Detection of Genetic Alterations in Oral Squamous Cell Carcinoma Using Multiplex Ligation-Dependent Probe Amplification (MLPA)

Authors

  • Zachary Wei Ern Yong
  • Lee Peng Karen-Ng Universiti Malaya
  • Thomas George Kallarakkal Universiti Malaya
  • Zainal Ariff Abdul Rahman Universiti Malaya
  • Siti Mazlipah Ismail Universiti Malaya
  • Mannil Thomas Abraham Hospital Tengku Ampuan Rahimah, Klang
  • Keng Kiong Tay Hospital Umum Sarawak, Kuching
  • Rosnah Binti Zain MAHSA University
  • Zuraiza Mohamad Zaini Universiti Malaya

DOI:

https://doi.org/10.22452/adum.vol29no6

Keywords:

Biomarkers, DNA copy number, Dysplasia, Chromosome alteration

Abstract

Deletions and amplifications of genes often occur during multistep progression from oral precancer, seen as oral epithelial dysplasia (OED) to cancerous stage. These genetic alterations could be used as markers to aid in detection of oral squamous cell carcinomas (OSCC). This study explored the use of multiplex ligation-dependent probe amplification (MLPA) technique in detecting OSCC and OED specific genetic alterations. MLPA was used to detect gains and losses of 106 genes in DNA extracted from frozen tissue samples of 10 OSCC and 10 non-cancer patients. Two biopsies of OED were analyzed to explore the alterations in oral potentially malignant disorders. There were significant differences (p<0.001) in the number of alterations in OSCC and dysplasia compared to non-cancer samples respectively.  The most frequently altered genes in OSCC were PTP4A3, RECQL4, ATM, and KLK3 (60%). Five genes (MYC, SLA, TNFRSF1A, MESDC1, MIF) were altered in 50% of OSCC samples. These nine genes were specific to OSCC samples (p<0.05). Some genes, including MYB, MET, CASP2, SLA and PTEN occurred in 50% of OED samples. MLPA was able to detect genetic alterations, that are present only in OSCC samples and showed potential to be used as an adjunctive tool in early diagnosis of OSCC.

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References

Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, et al. Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries. CA: A Cancer Journal for Clinicians. 2021;71(3):209-49.

Graveland AP, Bremmer JF, de Maaker M, Brink A, Cobussen P, Zwart M, et al. Molecular screening of oral precancer. Oral Oncol. 2013;49(12):1129-35.

Bremmer JF, Graveland AP, Brink A, Braakhuis BJ, Kuik DJ, Leemans CR, et al. Screening for oral precancer with noninvasive genetic cytology. Cancer prevention research (Philadelphia, Pa). 2009;2(2):128-33.

Carreras-Torras C, Gay-Escoda C. Techniques for early diagnosis of oral squamous cell carcinoma: Systematic review. Medicina oral, patologia oral y cirugia bucal. 2015;20(3):e305-15.

Sansregret L, Vanhaesebroeck B, Swanton C. Determinants and clinical implications of chromosomal instability in cancer. Nature reviews Clinical oncology. 2018;15(3):139-50.

Vincent-Chong VK, Ismail SM, Rahman ZA, Sharifah NA, Anwar A, Pradeep PJ, et al. Genome-wide analysis of oral squamous cell carcinomas revealed over expression of ISG15, Nestin and WNT11. Oral diseases. 2012;18(5):469-76.

Vincent-Chong VK, Salahshourifar I, Woo KM, Anwar A, Razali R, Gudimella R, et al. Genome wide profiling in oral squamous cell carcinoma identifies a four genetic marker signature of prognostic significance. PloS one. 2017;12(4):e0174865.

Freier K, Schwaenen C, Sticht C, Flechtenmacher C, Mühling J, Hofele C, et al. Recurrent FGFR1 amplification and high FGFR1 protein expression in oral squamous cell carcinoma (OSCC). Oral oncology. 2007;43(1):60-6.

V SP, Kyrodimos E, Tsiambas E, Giotakis E, Psyrri A, Ragos V, et al. Chromosomal instability in oral squamous cell carcinoma. Journal of BUON : official journal of the Balkan Union of Oncology. 2018;23(6):1580-2.

Fox EJ, Salk JJ, Loeb LA. Cancer genome sequencing--an interim analysis. Cancer research. 2009;69(12):4948-50.

Schouten JP, McElgunn CJ, Waaijer R, Zwijnenburg D, Diepvens F, Pals G. Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification. Nucleic acids research. 2002;30(12):e57.

Stuppia L, Antonucci I, Palka G, Gatta V. Use of the MLPA assay in the molecular diagnosis of gene copy number alterations in human genetic diseases. International journal of molecular sciences. 2012;13(3):3245-76.

Bremmer JF, Braakhuis BJ, Ruijter-Schippers HJ, Brink A, Duarte HM, Kuik DJ, et al. A noninvasive genetic screening test to detect oral preneoplastic lesions. Laboratory investigation; a journal of technical methods and pathology. 2005;85(12):1481-8.

Sethi S, Benninger MS, Lu M, Havard S, Worsham MJ. Noninvasive molecular detection of head and neck squamous cell carcinoma: an exploratory analysis. Diagnostic molecular pathology : the American journal of surgical pathology, part B. 2009;18(2):81-7.

Chen YJ, Lin SC, Kao T, Chang CS, Hong PS, Shieh TM, et al. Genome-wide profiling of oral squamous cell carcinoma. The Journal of pathology. 2004;204(3):326-32.

