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Bach K, Dohnálek J, Škerlová J, Kuzmík J, Poláchová E, Stanchev S, Majer P, Fanfrlík J, Pecina A, Řezáč J, Lepšík M, Borshchevskiy V, Polovinkin V, Strisovsky K. Extensive targeting of chemical space at the prime side of ketoamide inhibitors of rhomboid proteases by branched substituents empowers their selectivity and potency. Eur J Med Chem 2024; 275:116606. [PMID: 38901105 DOI: 10.1016/j.ejmech.2024.116606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 06/10/2024] [Accepted: 06/14/2024] [Indexed: 06/22/2024]
Abstract
Rhomboid intramembrane serine proteases have been implicated in several pathologies, and emerge as attractive pharmacological target candidates. The most potent and selective rhomboid inhibitors available to date are peptidyl α-ketoamides, but their selectivity for diverse rhomboid proteases and strategies to modulate it in relevant contexts are poorly understood. This gap, together with the lack of suitable in vitro models, hinders ketoamide development for relevant eukaryotic rhomboid enzymes. Here we explore the structure-activity relationship principles of rhomboid inhibiting ketoamides by medicinal chemistry and enzymatic in vitro and in-cell assays with recombinant rhomboid proteases GlpG, human mitochondrial rhomboid PARL and human RHBDL2. We use X-ray crystallography in lipidic cubic phase to understand the binding mode of one of the best ketoamide inhibitors synthesized here containing a branched terminal substituent bound to GlpG. In addition, to extend the interpretation of the co-crystal structure, we use quantum mechanical calculations and quantify the relative importance of interactions along the inhibitor molecule. These combined experimental analyses implicates that more extensive exploration of chemical space at the prime side is unexpectedly powerful for the selectivity of rhomboid inhibiting ketoamides. Together with variations in the peptide sequence at the non-prime side, or its non-peptidic alternatives, this strategy enables targeted tailoring of potent and selective ketoamides towards diverse rhomboid proteases including disease-relevant ones such as PARL and RHBDL2.
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Affiliation(s)
- Kathrin Bach
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic; Department of Molecular Genetics, Faculty of Science, Charles University, Viničná 5, Prague, 128 44, Czech Republic
| | - Jan Dohnálek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic; University of Chemistry and Technology, Technická 5, Prague, 166 28, Czech Republic
| | - Jana Škerlová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic
| | - Ján Kuzmík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic
| | - Edita Poláchová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic; First Faculty of Medicine, Charles University, Kateřinská 32, Prague, 121 08, Czech Republic
| | - Stancho Stanchev
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic
| | - Pavel Majer
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic
| | - Adam Pecina
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic
| | - Jan Řezáč
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic
| | - Valentin Borshchevskiy
- Institute of Biological Information Processing 7, IBI-7 (Structural Biochemistry) Forschungszentrum Jülich 52428 Jülich, Germany
| | - Vitaly Polovinkin
- ELI Beamlines Centre, ELI ERIC, Za Radnicí 835, 252 41, Dolní Břežany, Czech Republic
| | - Kvido Strisovsky
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic.
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Chen S, Cai K, Zheng D, Liu Y, Li L, He Z, Sun C, Yu C. RHBDL2 promotes the proliferation, migration, and invasion of pancreatic cancer by stabilizing the N1ICD via the OTUD7B and activating the Notch signaling pathway. Cell Death Dis 2022; 13:945. [PMID: 36351890 PMCID: PMC9646733 DOI: 10.1038/s41419-022-05379-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 10/21/2022] [Accepted: 10/26/2022] [Indexed: 11/11/2022]
Abstract
Pancreatic cancer (PC) is one of the most malignant types of cancer, and is characterized by early metastasis, limited response to chemotherapeutics, and poor prognosis. Therefore, there is an urgent need to explore new therapeutic strategies for PC treatment. Human rhomboid-like 2 (RHBDL2) is differentially expressed in cervical and breast cancer. However, the correlation between RHBDL2 and PC remains unclear. We found that RHBDL2 is highly expressed in human PC cells and tissues and is significantly associated with distant metastasis and poor survival of patients with PC. Gain- and loss-of-function assays indicated that RHBDL2 could accelerate PC cell proliferation and mobility in vitro and in vivo. The RNA-Seq results suggest that RHBDL2 may be involved in the activation of Notch signaling pathway. IMR-1 could restore the proliferation and metastatic capacity of PC cells mediated by RHBDL2. RHBDL2 interacted with and cleaved Notch1, resulting in the release of N1ICD. RHBDL2 decreased the ubiquitination level of N1ICD and collaborated with Ovarian tumor domain-containing 7B (OTUD7B) to stabilize N1ICD via the ubiquitin-proteasome pathway. RHBDL2 facilitated PC cell proliferation and mobility by stabilizing the N1ICD via the OTUD7B and activating the Notch signaling pathway. Thus, targeting this novel pathway may be a potential therapeutic strategy for PC.
