Display options
Cite
Kitamura E, Cowell JK, Chang CS, et al. Variant profiles of genes mapping to chromosome 16q loss in Wilms tumors reveals link to cilia-related genes and pathways. Genes Cancer. 2020;11(3):137-153doi: 10.18632/genesandcancer.207.
Kitamura, E., Cowell, J. K., Chang, C. S., & Hawthorn, L. (2020). Variant profiles of genes mapping to chromosome 16q loss in Wilms tumors reveals link to cilia-related genes and pathways. Genes & cancer, 11(3), 137-153. https://doi.org/10.18632/genesandcancer.207
Kitamura, Eiko, et al. "Variant profiles of genes mapping to chromosome 16q loss in Wilms tumors reveals link to cilia-related genes and pathways." Genes & cancer vol. 11,3 (2020): 137-153. doi: https://doi.org/10.18632/genesandcancer.207
Kitamura E, Cowell JK, Chang CS, Hawthorn L. Variant profiles of genes mapping to chromosome 16q loss in Wilms tumors reveals link to cilia-related genes and pathways. Genes Cancer. 2020 Oct 06;11(3):137-153. doi: 10.18632/genesandcancer.207. eCollection 2020 Dec 31. PMID: 33488951; PMCID: PMC7805536.
Copy Download .nbib Format: NLM
Share it on

Genes Cancer. 2020 Oct 06;11(3):137-153. doi: 10.18632/genesandcancer.207. eCollection 2020 Dec 31.

Variant profiles of genes mapping to chromosome 16q loss in Wilms tumors reveals link to cilia-related genes and pathways.

Genes & cancer

Eiko Kitamura, John K Cowell, Chang-Sheng Chang, Lesleyann Hawthorn

Affiliations

  1. Georgia Cancer Center, Augusta University, Augusta, GA, USA.

PMID: 33488951 PMCID: PMC7805536 DOI: 10.18632/genesandcancer.207

Abstract

BACKGROUND: Wilms tumor is the most common pediatric renal tumor and the fourth most common malignancy in children. Chromosome 16q deletion(del) or loss of heterozygosity (LOH) has been correlated with recurrence and overall poor prognosis, such that patients with 16qLOH and 1p allelic loss are treated with more aggressive chemotherapeutic regimens.

METHODS: In the present study, we have compared the variant profiles of Wilms tumors with and without 16q del/LOH using both data available from the TARGET database (42 samples) and tumors procured from our legacy collection (8 samples). Exome-Seq data was analyzed for tumor specific variants mapping to 16q. Whole exome analysis was also performed. An unbiased approach for somatic variant analysis was used to detect tumor-specific, somatic variants.

RESULTS: Of the 72 genes mapping to 16q, 42% were cilia-related genes and 28% of these were found to carry somatic variants specific to those tumors with 16qdel/LOH. Whole exome analyses further revealed that 30% of cilia-related genes across the genome carried alterations in tumors both with and without 16qdel/LOH. Additional pathway analyses revealed that many cilia-related pathway members also carried deleterious variant in these tumors including Sonic Hedgehog (SHh), Wnt, and Notch signaling pathways.

CONCLUSIONS: The data suggest that cilia-related genes and pathways are compromised in Wilms tumors. The genes on chromosome 16q that carry deleterious variants in cilia-related genes may account for the more aggressive nature of tumors with 16q del/LOH.

Copyright: © 2020 Kitamura et al.

Keywords: Wilms tumor; chromosome 16q; cilia pathways; cilia-related genes

Conflict of interest statement

CONFLICT OF INTEREST There is no conflict of interests.

References

  1. Development. 2017 Dec 15;144(24):4530-4539 - PubMed
  2. Am J Kidney Dis. 2005 Jun;45(6):1096-9 - PubMed
  3. J Pediatr Surg. 2011 Dec;46(12):2233-8 - PubMed
  4. Development. 2016 Nov 1;143(21):3907-3913 - PubMed
  5. Cell Calcium. 2018 Jan;69:37-45 - PubMed
  6. Semin Nephrol. 2014 Jan;34(1):27-33 - PubMed
  7. Nat Rev Cancer. 2001 Nov;1(2):157-62 - PubMed
  8. PLoS Genet. 2016 Jul 29;12(7):e1006220 - PubMed
  9. Pediatr Pulmonol. 2017 Apr;52(4):487-493 - PubMed
  10. Nat Genet. 2017 Oct;49(10):1487-1494 - PubMed
  11. Am J Pathol. 1968 Oct;53(4):609-16 - PubMed
  12. Genome Res. 2001 May;11(5):863-74 - PubMed
  13. EMBO Rep. 2015 Oct;16(10):1275-87 - PubMed
  14. PLoS One. 2011 Apr 22;6(4):e18941 - PubMed
  15. Oncotarget. 2016 Mar 1;7(9):9975-92 - PubMed
  16. Med Pediatr Oncol. 1996 Nov;27(5):398-403 - PubMed
  17. J Natl Cancer Inst. 1969 Jan;42(1):77-99 - PubMed
  18. Genesis. 2016 Sep;54(9):457-69 - PubMed
  19. Pediatr Blood Cancer. 2011 Dec 1;57(6):930-8 - PubMed
  20. J Pediatr Hematol Oncol. 2010 Aug;32(6):e241-3 - PubMed
  21. Hum Mutat. 2016 Aug;37(8):776-85 - PubMed
  22. Prog Mol Biol Transl Sci. 2018 Jan;153:181-207 - PubMed
  23. Eur J Pharmacol. 2018 Feb 5;820:65-76 - PubMed
  24. Nucleic Acids Res. 2002 Sep 1;30(17):3894-900 - PubMed
  25. Oncotarget. 2017 Aug 11;8(39):66467-66475 - PubMed
  26. Ultrastruct Pathol. 1984;6(4):285-94 - PubMed
  27. Eur J Surg Oncol. 2000 Feb;26(1):61-6 - PubMed
  28. Genes Chromosomes Cancer. 2007 Feb;46(2):163-70 - PubMed
  29. Am Soc Clin Oncol Educ Book. 2014;:215-23 - PubMed
  30. Nat Cell Biol. 2017 Oct 31;19(11):1379 - PubMed
  31. PLoS One. 2014 Feb 06;9(2):e88216 - PubMed
  32. J Biol Chem. 2011 Aug 5;286(31):27676-86 - PubMed
  33. Cancer Res. 1994 May 1;54(9):2331-3 - PubMed
  34. PLoS One. 2017 Oct 17;12(10):e0186333 - PubMed
  35. Eur Respir J. 2014 Dec;44(6):1579-88 - PubMed
  36. Development. 2018 Sep 17;145(18): - PubMed
  37. Am J Hum Genet. 2015 Oct 1;97(4):546-54 - PubMed
  38. J Clin Oncol. 2005 Oct 10;23(29):7312-21 - PubMed
  39. Mol Biol Cell. 2011 Apr;22(7):976-87 - PubMed
  40. Int J Mol Sci. 2017 Oct 28;18(11): - PubMed
  41. Mol Cancer Res. 2009 Jun;7(6):821-31 - PubMed
  42. Eur J Cancer. 2009 Mar;45(5):819-26 - PubMed
  43. Cancer Sci. 2016 May;107(5):690-9 - PubMed
  44. J Mol Biol. 2004 Oct 1;342(5):1659-74 - PubMed
  45. Antioxid Redox Signal. 2016 May 20;24(15):867-83 - PubMed

Publication Types