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Cai H, Zhang B, Ahrenfeldt J, Joseph JV, Riedel M, Gao Z, Thomsen SK, Christensen DS, Bak RO, Hager H, Vendelbo MH, Gao X, Birkbak N, Thomsen MK. CRISPR/Cas9 model of prostate cancer identifies Kmt2c deficiency as a metastatic driver by Odam/Cabs1 gene cluster expression. Nat Commun 2024; 15:2088. [PMID: 38453924 PMCID: PMC10920892 DOI: 10.1038/s41467-024-46370-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 02/20/2024] [Indexed: 03/09/2024] Open
Abstract
Metastatic prostate cancer (PCa) poses a significant therapeutic challenge with high mortality rates. Utilizing CRISPR-Cas9 in vivo, we target five potential tumor suppressor genes (Pten, Trp53, Rb1, Stk11, and RnaseL) in the mouse prostate, reaching humane endpoint after eight weeks without metastasis. By further depleting three epigenetic factors (Kmt2c, Kmt2d, and Zbtb16), lung metastases are present in all mice. While whole genome sequencing reveals few mutations in coding sequence, RNA sequencing shows significant dysregulation, especially in a conserved genomic region at chr5qE1 regulated by KMT2C. Depleting Odam and Cabs1 in this region prevents metastasis. Notably, the gene expression signatures, resulting from our study, predict progression-free and overall survival and distinguish primary and metastatic human prostate cancer. This study emphasizes positive genetic interactions between classical tumor suppressor genes and epigenetic modulators in metastatic PCa progression, offering insights into potential treatments.
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Affiliation(s)
- Huiqiang Cai
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Bin Zhang
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Johanne Ahrenfeldt
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Justin V Joseph
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Maria Riedel
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Zongliang Gao
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Sofie K Thomsen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Ditte S Christensen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Rasmus O Bak
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Henrik Hager
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Mikkel H Vendelbo
- Department of Nuclear Medicine & PET Centre, Aarhus University Hospital, Aarhus, Denmark
| | - Xin Gao
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Nicolai Birkbak
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Martin K Thomsen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.
- Aarhus Institute of Advanced Studies (AIAS), Aarhus University, Aarhus, Denmark.
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2
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Trasierras AM, Luna JM, Ventura S. A contrast set mining based approach for cancer subtype analysis. Artif Intell Med 2023; 143:102590. [PMID: 37673572 DOI: 10.1016/j.artmed.2023.102590] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 05/24/2023] [Accepted: 05/30/2023] [Indexed: 09/08/2023]
Abstract
The task of detecting common and unique characteristics among different cancer subtypes is an important focus of research that aims to improve personalized therapies. Unlike current approaches mainly based on predictive techniques, our study aims to improve the knowledge about the molecular mechanisms that descriptively led to cancer, thus not requiring previous knowledge to be validated. Here, we propose an approach based on contrast set mining to capture high-order relationships in cancer transcriptomic data. In this way, we were able to extract valuable insights from several cancer subtypes in the form of highly specific genetic relationships related to functional pathways affected by the disease. To this end, we have divided several cancer gene expression databases by the subtype associated with each sample to detect which gene groups are related to each cancer subtype. To demonstrate the potential and usefulness of the proposed approach we have extensively analysed RNA-Seq gene expression data from breast, kidney, and colon cancer subtypes. The possible role of the obtained genetic relationships was further evaluated through extensive literature research, while its prognosis was assessed via survival analysis, finding gene expression patterns related to survival in various cancer subtypes. Some gene associations were described in the literature as potential cancer biomarkers while other results have been not described yet and could be a starting point for future research.
