Single-cell RNA-seq reveals the transcriptional program underlying tumor progression and metastasis in neuroblastoma
Zhe Nian1, Dan Wang1, Hao Wang1, Wenxu Liu1, Zhenyi Ma2, Jie Yan3, Yanna Cao3, Jie Li3, Qiang Zhao3(), Zhe Liu1,2,4()
1. Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China 2. Zhejiang Key Laboratory of Medical Epigenetics, Department of Cell Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou 311121, China 3. Department of Pediatric Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin 300060, China 4. Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
Neuroblastoma (NB) is one of the most common childhood malignancies. Sixty percent of patients present with widely disseminated clinical signs at diagnosis and exhibit poor outcomes. However, the molecular mechanisms triggering NB metastasis remain largely uncharacterized. In this study, we generated a transcriptomic atlas of 15 447 NB cells from eight NB samples, including paired samples of primary tumors and bone marrow metastases. We used time-resolved analysis to chart the evolutionary trajectory of NB cells from the primary tumor to the metastases in the same patient and identified a common ‘starter’ subpopulation that initiates tumor development and metastasis. The ‘starter’ population exhibited high expression levels of multiple cell cycle-related genes, indicating the important role of cell cycle upregulation in NB tumor progression. In addition, our evolutionary trajectory analysis demonstrated the involvement of partial epithelial-to-mesenchymal transition (p-EMT) along the metastatic route from the primary site to the bone marrow. Our study provides insights into the program driving NB metastasis and presents a signature of metastasis-initiating cells as an independent prognostic indicator and potential therapeutic target to inhibit the initiation of NB metastasis.
A Zafar, W Wang, G Liu, X Wang, W Xian, F McKeon, J Foster, J Zhou, R Zhang. Molecular targeting therapies for neuroblastoma: progress and challenges. Med Res Rev 2021; 41(2): 961–1021 https://doi.org/10.1002/med.21750
GM Brodeur, R Iyer, JL Croucher, T Zhuang, M Higashi, V Kolla. Therapeutic targets for neuroblastomas. Expert Opin Ther Targets 2014; 18(3): 277–292 https://doi.org/10.1517/14728222.2014.867946
4
S Ackermann, M Cartolano, B Hero, A Welte, Y Kahlert, A Roderwieser, C Bartenhagen, E Walter, J Gecht, L Kerschke, R Volland, R Menon, JM Heuckmann, M Gartlgruber, S Hartlieb, KO Henrich, K Okonechnikov, J Altmüller, P Nürnberg, S Lefever, Wilde B de, F Sand, F Ikram, C Rosswog, J Fischer, J Theissen, F Hertwig, AD Singhi, T Simon, W Vogel, S Perner, B Krug, M Schmidt, S Rahmann, V Achter, U Lang, C Vokuhl, M Ortmann, R Büttner, A Eggert, F Speleman, RJ O’Sullivan, RK Thomas, F Berthold, J Vandesompele, A Schramm, F Westermann, JH Schulte, M Peifer, M Fischer. A mechanistic classification of clinical phenotypes in neuroblastoma. Science 2018; 362(6419): 1165–1170 https://doi.org/10.1126/science.aat6768
5
IV Kholodenko, DV Kalinovsky, II Doronin, SM Deyev, RV Kholodenko. Neuroblastoma origin and therapeutic targets for immunotherapy. J Immunol Res 2018; 2018: 7394268 https://doi.org/10.1155/2018/7394268
6
KK Matthay, JM Maris, G Schleiermacher, A Nakagawara, CL Mackall, L Diller, WA Weiss. Neuroblastoma. Nat Rev Dis Primers 2016; 2(1): 16078 https://doi.org/10.1038/nrdp.2016.78
