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Snezhkina A, Pavlov V, Fedorova M, Kalinin D, Pudova E, Kobelyatskaya A, Bakhtogarimov I, Krasnov G, Kudryavtseva A. Comprehensive Genetic Study of Malignant Cervical Paraganglioma. Int J Mol Sci 2023; 24:ijms24098220. [PMID: 37175927 PMCID: PMC10179044 DOI: 10.3390/ijms24098220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
Malignant middle ear paraganglioma (MEPGL) is an exceedingly rare tumor of the neuroendocrine system. In general, MEPGLs represent as slow growing and hypervascularized benign neoplasms. The genetic basis of MEPGL tumorigenesis has been poorly investigated. We report a case of malignant MEPGL accompanied by the comprehensive genetic analysis of the primary tumor and metastasis. Based on whole-exome sequencing data, the germline pathogenic mutation p.R230H in the SDHB gene, encoding for subunit B of mitochondrial complex II, was found in a patient. Analysis of somatic mutation spectra revealed five novel variants in different genes, including a potentially deleterious variant in UNC13C that was common for the tumor and metastasis. Identified somatic variants clustered into SBS1 and SBS5 mutational signatures. Of note, the primary tumor was characterized by Ki-67 4% and had an elevated mutational load (1.4/Mb); the metastasis' mutational load was about 4.5 times higher (6.4/Mb). In addition, we revealed somatic loss of the wild-type SDHB allele, as well as loss of heterozygosity (LOH) at the 11p locus. Thus, germline mutation in SDHB combined with somatic LOH seem to be drivers that lead to the tumor's initiation and progression. Other somatic changes identified can be additional disease-causing factors. Obtained results expand our understanding of molecular genetic mechanisms associated with the development of this rare tumor.
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Affiliation(s)
- Anastasiya Snezhkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Vladislav Pavlov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Maria Fedorova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Dmitry Kalinin
- Vishnevsky Institute of Surgery, Ministry of Health of the Russian Federation, 117997 Moscow, Russia
| | - Elena Pudova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | | | - Ildar Bakhtogarimov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - George Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Anna Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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Martinelli S, Riverso M, Mello T, Amore F, Parri M, Simeone I, Mannelli M, Maggi M, Rapizzi E. SDHB and SDHD silenced pheochromocytoma spheroids respond differently to tumour microenvironment and their aggressiveness is inhibited by impairing stroma metabolism. Mol Cell Endocrinol 2022; 547:111594. [PMID: 35149119 DOI: 10.1016/j.mce.2022.111594] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 01/11/2022] [Accepted: 02/04/2022] [Indexed: 12/18/2022]
Abstract
Germline mutations in more than 20 genes, including those encoding for the succinate dehydrogenase (SDH), predispose to rare tumours, such as pheochromocytoma/paraganglioma (PPGL). Despite encoding for the same enzymatic complex, SDHC and SDHD mutated PHEO/PGLs are generally benign, while up to 80% of SDHB mutated ones are malignant. In this study, we evaluated the different effects of tumour microenvironment on tumour cell migration/invasion, by co-culturing SDHB or SDHD silenced tumour spheroids with primary cancer-associated fibroblasts (CAFs). We observed that SDHD silenced spheroids had an intermediate migration pattern, compared to the highest migration capability of SDHB and the lowest one of the wild type (Wt) spheroids. Interestingly, we noticed that co-culturing Wt, SDHB and SDHD silenced spheroids with CAFs in low glucose (1 g/l) medium, caused a decreased migration of all the spheroids, but only for SDHB silenced ones this reduction was significant. Moreover, the collective migration, observed in high glucose (4.5 g/l) and characteristic of the SDHB silenced cells, was completely lost in low glucose. Importantly, migration could not be recovered even adding glucose (3.5 g/l) to low glucose conditioned medium. When we investigated cell metabolism, we found that low glucose concentration led to a reduction of oxygen consumption rate (OCR), basal and maximal oxidative metabolism, and ATP production only in CAFs, but not in tumour cells. These results suggest that CAFs metabolism impairment was responsible for the decreased invasion process of tumour cells, most likely preventing the release of the pro-migratory factors produced by CAFs. In conclusion, the interplay between CAFs and tumour cells is distinctive depending on the gene involved, and highlights the possibility to inhibit CAF-induced migration by impairing CAFs metabolism, indicating new potential therapeutic scenarios for medical therapy.
