QuantSeq

A global genetic interaction network maps a wiring diagram of cellular function

Michael Costanzo, Benjamin VanderSluis, Elizabeth N. Koch, Anastasia Baryshnikova, Carles Pons, Guihong Tan, Wen Wang, Matej Usaj, Julia Hanchard, Susan D. Lee, Vicent Pelechano, Erin B. Styles, Maximilian Billmann, Jolanda van Leeuwen, Nydia van Dyk, Zhen-Yuan Lin, Elena Kuzmin, Justin Nelson, Jeff S. Piotrowski, Tharan Srikumar, Sondra Bahr, Yiqun Chen, Raamesh Deshpande, Christoph F. Kurat1, Sheena C. Li, Zhijian Li, Mojca Mattiazzi Usaj, Hiroki Okada, Natasha Pascoe, Bryan-Joseph San Luis, Sara Sharifpoor, Emira Shuteriqi, Scott W. Simpkins, Jamie Snider, Harsha Garadi Suresh, Yizhao Tan, Hongwei Zhu, Noel Malod-Dognin, Vuk Janjic, Natasa Przulj, Olga G. Troyanskaya, Igor Stagljar, Tian Xia, Yoshikazu Ohya, Anne-Claude Gingras, Brian Raught, Michael Boutros, Lars M. Steinmetz, Claire L. Moore, Adam P. Rosebrock, Amy A. Caudy, Chad L. Myers, Brenda Andrews, Charles Boone

Science. 2016 Sep 23, doi: 10.1126/science.aaf1420

We generated a global genetic interaction network for Saccharomyces cerevisiae, constructing more than 23 million double mutants, identifying about 550,000 negative and about 350,000 positive genetic interactions. This comprehensive network maps genetic interactions for essential gene pairs, highlighting essential genes as densely connected hubs. Genetic interaction profiles enabled assembly of a hierarchical model of cell function, including modules corresponding to protein complexes and pathways, biological processes, and cellular compartments. Negative interactions connected functionally related genes, mapped core bioprocesses, and identified pleiotropic genes, whereas positive interactions often mapped general regulatory connections among gene pairs, rather than shared functionality. The global network illustrates how coherent sets of genetic interactions connect protein complex and pathway modules to map a functional wiring diagram of the cell.

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Integrated Stress Response Mediates Epithelial Injury In Mechanical Ventilation

Tamas Dolinay, Blanca E Himes, Maya Shumyatcher, Gladys Gray Lawrence, and Susan S Margulies

Am J Respir Cell Mol Biol. 2017 Mar 31, doi: 10.1165/rcmb.2016-0404OC

RATIONALE:
Ventilator-induced lung injury (VILI) is a severe complication of mechanical ventilation that can lead to acute respiratory distress syndrome (ARDS). VILI is characterized by damage to the epithelial barrier with subsequent pulmonary edema and profound hypoxia. Available lung protective ventilator strategies offer only modest benefit in preventing VILI because they cannot impede alveolar overdistension and concomitant epithelial barrier dysfunction in the inflamed lung regions. There are currently no effective biochemical therapies to mitigate injury to the alveolar epithelium. We hypothesize that alveolar stretch activates the integrated stress response (ISR) pathway, and that the chemical inhibition of this pathway mitigates alveolar barrier disruption during stretch and mechanical ventilation.

METHODS:
Using our established rat primary type I-like alveolar epithelial cell monolayer stretch model and in vivo rat mechanical ventilation that mimics alveolar overdistension seen in ARDS we studied epithelial responses to mechanical stress.

RESULTS:
Our studies revealed that the ISR signaling pathway is a key modulator of epithelial permeability. We show that prolonged epithelial stretch and injurious mechanical ventilation activates ISR, leading to increased alveolar permeability, cell death and proinflammatory signaling. Chemical inhibition of protein kinase RNA-like endoplasmic reticulum kinase, an upstream regulator of the pathway, resulted in decreased injury signaling and improved barrier function following prolonged cyclic stretch and injurious mechanical ventilation.

CONCLUSIONS:
Our results provide new evidence that therapeutic targeting of the integrated stress response can mitigate VILI.