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Affiliation(s)
- Shiyu Chen
- grid.452244.1Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004 China ,Guizhou Provincial Institute of Hepatobiliary, Pancreatic and Splenic Diseases, Guiyang, Guizhou 550004 China ,Guizhou Provincial Clinical Medical Research Center of Hepatobiliary Surgery, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Key Laboratory of Liver, Gallbladder, Pancreas and Spleen of Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891School of Basic Medical Sciences, Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Department of Translational Medicine, College of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Guizhou Medical University, Guiyang, Guizhou 550004 China
| | - Kun Cai
- grid.452244.1Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004 China ,Guizhou Provincial Institute of Hepatobiliary, Pancreatic and Splenic Diseases, Guiyang, Guizhou 550004 China ,Guizhou Provincial Clinical Medical Research Center of Hepatobiliary Surgery, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Key Laboratory of Liver, Gallbladder, Pancreas and Spleen of Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Department of Surgery, College of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou 550004 China
| | - Dijie Zheng
- grid.452244.1Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004 China ,Guizhou Provincial Institute of Hepatobiliary, Pancreatic and Splenic Diseases, Guiyang, Guizhou 550004 China ,Guizhou Provincial Clinical Medical Research Center of Hepatobiliary Surgery, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Key Laboratory of Liver, Gallbladder, Pancreas and Spleen of Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891School of Basic Medical Sciences, Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Guizhou Medical University, Guiyang, Guizhou 550004 China
| | - Yanqing Liu
- grid.452244.1Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004 China ,Guizhou Provincial Institute of Hepatobiliary, Pancreatic and Splenic Diseases, Guiyang, Guizhou 550004 China ,Guizhou Provincial Clinical Medical Research Center of Hepatobiliary Surgery, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Key Laboratory of Liver, Gallbladder, Pancreas and Spleen of Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891School of Basic Medical Sciences, Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Department of Translational Medicine, College of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Guizhou Medical University, Guiyang, Guizhou 550004 China
| | - Lin Li
- grid.452244.1Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004 China ,Guizhou Provincial Institute of Hepatobiliary, Pancreatic and Splenic Diseases, Guiyang, Guizhou 550004 China ,Guizhou Provincial Clinical Medical Research Center of Hepatobiliary Surgery, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Key Laboratory of Liver, Gallbladder, Pancreas and Spleen of Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891School of Basic Medical Sciences, Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Department of Translational Medicine, College of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Guizhou Medical University, Guiyang, Guizhou 550004 China
| | - Zhiwei He
- grid.452244.1Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004 China ,Guizhou Provincial Institute of Hepatobiliary, Pancreatic and Splenic Diseases, Guiyang, Guizhou 550004 China ,Guizhou Provincial Clinical Medical Research Center of Hepatobiliary Surgery, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Key Laboratory of Liver, Gallbladder, Pancreas and Spleen of Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Department of Surgery, College of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou 550004 China
| | - Chengyi Sun
- grid.452244.1Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004 China ,Guizhou Provincial Institute of Hepatobiliary, Pancreatic and Splenic Diseases, Guiyang, Guizhou 550004 China ,Guizhou Provincial Clinical Medical Research Center of Hepatobiliary Surgery, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Key Laboratory of Liver, Gallbladder, Pancreas and Spleen of Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Department of Surgery, College of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou 550004 China
| | - Chao Yu
- grid.452244.1Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004 China ,Guizhou Provincial Institute of Hepatobiliary, Pancreatic and Splenic Diseases, Guiyang, Guizhou 550004 China ,Guizhou Provincial Clinical Medical Research Center of Hepatobiliary Surgery, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Key Laboratory of Liver, Gallbladder, Pancreas and Spleen of Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Department of Surgery, College of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou 550004 China