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Affiliation(s)
- Serena Martinelli
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Italy
| | - Maria Riverso
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Italy
| | - Tommaso Mello
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Italy
| | - Francesca Amore
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Italy
| | - Matteo Parri
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Italy
| | - Irene Simeone
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Italy
| | - Massimo Mannelli
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Italy
| | - Mario Maggi
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Italy
| | - Elena Rapizzi
- Department of Experimental and Clinical Medicine, University of Florence, Italy.
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Case Report: Genetic Alterations Associated with the Progression of Carotid Paraganglioma. Curr Issues Mol Biol 2021; 43:2266-2275. [PMID: 34940133 PMCID: PMC8928979 DOI: 10.3390/cimb43030159] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/19/2021] [Accepted: 12/06/2021] [Indexed: 11/16/2022] Open
Abstract
Paragangliomas (PGLs) are rare neuroendocrine tumors that can develop from any paraganglion across the body. The carotid body is the most often location of PGLs in the head and neck region. Carotid PGLs (CPGLs) are characterized by predominantly non-aggressive behavior; however, all tumors have the potential to metastasize. To date, molecular mechanisms of paraganglioma progression remain elusive. We report a case of a 38-year-old woman with metastatic CPGL manifesting as a recurrent tumor with lymph node metastasis. The tumor was fast-growing and had a high Ki-67 proliferation index. Immunohistochemical (IHC) examination and whole-exome sequencing were performed for both recurrent tumor and metastasis. A germline pathogenic splice acceptor variant in the SDHB gene was found in the patient. Immunoreactivity of the SDHB subunit was weak diffuse in both samples, indicating deficiency of the succinate dehydrogenase. Moreover, the recurrent tumor exhibited loss of heterozygosity (LOH) at the SDHB locus, that is according to Knudson's "two-hit" hypothesis of cancer causation. We also identified a rare somatic promotor mutation in the TERT gene associated with the tumor progression. Obtained results confirmed the indicative role of the germline SDHB mutation for metastatic CPGLs, as well as the potential prognostic value of the TERT promoter mutation.
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Snezhkina A, Pavlov V, Dmitriev A, Melnikova N, Kudryavtseva A. Potential Biomarkers of Metastasizing Paragangliomas and Pheochromocytomas. Life (Basel) 2021; 11:1179. [PMID: 34833055 PMCID: PMC8619623 DOI: 10.3390/life11111179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/28/2021] [Accepted: 10/30/2021] [Indexed: 02/07/2023] Open
Abstract
Paragangliomas and pheochromocytomas (PPGLs) are rare neuroendocrine tumors originating from paraganglionic tissue in many sites of the body. Most PPGLs are characterized by nonaggressive behavior but all of them have the potential to metastasize. PPGLs represent a great diagnostic dilemma as it is difficult to recognize tumors that are likely to be metastasizing; criteria of malignancy can be found both in benign and metastatic forms. This review aims to analyze the current knowledge of the nature of metastasizing PPGLs paying particular attention to head and neck paragangliomas (HNPGLs). Potential predictors of the malignancy risk for PPGLs were summarized and discussed. These data may also help in the development of diagnostic and prognostic strategies, as well as in the identification of novel potential therapeutic targets for patients with PPGLs.
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Affiliation(s)
- Anastasiya Snezhkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (V.P.); (A.D.); (N.M.)
| | | | | | | | - Anna Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (V.P.); (A.D.); (N.M.)
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5
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Snezhkina AV, Fedorova MS, Pavlov VS, Kalinin DV, Golovyuk AL, Pudova EA, Guvatova ZG, Melnikova NV, Dmitriev AA, Razmakhaev GS, Poloznikov AA, Alekseeva GS, Kaprin AD, Krasnov GS, Kudryavtseva AV. Mutation Frequency in Main Susceptibility Genes Among Patients With Head and Neck Paragangliomas. Front Genet 2020; 11:614908. [PMID: 33391357 PMCID: PMC7775293 DOI: 10.3389/fgene.2020.614908] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 11/26/2020] [Indexed: 11/13/2022] Open
Abstract
Head and neck paragangliomas (HNPGLs) are rare neuroendocrine tumors that have a high degree of heritability and are predominantly associated with mutations in ten genes, such as SDHx, SDHAF2, VHL, RET, NF1, TMEM127, MAX, FH, MEN2, and SLC25A11. Elucidating the mutation prevalence is crucial for the development of genetic testing. In this study, we identified pathogenic/likely pathogenic variants in the main susceptibility genes in 102 Russian patients with HNPGLs (82 carotid and 23 vagal paragangliomas) using whole exome sequencing. Pathogenic/likely pathogenic variants were detected in 43% (44/102) of patients. We identified the following variant distribution of the tested genes: SDHA (1%), SDHB (10%), SDHC (5%), SDHD (24.5%), and RET (5%). SDHD variants were observed in the majority of the patients with bilateral/multiple paragangliomas. Thus, among Russian patients with HNPGLs the most frequently mutated gene was SDHD followed by SDHB, SDHC, RET, and SDHA.