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MicroRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos

Dionna M. Kasper, Albertomaria Moro, Emma Ristori, Anand Narayanan, Guillermina Hill-Teran, Elizabeth Fleming, Miguel Moreno-Mateos, Charles E. Vejnar, Jing Zhang, Donghoon Lee, Mengting Gu, Mark Gerstein, Antonio Giraldez, Stefania Nicoli

Developmental Cell 2017, doi: 10.1016/j.devcel.2017.02.021.

Proper functioning of an organism requires cells and tissues to behave in uniform, well-organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here, we carried out a multi-faceted and single-cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi-gene microRNA (miRNA) families. We found that embryos lacking particular miRNA-dependent signaling pathways develop a vascular trait similar to wild-type, but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We discovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.

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Genome-wide transcriptome profiling of Carica papaya L. embryogenic callus

Jamaluddin, N.D., Mohd Noor, N. & Goh, HH.

Physiol Mol Biol Plants (2017). doi:10.1007/s12298-017-0429-8

Genome-wide transcriptome profiling is a powerful tool to study global gene expression patterns in plant development. We report the first transcriptome profile analysis of papaya embryogenic callus to improve our understanding on genes associated with somatic embryogenesis. By using 3′ mRNA-sequencing, we generated 6,190,687 processed reads and 47.0% were aligned to papaya genome reference, in which 21,170 (75.4%) of 27,082 annotated genes were found to be expressed but only 41% was expressed at functionally high levels. The top 10% of genes with high transcript abundance were significantly enriched in biological processes related to cell proliferation, stress response, and metabolism. Genes functioning in somatic embryogenesis such as SERK and LEA, hormone-related genes, stress-related genes, and genes involved in secondary metabolite biosynthesis pathways were highly expressed. Transcription factors such as NAC, WRKY, MYB, WUSCHEL, Agamous-like MADS-box protein and bHLH important in somatic embryos of other plants species were found to be expressed in papaya embryogenic callus. Abundant expression of enolase and ADH is consistent with proteome study of papaya somatic embryo. Our study highlights that some genes related to secondary metabolite biosynthesis, especially phenylpropanoid biosynthesis, were highly expressed in papaya embryogenic callus, which might have implication for cell factory applications. The discovery of all genes expressed in papaya embryogenic callus provides an important information into early biological processes during the induction of embryogenesis and useful for future research in other plant species.

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BET-Bromodomain Inhibitors Engage the Host Immune System and Regulate Expression of the Immune Checkpoint Ligand PD-L1

Simon J. Hogg, Stephin J. Vervoort, Sumit Deswal, Christopher J. Ott, Jason Li, Leonie A. Cluse, Paul A. Beavis, Phillip K. Darcy, Benjamin P. Martin, Andrew Spencer, Anna K. Traunbauer, Irina Sadovnik, Karin Bauer, Peter Valent, James E. Bradner, Johannes Zuber, Jake Shortt, Ricky W. Johnstone

Cell Reports 18, 2162–2174, February 28, 2017

BET inhibitors (BETi) target bromodomain-containing proteins and are currently being evaluated as anti-cancer agents. We find that maximal therapeutic effects of BETi in a Myc-driven B cell lymphoma model required an intact host immune system. Genome-wide analysis of the BETi-induced transcriptional response identified the immune checkpoint ligand Cd274 (Pd-l1) as a Myc-independent, BETi target-gene. BETi directly repressed constitutively expressed and interferon-gamma (IFN-γ) induced CD274 expression across different human and mouse tumor cell lines and primary patient samples. Mechanistically, BETi decreased Brd4 occupancy at the Cd274 locus without any change in Myc occupancy, resulting in transcriptional pausing and rapid loss of Cd274 mRNA production. Finally, targeted inhibition of the PD-1/PD-L1 axis by combining anti-PD-1 antibodies and the BETi JQ1 caused synergistic responses in mice bearing Myc-driven lymphomas. Our data uncover an interaction between BETi and the PD-1/PD-L1 immune-checkpoint and provide mechanistic insight into the transcriptional regulation of CD274.

