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Qi P, Yao QL, Lao IW, Ren M, Bai QM, Cai X, Xue T, Wei R, Zhou XY. A custom next-generation sequencing panel for 1p/19q codeletion and mutational analysis in gliomas. J Neuropathol Exp Neurol 2024; 83:258-267. [PMID: 38408388 DOI: 10.1093/jnen/nlae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024] Open
Abstract
The World Health Organization has updated their classification system for the diagnosis of gliomas, combining histological features with molecular data including isocitrate dehydrogenase 1 and codeletion of chromosomal arms 1p and 19q. 1p/19q codeletion analysis is commonly performed by fluorescence in situ hybridization (FISH). In this study, we developed a 57-gene targeted next-generation sequencing (NGS) panel including 1p/19q codeletion detection mainly to assess diagnosis and potential treatment response in melanoma, gastrointestinal stromal tumor, and glioma patients. Loss of heterozygosity analysis was performed using the NGS method on 37 formalin-fixed paraffin-embedded glioma tissues that showed 1p and/or 19q loss determined by FISH. Conventional methods were applied for the validation of some glioma-related gene mutations. In 81.1% (30 of 37) and 94.6% (35 of 37) of cases, 1p and 19q were found to be in agreement whereas concordance for 1p/19q codeletion and no 1p/19q codeletion was found in 94.7% (18 of 19) and 94.4% (17 of 18) of cases, respectively. Overall, comparing NGS results with those of conventional methods showed high concordance. In conclusion, the NGS panel allows reliable analysis of 1p/19q codeletion and mutation at the same time.
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Affiliation(s)
- Peng Qi
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Qian-Lan Yao
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - I Weng Lao
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Min Ren
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Qian-Ming Bai
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Xu Cai
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Tian Xue
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Ran Wei
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Xiao-Yan Zhou
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
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Abstract
Myxoid pleomorphic liposarcoma (MPLPS) shows a strong predilection for the mediastinum and can affect a wide age range. Clinically, MPLPS exhibits aggressive behavior and demonstrates a worse overall and progression-free survival than myxoid/round cell liposarcoma (MRLPS) and pleomorphic liposarcoma (PLPS). Histologically, MPLPS is characterized by hybrid morphologic features of MRLPS and PLPS, including myxoid stroma, chicken wire-like vasculature, univacuolated and multivacuolated lipoblasts, and high-grade pleomorphic sarcomatous components. In terms of molecular features, MPLPS is distinct from other lipomatous tumors as it harbors genome-wide loss of heterozygosity.
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Affiliation(s)
- Josephine K Dermawan
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, 9500 Euclid Avenue L25, Cleveland, OH 44195, USA.
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Cogliati M, Chidebelu PE, Hitchcock M, Chen M, Rickerts V, Ackermann S, Desnos Ollivier M, Inácio J, Nawrot U, Florek M, Kwon-Chung KJ, Yang DH, Firacative C, Puime CA, Escandon P, Bertout S, Roger F, Xu J. Multi-locus sequence typing and phylogenetics of Cryptococcus neoformans AD hybrids. Fungal Genet Biol 2024; 170:103861. [PMID: 38128716 DOI: 10.1016/j.fgb.2023.103861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/06/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
Hybrid AD strains of the human pathogenic Cryptococcus neoformans species complex have been reported from many parts of the world. However, their origin, diversity, and evolution are incompletely understood. In this study, we analyzed 102 AD hybrid strains representing 21 countries on five continents. For each strain, we obtained its mating type and its allelic sequences at each of the seven loci that have been used for genotyping haploid serotypes A and D strains of the species complex by the Cryptococcus research community. Our results showed that most AD hybrids exhibited loss of heterozygosity at one or more of the seven analyzed loci. Phylogenetic and population genetic analyses of the allelic sequences revealed multiple origins of the hybrids within each continent, dating back to one million years ago in Africa and up to the present in other continents. We found evidence for clonal reproduction and long-distance dispersal of these hybrids in nature. Comparisons with the global haploid serotypes A and D strains identified new alleles and new haploid multi-locus genotypes in AD hybrids, consistent with the presence of yet-to-be discovered genetic diversity in haploid populations of this species complex in nature. Together, our results indicate that AD hybrids can be effectively genotyped using the same multi-locus sequencing type approach as that established for serotypes A and D strains. Our comparisons of the AD hybrids among each other as well as with the global haploid serotypes A and D strains revealed novel genetic diversity as well as evidence for multiple origins and dynamic evolution of these hybrids in nature.