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Affiliation(s)
- A M Trasierras
- Department of Computer Science and Numerical Analysis, Andalusian Research Institute in Data Science and Computational Intelligence (DaSCI), Spain; Maimonides Biomedical Research Institute of Cordoba, IMIBIC, University of Cordoba, Córdoba, 14071, Spain; Phytoplant Research S.L.U, Departamento Tecnología y Control, Rabanales 21-Parque Científico Tecnológico de Córdoba, Calle Astrónoma Cecilia Payne, Córdoba, Spain
| | - J M Luna
- Department of Computer Science and Numerical Analysis, Andalusian Research Institute in Data Science and Computational Intelligence (DaSCI), Spain; Maimonides Biomedical Research Institute of Cordoba, IMIBIC, University of Cordoba, Córdoba, 14071, Spain
| | - S Ventura
- Department of Computer Science and Numerical Analysis, Andalusian Research Institute in Data Science and Computational Intelligence (DaSCI), Spain; Maimonides Biomedical Research Institute of Cordoba, IMIBIC, University of Cordoba, Córdoba, 14071, Spain.
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3
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Araujo-Abad S, Fuentes-Baile M, Rizzuti B, Bazán JF, Villamarin-Ortiz A, Saceda M, Fernández E, Vidal M, Abian O, Velazquez-Campoy A, de Juan Romero C, Neira JL. The intrinsically disordered, epigenetic factor RYBP binds to the citrullinating enzyme PADI4 in cancer cells. Int J Biol Macromol 2023; 246:125632. [PMID: 37399862 DOI: 10.1016/j.ijbiomac.2023.125632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/16/2023] [Accepted: 06/28/2023] [Indexed: 07/05/2023]
Abstract
RYBP (Ring1 and YY 1 binding protein) is a multifunctional, intrinsically disordered protein (IDP), best described as a transcriptional regulator. It exhibits a ubiquitin-binding functionality, binds to other transcription factors, and has a key role during embryonic development. RYBP, which folds upon binding to DNA, has a Zn-finger domain at its N-terminal region. By contrast, PADI4 is a well-folded protein and it is one the human isoforms of a family of enzymes implicated in the conversion of arginine to citrulline. As both proteins intervene in signaling pathways related to cancer development and are found in the same localizations within the cell, we hypothesized they may interact. We observed their association in the nucleus and cytosol in several cancer cell lines, by using immunofluorescence (IF) and proximity ligation assays (PLAs). Binding also occurred in vitro, as measured by isothermal titration calorimetry (ITC) and fluorescence, with a low micromolar affinity (~1 μM). AlphaFold2-multimer (AF2) results indicate that PADI4's catalytic domain interacts with the Arg53 of RYBP docking into its active site. As RYBP sensitizes cells to PARP (Poly (ADP-ribose) polymerase) inhibitors, we applied them in combination with an enzymatic inhibitor of PADI4 observing a change in cell proliferation, and the hampering of the interaction of both proteins. This study unveils for the first time the possible citrullination of an IDP, and suggests that this new interaction, whether it involves or not citrullination of RYBP, might have implications in cancer development and progression.
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Affiliation(s)
- Salomé Araujo-Abad
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain; Centro de Biotecnología, Universidad Nacional de Loja, Avda. Pío Jaramillo Alvarado s/n, 110111 Loja, Ecuador
| | - María Fuentes-Baile
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain; Unidad de Investigación, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Hospital General Universitario de Elche, Camí de l'Almazara 11, 03203 Elche, Alicante, Spain
| | - Bruno Rizzuti
- CNR-NANOTEC, SS Rende (CS), Department of Physics, University of Calabria, 87036 Rende, Italy; Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) - Unidad mixta GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - J Fernando Bazán
- ħ Bioconsulting, LLC, Stillwater, MN, USA; Unit for Structural Biology, Vlaams Instituut voor Biotechnologie-UGent Center for Inflammation Research, Technologiepark 71, 9052 Ghent, Belgium
| | | | - Miguel Saceda
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain; Unidad de Investigación, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Hospital General Universitario de Elche, Camí de l'Almazara 11, 03203 Elche, Alicante, Spain
| | - Eduardo Fernández
- Instituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain; Centro de Investigación Biomédica en Red CIBER-BBN, Av. Monforte de Lemos 3-5, 28029 Madrid, Spain
| | - Miguel Vidal
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Calle Ramiro de Maeztu, 9, 28040 Madrid, Spain
| | - Olga Abian
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) - Unidad mixta GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Adrián Velazquez-Campoy
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) - Unidad mixta GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Camino de Juan Romero
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain; Unidad de Investigación, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Hospital General Universitario de Elche, Camí de l'Almazara 11, 03203 Elche, Alicante, Spain.
| | - José L Neira
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) - Unidad mixta GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain.