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Targeting the PD-1/PD-L1 pathway potentiates immunoediting to counterbalance neutral evolution in a mouse model of colorectal cancer

Zlatko Trajanoski, Mirjana Efremova, Victoria Klepsch, Pornpimol Charoentong, Francesca Finotello, Dietmar Rieder, Hubert Hackl, Natasch Hermann-Kleiter, Gottfried Baier, Anne Krogsdam

BioRxiv, doi:10.1101/099747

Background: The cancer immunoediting hypothesis postulates a dual role of the immune system: protecting the host by eliminating tumor cells, and shaping the developing tumor by editing the cancer genome. However, to what extent immunoediting is shaping the cancer genome in common malignancies is still a matter of debate. Moreover, the impact of cancer immunotherapy with checkpoint blockers on modulating immunoediting remains largely unexplored. Results: Here we employed a mouse model of colorectal cancer (CRC), next-generation sequencing, and computational analyses to elucidate the impact of evolutionary and immune-related forces on editing the tumor. We first carried out genomic and transcriptomic analyses of a widely-used model, MC38 cell line and show that this is a valid model for hypermutated and microsatellite-unstable CRC. Analyses of the data from longitudinal samples of wild type and immunodeficient RAG1 knockout mice transplanted with MC38 cells revealed that upregulation of checkpoint molecules and infiltration of Tregs are the major tumor escape mechanisms. Strikingly, the impact of neutral evolution on sculpting the tumor outweighed immunoediting by T cell dependent and T cell independent mechanisms in the progressing tumors. We also show that targeting the PD-1/PD-L1 pathway potentiated immunoediting and rendered tumors more homogeneous. Conclusions: In summary, our study demonstrates that neutral evolution is the major force that sculpts the tumor during progression, and that checkpoint blockade effectively enforces T cell dependent immunoselective pressure in this model. The results have important implication for basic research studies on the mechanisms of resistance to checkpoint blockade and for clinical translation.

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Global analysis of regulatory divergence in the evolution of mouse alternative polyadenylation

Mei‐Sheng Xiao, Bin Zhang, Yi‐Sheng Li, Qingsong Gao, Wei Sun, Wei Chen

Molecular Systems Biology (2016), doi:10.15252/msb.20167375

Alternative polyadenylation (APA), which is regulated by both cis‐elements and trans‐factors, plays an important role in post‐transcriptional regulation of eukaryotic gene expression. However, comparing to the extensively studied transcription and alternative splicing, the extent of APA divergence during evolution and the relative cis‐ and trans‐contribution remain largely unexplored. To directly address these questions for the first time in mammals, by using deep sequencing‐based methods, we measured APA divergence between C57BL/6J and SPRET/EiJ mouse strains as well as allele‐specific APA pattern in their F1 hybrids. Among the 24,721 polyadenylation sites (pAs) from 7,271 genes expressing multiple pAs, we identified 3,747 pAs showing significant divergence between the two strains. After integrating the allele‐specific data from F1 hybrids, we demonstrated that these events could be predominately attributed to cis‐regulatory effects. Further systematic sequence analysis of the regions in proximity to cis‐divergent pAs revealed that the local RNA secondary structure and a poly(U) tract in the upstream region could negatively modulate the pAs usage.

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Genome-wide genetic screening with chemically mutagenized haploid embryonic stem cells

Josep V Forment, Mareike Herzog, Julia Coates, Tomasz Konopka, Bianca V Gapp, Sebastian M Nijman, David J Adams, Thomas M Keane & Stephen P Jackson

Nature Chemical Biology (2016), doi:10.1038/nchembio.2226

In model organisms, classical genetic screening via random mutagenesis provides key insights into the molecular bases of genetic interactions, helping to define synthetic lethality, synthetic viability and drug-resistance mechanisms. The limited genetic tractability of diploid mammalian cells, however, precludes this approach. Here, we demonstrate the feasibility of classical genetic screening in mammalian systems by using haploid cells, chemical mutagenesis and next-generation sequencing, providing a new tool to explore mammalian genetic interactions.