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Vizovisek M, Ristanovic D, Menghini S, Christiansen MG, Schuerle S. The Tumor Proteolytic Landscape: A Challenging Frontier in Cancer Diagnosis and Therapy. Int J Mol Sci 2021; 22:ijms22052514. [PMID: 33802262 PMCID: PMC7958950 DOI: 10.3390/ijms22052514] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/24/2021] [Accepted: 02/25/2021] [Indexed: 02/06/2023] Open
Abstract
In recent decades, dysregulation of proteases and atypical proteolysis have become increasingly recognized as important hallmarks of cancer, driving community-wide efforts to explore the proteolytic landscape of oncologic disease. With more than 100 proteases currently associated with different aspects of cancer development and progression, there is a clear impetus to harness their potential in the context of oncology. Advances in the protease field have yielded technologies enabling sensitive protease detection in various settings, paving the way towards diagnostic profiling of disease-related protease activity patterns. Methods including activity-based probes and substrates, antibodies, and various nanosystems that generate reporter signals, i.e., for PET or MRI, after interaction with the target protease have shown potential for clinical translation. Nevertheless, these technologies are costly, not easily multiplexed, and require advanced imaging technologies. While the current clinical applications of protease-responsive technologies in oncologic settings are still limited, emerging technologies and protease sensors are poised to enable comprehensive exploration of the tumor proteolytic landscape as a diagnostic and therapeutic frontier. This review aims to give an overview of the most relevant classes of proteases as indicators for tumor diagnosis, current approaches to detect and monitor their activity in vivo, and associated therapeutic applications.
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Lung MS, Mitchell CA, Doyle MA, Lynch AC, Gorringe KL, Bowtell DDL, Campbell IG, Trainer AH. Germline whole exome sequencing of a family with appendiceal mucinous tumours presenting with pseudomyxoma peritonei. BMC Cancer 2020; 20:369. [PMID: 32357859 PMCID: PMC7195761 DOI: 10.1186/s12885-020-6705-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 03/02/2020] [Indexed: 12/12/2022] Open
Abstract
Background Familial cases of appendiceal mucinous tumours (AMTs) are extremely rare and the underlying genetic aetiology uncertain. We identified potential predisposing germline genetic variants in a father and daughter with AMTs presenting with pseudomyxoma peritonei (PMP) and correlated these with regions of loss of heterozygosity (LOH) in the tumours. Methods Through germline whole exome sequencing, we identified novel heterozygous loss-of-function (LoF) (i.e. nonsense, frameshift and essential splice site mutations) and missense variants shared between father and daughter, and validated all LoF variants, and missense variants with a Combined Annotation Dependent Depletion (CADD) scaled score of ≥10. Genome-wide copy number analysis was performed on tumour tissue from both individuals to identify regions of LOH. Results Fifteen novel variants in 15 genes were shared by the father and daughter, including a nonsense mutation in REEP5. None of these germline variants were located in tumour regions of LOH shared by the father and daughter. Four genes (EXOG, RANBP2, RANBP6 and TNFRSF1B) harboured missense variants that fell in a region of LOH in the tumour from the father only, but none showed somatic loss of the wild type allele in the tumour. The REEP5 gene was sequenced in 23 individuals with presumed sporadic AMTs or PMP; no LoF or rare missense germline variants were identified. Conclusion Germline exome sequencing of a father and daughter with AMTs identified novel candidate predisposing genes. Further studies are required to clarify the role of these genes in familial AMTs.
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Affiliation(s)
- Mei Sim Lung
- Research Division, Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Victorian Comprehensive Cancer Centre Building, 305 Grattan St., Melbourne, Victoria, VIC 3000, Australia
| | - Catherine A Mitchell
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Maria A Doyle
- Research Computing Facility, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Andrew C Lynch
- Department of Surgical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Kylie L Gorringe
- Cancer Genomics Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Cancer Genetics and Genomics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - David D L Bowtell
- Cancer Genetics and Genomics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia.,Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, Australia
| | | | - Ian G Campbell
- Research Division, Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Victorian Comprehensive Cancer Centre Building, 305 Grattan St., Melbourne, Victoria, VIC 3000, Australia. .,Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia. .,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia.