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Affiliation(s)
- M Cogliati
- Lab. Medical Mycology, Dept. Biomedical Sciences for Health, Università degli Studi di Milano, Milano, Italy.
| | - P E Chidebelu
- Department of Microbiology, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - M Hitchcock
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - M Chen
- Shanghai Key Laboratory of Molecular Medical Mycology, Department of Dermatology, Chanzheng Hospital, Second Military Medical University, Shanghai, China
| | | | | | - M Desnos Ollivier
- Institut Pasteur, Université de Paris, CNRS UMR2000, Molecular Mycology Unit, National Reference Center for Invasive Mycoses and Antifungals, Paris, France
| | - J Inácio
- School of Applied Sciences, University of Brighton, Brighton, UK
| | - U Nawrot
- Department of Pharmaceutical Microbiology and Parasitology, Wroclaw Medical University, Wroclaw, Poland
| | - M Florek
- Department of Pathology, Faculty of Veterinary Medicine, Wroclaw University of Environmental and Life Sciences, Wroclaw, Poland
| | - K J Kwon-Chung
- Molecular Microbiology Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases NIH, Bethesda, USA
| | - D-H Yang
- Molecular Microbiology Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases NIH, Bethesda, USA
| | - C Firacative
- Studies in Translational Microbiology and Emerging Diseases (MICROS) Research Group, School of Medicine and Health Sciences, Universidad de Rosario, Bogotá, Colombia
| | - C A Puime
- Unidad de Parasitología y Micología, Departamento de Laboratorios de Salud Pública, Ministerio de Salud Pública, Montevideo, Uruguay
| | - P Escandon
- Grupo de Microbiología, Instituto Nacional de Salud, Bogotá, Colombia
| | - S Bertout
- Laboratoire de Parasitologie et Mycologie Médicale, UMI 233 TransVIHMI, University of Montpellier, IRD, INSERM, Montpellier, France
| | - F Roger
- Laboratoire de Parasitologie et Mycologie Médicale, UMI 233 TransVIHMI, University of Montpellier, IRD, INSERM, Montpellier, France
| | - J Xu
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
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Kobashi Y, Nakayama E, Fukumori N, Shimojima A, Tabira M, Nishimura Y, Mukae M, Muto A, Nakashima N, Okutsu K, Yoshizaki Y, Futagami T, Takamine K, Tamaki H. Homozygous gene disruption in diploid yeast through a single transformation. J Biosci Bioeng 2024; 137:31-37. [PMID: 37981488 DOI: 10.1016/j.jbiosc.2023.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 10/13/2023] [Accepted: 11/05/2023] [Indexed: 11/21/2023]
Abstract
As industrial shochu yeast is a diploid strain, obtaining a strain with mutations in both allelic genes was considered difficult. We investigated a method for disrupting two copies of a homozygous gene with a single transformation. We designed a disruption cassette containing an intact LYS5 flanked by nonfunctional ura3 gene fragments divided into the 5'- and 3'-regions. These fragments had overlapping sequences that enabled LYS5 removal as well as URA3 regeneration through loop-out. Furthermore, both ends of the disruption cassette had an additional repeat sequence that allowed the cassette to be removed from the chromosome through loop-out. First, 45 bases of 5'- and 3'-regions of target gene sequences were added on both ends of this cassette using polymerase chain reaction; the resultant disruption cassette was introduced into a shochu yeast strain (ura3/ura3 lys5/lys5); then, single allele disrupted strains were selected on Lys drop-out plates; and after cultivation in YPD medium, double-disrupted strains, in which replacement of another allelic gene with disruption cassette by loss of heterozygosity and regeneration of URA3 in one of the cassettes by loop-out, were obtained by selection on Ura and Lys drop-out plates. The disruption cassettes were removed from the double-disrupted strain via loop-out between repeat sequences in the disruption cassette. The strains that lost either URA3 or LYS5 were counter-selected on 5-fluoroorotic acid or α-amino adipic acid plates, respectively. Using this method, we obtained leu2/leu2 and leu2/leu2 his3/his3 strains in shochu yeast, demonstrating the effectiveness and repeatability of this gene disruption technique in diploid yeast Saccharomyces cerevisiae.