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Affiliation(s)
| | - Maria S Fedorova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Vladislav S Pavlov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry V Kalinin
- Vishnevsky Institute of Surgery, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Alexander L Golovyuk
- Vishnevsky Institute of Surgery, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Elena A Pudova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Zulfiya G Guvatova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Nataliya V Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexey A Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - George S Razmakhaev
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Andrey A Poloznikov
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Galina S Alekseeva
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Andrey D Kaprin
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - George S Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anna V Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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Immunohistochemistry and Mutation Analysis of SDHx Genes in Carotid Paragangliomas. Int J Mol Sci 2020; 21:ijms21186950. [PMID: 32971818 PMCID: PMC7576476 DOI: 10.3390/ijms21186950] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 12/12/2022] Open
Abstract
Carotid paragangliomas (CPGLs) are rare neuroendocrine tumors often associated with mutations in SDHx genes. The immunohistochemistry of succinate dehydrogenase (SDH) subunits has been considered a useful instrument for the prediction of SDHx mutations in paragangliomas/pheochromocytomas. We compared the mutation status of SDHx genes with the immunohistochemical (IHC) staining of SDH subunits in CPGLs. To identify pathogenic/likely pathogenic variants in SDHx genes, exome sequencing data analysis among 42 CPGL patients was performed. IHC staining of SDH subunits was carried out for all CPGLs studied. We encountered SDHx variants in 38% (16/42) of the cases in SDHx genes. IHC showed negative (5/15) or weak diffuse (10/15) SDHB staining in most tumors with variants in any of SDHx (94%, 15/16). In SDHA-mutated CPGL, SDHA expression was completely absent and weak diffuse SDHB staining was detected. Positive immunoreactivity for all SDH subunits was found in one case with a variant in SDHD. Notably, CPGL samples without variants in SDHx also demonstrated negative (2/11) or weak diffuse (9/11) SDHB staining (42%, 11/26). Obtained results indicate that SDH immunohistochemistry does not fully reflect the presence of mutations in the genes; diagnostic effectiveness of this method was 71%. However, given the high sensitivity of SDHB immunohistochemistry, it could be used for initial identifications of patients potentially carrying SDHx mutations for recommendation of genetic testing.
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Orlov YL, Voropaeva EN, Chen M, Baranova AV. Medical genomics at the Systems Biology and Bioinformatics (SBB-2019) school. BMC Med Genomics 2020; 13:127. [PMID: 32948185 PMCID: PMC7500028 DOI: 10.1186/s12920-020-00786-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- Yuriy L. Orlov
- The Digital Health Institute, I.M.Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia
- Novosibirsk State University, 630090 Novosibirsk, Russia
- Research Institute of Internal and Preventive Medicine - Branch of the Institute of Cytology and Genetics SB RAS, 630089 Novosibirsk, Russia
| | - Elena N. Voropaeva
- Research Institute of Internal and Preventive Medicine - Branch of the Institute of Cytology and Genetics SB RAS, 630089 Novosibirsk, Russia
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, First Affiliated Hospital of Medical School, Zhejiang University, Hangzhou, 310058 China
| | - Ancha V. Baranova
- George Mason University, Fairfax, VA 22030 USA
- Research Centre for Medical Genetics, 115522 Moscow, Russia
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8
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Kudryavtseva AV, Kalinin DV, Pavlov VS, Savvateeva MV, Fedorova MS, Pudova EA, Kobelyatskaya AA, Golovyuk AL, Guvatova ZG, Razmakhaev GS, Demidova TB, Simanovsky SA, Slavnova EN, Poloznikov AА, Polyakov AP, Melnikova NV, Dmitriev AA, Krasnov GS, Snezhkina AV. Mutation profiling in eight cases of vagal paragangliomas. BMC Med Genomics 2020; 13:115. [PMID: 32948195 PMCID: PMC7500026 DOI: 10.1186/s12920-020-00763-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 08/05/2020] [Indexed: 12/25/2022] Open
Abstract
Background Vagal paragangliomas (VPGLs) belong to a group of rare head and neck neuroendocrine tumors. VPGLs arise from the vagus nerve and are less common than carotid paragangliomas. Both diagnostics and therapy of the tumors raise significant challenges. Besides, the genetic and molecular mechanisms behind VPGL pathogenesis are poorly understood. Methods The collection of VPGLs obtained from 8 patients of Russian population was used in the study. Exome library preparation and high-throughput sequencing of VPGLs were performed using an Illumina technology. Results Based on exome analysis, we identified pathogenic/likely pathogenic variants of the SDHx genes, frequently mutated in paragangliomas/pheochromocytomas. SDHB variants were found in three patients, whereas SDHD was mutated in two cases. Moreover, likely pathogenic missense variants were also detected in SDHAF3 and SDHAF4 genes encoding for assembly factors for the succinate dehydrogenase (SDH) complex. In a patient, we found a novel variant of the IDH2 gene that was predicted as pathogenic by a series of algorithms used (such as SIFT, PolyPhen2, FATHMM, MutationTaster, and LRT). Additionally, pathogenic/likely pathogenic variants were determined for several genes, including novel genes and some genes previously reported as associated with different types of tumors. Conclusions Results indicate a high heterogeneity among VPGLs, however, it seems that driver events in most cases are associated with mutations in the SDHx genes and SDH assembly factor-coding genes that lead to disruptions in the SDH complex.
