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Characterization of Satellite-2 Repeat Element DNA Sequences in Blood Plasma

Yıl 2022, Sayı: 18, 787 - 796, 31.12.2022
https://doi.org/10.38079/igusabder.1105142

Öz

Aim: 'Liquid biopsy', which is one of the concepts frequently encountered in different disciplines of medical science in recent years, involves the use of molecular and epigenetic biomarkers in blood and various body fluids instead of interventional tissue biopsy in subjects such as diagnosis, prognosis analysis and evaluation of response to treatment. Detection of gene mutations specific to cancer cells in DNA ('cell-free DNA', cfDNA) circulating freely is accepted as definitive proof that the contents of cancer cells pass into body fluids. Sequencing studies to determine the composition of cfDNA have reported that pericentric satellite DNA sequences are overrepresented in cfDNA compared to genome ratios. In this study, aimed to further characterize Sat-2 sequences after amplification in a polymerase chain reaction (PCR) in order to detect cancer-specific sequences.
Method: In the study, the 1st and 10th chromosome-specific Sat-2 sequences from the plasma of healthy and metastatic breast cancer patients were amplified by PCR and separated in an automated electrophoresis system.
Results: In the size analysis, it was determined that a large number of amplicons were formed from the two regions, approximately 50% of which were 143 and 115 bp long products, respectively. The amount of these two PCR amplicons was calculated to be higher in patients with breast cancer. It was determined that there were significant differences between controls and patients in terms of Sat-2 sequences, except for the 115 bp fragment specific to the tenth chromosome.
Conclusion: The findings obtained within the scope of the study reveal that cancer-specific target regions can be detected after sequencing the DNA sequences of the Sat-2 repeat element.

Kaynakça

  • González-Masiá JA, García-Olmo D, García-Olmo DC. Circulating nucleic acids in plasma and serum (CNAPS): Applications in oncology. Onco Targets Ther. 2013;6:819-32. doi:10.2147/OTT.S44668.
  • Bronkhorst AJ, Ungerer V, Diehl F, et al. Towards systematic nomenclature for cell-free DNA. Hum Genet. 2021;140(4):565-578. doi:10.1007/s00439-020-02227-2.
  • Stroun M, Anker P, Maurice P, Lyautey J, Lederrey C, Beljanski M. Neoplastic characteristics of the DNA found in the plasma of cancer patients. Oncology. 1989;46(5):318-22. doi:10.1159/000226740.
  • Sidransky D, Von Eschenbach A, Tsai YC, et al. Identification of p53 gene mutations in bladder cancers and urine samples. Science. 1991;252(5006):706-9. doi:10.1126/science.2024123.
  • Crowley E, Di Nicolantonio F, Loupakis F, Bardelli A. Liquid biopsy: Monitoring cancer-genetics in the blood. Nat Rev Clin Oncol. 2013;10(8):472-84. doi:10.1038/nrclinonc.2013.110.
  • Bronkhorst AJ, Wentzel JF, Ungerer V, et al. Sequence analysis of cell-free DNA derived from cultured human bone osteosarcoma (143B) cells. Tumour Biol. 2018;40(9):1010428318801190. doi:10.1177/1010428318801190.
  • Beck J, Urnovitz HB, Riggert J, Clerici M, Schütz E. Profile of the circulating DNA in apparently healthy individuals. Clin Chem. 2009;55(4):730-8. doi:10.1373/clinchem.2008.113597.
  • Van der Vaart M, Semenov DV, Kuligina EV, Richter VA, Pretorius PJ. Characterisation of circulating DNA by parallel tagged sequencing on the 454 platform. Clin Chim Acta. 2009;409(1-2):21-7. doi:10.1016/j.cca.2009.08.011.
  • Bronkhorst AJ, Wentzel JF, Aucamp J, van Dyk E, du Plessis L, Pretorius PJ. Characterization of the cell-free DNA released by cultured cancer cells. Biochim Biophys Acta. 2016;1863(1):157-65. doi:10.1016/j.bbamcr.2015.10.022.
  • Grabuschnig S, Soh J, Heidinger P, et al. Circulating cell-free DNA is predominantly composed of retrotransposable elements and non-telomeric satellite DNA. J Biotechnol. 2020;313:48-56. doi:10.1016/j.jbiotec.2020.03.002.
  • Bersani F, Lee E, Kharchenko PV, et al. Pericentromeric satellite repeat expansions through RNA-derived DNA intermediates in cancer. Proc Natl Acad Sci U S A. 2015;112(49):15148-53. doi:10.1073/pnas.1518008112.
  • Özgür E, Mayer Z, Keskin M, Yörüker EE, Holdenrieder S, Gezer U. Satellite 2 repeat DNA in blood plasma as a candidate biomarker for the detection of cancer. Clin Chim Acta. 2021;514:74-79. doi:10.1016/j.cca.2020.12.008.
  • Gezer U, Ustek D, Yörüker EE, et al. Characterization of H3K9me3- and H4K20me3-associated circulating nucleosomal DNA by high-throughput sequencing in colorectal cancer. Tumour Biol. 2013;34(1):329-36. doi:10.1007/s13277-012-0554-5.
  • Ellinger J, Müller SC, Stadler TC, Jung A, von Ruecker A, Bastian PJ. The role of cell-free circulating DNA in the diagnosis and prognosis of prostate cancer. Urol Oncol. 2011;29(2):124-9. doi:10.1016/j.urolonc.2009.05.010.
  • Tissot C, Toffart AC, Villar S, et al. Circulating free DNA concentration is an independent prognostic biomarker in lung cancer. Eur Respir J. 2015;46(6):1773-80. doi:10.1183/13993003.00676-2015.
  • Croswell JM, Kramer BS, Kreimer AR et al. Cumulative incidence of false-positive results in repeated, multimodal cancer screening. Ann Fam Med. 2009;7(3):212-22. doi:10.1370/afm.942.
  • Prensner JR, Rubin MA, Wei JT, Chinnaiyan AM. Beyond PSA: The next generation of prostate cancer biomarkers. Sci Transl Med. 2012;4(127):127rv3. doi:10.1126/scitranslmed.3003180.

