used a subcellular spatial razor approach based on LC-MS/MS-based proteomics with SILAC isotope labeling to determine changes in protein abundances in the nuclear and cytoplasmic compartments of human IMR90 fibroblasts subjected to mild oxidative stress. We show that response to mild tert-butyl hydrogen peroxide treatment includes redistribution between the nucleus and cytoplasm of numerous proteins not previously associated with oxidative stress. The 121 proteins with the most significant changes encompass proteins with known functions in a wide variety of subcellular locations and of cellular functional processes (transcription, signal transduction, autophagy, iron metabolism, TCA cycle, ATP synthesis) and are consistent with functional networks that are spatially dispersed across the cell. Both nuclear respiratory factor 2 and the proline regulatory axis appear to contribute to the cellular metabolic response. Proteins involved in iron metabolism or with iron/heme as a cofactor as well as mitochondrial proteins are prominent in the response. Evidence suggesting that nuclear import/export and vesicle-mediated protein transport contribute to the cellular response was obtained. We suggest that measurements of global changes in total cellular protein abundances need to be complemented with measurements of the dynamic subcellular spatial redistribution of proteins to obtain comprehensive pictures of cellular function.

Identification of miR-494 direct targets involved in senescence of human diploid fibroblasts.

Cellular senescence is a permanent cell cycle arrest triggered by different stimuli. We recently identified up-regulation of microRNA (miR)-494 as a component of the genetic program leading to senescence of human diploid IMR90 fibroblasts. Here, we used 2-dimensional differential gel electrophoresis (2D-DIGE) coupled to mass spectrometry to profile protein expression changes induced by adoptive overexpression of miR-494 in IMR90 cells. miR-494 induced robust perturbation of the IMR90 proteome by significantly (P≤0.05) down-regulating a number of proteins. Combination of mass spectrometry-based identification of down-regulated proteins and bioinformatic prediction of the miR-494 binding sites on the relevant mRNAs identified 26 potential targets of miR-494. Among them, computational analysis identified 7 potential evolution-conserved miR-494 targets. Functional miR-494 binding sites were confirmed in 3'-untranslated regions (UTRs) of 4 of them [heterogeneous nuclear ribonucleoprotein A3 (hnRNPA3), protein disulfide isomerase A3 (PDIA3), UV excision repair protein RAD23 homolog B (RAD23B), and synaptotagmin-binding cytoplasmic RNA-interacting protein (SYNCRIP)/heterogeneous nuclear ribonucleoprotein Q (hnRNPQ)]. Their reduced expression correlated with miR-494 up-regulation in senescent cells. RNA interference-mediated knockdown of hnRNPA3 and, to a lesser extent, RAD23B mirrored the senescent phenotype induced by miR-494 overexpression, blunting cell proliferation and causing up-regulation of SA-β-galactosidase and DNA damage. Ectopic expression of hnRNPA3 or RAD23B slowed the appearance of the senescent phenotype induced by miR-494. Overall, these findings identify novel miR-494 direct targets that are involved in cellular senescence.

Off-target effects of sulforaphane include the derepression of long terminal repeats through histone acetylation events

Sulforaphane is a naturally occurring isothiocyanate in cruciferous vegetables. Sulforaphane inhibits histone deacetylases, leading to the transcriptional activation of genes including tumor suppressor genes. The compound has attracted considerable attention in the chemoprevention of prostate cancer. Here we tested the hypothesis that sulforaphane is not specific for tumor suppressor genes but also activates loci such as long terminal repeats (LTRs), which might impair genome stability. Studies were conducted using chemically pure sulforaphane in primary human IMR-90 fibroblasts and in broccoli sprout feeding studies in healthy adults. Sulforaphane (2.0 μM) caused an increase in LTR transcriptional activity in cultured cells. Consumption of broccoli sprouts (34, 68 or 102 g) by human volunteers caused a dose dependent elevation in LTR mRNA in circulating leukocytes, peaking at more than a 10-fold increase. This increase in transcript levels was associated with an increase in histone H3 K9 acetylation marks in LTR 15 in peripheral blood mononuclear cells from subjects consuming sprouts. Collectively, this study suggests that sulforaphane has off-target effects that warrant further investigation when recommending high levels of sulforaphane intake, despite its promising activities in chemoprevention.

