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Article Characterization of HMGB1/2 Interactome in Prostate Cancer by Yeast Two Hybrid Approach: Potential Pathobiological Implications

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Article Characterization of HMGB1/2 Interactome in Prostate Cancer by Yeast Two Hybrid Approach: Potential Pathobiological Implications Article Characterization of HMGB1/2 Interactome in Prostate Cancer by Yeast Two Hybrid Approach: Potential Pathobiological Implications Aida Barreiro-Alonso 1,†, María Cámara-Quílez 1,†, Martín Salamini-Montemurri 1, Mónica Lamas- Maceiras 1, Ángel Vizoso-Vázquez 1, Esther Rodríguez-Belmonte 1, María Quindós-Varela 2, Olaia Martínez-Iglesias 3, Angélica Figueroa 3 and María-Esperanza Cerdán 1,* Table S1. Association of proteins that interact with Hmgb1 or Hmgb2 to cancer hallmarks. Cancer Hallmark Protein Model Reference MAP1B Colorectal cancers [109] GENOMIC INSTABILITY AND Liver adenocarcinoma (SKHep1) and NOP53 [110] MUTATIONS/ CHANGES IN glioblastoma (T98G) cell lines TELOMERASE ACTIVITY RSF1 Ovarian cells [111] SRSF3 Ovarian cancer [112] C1QBP Breast cancer [54,113] cFOS Bladder cancer [114] cFOS Breast cancer [115] DLAT Gastric Cancer [116] Human melanoma (A7), Prostate cancer FLNA [117] (PC3) cell lines GOLM1 Hepatocellular carcinoma [118] GOLM1 Breast cancer [119] GOLM1 Lung proliferation [120] GOLM1 Prostate cancer [82] SUSTAINING PROLIFERATIVE Hox-A10 Prostate cancer cell line PC-3 [58] SIGNALLING/ CELL Hox-A10 Ovarian cancer cell lines [121,122] PROLIFERATION NOP53 Breast cancer [123] PSMA7 Cervical cancer [124] PTPN2 Epithelial carcinogenesis [125] RASAL2 hepatocellular carcinoma [126] RSF1 Prostate cancer [95] RSF1 Nasopharyngeal carcinoma [127] SPIN1 Glioma [128] TGM3 Esophageal cancer [129] UBE2E3 Retinal pigment epithelial (RPE) [130] Vigilin Hepatocellular carcinomas [131] WNK4 Kidney [100] C1QBP Prostate cancer [48] COMMD1 Neuroblastoma [132] EVADING GROWTH FLNA Pulmonary neuroendocrine tumors [133] SUPPRESSORS/ CELL CYCLE NOP53 Lung cancer A549 and H1299 cell lines [107] CONTROL RSF1 Nasopharyngeal carcinoma [127] SPIN1 Glioma [128] Vigilin Liver carcinoma HepG2 cells [134] FLNA bladder carcinoma [117] RESISTING CELL DEATH GOLM1 Prostate cancer [82] APOTOSIS /PHAGOCITOSIS Hox-A10 Epithelial ovarian cancer cell lines [122] IMBALANCE (continued) MAP1B Melanoma and colon carcinoma cell lines [135] MAPKAPK5 Hepatocellular carcinoma [136] Cancers 2019, 11, x; doi: www.mdpi.com/journal/cancers Cancers 2019, 11, x 2 of 15 MNAT1 Colorectal cancer [73] MT2A Colorectal