Predicting the Impact of Deleterious Mutations in the Protein Kinase Domain of FGFR2 in the Context of Function, Structure, and Pathogenesis—a Bioinformatics Approach

Fibroblast growth factor receptor 2 (FGFR2) controls a wide range of biological functions by regulating the cellular proliferation, survival, migration and differentiation. A growing body of preclinical data demonstrated that deregulation of the FGFR signalling through genetic modification was observed in various types of cancers. However, the extent to which genetic modifications interfere with gene regulation and their involvement in cancer susceptibility remains largely unknown. In this work, we performed in silico profiling of harmful non-synonymous single nucleotide polymorphisms (SNPs) in the protein kinase domain of FGFR2. Tolerance index, position-specific independent count score, change in free energy score (ΔΔG), Eris and FoldX indicated that seven mutations were found to be deleterious and may alter the protein function and structure. Furthermore, based on physico-chemical properties, two mutations K659N and R747H were found to be most deleterious in protein kinase domain and taken for further structural analysis. Docking study showed a complete loss of binding affinity followed by interference in hydrogen bonding and surrounding residues due to K659N and R747H mutations. In order to elucidate the mechanism behind the impact of mutation that can generate a ripple effect throughout the protein structure and ultimately affect the function, in-depth molecular dynamics simulation and principal component analysis were performed. The obtained results indicate that K659N and R747H mutations have a distinct effect on the dynamic behaviour of FGFR2 protein. Our strategy may be helpful for understanding SNP effects on proteins with function and their role in human genetic diseases and for the development of novel pharmacological strategies.     

Prediction of the structures of the plant-specific regions of vascular plant cellulose synthases and correlated functional analysis

Seed plants express cellulose synthase (CESA) protein isoforms with non-redundant functions, but how the isoforms function differently is unknown. Compared to bacterial cellulose synthases, CESAs have two insertions in the large cytosolic loop: the relatively well-conserved Plant Conserved Region (P-CR) and a Class Specific Region (CSR) that varies between CESAs. Absent any atomic structure of a plant CESA, we used ab initio protein structure prediction and molecular modeling to explore how these plant-specific regions may modulate CESA function. We modeled P-CR and CSR peptides from Arabidopsis thaliana CESAs representing the six clades of seed plant CESAs. As expected, the predicted wild type P-CR structures were similar. Modeling of the mutant P-CR of Atcesa8 ^R362K (fra6) suggested that changes in local structural stability and surface electrostatics may cause the mutant phenotype. Among CSRs within CESAs required for primary wall cellulose synthesis, the amino sequence and the modeled arrangement of helices was most similar in AtCESA1 and AtCESA3. Genetic complementation of known Arabidopsis mutants showed that the CSRs of AtCESA1 and AtCESA3 can function interchangeably in vivo. Analysis of protein surface electrostatics led to ideas about how the surface charges on CSRs may mediate protein–protein interactions. Refined modeling of the P-CR and CSR regions of GhCESA1 from cotton modified their tertiary structures, spatial relationships to the catalytic domain, and preliminary predictions about CESA oligomer formation. Cumulatively, the results provide structural clues about the function of plant-specific regions of CESA.     

Are Pro<Superscript>8</Superscript>/Pro<Superscript>18</Superscript> really critical for functional dynamic behavior of human endostatin N-terminal peptide? A comparative molecular dynamics study

Endostatin which is derived from the non-collagenous domain 1 of collagen XVIII and is a recently identified broad spectrum anti-angiogenesis agent, inhibits 65 different tumor types. The N-terminal fragment of endostatin protein (ES) has the same antitumor, antimigration and antipermeability effects as the entire protein. In the current study, we modeled two mutant variants of ES with two mutation sites (M1-ES (Pro⁸ → Ala) and M2-ES (Pro¹⁸ → Ala)) and tried to understand proline’s effect on the peptide structure/stability by introducing P⁸A/P¹⁸A mutations, and then in order to gain functional insight into mutation caused by amino acid substitution to the peptide structure/function, these effects were predicted using computational tools. From the RMSD analyses, it can be concluded that dynamic behavior of wild-type and mutant structures was not significantly different from each other and all systems reached equilibrium. The RMSF analysis also revealed that the M2-ES has smaller overall flexibility than the WT-ES and M1-ES structures. The radius of gyration analysis then confirmed the structure of M2-ES compared to wild-type and M1 variant becomes more compact during simulation of our systems. Finally, molecular dynamics simulation analysis shows that replacement of Pro residue with Ala is able to induce a distinct β-sheet in both mutant structures. Indeed, the docking analysis shows the WT-ES and M2-ES bind to the same region of α_vβ₃ integrin, suggesting similar interaction pattern with a relatively equal binding energy into this receptor. Our results speculated that the P⁸A/P¹⁸A replacements confer no improvement (or no tangible weakness) in the peptide biological activity although is able to change structural conformation of N-terminal fragment of human endostatin protein.     

