A Western blot analysis of lysates from stably transfected HEK cells. Open black histograms, secondary Ab only; grey filled histograms, anti-DDR1. The blot was probed with anti-phosphotyrosine mAb 4G10 upper panel , followed by stripping and reprobing with anti-DDR1 lower panel. The corresponding blots were probed with anti-phosphotyrosine mAb 4G10 upper panel or anti-DDR2 lower panel.
The positions of molecular weight markers in kDa are indicated. Dasatinib inhibits collagen I-induced DDR autophosphorylation. The remaining cell adhesion was measured and calculated as described in Materials and Methods. Sequences of synthetic triple-helical collagen-derived peptides used in this study. Performed the experiments: HX. Analyzed the data: HX BL.
Wrote the paper: HX BL. Browse Subject Areas? Click through the PLOS taxonomy to find articles in your field. Introduction The extracellular matrix ECM physically supports cells in multicellular organisms and also signals to these cells through cell surface receptors. Synthetic Triple-helical Collagen-derived Peptides The sequences of the peptides used in this study are shown in Table S1. Western Blotting Cells grown in well tissue culture plates were lysed as above. Download: PPT. Figure 1. Figure 2. Figure 3. Figure 4. Figure 5. DDR-overexpressing cells exhibit increased cell adhesion to medium-affinity integrin-selective collagen peptides.
Figure 6. Figure 7. Figure 8. Activation of DDRs enhances integrin-mediated cell adhesion to medium-affinity integrin ligands. Discussion The DDRs are thought to play major roles in cell adhesion in a variety of cell types and several studies have suggested that DDR1 functions as an adhesion receptor e. Supporting Information. Figure S1.
Figure S2. Figure S3. Table S1. References 1. Annu Rev Biochem — View Article Google Scholar 2. Leitinger B Transmembrane collagen receptors. Annu Rev Cell Dev Biol — View Article Google Scholar 3. Hynes R Integrins. Bidirectional, allosteric signaling machines.
Cell — View Article Google Scholar 4. Acta Physiol Oxf — View Article Google Scholar 5. Cell Tissue Res — View Article Google Scholar 6. Biochem Soc Trans — View Article Google Scholar 7. J Biol Chem — View Article Google Scholar 8. J Biol Chem 35— View Article Google Scholar 9.
View Article Google Scholar Embo J — Structure — Mol Cell 1: 13— Mol Cell 1: 25— Matrix Biol — J Mol Biol — Matrix Biol 16— Mol Cell Biol — EMBO Rep 2: — Am J Hum Genet 80— Hum Mol Genet — Cell Signal — Cancer Metastasis Rev — Faseb J — Yoshida D, Teramoto A Enhancement of pituitary adenoma cell invasion and adhesion is mediated by discoidin domain receptor J Neurooncol 29— J Neurooncol — J Clin Invest — J Am Soc Nephrol — Mol Biol Cell — J Cell Physiol — These include defects in active zone apposition, release sites, membrane and vesicle organization, and synaptic transmission.
Moreover, the presynaptic microtubule and postsynaptic spectrin cytoskeletons are severely disrupted, suggesting a mechanism whereby Teneurins organize the cytoskeleton, which in turn affects other aspects of synapse development. Supporting this, Ten-m phys. Genetic analyses of teneurin and neuroligin reveal that they have differential roles that synergize to promote synapse assembly. Finally, at elevated endogenous levels, Ten-m regulates target selection between specific motor neurons and muscles.
Our study identifies the Teneurins as a key bi-directional trans-synaptic signal involved in general synapse organization, and demonstrates that proteins such as these can also regulate target selection. Homozygous null mutation in ODZ3 causes microphthalmia in humans Genet. Aldahmesh, Mohammed A. Purpose: Microphthalmia is a condition in which eyes are small in size, often assocd. Isolated microphthalmia is a model disease for studying early development of the human eye, and mutations in several key genes related to eye development have been linked to this phenotype.
