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Nie F, Jiang J, Ning J. Exploration of the prognostic value of methylation regulators related to m5C in papillary thyroid carcinoma. Medicine (Baltimore) 2024; 103:e38623. [PMID: 38905403 PMCID: PMC11191899 DOI: 10.1097/md.0000000000038623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/28/2024] [Indexed: 06/23/2024] Open
Abstract
The incidence of papillary thyroid carcinoma (PTC) has increased significantly in recent years, and for patients with metastatic and recurrent PTC, the options for treatment currently available are insufficient. To date, the exact molecular mechanism underlying PTC is still not fully understood. 5-Methylcytosine (m5C) RNA methylation is associated with the prognosis of a variety of tumors. However, the molecular mechanisms and biomarkers associated with m5C in the diagnosis, treatment, and prognosis of this disease have not been fully elucidated. Ten m5C regulators with significantly different expression levels were included in this study. Immune infiltration analysis revealed significant negative correlations between most of these regulators and regulatory T cells. TRDMT1, NSUN5, and NSUN6 had high weights and strong correlations in the protein-protein interaction network. Using gene ontology, Kyoto Encyclopedia of Genes and Genomes, and gene set enrichment analysis, 1489 differentially expressed genes were screened from The Cancer Genome Atlas messenger RNA matrix, indicating that these differentially expressed genes were significantly enriched in various pathways and functions related to cancers. Four m5C regulators, NSUN2, NSUN4, NSUN6, and DNMT3B, were screened as prognostic markers by least absolute shrinkage and selection operator regression analysis, and NSUN2 and NSUN6 were identified as risk factors for poor prognosis. We found that the prognostic prediction model constructed using the m5C regulators NSUN2, NSUN4, NSUN6, and DNMT3B showed good prognostic prediction ability and diagnostic ability. This model was applied to predict the survival probability of patients with PTC, the prediction ability of 5-year survival was the best. The multi-factor prognostic prediction model combined with the tumor node metastasis stage and risk score grouping showed better prognostic predictive power.
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Affiliation(s)
- Furong Nie
- Department of Endocrinology, Shenzhen Longhua District Central Hospital, Shenzhen 518110, Guangdong, China
| | - Jiacheng Jiang
- Department of Hepatology, The First Hospital of Hunan University of Chinese Medicine, Changsha 410007, Hunan, China
| | - Jie Ning
- Department of Endocrinology, Shenzhen Longhua District Central Hospital, Shenzhen 518110, Guangdong, China
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2
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Sun C, Kathuria K, Emery SB, Kim B, Burbulis IE, Shin JH, Weinberger DR, Moran JV, Kidd JM, Mills RE, McConnell MJ. Mapping recurrent mosaic copy number variation in human neurons. Nat Commun 2024; 15:4220. [PMID: 38760338 PMCID: PMC11101435 DOI: 10.1038/s41467-024-48392-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/29/2024] [Indexed: 05/19/2024] Open
Abstract
When somatic cells acquire complex karyotypes, they often are removed by the immune system. Mutant somatic cells that evade immune surveillance can lead to cancer. Neurons with complex karyotypes arise during neurotypical brain development, but neurons are almost never the origin of brain cancers. Instead, somatic mutations in neurons can bring about neurodevelopmental disorders, and contribute to the polygenic landscape of neuropsychiatric and neurodegenerative disease. A subset of human neurons harbors idiosyncratic copy number variants (CNVs, "CNV neurons"), but previous analyses of CNV neurons are limited by relatively small sample sizes. Here, we develop an allele-based validation approach, SCOVAL, to corroborate or reject read-depth based CNV calls in single human neurons. We apply this approach to 2,125 frontal cortical neurons from a neurotypical human brain. SCOVAL identifies 226 CNV neurons, which include a subclass of 65 CNV neurons with highly aberrant karyotypes containing whole or substantial losses on multiple chromosomes. Moreover, we find that CNV location appears to be nonrandom. Recurrent regions of neuronal genome rearrangement contain fewer, but longer, genes.
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Affiliation(s)
- Chen Sun
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA
| | - Kunal Kathuria
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD, 21205, USA
| | - Sarah B Emery
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI, 48109, USA
| | - ByungJun Kim
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA
| | - Ian E Burbulis
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, 22902, USA
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Sede de la Patagonia, Puerto Montt, Chile
| | - Joo Heon Shin
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD, 21205, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences and Neuroscience, Johns Hopkins School of Medicine, 600 North Wolfe Street, Baltimore, MD, 21287, USA
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, 733 North Broadway, Baltimore, MD, 21230, USA
| | - John V Moran
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI, 48109, USA
- Department of Internal Medicine, University of Michigan Medical School, 1500 East Medical Center Drive, Ann Arbor, MI, 48109, USA
| | - Jeffrey M Kidd
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI, 48109, USA
| | - Ryan E Mills
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA.
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI, 48109, USA.
| | - Michael J McConnell
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD, 21205, USA.
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3
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Huang J, Wang J, Xv J, Wang J, Wang G, Zhao Y. Genetic alterations and allele frequency of BRAF V600E and TERT mutation in papillary thyroid carcinoma with intermediate-to-high recurrence risk: a retrospective study. Clin Exp Med 2024; 24:76. [PMID: 38607456 PMCID: PMC11014806 DOI: 10.1007/s10238-024-01320-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Accepted: 03/02/2024] [Indexed: 04/13/2024]
Abstract
The predictive value of allele frequency (AF) of BRAF V600E and TERT mutations in papillary thyroid carcinoma (PTC) remains controversial. We aimed to investigate the AF of BRAF V600E and TERT mutations in intermediate-to-high risk PTC and their association between tumor invasiveness, prognosis, and other mutations. Probe hybridization capture and high-throughput sequencing were used to quantitatively test 40 gene loci in 94 intermediate-to-high recurrence risk PTC patients, combined with clinical characteristics and follow-up for retrospective analysis. BRAF V600E mutation AF was linked to a increased risk of thyroid capsule penetration, recurrence, and concurrent mutations. Concurrent mutations could lead to a worse prognosis and increased invasiveness. TERT promoter mutation frequently accompanied other mutations and resulted in a poorer prognosis. However, there was no clear association between the TERT mutation AF and tumor invasiveness or recurrence. The sensitivity and specificity of predicting recurrence in intermediate-to-high risk PTC with BRAF V600E mutation AF > 28.2% were 60 and 80%. Although genetic alterations in PTC can differ among different ethnicities, the AF of BRAF V600E and TERT mutations may be similar. The AF of BRAF V600E has the potential to be a novel indicator in predicting PTC invasiveness and prognosis.
