VHL-P138R and VHL-L163R Novel Variants: Mechanisms of VHL Pathogenicity Involving HIF-Dependent and HIF-Independent Actions

The von Hippel–Lindau (VHL) disease is an autosomal dominant cancer syndrome caused by mutations in the VHL tumor suppressor gene. VHL protein (pVHL) forms a complex (VBC) with Elongins B-C, Cullin2, and Rbx1. Although other functions have been discovered, the most described function of pVHL is to recognize and target hypoxia-inducible factor (HIF) for degradation. This work comprises the functional characterization of two novel variants of the VHL gene (P138R and L163R) that have been described in our center in patients with VHL disease by in vitro, in vivo, and in silico approaches. In vitro, we found that these variants have a significantly shorter half-life compared to wild-type VHL but still form a functional VBC complex. Altered fibronectin deposition was evidenced for both variants using immunofluorescence. In vivo studies revealed that both variants failed to suppress tumor growth. By means of molecular dynamics simulations, we inspected in silico the nature of the changes introduced by each variant in the VBC complex. We have demonstrated the pathogenicity of P138R and L163R novel variants, involving HIF-dependent and HIF-independent mechanisms. These results provide the basis for future studies regarding the impact of structural alterations on posttranslational modifications that drive pVHL’s fate and functions.

[1]  Ryan L. Collins,et al.  The mutational constraint spectrum quantified from variation in 141,456 humans , 2020, Nature.

[2]  Alexandros Kouris,et al.  VarSome: the human genomic variant search engine , 2018, bioRxiv.

[3]  Torsten Schwede,et al.  SWISS-MODEL: homology modelling of protein structures and complexes , 2018, Nucleic Acids Res..

[4]  Chunlei Liu,et al.  ClinVar: improving access to variant interpretations and supporting evidence , 2017, Nucleic Acids Res..

[5]  Evan Bolton,et al.  Database resources of the National Center for Biotechnology Information , 2017, Nucleic Acids Res..

[6]  V. G. Antico Arciuch,et al.  Role of RSUME in inflammation and cancer , 2015, FEBS letters.

[7]  K. Chung,et al.  E2-EPF UCP regulates stability and functions of missense mutant pVHL via ubiquitin mediated proteolysis , 2015, BMC Cancer.

[8]  S. Genheden,et al.  The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities , 2015, Expert opinion on drug discovery.

[9]  Bale,et al.  Standards and Guidelines for the Interpretation of Sequence Variants: A Joint Consensus Recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology , 2015, Genetics in Medicine.

[10]  Y. Xiong,et al.  Insights into Cullin-RING E3 ubiquitin ligase recruitment: structure of the VHL-EloBC-Cul2 complex. , 2015, Structure.

[11]  F. Holsboer,et al.  RSUME inhibits VHL and regulates its tumor suppressor function , 2014, Oncogene.

[12]  G. Mills,et al.  Autophagy mediates HIF2α degradation and suppresses renal tumorigenesis , 2014, Oncogene.

[13]  P. Sarma,et al.  Novel three missense mutations observed in Von Hippel-Lindau gene in a patient reported with renal cell carcinoma , 2013, Indian journal of human genetics.

[14]  J. Prchal,et al.  Novel homozygous VHL mutation in exon 2 is associated with congenital polycythemia but not with cancer. , 2013, Blood.

[15]  W. Kaelin,et al.  The VHL/HIF axis in clear cell renal carcinoma. , 2013, Seminars in cancer biology.

[16]  Andreas Thomann,et al.  Dissecting fragment-based lead discovery at the von Hippel-Lindau protein:hypoxia inducible factor 1α protein-protein interface. , 2012, Chemistry & biology.

[17]  Jing Hu,et al.  SIFT web server: predicting effects of amino acid substitutions on proteins , 2012, Nucleic Acids Res..

[18]  G. Mills,et al.  Results of a high-throughput screen to identify compounds that modulate VHL proteostasis. , 2012, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[19]  S. Richard,et al.  von Hippel–Lindau disease: A clinical and scientific review , 2011, European Journal of Human Genetics.

[20]  Robert M. Hanson,et al.  Web servers and services for electrostatics calculations with APBS and PDB2PQR , 2011, J. Comput. Chem..