Boerhavia diffusa plant extract can be a new potent therapeutics against mutant nephrin protein responsible for type1 nephrotic syndrome: Insight into hydrate-ligand docking interactions and molecular dynamics simulation study

Nephrotic syndrome type 1 is an inherited condition in which mutation of NPHS1 gene, which encodes nephrin protein, results increase permeability of glomerular capillary wall for macromolecules causes heavy proteinuria, hypoproteinemia, and edema. Nephrotic syndrome patients are resistant to steroid and immunosuppressive treatment. Natural products have traditionally been used to treat a number of chronic diseases. Present study was focused to investigate potency of different phytochemicals found in Boerhavia diffusa (B.diffusa) plant against mutant nephrin protein. The study involves virtual screening of total 66 bioactive compounds from B.diffusa plant against wild type and mutant models of Ig4 domain of nephrin protein through AutoDock raccoon. Based on binding energy and drug-likeness property, seven phytocompounds were screened. Hydrate-ligand docking (addition of explicit waters in ligands) method was used to select potential phytocompounds that could bind to mutant model of Ig4 domain of nephrin protein. For further prediction, molecular dynamics simulations with 100ns trajectory of Ig4 domain of nephrin protein in glycolipid bilayer membrane for systems such as wild, mutant, mutant model complex with boeravinone M and mutant model complex with boeravinone E were thoroughly studied. Hydrate-ligand docking result predicted boeravinone M and boeravinone E have shown better binding performance with mutant model. It causes due to hydration force field that measures entropy and enthalpy for each water molecule separately, allowing for more exact estimations of their contribution to ligand-protein interaction. Boeravinone E shows lowest short-range Lennard-Jones (LJ-SR) interaction energies of ?47.78 ± 12.7 kJ/mol. The results showed reduced compactness and stability nature of mutant model of Ig4 domain of nephrin protein, however, binding with boeravinone E has effectively modulated its stability and function by increasing its compactness. Current study may provide insight into therapeutic development of boeravinone E as a potential inhibitor against NPHS1in near future.     

Enhancement of thermostability of the Luciola mingrelica firefly luciferase by site-directed mutagenesis of nonconservative cysteine residues Cys62 and Cys146

Mutant forms of the firefly (Luciola mingrela) luciferase with point mutations Cys62Ser and Cys146Ser were obtained by site-directed mutagenesis. The mutations did not affect the catalytic activity and fluorescence spectra of the enzyme. The rate constants of the fast (k ₁) and slow (k ₂) stages of thermoinactivation of the wild-type and mutant enzymes were determined at 37°C in the absence and presence of 12 mM dithiothreitol (DTT). The thermostability of the mutant forms of luciferase increased several times compared to the wild-type enzyme. In the presence of DTT, k ₂ of the wild-type enzyme decreased three times whereas neither k ₁ nor k ₂ of the mutant forms changed. It was concluded that amino acid residues Cys62 and Cys146 play a major role in luciferase inactivation and that their substitution with Ser stabilizes the enzyme.     

Structural prediction,whole exome sequencing and molecular dynamics simulation confirms p.G118D somatic mutation of PIK3CA as functionally important in breast cancer patients

To understand the structural and functional importance of PIK3CA somatic mutations, whole exome sequencing, molecular dynamics simulation techniques in combination with in silico prediction algorithms such as SIFT, PolyPhen, Provean and CADD were employed. Twenty out of eighty missense somatic mutations in PIK3CA gene were found to be pathogenic by all the four algorithms. Most recurrent mutations found were known hotspot PIK3CA mutations with known clinical significance like p.E545 K, p.E545A, p.E545 G and p.C420R. A missense mutation p.G118D was found to be recurrently mutated in 5 cases. Interestingly, this mutation was observed in one of the patients who underwent whole exome sequencing and was completely absent from the controls. To see the effect of this mutation on the structure of PIK3CA protein, molecular dynamics simulation was performed. By molecular dynamics approach, we have shown that p.G118D mutation deviated from the native structure which was supported by the decrease in the number of hydrogen bonds, difference in hydrogen bond distance and angle, difference in root mean square deviation between the native and the mutant structures.     