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Affiliation(s)
- Jiayu Huang
- Department of Thyroid Surgery, The Second Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Jiazhi Wang
- Department of Thyroid Surgery, The Second Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Jingchao Xv
- Department of Thyroid Surgery, The Second Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Jingran Wang
- Department of Thyroid Surgery, The Second Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Guangzhi Wang
- Department of Thyroid Surgery, The Second Hospital of Dalian Medical University, Dalian, Liaoning, China.
| | - Yongfu Zhao
- Department of Thyroid Surgery, The Second Hospital of Dalian Medical University, Dalian, Liaoning, China.
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4
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Tahara M, Kiyota N, Imai H, Takahashi S, Nishiyama A, Tamura S, Shimizu Y, Kadowaki S, Ito KI, Toyoshima M, Hirashima Y, Ueno S, Sugitani I. A Phase 2 Study of Encorafenib in Combination with Binimetinib in Patients with Metastatic BRAF-Mutated Thyroid Cancer in Japan. Thyroid 2024; 34:467-476. [PMID: 38343359 DOI: 10.1089/thy.2023.0547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/16/2024]
Abstract
Background: Driver mutations at BRAF V600 are frequently identified in papillary thyroid cancer and anaplastic thyroid cancer (ATC), in which BRAF inhibitors have shown clinical effectiveness. This Japanese phase 2 study evaluated the efficacy and safety of a BRAF inhibitor, encorafenib, combined with an MEK inhibitor, binimetinib, in patients with BRAF V600-mutated thyroid cancer. Methods: This phase 2, open-label, uncontrolled study was conducted at 10 institutions targeted patients with BRAF V600-mutated locally advanced or distant metastatic thyroid cancer not amenable to curative treatment who became refractory/intolerant to ≥1 previous vascular endothelial growth factor receptor-targeted regimen(s) or were considered ineligible for those. The primary endpoint was centrally assessed objective response rate (ORR). The secondary endpoints included duration of response (DOR), progression-free survival (PFS), overall survival (OS), and safety. Results: We enrolled 22 patients with BRAFV600E-mutated thyroid cancer: 17 had differentiated thyroid cancer (DTC), and 5 had ATC. At data cutoff (October 26, 2022), the median follow-up was 11.5 (range = 3.4-19.0) months. The primary endpoint of centrally assessed ORR was 54.5% (95% confidence interval [CI] 32.2-75.6; partial response in 12 patients and stable disease in 10). The ORRs in patients with DTC and ATC were 47.1% (8 of 17) and 80.0% (4 of 5), respectively. The medians for DOR and PFS by central assessment and for OS were not reached in the overall population, the DTC subgroup, or the ATC subgroup. At 12 months, the rate of ongoing response was 90.9%, and the PFS and OS rates were 78.8% and 81.8%, respectively. All patients developed ≥1 adverse events (AEs): grade 3 AEs in 6 patients (27.3%). No patients developed grade 4-5 AEs. The most common grade 3 AE was lipase increased (4 patients [18.2%]). Those toxicities were mostly manageable with appropriate monitoring and dose adjustment. Conclusions: Treatment with encorafenib plus binimetinib met the primary endpoint criteria and demonstrated clinical benefit in patients with BRAFV600E-mutated thyroid cancer regardless of its histological type, such as DTC or ATC, with no new safety concerns identified. Encorafenib plus binimetinib could thus be a new treatment option for BRAF V600-mutated thyroid cancer. Clinical Trial Registration number: Japan Registry of Clinical Trials: jRCT2011200018.
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Affiliation(s)
- Makoto Tahara
- Department of Head and Neck Medical Oncology, National Cancer Center Hospital East, Kashiwa, Chiba, Japan
| | - Naomi Kiyota
- Department of Medical Oncology and Hematology, Cancer Center, Kobe University Hospital, Kobe, Hyogo, Japan
| | - Hiroo Imai
- Department of Medical Oncology, Tohoku University Hospital, Sendai, Miyagi, Japan
| | - Shunji Takahashi
- Department of Medical Oncology, The Cancer Institute Hospital of JFCR, Koto-ku, Tokyo, Japan
| | - Akihiro Nishiyama
- Department of Medical Oncology, Kanazawa University Hospital, Kanazawa, Ishikawa, Japan
| | - Shingo Tamura
- Department of Medical Oncology, Clinical Research Institute, National Hospital Organization Kyushu Medical Center, Fukuoka, Fukuoka, Japan
| | - Yasushi Shimizu
- Department of Medical Oncology, Hokkaido University Hospital, Sapporo, Hokkaido, Japan
| | - Shigenori Kadowaki
- Department of Clinical Oncology, Aichi Cancer Center Hospital, Nagoya, Aichi, Japan
| | - Ken-Ichi Ito
- Division of Breast and Endocrine Surgery, Department of Surgery, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
| | | | | | | | - Iwao Sugitani
- Department of Endocrinology, Nippon Medical School Hospital, Bunkyo-ku, Tokyo, Japan
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5
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Fagin JA, Krishnamoorthy GP, Landa I. Pathogenesis of cancers derived from thyroid follicular cells. Nat Rev Cancer 2023; 23:631-650. [PMID: 37438605 PMCID: PMC10763075 DOI: 10.1038/s41568-023-00598-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/08/2023] [Indexed: 07/14/2023]
Abstract
The genomic simplicity of differentiated cancers derived from thyroid follicular cells offers unique insights into how oncogenic drivers impact tumour phenotype. Essentially, the main oncoproteins in thyroid cancer activate nodes in the receptor tyrosine kinase-RAS-BRAF pathway, which constitutively induces MAPK signalling to varying degrees consistent with their specific biochemical mechanisms of action. The magnitude of the flux through the MAPK signalling pathway determines key elements of thyroid cancer biology, including differentiation state, invasive properties and the cellular composition of the tumour microenvironment. Progression of disease results from genomic lesions that drive immortalization, disrupt chromatin accessibility and cause cell cycle checkpoint dysfunction, in conjunction with a tumour microenvironment characterized by progressive immunosuppression. This Review charts the genomic trajectories of these common endocrine tumours, while connecting them to the biological states that they confer.