| | - Alison H Trainer
- Research Division, Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Victorian Comprehensive Cancer Centre Building, 305 Grattan St., Melbourne, Victoria, VIC 3000, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia.,Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Department of Medicine, University of Melbourne, Parkville, Victoria, Australia
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Ngo S, Liang J, Su YH, O'Brien LE. Disruption of EGF Feedback by Intestinal Tumors and Neighboring Cells in Drosophila. Curr Biol 2020; 30:1537-1546.e3. [PMID: 32243854 PMCID: PMC7409949 DOI: 10.1016/j.cub.2020.01.082] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 12/11/2019] [Accepted: 01/29/2020] [Indexed: 12/20/2022]
Abstract
In healthy adult organs, robust feedback mechanisms control cell turnover to enforce homeostatic equilibrium between cell division and death [1, 2]. Nascent tumors must subvert these mechanisms to achieve cancerous overgrowth [3-7]. Elucidating the nature of this subversion can reveal how cancers become established and may suggest strategies to prevent tumor progression. In adult Drosophila intestine, a well-studied model of homeostatic cell turnover, the linchpin of cell equilibrium is feedback control of the epidermal growth factor (EGF) protease Rhomboid (Rho). Expression of Rho in apoptotic cells enables them to secrete EGFs, which stimulate nearby stem cells to undergo replacement divisions [8]. As in mammals, loss of adenomatous polyposis coli (APC) causes Drosophila intestinal stem cells to form adenomas [9]. Here, we demonstrate that Drosophila APC-/- tumors trigger widespread Rho expression in non-apoptotic cells, resulting in chronic EGF signaling. Initially, nascent APC-/- tumors induce rho in neighboring wild-type cells via acute, non-autonomous activation of Jun N-terminal kinase (JNK). During later growth and multilayering, APC-/- tumors induce rho in tumor cells by autonomous downregulation of E-cadherin (E-cad) and consequent activity of p120-catenin. This sequential dysregulation of tumor non-autonomous and -autonomous EGF signaling converts tissue-level feedback into feed-forward activation that drives cancerous overgrowth. Because Rho, EGF receptor (EGFR), and E-cad are associated with colorectal cancer in humans [10-17], our findings may shed light on how human colorectal tumors progress.
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Affiliation(s)
- Sang Ngo
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jackson Liang
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yu-Han Su
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lucy Erin O'Brien
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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Rhomboid-Like-2 Intramembrane Protease Mediates Metalloprotease-Independent Regulation of Cadherins. Int J Mol Sci 2019; 20:ijms20235958. [PMID: 31783481 PMCID: PMC6928865 DOI: 10.3390/ijms20235958] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 11/25/2019] [Accepted: 11/25/2019] [Indexed: 11/17/2022] Open
Abstract
Cadherins are a major family of cell-cell adhesive receptors, which are implicated in development, tissue homeostasis, and cancer. Here, we show a novel mechanism of post-translational regulation of E-cadherin in cancer cells by an intramembrane protease of the Rhomboid family, RHBDL2, which leads to the shedding of E-cadherin extracellular domain. In addition, our data indicate that RHBDL2 mediates a similar activity on VE-cadherin, which is selectively expressed by endothelial cells. We show that RHBDL2 promotes cell migration, which is consistent with its ability to interfere with the functional role of cadherins as negative regulators of motility; moreover, the two players appear to lie in the same functional pathway. Importantly, we show that RHBDL2 expression is induced by the inflammatory chemokine TNFα. The E-cadherin extracellular domain is known to be released by metalloproteases (MMPs); however, here, we provide evidence of a novel MMP-independent, TNFα inducible, E-cadherin processing mechanism that is mediated by RHBDL2. Thus, the intramembrane protease RHBDL2 is a novel regulator of cadherins promoting cell motility.
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The DCBLD receptor family: emerging signaling roles in development, homeostasis and disease. Biochem J 2019; 476:931-950. [PMID: 30902898 DOI: 10.1042/bcj20190022] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/20/2019] [Accepted: 03/04/2019] [Indexed: 02/08/2023]
Abstract
The discoidin, CUB, and LCCL domain-containing (DCBLD) receptor family are composed of the type-I transmembrane proteins DCBLD1 and DCBLD2 (also ESDN and CLCP1). These proteins are highly conserved across vertebrates and possess similar domain structure to that of neuropilins, which act as critical co-receptors in developmental processes. Although DCBLD1 remains largely uncharacterized, the functional and mechanistic roles of DCBLD2 are emerging. This review provides a comprehensive discussion of this presumed receptor family, ranging from structural and signaling aspects to their associations with cancer, physiology, and development.
