An In Silico Approach to Identify Candidate tRNA-Derived Fragments with Minimal Modifications as Potential Biomarkers for Early Cancer Detection Studies
- سال انتشار: 1403
- محل انتشار: دومین کنگره بین المللی کنسرژنومیکس
- کد COI اختصاصی: ICGCS02_302
- زبان مقاله: انگلیسی
- تعداد مشاهده: 97
نویسندگان
Department of Medical Genetics, School of Advanced Technologies in Medicine, Golestan University of Medical Sciences, Gorgan, Iran
Department of Medical Genetics, School of Medicine, Babol University of Medical Sciences, Babol, Iran
Department of Medical Genetics, School of Advanced Technologies in Medicine, Golestan University of Medical Sciences, Gorgan, Iran
Department of Medical Genetics, School of Advanced Technologies in Medicine, Golestan University of Medical Sciences, Gorgan, Iran
Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
Department of Medical Genetics, School of Advanced Technologies in Medicine, Golestan University of Medical Sciences, Gorgan, Iran
چکیده
tRNA-derived fragments (tRFs) have emerged as promising non-invasive biomarkers for various cancers. Understanding their diagnostic potential is crucial for enhancing early detection and improving patient outcomes. tRFs contain numerous chemical modifications, such as pseudouridylation and methylation, which enhance their stability and detectability in biofluids. However, these modifications—particularly methylation—can interfere with PCR amplification, leading to challenges such as non-specific product amplification and false positives, thereby complicating their clinical application. Methods: A bioinformatic approach was employed to screen for tRNAs and tRFs with minimal chemical modifications that could compromise the accurate amplification of tRFs using quantitative reverse transcription PCR (qRT-PCR) for the rapid and non-invasive diagnosis of cancer patients. The MODOMICS database was utilized to gather information on tRNA modifications. To identify the corresponding fragments and investigate the expression profiles of the candidates, we analyzed data from MINTBase V۲.۰, which includes ۱۲,۰۲۳ datasets. Real-time PCR was conducted to evaluate the expression levels of ۵’tRF-His in cancer patients compared to healthy individuals. Data were analyzed using an independent t-test with a significance threshold of p < ۰.۰۵. Results: From the MODOMICS database, we identified ۵۹ tRNA sequences with modified residues in Homo sapiens, comprising ۵۱ cytosolic tRNAs and ۸ mitochondrial tRNAs. Our analysis revealed that fragments derived from specific tRNAs (e.g., Ala, Glu, Phe, Gly, Leu, Met, Ser, Val, Tyr, Cys, Ile, Lys, Pro, Asp, Arg, Asn, Gln, Trp) may not be suitable for PCR amplification without pre-treatment due to high levels of chemical modifications, the locations and patterns of these modifications, and the presence of methylation. In-silico predictions indicated that these tRFs could not be used in further in vitro studies unless pre-treatment kits are employed, which would increase detection costs. Notably, tRNA-His emerged as a viable source of tRFs for clinical diagnostics due to its lower modification levels and distinct methylation patterns. Eight modifications were identified on tRNA-His, including pseudouridine at nucleotides ۱۴, ۳۳, and ۵۵; dihydrouridine at nucleotides ۱۷ and ۲۱; ۵-methylcytidine at nucleotides ۴۸ and ۴۹; and N۱-methyladenosine at nucleotide ۵۸. The ۵’tRFs derived from tRNA-His are promising candidates due to their lack of methylation and fewer chemical modifications (nucleotides ۱ to ۴۷), which could interfere with reverse transcription and PCR. Our RT-qPCR experiments demonstrated that ۵’tRF-His can be amplified using the stem-loop method for cDNA synthesis without pre-treatment kits (p < ۰.۰۰۱). Conclusion: Our study indicates that various ۵’tRF-His can be developed as novel diagnostic biomarkers due to their low methylation, detectability, and higher stability in biofluids, along with the absence of severely interfering modifications on the ۵' end. However, further in vitro and in vivo studies are necessary to confirm the exact modifications of tRNA-His, which were only predicted through in-silico analyses. This will help assess the potential for translating these findings into clinical practice based on the sensitivity and specificity of ۵’tRF-His.کلیدواژه ها
tRNA-derived Fragments, Cancer, Diagnosis, Biomarker, Methylationمقالات مرتبط جدید
اطلاعات بیشتر در مورد COI
COI مخفف عبارت CIVILICA Object Identifier به معنی شناسه سیویلیکا برای اسناد است. COI کدی است که مطابق محل انتشار، به مقالات کنفرانسها و ژورنالهای داخل کشور به هنگام نمایه سازی بر روی پایگاه استنادی سیویلیکا اختصاص می یابد.
کد COI به مفهوم کد ملی اسناد نمایه شده در سیویلیکا است و کدی یکتا و ثابت است و به همین دلیل همواره قابلیت استناد و پیگیری دارد.