Molecular dynamics characterization of the SAMHD1 Aicardi–Goutières Arg145Gln mutant: structural determinants for the impaired tetramerization

Aicardi–Goutières syndrome, a rare genetic disorder characterized by calcification of basal ganglia, results in psychomotor delays and epilepsy states from the early months of children life. This disease is caused by mutations in seven different genes encoding proteins implicated in the metabolism of nucleic acids, including SAMHD1. Twenty SAMHD1 gene variants have been discovered and in this work, a structural characterization of the SAMHD1 Aicardi–Goutières Arg145Gln mutant is reported by classical molecular dynamics simulation. Four simulations have been carried out and compared. Two concerning the wild-type SAMHD1 form in presence and absence of cofactors, in order to explain the role of cofactors in the SAMHD1 assembly/disassembly process and, two concerning the Arg145Gln mutant, also in presence and absence of cofactors, in order to have an accurate comparison with the corresponding native forms. Results show the importance of native residue Arg145 in maintaining the tetramer, interacting with GTP cofactor inside allosteric sites. Replacement of arginine in glutamine gives rise to a loosening of GTP–protein interactions, when cofactors are present in allosteric sites, whilst in absence of cofactors, the occurrence of intra and inter-chain interactions is observed in the mutant, not seen in the native enzyme, making energetically unfavourable the tetramerization process.     

Chartarolides A-C,novel meroterpenoids with antitumor activities

Three phenylspirodrimane-based meroterpenoids with novel scaffolds, namely chartarolides A-C (1–3), were isolated from a sponge (Niphates recondite) associated fungus Stachybotrys chartarum WGC-25C-6. Their structures were determined on the basis of comprehensive analyses of the spectroscopic data (IR, 1D and 2D NMR, HRESIMS), including the TDDFT-ECD calculation for the assignments of absolute configurations. The biogenetic generation of 1–3 through the conjunction of phenylspirodrimane and mollicellin-type analogues as the precursors was postulated. Chartarolides A-C exhibited significant cytotoxic activities against a panel of human tumor cell lines, and showed strong inhibitory activities against the human tumor related protein kinases of FGFR3, IGF1R, PDGFRb, and TrKB.     

Tissue-specific expression and subcellular localization of ALADIN, the absence of which causes human triple A syndrome

Triple A syndrome is a rare genetic disorder caused by mutations in the achalasia-addisonianism-alacrima syndrome (AAAS) gene which encodes a tryptophan aspartic acid (WD) repeat-containing protein named alacrima-achalasia-adrenal insufficiency neurologic disorder (ALADIN). Northern blot analysis shows that the 2.1 kb AAAS mRNA is expressed in various tissues with stronger expression in testis and pancreas. We show that human ALADIN is a protein with an apparent molecular weight of 60 kDa, and expressed in the adrenal gland, pituitary gland and pancreas. Furthermore, biochemical analysis using anti-ALADIN antibody supports the previous finding of the localization of ALADIN in the nuclear membrane. The mutations S544G and S544X show that alteration of S544 residue affects correct targeting of ALADIN to the nuclear membrane.     

Construction of a full three-dimensional model of the transpeptidase domain of Streptococcus pneumoniae PBP2x starting from its Cα-atom coordinates

A new method is described for generating all-atom protein structures from C-atom information. The method, which combines both local structural trace alignments and comparative side chain modeling with ab initio side chain modeling, makes use of both the virtual-bond and the dipole-path methods. Provided that 3D structures of structurally and functionally related proteins exist, the method presented here is highly suitable for generating all-atom coordinates of partly solved, low-resolution crystal structures. Particularly the active site region can be modeled accurately with this procedure, which enables investigation of the binding modes of different classes of ligands with molecular dynamics simulations. The method is applied to the trace of Streptococcus pneumoniae, in order to construct an all-atom structure of the transpeptidase domain. Since after generation of full coordinates of the transpeptidase domain the structure had been solved to 2.4 Å resolution, new X-ray coordinates for the worst modeled loop (residues T370 to M386; 17 out of a total number of 351 residues constituting the transpeptidase domain) were incorporated, as kindly provided by Dr. Dideberg. The structure was relaxed with molecular dynamics simulations and simulated annealing methods. The RMS deviation between the 144 aligned C-atoms and the corresponding ones in the originally solved 3.5 Å resolution crystal structure was 0.98. The 351 C-atoms of the whole transpeptidase domain of the final model showed an RMS deviation of 1.58. The Ramachandran plot showed that 79.3% of the residues are in the most favored regions, with only 1.0% occurring in disallowed regions. The model presented here can be used to investigate the three-dimensional influences of mutations around the active site of PBP2x.     