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Affiliation(s)
- James A Fagin
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Gnana P Krishnamoorthy
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Iñigo Landa
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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6
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Bu R, Siraj AK, Azam S, Iqbal K, Qadri Z, Al-Rasheed M, Al-Sobhi SS, Al-Dayel F, Al-Kuraya KS. Whole Exome-Wide Association Identifies Rare Variants in GALNT9 Associated with Middle Eastern Papillary Thyroid Carcinoma Risk. Cancers (Basel) 2023; 15:4235. [PMID: 37686511 PMCID: PMC10486701 DOI: 10.3390/cancers15174235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/17/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
Papillary thyroid carcinoma (PTC) is the commonest thyroid cancer. The majority of inherited causes of PTC remain elusive. However, understanding the genetic underpinnings and origins remains a challenging endeavor. An exome-wide association study was performed to identify rare germline variants in coding regions associated with PTC risk in the Middle Eastern population. By analyzing exome-sequencing data from 249 PTC patients (cases) and 1395 individuals without any known cancer (controls), GALNT9 emerged as being strongly associated with rare inactivating variants (RIVs) (4/249 cases vs. 1/1395 controls, OR = 22.75, p = 5.09 × 10-5). Furthermore, three genes, TRIM40, ARHGAP23, and SOX4, were enriched for rare damaging variants (RDVs) at the exome-wide threshold (p < 2.5 × 10-6). An additional seven genes (VARS1, ZBED9, PRRC2A, VWA7, TRIM31, TRIM40, and COL8A2) were associated with a Middle Eastern PTC risk based on the sequence kernel association test (SKAT). This study underscores the potential of GALNT9 and other implicated genes in PTC predisposition, illuminating the need for large collaborations and innovative approaches to understand the genetic heterogeneity of PTC predisposition.
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Affiliation(s)
- Rong Bu
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Center, P.O. Box 3354, Riyadh 11211, Saudi Arabia; (R.B.); (A.K.S.); (S.A.); (K.I.); (Z.Q.); (M.A.-R.)
| | - Abdul K. Siraj
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Center, P.O. Box 3354, Riyadh 11211, Saudi Arabia; (R.B.); (A.K.S.); (S.A.); (K.I.); (Z.Q.); (M.A.-R.)
| | - Saud Azam
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Center, P.O. Box 3354, Riyadh 11211, Saudi Arabia; (R.B.); (A.K.S.); (S.A.); (K.I.); (Z.Q.); (M.A.-R.)
| | - Kaleem Iqbal
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Center, P.O. Box 3354, Riyadh 11211, Saudi Arabia; (R.B.); (A.K.S.); (S.A.); (K.I.); (Z.Q.); (M.A.-R.)
| | - Zeeshan Qadri
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Center, P.O. Box 3354, Riyadh 11211, Saudi Arabia; (R.B.); (A.K.S.); (S.A.); (K.I.); (Z.Q.); (M.A.-R.)
| | - Maha Al-Rasheed
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Center, P.O. Box 3354, Riyadh 11211, Saudi Arabia; (R.B.); (A.K.S.); (S.A.); (K.I.); (Z.Q.); (M.A.-R.)
| | - Saif S. Al-Sobhi
- Department of Surgery, King Faisal Specialist Hospital and Research Center, P.O. Box 3354, Riyadh 11211, Saudi Arabia;
| | - Fouad Al-Dayel
- Department of Pathology, King Faisal Specialist Hospital and Research Center, P.O. Box 3354, Riyadh 11211, Saudi Arabia;
| | - Khawla S. Al-Kuraya
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Center, P.O. Box 3354, Riyadh 11211, Saudi Arabia; (R.B.); (A.K.S.); (S.A.); (K.I.); (Z.Q.); (M.A.-R.)
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7
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Sun C, Kathuria K, Emery SB, Kim B, Burbulis IE, Shin JH, Weinberger DR, Moran JV, Kidd JM, Mills RE, McConnell MJ. Mapping the Complex Genetic Landscape of Human Neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.07.531594. [PMID: 36945473 PMCID: PMC10028870 DOI: 10.1101/2023.03.07.531594] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
When somatic cells acquire complex karyotypes, they are removed by the immune system. Mutant somatic cells that evade immune surveillance can lead to cancer. Neurons with complex karyotypes arise during neurotypical brain development, but neurons are almost never the origin of brain cancers. Instead, somatic mutations in neurons can bring about neurodevelopmental disorders, and contribute to the polygenic landscape of neuropsychiatric and neurodegenerative disease. A subset of human neurons harbors idiosyncratic copy number variants (CNVs, "CNV neurons"), but previous analyses of CNV neurons have been limited by relatively small sample sizes. Here, we developed an allele-based validation approach, SCOVAL, to corroborate or reject read-depth based CNV calls in single human neurons. We applied this approach to 2,125 frontal cortical neurons from a neurotypical human brain. This approach identified 226 CNV neurons, as well as a class of CNV neurons with complex karyotypes containing whole or substantial losses on multiple chromosomes. Moreover, we found that CNV location appears to be nonrandom. Recurrent regions of neuronal genome rearrangement contained fewer, but longer, genes.
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Affiliation(s)
- Chen Sun
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA
| | - Kunal Kathuria
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | - Sarah B Emery
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA
| | - ByungJun Kim
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA
| | - Ian E. Burbulis
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA 22902, USA
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Sede de la Patagonia, Puerto Montt, Chile
| | - Joo Heon Shin
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | | | - Daniel R. Weinberger
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA
- Department of Psychiatry and Behavioral Sciences and Neuroscience, Johns Hopkins School of Medicine, 600 North Wolfe Street, Baltimore, MD 21287, USA
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, 733 North Broadway, Baltimore, MD 21230, USA
| | - John V. Moran
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, University of Michigan Medical School, 1500 East Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Jeffrey M. Kidd
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA
| | - Ryan E. Mills
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA
| | - Michael J. McConnell
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA
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Cui S, McGranahan N, Gao J, Chen P, Jiang W, Yang L, Ma L, Liao J, Xie T, Xie C, Enver T, Wu S. Tracking the evolution of esophageal squamous cell carcinoma under dynamic immune selection by multi-omics sequencing. Nat Commun 2023; 14:892. [PMID: 36807354 PMCID: PMC9938262 DOI: 10.1038/s41467-023-36558-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 02/06/2023] [Indexed: 02/19/2023] Open
Abstract
Intratumoral heterogeneity (ITH) has been linked to decreased efficacy of clinical treatments. However, although genomic ITH has been characterized in genetic, transcriptomic and epigenetic alterations are hallmarks of esophageal squamous cell carcinoma (ESCC), the extent to which these are heterogeneous in ESCC has not been explored in a unified framework. Further, the extent to which tumor-infiltrated T lymphocytes are directed against cancer cells, but how the immune infiltration acts as a selective force to shape the clonal evolution of ESCC is unclear. In this study, we perform multi-omic sequencing on 186 samples from 36 primary ESCC patients. Through multi-omics analyses, it is discovered that genomic, epigenomic, and transcriptomic ITH are underpinned by ongoing chromosomal instability. Based on the RNA-seq data, we observe diverse levels of immune infiltrate across different tumor sites from the same tumor. We reveal genetic mechanisms of neoantigen evasion under distinct selection pressure from the diverse immune microenvironment. Overall, our work offers an avenue of dissecting the complex contribution of the multi-omics level to the ITH in ESCC and thereby enhances the development of clinical therapy.