Methods: In our search for novel genes that cause autosomal recessive microphthalmia when mutated, we enrolled a family that consists of third-cousin parents and two children with isolated colobomatous microphthalmia. Results: Exome and autozygome anal. Conclusion: Our data highlight a role for ODZ3 in the early development of the human eye. Teneurins, a transmembrane protein family involved in cell communication during neuronal development Cell.
Life Sci. Birkhaeuser Verlag. Teneurins are a unique family of transmembrane proteins conserved from Caenorhabditis elegans and Drosophila melanogaster to vertebrates, in which 4 paralogs exist. In vertebrates, teneurin expression is most prominent in the developing brain. Based on their distinct, complementary expression patterns, the authors suggest a possible function in the establishment of proper connectivity in the brain.
Functional studies show that teneurins can stimulate neurite outgrowth, but they might also play a role in axon guidance as well as in target recognition and synaptogenesis, possibly mediated by homophilic interactions. Although teneurins are transmembrane proteins, there is evidence that the intracellular domain has a nuclear function, since it can interact with nuclear proteins and influence transcription.
Therefore, the authors speculate that teneurins might be processed by proteolytic cleavage possibly regulated intramembrane proteolysis , which is triggered by homophilic interactions or, alternatively, by the binding of a still unknown ligand. Teneurins: important regulators of neural circuitry J. Cell Biol. Elsevier Ltd. Each is expressed in distinct, and often interconnected, areas of the developing nervous system. Different Ten-ms have complementary expression patterns.
In vitro and in vivo studies support roles for teneurins in promoting neurite outgrowth and cell adhesion. Recent in vivo studies show that teneurins play important roles in regulating connectivity in the nervous system. Knockdown in Caenorhabditis elegans resulted in abnormal axon guidance and cell migration, while targeted deletion of Ten-m3 in mice revealed it is required for the guidance of retinal axons and generation of visual topog.
Receptors of Cell Adhesion and Cellular Recognition, Volume 3 - 1st Edition
It is likely that all teneurins play important roles during neural development. Rockefeller University Press. All four proteins Ten-m lack signal peptides at the N-terminus, but contain a short hydrophobic domain characteristic of transmembrane proteins, amino acids after the N-terminus. About amino acids C-terminal to this hydrophobic region are eight consecutive EGF-like domains. Cell transfection, biochem.
Expression of fusion proteins composed of the N-terminal and hydrophobic domain of ten-m1 attached to the alk. Electron microscopic and electrophoretic anal. Northern blot and immunohistochem. All four ten-m genes can be expressed in variously spliced mRNA isoforms. The extracellular domain of Ten-m1 fused to an alk. Far Western assays and electron microscopy demonstrated that Ten-m1 can bind to itself.
Rubin, Beatrix P. Company of Biologists Ltd. The transmembrane glycoprotein teneurin 2 is expressed by neurons in the developing avian thalamofugal visual system at periods that correspond with target recognition and synaptogenesis. Partial and full-length teneurin 2 constructs were expressed in cell lines in vitro. Expression of the cytoplasmic domain is required for the induction of filopodia, the transport of teneurin 2 into neurites, and the co-localization of teneurin 2 with the cortical actin cytoskeleton.
In addn. These observations indicate that the homophilic binding of teneurin 2 may play a role in the development of specific neuronal circuits in the developing visual system. Discrete interactions in cell adhesion measured by single-molecule force spectroscopy Nat.
Cell-cell adhesion mediated by specific cell-surface mols. Here de-adhesion forces at the resoln. Our measurements are focused on a glycoprotein, contact site A csA , as a prototype of cell-adhesion proteins. CsA is expressed in aggregating cells of Dictyostelium discoideum, which are engaged in development of a multicellular organism.
Force probing surfaces of living cells to molecular resolution Nat. Nature chemical biology , 5 6 , ISSN:. Biological processes rely on molecular interactions that can be directly measured using force spectroscopy techniques.
