A Direct In Vivo RNAi Screen Identifies MKK4 as a Key Regulator of Liver Regeneration

Wüestefeld, Torsten; Pešić, Marina; Rudalska, Ramona; Dauch, Daniel; Longerich, Thomas; Kang, Tae‐Won; Yevsa, Tetyana; Heinzmann, Florian; Hoenicke, Lisa; Hohmeyer, Anja; Wuestefeld, Anna; Rittelmeier, Ina; Jarek, Michael; Geffers, Robert; Scharfe, Maren; Klawonn, Frank; Schirmacher, Peter; Malek, Nisar P.; Ott, Michael; Nordheim, Alfred; Vogel, Arndt; Manns, Michael P.; Zender, Lars

doi:10.1016/j.cell.2013.03.026

Cited by 133 publications

(120 citation statements)

References 45 publications

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“…Indeed, in vivo RNA interference (RNAi) screens have identified MKK4 as a key regulator of liver regeneration (389), whereas studies in MKK7 Ϫ/Ϫ mice have revealed the critical need for MKK7 in axon elongation in the developing cerebral cortex (390). The compound disruption of both the MKK4 and MKK7 genes results in severe growth retardation and embryonic lethality (E9.5).…”

Section: Jnk Involvement In Embryonic Developmentmentioning

confidence: 99%

JNK Signaling: Regulation and Functions Based on Complex Protein-Protein Partnerships

Zeke

Misheva

Reményi

et al. 2016

Microbiol Mol Biol Rev

409

350

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SUMMARYThe c-Jun N-terminal kinases (JNKs), as members of the mitogen-activated protein kinase (MAPK) family, mediate eukaryotic cell responses to a wide range of abiotic and biotic stress insults. JNKs also regulate important physiological processes, including neuronal functions, immunological actions, and embryonic development, via their impact on gene expression, cytoskeletal protein dynamics, and cell death/survival pathways. Although the JNK pathway has been under study for >20 years, its complexity is still perplexing, with multiple protein partners of JNKs underlying the diversity of actions. Here we review the current knowledge of JNK structure and isoforms as well as the partnerships of JNKs with a range of intracellular proteins. Many of these proteins are direct substrates of the JNKs. We analyzed almost 100 of these target proteins in detail within a framework of their classification based on their regulation by JNKs. Examples of these JNK substrates include a diverse assortment of nuclear transcription factors (Jun, ATF2, Myc, Elk1), cytoplasmic proteins involved in cytoskeleton regulation (DCX, Tau, WDR62) or vesicular transport (JIP1, JIP3), cell membrane receptors (BMPR2), and mitochondrial proteins (Mcl1, Bim). In addition, because upstream signaling components impact JNK activity, we critically assessed the involvement of signaling scaffolds and the roles of feedback mechanisms in the JNK pathway. Despite a clarification of many regulatory events in JNK-dependent signaling during the past decade, many other structural and mechanistic insights are just beginning to be revealed. These advances open new opportunities to understand the role of JNK signaling in diverse physiological and pathophysiological states.

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Section: Jnk Involvement In Embryonic Developmentmentioning

confidence: 99%

JNK Signaling: Regulation and Functions Based on Complex Protein-Protein Partnerships

Zeke

Misheva

Reményi

et al. 2016

Microbiol Mol Biol Rev

409

350

View full text Add to dashboard Cite

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“…Plasmid-based expression of short hairpin RNA has been used to study the role(s) of HGF/c-Met and EGFR during liver regeneration in rats 15,16 , and stable delivery of pools of short hairpin RNAs into mouse livers lead to the identification of the kinase MKK4 as a major regulator of liver regeneration 17 . Additional siRNA delivery systems were invented to improve tissue specificity and low-dose efficacy.…”

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confidence: 99%

Knockdown and knockout of β1-integrin in hepatocytes impairs liver regeneration through inhibition of growth factor signalling

et al. 2014

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The liver has a unique regenerative capability, which involves extensive remodelling of cell-cell and cell-matrix contacts. Here we study the role of integrins in mouse liver regeneration using Cre/loxP-mediated gene deletion or intravenous delivery of b1-integrin siRNA formulated into nanoparticles that predominantly target hepatocytes. We show that although short-term loss of b1-integrin has no obvious consequences for normal livers, partial hepatectomy leads to severe liver necrosis and reduced hepatocyte proliferation. Mechanistically, loss of b1-integrin in hepatocytes impairs ligand-induced phosphorylation of the epidermal growth factor and hepatocyte growth factor receptors, thereby attenuating downstream receptor signalling in vitro and in vivo. These results identify a crucial role and novel mechanism of action of b1-integrins in liver regeneration and demonstrate that protein depletion by nanoparticle-based delivery of specific siRNA is a powerful strategy to study gene function in the regenerating liver.