Copper(ii) complexes of substituted salicylaldehyde dibenzyl semicarbazones: synthesis, cytotoxicity and interaction with quadruplex DNA

A series of substituted salicylaldehyde dibenzyl semicarbazones [RC6H3(OH)CH=N-NHCON(CH2Ph)2] and their copper(II) complexes were synthesized and characterized. The chloridocopper(II) complexes of the 4-OH and 5-OH substituted ligands (complexes 9 and 7) show modest affinity and good selectivity (over duplex DNA) for the quadruplex formed from the human telomeric (HTelo) DNA sequence. Substitution of the chlorido ligands of these two complexes with pyridine yielded derivatives (7-py and 9-py) with increased affinity for HTelo. These derivatives also show good selectivity for HTelo over calf-thymus DNA (170- and 211-fold, respectively). The X-ray crystal structures of 9 and 9-py were determined. Molecular docking studies based on these structures show that the complexes stack on the 5'-end of the HTelo quadruplex, with the hydroxyl group forming a hydrogen bond with a guanine residue. Complexes 7, 9, 7-py and 9-py display significant cytotoxicity against MOLT-4 human leukaemia cells. Interestingly, they have low to negligible cytotoxicity against the non-cancerous IMR-90 human fibroblasts.

Redox Control of the Senescence Regulator Interleukin-1α and the Secretory Phenotype

Senescent cells accumulate in aged tissue and are causally linked to age-associated tissue degeneration. These non-dividing, metabolically active cells are highly secretory and alter tissue homeostasis, creating an environment conducive to metastatic disease progression. IL-1α is a key senescence-associated (SA) proinflammatory cytokine that acts as a critical upstream regulator of the SA secretory phenotype (SASP). We established that SA shifts in steady-state H2O2 and intracellular Ca(2+) levels caused an increase in IL-1α expression and processing. The increase in intracellular Ca(2+) promoted calpain activation and increased the proteolytic cleavage of IL-1α. Antioxidants and low oxygen tension prevented SA IL-1α expression and restricted expression of SASP components IL-6 and IL-8. Ca(2+) chelation or calpain inhibition prevented SA processing of IL-1α and its ability to induce downstream cytokine expression. Conditioned medium from senescent cells treated with antioxidants or Ca(2+) chelators or cultured in low oxygen markedly reduced the invasive capacity of proximal metastatic cancer cells. In this paracrine fashion, senescent cells promoted invasion by inducing an epithelial-mesenchymal transition, actin reorganization, and cellular polarization of neighboring cancer cells. Collectively, these findings demonstrate how SA alterations in the redox state and Ca(2+) homeostasis modulate the inflammatory phenotype through the regulation of the SASP initiator IL-1α, creating a microenvironment permissive to tumor invasion.

A simple High-Throughput Technology Enables Gain-of-Function Screening of Human microRNAs

MicroRNAs (miRs) regulate cellular processes by modulating gene expression. Although transcriptomic studies have identified numerous miRs differentially expressed in diseased versus normal cells, expression analysis alone cannot distinguish miRs driving a disease phenotype from those merely associated with the disease. To address this limitation, we developed miR-HTS, a method for unbiased high-throughput screening of the miRNome to identify functionally relevant miRs. Herein, we applied miR-HTS to simultaneously analyze the effects of 578 lentivirally transduced human miRs or miR clusters on growth of the IMR90 human lung fibroblast cell line. Growth-regulatory miRs were identified by quantitating the representation (i.e., relative abundance) of cells overexpressing each miR over a one-month culture of IMR90, using a panel of custom-designed quantitative real-time PCR (qPCR) assays specific for each transduced miR expression cassette. The miR-HTS identified 4 miRs previously reported to inhibit the growth of human lung-derived cell lines and 55 novel growth-inhibitory miR candidates. Nine of 12 (75%) selected candidate miRs were validated and shown to inhibit IMR90 cell growth. Thus, this novel lentiviral library- and qPCR-based miR-HTS technology provides a sensitive platform for functional screening that is straightforward and relatively inexpensive.