[21]  William Y. Kim,et al.  Two sides to every story: the HIF-dependent and HIF-independent functions of pVHL , 2011, Journal of cellular and molecular medicine.

[22]  Jan H. Jensen,et al.  PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa Predictions. , 2011, Journal of chemical theory and computation.

[23]  P. Bork,et al.  A method and server for predicting damaging missense mutations , 2010, Nature Methods.

[24]  A. McNeill,et al.  Genotype–phenotype correlations in VHL exon deletions , 2009, American journal of medical genetics. Part A.

[25]  A. Schoenfeld,et al.  Differences in regulation of tight junctions and cell morphology between VHL mutations from disease subtypes , 2009, BMC Cancer.

[26]  C. Béroud,et al.  Human Splicing Finder: an online bioinformatics tool to predict splicing signals , 2009, Nucleic acids research.

[27]  C. Ki,et al.  Improved Detection of Germline Mutations in Korean VHL Patients by Multiple Ligation-dependent Probe Amplification Analysis , 2009, Journal of Korean medical science.

[28]  W. Rathmell,et al.  VHL Type 2B Mutations Retain VBC Complex Form and Function , 2008, PloS one.

[29]  M. Ohh,et al.  NEDD8 acts as a ‘molecular switch’ defining the functional selectivity of VHL , 2008, EMBO reports.

[30]  T. Benzing,et al.  Von hippel-lindau: a tumor suppressor links microtubules to ciliogenesis and cancer development. , 2007, Cancer research.

[31]  G. Mills,et al.  A retrovirus-based protein complementation assay screen reveals functional AKT1-binding partners , 2006, Proceedings of the National Academy of Sciences.

[32]  M. Ashcroft,et al.  Role of hypoxia-inducible factor (HIF)-1alpha versus HIF-2alpha in the regulation of HIF target genes in response to hypoxia, insulin-like growth factor-I, or loss of von Hippel-Lindau function: implications for targeting the HIF pathway. , 2006, Cancer research.

[33]  V. Haase,et al.  The VHL/HIF oxygen-sensing pathway and its relevance to kidney disease. , 2006, Kidney international.

[34]  R. Johnson,et al.  pVHL Function Is Essential for Endothelial Extracellular Matrix Deposition , 2006, Molecular and Cellular Biology.

[35]  J. Frydman,et al.  Folding and Quality Control of the VHL Tumor Suppressor Proceed through Distinct Chaperone Pathways , 2005, Cell.

[36]  Patrick D. Sutphin,et al.  Coordinate Regulation of the Oxygen-Dependent Degradation Domains of Hypoxia-Inducible Factor 1α , 2005, Molecular and Cellular Biology.

[37]  R. Osman,et al.  Inactivation of VHL by Tumorigenic Mutations That Disrupt Dynamic Coupling of the pVHL·Hypoxia-inducible Transcription Factor-1α Complex* , 2005, Journal of Biological Chemistry.

[38]  W. Kaelin,et al.  Role of VHL gene mutation in human cancer. , 2004, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[39]  W. Rathmell,et al.  In vitro and In vivo Models Analyzing von Hippel-Lindau Disease-Specific Mutations , 2004, Cancer Research.

[40]  M. Barontini,et al.  Familial isolated pheochromocytoma presenting a new mutation in the von Hippel-Lindau gene. , 2004, American journal of hypertension.

[41]  J. Klco,et al.  pVHL Modification by NEDD8 Is Required for Fibronectin Matrix Assembly and Suppression of Tumor Development , 2004, Molecular and Cellular Biology.

[42]  J. Åqvist,et al.  Molecular Dynamics Simulations of Water and Biomolecules with a Monte Carlo Constant Pressure Algorithm , 2004 .

[43]  Jayanta Debnath,et al.  Morphogenesis and oncogenesis of MCF-10A mammary epithelial acini grown in three-dimensional basement membrane cultures. , 2003, Methods.

[44]  J. Frydman,et al.  The Hsp70 and TRiC/CCT Chaperone Systems Cooperate In Vivo To Assemble the Von Hippel-Lindau Tumor Suppressor Complex , 2003, Molecular and Cellular Biology.