cancer [137] PSMA7 Cervical cancer [124] PSMA7 Colorectal cancer [138] RSF1 Nasopharyngeal carcinoma [127] SPIN1 Glioma [128] SRSF3 oral squamous cell carcinoma [139] Protein Model Reference [140] Human colon adenocarcinoma and SRSF3 Human osteosarcoma cell lines SRSF3 Ovarian cancer [141] TGM3 Esophageal cancer [129] Ba/F3 cells U2AF1 [80,142] Lung adenocarcinoma cell lines YY1 Several models [143] C1QBP Breast cancer metastasis in mouse model [144] COMMD1 Mouse melanoma cells [145] Human melanoma (A7), prostate cancer FLNA [117] (PC3) cell lines GOLM1 Hepatocellular carcinoma [118] GOLM1 Breast cancer [119] GOLM1 Cervical cancer [146] GOLM1 Prostate cancer [82] Hox-A10 Ovarian cancer cell line ES-2 [121] MAPKAPK5 Hela Cells [86] MIEN1 Breast cancer [147] ACTIVATING INVASION AND MIEN1 Prostate cancer [148] METASTASIS NOP53 Endometrial cancer [149] RASAL2 Colorectal cancer [150] RASAL2 hepatocellular carcinoma [126] RASAL2 Lung cancer [151] RSF1 Prostate cancer [95] RSF1 Non-small cell lung cancer [152] SRSF3 HeLa cells [153] TGM3 Esophageal cancer [129] UHRF2 Gastric cancer cell lines [154] Vigilin Hepatocellular carcinomas [131] YY1 Cancer cell lines [155] DEREGULATED CELLULAR C1QBP Human embryonic kidney HEK293T cells [69] ENERGETICS / DLAT Gastric cancer cell lines [116] CARBOHYDRATE METABOLISM SRSF3 Colon cancer cells [156] REPROGRAMMING 2 Cancers 2019, 11, x 3 of 15 Table S2. Prostate cancer studies available through cBioportal. DNA Survival cBioportal Name References Samples Sequenced Cna RNA Seq Arrays Studies Metastatic prostate adenocarcinoma [40] 61 61 61 (mctp, nature 2012) Metastatic prostate adenocarcinoma [41] 444 444 444 Yes (su2c/pcf dream team, pnas 2019) Metastatic prostate cancer (su2c/pcf [42] 150 150 150 118 dream team, cell 2015) Neuroendocrine prostate cancer [43] 114 114 114 49 (multi-institute, nat med 2016) Prostate adenocarcinoma [29] 57 57 56 (broad/cornell, cell 2013) Prostate adenocarcinoma [30] 112 112 109 (broad/cornell, nat genet 2012) Prostate adenocarcinoma (cpc-gene, [31] 477 477 0 nature 2017) Prostate adenocarcinoma (eururol, [32] 65 65 65 2017) Prostate adenocarcinoma (fred [33] 176 141 149 hutchinson crc, nat med 2016) Prostate adenocarcinoma (mskcc, [34] 216 103 194 150 Yes cancer cell 2010) Prostate adenocarcinoma [35] 1013 1013 1013 (mskcc/dfci, nature genetics 2018) Prostate adenocarcinoma (tcga, cell [157] 333 333 333 290 2015) Prostate adenocarcinoma (tcga, [36] 494 494 489 493 pancancer atlas) Prostate adenocarcinoma (tcga, 499 499 492 498 Yes provisional) Prostate adenocarcinoma cna study [37] 104 0 104 