Single Nuclear RNA Sequencing Highlights Intra-Tumoral Heterogeneity and Tumor Microenvironment Complexity in Testicular Embryonic Rhabdomyosarcoma

References

• Gamboa AC, Gronchi A, Cardona K. Soft-tissue sarcoma in adults: an update on the current state of histiotype-specific management in an era of personalized medicine. CA Cancer J Clin. 2020;70(3):200–229. doi:10.3322/caac.21605
   PubMed Web of Science ®Google Scholar
• Kashi VP, Hatley ME, Galindo RL. Probing for a deeper understanding of rhabdomyosarcoma: insights from complementary model systems. Nat Rev Cancer. 2015;15(7):426–439. doi:10.1038/nrc3961
   PubMed Web of Science ®Google Scholar
• Caballero Mora FJ, Munoz Calvo MT, Garcia Ros M, et al. Tumores testiculares y paratesticulares en la infancia y adolescencia. [Testicular and paratesticular tumors during childhood and adolescence]. An Pediatr. 2013;78(1):6–13. doi:10.1016/j.anpedi.2012.05.018
   Google Scholar
• Buckley KS. Pediatric genitourinary tumors. Curr Opin Oncol. 2011;23(3):297–302. doi:10.1097/CCO.0b013e3283458613
   PubMed Web of Science ®Google Scholar
• Ahmed HU, Arya M, Muneer A, Mushtaq I, Sebire NJ. Testicular and paratesticular tumours in the prepubertal population. Lancet Oncol. 2010;11(5):476–483. doi:10.1016/S1470-2045(10)70012-7
   PubMed Web of Science ®Google Scholar
• Stuart T, Satija R. Integrative single-cell analysis. Nat Rev Genet. 2019;20(5):257–272. doi:10.1038/s41576-019-0093-7
   PubMed Web of Science ®Google Scholar
• Kiselev VY, Andrews TS, Hemberg M. Challenges in unsupervised clustering of single-cell RNA-seq data. Nat Rev Genet. 2019;20(5):273–282. doi:10.1038/s41576-018-0088-9
   PubMed Web of Science ®Google Scholar
• Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014;30(7):923–930. doi:10.1093/bioinformatics/btt656
   PubMed Web of Science ®Google Scholar
• Butler A, Hoffman P, Smibert P, Papalexi E, Satija R. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat Biotechnol. 2018;36(5):411–420. doi:10.1038/nbt.4096
   PubMed Web of Science ®Google Scholar
• Meijer RJ, Goeman JJ. Multiple testing of gene sets from gene ontology: possibilities and pitfalls. Brief Bioinform. 2016;17(5):808–818. doi:10.1093/bib/bbv091
   PubMed Web of Science ®Google Scholar
• Yu G, Wang LG, Han Y, He QY. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012;16(5):284–287. doi:10.1089/omi.2011.0118
   PubMed Web of Science ®Google Scholar
• Sabnis AJ, Guerriero CJ, Olivas V, et al. Combined chemical-genetic approach identifies cytosolic HSP70 dependence in rhabdomyosarcoma. Proc Natl Acad Sci U S A. 2016;113(32):9015–9020. doi:10.1073/pnas.1603883113
   PubMed Web of Science ®Google Scholar
• Huang SC, Ghossein RA, Bishop JA, et al. Novel PAX3-NCOA1 fusions in biphenotypic sinonasal sarcoma with focal rhabdomyoblastic differentiation. Am J Surg Pathol. 2016;40(1):51–59. doi:10.1097/PAS.0000000000000492
   PubMed Web of Science ®Google Scholar
• Qian J, Olbrecht S, Boeckx B, et al. A pan-cancer blueprint of the heterogeneous tumor microenvironment revealed by single-cell profiling. Cell Res. 2020;30(9):745–762. doi:10.1038/s41422-020-0355-0
   PubMed Web of Science ®Google Scholar
• Johnson MB, Sun X, Kodani A, et al. Aspm knockout ferret reveals an evolutionary mechanism governing cerebral cortical size. Nature. 2018;556(7701):370–375. doi:10.1038/s41586-018-0035-0
   PubMed Web of Science ®Google Scholar
• Lokody I. Signalling: FOXM1 and CENPF: co-pilots driving prostate cancer. Nat Rev Cancer. 2014;14(7):451. doi:10.1038/nrc3772
   PubMed Web of Science ®Google Scholar
• Stastna J, Pan X, Wang H, et al. Differing and isoform-specific roles for the formin DIAPH3 in plasma membrane blebbing and filopodia formation. Cell Res. 2012;22(4):728–745. doi:10.1038/cr.2011.202
   PubMed Web of Science ®Google Scholar
• Friedman HS, Dolan ME, Kaufmann SH, et al. Elevated DNA polymerase alpha, DNA polymerase beta, and DNA topoisomerase II in a melphalan-resistant rhabdomyosarcoma xenograft that is cross-resistant to nitrosoureas and topotecan. Cancer Res. 1994;54(13):3487–3493.
