{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,20]],"date-time":"2026-01-20T03:04:29Z","timestamp":1768878269026,"version":"3.49.0"},"reference-count":35,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2021,4,9]],"date-time":"2021-04-09T00:00:00Z","timestamp":1617926400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004166","name":"Warszawski Uniwersytet Medyczny","doi-asserted-by":"publisher","award":["1M15\/NM3\/16"],"award-info":[{"award-number":["1M15\/NM3\/16"]}],"id":[{"id":"10.13039\/501100004166","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Melanoma tumors are the most heterogeneous of all tumor types. Tumor heterogeneity results in difficulties in diagnosis and is a frequent cause of failure in treatment. Novel techniques enable accurate examination of the tumor cells, considering their heterogeneity. The study aimed to determine the somatic variations among high and low proliferating compartments of melanoma tumors. In this study, 12 archival formalin-fixed paraffin-embedded samples of previously untreated primary cutaneous melanoma were stained with Ki-67 antibody. High and low proliferating compartments from four melanoma tumors were dissected using laser-capture microdissection. DNA was isolated and analyzed quantitatively and qualitatively. Libraries for amplicon-based next-generation sequencing (NGS) were prepared using NEBNext Direct Cancer HotSpot Panel. NGS detected 206 variants in 42 genes in melanoma samples. Most of them were located within exons (135, 66%) and were predominantly non-synonymous single nucleotide variants (99, 73.3%). The analysis showed significant differences in mutational profiles between high and low proliferation compartments of melanoma tumors. Moreover, a significantly higher percentage of variants were detected only in high proliferation compartments (39%) compared to low proliferation regions (16%, p &lt; 0.05). Our results suggest a significant functional role of genetic heterogeneity in melanoma.<\/jats:p>","DOI":"10.3390\/ijms22083886","type":"journal-article","created":{"date-parts":[[2021,4,9]],"date-time":"2021-04-09T10:05:21Z","timestamp":1617962721000},"page":"3886","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Higher Mutation Burden in High Proliferation Compartments of Heterogeneous Melanoma Tumors"],"prefix":"10.3390","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1809-248X","authenticated-orcid":false,"given":"Tomasz M.","family":"Grzywa","sequence":"first","affiliation":[{"name":"Center for Preclinical Research, The Department of Methodology, Medical University of Warsaw, 1B Banacha Str., 02-097 Warsaw, Poland"},{"name":"Doctoral School, Medical University of Warsaw, 61 Zwirki and Wigury Str., 02-091 Warsaw, Poland"},{"name":"Department of Immunology, Medical University of Warsaw, 5 Nielubowicza Str., 02-097 Warsaw, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Agnieszka A.","family":"Koppolu","sequence":"additional","affiliation":[{"name":"Department of Medical Genetics, Medical University of Warsaw, 3C Pawinskiego Str., 02-106 Warsaw, Poland"},{"name":"Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3051-5446","authenticated-orcid":false,"given":"Wiktor","family":"Paskal","sequence":"additional","affiliation":[{"name":"Center for Preclinical Research, The Department of Methodology, Medical University of Warsaw, 1B Banacha Str., 02-097 Warsaw, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3650-5401","authenticated-orcid":false,"given":"Klaudia","family":"Klicka","sequence":"additional","affiliation":[{"name":"Center for Preclinical Research, The Department of Methodology, Medical University of Warsaw, 1B Banacha Str., 02-097 Warsaw, Poland"},{"name":"Doctoral School, Medical University of Warsaw, 61 Zwirki and Wigury Str., 02-091 Warsaw, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ma\u0142gorzata","family":"Rydzanicz","sequence":"additional","affiliation":[{"name":"Department of Medical Genetics, Medical University of Warsaw, 3C Pawinskiego Str., 02-106 Warsaw, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0659-7322","authenticated-orcid":false,"given":"Jaros\u0142aw","family":"Wejman","sequence":"additional","affiliation":[{"name":"Department of Pathology, Medical Center of Postgraduate Education, 00-416 Warsaw, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rafa\u0142","family":"P\u0142oski","sequence":"additional","affiliation":[{"name":"Department of Medical Genetics, Medical University of Warsaw, 3C Pawinskiego Str., 02-106 Warsaw, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0683-1791","authenticated-orcid":false,"given":"Pawe\u0142 K.","family":"W\u0142odarski","sequence":"additional","affiliation":[{"name":"Center for Preclinical Research, The Department of Methodology, Medical University of Warsaw, 1B Banacha Str., 02-097 Warsaw, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2021,4,9]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"15003","DOI":"10.1038\/nrdp.2015.3","article-title":"Melanoma","volume":"1","author":"Schadendorf","year":"2015","journal-title":"Nat. Rev. Dis. Prim."