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Calender A, Rollat Farnier PA, Buisson A, Pinson S, Bentaher A, Lebecque S, Corvol H, Abou Taam R, Houdouin V, Bardel C, Roy P, Devouassoux G, Cottin V, Seve P, Bernaudin JF, Lim CX, Weichhart T, Valeyre D, Pacheco Y, Clement A, Nathan N. Whole exome sequencing in three families segregating a pediatric case of sarcoidosis. BMC Med Genomics 2018; 11:23. [PMID: 29510755 PMCID: PMC5839022 DOI: 10.1186/s12920-018-0338-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Accepted: 02/19/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Sarcoidosis (OMIM 181000) is a multi-systemic granulomatous disorder of unknown origin. Despite multiple genome-wide association (GWAS) studies, no major pathogenic pathways have been identified to date. To find out relevant sarcoidosis predisposing genes, we searched for de novo and recessive mutations in 3 young probands with sarcoidosis and their healthy parents using a whole-exome sequencing (WES) methodology. METHODS From the SARCFAM project based on a national network collecting familial cases of sarcoidosis, we selected three families (trios) in which a child, despite healthy parents, develop the disease before age 15 yr. Each trio was genotyped by WES (Illumina HiSEQ 2500) and we selected the gene variants segregating as 1) new mutations only occurring in affected children and 2) as recessive traits transmitted from each parents. The identified coding variants were compared between the three families. Allelic frequencies and in silico functional results were analyzed using ExAC, SIFT and Polyphenv2 databases. The clinical and genetic studies were registered by the ClinicalTrials.gov - Protocol Registration and Results System (PRS) ( https://clinicaltrials.gov ) receipt under the reference NCT02829853 and has been approved by the ethical committee (CPP LYON SUD EST - 2 - REF IRB 00009118 - September 21, 2016). RESULTS We identified 37 genes sharing coding variants occurring either as recessive mutations in at least 2 trios or de novo mutations in one of the three affected children. The genes were classified according to their potential roles in immunity related pathways: 9 to autophagy and intracellular trafficking, 6 to G-proteins regulation, 4 to T-cell activation, 4 to cell cycle and immune synapse, 2 to innate immunity. Ten of the 37 genes were studied in a bibliographic way to evaluate the functional link with sarcoidosis. CONCLUSIONS Whole exome analysis of case-parent trios is useful for the identification of genes predisposing to complex genetic diseases as sarcoidosis. Our data identified 37 genes that could be putatively linked to a pediatric form of sarcoidosis in three trios. Our in-depth focus on 10 of these 37 genes may suggest that the formation of the characteristic lesion in sarcoidosis, granuloma, results from combined deficits in autophagy and intracellular trafficking (ex: Sec16A, AP5B1 and RREB1), G-proteins regulation (ex: OBSCN, CTTND2 and DNAH11), T-cell activation (ex: IDO2, IGSF3), mitosis and/or immune synapse (ex: SPICE1 and KNL1). The significance of these findings needs to be confirmed by functional tests on selected gene variants.
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Affiliation(s)
- Alain Calender
- Genetics Department, Hospices Civils de LYON (HCL), University Hospital, East Pathology Center, LYON, B-A3, 59 Bld Pinel, 69677 BRON Cedex, France
- Inflammation & Immunity of the Respiratory Epithelium - EA7426 (PI3) – South Medical University Hospital – Lyon 1 Claude Bernard University, 165 Chemin du Grand Revoyet, 69310 Pierre-Bénite, France
| | | | - Adrien Buisson
- Genetics Department, Hospices Civils de LYON (HCL), University Hospital, East Pathology Center, LYON, B-A3, 59 Bld Pinel, 69677 BRON Cedex, France
| | - Stéphane Pinson
- Genetics Department, Hospices Civils de LYON (HCL), University Hospital, East Pathology Center, LYON, B-A3, 59 Bld Pinel, 69677 BRON Cedex, France
| | - Abderrazzaq Bentaher
- Inflammation & Immunity of the Respiratory Epithelium - EA7426 (PI3) – South Medical University Hospital – Lyon 1 Claude Bernard University, 165 Chemin du Grand Revoyet, 69310 Pierre-Bénite, France
| | - Serge Lebecque
- Cancer Research Center, INSERM U-1052, CNRS 5286, 69008 Lyon, France
| | - Harriet Corvol