[45]  V. Barr,et al.  Reduced expression of insulin-like growth factor I receptors in MCF-7 breast cancer cells leads to a more metastatic phenotype. , 2002, Cancer research.

[46]  Yigong Shi Faculty Opinions recommendation of Structure of an HIF-1alpha -pVHL complex: hydroxyproline recognition in signaling. , 2002 .

[47]  M. Seyfarth,et al.  Paraneoplastic erythrocytosis associated with an inactivating point mutation of the von Hippel-Lindau gene in a renal cell carcinoma. , 2002, Blood.

[48]  W. Kaelin,et al.  Diverse Effects of Mutations in Exon II of the von Hippel-Lindau (VHL) Tumor Suppressor Gene on the Interaction of pVHL with the Cytosolic Chaperonin and pVHL-Dependent Ubiquitin Ligase Activity , 2002, Molecular and Cellular Biology.

[49]  Nathan A. Baker,et al.  Electrostatics of nanosystems: Application to microtubules and the ribosome , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[50]  M. Ivan,et al.  von Hippel-Lindau protein mutants linked to type 2C VHL disease preserve the ability to downregulate HIF. , 2001, Human molecular genetics.

[51]  P. Ratcliffe,et al.  Contrasting effects on HIF-1alpha regulation by disease-causing pVHL mutations correlate with patterns of tumourigenesis in von Hippel-Lindau disease. , 2001, Human molecular genetics.

[52]  R. Burk,et al.  Elongin BC complex prevents degradation of von Hippel-Lindau tumor suppressor gene products. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[53]  R Stearman,et al.  Studying interactions of four proteins in the yeast two-hybrid system: structural resemblance of the pVHL/elongin BC/hCUL-2 complex with the ubiquitin ligase complex SKP1/cullin/F-box protein. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[54]  D. Louis,et al.  The von Hippel-Lindau tumor suppressor protein is required for proper assembly of an extracellular fibronectin matrix. , 1998, Molecular cell.

[55]  W. Kaelin,et al.  Regulation of Hypoxia-Inducible mRNAs by the von Hippel-Lindau Tumor Suppressor Protein Requires Binding to Complexes Containing Elongins B/C and Cul2 , 1998, Molecular and Cellular Biology.

[56]  R. Klausner,et al.  The von Hippel-Lindau tumor-suppressor gene product forms a stable complex with human CUL-2, a member of the Cdc53 family of proteins. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[57]  A. Webster,et al.  Phenotypic expression in von Hippel-Lindau disease: correlations with germline VHL gene mutations. , 1996, Journal of medical genetics.

[58]  T. Darden,et al.  A smooth particle mesh Ewald method , 1995 .

[59]  Fan,et al.  Cellular proteins that bind the von Hippel-Lindau disease gene product: mapping of binding domains and the effect of missense mutations. , 1995, Cancer research.

[60]  A. Kibel,et al.  Tumour suppression by the human von Hippel-Lindau gene product , 1995, Nature Medicine.

[61]  J. Gnarra,et al.  Identification of the von Hippel-Lindau disease tumor suppressor gene. , 1993, Science.

[62]  G. Ciccotti,et al.  Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .

[63]  P. Jemth,et al.  Renal cell carcinoma risk in type 2 von Hippel-Lindau disease correlates with defects in pVHL stability and HIF-1alpha interactions. , 2006, Oncogene.

[64]  W. Krek,et al.  Regulation of microtubule stability by the von Hippel-Lindau tumour suppressor protein pVHL , 2003, Nature Cell Biology.

[65]  David I Stuart,et al.  Structural basis for the recognition of hydroxyproline in HIF-1 alpha by pVHL. , 2002, Nature.

[66]  A. Sakurai,et al.  [von Hippel-Lindau syndrome]. , 2001, Ryoikibetsu shokogun shirizu.

[67]  W. Linehan,et al.  Improved detection of germline mutations in the von Hippel‐Lindau disease tumor suppressor gene , 1998, Human mutation.

[68]  N. Guex,et al.  SWISS‐MODEL and the Swiss‐Pdb Viewer: An environment for comparative protein modeling , 1997, Electrophoresis.

[69]  C. Brooks Computer simulation of liquids , 1989 .