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Affiliation(s)
- Sijia Cui
- Department of Radiation and Medical Oncology, Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | | | - Jing Gao
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Peng Chen
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Wei Jiang
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Lingrong Yang
- Hangzhou Cancer Institution, Hangzhou Cancer Hospital, Hangzhou, China
| | - Li Ma
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Junfang Liao
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Tian Xie
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Congying Xie
- Department of Radiation and Medical Oncology, Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.
| | - Tariq Enver
- Cancer Institute, University College London, London, UK.
| | - Shixiu Wu
- Department of Radiation and Medical Oncology, Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China. .,National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China.
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9
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Schiantarelli J, Pappa T, Conway J, Crowdis J, Reardon B, Dietlein F, Huang J, Stanizzi D, Carey E, Bosma-Moody A, Imamovic A, Han S, Camp S, Kofman E, Shannon E, Barletta JA, He MX, Liu D, Park J, Lorch JH, Van Allen EM. Mutational Footprint of Platinum Chemotherapy in a Secondary Thyroid Cancer. JCO Precis Oncol 2022; 6:e2200183. [PMID: 36075011 PMCID: PMC9489159 DOI: 10.1200/po.22.00183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/27/2022] [Accepted: 07/19/2022] [Indexed: 11/20/2022] Open
Affiliation(s)
- Julia Schiantarelli
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of Harvard and MIT, Cambridge, MA
| | - Theodora Pappa
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of Harvard and MIT, Cambridge, MA
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women's Hospital, Boston, MA
| | - Jake Conway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of Harvard and MIT, Cambridge, MA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - Jett Crowdis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of Harvard and MIT, Cambridge, MA
| | - Brendan Reardon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of Harvard and MIT, Cambridge, MA
| | - Felix Dietlein
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of Harvard and MIT, Cambridge, MA
| | | | - Darren Stanizzi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Evan Carey
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Alice Bosma-Moody
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of Harvard and MIT, Cambridge, MA
| | - Alma Imamovic
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of Harvard and MIT, Cambridge, MA
| | - Seunghun Han
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of Harvard and MIT, Cambridge, MA
- Department of Biological and Biomedical Sciences, Harvard Medical School, Boston, MA
| | - Sabrina Camp
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of Harvard and MIT, Cambridge, MA
| | - Eric Kofman
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA
| | - Erin Shannon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of Harvard and MIT, Cambridge, MA
| | - Justine A. Barletta
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Meng Xiao He
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of Harvard and MIT, Cambridge, MA
- Harvard Graduate Program in Biophysics, Boston, MA
| | - David Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of Harvard and MIT, Cambridge, MA
| | - Jihye Park
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of Harvard and MIT, Cambridge, MA
| | - Jochen H. Lorch
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Eliezer M. Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of Harvard and MIT, Cambridge, MA
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10
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Cheng P, Lan Y, Liao J, Zhao E, Yan H, Xu L, A S, Ping Y, Xu J. Systematic investigation of the prognostic impact of clonal status of somatic mutations across multiple cancer types. Genomics 2022; 114:110412. [PMID: 35714828 DOI: 10.1016/j.ygeno.2022.110412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 05/15/2022] [Accepted: 06/10/2022] [Indexed: 11/18/2022]
Abstract
Tumors are genetically heterogeneous and many mutations are actually present in subclonal populations. The clonal status of mutations is valuable for accurate prognosis, clinical management. The aim of this study was to identify the clonal status of somatic mutations and systematically evaluate their prognostic values across various cancer types. We totally identified 227 clonal and 432 subclonal mutations contributed to prognosis and demonstrated the importance of clonal status in improving mutation-related clinical guidance. We further developed a customized multi-step approach to identify gene-specific prognostic patterns of clonal status at pan-cancer level and found some cancer-specific prognostic patterns. The 'subclonal-dependent risk' subpattern was one of the most common subpatterns, it usually accompanied by high genomic in-stability and high extent of intra-tumor heterogeneity and could be used to improve the accuracy of prognostic analysis. Our results revealed the importance of clonal status, especially subclonal mutation in clinical survival.
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Affiliation(s)
- Peng Cheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Yujia Lan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Jianlong Liao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Erjie Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Haoteng Yan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China; Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
| | - Liwen Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Suru A
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Yanyan Ping
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China.
| | - Jinyuan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China.
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11
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Siraj S, Masoodi T, Siraj AK, Azam S, Qadri Z, Parvathareddy SK, Bu R, Siddiqui KS, Al-Sobhi SS, AlDawish M, Al-Kuraya KS. APOBEC SBS13 Mutational Signature-A Novel Predictor of Radioactive Iodine Refractory Papillary Thyroid Carcinoma. Cancers (Basel) 2022; 14:cancers14061584. [PMID: 35326735 PMCID: PMC8946015 DOI: 10.3390/cancers14061584] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/03/2022] [Accepted: 03/15/2022] [Indexed: 02/04/2023] Open
Abstract
Standard surgery followed by radioactive iodine (131I, RAI) therapy are not curative for 5−20% of papillary thyroid carcinoma (PTC) patients with RAI refractory disease. Early predictors indicating therapeutic response to RAI therapy in PTC are yet to be elucidated. Whole-exome sequencing was performed (at median depth 198x) on 66 RAI-refractory and 92 RAI-avid PTCs with patient-matched germline. RAI-refractory tumors were significantly associated with distinct aggressive clinicopathological features, including positive surgical margins (p = 0.016) and the presence of lymph node metastases at primary diagnosis (p = 0.012); higher nonsilent tumor mutation burden (p = 0.011); TERT promoter (TERTp) mutation (p < 0.0001); and the enrichment of the APOBEC-related single-base substitution (SBS) COSMIC mutational signatures 2 (p = 0.030) and 13 (p < 0.001). Notably, SBS13 (odds ratio [OR] 30.4, 95% confidence intervals [CI] 1.43−647.22) and TERTp mutation (OR 41.3, 95% CI 4.35−391.60) were revealed to be independent predictors of RAI refractoriness in PTC (p = 0.029 and 0.001, respectively). Although SBS13 and TERTp mutations alone highly predicted RAI refractoriness, when combined, they significantly increased the likelihood of predicting RAI refractoriness in PTC. This study highlights the APOBEC SBS13 mutational signature as a novel independent predictor of RAI refractoriness in a distinct subgroup of PTC.