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Transgenic Expression of Mitochondrial Chaperone TRAP1 Accelerates Prostate Cancer Development

Sofia Lisanti, David S. Garlick, Kelly G. Bryant, Michele Tavecchio, Gordon B. Mills, Yiling Lu, Andrew V. Kossenkov, Louise C. Showe, Lucia R. Languino and Dario C. Altieri

JBC, doi: 10.1074/jbc.M116.745950

Protein homeostasis, or proteostasis is required for mitochondrial function, but its role in cancer is controversial. Here, we show that transgenic mice expressing the mitochondrial chaperone, TRAP1 in the prostate develop epithelial hyperplasia and cellular atypia. When examined on a Pten+/- background, a common alteration in human prostate cancer, TRAP1 transgenic mice showed accelerated incidence of invasive prostatic adenocarcinoma, characterized by increased cell proliferation and reduced apoptosis, in situ. Conversely, homozygous deletion of TRAP1 delays prostatic tumorigenesis in Pten+/- mice, without affecting hyperplasia or prostatic intraepithelial neoplasia. Global profiling of Pten+/–TRAP1 transgenic mice by RNA sequencing and reverse phase protein array reveals modulation of oncogenic networks of cell proliferation, apoptosis, cell motility, and DNA damage. Mechanistically, reconstitution of Pten+/- prostatic epithelial cells with TRAP1 increases cell proliferation, reduces apoptosis, and promotes cell invasion, without changes in mitochondrial bioenergetics. Therefore, TRAP1 is a driver of prostate cancer, in vivo, and “actionable” therapeutic target.

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Dissecting cis-regulatory effect on alternative polyadenylation using hybrid mice * DISSERTATION

Meisheng Xiao

Department of Biology, Chemistry and Pharmacy of the Freie Universität Berlin

The 3’ ends of most eukaryotic mRNAs are cleaved and polyadenylated at the last step of transcription. Recent studies revealed that more than 70% mammalian genes have multiple polyadenylation sites (pAs) leading to the generation of multiple mRNA isoforms with different coding region or 3’ untranslated region (3’ UTR) from the same gene locus and contributes to the complexity of transcriptome and proteome by regulating their stability, localization, translation, and function. Boosted by the large-scale analysis technologies, extensive and dynamic regulation of 3’ UTR by alternative polyadenylation (APA) has been observed in different tissues; different cellular conditions (proliferation, differentiation, and development); and response to stimuli. Although the exact underlying mechanisms of APA remains under investigation, it should be in general regulated via the interaction between cisregulatory elements residing at the DNA/RNA and trans-factors including polyadenylation cleavage core protein complex as well as other accessory RNA binding proteins (RBP). Change of APA pattern during evolution remains underexplored. Such changes could arise from the divergence in cis-regulatory elements and/or transacting RBPs. The divergences of the two factors with different extent of pleiotropic consequences undergo distinct evolutionary trajectories. Therefore, to better understand evolution in APA, it is important to distinguish the relative contribution of cis– and trans-effects. In this project, to comprehensively investigate the contribution of cis-elements and trans-factors in the process of APA in a mammalian system, we identified and quantified pAs usage difference between two parental strains (C57BL/6J and SPRET/EiJ) and between the two alleles in the F1 hybrids with 3’ read capturing and sequencing (3’ READS) and 3’ mRNA-Seq methods, respectively. In total, we identified 3747 parental divergent pAs across five types of APA, between the two parental mouse strains. By comparing the parental divergent pAs with those in F1 hybrids, we observed a predominant contribution of cis-regulatory effect on pAs usage, which is mediated by genetic variants between two species around the pAs. Further sequence feature analysis demonstrated that the unstable secondary structure and a novel hexamer UUUUUU in the upstream region of pAs could enhance and inhibit the pAs usage, respectively.