Loss of glucocerebrosidase 1 activity causes lysosomal dysfunction and α-synuclein aggregation

Lysosomal dysfunction is a common pathological feature of neurodegenerative diseases. GTP-binding protein type A1 (GBA1) encodes β-glucocerebrosidase 1 (GCase 1), a lysosomal hydrolase. Homozygous mutations in GBA1 cause Gaucher disease, the most common lysosomal storage disease, while heterozygous mutations are strong risk factors for Parkinson''s disease. However, whether loss of GCase 1 activity is sufficient for lysosomal dysfunction has not been clearly determined. Here, we generated human neuroblastoma cell lines with nonsense mutations in the GBA1 gene using zinc-finger nucleases. Depending on the site of mutation, GCase 1 activity was lost or maintained. The cell line with GCase 1 deficiency showed indications of lysosomal dysfunction, such as accumulation of lysosomal substrates, reduced dextran degradation and accumulation of enlarged vacuolar structures. In contrast, the cell line with C-terminal truncation of GCase 1 but with intact GCase 1 activity showed normal lysosomal function. When α-synuclein was overexpressed, accumulation and secretion of insoluble aggregates increased in cells with GCase 1 deficiency but did not change in mutant cells with normal GCase 1 activity. These results demonstrate that loss of GCase 1 activity is sufficient to cause lysosomal dysfunction and accumulation of α-synuclein aggregates.     

Rational coupled dynamics network manipulation rescues disease-relevant mutant cystic fibrosis transmembrane conductance regulator

Many cellular functions necessary for life are tightly regulated by protein allosteric conformational change, and correlated dynamics between protein regions has been found to contribute to the function of proteins not previously considered allosteric. The ability to map and control such dynamic coupling would thus create opportunities for the extension of current therapeutic design strategy. Here, we present an approach to determine the networks of residues involved in the transfer of correlated motion across a protein, and apply our approach to rescue disease-causative mutant cystic fibrosis transmembrane regulator (CFTR) ion channels, ΔF508 and ΔI507, which together constitute over 90% of cystic fibrosis cases. We show that these mutations perturb dynamic coupling within the first nucleotide-binding domain (NBD1), and uncover a critical residue that mediates trans-domain coupled dynamics. By rationally designing a mutation to this residue, we improve aberrant dynamics of mutant CFTR as well as enhance surface expression and function of both mutants, demonstrating the rescue of a disease mutation by rational correction of aberrant protein dynamics.     

NLIP and HAD-like Domains of Pah1 and Lipin 1 Phosphatidate Phosphatases Are Essential for Their Catalytic Activities

Saccharomyces cerevisiae Pah1 phosphatidate phosphatase (PAP) catalyzes the dephosphorylation of phosphatidate to yield diacylglycerol, controlling phospholipids and triacylglycerol metabolisms. Pah1 and human Lipin 1 are intrinsically disordered proteins with 56% and 43% unfolded regions, respectively. Truncation analysis of the conserved and non-conserved regions showed that N- and C-conserved regions are essential for the catalytic activity of Pah1. PAP activities can be detected in the conserved N-terminal Lipin (NLIP) domain and C-terminal Lipin (CLIP)/haloacid dehalogenase (HAD)-like domain of Pah1 and Lipin 1, suggesting that the evolutionarily conserved domains are essential for the catalytic activity. The removal of disordered hydrophilic regions drastically reduced the protein solubility of Pah1. Thioredoxin is an efficient fusion protein for production of soluble NLIP–HAD recombinant proteins in Escherichia coli.     

Mass spectrometric measurement of changes in protein hydrogen exchange rates that result from point mutations

Point mutations, as well as additions or deletions of entire domains, are frequently produced to study protein function; however, to infer function from mutant proteins, it is imperative that their structural integrity be verified. Although detailed structural studies can be performed by using NMR or crystallography, for practical reasons mutant proteins usually are characterized by using less rigorous techniques. Here it is shown that measurement of hydrogen exchange rates via electrospray ionization mass spectrometry is a sensitive and generally applicable method for detection of conformational or dynamic changes that result from point mutations. Hydrogen exchange experiments were performed on a bacterial phosphocarrier protein (HPr) and two variants produced by conversion of either serine-46 to aspartic acid (S46D) or serine-31 to alanine (S31A), where the differences in the ΔG of folding relative to the wild type were 1.5 and 0.5 kcal/mol, respectively. Whereas no significant differences were found for the intact mutant and wild-type proteins, changes in deuterium incorporation could be detected within specific regions produced by peptic proteolysis of the deuterium-labeled proteins. Thus, energetically small changes in conformation (or dynamics) that result from point mutations can be characterized by mass spectrometric measurements of hydrogen exchange rates. Furthermore, these changes can be localized to specific regions within the protein.     