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Affiliation(s)
- Sarah Siraj
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.K.P.); (R.B.)
| | - Tariq Masoodi
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.K.P.); (R.B.)
| | - Abdul K. Siraj
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.K.P.); (R.B.)
| | - Saud Azam
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.K.P.); (R.B.)
| | - Zeeshan Qadri
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.K.P.); (R.B.)
| | - Sandeep K. Parvathareddy
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.K.P.); (R.B.)
| | - Rong Bu
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.K.P.); (R.B.)
| | - Khawar S. Siddiqui
- Department of Pediatric Hematology-Oncology, King Faisal Specialist Hospital and Research Center, P.O. Box 3354, Riyadh 11211, Saudi Arabia;
| | - Saif S. Al-Sobhi
- Department of Surgery, King Faisal Specialist Hospital and Research Center, P.O. Box 3354, Riyadh 11211, Saudi Arabia;
| | - Mohammed AlDawish
- Department of Endocrinology and Diabetes, Prince Sultan Military Medical City, P.O. Box 261370, Riyadh 11342, Saudi Arabia;
| | - Khawla S. Al-Kuraya
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.K.P.); (R.B.)
- Correspondence: ; Tel.: +966-112-055-2167
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12
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Wang Z, Tang P, Hua S, Gao J, Zhang B, Wan H, Wu Q, Zhang J, Chen G. Genetic and Clinicopathologic Characteristics of Papillary Thyroid Carcinoma in the Chinese Population: High BRAF Mutation Allele Frequency, Multiple Driver Gene Mutations, and RET Fusion May Indicate More Advanced TN Stage. Onco Targets Ther 2022; 15:147-157. [PMID: 35173448 PMCID: PMC8841610 DOI: 10.2147/ott.s339114] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 01/02/2022] [Indexed: 11/23/2022] Open
Affiliation(s)
- Zhihong Wang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
| | - Peng Tang
- Department of Breast and Thyroid Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, People’s Republic of China
| | - Surong Hua
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
| | - Junyi Gao
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
| | - Bin Zhang
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, People’s Republic of China
| | - Hua Wan
- Research and Development Department, Beijing USCI Medical Laboratory, Beijing, People’s Republic of China
| | - Qixi Wu
- Research and Development Department, Beijing USCI Medical Laboratory, Beijing, People’s Republic of China
| | - Jiaxin Zhang
- Department of Thyroid and Breast Surgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, People’s Republic of China
- Correspondence: Ge Chen, Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, No. 1 Shuai Fu Yuan Hu Tong, Beijing, 100730, People’s Republic of China, Tel +86 156 1123 3738, Fax +86 156 69152600, Email ; Jiaxin Zhang, Department of Thyroid and Breast Surgery, Affiliated Hospital of Xuzhou Medical University, No. 99, Huaihai West Road, Xuzhou, 221004, People’s Republic of China, Tel +86 180 5226 8693, Fax +86 180 85802306, Email
| | - Ge Chen
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
- Correspondence: Ge Chen, Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, No. 1 Shuai Fu Yuan Hu Tong, Beijing, 100730, People’s Republic of China, Tel +86 156 1123 3738, Fax +86 156 69152600, Email ; Jiaxin Zhang, Department of Thyroid and Breast Surgery, Affiliated Hospital of Xuzhou Medical University, No. 99, Huaihai West Road, Xuzhou, 221004, People’s Republic of China, Tel +86 180 5226 8693, Fax +86 180 85802306, Email
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13
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Alexander EK. Novel Genomic Roadmaps and Their Clinical Translation Ahead. J Clin Endocrinol Metab 2022; 107:e886-e887. [PMID: 34131747 PMCID: PMC8764213 DOI: 10.1210/clinem/dgab423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Indexed: 11/22/2022]
Affiliation(s)
- Erik K Alexander
- Chief, Thyroid Section, Brigham & Women’s Hospital; Professor of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Correspondence: Erik K. Alexander, MD, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA.
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14
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Jacquemin V, Antoine M, Dom G, Detours V, Maenhaut C, Dumont JE. Dynamic Cancer Cell Heterogeneity: Diagnostic and Therapeutic Implications. Cancers (Basel) 2022; 14:280. [PMID: 35053446 PMCID: PMC8773841 DOI: 10.3390/cancers14020280] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 12/12/2022] Open
Abstract
Though heterogeneity of cancers is recognized and has been much discussed in recent years, the concept often remains overlooked in different routine examinations. Indeed, in clinical or biological articles, reviews, and textbooks, cancers and cancer cells are generally presented as evolving distinct entities rather than as an independent heterogeneous cooperative cell population with its self-oriented biology. There are, therefore, conceptual gaps which can mislead the interpretations/diagnostic and therapeutic approaches. In this short review, we wish to summarize and discuss various aspects of this dynamic evolving heterogeneity and its biological, pathological, clinical, diagnostic, and therapeutic implications, using thyroid carcinoma as an illustrative example.
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Affiliation(s)
- Valerie Jacquemin
- Correspondence: (V.J.); (J.E.D.); Tel.: +32-2-555-32-26 (V.J.); +32-2-555-41-34 (J.E.D.)
| | | | | | | | | | - Jacques E. Dumont
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), Université Libre de Bruxelles, 1070 Brussels, Belgium; (M.A.); (G.D.); (V.D.); (C.M.)
