scholarly journals The functional landscape of patient derived RNF43 mutations predicts Wnt inhibitor sensitivity

2020 ◽  
Author(s):  
Jia Yu ◽  
Permeen Akhtar Bt Mohamed Yuso ◽  
Pamela Goh ◽  
Nathan Harmston ◽  
David M. Epstein ◽  
...  

AbstractA subset of Wnt-addicted cancers are sensitive to targeted therapies that block Wnt secretion or receptor engagement. RNF43 loss-of-function mutations that increase cell surface Wnt receptor abundance cause sensitivity to Wnt inhibitors. However, it is not clear which of the clinically identified RNF43 mutations affect its function in vivo. We assayed 90 missense and 45 truncating RNF43 mutations found in human cancers, using a combination of cell-based reporter assays, genome editing, flow cytometry and immunofluorescence microscopy. Patent-derived xenograft (PDX) models with C-terminal truncating RNF43 mutations were tested for Wnt inhibitor sensitivity. We find that five common germline variants of RNF43 have wild-type activity. The majority of cancer-associated missense mutations in the RING and PA domains are either loss of function or hyperactivating. Hyperactivating mutants appear to function through formation of inactive dimers with endogenous RNF43 and/or ZNRF3. C-terminal truncation mutants including the common G659fs mutant, have discordant behavior in in vitro versus in vivo assays. PDXs and cell lines with C-terminal truncations show increased cell surface FZD, Wnt/β-catenin signaling and are responsive to PORCN inhibition in vivo, providing clear evidence of RNF43 loss of function. In conclusion, RNF43 nonsense and frameshift mutations, including those in the C-terminal domain, and specific missense mutations in RING and PA are loss of function and predict response to upstream Wnt inhibitors in microsatellite stable cancers. This study expands the landscape of actionable RNF43 mutations, potentially extending the benefit of these therapies to additional patients.Statement of SignificanceLoss of function RNF43 mutations, first described in pancreatic cancers, drive progression of multiple cancers by increasing cellular sensitivity to Wnt ligands. These cancers are therefore uniquely sensitive to agents such as PORCN inhibitors that block Wnt production. As the PORCN inhibitors and other upstream inhibitors advance into clinical trials it is important to identify the right patients to treat with these upstream Wnt inhibitors. Hence a detailed map of mutations that are actionable is required.Here we systematically examined a spectrum of 135 patient-derived RNF43 mutations from multiple cancers. Using cell-based reporter assays, genome editing and patient-derived xenografts, we identify rules to guide patient selection. MSS cancers with either truncating mutations anywhere in the gene, including C-terminal truncations around the G659 position, or point mutations in well-defined functional domains, are likely to have RNF43 loss of function and hence a response to therapy.

Development ◽  
2000 ◽  
Vol 127 (22) ◽  
pp. 4981-4992 ◽  
Author(s):  
O. Kazanskaya ◽  
A. Glinka ◽  
C. Niehrs

Dickkopf1 (dkk1) encodes a secreted WNT inhibitor expressed in Spemann's organizer, which has been implicated in head induction in Xenopus. Here we have analyzed the role of dkk1 in endomesoderm specification and neural patterning by gain- and loss-of-function approaches. We find that dkk1, unlike other WNT inhibitors, is able to induce functional prechordal plate, which explains its ability to induce secondary heads with bilateral eyes. This may be due to differential WNT inhibition since dkk1, unlike frzb, inhibits Wnt3a signalling. Injection of inhibitory antiDkk1 antibodies reveals that dkk1 is not only sufficient but also required for prechordal plate formation but not for notochord formation. In the neural plate dkk1 is required for anteroposterior and dorsoventral patterning between mes- and telencephalon, where dkk1 promotes anterior and ventral fates. Both the requirement of anterior explants for dkk1 function and their ability to respond to dkk1 terminate at late gastrula stage. Xenopus embryos posteriorized with bFGF, BMP4 and Smads are rescued by dkk1. dkk1 does not interfere with the ability of bFGF to induce its immediate early target gene Xbra, indicating that its effect is indirect. In contrast, there is cross-talk between BMP and WNT signalling, since induction of BMP target genes is sensitive to WNT inhibitors until the early gastrula stage. Embryos treated with retinoic acid (RA) are not rescued by dkk1 and RA affects the central nervous system (CNS) more posterior than dkk1, suggesting that WNTs and retinoids may act to pattern anterior and posterior CNS, respectively, during gastrulation.


