Helicase-like transcription factor at the intersection of replication independent non-coding RNAs and histone subtype in a cell-line derived xenograft model of colorectal cancer
Main Article Content
Abstract
New strategies are desperately needed for the treatment of metastatic colorectal cancer. Early diagnostic techniques have improved the survival rate for individuals with early stage disease; however, the five-year survival rate for patients with metastatic disease is less than 10%. Understanding the mechanisms responsible for disease progression and metastasis is a critical need for these patients. Human helicase-like transcription factor is a tumor suppressor epigenetically silenced during the progression of colorectal cancer. To examine how exactly does silencing HLTF contribute to tumorigenesis, we developed a cell-line derived xenograft model to compare the extremes of disease development. We compared the initial phase in which cancer cells that express helicase-like transcription factor are located in a tumor microenvironment where helicase-like transcription factor is absent vs the final metastatic phase in which neither the cancer cells nor the cells of the tumor microenvironment express helicase-like transcription factor. Combinatorial use of RNA sequencing technology with species-specific mapping, spatial transcriptomics, immunohistochemistry and mass spectrometry provided a holistic understanding of glutathione-based antioxidant defense in the model. The collective re-evaluation of the data revealed changes in replication independent non-coding RNAs and a histone subtype previously unreported.
Keywords:
Colorectal cancer (CRC), helicase-like transcription factor (HLTF), SWI-SNF-related, Matrix-Associated, Actin-dependent regulator of chromatin, Subfamily A, Member 3 (SMARCA3), tumor microenvironment (TME), cell-line derived xenograft (CDX), non-coding RNA U2, snoRNA U3, SNORD3A
Article Details
How to Cite
HELMER, Rebecca A; CHILTON, Beverly S..
Helicase-like transcription factor at the intersection of replication independent non-coding RNAs and histone subtype in a cell-line derived xenograft model of colorectal cancer.
Medical Research Archives, [S.l.], v. 13, n. 10, oct. 2025.
ISSN 2375-1924.
Available at: <https://esmed.org/MRA/mra/article/view/7004>. Date accessed: 06 dec. 2025.
doi: https://doi.org/10.18103/mra.v13i10.7004.
Section
Research Articles
The Medical Research Archives grants authors the right to publish and reproduce the unrevised contribution in whole or in part at any time and in any form for any scholarly non-commercial purpose with the condition that all publications of the contribution include a full citation to the journal as published by the Medical Research Archives.
References
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20. Reginato G, Dello Stritto MR, Wang Y, et al. HLTF disrupts Cas9-DNA post-cleavage complexes to allow DNA break processing. Nat Commun. 2024;15(1):5789. doi: 10.1038/s41467-024-50080-y.
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22. Bai G, Endres T, Kuhbacher U, et al. HLTF resolves G4s and promotes G4-induced replication fork slowing to maintain genome stability. Mol Cell. 2024;86(16): 3044-3060.e11. doi: 10.1016/j.molcel.2024.07.018.
23. Dusek CO, Dash RC, McPherson KS, et al. DNA sequence specificity reveals a role of the HLTF HIRAN domain in the recognition of trinucleotide repeats. Biochemistry. 2022;24: 10.1021/acs.biochem.2c00027. doi: 10.1021/acs.biochem.2c00027.
24. Martinez-Marin D, Helmer RA, Kaur G, et al. Helicase-like transcription factor (HLTF)-deleted CDX/TME model of colorectal cancer increased transcription of oxidative phosphorylation genes and diverted glycolysis to boost S-glutathionylation in lymphatic intravascular metastatic niches. PLoS One. 2023;18(9):e0291023. doi: 10.1371/journal.pone.0291023.
25. Wallner M, Herbst A, Behrens A, et al. Methylation of serum DNA is an independent prognostic marker in colorectal cancer. Clin Cancer Res. 2006;12(24):7347–7352. doi: 10.1158/1078-0432.CCR-06-1264.
26. Herbst A, Wallner M, Rahmig K,et al. Methylation of helicase-like transcription factor in serum of patients with colorectal cancer is an independent predictor of disease recurrence. Eur J Gastroenterol Hepatol. 2009; 21(5):565–569. doi: 10.1097/MEG.0b013e328318ecf2.
27. Ahmad, K. & Henikoff, S. The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly. Mol. Cell 9, 1191–1200 (2002).
28. Goldberg AD, Banaszynski LA, NohK-M et al. Distinct factors control histone variant H3.3 localization at specific genomic regions. Cell. 2010;140(5): 678–691. doi: 10.1016/j.cell.2010.01.003
29. Dutca LM, Gallagher JEG, Saserga SJ. The initial U3 snoRNA:pre-rRNA base pairing interaction required for pre-18S rRNA folding revealed by in vivo chemical probing. Nucleic Acids Res. 2011;39(12):5164-80. doi: 10.1093/nar/gkr044.