Li J, Wang K, Jensen TD, Li S, Bolund L, Wiuf C. Tumor heterogeneity in neoplasms of breast, colon, and skin. BMC research notes. 2010;3:321.

Cha JD, Kim HJ, Cha IH. Genetic alterations in oral squamous cell carcinoma progression detected by combining array-based comparative genomic hybridization and multiplex ligation-dependent probe amplification. Oral surgery, oral medicine, oral pathology, oral radiology, and endodontics. 2011;111(5):594-607.

Ribeiro IP, Marques F, Caramelo F, Ferrão J, Prazeres H, Julião MJ, et al. Genetic imbalances detected by multiplex ligation-dependent probe amplification in a cohort of patients with oral squamous cell carcinoma-the first step towards clinical personalized medicine. Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine. 2014;35(5):4687-95.

Vincent-Chong VK, Anwar A, Karen-Ng LP, Cheong SC, Yang YH, Pradeep PJ, et al. Genome wide analysis of chromosomal alterations in oral squamous cell carcinomas revealed over expression of MGAM and ADAM9. PloS one. 2013;8(2):e54705.

Alonso Guervós M, Alvarez Marcos C, Llorente JL, Sampedro Nuño A, Suárez C, Hermsen M. Genetic differences between primary larynx and pharynx carcinomas and their matched lymph node metastases by multiplex ligation-dependent probe amplification. Oral oncology. 2009;45(7):600-4.

Worsham MJ, Lu M, Chen KM, Stephen JK, Havard S, Schweitzer VP. Malignant and nonmalignant gene signatures in squamous head and neck cancer. Journal of oncology. 2012;2012:752860.

Miskad UA, Semba S, Kato H, Yokozaki H. Expression of PRL-3 phosphatase in human gastric carcinomas: close correlation with invasion and metastasis. Pathobiology : journal of immunopathology, molecular and cellular biology. 2004;71(4):176-84.

Buffart TE, Coffa J, Hermsen MA, Carvalho B, van der Sijp JR, Ylstra B, et al. DNA copy number changes at 8q11-24 in metastasized colorectal cancer. Cellular oncology : the official journal of the International Society for Cellular Oncology. 2005;27(1):57-65.

Ambatipudi S, Gerstung M, Gowda R, Pai P, Borges AM, Schäffer AA, et al. Genomic profiling of advanced-stage oral cancers reveals chromosome 11q alterations as markers of poor clinical outcome. PloS one. 2011;6(2):e17250.

Parikh RA, White JS, Huang X, Schoppy DW, Baysal BE, Baskaran R, et al. Loss of distal 11q is associated with DNA repair deficiency and reduced sensitivity to ionizing radiation in head and neck squamous cell carcinoma. Genes, chromosomes & cancer. 2007;46(8):761-75.

Lim AM, Young RJ, Collins M, Fox SB, McArthur GA, Corry J, et al. Correlation of Ataxia-Telangiectasia-Mutated (ATM) gene loss with outcome in head and neck squamous cell carcinoma. Oral oncology. 2012;48(8):698-702.

Ishikawa T, Kashiwagi H, Iwakami Y, Hirai M, Kawamura T, Aiyoshi Y, et al. Expression of alpha-fetoprotein and prostate-specific antigen genes in several tissues and detection of mRNAs in normal circulating blood by reverse transcriptase-polymerase chain reaction. Japanese journal of clinical oncology. 1998;28(12):723-8.

Rodriguez S, Al-Ghamdi OA, Burrows K, Guthrie PA, Lane JA, Davis M, et al. Very low PSA concentrations and deletions of the KLK3 gene. Clinical chemistry. 2013;59(1):234-44.

Milne AN, Sitarz R, Carvalho R, Polak MM, Ligtenberg M, Pauwels P, et al. Molecular analysis of primary gastric cancer, corresponding xenografts, and 2 novel gastric carcinoma cell lines reveals novel alterations in gastric carcinogenesis. Human pathology. 2007;38(6):903-13.

Worsham MJ, Pals G, Schouten JP, Miller F, Tiwari N, van Spaendonk R, et al. High-resolution mapping of molecular events associated with immortalization, transformation, and progression to breast cancer in the MCF10 model. Breast cancer research and treatment. 2006;96(2):177-86.

Pettus JR, Johnson JJ, Shi Z, Davis JW, Koblinski J, Ghosh S, et al. Multiple kallikrein (KLK 5, 7, 8, and 10) expression in squamous cell carcinoma of the oral cavity. Histology and histopathology. 2009;24(2):197-207.

Warnakulasuriya S, Johnson NW, van der Waal I. Nomenclature and classification of potentially malignant disorders of the oral mucosa. Journal of oral pathology & medicine : official publication of the International Association of Oral Pathologists and the American Academy of Oral Pathology. 2007;36(10):575-80.

Califano J, van der Riet P, Westra W, Nawroz H, Clayman G, Piantadosi S, et al. Genetic progression model for head and neck cancer: implications for field cancerization. Cancer research. 1996;56(11):2488-92.

Nagata S, Hamada T, Yamada N, Yokoyama S, Kitamoto S, Kanmura Y, et al. Aberrant DNA methylation of tumor-related genes in oral rinse: a noninvasive method for detection of oral squamous cell carcinoma. Cancer. 2012;118(17):4298-308.

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Published

2022-09-12

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Original/Research Article