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Affiliation(s)
- Anna V Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
| | - Dmitry V Kalinin
- Vishnevsky Institute of Surgery, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Vladislav S Pavlov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Maria V Savvateeva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Maria S Fedorova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Elena A Pudova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Alexander L Golovyuk
- Vishnevsky Institute of Surgery, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Zulfiya G Guvatova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - George S Razmakhaev
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Tatiana B Demidova
- A. N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Sergey A Simanovsky
- A. N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Elena N Slavnova
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Andrey А Poloznikov
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Andrey P Polyakov
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Nataliya V Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexey A Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - George S Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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Pavlov VS, Kalinin DV, Lukyanova EN, Golovyuk AL, Fedorova MS, Pudova EA, Savvateeva MV, Lipatova AV, Guvatova ZG, Kaprin AD, Kiseleva MV, Demidova TB, Simanovsky SA, Melnikova NV, Dmitriev AA, Krasnov GS, Snezhkina AV, Kudryavtseva AV. Multiple paragangliomas: a case report. BMC Med Genomics 2020; 13:125. [PMID: 32948182 PMCID: PMC7500000 DOI: 10.1186/s12920-020-00789-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 08/31/2020] [Indexed: 02/06/2023] Open
Abstract
Background Carotid and vagal paragangliomas (CPGLs and VPGLs) are rare neoplasms that arise from the paraganglia located at the bifurcation of carotid arteries and vagal trunk, respectively. Both tumors can occur jointly as multiple paragangliomas accounting for approximately 10 to 20% of all head and neck paragangliomas. However, molecular and genetic mechanisms underlying the pathogenesis of multiple paragangliomas remain elusive. Case presentation We report a case of multiple paragangliomas in a patient, manifesting as bilateral CPGL and unilateral VPGL. Tumors were revealed via computed tomography and ultrasound study and were resected in two subsequent surgeries. Both CPGLs and VPGL were subjected to immunostaining for succinate dehydrogenase (SDH) subunits and exome analysis. A likely pathogenic germline variant in the SDHD gene was indicated, while likely pathogenic somatic variants differed among the tumors. Conclusions The identified germline variant in the SDHD gene seems to be a driver in the development of multiple paragangliomas. However, different spectra of somatic variants identified in each tumor indicate individual molecular mechanisms underlying their pathogenesis.
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Affiliation(s)
- Vladislav S Pavlov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova str, Moscow, 119991, Russia
| | - Dmitry V Kalinin
- Vishnevsky Institute of Surgery, Ministry of Health of the Russian Federation, 27 Bol'shaya Serpukhovskaya str, Moscow, 117997, Russia
| | - Elena N Lukyanova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova str, Moscow, 119991, Russia
| | - Alexander L Golovyuk
- Vishnevsky Institute of Surgery, Ministry of Health of the Russian Federation, 27 Bol'shaya Serpukhovskaya str, Moscow, 117997, Russia
| | - Maria S Fedorova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova str, Moscow, 119991, Russia
| | - Elena A Pudova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova str, Moscow, 119991, Russia
| | - Maria V Savvateeva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova str, Moscow, 119991, Russia
| | - Anastasiya V Lipatova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova str, Moscow, 119991, Russia
| | - Zulfiya G Guvatova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova str, Moscow, 119991, Russia
| | - Andrey D Kaprin
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, 3 2nd Botkinski drive, Moscow, 125284, Russia
| | - Marina V Kiseleva
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, 3 2nd Botkinski drive, Moscow, 125284, Russia
| | - Tatiana B Demidova
- A. N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 33 Leninskij prosp, Moscow, 119071, Russia
| | - Sergey A Simanovsky
- A. N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 33 Leninskij prosp, Moscow, 119071, Russia
| | - Nataliya V Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova str, Moscow, 119991, Russia
| | - Alexey A Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova str, Moscow, 119991, Russia
| | - George S Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova str, Moscow, 119991, Russia
| | - Anastasiya V Snezhkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova str, Moscow, 119991, Russia.