30. Lemus-Diaz N, Ferreira RR, Bohnsack KE, Gruber J, Bohnsack MT. The human box C/D snoRNA U3 regulates expression of sortin nexin 27. Nucleic Acids Res. 2020;48(14):8074-8089. doi: 10.1093/nar/gkaa549.
31. Singh MK, Shin Y, Han S, et al. Molecular chaperonin HSP60: Current understanding and future prospects. Int J Mol Sci. 2024;25(10): 5483; https://doi.org/10.3390/ijms25105483.
32. Feng Y, Endo M, Sugiyama H. Nucleosomes and epigenetics from a chemical perspective. Chembiochem. 2021;22(4):595-612. doi.org/10.1002/cbic.202000332.
33. Garcia-Gimenez JL, Olaso G, Hake SB, et al. Histone H3 glutathionylation in proliferating mammalian cells destabilizes nucleosomal structure. Antioxid. Redox Signal. 2013;19(12):1305–1320. doi: 10.1089/ars.2012.5021.
34. Garcia-Gimenez JL, Pallardo FV. Maintenance of glutathione levels and its importance in epigenetic regulation. Front Pharmacol. 2014;5:88. doi: 10.3389/fphar.2014.00088.
35. Guiro J, Fagbemi M, Tellier M, et al. CAPTURE of the human U2 snRNA genes expands the repertoire of associated factors. Biomolecules 2022;12(5):704. doi: 10.3390/biom12050704.
36. Song Z, Bae B, Schnabl S, et al., Mapping snoRNA-target RNA interactions in an RNA-binding protein-dependent manner with chimeric eCLIP. Genome Biol. 2025; 26:39. doi: 10.1186/s13059-025-03508-7
37. Maqbool M, Khan A, Shahzad. Predictive biomarkers for colorectal cancer: a state-of-the-art systematic review. Biomarkers 2023;28(6):562-598. doi: 10.1080/1354750X.2023.2247185.
38. Zhu H, Wang J, Miao J, et al. SNORD3A regulates STING transcription to promote ferroptosis in acute kidney injury. Adv Sci (Weinh). 2024 Sep;11(33):e2400305. doi: 10.1002/advs.202400305.
39. Luo, L, Zhang, J, Tang, H, et al. LncRNA SNORD3A specifically sensitizes breast cancer cells to 5-FU by sponging miR-185-5p to enhance UMPS expression. Cell death & disease, 2020;11,329. doi:10.1038/s41419-020-2557-2.
40. Yun, H, Zoller, J, Zhou, F, et al. The landscape of RNA-chromatin interaction reveals small non-coding RNAs as essential mediators of leukemia maintenance. Leukemia. 2024; 38, 1688-1698. doi:10.1038/s41375-024-02322-7.
41. Gomes AP, Llter D, Low V, et al. Dynamic incorporation of Histone H3 variants into chromatin is essential for acquisition of aggressive traits and metastatic colonization. Cancer Cell. 2019; 36(4): 402–417.e13. doi:10.1016/j.ccell.2019.08.006.
2. Maida M, Dahiya DS, Shah YR, et al. Screening and surveillance of colorectal cancer: A review of the literature. Cancers (Basel), 2024;16(15):2746. doi: 10.3390/cancers16152746.
3. Waheed Y, Mojumdar A, Shafiq M, de Marco A, De March M. The fork remodeler helicase-like transcription factor in cancer development: all at once. Biochim Biophys Acta Mol Basis Dis. 2024;1870(7):167280. doi: 10.1016/j.bbadis.2024.167280.
4. Dhont L, Mascaux C, Belayew A. The helicase-like transcription factor (HLTF) in cancer: loss of function or oncomorphic conversion of a tumor suppressor. Cell Mol Life Sci. 2016;73(1):129–145. doi: 10.1007/s00018-015-2060-6.
5. Moinova HR, Chen WD, Shen L, et al. HLTF gene silencing in human colon cancer. Proc Natl Acad Sci USA. 2002;99(7):4562–4567. https://doi.org/10.1073/pnas.062459899. PMID:11904375.
6. Leung WK, To KF, Man EP, et al. Detection of hypermethylated DNA or cyclooxygenase-2 messenger RNA in fecal samples of patients with colorectal cancer or polyps. Am J Gastroenterol. 2007;102(5):1070–1076.