- Pediatric pulmonology and Reference Center for rare lung diseases RespiRare, Hôpital Trousseau, AP-HP, INSERM UMR-S938, Sorbonne University, Paris, France
| | - Rola Abou Taam
- Pediatric pulmonology and Reference Center for rare lung diseases RespiRare, Hôpital Necker, Paris, France
| | - Véronique Houdouin
- Pediatric pulmonology and Reference Center for rare lung diseases RespiRare, Hôpital Robert Debré, INSERM U-1142, University Paris Diderot VII, Paris, France
| | - Claire Bardel
- Department of biostatistics, University Hospital, Hospices Civils de LYON (HCL), Lyon, France
| | - Pascal Roy
- Department of biostatistics, University Hospital, Hospices Civils de LYON (HCL), Lyon, France
| | - Gilles Devouassoux
- Department of Pulmonology, University Hospital, Hôpital Croix Rousse, Lyon, France
| | - Vincent Cottin
- Department of Pulmonology, University Hospital, Hôpital Louis Pradel, Lyon, France
| | - Pascal Seve
- Department of Internal medicine, University Hospital, Hôpital Croix Rousse, Lyon, France
| | | | - Clarice X. Lim
- Medical University of Vienna, Center for Pathobiochemistry and Genetics, Institute of Medical Genetics, Währinger Straße 10, 1090 Vienna, Austria
| | - Thomas Weichhart
- Medical University of Vienna, Center for Pathobiochemistry and Genetics, Institute of Medical Genetics, Währinger Straße 10, 1090 Vienna, Austria
| | - Dominique Valeyre
- EA2363, University Paris 13, COMUE Sorbonne-Paris-Cité, 74 rue Marcel Cachin, 93009 Bobigny, France
- Assistance Publique Hôpitaux de Paris, Department of Pulmonology, Avicenne University Hospital, 93009 Bobigny, France
| | - Yves Pacheco
- Inflammation & Immunity of the Respiratory Epithelium - EA7426 (PI3) – South Medical University Hospital – Lyon 1 Claude Bernard University, 165 Chemin du Grand Revoyet, 69310 Pierre-Bénite, France
| | - Annick Clement
- AP-HP Pediatric pulmonology and Reference Center for rare lung diseases RespiRare, Hôpital Trousseau, INSERM UMR-S933, Sorbonne University, Paris, France
| | - Nadia Nathan
- AP-HP Pediatric pulmonology and Reference Center for rare lung diseases RespiRare, Hôpital Trousseau, INSERM UMR-S933, Sorbonne University, Paris, France
| | - in the frame of GSF (Groupe Sarcoïdose France)
- Genetics Department, Hospices Civils de LYON (HCL), University Hospital, East Pathology Center, LYON, B-A3, 59 Bld Pinel, 69677 BRON Cedex, France
- Department of biostatistics, University Hospital, Hospices Civils de LYON (HCL), Lyon, France
- Inflammation & Immunity of the Respiratory Epithelium - EA7426 (PI3) – South Medical University Hospital – Lyon 1 Claude Bernard University, 165 Chemin du Grand Revoyet, 69310 Pierre-Bénite, France
- Cancer Research Center, INSERM U-1052, CNRS 5286, 69008 Lyon, France
- Pediatric pulmonology and Reference Center for rare lung diseases RespiRare, Hôpital Trousseau, AP-HP, INSERM UMR-S938, Sorbonne University, Paris, France
- Pediatric pulmonology and Reference Center for rare lung diseases RespiRare, Hôpital Necker, Paris, France
- Pediatric pulmonology and Reference Center for rare lung diseases RespiRare, Hôpital Robert Debré, INSERM U-1142, University Paris Diderot VII, Paris, France
- Department of Pulmonology, University Hospital, Hôpital Croix Rousse, Lyon, France
- Department of Pulmonology, University Hospital, Hôpital Louis Pradel, Lyon, France
- Department of Internal medicine, University Hospital, Hôpital Croix Rousse, Lyon, France
- Histology and Tumor Biology, ER2 UPMC, Hôpital Tenon, Paris, France
- Medical University of Vienna, Center for Pathobiochemistry and Genetics, Institute of Medical Genetics, Währinger Straße 10, 1090 Vienna, Austria
- EA2363, University Paris 13, COMUE Sorbonne-Paris-Cité, 74 rue Marcel Cachin, 93009 Bobigny, France
- Assistance Publique Hôpitaux de Paris, Department of Pulmonology, Avicenne University Hospital, 93009 Bobigny, France
- AP-HP Pediatric pulmonology and Reference Center for rare lung diseases RespiRare, Hôpital Trousseau, INSERM UMR-S933, Sorbonne University, Paris, France
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9
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Johnson N, Březinová J, Stephens E, Burbridge E, Freeman M, Adrain C, Strisovsky K. Quantitative proteomics screen identifies a substrate repertoire of rhomboid protease RHBDL2 in human cells and implicates it in epithelial homeostasis. Sci Rep 2017; 7:7283. [PMID: 28779096 PMCID: PMC5544772 DOI: 10.1038/s41598-017-07556-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 06/21/2017] [Indexed: 01/01/2023] Open