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Affiliation(s)
- Yuki Kobashi
- United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Eri Nakayama
- Graduate School of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Naoki Fukumori
- Graduate School of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Ayane Shimojima
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Manami Tabira
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Yuki Nishimura
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Manami Mukae
- Graduate School of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Ai Muto
- Graduate School of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Naoto Nakashima
- Graduate School of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Kayu Okutsu
- Education and Research Center for Fermentation Studies, Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Yumiko Yoshizaki
- United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan; Education and Research Center for Fermentation Studies, Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Taiki Futagami
- United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan; Education and Research Center for Fermentation Studies, Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Kazunori Takamine
- United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan; Education and Research Center for Fermentation Studies, Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Hisanori Tamaki
- United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan; Education and Research Center for Fermentation Studies, Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan.
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Ghazali N, Rahman NA, Kannan TP, Ahmad A, Sulong S. Identification of copy neutral loss of heterozygosity on chromosomes 1p, 1q, and 6p among nonsyndromic cleft lip and/or without cleft palate with hypodontia. BMC Oral Health 2023; 23:945. [PMID: 38031027 PMCID: PMC10685534 DOI: 10.1186/s12903-023-03464-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 09/27/2023] [Indexed: 12/01/2023] Open
Abstract
BACKGROUND Nonsyndromic cleft lip and/or without cleft palate (NSCL/P) with or without hypodontia is a common developmental aberration in humans and animals. This study aimed to identify the loss of heterozygosity (LOH) involved in hypodontia and NSCL/P pathogenesis. METHODS This is a cross-sectional study that conducted genome-wide copy number analysis using CytoScan 750K array on salivary samples from Malay subjects with NSCL/P with or without hypodontia aged 7-13 years. To confirm the significant results, simple logistic regression was employed to conduct statistical data analysis using SPSS software. RESULTS The results indicated the most common recurrent copy neutral LOH (cnLOH) observed at 1p33-1p32.3, 1q32.2-1q42.13 and 6p12.1-6p11.1 loci in 8 (13%), 4 (7%), and 3 (5%) of the NSCL/P subjects, respectively. The cnLOHs at 1p33-1p32.3 (D1S197), 1q32.2-1q42.13 (D1S160), and 6p12.1-6p11.1 (D1S1661) were identified observed in NSCL/P and noncleft children using microsatellite analysis markers as a validation analysis. The regions affected by the cnLOHs at 1p33-1p32.3, 1q32.2-1q42.13, and 6p12.1-6p11.1 loci contained selected genes, namely FAF1, WNT3A and BMP5, respectively. There was a significant association between the D1S197 (1p33-32.3) markers containing the FAF1 gene among NSCL/P subjects with or without hypodontia compared with the noncleft subjects (p-value = 0.023). CONCLUSION The results supported the finding that the genetic aberration on 1p33-32.3 significantly contributed to the development of NSCL/P with or without hypodontia. These results have an exciting prospect in the promising field of individualized preventive oral health care.
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Affiliation(s)
- Norliana Ghazali
- School of Dental Sciences, Universiti Sains Malaysia (USM), Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia
| | - Normastura Abd Rahman
- School of Dental Sciences, Universiti Sains Malaysia (USM), Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia.