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4
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Araujo-Abad S, Neira JL, Rizzuti B, García-Morales P, de Juan Romero C, Santofimia-Castaño P, Iovanna J. Intrinsically Disordered Chromatin Protein NUPR1 Binds to the Enzyme PADI4. J Mol Biol 2023; 435:168033. [PMID: 36858171 DOI: 10.1016/j.jmb.2023.168033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 02/18/2023] [Accepted: 02/21/2023] [Indexed: 03/02/2023]
Abstract
The nuclear protein 1 (NUPR1) is an intrinsically disordered protein involved in stress-mediated cellular conditions. Its paralogue nuclear protein 1-like (NUPR1L) is p53-regulated, and its expression down-regulates that of the NUPR1 gene. Peptidyl-arginine deiminase 4 (PADI4) is an isoform of a family of enzymes catalyzing arginine to citrulline conversion; it is also involved in stress-mediated cellular conditions. We characterized the interaction between NUPR1 and PADI4 in vitro, in silico, and in cellulo. The interaction of NUPR1 and PADI4 occurred with a dissociation constant of 18 ± 6 μM. The binding region of NUPR1, mapped by NMR, was a hydrophobic polypeptide patch surrounding the key residue Ala33, as pinpointed by: (i) computational results; and, (ii) site-directed mutagenesis of residues of NUPR1. The association between PADI4 and wild-type NUPR1 was also assessed in cellulo by using proximity ligation assays (PLAs) and immunofluorescence (IF), and it occurred mainly in the nucleus. Moreover, binding between NUPR1L and PADI4 also occurred in vitro with an affinity similar to that of NUPR1. Molecular modelling provided information on the binding hot spot for PADI4. This is an example of a disordered partner of PADI4, whereas its other known interacting proteins are well-folded. Altogether, our results suggest that the NUPR1/PADI4 complex could have crucial functions in modulating DNA-repair, favoring metastasis, or facilitating citrullination of other proteins.
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Affiliation(s)
- Salomé Araujo-Abad
- IDIBE, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain; Centro de Biotecnología, Universidad Nacional de Loja, Avda. Pío Jaramillo Alvarado s/n, Loja, 110111 Loja, Ecuador
| | - José L Neira
- IDIBE, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain; Institute of Biocomputation and Physics of Complex Systems - Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain.
| | - Bruno Rizzuti
- Institute of Biocomputation and Physics of Complex Systems - Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; CNR-NANOTEC, SS Rende (CS), Department of Physics, University of Calabria, 87036 Rende, Italy
| | | | - Camino de Juan Romero
- IDIBE, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain; Unidad de Investigación, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Hospital General Universitario de Elche, Camí de l'Almazara 11, 03203 Elche (Alicante), Spain
| | - Patricia Santofimia-Castaño
- Centre de Recherche en Cancérologie de Marseille, INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, 13288 Marseille, France.
| | - Juan Iovanna
- Centre de Recherche en Cancérologie de Marseille, INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, 13288 Marseille, France
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5
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Effects of TP53 Mutations and miRs on Immune Responses in the Tumor Microenvironment Important in Pancreatic Cancer Progression. Cells 2022; 11:cells11142155. [PMID: 35883598 PMCID: PMC9318640 DOI: 10.3390/cells11142155] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 01/27/2023] Open
Abstract
Approximately 90% of pancreatic cancers are pancreatic ductal adenocarcinomas (PDAC). PDAC is the fourth leading cause of cancer death world-wide. Therapies for PDAC are largely ineffective due to the dense desmoplastic tumor microenvironment which prevents chemotherapeutic drugs and small molecule inhibitors from exerting effective anti-cancer effects. In this review, we will discuss the roles of TP53 and miRs on the PDAC tumor microenvironment and how loss of the normal functions of TP53 promote tumor progression. The TP53 gene is mutated in approximately 50% of pancreatic cancers. Often, these TP53 mutations are point mutations which confer additional functions for the TP53 proteins. These are called gain of function (GOF) mutations (mut). Another class of TP53 mutations are deletions which result in loss of the TP53 protein; these are referred to TP53-null mutations. We have organized this review into various components/properties of the PDAC microenvironment and how they may be altered in the presence of mutant TP53 and loss of certain miR expression.