BioSpotlight

BioTechniquesVol. 54, No. 2 BioSpotlightOpen AccessBioSpotlightPatrick C.H. Lo & Kristie NyboPatrick C.H. LoSearch for more papers by this author & Kristie NyboSearch for more papers by this authorPublished Online:3 Apr 2018https://doi.org/10.2144/000113985AboutSectionsPDF/EPUB ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinkedInRedditEmail Breaking pointChromosomal rearrangements often disrupt specific genes, potentially leading to genetic disorders or syndromes. Defining the molecular nature of these syndromes often requires mapping the breakpoint locations, but traditional methods for mapping breakpoints such as fluorescence in situ hybridization (FISH) lack the resolution to precisely pinpoint a break at the nucleotide level. Multiplex ligation-dependent probe amplification (MLPA) and Sanger sequencing offer that single nucleotide resolution, but are laborious and time consuming. In the search for a more effective way to localize chromosomal breakpoints, Okoniewski et al. from the University of Zurich, Switzerland tested the capabilities of two next-generation sequencing platforms in identifying breakpoints, and present their conclusions in this issue of BioTechniques. The authors selected the Illumina HiSeq 2000 and PacBio RS platforms, which offer a significant number of short 100 bp reads and long 2 kb reads, respectively, and compared their abilities to characterize large deletions previously identified by MLPA and microarray analyses. The authors found that both platforms provided sufficient read depths to identify precise breakpoint locations at the nucleotide level with comparable sample preparation costs. The approaches differed in preparation time -- with the Illumina methodology requiring more time for sample preparation and sequencing -- and in the approach to breakpoint detection. With the Illumina system, breakpoints were seen as an increase in mismatches, in part because the short reads were able to map across the breakpoints since the mapping software allowed several mismatches. In contrast, PacBio data showed a clear drop of read depth in the deleted region. During this study, the authors found data analysis particularly challenging since few dedicated computational techniques were available for characterizing large deletions using next-generation sequencing. Therefore, Okoniewski et al. decided to create a new script to count matches at putative breakpoint sites. This script, along with the validating data for the Illumina HiSeq and PacBio platforms, comprise a new alternative for rapid breakpoint identification that requires fewer resources and less time than traditional Sanger sequencing.Experimental design of the miR-HTS method.See “Precise breakpoint localization of large genomic deletions using PacBio and Illumina next-generation sequencers”Functional miRNA screens using qPCRMicroRNAs (miRNAs) are involved in the regulation of developmental, physiological, and pathophysiological processes. Observing the differential expression of an miRNA during development or pathogenesis, however, does not prove a direct role for that miRNA in regulating the process since changes in abundance could be the consequence and not the cause. Functional miRNA screens can determine whether candidate miRNAs with altered expression levels are in fact regulating a specific biological process, and high-throughput functional assays are critical for screening large numbers of candidate miRNAs to identify clinically relevant targets. Such high-throughput screens typically take advantage of large libraries of miRNA mimics or lentiviral miRNA overexpression constructs that are individually arrayed in microplates, but this approach requires expensive robotics and is subject to the variations and errors inherent in large-scale, multiwell HTP screens. A simpler alternative is to use pooled lentiviral or retroviral miRNA libraries to infect a population of cells such that each infected cell only has a single virus overexpressing a unique miRNA or miRNA cluster. Specific miRNAs in the pool whose overexpression in cells then causes either over- or under-representation of a specific phenotype can be identified by quantitating unique miRNA expression cassette “barcodes”. Methods to quantify barcodes include next-generation sequencing, bead-based assays, and custom-made microarrays, but all of these approaches require expensive instrumention and complicated bioinformatic analyses. In this issue of BioTechniques, C. Civin and colleagues at the University of Maryland School of Medicine demonstrate how quantitative PCR can used as a simpler means to assay for specific miRNA barcodes in functional screens of pooled lentiviral miRNA libraries. As a proof of principle, the authors used their “miR-HTS” method to screen for miRNAs regulating cell growth in the IMR90 human lung fibroblast cell line using a pooled human lenti-miRNA library and custom qPCR assays. Fifty nine growth-inhibitory miRNAs were isolated, of which only four were previously identified as inhibiting growth in human lung cells. Nine of twelve miRNAs randomly selected from among the 55 novel candidate growth-inhibitory miRNAs were validated in follow-up experiments to inhibit IMR90 cell growth. This miR-HTS method is simpler, less expensive, and presents a more flexible approach for functional miRNA screening using pooled lenti- or retro-viral miRNA libraries.See “A simple high-throughput technology enables gain-of-function screening of human microRNAs”FiguresReferencesRelatedDetails Vol. 54, No. 2 Follow us on social media for the latest updates Metrics History Published online 3 April 2018 Published in print February 2013 Information© 2013 Author(s)PDF download

