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Supplementary Figures Mena regulates the LINC complex to control actin–nuclear lamina associations, trans-nuclear membrane signalling and cancer gene expression Frederic Li Mow Chee!, Bruno Beernaert!, Alexander Loftus!, Yatendra Kumar", Billie G. C. Griffith!, Jimi C. Wills!, Ann P. Wheeler#, J. Douglas Armstrong$, Maddy Parsons%, Irene M. Leigh,(, Charlotte M. Proby&, Alex von Kriegsheim!, Wendy A. Bickmore", Margaret C. Frame,* & Adam Byron,* Supplementary Information Supplementary Figure 1 Supplementary Figure 2 Supplementary Figure 3 Supplementary Table 1 Supplementary Table 2 Supplementary Table 3 Supplementary Table 4 !Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH< =XR, UK. "MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH< =XU, UK. #Advanced Imaging Resource, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH< =XU, UK. $Simons Initiative for the Developing Brain, School of Informatics, University of Edinburgh, Edinburgh EHH IYL, UK. %Randall Centre for Cell and Molecular Biophysics, King’s College London, London SEM MUL, UK. &Division of Molecular and Clinical Medicine, School of Medicine, University of Dundee, Dundee DD <HN, UK. 'Institute of Dentistry, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EM =AT, UK. *email: [email protected] or [email protected] 1 a cSCC IAC correlation b cSCC IAC pathways c Core adhesome network ENAH −log10(q) MACF1 CSRP1 Met1 Met4 0 5 10 + + CORO2A Integrin signalling + CFL1 pathway PRNP ILK + HSPB1 PALLD PPFIA1 TES RDX Cytoskeletal regulation + VASP + + ARPC2 by Rho GTPase PPP2CA + Met1 + LASP1 MYH9 + VIM TUBA4A Huntington ITGA3 + disease ITGB4 VCL CAV1 ACTB ROCK1 KTN1 FLNA+ CALR DNA FBLIM1 CORO1B RAC1 + replication +ACTN1 ITGA6 + Met4 ITGAV Parkinson ITGB1 disease Actin cytoskel. PXN + SVIL + MSN ABI1 + LIMS1 + CTTN Cell + Actin binding PLEC + RHOA cycle q + TLN1 + ARHGEF2 log10 PARVA + PTK2 mRNA scale EZR Pearson splicing ≥0.05 0.001 CAPN2 correlation TRIP6 TUBA1B + coefficient Overlap log (Met4/Met1) SLC3A2 2 RAVER1 MARCKS 0.7 1.0 0 >50 ≤−3 0 ≥3 FHL2 FERMT3 Physical interaction Pathway association d IAC principal component analysis e Core adhesome clustering 20 Met4 Actin cytoskeleton Met1 10 Actin binding Actin organisation 0 −10 ENAH TRIP6 CAV1 KTN1 SLC3A2 MARCKS LASP1 TUBA1B ABI1 FBLIM1 EZR VCL HSPB1 TES PRNP ARHGEF2 RAVER1 RAC1 SVIL PPP2CA PALLD CAPN2 PLEC MYH9 MACF1 CTTN CFL1 CSRP1 CORO2A ITGB1 RHOA TUBA4A ITGB4 FLNA ITGA6 FERMT3 ACTB ARPC2 ACTN1 PARVA VASP RDX ITGA3 LIMS1 PTK2 TLN1 CORO1B CALR PXN FHL2 MSN ILK ITGAV ROCK1 VIM PPFIA1 Component 2 (5.5%) −20 −25 0 25 50 Component 1 (83.4%) f IAC Mena validation IAC Lysate cSCC: Met1Met4 Met1Met4 Met1 Met4 100 Mena IAC 75 100 High exp. 75 High exp. Z-score Cyto. 37 GAPDH −1.3 0 1.3 20 Mito. 15 COX IV Meta-adhesome 20 dataset occurrence Nucl. 15 Histone H3 kDa 1 7 g IAC active module: alternative clustering h Actin regulation cluster: alternative Transcription Mena coactivator Network view Nesprin-2 Protein complex activity TCP-1ε + scaffold activity + WDR76 + GTPase activity HSPA6 hPrp4 snRNA 9 1 Helicase activity binding ATPase activity CDK9 + DNA binding DnaJA2 