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6
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Zhao H, Zhang J, Fu X, Mao D, Qi X, Liang S, Meng G, Song Z, Yang R, Guo Z, Tong B, Sun M, Zuo B, Li G. Integrated bioinformatics analysis of the NEDD4 family reveals a prognostic value of NEDD4L in clear-cell renal cell cancer. PeerJ 2021; 9:e11880. [PMID: 34458018 PMCID: PMC8378337 DOI: 10.7717/peerj.11880] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 07/07/2021] [Indexed: 12/20/2022] Open
Abstract
The members of the Nedd4-like E3 family participate in various biological processes. However, their role in clear cell renal cell carcinoma (ccRCC) is not clear. This study systematically analyzed the Nedd4-like E3 family members in ccRCC data sets from multiple publicly available databases. NEDD4L was identified as the only NEDD4 family member differentially expressed in ccRCC compared with normal samples. Bioinformatics tools were used to characterize the function of NEDD4L in ccRCC. It indicated that NEDD4L might regulate cellular energy metabolism by co-expression analysis, and subsequent gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. A prognostic model developed by the LASSO Cox regression method showed a relatively good predictive value in training and testing data sets. The result revealed that NEDD4L was associated with biosynthesis and metabolism of ccRCC. Since NEDD4L is downregulated and dysregulation of metabolism is involved in tumor progression, NEDD4L might be a potential therapeutic target in ccRCC.
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Affiliation(s)
- Hui Zhao
- Department of Urology, Affiliated Hospital of Weifang Medical University, Weifang, China.,Department of Urology, China Rehabilitation Research Centre, Rehabilitation School of Capital Medical University, Beijing, China
| | - Junjun Zhang
- Department of Oncology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Xiaoliang Fu
- Department of Urology, The Second Affiliated Hospital of Air Force Medical University, Xian, China
| | - Dongdong Mao
- Department of Urology, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Xuesen Qi
- Department of Urology, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Shuai Liang
- Department of Urology, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Gang Meng
- Department of Urology, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Zewen Song
- Department of Oncology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Ru Yang
- Henan Key Laboratory of Neurorestoratology, The First Affliated Hospital of Xinxiang Medical University, Weihui, China
| | - Zhenni Guo
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Binghua Tong
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Meiqing Sun
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Baile Zuo
- Tumor Molecular Immunology and Immunotherapy Laboratory, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
| | - Guoyin Li
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China.,Academy of Medical Science, Zhengzhou University, Zhengzhou, China
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7