Abstract
Rhomboids are intramembrane serine proteases conserved in all kingdoms of life. They regulate epidermal growth factor receptor signalling in Drosophila by releasing signalling ligands from their transmembrane tethers. Their functions in mammals are poorly understood, in part because of the lack of endogenous substrates identified thus far. We used a quantitative proteomics approach to investigate the substrate repertoire of rhomboid protease RHBDL2 in human cells. We reveal a range of novel substrates that are specifically cleaved by RHBDL2, including the interleukin-6 receptor (IL6R), cell surface protease inhibitor Spint-1, the collagen receptor tyrosine kinase DDR1, N-Cadherin, CLCP1/DCBLD2, KIRREL, BCAM and others. We further demonstrate that these substrates can be shed by endogenously expressed RHBDL2 and that a subset of them is resistant to shedding by cell surface metalloproteases. The expression profiles and identity of the substrates implicate RHBDL2 in physiological or pathological processes affecting epithelial homeostasis.
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Affiliation(s)
- Nicholas Johnson
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Flemingovo n. 2, Prague, 166 10, Czech Republic
| | - Jana Březinová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Flemingovo n. 2, Prague, 166 10, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Elaine Stephens
- MRC Laboratory of Molecular Biology, Cambridge, CB2 2QH, United Kingdom
| | | | - Matthew Freeman
- MRC Laboratory of Molecular Biology, Cambridge, CB2 2QH, United Kingdom.,Sir William Dunn School of Pathology, Oxford, OX1 3RE, United Kingdom
| | - Colin Adrain
- Instituto Gulbenkian de Ciência, Lisbon, Portugal.
| | - Kvido Strisovsky
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Flemingovo n. 2, Prague, 166 10, Czech Republic.
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10
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Düsterhöft S, Künzel U, Freeman M. Rhomboid proteases in human disease: Mechanisms and future prospects. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:2200-2209. [PMID: 28460881 DOI: 10.1016/j.bbamcr.2017.04.016] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 04/24/2017] [Accepted: 04/26/2017] [Indexed: 01/19/2023]
Abstract
Rhomboids are intramembrane serine proteases that cleave the transmembrane helices of substrate proteins, typically releasing luminal/extracellular domains from the membrane. They are conserved in all branches of life and there is a growing recognition of their association with a wide range of human diseases. Human rhomboids, for example, have been implicated in cancer, metabolic disease and neurodegeneration, while rhomboids in apicomplexan parasites appear to contribute to their invasion of host cells. Recent advances in our knowledge of the structure and the enzyme function of rhomboids, and increasing efforts to identify specific inhibitors, are beginning to provide important insight into the prospect of rhomboids becoming future therapeutic targets. This article is part of a Special Issue entitled: Proteolysis as a Regulatory Event in Pathophysiology edited by Stefan Rose-John.
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Affiliation(s)
- Stefan Düsterhöft
- Dunn School of Pathology, University of Oxford, OX1 3RE, United Kingdom
| | - Ulrike Künzel
- Dunn School of Pathology, University of Oxford, OX1 3RE, United Kingdom
| | - Matthew Freeman
- Dunn School of Pathology, University of Oxford, OX1 3RE, United Kingdom.
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11
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Abstract
Intramembrane serine proteases of the rhomboid family are widespread, and their gradually uncovered functions in different organisms already suggest medical relevance for infectious diseases and cancer. However, selective inhibitors that could serve as research tools for rhomboids, for validation of their disease relevance, or as templates for drug development are lacking. Here I summarize the current knowledge about rhomboid protease mechanism and specificity, overview the currently used inhibitors, and conclude by proposing avenues for future development of rhomboid protease inhibitors.