Here we review how atomic force microscopy can be applied to force probe surfaces of living cells to single-molecule resolution. Such probing of individual interactions can be used to map cell surface receptors, and to assay the receptors' functional states, binding kinetics and landscapes. This information provides unique insight into how cells structurally and functionally modulate the molecules of their surfaces to interact with the cellular environment.
Tensile forces govern germ-layer organization in zebrafish Nat. Krieg, M. Understanding the factors that direct tissue organization during development is one of the most fundamental goals in developmental biol. Various hypotheses explain cell sorting and tissue organization on the basis of the adhesive and mech. However, validating these hypotheses has been difficult due to the lack of appropriate tools to measure these parameters. Here the authors use at. These results demonstrate a previously unrecognized role for Nodal-controlled cell-cortex tension in germ-layer organization during gastrulation.
Cell Res. Nunes, Samantha M. Teneurin-1 is a type II transmembrane protein expressed in neurons of the developing and adult central nervous system. To investigate the intracellular signaling of teneurin-1, we searched for proteins interacting with its intracellular domain. One of the proteins identified is the c-Cbl-assocd. SH3 domains.
This interaction results on one hand in the recruitment of the sol.
In the nucleus, the intracellular domain of teneurin-1 colocalizes with this transcriptional repressor in foci assocd. We propose that these interactions are part of a specific signaling pathway. Evidence for cleavage and nuclear translocation of the intracellular domain has been obtained by the detection of endogenous teneurin-1 immunoreactivity in nuclear speckles in chick embryo fibroblasts.
Furthermore, in the nuclear matrix fraction of these cells as well as in cells expressing a hormone-inducible full-length teneurin-1 protein, a teneurin-1 fragment of identical size could be detected as in cells transfected with the intracellular domain alone. In cultured mouse neuroblastoma and fibroblast cells, submicromolar latrunculin A I  and latrunculin B II  concns. Immunofluorescence studies with antibiotics specific for cytoskeletal proteins reveal that the toxins cause major alterations in the organization of microfilaments without obvious effects on the organization of the microtubular system.
Straight, Aaron F. American Association for the Advancement of Science. Completion of cell division during cytokinesis requires temporally and spatially regulated communication from the microtubule cytoskeleton to the actin cytoskeleton and the cell membrane. We identified a specific inhibitor of nonmuscle myosin II, blebbistatin, that inhibited contraction of the cleavage furrow without disrupting mitosis or contractile ring assembly. Using blebbistatin and other drugs, we showed that exit from the cytokinetic phase of the cell cycle depends on ubiquitin-mediated proteolysis.
Continuous signals from microtubules are required to maintain the position of the cleavage furrow, and these signals control the localization of myosin II independently of other furrow components. Phototoxicity and photoinactivation of blebbistatin in UV and visible light Biochem. Elsevier Science. Blebbistatin was recently identified as a selective, cell-permeant inhibitor of myosin II. Because blebbistatin is likely to be used extensively with fluorescence imaging in studies of cytoskeletal dynamics, its compatibility with common excitation wavelengths was examd.
Illumination of blebbistatin-treated bovine aortic endothelial cells at and nm, but not or nm, caused dose-dependent cell death. Illumination of blebbistatin alone at and nm changed its absorption and emission spectra, but the resultant compds. Fluorescence microscopy showed that upon illumination, blebbistatin became bound to cells and to protein-coated glass, suggesting that toxicity may arise from light-induced reaction of blebbistatin with cell proteins. Blebbistatin should be used only with careful consideration of these photochem. Neuroblastoma is the second most common pediatric malignancy, characterized by a high rate of unexplained spontaneous remissions.
Much progress has been made in understanding neuroblastoma differentiation triggered by certain agents such as retinoic acid. However, little is known about the signaling pathways that lead to differentiation of neuroblastoma cells due to serum withdrawal. Interestingly, addn. Our results demonstrate a novel role for serum-derived lipoproteins in the control of receptor tyrosine kinase activity. Structure and mechanism of cadherins and catenins in cell-cell contacts Annu.