Blood ◽  
2013 ◽  
Vol 121 (1) ◽  
pp. 72-84 ◽  
Author(s):  
Austen J. J. Worth ◽  
Joao Metelo ◽  
Gerben Bouma ◽  
Dale Moulding ◽  
Marco Fritzsche ◽  
...  

Abstract Wiskott Aldrich syndrome (WAS), an X-linked immunodeficiency, results from loss-of-function mutations in the human hematopoietic cytoskeletal regulator gene WAS. Many missense mutations in the Ena Vasp homology1 (EVH1) domain preserve low-level WAS protein (WASp) expression and confer a milder clinical phenotype. Although disrupted binding to WASp-interacting protein (WIP) leads to enhanced WASp degradation in vivo, the intrinsic function of EVH1-mutated WASp is poorly understood. In the present study, we show that, despite mediating enhanced actin polymerization compared with wild-type WASp in vitro, EVH1 missense mutated proteins did not support full biologic function in cells, even when levels were restored by forced overexpression. Podosome assembly was aberrant and associated with dysregulated lamellipodia formation and impaired persistence of migration. At sites of residual podosome-associated actin polymerization, localization of EVH1-mutated proteins was preserved even after deletion of the entire domain, implying that WIP-WASp complex formation is not absolutely required for WASp localization. However, retention of mutant proteins in podosomes was significantly impaired and associated with reduced levels of WASp tyrosine phosphorylation. Our results indicate that the EVH1 domain is important not only for WASp stability, but also for intrinsic biologic activity in vivo.


Viruses ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 237
Author(s):  
Hye Jin Shin ◽  
Keun Bon Ku ◽  
Soojin Kim ◽  
Heon Seok Kim ◽  
Yeon-Soo Kim ◽  
...  

Genetic screens using CRISPR/Cas9 have been exploited to discover host–virus interactions. These screens have identified viral dependencies on host proteins during their life cycle and potential antiviral strategies. The acyl-CoA binding domain containing 3 (ACBD3) was identified as an essential host factor for the Coxsackievirus B3 (CVB3) infection. Other groups have also investigated the role of ACBD3 as a host factor for diverse enteroviruses in cultured cells. However, it has not been tested if ACBD3 is required in the animal model of CVB3 infection. Owing to embryonic lethality, conventional knockout mice were not available for in vivo study. As an alternative approach, we used adeno-associated virus (AAV)-mediated CRISPR genome editing to generate mice that lacked ACBD3 within the pancreas, the major target organ for CVB3. Delivery of sgRNAs using self-complementary (sc) AAV8 efficiently induced a loss-of-function mutation in the pancreas of the Cas9 knock-in mice. Loss of ACBD3 in the pancreas resulted in a 100-fold reduction in the CVB3 titer within the pancreas and a noticeable reduction in viral protein expression. These results indicate a crucial function of ACBD3 in CVB3 infection in vivo. AAV-mediated CRISPR genome editing may be applicable to many in vivo studies on the virus–host interaction and identify a novel target for antiviral therapeutics.


2021 ◽  
Vol 118 (10) ◽  
pp. e2020401118
Author(s):  
Min Qiu ◽  
Zachary Glass ◽  
Jinjin Chen ◽  
Mary Haas ◽  
Xin Jin ◽  
...  

Loss-of-function mutations in Angiopoietin-like 3 (Angptl3) are associated with lowered blood lipid levels, making Angptl3 an attractive therapeutic target for the treatment of human lipoprotein metabolism disorders. In this study, we developed a lipid nanoparticle delivery platform carrying Cas9 messenger RNA (mRNA) and guide RNA for CRISPR-Cas9–based genome editing of Angptl3 in vivo. This system mediated specific and efficient Angptl3 gene knockdown in the liver of wild-type C57BL/6 mice, resulting in profound reductions in serum ANGPTL3 protein, low density lipoprotein cholesterol, and triglyceride levels. Our delivery platform is significantly more efficient than the FDA-approved MC-3 LNP, the current gold standard. No evidence of off-target mutagenesis was detected at any of the nine top-predicted sites, and no evidence of toxicity was detected in the liver. Importantly, the therapeutic effect of genome editing was stable for at least 100 d after a single dose administration. This study highlights the potential of LNP-mediated delivery as a specific, effective, and safe platform for Cas9-based therapeutics.