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"7","DOI":"10.3322\/caac.21590","article-title":"Cancer statistics, 2020","volume":"70","author":"Siegel","year":"2020","journal-title":"CA Cancer J. Clin."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1007\/978-3-030-41008-7_3","article-title":"Immunotherapy for Melanoma","volume":"1244","author":"Albittar","year":"2020","journal-title":"Adv. Exp. Med. Biol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"956","DOI":"10.1016\/j.tranon.2017.09.007","article-title":"Intratumor and Intertumor Heterogeneity in Melanoma","volume":"10","author":"Grzywa","year":"2017","journal-title":"Transl. Oncol."},{"key":"ref_5","first-page":"338","article-title":"The causes and consequences of genetic heterogeneity in cancer evolution","volume":"501","author":"Burrell","year":"2013","journal-title":"Nat. Cell Biol."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Lovly, C.M., Salama, A.K.S., and Salgia, R. (2016). Tumor Heterogeneity and Therapeutic Resistance. Am. Soc. Clin. Oncol. Educ. Book, e585\u2013e593.","DOI":"10.14694\/EDBK_158808"},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Mancini, I., Simi, L., Salvianti, F., Castiglione, F., Sonnati, G., and Pinzani, P. (2019). Analytical Evaluation of an NGS Testing Method for Routine Molecular Diagnostics on Melanoma Formalin-Fixed, Paraffin-Embedded Tumor-Derived DNA. Diagnostics, 9.","DOI":"10.3390\/diagnostics9030117"},{"key":"ref_8","first-page":"1","article-title":"Towards Personalized Medicine in Melanoma: Implementation of a Clinical Next-Generation Sequencing Panel","volume":"7","author":"Bustos","year":"2017","journal-title":"Sci. Rep."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"McDonough, S.J., Bhagwate, A., Sun, Z., Wang, C., Zschunke, M., Gorman, J.A., Kopp, K.J., and Cunningham, J.M. (2019). Use of FFPE-derived DNA in next generation sequencing: DNA extraction methods. PLoS ONE, 14.","DOI":"10.1101\/521534"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Reiman, A., Kikuchi, H., Scocchia, D., Smith, P., Tsang, Y.W., Snead, D., and Cree, I.A. (2017). Validation of an NGS mutation detection panel for melanoma. BMC Cancer, 17.","DOI":"10.1186\/s12885-017-3149-0"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"691","DOI":"10.1111\/cup.13695","article-title":"Targeted next generation sequencing (NGS) to classify melanocytic neoplasms","volume":"47","author":"Zarabi","year":"2020","journal-title":"J. Cutan. Pathol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.ejcb.2013.12.002","article-title":"Oncogenes in melanoma: An update","volume":"93","author":"Kunz","year":"2014","journal-title":"Eur. J. Cell Biol."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Kunz, M., and Vera, J. (2019). Modelling of Protein Kinase Signaling Pathways in Melanoma and Other Cancers. Cancers, 11.","DOI":"10.3390\/cancers11040465"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"770","DOI":"10.1016\/j.bbamcr.2016.01.025","article-title":"Roads to melanoma: Key pathways and emerging players in melanoma progression and oncogenic signaling","volume":"1863","author":"Paluncic","year":"2016","journal-title":"Biochim. Biophys. Acta (BBA) Bioenerg."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1111\/php.12377","article-title":"UV Signature Mutations","volume":"91","author":"Brash","year":"2015","journal-title":"Photochem. Photobiol."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Czarnecka, A.M., Bartnik, E., Fiedorowicz, M., and Rutkowski, P. (2020). Targeted Therapy in Melanoma and Mechanisms of Resistance. Int. J. Mol. Sci., 21.","DOI":"10.3390\/ijms21134576"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"14744","DOI":"10.18632\/oncotarget.4539","article-title":"Genetic heterogeneity in cholangiocarcinoma: A major challenge for targeted therapies","volume":"6","author":"Brandi","year":"2015","journal-title":"Oncotarget"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1038\/nm.3984","article-title":"Pan-cancer analysis of the extent and consequences of intratumor heterogeneity","volume":"22","author":"Andor","year":"2016","journal-title":"Nat. Med."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1007\/s00109-020-01874-2","article-title":"Clinical implications of intratumor heterogeneity: Challenges and opportunities","volume":"98","author":"Cajal","year":"2020","journal-title":"J. Mol. Med."