Cell Dev. Most cadherins are single-pass transmembrane proteins whose extracellular regions mediate specific cell-cell interactions. The intracellular faces of these contacts are assocd. The close coordination of the transmembrane adhesion mols. Structural, biochem. Synapses are specialized adhesion sites between neurons that are connected by protein complexes spanning the synaptic cleft. These trans-synaptic interactions can organize synapse formation, but their macromol. Here, we demonstrate that the synaptic cell adhesion mol.
SynCAM 1 self-assembles laterally via its extracellular, membrane-proximal Ig domains 2 and 3. This cis oligomerization generates SynCAM oligomers with increased adhesive capacity and instructs the interactions of this mol. In immature neurons, cis assembly promotes the adhesive clustering of SynCAM 1 at new axo-dendritic contacts. Interfering with the lateral self-assembly of SynCAM 1 in differentiating neurons strongly impairs its synaptogenic activity.
At later stages, the lateral oligomerization of SynCAM 1 restricts synaptic size, indicating that this adhesion mol. These results support the notion that lateral interactions assemble SynCAM complexes within the synaptic cleft to promote synapse induction and modulate their structure. These findings provide novel insights into synapse development and the adhesive mechanisms of Ig superfamily members. Cooperative role of nectin-nectin and nectin-afadin interactions in formation of nectin-based cell-cell adhesion J.
American Society for Biochemistry and Molecular Biology. The nectin cell adhesion mols. In a single cell, Necl-5 nectin-like mol. In such a single cell, afadin also localizes at the leading edge without interacting with nectins or Necl It remains unknown how the nectin-nectin and nectin-afadin interactions are initiated when moving cells contact each other to initiate the formation of adherens junctions.
We show here that the Neclnectin interaction induced by cell-cell contact enhances the nectin-afadin interaction. This interaction then enhances the nectin-nectin interaction, which further enhances the nectin-afadin interaction in a pos. Thus, the Neclnectin, nectin-nectin, and nectin-afadin interactions cooperatively increase the clustering of the nectin-afadin complex at the cell-cell contact sites, promoting the formation of the nectin-based cell-cell adhesion. Their extracellular domains are composed of an array of eight consecutive EGF modules followed by a large globular domain. Two of the eight modules contain only 5 instead of the typical 6 cysteine residues and have the capability to dimerize in a covalent, disulfide-linked fashion.
The structural properties of the extracellular domains of all four mouse Ten-m proteins have been analyzed using secreted, recombinant mols. Electron microscopic anal. Cotransfection expts. Model of the brain tumor-Pumilio translation repressor complex Genes Dev. Edwards, Thomas A.
Cold Spring Harbor Laboratory Press. Recruitment is mediated by interactions between the Pumilio RNA-binding Puf repeats and the NHL domain of Brat, a conserved structural motif present in a large family of growth regulators. In this report, we describe the crystal structure of the Brat NHL domain and present a model of the Pumilio-Brat complex derived from in silico docking expts. A key feature of the model is recognition of the outer, convex surface of the Pumilio Puf domain by the top, electropos. Together, these interactions are likely to be prototypic of the recruitment strategies of other NHL-contg.
Liu, Heli; Juo, Z. Christopher; He, Xiaolin. Cell Press. Repulsive signaling by Semaphorins and Plexins is crucial for the development and homeostasis of the nervous, immune, and cardiovascular systems. Both structures show two PlexinC1 mols. Both binding interfaces are dominated by the insertion of the Semaphorin's 4c-4d loop into a deep groove in blade 3 of the PlexinC1 propeller. A39R appears to achieve Sema7A mimicry by preserving key Plexin-binding determinants seen in the mammalian Sema7A complex that have evolved to achieve higher affinity binding to the host-derived PlexinC1.
The complex structures support a conserved Semaphorin-Plexin recognition mode and suggest that Plexins are activated by dimerization. Janssen, Bert J. Cell-cell signalling of semaphorin ligands through interaction with plexin receptors is important for the homeostasis and morphogenesis of many tissues and is widely studied for its role in neural connectivity, cancer, cell migration and immune responses. SEMA4D and Sema6A exemplify two diverse vertebrate, membrane-spanning semaphorin classes that are capable of direct signalling through members of the two largest plexin classes, B and A, resp.