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The role of the microbiota in prey capture behavior * DISSERTATION

Levi W. Simonson

Department of Biology and the Graduate School of the University of Oregon

There is a growing body of evidence that normal nervous system activity requires signals from resident microbes. We have yet to discover the mechanisms by which the microbiota influence brain function. However, we know that the enteric nervous system (ENS) serves as an important interface between the developing host and its microbiota. In this dissertation I will introduce a novel computer-assisted method for ENS characterization and a novel, incredibly specific mechanism of host-microbe interactions. With new ENS characterization method I developed, it will be possible to better understand the role of the ENS during development, by more rapidly and algorithmically assessing ENS phenotypes. Furthermore, my discovery of a single microbially-sourced protein that influences vertebrate host prey capture behavior and visual system development, will provide a new appreciation for the role resident microbes, both in model organisms and in ourselves. By both establishing a new, less biased, approach to image analysis and describing a surprising new regulatory host-microbe interaction, the work I describe in this dissertation should provide the foundation for an explosion of exciting discoveries in the near future.

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Pan-cancer analysis of the Mediator complex transcriptome identifies CDK19 and CDK8 as therapeutic targets in advanced prostate cancer.

Brägelmann J, Klümper N, Offermann A, von Mässenhausen A, Böhm D, Deng M, Queisser A, Sanders C, Syring I, Merseburger AS, Vogel W, Sievers E, Vlasic I, Carlsson J, Andrén O, Brossart P, Duensing S, Svensson MA, Shaikhibrahim Z, Kirfel J, Perner S.

Clinical Cancer Research, doi: 10.1158/1078-0432.CCR-16-0094

PURPOSE:
The Mediator complex is a multi-protein assembly, which serves as a hub for diverse signaling pathways to regulate gene expression. Since gene expression is frequently altered in cancer a systematic understanding of the Mediator complex in malignancies could foster the development of novel targeted therapeutic approaches.

EXPERIMENTAL DESIGN:
We performed a systematic deconvolution of the Mediator subunit expression profiles across 23 cancer entities (n=8568) using data from The Cancer Genome Atlas (TCGA). Prostate cancer (PCa) specific findings were validated in two publicly available gene expression cohorts and a large cohort of primary and advanced PCa (n=622) stained by immunohistochemistry. The role of CDK19 and CDK8 was evaluated by siRNA mediated gene knock-down and inhibitor treatment in PCa cell lines with functional assays and gene expression analysis by RNAseq.

RESULTS:
Cluster analysis of TCGA expression data segregated tumor entities, indicating tumor-type specific Mediator complex compositions. Only PCa was marked by high expression of CDK19. In primary PCa CDK19 was associated with increased aggressiveness and shorter disease free survival. During cancer progression highest levels of CDK19 and of its paralog CDK8 were present in metastases. In vitro, inhibition of CDK19 and CDK8 by knock-down or treatment with a selective CDK8/CDK19 inhibitor significantly decreased migration and invasion.

CONCLUSIONS:
Our analysis revealed distinct transcriptional expression profiles of the Mediator complex across cancer entities indicating differential modes of transcriptional regulation. Moreover it identified CDK19 and CDK8 to be specifically overexpressed during PCa progression, highlighting their potential as novel therapeutic targets in advanced PCa.

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Molecular basis for cytoplasmic RNA surveillance by uridylation‐triggered decay in Drosophila

Madalena M Reimão‐Pinto, Raphael A Manzenreither, Thomas R Burkard, Pawel Sledz, Martin Jinek, Karl Mechtler, Stefan L Ameres

The EMBO Journal (2016) e201695164; doi: 10.15252/embj.201695164

The posttranscriptional addition of nucleotides to the 3′ end of RNA regulates the maturation, function, and stability of RNA species in all domains of life. Here, we show that in flies, 3′ terminal RNA uridylation triggers the processive, 3′‐to‐5′ exoribonucleolytic decay via the RNase II/R enzyme CG16940, a homolog of the human Perlman syndrome exoribonuclease Dis3l2. Together with the TUTase Tailor, dmDis3l2 forms the cytoplasmic, terminal RNA uridylation‐mediated processing (TRUMP) complex that functionally cooperates in the degradation of structured RNA. RNA immunoprecipitation and high‐throughput sequencing reveals a variety of TRUMP complex substrates, including abundant non‐coding RNA, such as 5S rRNA, tRNA, snRNA, snoRNA, and the essential RNase MRP. Based on genetic and biochemical evidence, we propose a key function of the TRUMP complex in the cytoplasmic quality control of RNA polymerase III transcripts. Together with high‐throughput biochemical characterization of dmDis3l2 and bacterial RNase R, our results imply a conserved molecular function of RNase II/R enzymes as “readers” of destabilizing posttranscriptional marks—uridylation in eukaryotes and adenylation in prokaryotes—that play important roles in RNA surveillance.