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Jiang W, Zhang C, Zhang X, Sun L, Li J, Zuo J. CircRNA HIPK3 promotes the progression of oral squamous cell carcinoma through upregulation of the NUPR1/PI3K/AKT pathway by sponging miR-637. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:860. [PMID: 34164494 PMCID: PMC8184441 DOI: 10.21037/atm-21-1908] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Background To investigate the expression, function, and related mechanisms of circHIPK3 in oral squamous cell carcinoma (OSCC). Methods CircHIPK3 expression was determined by quantitative reverse transcription polymerized chain reaction (QRT-PCR) in OSCC and adjacent tissues, and the correlation between the circHIPK3 level and clinicopathological indexes of OSCC was analyzed. CircHIPK3 expressions in different OSCC cell lines were detected, cell counting kit-8 (CCK-8) and 5-bromodeoxyuridine (BrdU) assays were utilized to monitor cell proliferation and activity. Flow cytometry was adopted to detect apoptosis and transwell assay was used to detect cell invasion. The expressions of nuclear protein 1 (NUPR1), phosphatidylinositol 3 kinase (PI3K)/protein kinase B (AKT) (PI3K/AKT) pathway proteins, and E-cadherin, Vimentin, and N-cadherin markers of epithelial-mesenchymal transformation (EMT) were detected by Western blot or Quantitative Real-time PCR (QRT-PCR). Results Upregulated circHIPK3 was noted in OSCC tissues (compared with adjacent tissues), and its overexpression was related to OSCC size and histopathological grade. Functionally, overexpressed circHIPK3 can significantly promote EMT, proliferation, and invasion of OSCC cells and can inhibit cell apoptosis in vivo and in vitro. In addition, CircHIPK3 upregulated the activation of NUPR1 and PI3K/AKT. Bioinformatics analyses showed that miR-637 was the common target of circHIPK3 and NUPR1, while a dual luciferase reporting assay and RIP assay further demonstrated that circHIPK3 targeted miR-637 and bound to 3' UTR of NUPR1. Conclusions CircHIPK3 demonstrates potential as a prognostic marker of OSCC and mediates OSCC progression via the miR-637-mediated NUPR1/PI3K/AKT axis.
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Affiliation(s)
- Weipeng Jiang
- Department of Outpatient Oral and Maxillofacial Surgery, Hospital of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Health Science Center, School of Dentistry, Shenzhen University, Shenzhen, China
| | - Chunxiao Zhang
- Department of Medical Genetics, Weihai Maternity and Child Care Hospital, Weihai, China.,Department of Medical Genetics, Weihai Municipal Second Hospital Affiliated to Qingdao University, Weihai, China
| | - Xiaoming Zhang
- School of Dentistry, Binzhou Medical University, Binzhou, China
| | - Legang Sun
- School of Dentistry, Binzhou Medical University, Binzhou, China
| | - Jikui Li
- School of Dentistry, Binzhou Medical University, Binzhou, China
| | - Jinhua Zuo
- School of Dentistry, Binzhou Medical University, Binzhou, China.,Department of Oral and Maxillofacial Surgery, The Affiliated Hospital of Binzhou Medical College, Binzhou, China
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Mansour SMA, Ali SA, Nofal S, Soror SH. Targeting NUPR1 for Cancer Treatment: A Risky Endeavor. Curr Cancer Drug Targets 2020; 20:768-778. [PMID: 32619170 DOI: 10.2174/1568009620666200703152523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 05/10/2020] [Accepted: 05/11/2020] [Indexed: 02/06/2023]
Abstract
NUPR1 is a transcription factor that has attracted great attention because of its various roles in cancer. Several studies were carried out to determine its molecular targets and mechanism of action to develop novel therapies against cancer. Here, we shed light on the role of NUPR1 in different types of cancer. NUPR1 regulates a complex network of pathways that may be affected by its silencing, which can cause varying effects. Its role in some types of cancer has been reported but remains incompletely understood, whereas its roles in other types of cancers have not been reported yet. Therefore, targeting NUPR1 for cancer treatment remains challenging and risky.