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Affiliation(s)
- K Strisovsky
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
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12
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Strisovsky K. Rhomboid protease inhibitors: Emerging tools and future therapeutics. Semin Cell Dev Biol 2016; 60:52-62. [PMID: 27567709 DOI: 10.1016/j.semcdb.2016.08.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 08/16/2016] [Accepted: 08/24/2016] [Indexed: 02/01/2023]
Abstract
Rhomboid-family intramembrane serine proteases are evolutionarily widespread. Their functions in different organisms are gradually being uncovered and already suggest medical relevance for infectious diseases and cancer. In contrast to these advances, selective inhibitors that could serve as efficient tools for investigation of physiological functions of rhomboids, validation of their disease relevance or as templates for drug development are lacking. In this review I extract what is known about rhomboid protease mechanism and specificity, examine the currently used inhibitors, their mechanism of action and limitations, and conclude by proposing routes for future development of rhomboid protease inhibitors.
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Affiliation(s)
- Kvido Strisovsky
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo n. 2, Prague 166 10, Czech Republic.
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13
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Substrates and physiological functions of secretase rhomboid proteases. Semin Cell Dev Biol 2016; 60:10-18. [PMID: 27497690 DOI: 10.1016/j.semcdb.2016.07.033] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 07/26/2016] [Accepted: 07/31/2016] [Indexed: 02/01/2023]
Abstract
Rhomboids are conserved intramembrane serine proteases with widespread functions. They were the earliest discovered members of the wider rhomboid-like superfamily of proteases and pseudoproteases. The secretase class of rhomboid proteases, distributed through the secretory pathway, are the most numerous in eukaryotes, but our knowledge of them is limited. Here we aim to summarise all that has been published on secretase rhomboids in a concise encyclopaedia of the enzymes, their substrates, and their biological roles. We also discuss emerging themes of how these important enzymes are regulated.
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14
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Wood S, Goldufsky J, Shafikhani SH. Pseudomonas aeruginosa ExoT Induces Atypical Anoikis Apoptosis in Target Host Cells by Transforming Crk Adaptor Protein into a Cytotoxin. PLoS Pathog 2015; 11:e1004934. [PMID: 26020630 PMCID: PMC4447348 DOI: 10.1371/journal.ppat.1004934] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 05/04/2015] [Indexed: 11/19/2022] Open
Abstract
Previously, we demonstrated that Pseudomonas aeruginosa ExoT induces potent apoptosis in host epithelial cells in a manner that primarily depends on its ADP-ribosyltransferase domain (ADPRT) activity. However, the mechanism underlying ExoT/ADPRT-induced apoptosis remains undetermined. We now report that ExoT/ADPRT disrupts focal adhesion sites, activates p38β and JNK, and interferes with integrin-mediated survival signaling; causing atypical anoikis. We show that ExoT/ADPRT-induced anoikis is mediated by the Crk adaptor protein. We found that Crk-/- knockout cells are significantly more resistant to ExoT-induced apoptosis, while Crk-/- cells complemented with Crk are rendered sensitive to ExoT-induced apoptosis. Moreover, a dominant negative (DN) mutant form of Crk phenocopies ExoT-induced apoptosis both kinetically and mechanistically. Crk is generally believed to be a component of focal adhesion (FA) and its role in cellular survival remains controversial in that it has been found to be either pro-survival or pro-apoptosis. Our data demonstrate that although Crk is recruited to FA sites, its function is likely not required for FA assembly or for survival per se. However, when modified by ExoT or by mutagenesis, it can be transformed into a cytotoxin that induces anoikis by disrupting FA sites and interfering with integrin survival signaling. To our knowledge, this is the first example whereby a bacterial toxin exerts its cytotoxicity by subverting the function of an innocuous host cellular protein and turning it against the host cell.
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Affiliation(s)
- Stephen Wood
- Department of Immunology/Microbiology, Rush University Medical Center, Chicago, Illinois, United States of America
| | - Josef Goldufsky
- Department of Immunology/Microbiology, Rush University Medical Center, Chicago, Illinois, United States of America
| | - Sasha H. Shafikhani
- Department of Immunology/Microbiology, Rush University Medical Center, Chicago, Illinois, United States of America
- Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois, United States of America
- Cancer Center, Rush University Medical Center, Chicago, Illinois, United States of America
- * E-mail:
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