7
T Teitz, M Inoue, MB Valentine, K Zhu, JE Rehg, W Zhao, D Finkelstein, YD Wang, MD Johnson, C Calabrese, M Rubinstein, R Hakem, WA Weiss, JM Lahti. Th-MYCN mice with caspase-8 deficiency develop advanced neuroblastoma with bone marrow metastasis. Cancer Res 2013; 73(13): 4086–4097 https://doi.org/10.1158/0008-5472.CAN-12-2681
S Zhu, X Zhang, N Weichert-Leahey, Z Dong, C Zhang, G Lopez, T Tao, S He, AC Wood, D Oldridge, CY Ung, JH van Ree, A Khan, BM Salazar, E Lummertz da Rocha, MW Zimmerman, F Guo, H Cao, X Hou, SJ Weroha, AR Perez-Atayde, DS Neuberg, A Meves, MA McNiven, JM van Deursen, H Li, JM Maris, AT Look. LMO1 synergizes with MYCN to promote neuroblastoma initiation and metastasis. Cancer Cell 2017; 32(3): 310–323.e5 https://doi.org/10.1016/j.ccell.2017.08.002
10
J Massagué, AC Obenauf. Metastatic colonization by circulating tumour cells. Nature 2016; 529(7586): 298–306 https://doi.org/10.1038/nature17038
11
J Peng, BF Sun, CY Chen, JY Zhou, YS Chen, H Chen, L Liu, D Huang, J Jiang, GS Cui, Y Yang, W Wang, D Guo, M Dai, J Guo, T Zhang, Q Liao, Y Liu, YL Zhao, DL Han, Y Zhao, YG Yang, W Wu. Single-cell RNA-seq highlights intra-tumoral heterogeneity and malignant progression in pancreatic ductal adenocarcinoma. Cell Res 2019; 29(9): 725–738 https://doi.org/10.1038/s41422-019-0195-y
12
SV Puram, I Tirosh, AS Parikh, AP Patel, K Yizhak, S Gillespie, C Rodman, CL Luo, EA Mroz, KS Emerick, DG Deschler, MA Varvares, R Mylvaganam, O Rozenblatt-Rosen, JW Rocco, WC Faquin, DT Lin, A Regev, BE Bernstein. Single-cell transcriptomic analysis of primary and metastatic tumor ecosystems in head and neck cancer. Cell 2017; 171(7): 1611–1624.e24 https://doi.org/10.1016/j.cell.2017.10.044
13
T Kan, S Zhang, S Zhou, Y Zhang, Y Zhao, Y Gao, T Zhang, F Gao, X Wang, L Zhao, M Yang. Single-cell RNA-seq recognized the initiator of epithelial ovarian cancer recurrence. Oncogene 2022; 41(6): 895–906 https://doi.org/10.1038/s41388-021-02139-z
14
R Dong, R Yang, Y Zhan, HD Lai, CJ Ye, XY Yao, WQ Luo, XM Cheng, JJ Miao, JF Wang, BH Liu, XQ Liu, LL Xie, Y Li, M Zhang, L Chen, WC Song, W Qian, WQ Gao, YH Tang, CY Shen, W Jiang, G Chen, W Yao, KR Dong, XM Xiao, S Zheng, K Li, J Wang. Single-cell characterization of malignant phenotypes and developmental trajectories of adrenal neuroblastoma. Cancer Cell 2020; 38(5): 716–733.e6 https://doi.org/10.1016/j.ccell.2020.08.014
15
S Jansky, AK Sharma, V Körber, A Quintero, UH Toprak, EM Wecht, M Gartlgruber, A Greco, E Chomsky, TGP Grünewald, KO Henrich, A Tanay, C Herrmann, T Höfer, F Westermann. Single-cell transcriptomic analyses provide insights into the developmental origins of neuroblastoma. Nat Genet 2021; 53(5): 683–693 https://doi.org/10.1038/s41588-021-00806-1
16
G Kildisiute, WM Kholosy, MD Young, K Roberts, R Elmentaite, SR van Hooff, CN Pacyna, E Khabirova, A Piapi, C Thevanesan, E Bugallo-Blanco, C Burke, L Mamanova, KM Keller, KPS Langenberg-Ververgaert, P Lijnzaad, T Margaritis, FCP Holstege, ML Tas, M Wijnen, MM van Noesel, I Del Valle, G Barone, R van der Linden, C Duncan, J Anderson, JC Achermann, M Haniffa, SA Teichmann, D Rampling, NJ Sebire, X He, RR de Krijger, RA Barker, KB Meyer, O Bayraktar, K Straathof, JJ Molenaar, S Behjati. Tumor to normal single-cell mRNA comparisons reveal a pan-neuroblastoma cancer cell. Sci Adv 2021; 7(6): eabd3311 https://doi.org/10.1126/sciadv.abd3311