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BET Bromodomain Inhibition Promotes Anti-tumor Immunity by Suppressing PD-L1 Expression

Hengrui Zhu, Fee Bengsch, Nikolaos Svoronos, Melanie R. Rutkowski, Benjamin G. Bitler, Michael J. Allegrezza, Yuhki Yokoyama, Andrew V. Kossenkov, James E. Bradner, Jose R. Conejo-Garcia, Rugang Zhang

Cell Reports 16, 2829–2837, September 13, 2016; doi: 10.1016/j.celrep.2016.08.032

Restoration of anti-tumor immunity by blocking PD-L1 signaling through the use of antibodies has proven to be beneficial in cancer therapy. Here, we show that BET bromodomain inhibition suppresses PD-L1 expression and limits tumor progression in ovarian cancer. CD274 (encoding PD-L1) is a direct target of BRD4-mediated gene transcription. In mouse models, treatment with the BET inhibitor JQ1 significantly reduced PD-L1 expression on tumor cells and tumor-associated dendritic cells and macrophages, which correlated with an increase in the activity of anti-tumor cytotoxic T cells. The BET inhibitor limited tumor progression in a cytotoxic T-cell-dependent manner. Together, these data demonstrate a small-molecule approach to block PD-L1 signaling. Given the fact that BET inhibitors have been proven to be safe with manageable reversible toxicity in clinical trials, our findings indicate that pharmacological BET inhibitors represent a treatment strategy for targeting PD-L1 expression.

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An siRNA screen for ATG protein depletion reveals the extent of the unconventional functions of the autophagy proteome in virus replication

Mario Mauthe, Martijn Langereis, Jennifer Jung, Xingdong Zhou, Alex Jones, Wienand Omta, Sharon A. Tooze, Björn Stork, Søren Riis Paludan, Tero Ahola, Dave Egan, Christian Behrends, Michal Mokry, Cornelis de Haan, Frank van Kuppevel, Fulvio Reggiori

The Rockefeller University Press / JCB vol. 214 no. 5 619-635 / doi: 10.1083/jcb.201602046

Autophagy is a catabolic process regulated by the orchestrated action of the autophagy-related (ATG) proteins. Recent work indicates that some of the ATG proteins also have autophagy-independent roles. Using an unbiased siRNA screen approach, we explored the extent of these unconventional functions of ATG proteins. We determined the effects of the depletion of each ATG proteome component on the replication of six different viruses. Our screen reveals that up to 36% of the ATG proteins significantly alter the replication of at least one virus in an unconventional fashion. Detailed analysis of two candidates revealed an undocumented role for ATG13 and FIP200 in picornavirus replication that is independent of their function in autophagy as part of the ULK complex. The high numbers of unveiled ATG gene-specific and pathogen-specific functions of the ATG proteins calls for caution in the interpretation of data, which rely solely on the depletion of a single ATG protein to specifically ablate autophagy.

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Parallel reverse genetic screening in mutant human cells using transcriptomics

Bianca V Gapp, Tomasz Konopka, Thomas Penz, Vineet Dalal, Tilmann Bürckstümmer, Christoph Bock, Sebastian MB Nijman

Molecular Systems Biology (2016) 12, 879; doi: 10.15252/msb.20166890

Reverse genetic screens have driven gene annotation and target discovery in model organisms. However, many disease‐relevant genotypes and phenotypes cannot be studied in lower organisms. It is therefore essential to overcome technical hurdles associated with large‐scale reverse genetics in human cells. Here, we establish a reverse genetic approach based on highly robust and sensitive multiplexed RNA sequencing of mutant human cells. We conduct 10 parallel screens using a collection of engineered haploid isogenic cell lines with knockouts covering tyrosine kinases and identify known and unexpected effects on signaling pathways. Our study provides proof of concept for a scalable approach to link genotype to phenotype in human cells, which has broad applications. In particular, it clears the way for systematic phenotyping of still poorly characterized human genes and for systematic study of uncharacterized genomic features associated with human disease.