Gut ◽  
2019 ◽  
Vol 69 (7) ◽  
pp. 1309-1321 ◽  
Author(s):  
Wen-Ping Xu ◽  
Jin-Pei Liu ◽  
Ji-Feng Feng ◽  
Chang-Peng Zhu ◽  
Yuan Yang ◽  
...  

ObjectiveAutophagy participates in the progression of hepatocellular carcinoma (HCC) and the resistance of HCC cells to sorafenib. We investigated the feasibility of sensitising HCC cells to sorafenib by modulating miR-541-initiated microRNA-autophagy axis.DesignGain- and loss-of-function assays were performed to evaluate the effects of miR-541 on the malignant properties and autophagy of human HCC cells. Autophagy was quantified by western blotting of LC3, transmission electron microscopy analyses and confocal microscopy scanning of mRFP-GFP-LC3 reporter construct. Luciferase reporter assays were conducted to confirm the targets of miR-541. HCC xenograft tumours were established to analyse the role of miR-541 in sorafenib-induced lethality.ResultsThe expression of miR-541 was downregulated in human HCC tissues and was associated with malignant clinicopathologic phenotypes, recurrence and survival of patients with HCC. miR-541 inhibited the growth, metastasis and autophagy of HCC cells both in vitro and in vivo. Prediction software and luciferase reporter assays identified autophagy-related gene 2A (ATG2A) and Ras-related protein Rab-1B (RAB1B) as the direct targets of miR-541. Consistent with the effects of the miR-541 mimic, inhibition of ATG2A or RAB1B suppressed the malignant phenotypes and autophagy of HCC cells. Furthermore, siATG2A and siRAB1B partially reversed the enhancement of the malignant properties and autophagy in HCC cells mediated by the miR-541 inhibitor. More interestingly, higher miR-541 expression predicted a better response to sorafenib treatment, and the combination of miR-541 and sorafenib further suppressed the growth of HCC cells in vivo compared with the single treatment.ConclusionsDysregulation of miR-541-ATG2A/RAB1B axis plays a critical role in patients’ responses to sorafenib treatment. Manipulation of this axis might benefit survival of patients with HCC, especially in the context of the highly pursued strategies to eliminate drug resistance.


2020 ◽  
Vol 48 (7) ◽  
pp. e38-e38 ◽  
Author(s):  
Sara E DiNapoli ◽  
Raul Martinez-McFaline ◽  
Caitlin K Gribbin ◽  
Paul J Wrighton ◽  
Courtney A Balgobin ◽  
...  

Abstract CRISPR/Cas9 has become a powerful tool for genome editing in zebrafish that permits the rapid generation of loss of function mutations and the knock-in of specific alleles using DNA templates and homology directed repair (HDR). We examined the efficiency of synthetic, chemically modified gRNAs and demonstrate induction of indels and large genomic deletions in combination with recombinant Cas9 protein. We developed an in vivo genetic assay to measure HDR efficiency and we utilized this assay to test the effect of altering template design on HDR. Utilizing synthetic gRNAs and linear dsDNA templates, we successfully performed knock-in of fluorophores at multiple genomic loci and demonstrate transmission through the germline at high efficiency. We demonstrate that synthetic HDR templates can be used to knock-in bacterial nitroreductase (ntr) to facilitate lineage ablation of specific cell types. Collectively, our data demonstrate the utility of combining synthetic gRNAs and dsDNA templates to perform homology directed repair and genome editing in vivo.


2019 ◽  
Vol 40 (Supplement_1) ◽  
Author(s):  
J Li ◽  
L J Wang ◽  
F Wang ◽  
H F Tang ◽  
R Chen ◽  
...  