17
ES Hanemaaijer, T Margaritis, K Sanders, FL Bos, T Candelli, H Al-Saati, MM van Noesel, FAG Meyer-Wentrup, M van de Wetering, FCP Holstege, H Clevers. Single-cell atlas of developing murine adrenal gland reveals relation of Schwann cell precursor signature to neuroblastoma phenotype. Proc Natl Acad Sci USA 2021; 118(5): e2022350118 https://doi.org/10.1073/pnas.2022350118
18
OC Bedoya-Reina, W Li, M Arceo, M Plescher, P Bullova, H Pui, M Kaucka, P Kharchenko, T Martinsson, J Holmberg, I Adameyko, Q Deng, C Larsson, CC Juhlin, P Kogner, S Schlisio. Single-nuclei transcriptomes from human adrenal gland reveal distinct cellular identities of low and high-risk neuroblastoma tumors. Nat Commun 2021; 12(1): 5309 https://doi.org/10.1038/s41467-021-24870-7
19
P Kameneva, AV Artemov, ME Kastriti, L Faure, TK Olsen, J Otte, A Erickson, B Semsch, ER Andersson, M Ratz, J Frisén, AS Tischler, Krijger RR de, T Bouderlique, N Akkuratova, M Vorontsova, O Gusev, K Fried, E Sundström, S Mei, P Kogner, N Baryawno, PV Kharchenko, I Adameyko. Single-cell transcriptomics of human embryos identifies multiple sympathoblast lineages with potential implications for neuroblastoma origin. Nat Genet 2021; 53(5): 694–706 https://doi.org/10.1038/s41588-021-00818-x
20
X Yuan, JA Seneviratne, S Du, Y Xu, Y Chen, Q Jin, X Jin, A Balachandran, S Huang, Y Xu, Y Zhai, L Lu, M Tang, Y Dong, BB Cheung, GM Marshall, W Shi, DR Carter, C Zhang. Single-cell profiling of peripheral neuroblastic tumors identifies an aggressive transitional state that bridges an adrenergic-mesenchymal trajectory. Cell Rep 2022; 41(1): 111455 https://doi.org/10.1016/j.celrep.2022.111455
21
IS Fetahu, W Esser-Skala, R Dnyansagar, S Sindelar, F Rifatbegovic, A Bileck, L Skos, E Bozsaky, D Lazic, L Shaw, M Tötzl, D Tarlungeanu, M Bernkopf, M Rados, W Weninger, EM Tomazou, C Bock, C Gerner, R Ladenstein, M Farlik, N Fortelny, S Taschner-Mandl. Single-cell transcriptomics and epigenomics unravel the role of monocytes in neuroblastoma bone marrow metastasis. Nat Commun 2023; 14(1): 3620 https://doi.org/10.1038/s41467-023-39210-0
22
CS McGinnis, LM Murrow, ZJ Gartner. DoubletFinder: doublet detection in single-cell RNA sequencing data using artificial nearest neighbors. Cell Syst 2019; 8(4): 329–337.e4 https://doi.org/10.1016/j.cels.2019.03.003
23
I Korsunsky, N Millard, J Fan, K Slowikowski, F Zhang, K Wei, Y Baglaenko, M Brenner, PR Loh, S Raychaudhuri. Fast, sensitive and accurate integration of single-cell data with Harmony. Nat Methods 2019; 16(12): 1289–1296 https://doi.org/10.1038/s41592-019-0619-0
24
I Tirosh, AS Venteicher, C Hebert, LE Escalante, AP Patel, K Yizhak, JM Fisher, C Rodman, C Mount, MG Filbin, C Neftel, N Desai, J Nyman, B Izar, CC Luo, JM Francis, AA Patel, ML Onozato, N Riggi, KJ Livak, D Gennert, R Satija, BV Nahed, WT Curry, RL Martuza, R Mylvaganam, AJ Iafrate, MP Frosch, TR Golub, MN Rivera, G Getz, O Rozenblatt-Rosen, DP Cahill, M Monje, BE Bernstein, DN Louis, A Regev, ML Suvà. Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma. Nature 2016; 539(7628): 309–313 https://doi.org/10.1038/nature20123
FJ Sedlazeck, P Rescheneder, M Smolka, H Fang, M Nattestad, A von Haeseler, MC Schatz. Accurate detection of complex structural variations using single-molecule sequencing. Nat Methods 2018; 15(6): 461–468 https://doi.org/10.1038/s41592-018-0001-7