In the absence of any structural information on the plexin ectodomain or its interaction with semaphorins the extracellular specificity and mechanism controlling plexin signalling has remained unresolved. These structures, together with biophys. In combination, our data favor a cell-cell signalling mechanism involving semaphorin-stabilized plexin dimerization, possibly followed by clustering, which is consistent with previous functional data.
Force measurements in E-cadherin-mediated cell doublets reveal rapid adhesion strengthened by actin cytoskeleton remodeling through Rac and Cdc42 J. We have used a modified, dual pipet assay to quantify the strength of cadherin-dependent cell-cell adhesion. The force required to sep. E-cadherin-expressing paired cells in suspension was measured as an index of intercellular adhesion. Severing the link between cadherin and the actin cytoskeleton or disrupting actin polymn. Rac and Cdc42, the Rho-like small GTPases, were activated when E-cadherin-expressing cells formed aggregates in suspension.
Our findings highlight the crucial roles played by Rac, Cdc42, and actin cytoskeletal dynamics in the development and regulation of strong cell adhesion, defined in terms of mech. Teneurin-1 is expressed in interconnected regions of the developing brain and is processed in vivo BMC Develop. In vertebrates there are four paralogs teneurin-1 to -4 , all of which are expressed prominently in the developing central nervous system. RESULTS: Analysis of teneurin-1 expression in the developing chick brain by in situ hybridization and immunohistochemistry defined a unique, distinct expression pattern in interconnected regions of the brain.
Moreover we found complementary patterns of teneurin-1 and-2 expression in many parts of the brain, including the retina, optic tectum, olfactory bulb, and cerebellum as well as in brain nuclei involved in processing of sensory information. Based on these expression patterns, we suspect a role for teneurins in neuronal connectivity. In contrast to the cell-surface staining of the antibody against the extracellular domain, an antibody recognizing the intracellular domain revealed nuclear staining in subpopulations of neurons and in undifferentiated mesenchyme.
Western blot analysis of brain lysates showed the presence of N-terminal fragments of teneurin-1 containing the intracellular domain indicating that proteolytic processing occurs. Finally, the teneurin-1 intracellular domain was found to contain a nuclear localization signal, which is required for nuclear localization in transfected cells. Our data support the hypothesis that teneurins can be proteolytically processed leading to the release of the intracellular domain and its translocation to the nucleus.
Teneurins: a novel family of neuronal cell surface proteins in vertebrates, homologous to the drosophila pair-rule gene product Ten-m Dev. Academic Press. We have characterized chicken teneurin-1 and teneurin-2, 2 homologs of the Drosophila pair-rule gene product Ten-m and Drosophila Ten-a. The high degree of conservation between the vertebrate and invertebrate proteins suggests that these belong to a novel family.
We propose to name the vertebrate members of this family teneurins, because of their predominant expression in the nervous system. The expression of teneurin-1 and -2 was investigated by in situ hybridization. Teneurin-1 and -2 are expressed by distinct populations of neurons during the time of axonal growth.
The most prominent site of expression of chicken teneurins is the developing visual system. The junctional markers also displayed reduced colocalization with F-actin Figure 7—figure supplement 1G—H. B Quantification of cell height relative to transwell filter. Three measurements per image were averaged. Each data point relates to one EM image. A representative confocal microscopy image is shown. E Quantification of relative F-actin staining intensity. See also Figure 7—figure supplement 1.
When we collected intact spheroids for immunostaining we found normal apical polarization of the Golgi Figure 8C. Overall, our results support a role for PTPRK in promoting cell-cell junctions and repressing invasive behavior, probably through recruitment and dephosphorylation of several cell junction organizers. MCF10A spheroids after 14 day culture in Matrigel.