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1038\/nrclinonc.2017.166","article-title":"Tumour heterogeneity and resistance to cancer therapies","volume":"15","author":"Shaw","year":"2018","journal-title":"Nat. Rev. Clin. Oncol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1016\/j.cell.2012.06.024","article-title":"A Landscape of Driver Mutations in Melanoma","volume":"150","author":"Hodis","year":"2012","journal-title":"Cell"},{"key":"ref_22","first-page":"502","article-title":"Melanoma genome sequencing reveals frequent PREX2 mutations","volume":"485","author":"Berger","year":"2012","journal-title":"Nat. Cell Biol."},{"key":"ref_23","first-page":"191","article-title":"A comprehensive catalogue of somatic mutations from a human cancer genome","volume":"463","author":"Pleasance","year":"2009","journal-title":"Nat. Cell Biol."},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Takahashi, H., Asaoka, M., Yan, L., Rashid, O.M., Oshi, M., Ishikawa, T., Nagahashi, M., and Takabe, K. (2020). Biologically Aggressive Phenotype and Anti-cancer Immunity Counterbalance in Breast Cancer with High Mutation Rate. Sci. Rep., 10.","DOI":"10.1038\/s41598-020-58995-4"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1115","DOI":"10.1001\/jamaophthalmol.2018.2986","article-title":"Association of Uveal Melanoma Metastatic Rate With Stochastic Mutation Rate and Type of Mutation","volume":"136","author":"Szalai","year":"2018","journal-title":"JAMA Ophthalmol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1221","DOI":"10.1073\/pnas.0336397100","article-title":"Components of the Rb pathway are critical targets of UV mutagenesis in a murine melanoma model","volume":"100","author":"Kannan","year":"2003","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1242","DOI":"10.1111\/j.0022-202X.2005.23931.x","article-title":"Recurrent Patterns of Dual RB and p53 Pathway Inactivation in Melanoma","volume":"125","author":"Yang","year":"2005","journal-title":"J. Investig. Dermatol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"6935","DOI":"10.1158\/1078-0432.CCR-13-1266","article-title":"Large-scale Analysis of PDGFRA Mutations in Melanomas and Evaluation of Their Sensitivity to Tyrosine Kinase Inhibitors Imatinib and Crenolanib","volume":"19","author":"Dai","year":"2013","journal-title":"Clin. Cancer Res."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1002\/cbf.3120","article-title":"Platelet-derived growth factor (PDGF) signalling in cancer: Rapidly emerging signalling landscape","volume":"33","author":"Farooqi","year":"2015","journal-title":"Cell Biochem. Funct."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1127","DOI":"10.1038\/ng.438","article-title":"Analysis of the tyrosine kinome in melanoma reveals recurrent mutations in ERBB4","volume":"41","author":"Prickett","year":"2009","journal-title":"Nat. Genet."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"1002","DOI":"10.1158\/1535-7163.MCT-16-0535","article-title":"The Slow Cycling Phenotype: A Growing Problem for Treatment Resistance in Melanoma","volume":"16","author":"Ahn","year":"2017","journal-title":"Mol. Cancer Ther."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"9339","DOI":"10.1158\/0008-5472.CAN-06-3126","article-title":"Cancer Stem Cells\u2014Perspectives on Current Status and Future Directions: AACR Workshop on Cancer Stem Cells","volume":"66","author":"Clarke","year":"2006","journal-title":"Cancer Res."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Pe\u0142ka, K., Klicka, K., Grzywa, T.M., Gondek, A., Marczewska, J.M., Garbicz, F., Szczepaniak, K., Paskal, W., and W\u0142odarski, P.K. (2020). miR-96-5p, miR-134-5p, miR-181b-5p and miR-200b-3p heterogenous expression in sites of prostate cancer versus benign prostate hyperplasia\u2014Archival samples study. Histochem. Cell Biol., 1\u201311.","DOI":"10.1007\/s00418-020-01941-2"},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Grzywa, T., Klicka, K., Paskal, W., Dudkiewicz, J., Wejman, J., Pyzlak, M., and W\u0142odarski, P.K. (2020). miR-410-3p is induced by vemurafenib via ER stress and contributes to resistance to BRAF inhibitor in melanoma. PLoS ONE, 15.","DOI":"10.1371\/journal.pone.0234707"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"761","DOI":"10.1093\/bioinformatics\/btu703","article-title":"DANN: A deep learning approach for annotating the pathogenicity of genetic variants","volume":"31","author":"Quang","year":"2015","journal-title":"Bioinformatics"}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/22\/8\/3886\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,13]],"date-time":"2025-10-13T13:59:11Z","timestamp":1760363951000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/22\/8\/3886"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,4,9]]},"references-count":35,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2021,4]]}},"alternative-id":["ijms22083886"],"URL":"https:\/\/doi.org\/10.3390\/ijms22083886","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,4,9]]}}}