Abstract Background Muscle atrophy is the loss of skeletal muscle mass and strength in response to diversity catabolic stimuli, such as heart failure. At present, no effective treatment except exercise is validated on reducing multiple muscle atrophy clinically. We have recently reported that microRNA-29b (miR-29b) promotes multiple types of muscle atrophy. Purpose The goal of this study was to assess whether genome editing using a clustered regularly interspaced short palindromic repeat/Cas9 (CRISPR/Cas9) system can efficiently introduce loss-of-function mutations into the endogenous miR-29b in vivo and as a potential therapy by treating muscle atrophy. Methods We used lentivirus to express CRISPR-associated 9 and a CRISPR guide RNA targeting miR-29b. Mutagenesis rate of miR-29b and off-target mutagenesis were detected by T7 Endonuclease I (T7EI) Assay. The expression level of miR-29b were measured in vitro and vivo after administration of the virus by using qRT-PCR. After intramuscular administration of the virus, the angiotensin II (AngII), immobilization and denervation-induced muscle atrophy were performed. Then muscle function was assessed in exercise capacity, the appearance and weight of muscle, the size of the muscle fibers, molecular and cellular detection. Results Here, we report that CRISPR/Cas9 mediated genome editing through intramuscular administration efficiently targeting the biogenesis processing sites in pre-miR-29b. No off-target mutagenesis was detected in 10 selected sites. This CRISPR-based treatment resulted in decreased miR-29b levels specifically. In vivo, this CRISPR-based treatment could ameliorate the muscle atrophy induced by angiotensin II (AngII), immobilization and denervation via activation of PI3K-AKT-mTOR signaling pathway and protect against AngII-induced apoptosis in mice. Moreover, the exercise capacity is also significantly enhanced. Conclusion Our work establishes CRISPR/Cas9 based gene targeting on miRNA as a potential durable therapy for treatment of muscle atrophy and expands the strategies available interrogating miRNA function in vivo. Acknowledgement/Funding The grants from National Natural Science Foundation of China (81722008, 91639101 and 81570362 to JJ Xiao)


Author(s):  
Caiqiang Huang ◽  
Runguang Li ◽  
Changsheng Yang ◽  
Rui Ding ◽  
Qingchu Li ◽  
...  

AbstractOsteoporosis (OP) is the most common systematic bone disorder among elderly individuals worldwide. Long noncoding RNAs (lncRNAs) are involved in biological processes in various human diseases. It has been previously revealed that PAX8 antisense RNA 1 (PAX8-AS1) is upregulated in OP. However, its molecular mechanism in OP remains unclear. Therefore, we specifically designed this study to determine the specific role of PAX8-AS1 in OP. We first established a rat model of OP and then detected PAX8-AS1 expression in the rats with RT-qPCR. Next, to explore the biological function of PAX8-AS1 in osteoblasts, in vitro experiments, such as Cell Counting Kit-8 (CCK-8) assays, flow cytometry, western blotting and immunofluorescence (IF) staining, were conducted. Subsequently, we performed bioinformatic analysis and luciferase reporter assays to predict and identify the relationships between microRNA 1252-5p (miR-1252-5p) and both PAX8-AS1 and G protein subunit beta 1 (GNB1). Additionally, rescue assays in osteoblasts clarified the regulatory network of the PAX8-AS1/miR-1252-5p/GNB1 axis. Finally, in vivo loss-of-function studies verified the role of PAX8-AS1 in OP progression. The results illustrated that PAX8-AS1 was upregulated in the proximal tibia of OP rats. PAX8-AS1 silencing promoted the viability and inhibited the apoptosis and autophagy of osteoblasts. PAX8-AS1 interacted with miR-1252-5p. GNB1 was negatively regulated by miR-1252-5p. In addition, the impacts of PAX8-AS1 knockdown on osteoblasts were counteracted by GNB1 overexpression. PAX8-AS1 depletion suppressed OP progression by inhibiting apoptosis and autophagy in osteoblasts. In summary, PAX8-AS1 suppressed the viability and activated the autophagy of osteoblasts via the miR-1252-5p/GNB1 axis in OP.


2015 ◽  
Vol 112 (37) ◽  
pp. E5189-E5198 ◽  
Author(s):  
Lisa A. Miosge ◽  
Matthew A. Field ◽  
Yovina Sontani ◽  
Vicky Cho ◽  
Simon Johnson ◽  
...  