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Affiliation(s)
- Salma M A Mansour
- Egyptian Patent Office, Academy of Scientific Research and Technology (ASRT), 101 Kaser Al-Ainy Street, Cairo, Egypt
| | - Sahar A Ali
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Helwan University, Ain Helwan, Helwan Cairo 11795, Egypt
| | - Shaira Nofal
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Helwan University, Ain Helwan, Helwan Cairo 11795, Egypt
| | - Sameh H Soror
- Egyptian Patent Office, Academy of Scientific Research and Technology (ASRT), 101 Kaser Al-Ainy Street, Cairo, Egypt.,Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Helwan University, Ain Helwan, Helwan Cairo 11795, Egypt
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9
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Neira JL, Rizzuti B, Jiménez-Alesanco A, Abián O, Velázquez-Campoy A, Iovanna JL. The Paralogue of the Intrinsically Disordered Nuclear Protein 1 Has a Nuclear Localization Sequence that Binds to Human Importin α3. Int J Mol Sci 2020; 21:ijms21197428. [PMID: 33050086 PMCID: PMC7583046 DOI: 10.3390/ijms21197428] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 09/28/2020] [Accepted: 10/03/2020] [Indexed: 02/07/2023] Open
Abstract
Numerous carrier proteins intervene in protein transport from the cytoplasm to the nucleus in eukaryotic cells. One of those is importin α, with several human isoforms; among them, importin α3 (Impα3) features a particularly high flexibility. The protein NUPR1L is an intrinsically disordered protein (IDP), evolved as a paralogue of nuclear protein 1 (NUPR1), which is involved in chromatin remodeling and DNA repair. It is predicted that NUPR1L has a nuclear localization sequence (NLS) from residues Arg51 to Gln74, in order to allow for nuclear translocation. We studied in this work the ability of intact NUPR1L to bind Impα3 and its depleted species, ∆Impα3, without the importin binding domain (IBB), using fluorescence, isothermal titration calorimetry (ITC), circular dichroism (CD), nuclear magnetic resonance (NMR), and molecular docking techniques. Furthermore, the binding of the peptide matching the isolated NLS region of NUPR1L (NLS-NUPR1L) was also studied using the same methods. Our results show that NUPR1L was bound to Imp α3 with a low micromolar affinity (~5 μM). Furthermore, a similar affinity value was observed for the binding of NLS-NUPR1L. These findings indicate that the NLS region, which was unfolded in isolation in solution, was essentially responsible for the binding of NUPR1L to both importin species. This result was also confirmed by our in silico modeling. The binding reaction of NLS-NUPR1L to ∆Impα3 showed a larger affinity (i.e., lower dissociation constant) compared with that of Impα3, confirming that the IBB could act as an auto-inhibition region of Impα3. Taken together, our findings pinpoint the theoretical predictions of the NLS region in NUPR1L and, more importantly, suggest that this IDP relies on an importin for its nuclear translocation.
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Affiliation(s)
- José L. Neira
- IDIBE, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain
- Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain; (A.J.-A.); (O.A.); (A.V.-C.)
- Correspondence: (J.L.N.); (J.L.I.); Tel.: +34-966-65-8475 (J.L.N.); +33(0)491-82-8803 (J.L.I.)
| | - Bruno Rizzuti
- CNR-NANOTEC, Licryl-UOS Cosenza and CEMIF.Cal, Department of Physics, University of Calabria, Via P. Bucci, Cubo 31 C, Arcavacata di Rende, 87036 Cosenza, Italy;
| | - Ana Jiménez-Alesanco
- Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain; (A.J.-A.); (O.A.); (A.V.-C.)
| | - Olga Abián
- Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain; (A.J.-A.); (O.A.); (A.V.-C.)
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
- Instituto Aragonés de Ciencias de la Salud (IACS), 50009 Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain; (A.J.-A.); (O.A.); (A.V.-C.)
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
- Fundacion ARAID, Gobierno de Aragon, 50009 Zaragoza, Spain
| | - Juan L. Iovanna
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, 163 Avenue de Luminy, 13288 Marseille, France
- Correspondence: (J.L.N.); (J.L.I.); Tel.: +34-966-65-8475 (J.L.N.); +33(0)491-82-8803 (J.L.I.)