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Nuclear Innate Immune DNA Sensor IFI16 is Degraded During Lytic Reactivation of Kaposi’s Sarcoma-Associated Herpesvirus (KSHV): Role of IFI16 in Maintenance of KSHV Latency

Arunava Roy, Dipanjan Dutta, Jawed Iqbal, Gina Pisano, Olsi Gjyshi, Mairaj Ahmed Ansari, Binod Kumar and Bala Chandran

JVI.01003-16; doi: 10.1128/JVI.01003-16

IFI16 (Interferon-γ-inducible protein 16) recognizes the nuclear episomal herpes virus (KSHV, EBV and HSV-1) genomes and induces the inflammasome and interferon-β responses. It also acts as a lytic replication restriction factor and inhibits viral DNA replication (HCMV and HPV) and transcription (HSV-1, HCMV and HPV) through epigenetic modifications of the viral genomes. To date, the role of IFI16 in the biology of latent viruses is not known. Here, we demonstrate that knockdown of IFI16 in KSHV latently infected B-lymphoma BCBL-1 and BC-3 cell lines results in lytic reactivation, increase in KSHV lytic transcripts, proteins, and viral genome replication. Similar results were also observed during KSHV lytic cycle induction in TREX-BCBL-1 cells with the doxycycline-inducible lytic cycle switch RTA gene. Overexpression of IFI16 reduced lytic gene induction by chemical agent TPA. IFI16 protein levels were significantly reduced or absent in TPA or doxycycline induced cells expressing lytic KSHV proteins. IFI16 is polyubiquitinated and degraded via the proteasomal pathway. IFI16’s degradation was absent in phosphonoacetic acid treated cells that blocks KSHV DNA replication and consequently late lytic gene expression. Chromatin immunoprecipitation assays of BCBL-1 and BC-3 cells demonstrated that IFI16 binds to KSHV gene promoters. Uninfected epithelial SLK and osteosarcoma U2OS cells transfected with KSHV luciferase promoter constructs confirmed that IFI16 functions as a transcriptional repressor. These results reveal that KSHV utilizes the innate immune nuclear DNA sensor IFI16 to maintain its latency and repression of lytic transcripts, and a late lytic KSHV gene product(s) targets IFI16 for degradation during lytic reactivation.

Importance Like all herpesviruses, latency is an integral part of Kaposi’s sarcoma-associated herpesvirus (KSHV) life cycle, an etiological agent for many human cancers. Herpesviruses utilize viral and host factors to successfully evade the host immune system to maintain latency. Reactivation is a complex event where the latent episomal viral genome springs back to an active transcription of lytic cycle genes. Our studies reveal that KSHV has evolved to utilize the innate immune sensor IFI16 to keep lytic cycle transcription in dormancy. We demonstrate that IFI16 binds to the lytic gene promoters and acts as a transcriptional repressor, and thereby helps to maintain latency. We also discovered that during the late stage of lytic replication, KSHV selectively degrades IFI16, thus relieving the transcriptional repression. This is the first report to demonstrate IFI16’s role in latency maintenance of a herpes virus and further understanding will lead to the development of strategies to eliminate latent infection.

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Differences in DNA Repair Capacity, Cell Death and Transcriptional Response after Irradiation between a Radiosensitive and a Radioresistant Cell Line

Mireia Borràs-Fresneda, Joan-Francesc Barquinero, Maria Gomolka, Sabine Hornhardt, Ute Rössler, Gemma Armengol & Leonardo Barrios

Sci. Rep. 6, 27043; doi:10.1038/srep27043 (2016)