Yes (mskcc, pnas 2014) Prostate adenocarcinoma organoids [38] 12 12 0 10 (mskcc, cell 2014) Prostate cancer (mskcc, jco precis [39] 504 504 504 oncol 2017) The metastatic prostate cancer 19 19 19 project (provisional, december 2018) 3 Cancers 2019, 11, x 4 of 15 Table S3. qPCR primer list. Hybridization Amplicon Gene Name Sequence TM (°C) * Site ** Size (bp) AGER F: 5′-TGTGTGGCCACCCATTCC-3′ 60.47 901–918 109 (RAGE) R: 5′-CTGATCCTCCCACAGAGCC-3′ 59.75 991–1009 F: 5′-AACAGCGTGACTACAGGGTATG-3′ 60.68 795–816 DLAT 101 R: 5′-CCCAAAAGCTGCAGCAGTAAG-3′ 60.64 875–895 F: 5′-ACAGTGTCAATCGGAGGTCAC-3′ 60.58 4942–4961 FLNA 118 R: 5′-TGCACGTCACTTTGCCTTTG-3′ 60.47 5040–5059 F: 5′-GGGATAGCCTCTCTTACTACCAC-3′ 59.77 71–93 CFOS 124 R: 5′-GTGACCGTGGGAATGAAGTTG-3′ 60.04 174–194 F: 5′-CCTCCTGCACCACCAACTG-3′ 61.18 449–467 GAPDH 102 R: 5′-TGGCAGTGATGGCATGGA-3′ 59.50 533–550 F: 5′-TCAAAGGAGAACATCCTGGCC-3′ 60.59 338–358 HMGB1 87 R: 5′- GCTTGTCATCTGCAGCAGTGTT-3′ 62.54 403–424 F: 5′-GAGCAGTCAGCCAAAGATAAACAA-3′ 60.37 403–426 HMGB2 111 R: 5′-TCCTGCTTCACTTTTGCCCTT-3′ 61.01 493–513 F: 5′-CTCCCACACTCGCCATCTC-3′ 60.43 1341–1359 HOXA10 187 R: 5′-CAAACCCAGCCCAGTCAGG-3′ 61.19 1509–1527 F: 5′-ACCCTGGCAGGTGCTTG-3′ 60.08 108–124 KLK3 (PSA) 116 R: 5′-GCAAGATCACGCTTTTGTTCCT-3′ 60.61 202–223 F: 5′-TGAATGATGAGATCAACTTCCTCAG-3′ 59.25 653–677 KRT7 75 R: 5′-TGTCGGAGATCTGGGACTGC-3′ 61.91 708–727 F: 5′-ACATCTTGGAACCTCCCACATC-3′ 60.62 731–752 MAP1B 98 R: 5′-TGCAAACAAGGCAGAATCGC-3′ 60.61 809–828 F: 5′-TTGGGGGCAGGAGAGAGAC-3′ 61.21 519–537 MIEN1 107 R: 5′-TTACCGAGGCGAAGAGTGG-3′ 59.68 607–625 F: 5′-TGTGCGGACACACTCTCTGTGAAA-3′ 65.09 74–97 MNAT1 145 R: 5′-TCAACCTCCTTGTCAACAGTGGGA-3′ 64.37 195–218 F: 5′-AAAGGGGCGTCGGACAAG-3′ 60.54 223–240 MT2A 118 R: 5′- GGTCACGGTCAGGGTTGTAC-3′ 60.90 321–340 F: 5′-ACCAGTTCCTGGAAGACGTG-3′ 60.19 182–201 NOP53 109 R: 5′-CCTTTTTCCTTGGAGCCAG-3′ 56.66 272–290 F: 5′-AAGAGGAGTGAGAGGAAGGC-3′ 59.02 929–948 PMEPA1 110 R: 5′-GCTTGTGCATTCAGACCAGA-3′ 59.05 1019–1038 F: 5′-TGACAACCTAGCCACAGAACTG-3′ 60.81 174–195 SNAPIN 97 R: 5′-TCGCCGGGCATTAAGTAGC-3′ 60.80 252–270 F: 5′-AAGGTTACTTTCCGCACCAG-3′ 58.69 376–395 UBE2E3 102 R: 5′-AATAGTCAAAGCGGGACTCCA-3′ 59.69 457–477 F: 5′-GGACCTTCCAATCAGCCATC-3′ 58.90 316–335 UHRF2 99 R: 5′-GACATCTCTGGCATCCACCA-3′ 60.04 395–414 F: 5′-AGCGGCAAGAAGAGTTACCTC-3′ 60.65 538–558 YY1 103 R: 5′-TCTTGATCTGCACCTGCTTCTG-3′ 61.20 619–640 F: 5′-CCCGAGCATTCCTCTGATTC-3′ 58.70 79–98 ZNF428 95 R: 5′-TCGTCAGTGGTCTCCTCTTC-3′ 59.04 154–173 4 Cancers 2019, 11, x 5 of 15 * Tms were calculated using MFEprimer3.0 (http://mfeprimer.igenetech.com/) ** Hybridization sites are referenced to