Triple-helical target sites of oncogenes to direct therapeutic triplex-forming oligonucleotides for the management of colorectal cancer

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Published Sep 11, 2021
Rajeswari Kalepu



Colorectal cancer (CRC) has been evolved as the most predominant cancer type in western countries by the 21st century and covers about 10% of cancer-related mortality. The factors that caused increased incidence may include aging, poor dietary habits, usage of nicotine, hindered physical activity, and obesity. Also, it is noted the influence of some familial cancer syndromes [1]. Several genes are responsible for the development of CRC and their mutations can make CRC more complex to treat by the cancer medicine fraternity. Deoxyribonucleic acid (DNA) can form non-canonical structures by folding any one of the strands or association of other strands to form a triple helix or quadruple structure [2]. The DNA triple helices are formed to the major groove of the DNA where purine or pyrimidine bases are present [3]. The DNA triple helix structures can be formed in two forms. The first one is the intra-molecular triple-helical DNA (or Hinge-DNA/H-DNA) structure and, the second one is the intermolecular triplex that can be formed with triple helix forming oligonucleotide (TFO)-targeted pairs with the major groove of the double-stranded DNA. The triple helix formation can modulate the transcription level of the target gene [4]. Antigene Technology (AT) is one of the applications to control gene expression selectively by forming triple helices with triple helix target sequences. It is also proved by targeting genomic sequences using TFOs in few studies. This is also being termed as local mutagenesis by applying TFOs on cell cultures [5]. With this, it is well understood that gene expression can be controlled by using TFO at the transcription level. The current study is intended to identify the number of oncogenes expressed in CRC and their potential TTS with special interest to promotor and protein-coding regions to direct the in vitro TFO synthesis for the therapeutic betterment of CRC.





In this study, TTS Mapping, and integration (TTSMI) database [6] was employed to identify the TTS sites as it provides a unique TTS location in the human genome with different annotation tracks. TTSMI is a user-friendly database to fetch the data in different regions. By setting up a percentage of guanine content (%G) as the default value (>=40%) since GA motif TFOs are more stable triple helices with higher %G with pyrimidine interruption setting to 1 because less pyrimidine content gives more stable triple helix. The different gene region annotations were selected from the filter options for each of the chromosomes and the number of TTS counts were noted from the result of annotation tracks data. The default sequence length was maintained between 15-30 nucleotide per TTS.


The highest number of TTS sites were found in each chromosome and the highest number of TTS was noted in chromosome 1 (126567) whereas, the least number was found in chromosome Y (1359) (fig. 1). The total number of oncogenes associated with TTS sites at protein-coding region include 216 and at promoter region was 502 (fig. 2). After narrow down, the oncogenes with TTS involved in the pathogenesis of CRC were 16 (fig.3). Further, the TTS sequences associated with the 16 oncogenes of CRC were retrieved from the database and tabulated (table 1). At the end of the study, we found KRAS, BRAF, FGFR2, MYC, IDH1, ERBB2, and EGFR have zero off-target sites.


KRAS, BRAF, FGFR2, MYC, IDH1, ERBB2, and EGFR genes would be more appropriate targets as they have TTS sequences with zero off-target sites. The identified TTS sequences located on the oncogenes of CRC would become the potential therapeutic targets and compatible TFOs can be synthesized in vitro to target these genes.

How to Cite

Kalepu, R. (2021). Triple-helical target sites of oncogenes to direct therapeutic triplex-forming oligonucleotides for the management of colorectal cancer. SPAST Abstracts, 1(01). Retrieved from
Abstract 13 |

Article Details

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