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15
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Yu T, Gao X, Zheng Z, Zhao X, Zhang S, Li C, Liu G. Intratumor Heterogeneity as a Prognostic Factor in Solid Tumors: A Systematic Review and Meta-Analysis. Front Oncol 2021; 11:744064. [PMID: 34722299 PMCID: PMC8554141 DOI: 10.3389/fonc.2021.744064] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/17/2021] [Indexed: 11/13/2022] Open
Abstract
Background The landscape of intratumor heterogeneity (ITH) is present from the tumor evolution. ITH is a promising clinical indicator, but the association between ITH and prognosis remains controversial. Therefore, a meta-analysis was performed to explore whether ITH can serve as a valuable prognostic indicator in solid tumors. Methods All included studies were from PubMed, Embase, Cochrane, and Web of Science databases up to October 10, 2020. Studies based on ITH with available prognostic information were included. Three researchers independently completed study selection and data extraction following PRISMA guidelines. The random-effect model was used for synthesis. Hazard ratio (HR) and 95% confidence intervals (CI) were used with the endpoint defined by overall survival (OS), disease-specific survival (DFS), and progression-free survival (PFS). Results A total of 9,804 solid tumor patients from 21 studies were included. Analysis of specific cancers in the TCGA database showed similar results based on different ITH assessment methods, which provided the logical support for data consolidation. Available evidence revealed a negative relationship between ITH and prognosis for a specific cancer (such as lung cancer). However, the OS results from 14 tumor types showed that high ITH associated with shorter survival time [HR 1.65 (95% CI, 1.42-1.91)]. PFS and DFS analyses showed similar results [HR 1.89 (95% CI, 1.41-2.54) and HR 1.87 (95% CI, 1.15-3.04)] in general. The status of tumor metastasis and sampling models were not the confounding factors. Conclusions High ITH is associated with worse prognosis in many solid tumors in general although this association was absent for some cancers. ITH is expected to be a promising clinical prognostic factor for the improvement of assessment, treatment, and surveillance strategy.
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Affiliation(s)
- Tao Yu
- Department of Oncology, Tianjin Medical University General Hospital, Tianjin, China
| | - Xin Gao
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, China.,Institute of General Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Zicheng Zheng
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, China.,Institute of General Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Xinyu Zhao
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, China.,Institute of General Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Shiyao Zhang
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, China.,Institute of General Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Chunqiang Li
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, China.,Institute of General Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Gang Liu
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, China.,Institute of General Surgery, Tianjin Medical University General Hospital, Tianjin, China
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16
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Wang Q, Zhao N, Zhang J. Gene Mutation Analysis in Papillary Thyroid Carcinoma Using a Multi-Gene Panel in China. Int J Gen Med 2021; 14:5139-5148. [PMID: 34511996 PMCID: PMC8421255 DOI: 10.2147/ijgm.s327409] [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: 07/14/2021] [Accepted: 08/17/2021] [Indexed: 01/15/2023] Open
Abstract
Purpose To detect low-frequency mutation in the 57 genes of small panels that are associated with developing thyroid cancer in papillary thyroid carcinoma (PTC) patients and provide patients with precise-targeted therapy. Patients and Methods This study included 144 patients diagnosed with PTC who underwent total thyroidectomy and lymph node dissection in the central area of the neck between May 2017 and October 2018. We performed ultra-deep sequencing of 57 genes from 144 patients and detected the 57 genes mutations with bioinformatics. Results There were 698 mutations in 45 genes from 138 PTC patients. A high frequency of mutations was detected in the RBM10 gene (44%) and TERT (43%), and some hotspot mutations, such as RBM10:p.E119D and TERT:p.P112fs, were also found. Conclusion Ultra-deep sequencing of small gene panels can find some low-frequency mutation genes, which can provide targeted therapy for patients.
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Affiliation(s)
- Qiang Wang
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, People's Republic of China.,Department of Thyroid surgery, Shanxi Provincial People's Hospital Affiliated to Shanxi Medical University, Taiyuan, 030000, People's Republic of China
| | - Ning Zhao
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Jun Zhang
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, People's Republic of China
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17
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Muzza M, Pogliaghi G, Persani L, Fugazzola L, Colombo C. Combined Mutational and Clonality Analyses Support the Existence of Intra-Tumor Heterogeneity in Papillary Thyroid Cancer. J Clin Med 2021; 10:jcm10122645. [PMID: 34208446 PMCID: PMC8234519 DOI: 10.3390/jcm10122645] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/27/2021] [Accepted: 06/11/2021] [Indexed: 12/13/2022] Open
Abstract
Despite its potential clinical impact, intra-tumor genetic heterogeneity (ITH) has been scantly investigated in papillary thyroid cancer (PTC). We studied ITH in PTC by combining, for the first time, data derived from the evaluation of the normalized allelic frequencies (NAF) of the mutation/s, using a customized MassARRAY panel, and those obtained by the HUMARA clonality assay. Among tumors with a single mutation, 80% of cases with NAF 50 ± 5% were clonal, consistent with the presence of a single mutated clone, while 20% of cases showed a polyclonal pattern, suggesting the presence of the same mutation in two or more clones. Differently, all cases with NAF < 45% were polyclonal. Among tumors with double mutation, cases with both mutations showing NAF 50 ± 5% were monoclonal, consistent with the presence of a single clone harboring both mutations. On the other hand, all cases with double mutation at NAF < 45% were polyclonal, indicating the presence of two clones with different mutations. Finally, no significant differences in the clinico-pathological characteristics were found between monoclonal and polyclonal tumors. In conclusion, the present study adds insights into the concept of ITH in PTC, which warrants attention because the occurrence of this phenomenon is likely to affect the response to targeted drugs.
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Affiliation(s)
- Marina Muzza
- Laboratory of Endocrine and Metabolic Research, Istituto Auxologico Italiano IRCCS, 20095 Milan, Italy; (M.M.); (G.P.)
| | - Gabriele Pogliaghi
- Laboratory of Endocrine and Metabolic Research, Istituto Auxologico Italiano IRCCS, 20095 Milan, Italy; (M.M.); (G.P.)
| | - Luca Persani
- Division of Endocrine and Metabolic Diseases, Istituto Auxologico Italiano IRCCS, 20095 Milan, Italy; (L.P.); (C.C.)
- Department of Medical Biotechnology and Translational Medicine, University of Milan, 20133 Milan, Italy
| | - Laura Fugazzola
- Division of Endocrine and Metabolic Diseases, Istituto Auxologico Italiano IRCCS, 20095 Milan, Italy; (L.P.); (C.C.)
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy
- Correspondence:
| | - Carla Colombo
- Division of Endocrine and Metabolic Diseases, Istituto Auxologico Italiano IRCCS, 20095 Milan, Italy; (L.P.); (C.C.)