27
D Aran, AP Looney, L Liu, E Wu, V Fong, A Hsu, S Chak, RP Naikawadi, PJ Wolters, AR Abate, AJ Butte, M Bhattacharya. Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage. Nat Immunol 2019; 20(2): 163–172 https://doi.org/10.1038/s41590-018-0276-y
28
Q Zhang, Y He, N Luo, SJ Patel, Y Han, R Gao, M Modak, S Carotta, C Haslinger, D Kind, GW Peet, G Zhong, S Lu, W Zhu, Y Mao, M Xiao, M Bergmann, X Hu, SP Kerkar, AB Vogt, S Pflanz, K Liu, J Peng, X Ren, Z Zhang. Landscape and dynamics of single immune cells in hepatocellular carcinoma. Cell 2019; 179(4): 829–845.e20 https://doi.org/10.1016/j.cell.2019.10.003
29
C Trapnell, D Cacchiarelli, J Grimsby, P Pokharel, S Li, M Morse, NJ Lennon, KJ Livak, TS Mikkelsen, JL Rinn. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat Biotechnol 2014; 32(4): 381–386 https://doi.org/10.1038/nbt.2859
30
K Street, D Risso, RB Fletcher, D Das, J Ngai, N Yosef, E Purdom, S Dudoit. Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics. BMC Genomics 2018; 19(1): 477 https://doi.org/10.1186/s12864-018-4772-0
31
L Garcia-Alonso, CH Holland, MM Ibrahim, D Turei, J Saez-Rodriguez. Benchmark and integration of resources for the estimation of human transcription factor activities. Genome Res 2019; 29(8): 1363–1375 https://doi.org/10.1101/gr.240663.118
32
MJ Alvarez, Y Shen, FM Giorgi, A Lachmann, BB Ding, BH Ye, A Califano. Functional characterization of somatic mutations in cancer using network-based inference of protein activity. Nat Genet 2016; 48(8): 838–847 https://doi.org/10.1038/ng.3593
33
CH Holland, J Tanevski, J Perales-Patón, J Gleixner, MP Kumar, E Mereu, BA Joughin, O Stegle, DA Lauffenburger, H Heyn, B Szalai, J Saez-Rodriguez. Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data. Genome Biol 2020; 21(1): 36 https://doi.org/10.1186/s13059-020-1949-z
34
BM Verhoeven, S Mei, TK Olsen, K Gustafsson, A Valind, A Lindström, D Gisselsson, SS Fard, C Hagerling, PV Kharchenko, P Kogner, JI Johnsen, N Baryawno. The immune cell atlas of human neuroblastoma. Cell Rep Med 2022; 3(6): 100657 https://doi.org/10.1016/j.xcrm.2022.100657
35
S Jin, CF Guerrero-Juarez, L Zhang, I Chang, R Ramos, CH Kuan, P Myung, MV Plikus, Q Nie. Inference and analysis of cell-cell communication using CellChat. Nat Commun 2021; 12(1): 1088 https://doi.org/10.1038/s41467-021-21246-9
36
J Zhang, M Guan, Q Wang, J Zhang, T Zhou, X Sun. Single-cell transcriptome-based multilayer network biomarker for predicting prognosis and therapeutic response of gliomas. Brief Bioinform 2020; 21(3): 1080–1097 https://doi.org/10.1093/bib/bbz040
37
AP Patel, I Tirosh, JJ Trombetta, AK Shalek, SM Gillespie, H Wakimoto, DP Cahill, BV Nahed, WT Curry, RL Martuza, DN Louis, O Rozenblatt-Rosen, ML Suvà, A Regev, BE Bernstein. Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma. Science 2014; 344(6190): 1396–1401 https://doi.org/10.1126/science.1254257
38
GM Brodeur. Neuroblastoma: biological insights into a clinical enigma. Nat Rev Cancer 2003; 3(3): 203–216 https://doi.org/10.1038/nrc1014
39
XW Pan, H Zhang, D Xu, JX Chen, WJ Chen, SS Gan, FJ Qu, CM Chu, JW Cao, YH Fan, X Song, JQ Ye, W Zhou, XG Cui. Identification of a novel cancer stem cell subpopulation that promotes progression of human fatal renal cell carcinoma by single-cell RNA-seq analysis. Int J Biol Sci 2020; 16(16): 3149–3162 https://doi.org/10.7150/ijbs.46645