See also Figure 8—figure supplement 1. These substrates are linked to cell-cell junction organization, which is perturbed when PTPRK is deleted. Importantly, our findings demonstrate the substrate selectivity of this receptor, which requires both its active and inactive PTP domains. Our conclusions have implications not only for understanding PTP biology and cell-cell junction phosphoregulation, but also provide molecular insight into how PTPRK might function as a tumor suppressor. Cross-referencing the PTPRK interactome with the PTPRK-dependent tyrosine phosphoproteome enabled us to identify candidate substrates to assay for cellular interactions and direct dephosphorylation.
Substrate-trapping methods in combination with mass spectrometry are commonly used to identify PTP substrates Blanchetot et al. Both were partially competed from traps with the phosphate mimetic vanadate, suggesting phosphorylation-dependent interaction. An interesting future line of research will be to determine whether PTPRK is an upstream regulator of this new mechanotransduction pathway.
Our immunoblots also highlighted phosphorylation-dependent enrichment of p Cat and PKP4 on this trap.
Signal Transduction by Adhesion Receptors
However, we also found hyperphosphorylation of other PTPRK-binding partners in KO cells, indicating the traps alone were too restrictive in identifying substrates. Indeed, the PTPRK pseudophosphatase D2 domain was sufficient for substrate recognition, which may have masked the effect of the substrate traps, particularly as we have shown that D2 domain binding to most proteins is independent of tyrosine phosphorylation. Furthermore, we cannot rule out the existence of additional PTPRK substrates, for example, that are expressed in different cellular contexts, particularly as we observed divergent interactomes between epithelial and fibroblast cells.
This suggests that rather than co-evolving with its substrates, PTPRK regulates pre-established functional protein complexes. In this way, PTPRK would have introduced new regulation, and perhaps function, to existing signaling networks for chordate and vertebrate-specific organization. PKP3 has been proposed to promote the stability of desmosomes upon overexpression Gurjar et al.
PKP4 is targeted to both adherens junctions and desmosomes, but its role is less well understood Hatzfeld et al. Our finding that PTPRK promotes junctional integrity raises the possibility that dephosphorylation of substrates, such as p Cat , would stabilize cadherin-based junctional assemblies.
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This is reminiscent of the proposed role of p Cat in controlling epithelial cell lateral domain expansion and shape maturation by balancing junctional contractility and maturation through regulation of E-Cadherin and RhoA Yu et al. In line with this, we found little evidence for a PTPRK substrate consensus sequence other than a bias against basic residues immediately adjacent to the phosphotyrosine site, similar to previous reports for other PTPs Barr et al. The Janus kinases have a similar tandem arrangement where a pseudokinase domain regulates kinase activity Babon et al.
However, when free D2 domain was added to free D1 domain, we saw no impact on activity. We further show that unlike LAR Nam et al. Additionally, we rule out a role for the D2 domain in phosphotyrosine recognition using dephosphorylated lysates, vanadate competition and a PTPRK homology model. Several previous reports have shown that wildtype PTPs can interact with substrates, which are presumably in a dephosphorylated state Chen et al.
Thus, PTPRK might serve as a scaffold for dephosphorylated proteins either by recruiting non-phosphorylated proteins, or by dephosphorylating already phosphorylated proteins upon recruitment. It is likely that the combination of recognition and dephosphorylation is important for full PTPRK function.
Vertebrate genomes all encode at least 4 R2B family members, with distinct expression profiles Figure 1—figure supplement 1A. For example, by in situ hybridization the receptors display divergent expression patterns in the adult mouse cerebellum Besco et al. Assuming they are regulated similarly by cell-cell contact, our results indicate that receptor expression patterns will determine subtly distinct responses to cell contact.
Afadin Y phosphorylation, the rat equivalent of Human Afadin Y, has been shown to mediate recruitment of SHP2, implicating it in Ras-Mitogen activated protein kinase signaling Nakata et al. PTPRK is the only R2B family member implicated by transposon-based mouse forward genetics in the progression of several cancers March et al. Moreover, specific gene fusions result in its promoter driving the expression of oncogenic RSPO3 in a subset of colorectal cancers Seshagiri et al. Our findings of abrogated junction organization, spheroid overgrowth and invasive behavior in PTPRK-deficient cells support its role as a tumor suppressor.