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“…RNAi-based high-throughput screening has become a widely used method for identification of new components of diverse biological processes, including signal transduction, cancer, and host cell responses to infection (1,2). Genome-scale RNAi screens have led to identification of tumor suppressors (3), oncogenes (4), therapeutic targets (5), and regulators of ES cell (ESC) maintenance (6)(7)(8)(9)(10), tissue regeneration (11), viral infection (12), and antiviral response (13).…”

mentioning

confidence: 99%

Integrative framework for identification of key cell identity genes uncovers determinants of ES cell identity and homeostasis

Cinghu

Yellaboina

Freudenberg

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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Identification of genes associated with specific biological phenotypes is a fundamental step toward understanding the molecular basis underlying development and pathogenesis. Although RNAibased high-throughput screens are routinely used for this task, false discovery and sensitivity remain a challenge. Here we describe a computational framework for systematic integration of published gene expression data to identify genes defining a phenotype of interest. We applied our approach to rank-order all genes based on their likelihood of determining ES cell (ESC) identity. RNAi-mediated loss-of-function experiments on top-ranked genes unearthed many novel determinants of ESC identity, thus validating the derived gene ranks to serve as a rich and valuable resource for those working to uncover novel ESC regulators. Underscoring the value of our gene ranks, functional studies of our top-hit Nucleolin (Ncl), abundant in stem and cancer cells, revealed Ncl's essential role in the maintenance of ESC homeostasis by shielding against differentiation-inducing redox imbalance-induced oxidative stress. Notably, we report a conceptually novel mechanism involving a Nucleolin-dependent Nanog-p53 bistable switch regulating the homeostatic balance between self-renewal and differentiation in ESCs. Our findings connect the dots on a previously unknown regulatory circuitry involving genes associated with traits in both ESCs and cancer and might have profound implications for understanding cell fate decisions in cancer stem cells. The proposed computational framework, by helping to prioritize and preselect candidate genes for tests using complex and expensive genetic screens, provides a powerful yet inexpensive means for identification of key cell identity genes.C ell identity is governed by a set of key regulators, which maintain the gene expression program characteristic of that cell state while restricting the induction of alternate programs that could lead to a new cell state. Identification of cell identity genes is a fundamental step toward understanding the mechanisms that underlie cellular homeostasis, differentiation, development, and pathogenesis. RNAi-based high-throughput screening has become a widely used method for identification of new components of diverse biological processes, including signal transduction, cancer, and host cell responses to infection (1, 2). Genome-scale RNAi screens have led to identification of tumor suppressors (3), oncogenes (4), therapeutic targets (5), and regulators of ES cell (ESC) maintenance (6-10), tissue regeneration (11), viral infection (12), and antiviral response (13).Despite the success of RNAi screens, false discovery and sensitivity remain a significant and difficult problem to address, with surprisingly small overlap among screen hits from independent but related screens (1). For example, multiple genomescale RNAi screens for host proteins required for HIV infection/ replication resulted in a limited overlap among screen hits at the gene level (1). Similarly, screens performed in mous...

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A Direct In Vivo RNAi Screen Identifies MKK4 as a Key Regulator of Liver Regeneration

Cited by 133 publications

References 45 publications

JNK Signaling: Regulation and Functions Based on Complex Protein-Protein Partnerships

JNK Signaling: Regulation and Functions Based on Complex Protein-Protein Partnerships

Knockdown and knockout of β1-integrin in hepatocytes impairs liver regeneration through inhibition of growth factor signalling

Integrative framework for identification of key cell identity genes uncovers determinants of ES cell identity and homeostasis

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