40
Manno G La, R Soldatov, A Zeisel, E Braun, H Hochgerner, V Petukhov, K Lidschreiber, ME Kastriti, P Lönnerberg, A Furlan, J Fan, LE Borm, Z Liu, Bruggen D van, J Guo, X He, R Barker, E Sundström, G Castelo-Branco, P Cramer, I Adameyko, S Linnarsson, PV Kharchenko. RNA velocity of single cells. Nature 2018; 560(7719): 494–498 https://doi.org/10.1038/s41586-018-0414-6
41
B Spanjaard, B Hu, N Mitic, P Olivares-Chauvet, S Janjuha, N Ninov, JP Junker. Simultaneous lineage tracing and cell-type identification using CRISPR-Cas9-induced genetic scars. Nat Biotechnol 2018; 36(5): 469–473 https://doi.org/10.1038/nbt.4124
H Lee-Six, NF Øbro, MS Shepherd, S Grossmann, K Dawson, M Belmonte, RJ Osborne, BJP Huntly, I Martincorena, E Anderson, L O’Neill, MR Stratton, E Laurenti, AR Green, DG Kent, PJ Campbell. Population dynamics of normal human blood inferred from somatic mutations. Nature 2018; 561(7724): 473–478 https://doi.org/10.1038/s41586-018-0497-0
44
TE Miller, CA Lareau, JA Verga, EAK DePasquale, V Liu, D Ssozi, K Sandor, Y Yin, LS Ludwig, CA El Farran, DM Morgan, AT Satpathy, GK Griffin, AA Lane, JC Love, BE Bernstein, VG Sankaran, P van Galen. Mitochondrial variant enrichment from high-throughput single-cell RNA sequencing resolves clonal populations. Nat Biotechnol 2022; 40(7): 1030–1034 https://doi.org/10.1038/s41587-022-01210-8
45
B Nguyen, C Fong, A Luthra, SA Smith, RG DiNatale, S Nandakumar, H Walch, WK Chatila, R Madupuri, R Kundra, CM Bielski, B Mastrogiacomo, MTA Donoghue, A Boire, S Chandarlapaty, K Ganesh, JJ Harding, CA Iacobuzio-Donahue, P Razavi, E Reznik, CM Rudin, D Zamarin, W Abida, GK Abou-Alfa, C Aghajanian, A Cercek, P Chi, D Feldman, AL Ho, G Iyer, YY Janjigian, M Morris, RJ Motzer, EM O’Reilly, MA Postow, NP Raj, GJ Riely, ME Robson, JE Rosenberg, A Safonov, AN Shoushtari, W Tap, MY Teo, AM Varghese, M Voss, R Yaeger, MG Zauderer, N Abu-Rustum, J Garcia-Aguilar, B Bochner, A Hakimi, WR Jarnagin, DR Jones, D Molena, L Morris, E Rios-Doria, P Russo, S Singer, VE Strong, D Chakravarty, LH Ellenson, A Gopalan, JS Reis-Filho, B Weigelt, M Ladanyi, M Gonen, SP Shah, J Massague, J Gao, A Zehir, MF Berger, DB Solit, SF Bakhoum, F Sanchez-Vega, N Schultz. Genomic characterization of metastatic patterns from prospective clinical sequencing of 25,000 patients. Cell 2022; 185(3): 563–575.e11 https://doi.org/10.1016/j.cell.2022.01.003
K Lundgren, B Nordenskjöld, G Landberg. Hypoxia, Snail and incomplete epithelial-mesenchymal transition in breast cancer. Br J Cancer 2009; 101(10): 1769–1781 https://doi.org/10.1038/sj.bjc.6605369
M Li, C Sun, X Bu, Y Que, L Zhang, Y Zhang, L Zhang, S Lu, J Huang, J Zhu, J Wang, F Sun, Y Zhang. ISL1 promoted tumorigenesis and EMT via Aurora kinase A-induced activation of PI3K/AKT signaling pathway in neuroblastoma. Cell Death Dis 2021; 12(6): 620 https://doi.org/10.1038/s41419-021-03894-3
50
T Ferronha, MA Rabadán, E Gil-Guiñon, Dréau G Le, Torres C de, E Martí. LMO4 is an essential cofactor in the Snail2-mediated epithelial-to-mesenchymal transition of neuroblastoma and neural crest cells. J Neurosci 2013; 33(7): 2773–2783 https://doi.org/10.1523/JNEUROSCI.4511-12.2013
51