KIFC1 Is Essential for Bipolar Spindle Formation and Genomic Stability in the Primary Human Fibroblast IMR-90 Cell

Kinesin family member C1 (KIFC1) is the only member of the minus-end-directed kinesin-14 family in human cells. In cancer cells, KIFC1 plays an essential role in bipolar spindle formation by clustering the multiple poles during mitosis. However, it has not been clearly demonstrated whether KIFC1 also functions to mediate bipolar spindle formation and to maintain genomic stability in normal cells. In this study, by using human primary lung fibroblast IMR-90 cells, we showed that KIFC1 knock-down with lentiviral KIFC1 shRNA induced 17% of cells with multiple microtubule organizing centers (MTOCs) and delayed cyclin A degradation for more than 2 hr in early mitosis. However, these cells eventually carried out mitosis, resulting in 24% of cells with lagging chromosomes and 9% of cells with micronuclei after mitosis. Karyotyping of KIFC1-depleted IMR-90 cells demonstrated that cells with various abnormal numbers of chromosomes are produced. When IMR-90 cells treated with KIFC1 or the control shRNA for 60 hr were compared, 20% less cells were observed in KIFC1-depleted cells without an obvious immediate cell death. As reported for Mad2 depletion in IMR-90 cells, KIFC1-depleted IMR-90 cells showed typical features of senescence, like senescence-associated (SA) β-galactosidase expression, when incubated 6 days or more. However, IMR-90 cells knocked down with both KIFC1 and Mad2 underwent apoptosis, suggesting that KIFC1 and Mad2 likely function in different pathways during mitosis. Taken together, we suggest that KIFC1 plays an essential role for bipolar MTOC formation and maintaining chromosomal stability in the mitosis of human primary fibroblast IMR-90.

Cationic, helical polypeptide-based gene delivery for IMR-90 fibroblasts and human embryonic stem cells