Kan Plazmasında Satellit-2 Tekrar Elementi DNA Dizilerinin Karakterizasyonu

Yıl 2022, Sayı: 18, 787 - 796, 31.12.2022
https://doi.org/10.38079/igusabder.1105142

Öz

Amaç: Son yıllarda tıp biliminin farklı disiplinlerinde sıkça karşılaşılan kavramlardan biri olan “sıvı biyopsi”, hastaların tanı, prognoz analizi ve tedaviye cevabını değerlendirme gibi konularda girişimsel doku biyopsisi yerine, kan ve çeşitli vücut sıvılarındaki moleküler ve epigenetik biyobelirteçlerin kullanılmasını içerir. Dolaşımda serbest halde dolaşan DNA’da (‘cell-free DNA’, cfDNA) kanser hücrelerine özgü gen mutasyonlarının saptanması, kanser hücrelerinin içeriğinin vücut sıvılarına geçtiğinin kesin kanıtı olarak kabul edilmektedir. cfDNA’nın bileşiminin belirlenmesine yönelik dizileme çalışmaları, perisentrik satellit DNA dizilerinin, cfDNA’da genom oranlarına kıyasla daha fazla oranda temsil edildiğini bildirmiştir. Bu çalışmada, kanser açısından spesifik dizilerin saptanması amacıyla, Sat-2 dizilerinin polimeraz zincir reaksiyonunda (PCR) çoğaltılmaları sonrasında daha detaylı karakterizasyonu amaçlanmıştır.
Yöntem: Çalışmada, sağlıklı ve metastatik meme kanserli hastaların plazmalarından 1. ve 10. kromozoma spesifik Sat-2 dizileri PCR ile çoğaltıldıktan sonra, otomatik elektroforez sisteminde ayrıştırıldılar.
Bulgular: Yapılan büyüklük analizinde, iki bölgeden çok sayıda amplikon oluştuğu, bunların yaklaşık %50’ni sırasıyla 143 ve 115 bç uzunluğunda ürünlerin oluşturduğu belirlenmiştir. Bu iki PCR amplikonunun miktarı meme kanserli hastalarda daha yüksek olarak hesaplandı. Onuncu kromozoma özgü 115 bç’lik fargman dışındaki Sat-2 dizileri açısından kontroller ile hastalar arasında önemli farklar olduğu belirlenmiştir.
Sonuç: Çalışma kapsamında elde edilen bulgular, Sat-2 tekrar elementine ait DNA dizilerinin sekanslanması sonrası kansere spesifik hedef bölgelerin saptanabileceğini ortaya koymaktadır. 