P Missios, EL da Rocha, DS Pearson, J Philipp, MM Aleman, M Pirouz, D Farache, JW Franses, C Kubaczka, KM Tsanov, DK Jha, B Pepe-Mooney, JT Powers, RI Gregory, AS Lee, D Dominguez, DT Ting, GQ Daley. LIN28B alters ribosomal dynamics to promote metastasis in MYCN-driven malignancy. J Clin Invest 2021; 131(22): e145142 https://doi.org/10.1172/JCI145142
52
CY Tan, CL Chang. NDPKA is not just a metastasis suppressor—be aware of its metastasis-promoting role in neuroblastoma. Lab Invest 2018; 98(2): 219–227 https://doi.org/10.1038/labinvest.2017.105
53
SK Das, S Maji, SL Wechman, P Bhoopathi, AK Pradhan, S Talukdar, D Sarkar, J Landry, C Guo, XY Wang, WK Cavenee, L Emdad, PB Fisher. MDA-9/Syntenin (SDCBP): novel gene and therapeutic target for cancer metastasis. Pharmacol Res 2020; 155: 104695 https://doi.org/10.1016/j.phrs.2020.104695
CJ Barger, C Branick, L Chee, AR Karpf. Pan-cancer analyses reveal genomic features of FOXM1 overexpression in cancer. Cancers (Basel) 2019; 11(2): 251 https://doi.org/10.3390/cancers11020251
56
J Musa, MM Aynaud, O Mirabeau, O Delattre, TG Grünewald. MYBL2 (B-Myb): a central regulator of cell proliferation, cell survival and differentiation involved in tumorigenesis. Cell Death Dis 2017; 8(6): e2895 https://doi.org/10.1038/cddis.2017.244
LR Bandara, EW Lam, TS Sørensen, M Zamanian, R Girling, Thangue NB La. DP-1: a cell cycle-regulated and phosphorylated component of transcription factor DRTF1/E2F which is functionally important for recognition by pRb and the adenovirus E4 orf 6/7 protein. EMBO J 1994; 13(13): 3104–3114 https://doi.org/10.1002/j.1460-2075.1994.tb06609.x
59
E Fang, X Wang, F Yang, A Hu, J Wang, D Li, H Song, M Hong, Y Guo, Y Liu, H Li, K Huang, L Zheng, Q Tong. Therapeutic targeting of MZF1–AS1/PARP1/E2F1 axis inhibits proline synthesis and neuroblastoma progression. Adv Sci (Weinh) 2019; 6(19): 1900581 https://doi.org/10.1002/advs.201900581
60
Z Wang, HJ Park, JR Carr, YJ Chen, Y Zheng, J Li, AL Tyner, RH Costa, S Bagchi, P Raychaudhuri. FoxM1 in tumorigenicity of the neuroblastoma cells and renewal of the neural progenitors. Cancer Res 2011; 71(12): 4292–4302 https://doi.org/10.1158/0008-5472.CAN-10-4087
61
G Raschellà, V Cesi, R Amendola, A Negroni, B Tanno, P Altavista, GP Tonini, Bernardi B De, B Calabretta. Expression of B-myb in neuroblastoma tumors is a poor prognostic factor independent from MYCN amplification. Cancer Res 1999; 59(14): 3365–3368
62
J Xu, S Lamouille, R Derynck. TGF-beta-induced epithelial to mesenchymal transition. Cell Res 2009; 19(2): 156–172 https://doi.org/10.1038/cr.2009.5
R Derynck, SJ Turley, RJ Akhurst. TGFβ biology in cancer progression and immunotherapy. Nat Rev Clin Oncol 2021; 18(1): 9–34 https://doi.org/10.1038/s41571-020-0403-1
65
J Cheng, J Zhang, Z Wu, X Sun. Inferring microenvironmental regulation of gene expression from single-cell RNA sequencing data using scMLnet with an application to COVID-19. Brief Bioinform 2021; 22(2): 988–1005 https://doi.org/10.1093/bib/bbaa327
66
J Luo, M Deng, X Zhang, X Sun. ESICCC as a systematic computational framework for evaluation, selection, and integration of cell-cell communication inference methods. Genome Res 2023; 33(10): 1788–1805 https://doi.org/10.1101/gr.278001.123
67
X HeX Sun Y Shao. Multicellular network-informed survival model for identification of drug targets of gliomas. IEEE J Biomed Health Inform 2023; [Epub ahead of print] doi: 10.1109/JBHI.2023.3309825