Actin regulation/ TCP-1δ + 8 2 protein binding + + TCP-1α Cell 7 6 TCP-1θ adhesion 3 Core cSCC molecule TRIM28 adhesome binding 5 4 ERK signalling Meta-adhesome + Actin binding log2(Met4/Met1) ECM Cell adhesion/ ≤−3 0 ≥3 Growth factor protein binding Core cSCC binding adhesome Hub 1 Nucleotidyl- 4 Ribosome 8 Actin binding Non-hub transferase rRNA binding Cytoskeleton log (Met4/Met1) activity 2 5 Lyase activity 9 Transcription 2 Cell adhesion ≤−3 0 ≥3 6 mRNA binding coactivator molecule binding activity Ribosome 3 Histone Nucleosome binding 7 Actin binding binding Supplementary Figure 1. See next page for caption. 2 Supplementary Figure 1. Proteomic analysis of patient-derived cSCC IACs. (a) Sample correlation analysis of mass spectrometric analyses of Met1 and Met4 IACs (n = 3 independent biological replicates). Pearson correlation coecients for all pairwise sample comparisons were subjected to hierarchical clustering. (b) Over-representation analysis of Panther pathways in the cSCC IAC subproteome. Purple shading intensity indicates size of subproteome overlap with respective gene sets (q < 0.05, hypergeometric test with Benjamini–Hochberg correction). (c) Functional association network of the core cSCC adhesome. Proteins (nodes) are coloured according to protein enrichment in Met1 or Met4 IACs and annotated with gene names for clarity. Node size represents signicance of dierential enrichment between Met1 and Met4 IACs (two-sided t-test with Benjamini–Hochberg correction; n = 3 independent biological replicates). Black node borders indicate actin-cytoskeletal proteins; actin-binding proteins are indicated by a plus sign. (d) Principal component analysis of Met1 and Met4 IACs. (e) Hierarchical cluster analysis of the core cSCC adhesome. Data are as for Fig. 1e with additional annotation. Frequency of occurrence in meta-adhesome datasets is indicated, and proteins are annotated with gene names for clarity. (f) Isolation of Mena in Met4 IACs as determined by western blotting. GAPDH (cyto., cytoplasmic), COX IV (mito., mitochondrial) and histone H3 (nucl., nuclear) were probed as non-adhesion control proteins. High exp., high exposure of blot. (g) Maximal-scoring active module of the cSCC IAC interactome. e network is based on that in Fig. 1g, but it was partitioned using the constant Potts model, resolved for maximum Surprise quality function. Proteins (nodes) are coloured according to assigned cluster (le panel). Molecular functions enriched in protein clusters were determined by Gene Ontology over-representation analysis (the two most signicant functional categories are labelled). For protein clusters with fewer than two signicant functional categories, clusters were annotated manually with a single representative term. Network view (right panel) shows corresponding protein interactions (edge densities) in the partitioned network; nodes are coloured according to protein enrichment in Met1 or Met4 IACs. e actin regulation cluster detailed in h is indicated with a red arrowhead. Large nodes indicate kinless and connector hubs; black node borders indicate core adhesome proteins. (h) Subnetwork analysis of the actin regulation cluster