| | - Thirumulu Ponnuraj Kannan
- School of Dental Sciences, Universiti Sains Malaysia (USM), Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia
| | - Azlina Ahmad
- School of Dental Sciences, Universiti Sains Malaysia (USM), Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia
| | - Sarina Sulong
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia (USM), Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia
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Finkelstein S, Timmaraju VA, Samankan S, O'Malley Q, Kapustin D, Spaulding S, Xing M, Matloob A, Beute J, Seo G, Saturno M, Greenberg L, Wein L, Gonzalez-Velazquez C, Doyle S, Levine J, Urken M, Brandwein-Weber M. Functional loss of tumor suppressor genes detected by loss of heterozygosity, but not driver mutations, predicts aggressive lymph node status in papillary thyroid carcinoma. Pathol Res Pract 2023; 251:154842. [PMID: 37890270 DOI: 10.1016/j.prp.2023.154842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 09/30/2023] [Indexed: 10/29/2023]
Abstract
BACKGROUND Recognizing aggressive tumor biology is essential to optimizing patient management for papillary thyroid carcinomas (PTC). Aggressive lymph node (ALN) status is one feature that influences decision-making. We evaluated genomic deletions in regions of tumor suppressor genes, detected by loss of heterozygosity (LOH) analysis, to understand causal alterations linked to thyroid cancer aggressiveness and to serve as a molecular diagnostic biomarker for ALN status. METHODS We analyzed 105 primary PTC enriched for patients with ALN (64% with, 36% without). We also analyzed 39 positive lymph nodes (79% with, 21% without ALN). LOH was determined using a panel of 25 polymorphic microsatellite alleles targeting 10 genomic loci harboring common tumor suppressor genes. Additionally, ThyGeNEXT® and ThyraMIR® assays were performed. RESULTS LOH was detected in 43/67 primary PTC from patients with ALN status, compared with only 5/38 primary PTC without ALN (minimal metastatic burden) (P=0.0000003). This is further supported by post hoc analyses of paired primary and metastatic samples. Paired samples from patients with ALN are more likely to harbor LOH, compared to the ALN negative group (P=0.0125). Additionally, 12/31 paired samples from patients with ALN demonstrated additional or different LOH loci in metastatic samples compared to the primary tumor samples. No association was seen between ALN and mutational, translocation, or microRNA data. CONCLUSIONS LOH detected in primary PTC significantly predicts ALN status. Analysis of paired primary and metastatic samples from patients with / without ALN status further supports this relationship. The acquisition of LOH at additional loci is common in lymph nodes from patients with ALN status. SIMPLE SUMMARY A subset of patients with papillary thyroid carcinoma (PTC) will develop recurrent disease. One known predictor of recurrence is the American Thyroid Association category "Aggressive Lymph Node" (ALN) disease, considering metastatic burden. Loss of heterozygosity (LOH) - chromosomal loss in regions of tumor suppressor genes - has yet to be investigated as a possible mechanism driving ALN status in PTC. The ability to predict ALN status prior to surgery can guide the extent of surgery and postoperative treatment options. We found that paired samples from patients with ALN are more likely to harbor LOH, compared to patients without ALN disease. 38% of patients with ALN demonstrated additional or different LOH loci in metastatic samples compared to the primary tumor samples. LOH complements current molecular analysis of thyroid cancer when searching for evidence of aggressive biology.