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy
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18
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Yang K, Yu W, Liu H, Ding F, Zhang Y, Zhang Y, Wang W, Lou F, Cao S, Wang H, He Z. Comparison of Genomic Characterization in Upper Tract Urothelial Carcinoma and Urothelial Carcinoma of the Bladder. Oncologist 2021; 26:e1395-e1405. [PMID: 34050578 DOI: 10.1002/onco.13839] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 05/05/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Different genomic characterization in urothelial carcinoma (UC) by site of origin may imply contrasting therapeutic opportunities and pathogenetic mechanisms. The aim of this study was to investigate whether differences between upper tract UC (UTUC) and UC of the bladder (UCB) result from intrinsic biological diversity. MATERIALS AND METHODS We prospectively sequenced 118 tumors and matched blood DNA from Chinese patients with UC using next-generation sequencing techniques, including 45 UTUC and 73 UCB. Two hundred twenty-six patients with UTUC and 350 patients with UCB for The Cancer Genome Atlas were acquired from the cbioportal. RESULTS There were marked disparities in the mutational landscape for UC according to race and site of origin. Signature 22 for exposure to aristolochic acid was only observed in the UTUC cohort. Conversely, signature 6 for defective DNA mismatch repair only existed in the UCB cohort. Compared with UCB, UTUC had higher clonal and subclonal mutation numbers. TP53, PIK3CA, and FGFR3 mutations may be the driver genes for UTUC, whereas for UCB, the driver gene may be BRCA1. Patients with UTUC had lower PD-L1 than those with UCB. There was no significant difference in the number of DDR mutations, copy number variation counts, and tumor mutational burden between UTUC and UCB. CONCLUSION UTUC and UCB exhibit significant differences in the prevalence of genomic landscape and carcinogenesis. Consequently, molecular subtypes differ according to location, and these results may imply the site-specific management of patients with urothelial carcinoma. Mutational signature may be used as a screening tool to assist clinical differential diagnosis between UTUC and UCB. IMPLICATIONS FOR PRACTICE This study's findings lay the foundation for a deeper understanding of distinct molecular mechanisms and similar treatment opportunities between upper tract urothelial carcinoma (UTUC) and urothelial carcinoma of the bladder (UCB) and had important implications for the site-specific management of patients with urothelial carcinoma. A comprehensive understanding of the biology of UTUC and UCB is needed to identify new drug targets in order to improve clinical outcomes.
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Affiliation(s)
- Kaiwei Yang
- Department of Urology, Peking University First Hospital, Beijing, People's Republic of China
| | - Wei Yu
- Department of Urology, Peking University First Hospital, Beijing, People's Republic of China
| | - Huanhuan Liu
- Acornmed Biotechnology Co., Ltd., Beijing, People's Republic of China
| | - Feng Ding
- Acornmed Biotechnology Co., Ltd., Beijing, People's Republic of China
| | - Yanrui Zhang
- Acornmed Biotechnology Co., Ltd., Beijing, People's Republic of China
| | - Yun Zhang
- Acornmed Biotechnology Co., Ltd., Beijing, People's Republic of China
| | - Wang Wang
- Acornmed Biotechnology Co., Ltd., Beijing, People's Republic of China
| | - Feng Lou
- Acornmed Biotechnology Co., Ltd., Beijing, People's Republic of China
| | - Shanbo Cao
- Acornmed Biotechnology Co., Ltd., Beijing, People's Republic of China
| | - Huina Wang
- Acornmed Biotechnology Co., Ltd., Beijing, People's Republic of China
| | - Zhisong He
- Department of Urology, Peking University First Hospital, Beijing, People's Republic of China
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19
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Eszlinger M, Khalil M, Gillmor AH, Huang H, Stewardson P, McIntyre JB, Morrissy S, Paschke R. Histology-based molecular profiling improves mutation detection for advanced thyroid cancer. Genes Chromosomes Cancer 2021; 60:531-545. [PMID: 33749950 DOI: 10.1002/gcc.22949] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 01/21/2023] Open
Abstract
Advanced cancers frequently show histologic and molecular intratumoral heterogeneity. Therefore, we comprehensively characterized advanced, metastatic, radioiodine-resistant (RAIR) thyroid carcinomas at the molecular level in the context of histologic heterogeneity with the aim to identify potentially actionable mutations that may guide the use of specific tyrosine kinase inhibitor (TKI) treatment. Whole exome sequencing (WES) was applied to 29 macrodissected tissue samples of histologically heterogeneous and homogeneous areas, lymph node and lung metastases from six clinically and histologically well-characterized metastatic RAIR thyroid cancer patients with structural incomplete response to treatment. WES data were analyzed to identify potential driver mutations in oncogenic pathways, copy number alterations, microsatellite instability, mutant-allele tumor heterogeneity, and the relevance of histologic heterogeneity to molecular profiling. In addition to known driver mutations in BRAF, NRAS, EIF1AX, NCOA4-RET, and TERT, further potentially actionable drivers were identified in AKT1, ATM, E2F1, HTR2A, and MLH3. The analysis of the evolutionary history of the mutations and the reconstruction of the molecular phylogeny of the cancers show a remarkable association between histologic and molecular heterogeneity. A comprehensive molecular analysis of the primary tumor guided by histologic analysis may help to better stratify patients for precision medicine approaches. Given the association between the molecular and the histologic heterogeneity, the selection of tumor samples for molecular analysis should be based on meticulous histologic evaluation of the entire tumor.