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10
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Sallee NA, Lee E, Leffert A, Ramirez S, Brace AD, Halenbeck R, Kavanaugh WM, Sullivan KMC. A Pilot Screen of a Novel Peptide Hormone Library Identified Candidate GPR83 Ligands. SLAS DISCOVERY 2020; 25:1047-1063. [PMID: 32713278 DOI: 10.1177/2472555220934807] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The identification of novel peptide hormones by functional screening is challenging because posttranslational processing is frequently required to generate biologically active hormones from inactive precursors. We developed an approach for functional screening of novel potential hormones by expressing them in endocrine host cells competent for posttranslational processing. Candidate preprohormones were selected by bioinformatics analysis, and stable endocrine host cell lines were engineered to express the preprohormones. The production of mature hormones was demonstrated by including the preprohormones insulin and glucagon, which require the regulated secretory pathway for production of the active forms. As proof of concept, we screened a set of G-protein-coupled receptors (GPCRs) and identified protein FAM237A as a specific activator of GPR83, a GPCR implicated in central nervous system and regulatory T-cell function. We identified the active form of FAM237A as a C-terminally cleaved, amidated 9 kDa secreted protein. The related protein FAM237B, which is 64% homologous to FAM237A, demonstrated similar posttranslational modification and activation of GPR83, albeit with reduced potency. These results demonstrate that our approach is capable of identifying and characterizing novel hormones that require processing for activity.
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Affiliation(s)
- Nathan A Sallee
- Five Prime Therapeutics Inc., South San Francisco, CA, USA.,Maze Therapeutics Inc., South San Francisco, CA, USA
| | - Ernestine Lee
- Five Prime Therapeutics Inc., South San Francisco, CA, USA
| | - Atossa Leffert
- Five Prime Therapeutics Inc., South San Francisco, CA, USA
| | - Silvia Ramirez
- Five Prime Therapeutics Inc., South San Francisco, CA, USA.,BioMarin Pharmaceutical Inc., San Rafael, CA, USA
| | - Arthur D Brace
- Five Prime Therapeutics Inc., South San Francisco, CA, USA
| | - Robert Halenbeck
- Five Prime Therapeutics Inc., South San Francisco, CA, USA.,BioMarin Pharmaceutical Inc., San Rafael, CA, USA
| | - W Michael Kavanaugh
- Five Prime Therapeutics Inc., South San Francisco, CA, USA.,CytomX Therapeutics Inc., South San Francisco, CA, USA
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11
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Comparative analysis of peripheral blood reveals transcriptomic adaptations to extreme environments on the Qinghai-Tibetan Plateau in the gray wolf (Canis lupus chanco). ORG DIVERS EVOL 2019. [DOI: 10.1007/s13127-019-00405-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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12
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The chromatin nuclear protein NUPR1L is intrinsically disordered and binds to the same proteins as its paralogue. Biochem J 2018; 475:2271-2291. [DOI: 10.1042/bcj20180365] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/16/2018] [Accepted: 06/19/2018] [Indexed: 12/24/2022]
Abstract
NUPR1 is a protumoral multifunctional intrinsically disordered protein (IDP), which is activated during the acute phases of pancreatitis. It interacts with other IDPs such as prothymosin α, as well as with folded proteins such as the C-terminal region of RING1-B (C-RING1B) of the Polycomb complex; in all those interactions, residues around Ala33 and Thr68 (the ‘hot-spot’ region) of NUPR1 intervene. Its paralogue, NUPR1L, is also expressed in response to DNA damage, it is p53-regulated, and its expression down-regulates that of the NUPR1 gene. In this work, we characterized the conformational preferences of isolated NUPR1L and its possible interactions with the same molecular partners of NUPR1. Our results show that NUPR1L was an oligomeric IDP from pH 2.0 to 12.0, as judged by steady-state fluorescence, circular dichroism (CD), dynamic light scattering, 1D 1H-NMR (nuclear magnetic resonance), and as indicated by structural modelling. However, in contrast with NUPR1, there was evidence of local helical- or turn-like structures; these structures were not rigid, as judged by the lack of sigmoidal behaviour in the chemical and thermal denaturation curves obtained by CD and fluorescence. Interestingly enough, NUPR1L interacted with prothymosin α and C-RING1B, and with a similar affinity to that of NUPR1 (in the low micromolar range). Moreover, NUPR1L hetero-associated with NUPR1 with an affinity of 0.4 µM and interacted with the ‘hot-spot’ region of NUPR1. Thus, we suggest that the regulation of NUPR1 gene by NUPR1L does not only happen at the DNA level, but it could also involve direct interactions with NUPR1 natural partners.
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