   PubMed Web of Science ®Google Scholar
• Smith LM, Anderson JR, Coffin CM. Cytodifferentiation and clinical outcome after chemotherapy and radiation therapy for rhabdomyosarcoma (RMS). Med Pediatr Oncol. 2002;38(6):398–404. doi:10.1002/mpo.10060
   PubMedGoogle Scholar
• Coffin CM, Rulon J, Smith L, Bruggers C, White FV. Pathologic features of rhabdomyosarcoma before and after treatment: a clinicopathologic and immunohistochemical analysis. Mod Pathol. 1997;10(12):1175–1187.
   PubMed Web of Science ®Google Scholar
• Tonin PN, Scrable H, Shimada H, Cavenee WK. Muscle-specific gene expression in rhabdomyosarcomas and stages of human fetal skeletal muscle development. Cancer Res. 1991;51(19):5100–5106.
   PubMed Web of Science ®Google Scholar
• Osborn M, Hill C, Altmannsberger M, Weber K. Monoclonal antibodies to titin in conjunction with antibodies to desmin separate rhabdomyosarcomas from other tumor types. Lab Invest. 1986;55(1):101–108.
   PubMed Web of Science ®Google Scholar
• Barlow JW, Wiley JC, Mous M, et al. Differentiation of rhabdomyosarcoma cell lines using retinoic acid. Pediatr Blood Cancer. 2006;47(6):773–784. doi:10.1002/pbc.20650
   PubMed Web of Science ®Google Scholar
• Peters K, Caracciolo JT, Henderson-Jackson E, Binitie O. Myopericytoma/myopericytomatosis of the lower extremity in two young patients: a recently designated rare soft tissue neoplasm. Radiol Case Rep. 2018;13(1):275–280. doi:10.1016/j.radcr.2017.10.010
   PubMedGoogle Scholar
• Bo H, Cao K, Tang R, et al. A network-based approach to identify DNA methylation and its involved molecular pathways in testicular germ cell tumors. J Cancer. 2019;10(4):893–902. doi:10.7150/jca.27491
   PubMed Web of Science ®Google Scholar
• Bo H, Fan L, Li J, et al. High expression of lncRNA AFAP1-AS1 promotes the progression of colon cancer and predicts poor prognosis. J Cancer. 2018;9(24):4677–4683. doi:10.7150/jca.26461
   PubMed Web of Science ®Google Scholar
• Charville GW, Varma S, Forgo E, et al. PAX7 expression in rhabdomyosarcoma, related soft tissue tumors, and small round blue cell neoplasms. Am J Surg Pathol. 2016;40(10):1305–1315. doi:10.1097/PAS.0000000000000717
   PubMed Web of Science ®Google Scholar
• Parham DM, Barr FG. Classification of rhabdomyosarcoma and its molecular basis. Adv Anat Pathol. 2013;20(6):387–397. doi:10.1097/PAP.0b013e3182a92d0d
   PubMed Web of Science ®Google Scholar
• Blake J, Ziman MR. Aberrant PAX3 and PAX7 expression. A link to the metastatic potential of embryonal rhabdomyosarcoma and cutaneous malignant melanoma? Histol Histopathol. 2003;18(2):529–539. doi:10.14670/HH-18.529
   PubMed Web of Science ®Google Scholar