Kaynakça

  • González-Masiá JA, García-Olmo D, García-Olmo DC. Circulating nucleic acids in plasma and serum (CNAPS): Applications in oncology. Onco Targets Ther. 2013;6:819-32. doi:10.2147/OTT.S44668.
  • Bronkhorst AJ, Ungerer V, Diehl F, et al. Towards systematic nomenclature for cell-free DNA. Hum Genet. 2021;140(4):565-578. doi:10.1007/s00439-020-02227-2.
  • Stroun M, Anker P, Maurice P, Lyautey J, Lederrey C, Beljanski M. Neoplastic characteristics of the DNA found in the plasma of cancer patients. Oncology. 1989;46(5):318-22. doi:10.1159/000226740.
  • Sidransky D, Von Eschenbach A, Tsai YC, et al. Identification of p53 gene mutations in bladder cancers and urine samples. Science. 1991;252(5006):706-9. doi:10.1126/science.2024123.
  • Crowley E, Di Nicolantonio F, Loupakis F, Bardelli A. Liquid biopsy: Monitoring cancer-genetics in the blood. Nat Rev Clin Oncol. 2013;10(8):472-84. doi:10.1038/nrclinonc.2013.110.
  • Bronkhorst AJ, Wentzel JF, Ungerer V, et al. Sequence analysis of cell-free DNA derived from cultured human bone osteosarcoma (143B) cells. Tumour Biol. 2018;40(9):1010428318801190. doi:10.1177/1010428318801190.
  • Beck J, Urnovitz HB, Riggert J, Clerici M, Schütz E. Profile of the circulating DNA in apparently healthy individuals. Clin Chem. 2009;55(4):730-8. doi:10.1373/clinchem.2008.113597.
  • Van der Vaart M, Semenov DV, Kuligina EV, Richter VA, Pretorius PJ. Characterisation of circulating DNA by parallel tagged sequencing on the 454 platform. Clin Chim Acta. 2009;409(1-2):21-7. doi:10.1016/j.cca.2009.08.011.
  • Bronkhorst AJ, Wentzel JF, Aucamp J, van Dyk E, du Plessis L, Pretorius PJ. Characterization of the cell-free DNA released by cultured cancer cells. Biochim Biophys Acta. 2016;1863(1):157-65. doi:10.1016/j.bbamcr.2015.10.022.
  • Grabuschnig S, Soh J, Heidinger P, et al. Circulating cell-free DNA is predominantly composed of retrotransposable elements and non-telomeric satellite DNA. J Biotechnol. 2020;313:48-56. doi:10.1016/j.jbiotec.2020.03.002.
  • Bersani F, Lee E, Kharchenko PV, et al. Pericentromeric satellite repeat expansions through RNA-derived DNA intermediates in cancer. Proc Natl Acad Sci U S A. 2015;112(49):15148-53. doi:10.1073/pnas.1518008112.
  • Özgür E, Mayer Z, Keskin M, Yörüker EE, Holdenrieder S, Gezer U. Satellite 2 repeat DNA in blood plasma as a candidate biomarker for the detection of cancer. Clin Chim Acta. 2021;514:74-79. doi:10.1016/j.cca.2020.12.008.
  • Gezer U, Ustek D, Yörüker EE, et al. Characterization of H3K9me3- and H4K20me3-associated circulating nucleosomal DNA by high-throughput sequencing in colorectal cancer. Tumour Biol. 2013;34(1):329-36. doi:10.1007/s13277-012-0554-5.
  • Ellinger J, Müller SC, Stadler TC, Jung A, von Ruecker A, Bastian PJ. The role of cell-free circulating DNA in the diagnosis and prognosis of prostate cancer. Urol Oncol. 2011;29(2):124-9. doi:10.1016/j.urolonc.2009.05.010.
  • Tissot C, Toffart AC, Villar S, et al. Circulating free DNA concentration is an independent prognostic biomarker in lung cancer. Eur Respir J. 2015;46(6):1773-80. doi:10.1183/13993003.00676-2015.
  • Croswell JM, Kramer BS, Kreimer AR et al. Cumulative incidence of false-positive results in repeated, multimodal cancer screening. Ann Fam Med. 2009;7(3):212-22. doi:10.1370/afm.942.
  • Prensner JR, Rubin MA, Wei JT, Chinnaiyan AM. Beyond PSA: The next generation of prostate cancer biomarkers. Sci Transl Med. 2012;4(127):127rv3. doi:10.1126/scitranslmed.3003180.
Toplam 17 adet kaynakça vardır.

Ayrıntılar

Birincil Dil Türkçe
Konular Klinik Tıp Bilimleri
Bölüm Makaleler
Yazarlar

Emre Özgür 0000-0002-4995-4759

Anıl Yıldız 0000-0002-6402-4445

Süleyman Bademler 0000-0002-0221-7153

Uğur Gezer 0000-0001-8471-5254

Yayımlanma Tarihi 31 Aralık 2022
Kabul Tarihi 16 Aralık 2022
Yayımlandığı Sayı Yıl 2022 Sayı: 18

Kaynak Göster

JAMA Özgür E, Yıldız A, Bademler S, Gezer U. Kan Plazmasında Satellit-2 Tekrar Elementi DNA Dizilerinin Karakterizasyonu. IGUSABDER. 2022;:787–796.

 Alıntı-Gayriticari-Türetilemez 4.0 Uluslararası (CC BY-NC-ND 4.0)