Thus, their combined dysregulation could contribute to pathological phenotypes in a PTPRK mutant setting. Compromised epithelial barrier integrity is also linked to inflammatory bowel disease susceptibility; therefore, PTPRK SNPs linked to celiac disease should be investigated Trynka et al. PTPs are well-placed to fine-tune and tailor responses to particular cellular contexts.
PTPRK might therefore provide feedback in the context of cell contact by dephosphorylating its substrates to promote junctional integrity. Indeed, overexpression of v-Src in epithelial cells leads to junction disassembly and EMT Woodcock et al. Thus, such PTPs could act as interpreters of the cellular context. In summary, by defining the substrate repertoire of human PTPRK, we reveal mechanistic insight into its putative tumor suppressor role through its control of cell-cell junctions and suppression of EMT.
Our study raises new questions about the phosphoregulation of junctional proteins and implicates PTPRK as a direct sensor and mediator of cell adhesion. We show that the PTPRK D2 domain is critical for substrate recognition, yet binds proteins independently of phosphorylation status. It will be of great interest to determine whether these findings hold true for other RPTPs. In addition, it is unknown whether the R2B receptor extracellular regions, which were previously described as spacer clamps Aricescu et al. Thus, we provide a framework for systematically identifying RPTP substrates, which in turn will advance our knowledge of these poorly characterized, yet important enzymes.
Hs27 cells were cultured in Fibroblast growth medium Promocell, UK. Cell lines were tested for the presence of Mycoplasma using commercially available kits see Key Resources table. Isotopic labeling was assessed by mass spectrometry, following in-gel tryptic digest. Rabbits were housed and immunized in Josman, LLC. Rabbit anti-PTPRK mAb were generated from an antigen-specific single B cell cultivation and cloning platform based on a modified protocol Seeber et al.
Variable regions VH and VL of each monoclonal antibody from rabbit B cells were then cloned into expression vectors from extracted mRNA as previously described Seeber et al. Individual recombinant rabbit antibodies were expressed in Expi cells and subsequently purified with protein A. Purified anti-PTPRK antibodies were then subjected to functional activity assays and kinetic screening.
Lead clones were selected for large scale antibody production. Cells were seeded at 1. Cells were returned to the incubator after 30 min at RT. After 24 hr total incubation, media were replaced for complete growth medium. Cells were allowed to recover for 48—72 hr prior to treatment or processing for analysis. After 48 hr eGFP positive cells were single-cell sorted using flow cytometry. Clones were expanded and protein levels assessed by Western blot. Targeted regions of the genome were amplified by PCR and sequenced to confirm editing.
After 24 hr media was then replaced with 16 ml complete growth medium. Viral particles were pelleted via ultracentrifugation at , x g for 1. For lentiviral infections, 1. After 30 min at room temperature RT , cells were returned to the incubator. Lysates were harvested, followed by the addition of DTT to a final concentration of 10 mM and incubated for 15 min on ice.
After 5 min, a small amount of catalase Sigma-Aldrich was added to the pervanadate solution using a pipette tip and mixed by gentle inversion to quench unreacted H 2 O 2. Freshly made pervanadate solution was used within 5 min to avoid decomposition of the complex. Expression levels were normalized to the reference gene RPL Gene specific primers are listed in the Key Resources table. Proteins were transferred onto 0. Prior to lysis, cells were subjected to one round of freeze-thaw. The supernatant was removed and incubated with 0.
Ni-NTA agarose was then washed with 10 volumes of purification buffer containing 5 mM imidazole, followed by 20 volumes of purification buffer containing 20 mM imidazole; prior to elution in purification buffer containing mM imidazole. Samples were then cooled to RT and allowed to equilibrate for 5 min.