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Affiliation(s)
- Sydney Finkelstein
- Interpace Diagnostics, Interpace Biosciences, Pittsburgh, PA, United States
| | | | - Shabnam Samankan
- Department of Pathology, Icahn School of Medicine, Mount Sinai Health System, New York, United States
| | - Quinn O'Malley
- THANC (Thyroid, Head and Neck Cancer) Foundation, 10 Union Square East, New York, NY 10003, United States
| | - Danielle Kapustin
- THANC (Thyroid, Head and Neck Cancer) Foundation, 10 Union Square East, New York, NY 10003, United States; Department of Otolaryngology - Head and Neck Surgery, Icahn School of Medicine, Mount Sinai Health System, New York, NY, United State
| | - Sarah Spaulding
- THANC (Thyroid, Head and Neck Cancer) Foundation, 10 Union Square East, New York, NY 10003, United States
| | - Monica Xing
- THANC (Thyroid, Head and Neck Cancer) Foundation, 10 Union Square East, New York, NY 10003, United States
| | - Ammar Matloob
- Department of Pathology, Icahn School of Medicine, Mount Sinai Health System, New York, United States
| | - John Beute
- THANC (Thyroid, Head and Neck Cancer) Foundation, 10 Union Square East, New York, NY 10003, United States
| | - Gabriella Seo
- THANC (Thyroid, Head and Neck Cancer) Foundation, 10 Union Square East, New York, NY 10003, United States
| | - Michael Saturno
- THANC (Thyroid, Head and Neck Cancer) Foundation, 10 Union Square East, New York, NY 10003, United States
| | - Lily Greenberg
- THANC (Thyroid, Head and Neck Cancer) Foundation, 10 Union Square East, New York, NY 10003, United States
| | - Lauren Wein
- THANC (Thyroid, Head and Neck Cancer) Foundation, 10 Union Square East, New York, NY 10003, United States
| | - Camilo Gonzalez-Velazquez
- THANC (Thyroid, Head and Neck Cancer) Foundation, 10 Union Square East, New York, NY 10003, United States
| | - Scott Doyle
- Department of Pathology and Anatomical Sciences, University at Buffalo, Jacobs School of Medicine, Buffalo, NY, United States
| | - Jonathan Levine
- Interpace Diagnostics, Interpace Biosciences, Pittsburgh, PA, United States
| | - Mark Urken
- THANC (Thyroid, Head and Neck Cancer) Foundation, 10 Union Square East, New York, NY 10003, United States; Department of Otolaryngology - Head and Neck Surgery, Icahn School of Medicine, Mount Sinai Health System, New York, NY, United State
| | - Margaret Brandwein-Weber
- Department of Pathology, Icahn School of Medicine, Mount Sinai Health System, New York, United States.
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Habara K, Nishikori A, Kiyama J, Nakashima M, Koda M, Sasaki K, Sakashita T, Tanaka N, Yonehara S. A case of coexistent poorly differentiated adenosquamous carcinoma (glassy cell carcinoma), usual-type adenocarcinoma, and squamous cell carcinoma in situ of the cervix. Med Mol Morphol 2023; 56:217-224. [PMID: 37129713 PMCID: PMC10415468 DOI: 10.1007/s00795-023-00354-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/16/2023] [Indexed: 05/03/2023]
Abstract
Poorly differentiated adenosquamous carcinoma (glassy cell carcinoma) of the cervix is extremely rare, accounting for 1-2% of all cervical cancers. Herein, we report a case with coexistent poorly differentiated adenosquamous carcinoma (glassy cell carcinoma), "usual-type" adenocarcinoma, and squamous cell carcinoma in situ of the cervix. A female patient in her 60 s was referred to our hospital and diagnosed with poorly differentiated adenosquamous carcinoma based on cervical cytology and biopsy. The tumor was classified as clinical stage IB1 cervical cancer following magnetic resonance imaging; radical hysterectomy was performed. Histopathological examination revealed poorly differentiated adenosquamous carcinoma (glassy cell carcinoma), usual-type adenocarcinoma, and squamous cell carcinoma in situ, all coexisting. All carcinoma regions showed identical sizes to high-risk human papillomavirus (HPV) in fragment analysis. The patient is currently alive, without evidence of recurrence, 31 months post surgery. In this case, three different carcinomas coexisted. Fragment analysis of the patient's HPV status suggested that all carcinomas were related to an infection with the same high-risk HPV type. To determine the precise mechanism of tumor development, i.e., whether the tumors were of the mixed or collision type, further studies are needed, including clonal analysis for the loss of heterozygosity pattern.