GM Brodeur, J Pritchard, F Berthold, NL Carlsen, V Castel, RP Castelberry, B De Bernardi, AE Evans, M Favrot, F Hedborg. Revisions of the international criteria for neuroblastoma diagnosis, staging, and response to treatment. J Clin Oncol 1993; 11(8): 1466–1477 https://doi.org/10.1200/JCO.1993.11.8.1466
70
WB London, RP Castleberry, KK Matthay, AT Look, RC Seeger, H Shimada, P Thorner, G Brodeur, JM Maris, CP Reynolds, SL Cohn. Evidence for an age cutoff greater than 365 days for neuroblastoma risk group stratification in the Children’s Oncology Group. J Clin Oncol 2005; 23(27): 6459–6465 https://doi.org/10.1200/JCO.2005.05.571
JP Thiery, H Acloque, RY Huang, MA Nieto. Epithelial-mesenchymal transitions in development and disease. Cell 2009; 139(5): 871–890 https://doi.org/10.1016/j.cell.2009.11.007
73
X Ye, RA Weinberg. Epithelial-mesenchymal plasticity: a central regulator of cancer progression. Trends Cell Biol 2015; 25(11): 675–686 https://doi.org/10.1016/j.tcb.2015.07.012
74
Q Zhang, L Fei, R Han, R Huang, Y Wang, H Chen, B Yao, N Qiao, Z Wang, Z Ma, Z Ye, Y Zhang, W Wang, Y Wang, L Kong, X Shou, X Cao, X Zhou, M Shen, H Cheng, Z Yao, C Zhang, G Guo, Y Zhao. Single-cell transcriptome reveals cellular hierarchies and guides p-EMT-targeted trial in skull base chordoma. Cell Discov 2022; 8(1): 94 https://doi.org/10.1038/s41421-022-00459-2
75
EM Grasset, M Dunworth, G Sharma, M Loth, J Tandurella, A Cimino-Mathews, M Gentz, S Bracht, M Haynes, EJ Fertig, AJ Ewald. Triple-negative breast cancer metastasis involves complex epithelial-mesenchymal transition dynamics and requires vimentin. Sci Transl Med 2022; 14(656): eabn7571 https://doi.org/10.1126/scitranslmed.abn7571
76
I Pastushenko, C Blanpain. EMT transition states during tumor progression and metastasis. Trends Cell Biol 2019; 29(3): 212–226 https://doi.org/10.1016/j.tcb.2018.12.001
77
AM Krebs, J Mitschke, M Lasierra Losada, O Schmalhofer, M Boerries, H Busch, M Boettcher, D Mougiakakos, W Reichardt, P Bronsert, VG Brunton, C Pilarsky, TH Winkler, S Brabletz, MP Stemmler, T Brabletz. The EMT-activator Zeb1 is a key factor for cell plasticity and promotes metastasis in pancreatic cancer. Nat Cell Biol 2017; 19(5): 518–529 https://doi.org/10.1038/ncb3513
78
Y Hao, D Baker, P Ten Dijke. TGF-β-mediated epithelial-mesenchymal transition and cancer metastasis. Int J Mol Sci 2019; 20(11): 2767 https://doi.org/10.3390/ijms20112767
79
Y Zhang, X Zou, W Qian, X Weng, L Zhang, L Zhang, S Wang, X Cao, L Ma, G Wei, Y Wu, Z Hou. Enhanced PAPSS2/VCAN sulfation axis is essential for Snail-mediated breast cancer cell migration and metastasis. Cell Death Differ 2019; 26(3): 565–579 https://doi.org/10.1038/s41418-018-0147-y
80
JL Carstens, S Yang, P Correa de Sampaio, X Zheng, S Barua, KM McAndrews, A Rao, JK Burks, AD Rhim, R Kalluri. Stabilized epithelial phenotype of cancer cells in primary tumors leads to increased colonization of liver metastasis in pancreatic cancer. Cell Rep 2021; 35(2): 108990 https://doi.org/10.1016/j.celrep.2021.108990
81
MV Sepporta, V Praz, Bourloud K Balmas, JM Joseph, N Jauquier, N Riggi, K Nardou-Auderset, A Petit, JY Scoazec, H Sartelet, R Renella, A Mühlethaler-Mottet. TWIST1 expression is associated with high-risk neuroblastoma and promotes primary and metastatic tumor growth. Commun Biol 2022; 5(1): 42 https://doi.org/10.1038/s42003-021-02958-6