7. Philipp AB, Stieber P, Nagel D, et al. Prognostic role of methylated free circulating DNA in colorectal cancer. Int J Cancer 2012;131:2308-2319. doi: 10.1002/ijc.27505. PMID: 22362391.
8. Jung G, Hernandez-Illan E, Moreira L, Balaguer F, Goel A. Epigenetics of colorectal cancer: biomarker and therapeutic potential. Nat Rev Gastroenterol Hepato. 2020;17(2):111-130. doi: 10.1038/s41575-019-0230-y. PMID:31900466.
9. Dhont L, Belayew A. HLTF (helicase-like transcription factor). Atlas Genet Cytogenet Oncol Haematol. 2016-11-01. Online version: http://atlasgeneticsoncology.org/gene/42332/hltf.
10. Sheridan PL, Schorpp M, Voz ML, Jones KA. Cloning of an SNF2/SWI2-related protein that binds specifically to the SPH motifs of the SV40 enhancer and to the HIV-1 promoter. J Biol Chem. 1995;270(9):4575–4587. 10.1074/jbc.270.9.4575;
11. Hayward-Lester A, Hewetson A, Beale EG, Oefner PJ, Doris PA, Chilton BS. Cloning, characterization and steroid-dependent posttranslational processing of RUSH-1α and β, two uteroglobin promoter binding proteins. Mol Endocrinol 1996; 10:1335–1349. 10.1210/mend.10.11.8923460;
12. Ding H, Descheemaeker K, Marynen P, et al. Characterization of helicase-like transcription factor involved in the suppression of the human plasminogen activator inhibitor-1 gene. DNA Cell Biol. 1996;15(6):429–442. 10.1089/dna.1996.15.429;
13. Hewetson A, Hendrix EC, Mansharamani M, Lee VH, Chilton BS. Identification of the RUSH consensus-binding site by cyclic amplification and selection of targets: demonstration that RUSH mediates the ability of prolactin to augment progesterone-dependent gene expression. Mol Endocrinol. 2002;16(9):2101-12. doi: 10.1210/me.2002-0064.
14. Unk I, Hajdu I, Fatyol K, et al. Human HLTF functions as a ubiquitin ligase for proliferating cell nuclear antigen polyubiquitination. Proc Natl Acad Sci USA 2008;105(10):3768-3773. doi: 10.1073/pnas.0800563105.
15. Kang S, Yoo J, Myung K. PCNA cycling dynamics during DNA replication and repair in mammals. Trends Genet. 2024;40(6):526-539. doi: 10.1016/j.tig.2024.02.006.
16. Kile AC, Chavez DA, Bacal J, et al. HLTF’s Ancient HIRAN domain binds 3' DNA ends to drive replication fork reversal. Mol Cell 2015;58(6):1090-1100.
17. Chavez DA, Greer BH, Eichman BF. The HIRAN domain of helicase-like transcription factor positions the DNA translocase motor to drive efficient DNA fork regression. J Biol Chem. 2018; 293(22):8484-8494. doi: 10.1074/jbc.RA118.002905.
18. van Toorn M, Turkyilmaz Y, Han S, et al. Active DNA damage eviction by HLTF stimulates nucleotide excision repair. Mol Cell. 2022;82(7): 1343–1358. e8. doi: 10.1016/j.molcel.2022.02.020.
19. Akano I, Hebert JM, Tiedmann RL, et al. The SWI-SNF related protein SMARCA3 is a histone H3K23 ubiquitin ligase that regulates H3K9me3 in cancer. Mol Cell. 2025;85(15):2885-2899. e8. doi: 10.1016/j.molcel.2025.06.020.
20. Reginato G, Dello Stritto MR, Wang Y, et al. HLTF disrupts Cas9-DNA post-cleavage complexes to allow DNA break processing. Nat Commun. 2024;15(1):5789. doi: 10.1038/s41467-024-50080-y.
21. Spiegel J, Adhikari S, Balasubramanian S. The structure and function of DNA G-quadruplexes. Trends Chem. 2020;2(2):123-136. doi: 10.1016/j.trechm.2019.07.002.
22. Bai G, Endres T, Kuhbacher U, et al. HLTF resolves G4s and promotes G4-induced replication fork slowing to maintain genome stability. Mol Cell. 2024;86(16): 3044-3060.e11. doi: 10.1016/j.molcel.2024.07.018.
23. Dusek CO, Dash RC, McPherson KS, et al. DNA sequence specificity reveals a role of the HLTF HIRAN domain in the recognition of trinucleotide repeats. Biochemistry. 2022;24: 10.1021/acs.biochem.2c00027. doi: 10.1021/acs.biochem.2c00027.