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Protein only and streptavidin only controls should be included. A beads-only control was treated identically. Samples were briefly spun, transferred onto a magnetic stand and washed 3 times with 1 ml of ice-cold size exclusion buffer, followed by two washes with 1 ml of ice-cold mM NaCl wash buffer 20 mM Tris-HCl pH 7. In a cold room, beads were pulled to a magnet and supernatant removed.
Beads were then washed twice in 1 ml ice-cold mM NaCl wash buffer including a brief spin and separation by magnet. Beads were then washed once with 1 ml ice-cold mM NaCl wash buffer without resuspension and washed twice more in 1 ml ice-cold mM NaCl wash buffer with resuspension. For analysis by mass spectrometry, beads were subject to two further washes without resuspension and one further wash with resuspension in 1 ml ice-cold 50 mM ammonium bicarbonate pH 8. Next, Samples were briefly spun and placed onto a magnetic stand, supernatant was then transferred into a low protein-binding tube Eppendorf, Thermo Fisher Scientific.
All buffers were made using proteomics grade water. Samples were then slowly loaded onto each Sep-Pak; flow-through was reapplied once. Sep-Paks were then washed three times with 1 ml 0. Raw files were processed on MaxQuant v. Quantification was carried out using Perseus ver. For label-free quantification LFQ , LFQ intensities from MaxQuant were log2 x transformed prior to filtering out proteins branded as identified only by site, reverse or potential contaminants.
Proteins were then further filtered out based on the minimum number of valid values in one group, to be stringent we required a minimum of three MCF10A experiments or two Hs27 experiments valid values. Missing values were then imputed from the normal distribution and statistical significance was calculated via a two-sample, two-sided t test performed with truncation by a permutation-based FDR threshold value 0. All buffers were made in phosphate-free water Thermo Fisher Scientific. The assay was then incubated at RT for 2. The absorbance was then read at nm using a well plate reader SpectraMax M5, Molecular Devices.
Enzyme activity was compared against a standard curve from serial dilutions of a phosphate standard ENZO. Cells were cultured for 7 days with a media change on days 2 10 ml , 4 12 ml , 5 12 ml and 6 12 ml. A total of 10 mg of protein from heavy and light lysates was processed per replicate. Proteins were then alkylated by addition of Samples were diluted to a final concentration of 1.
Next, 0. Samples were split in half and transferred to two new 5 ml low protein-binding tubes. Samples were diluted to a final concentration of 0. Tryptic digests were then acidified via the addition of Samples were then split into two new 2 ml low protein-binding tubes Thermo Fisher Scientific , prior to centrifugation at x g for 10 min.
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Sep-Paks were equilibrate, washed and loaded as described above. Peptides were eluted in a stepwise manner into new 1. Beads were pelleted via at x g for 30 s and washed three times with 1 ml ice-cold IAP buffer followed by two washes with 1 ml ice-cold proteomics grade water. This step was repeated for a total of three elutions and supernatants combined.
Total peptides were resolved using four different gradients. Phosphopeptides were resolved using four different gradients. Data were processed using MaxQuant v. Proteins were then further filtered out based on the minimum number of valid values; a minimum of two valid values were required for high confidence analysis. Statistical significance was calculated via a one-sample, two-sided t test performed with truncation by a Benjamini Hochberg FDR threshold value 0.
Equal amounts 3—4 mg of lysate were transferred into 1. All steps were performed on ice unless indicated. Samples were mixed by gentle inversion and reactions were then incubated for 1. Beads were pelleted at x g for 30 s and the supernatant transferred into a new microfuge tube. Cells were cultured for 6 days, with a media change on day 3, and then every day thereafter.
Coverslips were then incubated with primary antibody dilution for 1—5 hr at RT. Coverslips were then mounted onto 1. Spheroids were extracted from Matrigel as previously described Lee et al. Media was aspirated and wells washed twice with PBS. Spheroids were then briefly centrifuged at x g and the majority of supernatant aspirated. The remaining supernatant was used to resuspend the spheroids prior to transferring them onto a glass slide. The fixed spheroids were then washed three times in mM glycine in PBS with 10 min per wash. Next, the spheroids were blocked in IF buffer 0.
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