| | - Anna V Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova str, Moscow, 119991, Russia
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10
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Chen G, Wang L, Diao T, Chen Y, Cao C, Zhang X. Analysis of immune-related signatures of colorectal cancer identifying two different immune phenotypes: Evidence for immune checkpoint inhibitor therapy. Oncol Lett 2020; 20:517-524. [PMID: 32565977 PMCID: PMC7285802 DOI: 10.3892/ol.2020.11605] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 02/05/2020] [Indexed: 12/24/2022] Open
Abstract
Immune checkpoint inhibitor (ICI) therapy has revolutionized the treatment of numerous types of cancer, including colorectal cancer (CRC). Patients with CRC and deficient mismatch repair or high microsatellite instability could benefit from ICI treatment, although the response rate of most patients is low. Therefore, the immune subtyping of patients with CRC is required in order to determine the subtypes suitable for ICI treatment. The present study used a cohort of patients with CRC from The Cancer Genome Atlas (TCGA) to perform molecular subtyping, with results validated in three CRC cohorts from the Gene Expression Omnibus. Non-negative matrix factorization was used to achieve consensus molecular subtyping. The tumor immune dysfunction and exclusion algorithm was used to predict potential ICI therapy responses and gene set enrichment analysis was performed to define different pathways associated with the immune response. Two distinct subtypes of CRC were finally identified in TCGA cohorts, which were characterized as significantly different prognostic subtypes (low-risk and high-risk subtypes). Higher expression of programmed death-ligand 1, higher proportion of tumor-infiltrating lymphocytes and tumor mutation burden were significantly enriched in the low-risk subtype. Further pathway analysis revealed that the low-risk subtype was associated with immune response activation and signaling pathways involved in ‘antigen processing and presentation’. Three independent CRC cohorts were used to validate the above findings. In summary, two clinical CRC subtypes were identified, which are characterized by significantly different survival outcomes and immune infiltration patterns. The findings of the present study suggest that ICI treatment may be more effective in the low-risk CRC subtype.
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Affiliation(s)
- Gang Chen
- Department of Anal and Intestinal Surgery, Tengzhou Central People's Hospital, Tengzhou, Shandong 277500, P.R. China
| | - Lin Wang
- Department of Surgery Operating Room, Tengzhou Central People's Hospital, Tengzhou, Shandong 277500, P.R. China
| | - Tongwei Diao
- Department of Anal and Intestinal Surgery, Tengzhou Central People's Hospital, Tengzhou, Shandong 277500, P.R. China
| | - Ying Chen
- Department of Anal and Intestinal Surgery, Tengzhou Central People's Hospital, Tengzhou, Shandong 277500, P.R. China
| | - Chengbo Cao
- Department of Anal and Intestinal Surgery, Tengzhou Central People's Hospital, Tengzhou, Shandong 277500, P.R. China
| | - Xindong Zhang
- Department of Pathology, Tengzhou Central People's Hospital, Tengzhou, Shandong 277500, P.R. China
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Baranova AV, Klimontov VV, Letyagin AY, Orlov YL. Medical genomics research at BGRS-2018. BMC Med Genomics 2019; 12:36. [PMID: 30871564 PMCID: PMC6416836 DOI: 10.1186/s12920-019-0480-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- Ancha V Baranova
- School of Systems Biology, George Mason University, Fairfax, VA, USA.,Research Centre for Medical Genetics, Moscow, 115478, Russia
| | - Vadim V Klimontov
- Institute of Cytology and Genetics SB RAS, 630090, Novosibirsk, Russia
| | - Andrey Y Letyagin
- Institute of Cytology and Genetics SB RAS, 630090, Novosibirsk, Russia
| | - Yuriy L Orlov
- Institute of Cytology and Genetics SB RAS, 630090, Novosibirsk, Russia. .,Novosibirsk State University, 630090, Novosibirsk, Russia.
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