Insight into herbicide resistance of W574L mutant Arabidopsis thaliana acetohydroxyacid synthase: molecular dynamics simulations and binding free energy calculations

Acetohydroxyacid synthase (AHAS) is the target enzyme of several classes of herbicides, such as sulfonylureas and imidazolinones. Now many mutant AHASs with herbicide resistance have emerged along with extensive use of herbicides, therefore it is imperative to understand the detailed interaction mechanism and resistance mechanism so as to develop new potent inhibitors for wild-type or resistant AHAS. With the aid of available crystal structures of the Arabidopsis thaliana (At) AHAS-inhibitor complex, molecular dynamics (MD) simulations were used to investigate the interaction and resistance mechanism directly and dynamically at the atomic level. Nanosecond-level MD simulations were performed on six systems consisting of wild-type or W574L mutant AtAHAS in the complex with three sulfonylurea inhibitors, separately, and binding free energy was calculated for each system using the MM-GBSA method. Comprehensive analyses from structural and energetic aspects confirmed the importance of residue W574, and also indicated that W574L mutation might alert the structural charactersistic of the substrate access channel and decrease the binding affinity of inhibitors, which cooperatively weaken the effective channel-blocked effect and finally result in weaker inhibitory effect of inhibitor and corresponding herbicide resistance of W574L mutant. To our knowledge, it is the first report about MD simulations study on the AHAS-related system, which will pave the way to study the interactions between herbicides and wild-type or mutant AHAS dynamically, and decipher the resistance mechanism at the atomic level for better designing new potent anti-resistance herbicides.     

Effects of a chemical chaperone on genetic mutations in ��-galactosidase A in Korean patients with Fabry disease

Fabry disease is an X-linked inborn error of glycosphingolipid catabolism that results from mutations in the gene encoding the α-galactosidase A (GLA) enzyme. We have identified 15 distinct mutations in the GLA gene in 13 unrelated patients with classic Fabry disease and 2 unrelated patients with atypical Fabry disease. Two of the identified mutations were novel (i.e., the D231G missense mutation and the L268delfsX1 deletion mutation). This study evaluated the effects of the chemical chaperones 1-deoxygalactonojirimycin (DGJ) on the function of GLA in vitro, in cells containing missense mutations in the GLA gene. Nine missense and a nonsense mutations, including one novel mutation were cloned into mammalian expression vectors. After transient expression in COS-7 cells, GLA enzyme activity and protein expression were analyzed using fluorescence spectrophotometry and Western blot analysis, respectively. DGJ enhanced GLA enzyme activity in the M42V, I91T, R112C and F113L mutants. Interestingly, the I91T and F113L mutations are associated with the atypical form of Fabry disease. However, DGJ treatment did not have any significant effect on the GLA enzyme activity and protein expression of other mutants, including C142W, D231G, D266N, and S297F. Of note, GLA enzyme activity was not detected in the novel mutant (i.e., D231G), although protein expression was similar to the wild type. In the absence of DGJ, the E66Q mutant had wild-type levels of GLA protein expression and approximately 40% GLA activity, indicating that E66Q is either a mild mutation or a functional single nucleotide polymorphism (SNP). Thus, the results of this study suggest that the chemical chaperone DGJ enhances GLA enzyme activity and protein expression in milder mutations associated with the atypical form of Fabry disease.     