identied by active module partitioning in g. e weighted subnetwork was clustered using a force-directed algorithm. Nodes are coloured according to protein enrichment in Met1 or Met4 IACs. a Mena re-expression b Mena sequence alignment −/− −/− Met4 GGATCAACAATAGAAACAGAACAAAAAGAGGACAAAGGTGAAGATTCAGAGCCTGTAACT 355 Pan-Mena GGATCAACAATAGAAACAGAACAAAAAGAGGACAAAGGTGAAGATTCAGAGCCTGTAACT 1500 Mena11a GGATCAACAATAGAAACAGAACAAAAAGAGGACAAAGGTGAAGATTCAGAGCCTGTAACT 1500 Met4 Met4 MenaMet4 Mena ************************************************************ +Mena11a 100 75 Mena Met4 TCTAAGGCCTCTTCAACAAGTACACCTGAACCAACAAGAAAACCTTGGGAAAGAACAAAT 415 Pan-Mena TCTAAGGCCTCTTCAACAAGTACACCTGAACCAACAAGAAAACCTTGGGAAAGAACAAAT 1560 Lysate 37 Mena11a kDa GAPDH TCTAAGGCCTCTTCAACAAGTACACCTGAACCAACAAGAAAACCTTGGGAAAGAACAAAT 1560 ************************************************************ Met4 ACAATGAATGGCAGCAAGTCACCTGTTATCTCCAGACGGGATTCTCCAAGGAAAAATCAG 475 Pan-Mena ACAATGAATGGCAGCAAGTCACCTGTTATCTCCAGA------------------------ 1596 Mena11a ACAATGAATGGCAGCAAGTCACCTGTTATCTCCAGACGGGATTCTCCAAGGAAAAATCAG 1620 ************************************ Met4 ATTGTTTTTGACAACAGGTCCTATGATTCATTACACAGACCAAAATCCACACCCTTATCA 535 Pan-Mena ---------------------------------------CCAAAATCCACACCCTTATCA 1617 Mena11a ATTGTTTTTGACAACAGGTCCTATGATTCATTACACAGACCAAAATCCACACCCTTATCA 1680 ********************* Met4 CAGCCCAGTGCCAATGGAGTCCAGACGGAAGGACTTGACTATGACAGGCTGAAGCAGGAC 595 Pan-Mena CAGCCCAGTGCCAATGGAGTCCAGACGGAAGGACTTGACTATGACAGGCTGAAGCAGGAC 1677 Mena11a CAGCCCAGTGCCAATGGAGTCCAGACGGAAGGACTTGACTATGACAGGCTGAAGCAGGAC 1740 ************************************************************ Met4 ATTTTAGATGAAATGAGAAAAGAATTAACAAAGCTAAAAGAAGAGCTCATTGATGCAATC 655 Pan-Mena ATTTTAGATGAAATGAGAAAAGAATTAACAAAGCTAAAAGAAGAGCTCATTGATGCAATC 1737 Mena11a ATTTTAGATGAAATGAGAAAAGAATTAACAAAGCTAAAAGAAGAGCTCATTGATGCAATC 1800 ************************************************************ Supplementary Figure 2. Analysis of Mena expression in Met4 cSCC cells. (a) Western blot analysis of endogenous Mena in parental Met4 cells, absence of Mena in Mena-depleted Met4 cells (Met4 Mena−/−) and re-expression of Mena11a in Met4 Mena−/− cells (Met4 Mena−/− +Mena11a). (b) Nucleotide sequence alignment of endogenous Mena transcript sequenced from Met4 cells. Mena sequence compared to pan-Mena (GenBank accession KM214203.1) and Mena11a (GenBank accession KM214204.1) coding sequences. Grey boxes indicate the additional Mena11a exon coding sequence. Asterisks indicate exact residue conservation. 3 a H3K27me3 quantification b Multiplexed gene expression data normalisation −/− −/− H3K27me3 rel. intensity 2 (norm. to histone H3) n.s. * Met4 Met4 MenaMet4 Mena ** 20 +GFP-Mena11a H3K27me3 1.00 0 15 expression 2 20 0.75 15 Histone H3 0.50 Relative log −2 100 GFP-Mena11a 0.25 75 Mena kDa 0 −/− −/− Rep.: 1 2 3 4 1 2 3 4 Met4 Met4 Met4 Mena−/− Met4 MenaMet4 Mena +GFP-Mena11a c Gene expression principal component analysis d Gene expression clustering Cell migration Met4 Mena−/− ECM organisation Immune response Met4 25 CHAD CD24 COL18A1 ARAP2 GPR56 CTSH ARHGDIB ID1 ID2 LAMA5 NOTCH1 EPAS1 SRC TLR4 CLU ADAP1
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