• Wan X, Yeung C, Kim SY, et al. Identification of FoxM1/Bub1b signaling pathway as a required component for growth and survival of rhabdomyosarcoma. Cancer Res. 2012;72(22):5889–5899. doi:10.1158/0008-5472.CAN-12-1991
   PubMed Web of Science ®Google Scholar
• Cheng H, Zhang N, Pati D. Cohesin subunit RAD21: from biology to disease. Gene. 2020;758:144966. doi:10.1016/j.gene.2020.144966
   PubMed Web of Science ®Google Scholar
• Wu Q, Lian JB, Stein JL, Stein GS, Nickerson JA, Imbalzano AN. The BRG1 ATPase of human SWI/SNF chromatin remodeling enzymes as a driver of cancer. Epigenomics. 2017;9(6):919–931. doi:10.2217/epi-2017-0034
   PubMed Web of Science ®Google Scholar
• Bharathy N, Berlow NE, Wang E, et al. The HDAC3-SMARCA4-miR-27a axis promotes expression of the PAX3: FOXO1fusion oncogene in rhabdomyosarcoma. Sci Signal. 2018;11(557). doi:10.1126/scisignal.aau7632
   PubMed Web of Science ®Google Scholar
• Wang C. Childhood rhabdomyosarcoma: recent advances and prospective views. J Dent Res. 2012;91(4):341–350. doi:10.1177/0022034511421490
   PubMed Web of Science ®Google Scholar
• Becker M, Moczar M, Poupon MF, Moczar E. Solubilization and degradation of extracellular matrix by various metastatic cell lines derived from a rat rhabdomyosarcoma. J Natl Cancer Inst. 1986;77(2):417–424.
   PubMedGoogle Scholar
• Almacellas-Rabaiget O, Monaco P, Huertas-Martinez J, et al. LOXL2 promotes oncogenic progression in alveolar rhabdomyosarcoma independently of its catalytic activity. Cancer Lett. 2020;474:1–14. doi:10.1016/j.canlet.2019.12.040
   PubMed Web of Science ®Google Scholar
• Haydn T, Kehr S, Willmann D, Metzger E, Schule R, Fulda S. Next-generation sequencing reveals a novel role of lysine-specific demethylase 1 in adhesion of rhabdomyosarcoma cells. Int J Cancer. 2020;146(12):3435–3449. doi:10.1002/ijc.32806
   PubMed Web of Science ®Google Scholar
• Wu YF, Matsuo N, Sumiyoshi H. Yoshioka H. Sp7/Osterix is involved in the up-regulation of the mouse pro-alpha1(V) collagen gene (Col5a1) in osteoblastic cells. Matrix Biol. 2010;29(8):701–706. doi:10.1016/j.matbio.2010.09.002
   PubMed Web of Science ®Google Scholar
• Iyengar P, Espina V, Williams TW, et al. Adipocyte-derived collagen VI affects early mammary tumor progression in vivo, demonstrating a critical interaction in the tumor/stroma microenvironment. J Clin Invest. 2005;115(5):1163–1176. doi:10.1172/JCI23424
   PubMed Web of Science ®Google Scholar
• Cattaruzza S, Nicolosi PA, Braghetta P, et al. NG2/CSPG4-collagen type VI interplays putatively involved in the microenvironmental control of tumour engraftment and local expansion. J Mol Cell Biol. 2013;5(3):176–193. doi:10.1093/jmcb/mjt010
   PubMed Web of Science ®Google Scholar