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Affiliation(s)
- Markus Eszlinger
- Departments of Oncology, Pathology and Laboratory Medicine, Biochemistry and Molecular Biology, and Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Institute of Pathology, University Hospital Halle, Halle, Germany
| | - Moosa Khalil
- Department of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Aaron Hill Gillmor
- Department of Graduate Sciences and Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Helen Huang
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Paul Stewardson
- Department of Medical Science and Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - John B McIntyre
- Precision Oncology Hub Laboratory, Alberta Health Services, Tom Baker Cancer Centre, Calgary, Alberta, Canada
| | - Sorana Morrissy
- Department of Biochemistry and Molecular Biology, and Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Ralf Paschke
- Departments of Medicine, Oncology, Pathology and Laboratory Medicine, Biochemistry and Molecular Biology, and Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
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Hysek M, Jatta K, Hellgren LS, Stenman A, Larsson C, Zedenius J, Juhlin CC. Spatial Distribution Patterns of Clinically Relevant TERT Promoter Mutations in Follicular Thyroid Tumors of Uncertain Malignant Potential: Advantages of the Digital Droplet PCR Technique. J Mol Diagn 2020; 23:212-222. [PMID: 33197629 DOI: 10.1016/j.jmoldx.2020.10.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 10/15/2020] [Accepted: 10/23/2020] [Indexed: 01/17/2023] Open
Abstract
In thyroid carcinomas, telomerase reverse transcriptase (TERT) promoter mutations C228T and C250T predict an unfavorable clinical outcome. The analysis is particularly valuable when assessing histologically equivocal follicular thyroid tumors of uncertain malignant potential (FT-UMPs). Given recent findings of TERT promoter mutational heterogeneity in thyroid cancer, we determined the frequency of this phenomenon in FT-UMPs and minimally invasive follicular thyroid carcinomas. DNA was extracted from several tissue blocks from 16 FT-UMPs as well as 10 minimally invasive follicular thyroid carcinomas, and interrogated using Sanger sequencing as well as digital droplet PCR (ddPCR). Mutational heterogeneity was observed by Sanger sequencing in four of seven (57%) FT-UMPs. In two FT-UMPs with C228T mutations, analyses of additional blocks gave wild-type results using Sanger sequencing in one or several blocks interrogated, whereas ddPCR found low-frequency C228T mutations in one of these fractions. In two additional FT-UMPs with the C228T and C250T mutation, respectively, sequencing of additional blocks revealed the opposite mutation. Moreover, in the C250T mutated area in one of these tumors, the ddPCR displayed a co-occurring C228T mutation that failed detection through Sanger sequencing. To conclude, most TERT promoter mutated FT-UMPs display mutational heterogeneity when analyzed by Sanger sequencing, thereby emphasizing the importance of the tissue sampling process. The ddPCR technique might overcome this phenomenon because of increased sensitivity and should be considered for clinical screening purposes.
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Affiliation(s)
- Martin Hysek
- Departments of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden; Departments of Pathology and Cytology, Karolinska University Hospital, Stockholm, Sweden
| | - Kenbugul Jatta
- Departments of Pathology and Cytology, Karolinska University Hospital, Stockholm, Sweden
| | - L Samuel Hellgren
- Departments of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden; Departments of Pathology and Cytology, Karolinska University Hospital, Stockholm, Sweden
| | - Adam Stenman
- Departments of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden; Breast, Endocrine Tumors and Sarcoma, Karolinska University Hospital, Stockholm, Sweden; Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Catharina Larsson
- Departments of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Jan Zedenius
- Breast, Endocrine Tumors and Sarcoma, Karolinska University Hospital, Stockholm, Sweden; Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - C Christofer Juhlin
- Departments of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden; Departments of Pathology and Cytology, Karolinska University Hospital, Stockholm, Sweden.
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Muzza M. The clonal origin of multifocal papillary thyroid cancer: intrathyroidal spread or independent tumors? Minerva Endocrinol (Torino) 2020; 46:35-44. [PMID: 33045819 DOI: 10.23736/s2724-6507.20.03302-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Multifocality is a common finding in papillary thyroid cancer but the molecular pathogenesis, prognosis and management of multifocal papillary thyroid cancer are debated. The clonal origin of multifocal papillary thyroid cancer represents a controversial aspect, as two opposite viewpoints have been proposed: independent origin or intraglandular spread. Different approaches have been used for inferring the clonality of multifocal papillary thyroid cancer, including X-chromosome inactivation, mutational analysis, determination of loss of heterozygosity and, more recently, next-generation sequencing. Next-generation sequencing, able to provide information on genetic heterogeneity and phylogenetic evolution in multifocal tumors, represents the most reliable approach. While most evidences indicated an independent origin of multifocal papillary thyroid cancer, a minority of studies suggested that multifocal papillary thyroid tumors might be monoclonally derived. This discrepancy may reflect technical limitations; nevertheless, studies based on next-generation sequencing indicated that both independent and clonal origins are possible. The co-existence of multiple tumors implies a high degree of genetic heterogeneity, which may influence the best and targeted therapeutic strategy. On the other hand, intrathyroidal dissemination may indicate metastatic potential of the dominant tumor, thereby prompting more aggressive treatments. In conclusion, data available in the literature indicated that multifocal papillary thyroid cancer may derived from both intraglandular spread and independent tumor foci. The understanding of the clonal origin of multifocal papillary thyroid tumors might represent an important issue in patient treatment.
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Affiliation(s)
- Marina Muzza
- Division of Endocrine and Metabolic Diseases, IRCCS Istituto Auxologico Italiano, Milan, Italy -
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Yehia L, Eng C. The "APCs" of PTCs: Adenomatous Polyposis Syndrome and the Thyroid. Thyroid 2020; 30:355-356. [PMID: 32041494 DOI: 10.1089/thy.2020.0109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Lamis Yehia
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
- Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio
- Germline High Risk Cancer Focus Group, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio
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Intratumoral Genetic Heterogeneity in Papillary Thyroid Cancer: Occurrence and Clinical Significance. Cancers (Basel) 2020; 12:cancers12020383. [PMID: 32046148 PMCID: PMC7072350 DOI: 10.3390/cancers12020383] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/04/2020] [Accepted: 02/06/2020] [Indexed: 12/16/2022] Open
Abstract
Intratumoral heterogeneity (ITH) refers to a subclonal genetic diversity observed within a tumor. ITH is the consequence of genetic instability and accumulation of genetic alterations, two mechanisms involved in the progression from an early tumor stage to a more aggressive cancer. While this process is widely accepted, the ITH of early stage papillary thyroid carcinoma (PTC) is debated. By different genetic analysis, several authors reported the frequent occurrence of PTCs composed of both tumor cells with and without RET/PTC or BRAFV600E genetic alterations. While these data, and the report of discrepancies in the genetic pattern between metastases and the primary tumor, demonstrate the existence of ITH in PTC, its extension and biological significance is debated. The ITH takes on a great significance when involves oncogenes, such as RET rearrangements and BRAFV600E as it calls into question their role of driver genes. ITH is also predicted to play a major clinical role as it could have a significant impact on prognosis and on the response to targeted therapy. In this review, we analyzed several data indicating that ITH is not a marginal event, occurring in PTC at any step of development, and suggesting the existence of unknown genetic or epigenetic alterations that still need to be identified.
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