Normal tissue toxicity after radiotherapy shows variability between patients, indicating inter-individual differences in radiosensitivity. Genetic variation probably contributes to these differences. The aim of the present study was to determine if two cell lines, one radiosensitive (RS) and another radioresistant (RR), showed differences in DNA repair capacity, cell viability, cell cycle progression and, in turn, if this response could be characterised by a differential gene expression profile at different post-irradiation times. After irradiation, the RS cell line showed a slower rate of γ-H2AX foci disappearance, a higher frequency of incomplete chromosomal aberrations, a reduced cell viability and a longer disturbance of the cell cycle when compared to the RR cell line. Moreover, a greater and prolonged transcriptional response after irradiation was induced in the RS cell line. Functional analysis showed that 24 h after irradiation genes involved in “DNA damage response”, “direct p53 effectors” and apoptosis were still differentially up-regulated in the RS cell line but not in the RR cell line. The two cell lines showed different response to IR and can be distinguished with cell-based assays and differential gene expression analysis. The results emphasise the importance to identify biomarkers of radiosensitivity for tailoring individualized radiotherapy protocols.

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The effector AWR5 from the plant pathogen Ralstonia solanacearum is an inhibitor of the TOR signalling pathway

Crina Popa, Liang Li, Sergio Gil, Laura Tatjer, Keisuke Hashii, Mitsuaki Tabuchi, Núria S. Coll, Joaquín Ariño & Marc Valls

Sci. Rep. 6, 27058; doi: 10.1038/srep27058 (2016)

Bacterial pathogens possess complex type III effector (T3E) repertoires that are translocated inside the host cells to cause disease. However, only a minor proportion of these effectors have been assigned a function. Here, we show that the T3E AWR5 from the phytopathogen Ralstonia solanacearum is an inhibitor of TOR, a central regulator in eukaryotes that controls the switch between cell growth and stress responses in response to nutrient availability. Heterologous expression of AWR5 in yeast caused growth inhibition and autophagy induction coupled to massive transcriptomic changes, unmistakably reminiscent of TOR inhibition by rapamycin or nitrogen starvation. Detailed genetic analysis of these phenotypes in yeast, including suppression of AWR5-induced toxicity by mutation of CDC55 and TPD3, encoding regulatory subunits of the PP2A phosphatase, indicated that AWR5 might exert its function by directly or indirectly inhibiting the TOR pathway upstream PP2A. We present evidence in planta that this T3E caused a decrease in TOR-regulated plant nitrate reductase activity and also that normal levels of TOR and the Cdc55 homologues in plants are required for R. solanacearum virulence. Our results suggest that the TOR pathway is a bona fide T3E target and further prove that yeast is a useful platform for T3E function characterisation.

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Transcriptional profiling and muscle cross‐section analysis reveal signs of ischemia reperfusion injury following total knee arthroplasty with tourniquet

Jonathan B. Muyskens, Austin D. Hocker, Douglas W. Turnbull, Steven N. Shah, Brick A. Lantz, Brian A. Jewett, Hans C. Dreyer

Physiological Reports Published 5 January 2016 Vol. 4 no. e12671 DOI: 10.14814/phy2.12671

Total knee arthroplasty (TKA) is the most common and cost‐effective treatment for older adults with long‐standing osteoarthritis. Projections indicate that nearly 3.5 million older adults will undergo this procedure annually by the year 2030. Thus, understanding the factors that lead to optimal outcomes is of great clinical interest. In the majority of cases, tourniquet is applied during surgery to maintain a clear surgical field, however, there is debate as to whether this intervention is completely benign. In particular, muscle atrophy is a significant factor in preventing full functional recovery following surgery, and some evidence suggests that tourniquet application and the associated ischemia–reperfusion injury that results contributes to muscle atrophy. For this reason, we examined tissue level changes in muscle in TKA patients following surgery and found that there was a significant increase in cross‐sectional area of muscle fibers of all types. Furthermore, to detect changes not evident at the tissue level, we performed NextSeq analysis to assess the transcriptional landscape of quadriceps muscle cells following TKA with tourniquet and found 72 genes that were significantly upregulated. A large proportion of those genes regulate cell stress pathways, suggesting that muscle cells in our cohort of older adults were capable of mounting a significant response to cell stress. Furthermore, factors related to complement were upregulated, suggesting tourniquet may play a role in priming cells to ischemia reperfusion injury. Therefore, our analysis reveals potential harms of tourniquet during TKA, thus suggesting that surgeons should consider limiting its use.

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