Diblock copolymers consisting of poly(ethylene glycol)-block-poly(γ-4-(((2-(piperidin-1-yl)ethyl)amino)methyl)benzyl-L-glutamate) (PEG-b-PVBLG-8) were synthesized and evaluated for their ability to mediate gene delivery in hard-to-transfect cells like IMR-90 human fetal lung fibroblasts and human embryonic stem cells (hESCs). The PEG-b-PVBLG-8 contained a membrane-disruptive, cationic, helical polypeptide block (PVBLG-8) for complexing with DNA and a hydrophilic PEG block to improve the biocompatibility of the gene delivery vehicle. The incorporation of PEG effectively reduced the toxicity of the helical PVBLG-8 block without dramatically compromising the polymer's ability to destabilize membranes or form complexes with DNA. PEG-b-PVBLG-8 copolymers with low (n = 76) and high (n = 287) degrees of polymerization (n) of the PVBLG-8 block were synthesized and evaluated for gene delivery. PEG-b-PVBLG-8 diblock polymers with a high degree of polymerization have a greater transfection efficiency and lower toxicity in IMR-90 cells than the commercial reagent Lipofectamine 2000. The usefulness of PEG-b-PVBLG-8 was further demonstrated via the successful transfection of hESCs without a measured loss in cell pluripotency markers.

Evaluating the potential of poly(beta-amino ester) nanoparticles for reprogramming human fibroblasts to become induced pluripotent stem cells

BackgroundGene delivery can potentially be used as a therapeutic for treating genetic diseases, including neurodegenerative diseases, as well as an enabling technology for regenerative medicine. A central challenge in many gene delivery applications is having a safe and effective delivery method. We evaluated the use of a biodegradable poly(beta-amino ester) nanoparticle-based nonviral protocol and compared this with an electroporation-based approach to deliver episomal plasmids encoding reprogramming factors for generation of human induced pluripotent stem cells (hiPSCs) from human fibroblasts.MethodsA polymer library was screened to identify the polymers most promising for gene delivery to human fibroblasts. Feeder-independent culturing protocols were developed for nanoparticle-based and electroporation-based reprogramming. The cells reprogrammed by both polymeric nanoparticle-based and electroporation-based nonviral methods were characterized by analysis of pluripotency markers and karyotypic stability. The hiPSC-like cells were further differentiated toward the neural lineage to test their potential for neurodegenerative retinal disease modeling.Results1-(3-aminopropyl)-4-methylpiperazine end-terminated poly(1,4-butanediol diacry-late-co-4-amino-1-butanol) polymer (B4S4E7) self-assembled with plasmid DNA to form nanoparticles that were more effective than leading commercially available reagents, including Lipofectamine® 2000, FuGENE® HD, and 25 kDa branched polyethylenimine, for nonviral gene transfer. B4S4E7 nanoparticles showed effective gene delivery to IMR-90 human primary fibroblasts and to dermal fibroblasts derived from a patient with retinitis pigmentosa, and enabled coexpression of exogenously delivered genes, as is needed for reprogramming. The karyotypically normal hiPSC-like cells generated by conventional electroporation, but not by poly(beta-amino ester) reprogramming, could be differentiated toward the neuronal lineage, specifically pseudostratified optic cups.ConclusionThis study shows that certain nonviral reprogramming methods may not necessarily be safer than viral approaches and that maximizing exogenous gene expression of reprogramming factors is not sufficient to ensure successful reprogramming.

RRM2B Suppresses Activation of the Oxidative Stress Pathway and is Up-regulated by P53 During Senescence

RRM2B is the DNA damage-inducible small subunit of ribonucleotide reductase, the rate-limiting enzyme in de novo deoxyribonucleoside triphosphate synthesis. Although RRM2B is implicated in DNA repair and the maintenance of mitochondrial DNA content, the regulation and function of RRM2B in senescence have not been previously established. Here, we show that RRM2B is highly induced in a p53-dependent manner during senescence in primary human fibroblast IMR90 cells and is expressed at higher levels in senescent precancerous human prostatic intraepithelial neoplasm lesions compared to adjacent normal prostate glands. Paradoxically, silencing RRM2B expression leads to an increase in the level of reactive oxygen species, mitochondrial membrane depolarization, and premature senescence in a p38MAPK- and p53-dependent manner in young fibroblasts. Consistently, induction of senescence is accelerated in Rrm2b deficient mouse embryo fibroblasts. Our data demonstrate that RRM2B is induced by stress signals prior to the onset of senescence and prevents premature oxidative stress-induced senescence.