the starting codon (cDNA) for each gene (Ensembl database). Figure S1. Re-screening of Y2H candidates and triple selection for positive growth in media without histidine, adenine or reporting alfa-galactosidase activity. Single colonies which were positive in the first screening as described in Materials and Methods were re-plated on selective media. CL, candidates from PC-3 libraries; TJ, candidates from PCa tissue libraries. Control represent cells transformed with the corresponding bait plasmid and an empty prey-plasmid. Upper panel: a, DLAT; b, DANNAF; c, HDLBP; d, HOXA10; e, KRT7; f, UBE2E3; g, UHRF2; h, ZNF428. Middle panel: a, FOS; b, GOLM1; c, HNRHPU; d, MAP1B; e, MAPKAPK5; f, MIEN1; g, MT2A; h, PSMA7; i, PTPN2; j, RASAL2; k, RSF1; l, SRSF3; m, TAF3; n, TGM3; o, UBC; p, WINK4; q, YY1; r, ZNF48. Lower panel: a, C1QBP; b, SNAPIN; c, UHRF2; d, ZNF428; e, C1QBP; f, COMMD1; g, FLNA; h, MIEN1; i, NOP53; j, RSP28. 5 Cancers 2019, 11, x 6 of 15 Image S1. Whole Blots accompanying Figure 2A 0.276± Cytokeratin-7 co- 0.3 0.016 inmunopercipitation 0.25 0.2 0.15 0.1 0.047±0.004 0.05 bandsarbitrary in units 0 Densitometric Densitometric analisis immunoof IP-HMGB1 IP-IgG n=3 6 Cancers 2019, 11, x 7 of 15 Image S2. Whole Blots accompanying Figure 6. 7 Cancers 2019, 11, x 8 of 15 References 1. Catena, R.; Escoffier, E.; Caron, C.; Khochbin, S.; Martianov, I.; Davidson, I. HMGB4, a Novel Member of the HMGB Family, is Preferentially Expressed in the Mouse Testis and Localizes to the Basal Pole of Elongating Spermatids. Biol. Reprod. 2009, 80, 358–366. 2. Pusterla, T.; de Marchis, F.; Palumbo, R.; Bianchi, M.E. High Mobility Group B2 is Secreted by Myeloid Cells and has Mitogenic and Chemoattractant Activities Similar to High Mobility Group B1. Autoimmunity 2009, 42, 308–310. 3. Ugrinova, I.; Pashev, I.G.; Pasheva, E.A. Nucleosome Binding Properties and Co-Remodeling Activities of Native and in Vivo Acetylated HMGB-1 and HMGB-2 Proteins. Biochemistry 2009, 48, 6502–6507. 4. Swanson, P.C. Fine Structure and Activity of Discrete RAG-HMG Complexes on V(D)J Recombination Signals. Mol. Cell. Biol. 2002, 22, 1340–1351. 5. Bagherpoor, A.J.; Dolezalova, D.; Barta, T.; Kucirek, M.; Sani, S.A.; Esner, M.; Kunova Bosakova, M.; Vinarsky, V.; Peskova, L.; Hampl, A.; et al. Properties of Human Embryonic Stem Cells and their Differentiated Derivatives Depend on Nonhistone DNA-Binding HMGB1 and HMGB2 Proteins. Stem Cells Dev. 2017, 26, 328–340. 6. Ke, S.; Zhou, F.; Yang, H.; Wei, Y.; Gong, J.; Mei, Z.; Wu, L.; Yu, H.; Zhou, Y.
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