24. Martinez-Marin D, Helmer RA, Kaur G, et al. Helicase-like transcription factor (HLTF)-deleted CDX/TME model of colorectal cancer increased transcription of oxidative phosphorylation genes and diverted glycolysis to boost S-glutathionylation in lymphatic intravascular metastatic niches. PLoS One. 2023;18(9):e0291023. doi: 10.1371/journal.pone.0291023.
25. Wallner M, Herbst A, Behrens A, et al. Methylation of serum DNA is an independent prognostic marker in colorectal cancer. Clin Cancer Res. 2006;12(24):7347–7352. doi: 10.1158/1078-0432.CCR-06-1264.
26. Herbst A, Wallner M, Rahmig K,et al. Methylation of helicase-like transcription factor in serum of patients with colorectal cancer is an independent predictor of disease recurrence. Eur J Gastroenterol Hepatol. 2009; 21(5):565–569. doi: 10.1097/MEG.0b013e328318ecf2.
27. Ahmad, K. & Henikoff, S. The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly. Mol. Cell 9, 1191–1200 (2002).
28. Goldberg AD, Banaszynski LA, NohK-M et al. Distinct factors control histone variant H3.3 localization at specific genomic regions. Cell. 2010;140(5): 678–691. doi: 10.1016/j.cell.2010.01.003
29. Dutca LM, Gallagher JEG, Saserga SJ. The initial U3 snoRNA:pre-rRNA base pairing interaction required for pre-18S rRNA folding revealed by in vivo chemical probing. Nucleic Acids Res. 2011;39(12):5164-80. doi: 10.1093/nar/gkr044.
30. Lemus-Diaz N, Ferreira RR, Bohnsack KE, Gruber J, Bohnsack MT. The human box C/D snoRNA U3 regulates expression of sortin nexin 27. Nucleic Acids Res. 2020;48(14):8074-8089. doi: 10.1093/nar/gkaa549.
31. Singh MK, Shin Y, Han S, et al. Molecular chaperonin HSP60: Current understanding and future prospects. Int J Mol Sci. 2024;25(10): 5483; https://doi.org/10.3390/ijms25105483.
32. Feng Y, Endo M, Sugiyama H. Nucleosomes and epigenetics from a chemical perspective. Chembiochem. 2021;22(4):595-612. doi.org/10.1002/cbic.202000332.
33. Garcia-Gimenez JL, Olaso G, Hake SB, et al. Histone H3 glutathionylation in proliferating mammalian cells destabilizes nucleosomal structure. Antioxid. Redox Signal. 2013;19(12):1305–1320. doi: 10.1089/ars.2012.5021.
34. Garcia-Gimenez JL, Pallardo FV. Maintenance of glutathione levels and its importance in epigenetic regulation. Front Pharmacol. 2014;5:88. doi: 10.3389/fphar.2014.00088.
35. Guiro J, Fagbemi M, Tellier M, et al. CAPTURE of the human U2 snRNA genes expands the repertoire of associated factors. Biomolecules 2022;12(5):704. doi: 10.3390/biom12050704.
36. Song Z, Bae B, Schnabl S, et al., Mapping snoRNA-target RNA interactions in an RNA-binding protein-dependent manner with chimeric eCLIP. Genome Biol. 2025; 26:39. doi: 10.1186/s13059-025-03508-7
37. Maqbool M, Khan A, Shahzad. Predictive biomarkers for colorectal cancer: a state-of-the-art systematic review. Biomarkers 2023;28(6):562-598. doi: 10.1080/1354750X.2023.2247185.
38. Zhu H, Wang J, Miao J, et al. SNORD3A regulates STING transcription to promote ferroptosis in acute kidney injury. Adv Sci (Weinh). 2024 Sep;11(33):e2400305. doi: 10.1002/advs.202400305.
39. Luo, L, Zhang, J, Tang, H, et al. LncRNA SNORD3A specifically sensitizes breast cancer cells to 5-FU by sponging miR-185-5p to enhance UMPS expression. Cell death & disease, 2020;11,329. doi:10.1038/s41419-020-2557-2.
40. Yun, H, Zoller, J, Zhou, F, et al. The landscape of RNA-chromatin interaction reveals small non-coding RNAs as essential mediators of leukemia maintenance. Leukemia. 2024; 38, 1688-1698. doi:10.1038/s41375-024-02322-7.
41. Gomes AP, Llter D, Low V, et al. Dynamic incorporation of Histone H3 variants into chromatin is essential for acquisition of aggressive traits and metastatic colonization. Cancer Cell. 2019; 36(4): 402–417.e13. doi:10.1016/j.ccell.2019.08.006.