Each person’s genome sequence has thousands of missense variants. Practical interpretation of their functional significance must rely on computational inferences in the absence of exhaustive experimental measurements. Here we analyzed the efficacy of these inferences in 33 de novo missense mutations revealed by sequencing in first-generation progeny of N-ethyl-N-nitrosourea–treated mice, involving 23 essential immune system genes. PolyPhen2, SIFT, MutationAssessor, Panther, CADD, and Condel were used to predict each mutation’s functional importance, whereas the actual effect was measured by breeding and testing homozygotes for the expected in vivo loss-of-function phenotype. Only 20% of mutations predicted to be deleterious by PolyPhen2 (and 15% by CADD) showed a discernible phenotype in individual homozygotes. Half of all possible missense mutations in the same 23 immune genes were predicted to be deleterious, and most of these appear to become subject to purifying selection because few persist between separate mouse substrains, rodents, or primates. Because defects in immune genes could be phenotypically masked in vivo by compensation and environment, we compared inferences by the same tools with the in vitro phenotype of all 2,314 possible missense variants in TP53; 42% of mutations predicted by PolyPhen2 to be deleterious (and 45% by CADD) had little measurable consequence for TP53-promoted transcription. We conclude that for de novo or low-frequency missense mutations found by genome sequencing, half those inferred as deleterious correspond to nearly neutral mutations that have little impact on the clinical phenotype of individual cases but will nevertheless become subject to purifying selection.


2018 ◽  
Author(s):  
Xiaorong Zhou ◽  
Bret M. Evers ◽  
Mahesh S. Padanad ◽  
James A. Richardson ◽  
Emily Stein ◽  
...  

ABSTRACTPROTOCADHERIN 7 (PCDH7), a transmembrane receptor and member of the Cadherin superfamily, is frequently overexpressed in lung adenocarcinoma and is associated with poor clinical outcome. While PCDH7 was recently shown to promote transformation and facilitate brain metastasis in lung and breast cancers, decreased PCDH7 expression has also been documented in colorectal, gastric, and invasive bladder cancers. These data suggest context-dependent functions for PCDH7 in distinct tumor types. Given that PCDH7 is a potentially targetable molecule on the surface of cancer cells, further investigation of its role in tumorigenesisin vivois needed to evaluate the therapeutic potential of its inhibition. Here we report the analysis of novel PCDH7 gain- and loss-of-function mouse models and provide compelling evidence that this cell-surface protein acts as a potent lung cancer driver. Employing a Cre-inducible transgenic allele, we demonstrated that enforced PCDH7 expression significantly acceleratesKrasG12D-driven lung tumorigenesis and potentiates MAPK pathway activation. Furthermore, we performedin vivosomatic genome editing with CRISPR/Cas9 inKrasLSL-G12D;Tp53fl/fl(KP) mice to assess the consequences of PCDH7 loss of function. Inactivation of PCDH7 in KP mice significantly reduced lung tumor development, prolonged survival, and diminished phospho-activation of ERK1/2. Together, these findings establish a critical oncogenic function for PCDH7in vivoand highlight the therapeutic potential of PCDH7 inhibition for lung cancer. Moreover, given recent reports of elevated or reduced PCDH7 in distinct tumor types, the new inducible transgenic model described here provides a robust experimental system for broadly elucidating the effects of PCDH7 overexpressionin vivo.AUTHOR SUMMARYLung cancer is the leading cause of cancer-associated deaths worldwide. PROTOCADHERIN 7 (PCDH7), cell surface protein and member of the Cadherin superfamily, is frequently overexpressed in lung adenocarcinomas and is associated with poor clinical outcome. Nevertheless, it has yet to be shownin vivowhether PCDH7 plays a role in the initiation and progression of lung cancer, and whether it represents an actionable therapeutic target. Here we demonstrate, using a novel transgenic mouse model, that PCDH7 overexpression acceleratesKrasG12D-driven lung tumorigenesis. Furthermore, we validate PCDH7 as a therapeutic target by knocking it out usingin vivosomatic genome editing in theKrasLSL-G12D;Tp53fl/fl(KP) model. Our results provide new insight into the mechanisms that drive lung cancer pathogenesis and, because targeting oncogenic cell-surface proteins with antibodies has proven to be a highly effective anti-cancer therapeutic strategy, establish a new target for cancer treatment. Moreover, given recent reports of elevated or reduced PCDH7 in distinct tumor types, the transgenic PCDH7 model described here provides a robust experimental system for elucidating the effects of PCDH7 overexpression in differentin vivosettings. This model will also provide an ideal system for future testing of therapeutics directed at PCDH7.


Sign in / Sign up

Export Citation Format

Share Document