Temperature inducible beta-sheet structure in the transactivation domains of retroviral regulatory proteins of the Rev family

The interaction of the human immunodeficiency virus type 1 (HIV-1) regulatory protein Rev with cellular cofactors is crucial for the viral life cycle. The HIV-1 Rev transactivation domain is functionally interchangeable with analog regions of Rev proteins of other retroviruses suggesting common folding patterns. In order to obtain experimental evidence for similar structural features mediating protein-protein contacts we investigated activation domain peptides from HIV-1, HIV-2, VISNA virus, feline immunodeficiency virus (FIV) and equine infectious anemia virus (EIAV) by CD spectroscopy, secondary structure prediction and sequence analysis. Although different in polarity and hydrophobicity, all peptides showed a similar behavior with respect to solution conformation, concentration dependence and variations in ionic strength and pH. Temperature studies revealed an unusual induction of beta-structure with rising temperatures in all activation domain peptides. The high stability of beta-structure in this region was demonstrated in three different peptides of the activation domain of HIV-1 Rev in solutions containing 40% hexafluoropropanol, a reagent usually known to induce alpha-helix into amino acid sequences. Sequence alignments revealed similarities between the polar effector domains from FIV and EIAV and the leucine rich (hydrophobic) effector domains found in HIV-1, HIV-2 and VISNA. Studies on activation domain peptides of two dominant negative HIV-1 Rev mutants, M10 and M32, pointed towards different reasons for the biological behavior. Whereas the peptide containing the M10 mutation (L78E79-->D78L79) showed wild-type structure, the M32 mutant peptide (L78L81L83-->A78A81A83) revealed a different protein fold to be the reason for the disturbed binding to cellular cofactors. From our data, we conclude, that the activation domain of Rev proteins from different viral origins adopt a similar fold and that a beta-structural element is involved in binding to a cellular cofactor.     

Microarray-based detection of Korean-specific <Emphasis Type="Italic">BRCA1</Emphasis> mutations

A reliable multiplex assay procedure to detect human genetic mutations in the breast cancer susceptibility gene BRCA1 using zip-code microarrays and single base extension (SBE) reactions is described. Multiplex PCR amplification was performed to amplify the genomic regions containing the mutation sites. The PCR products were then employed as templates in subsequent multiplex SBE reactions using bifunctional primers carrying a unique complementary zip sequence in addition to a mutation-site-specific sequence. The SBE primers, terminating one base before their mutation sites, were extended by a single base at a mutation site with a corresponding biotin-labeled ddNTP. Hybridization of the SBE products to zip-code microarrays was followed by staining with streptavidin–Cy3, leading to successful genotyping of several selected BRCA1 mutation sites with wild-type and heterozygote mutant samples from breast cancer patients. This work has led to the development of a reliable DNA microarray-based system for the diagnosis of human genetic mutations. Cheulhee Jung and Seong-Chun Yim contributed equally to this work.     

Functional proteomics,human genetics and cancer biology of GIPC family members

GIPC1, GIPC2 and GIPC3 consist of GIPC homology 1 (GH1) domain, PDZ domain and GH2 domain. The regions around the GH1 and GH2 domains of GIPC1 are involved in dimerization and interaction with myosin VI (MYO6), respectively. The PDZ domain of GIPC1 is involved in interactions with transmembrane proteins [IGF1R, NTRK1, ADRB1, DRD2, TGFβR3 (transforming growth factorβ receptor type III), SDC4, SEMA4C, LRP1, NRP1, GLUT1, integrin α5 and VANGL2], cytosolic signaling regulators (APPL1 and RGS19) and viral proteins (HBc and HPV-18 E6). GIPC1 is an adaptor protein with dimerizing ability that loads PDZ ligands as cargoes for MYO6-dependent endosomal trafficking. GIPC1 is required for cell-surface expression of IGF1R and TGFβR3. GIPC1 is also required for integrin recycling during cell migration, angiogenesis and cytokinesis. On early endosomes, GIPC1 assembles receptor tyrosine kinases (RTKs) and APPL1 for activation of PI3K–AKT signaling, and G protein-coupled receptors (GPCRs) and RGS19 for attenuation of inhibitory Gα signaling. GIPC1 upregulation in breast, ovarian and pancreatic cancers promotes tumor proliferation and invasion, whereas GIPC1 downregulation in cervical cancer with human papillomavirus type 18 infection leads to resistance to cytostatic transforming growth factorβ signaling. GIPC2 is downregulated in acute lymphocytic leukemia owing to epigenetic silencing, while Gipc2 is upregulated in estrogen-induced mammary tumors. Somatic mutations of GIPC2 occur in malignant melanoma, and colorectal and ovarian cancers. Germ-line mutations of the GIPC3 or MYO6 gene cause nonsyndromic hearing loss. As GIPC proteins are involved in trafficking, signaling and recycling of RTKs, GPCRs, integrins and other transmembrane proteins, dysregulation of GIPCs results in human pathologies, such as cancer and hereditary deafness.