Shedding light on the DICER1 mutational spectrum of uncertain significance in malignant neoplasms
The Dicer protein is an indispensable player in such fundamental cell pathways as miRNA biogenesis and regulation of protein expression in a cell. Most recently, both germline and somatic mutations in DICER1 have been identified in diverse types of cancers, which suggests Dicer mutations can lead to...
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Frontiers Media S.A.
2024-10-01
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| author | D. S. Bug I. S. Moiseev Yu. B. Porozov Yu. B. Porozov N. V. Petukhova |
| author_facet | D. S. Bug I. S. Moiseev Yu. B. Porozov Yu. B. Porozov N. V. Petukhova |
| author_sort | D. S. Bug |
| collection | DOAJ |
| description | The Dicer protein is an indispensable player in such fundamental cell pathways as miRNA biogenesis and regulation of protein expression in a cell. Most recently, both germline and somatic mutations in DICER1 have been identified in diverse types of cancers, which suggests Dicer mutations can lead to cancer progression. In addition to well-known hotspot mutations in RNAase III domains, DICER1 is characterized by a wide spectrum of variants in all the functional domains; most are of uncertain significance and unstated clinical effects. Moreover, various new somatic DICER1 mutations continuously appear in cancer genome sequencing. The latest contemporary methods of variant effect prediction utilize machine learning algorithms on bulk data, yielding suboptimal correlation with biological data. Consequently, such analysis should be conducted based on the functional and structural characteristics of each protein, using a well-grounded targeted dataset rather than relying on large amounts of unsupervised data. Domains are the functional and evolutionary units of a protein; the analysis of the whole protein should be based on separate and independent examinations of each domain by their evolutionary reconstruction. Dicer represents a hallmark example of a multidomain protein, and we confirmed the phylogenetic multidomain approach being beneficial for the clinical effect prediction of Dicer variants. Because Dicer was suggested to have a putative role in hematological malignancies, we examined variants of DICER1 occurring outside the well-known hotspots of the RNase III domain in this type of cancer using phylogenetic reconstruction of individual domain history. Examined substitutions might disrupt the Dicer function, which was demonstrated by molecular dynamic simulation, where distinct structural alterations were observed for each mutation. Our approach can be utilized to study other multidomain proteins and to improve clinical effect evaluation. |
| format | Article |
| id | doaj-art-e0463cd7c0ab4a61874da5aef4048d61 |
| institution | OA Journals |
| issn | 2296-889X |
| language | English |
| publishDate | 2024-10-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Molecular Biosciences |
| spelling | doaj-art-e0463cd7c0ab4a61874da5aef4048d612025-08-20T02:28:32ZengFrontiers Media S.A.Frontiers in Molecular Biosciences2296-889X2024-10-011110.3389/fmolb.2024.14411801441180Shedding light on the DICER1 mutational spectrum of uncertain significance in malignant neoplasmsD. S. Bug0I. S. Moiseev1Yu. B. Porozov2Yu. B. Porozov3N. V. Petukhova4Bioinformatics Research Center, Pavlov First Saint Petersburg Medical State University, St. Petersburg, RussiaR. M. Gorbacheva Scientific Research Institute of Pediatric Hematology and Transplantation, Pavlov First Saint Petersburg State Medical University, St. Petersburg, RussiaSt. Petersburg School of Physics, Mathematics, and Computer Science, HSE University, Saint Petersburg, RussiaAdvitam Laboratory, Belgrade, SerbiaBioinformatics Research Center, Pavlov First Saint Petersburg Medical State University, St. Petersburg, RussiaThe Dicer protein is an indispensable player in such fundamental cell pathways as miRNA biogenesis and regulation of protein expression in a cell. Most recently, both germline and somatic mutations in DICER1 have been identified in diverse types of cancers, which suggests Dicer mutations can lead to cancer progression. In addition to well-known hotspot mutations in RNAase III domains, DICER1 is characterized by a wide spectrum of variants in all the functional domains; most are of uncertain significance and unstated clinical effects. Moreover, various new somatic DICER1 mutations continuously appear in cancer genome sequencing. The latest contemporary methods of variant effect prediction utilize machine learning algorithms on bulk data, yielding suboptimal correlation with biological data. Consequently, such analysis should be conducted based on the functional and structural characteristics of each protein, using a well-grounded targeted dataset rather than relying on large amounts of unsupervised data. Domains are the functional and evolutionary units of a protein; the analysis of the whole protein should be based on separate and independent examinations of each domain by their evolutionary reconstruction. Dicer represents a hallmark example of a multidomain protein, and we confirmed the phylogenetic multidomain approach being beneficial for the clinical effect prediction of Dicer variants. Because Dicer was suggested to have a putative role in hematological malignancies, we examined variants of DICER1 occurring outside the well-known hotspots of the RNase III domain in this type of cancer using phylogenetic reconstruction of individual domain history. Examined substitutions might disrupt the Dicer function, which was demonstrated by molecular dynamic simulation, where distinct structural alterations were observed for each mutation. Our approach can be utilized to study other multidomain proteins and to improve clinical effect evaluation.https://www.frontiersin.org/articles/10.3389/fmolb.2024.1441180/fullDicer1variant of uncertain significancevariant effect predictiongene evolutiononcologymolecular dynamics |
| spellingShingle | D. S. Bug I. S. Moiseev Yu. B. Porozov Yu. B. Porozov N. V. Petukhova Shedding light on the DICER1 mutational spectrum of uncertain significance in malignant neoplasms Frontiers in Molecular Biosciences Dicer1 variant of uncertain significance variant effect prediction gene evolution oncology molecular dynamics |
| title | Shedding light on the DICER1 mutational spectrum of uncertain significance in malignant neoplasms |
| title_full | Shedding light on the DICER1 mutational spectrum of uncertain significance in malignant neoplasms |
| title_fullStr | Shedding light on the DICER1 mutational spectrum of uncertain significance in malignant neoplasms |
| title_full_unstemmed | Shedding light on the DICER1 mutational spectrum of uncertain significance in malignant neoplasms |
| title_short | Shedding light on the DICER1 mutational spectrum of uncertain significance in malignant neoplasms |
| title_sort | shedding light on the dicer1 mutational spectrum of uncertain significance in malignant neoplasms |
| topic | Dicer1 variant of uncertain significance variant effect prediction gene evolution oncology molecular dynamics |
| url | https://www.frontiersin.org/articles/10.3389/fmolb.2024.1441180/full |
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