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Affiliation(s)
- Kouki Habara
- Department of Pathology, Japan Agricultural Cooperatives Onomichi General Hospital, 1-10-23 Hirahara, Onomichi, Hiroshima, Japan
| | - Asami Nishikori
- Department of Molecular Hematopathology, Faculty of Health Sciences, Okayama University School of Medicine, 2-5-1 Shikata, Kita-Ku, Okayama, Japan
| | - Jin Kiyama
- Department of Medical Technology, Okayama University Hospital, 2-5-1 Shikata, Kita-ku, Okayama, Japan
| | - Manami Nakashima
- Department of Pathology, Japan Agricultural Cooperatives Onomichi General Hospital, 1-10-23 Hirahara, Onomichi, Hiroshima, Japan
| | - Masanori Koda
- Department of Pathology, Japan Agricultural Cooperatives Onomichi General Hospital, 1-10-23 Hirahara, Onomichi, Hiroshima, Japan
| | - Kenji Sasaki
- Department of Pathology, Japan Agricultural Cooperatives Onomichi General Hospital, 1-10-23 Hirahara, Onomichi, Hiroshima, Japan
| | - Tomohisa Sakashita
- Department of Obstetrics and Gynecology, Japan Agricultural Cooperatives Onomichi General Hospital, 1-10-23 Hirahara, Onomichi, Hiroshima, Japan
| | - Norifumi Tanaka
- Department of Obstetrics and Gynecology, National Hospital Organization East Hiroshima Medical Center, 513 Jike, Saijo, Higashihiroshima, Hiroshima, Japan
| | - Shuji Yonehara
- Department of Pathology, Japan Agricultural Cooperatives Onomichi General Hospital, 1-10-23 Hirahara, Onomichi, Hiroshima, Japan
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Sokolenko A, Preobrazhenskaya E, Marchetti C, Piermattei A, Zagrebin F, Kuligina E, Gorodnova T, Pavone M, Ivantsov A, Bizin I, Scambia G, Berlev I, Fagotti A, Imyanitov E. Origin of Residual Tumor Masses in BRCA1/2-Driven Ovarian Carcinomas Treated by Neoadjuvant Chemotherapy: Selection of Preexisting BRCA1/2-Proficient Tumor Cells but Not the Gain of Second ORF-Restoring Mutation. Pathobiology 2023; 91:108-113. [PMID: 37579727 DOI: 10.1159/000533591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 08/07/2023] [Indexed: 08/16/2023] Open
Abstract
INTRODUCTION Tubo-ovarian carcinomas (OCs) are highly sensitive to platinum-based neoadjuvant chemotherapy (NACT) but almost never demonstrate complete pathologic response. METHODS We analyzed paired primary and residual tumor tissues from 30 patients with hereditary BRCA1/2-driven OCs (BRCA1: 17; BRCA2: 13), who were treated by carboplatin/paclitaxel NACT (median number of cycles: 3, range: 3-6). BRCA1/2 and TP53 genes were analyzed by the next-generation sequencing. The ratio between TP53 mutation-specific versus wild-type reads was considered to monitor the proportion of tumor and non-tumor cells in the tissue sample, and the ratio between BRCA1/2-mutated and wild-type reads was used to estimate the presence of cells with the loss or retention of heterozygosity (LOH or ROH, respectively). RESULTS All 30 OCs had BRCA1/2 LOH in primary tumor and carried somatic TP53 mutation. Twenty-eight OCs had sufficient tumor cell cellularity in the post-NACT tissue to evaluate the ratio between mutated and wild-type BRCA1/2 alleles. Five (18%) out of 28 informative tumor pairs showed transition from LOH to ROH during NACT presumably affecting all or the vast majority of residual tumor cells. There were no signals of the emergence of a second open reading frame-restoring BRCA1/2 mutation. CONCLUSION Chemonaive BRCA1/2-driven carcinomas may contain a fraction of tumor cells with preserved BRCA1/2 heterozygosity. NACT can cause a selection of pre-existing BRCA1/2-proficient tumor cells, without gaining secondary reversal BRCA1/2 mutations.
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Affiliation(s)
- Anna Sokolenko
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St. Petersburg, Russian Federation
- Department of Medical Genetics, St. Petersburg Pediatric Medical University, St. Petersburg, Russian Federation
| | - Elena Preobrazhenskaya
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St. Petersburg, Russian Federation
| | - Claudia Marchetti
- Dipartimento Scienze della Salute della Donna e del Bambino, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Roma, Italy
- Dipartimento Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Roma, Italy
| | - Alessia Piermattei
- Dipartimento Scienze della Salute della Donna e del Bambino, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Roma, Italy
| | - Fedor Zagrebin
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St. Petersburg, Russian Federation
| | - Ekatherina Kuligina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St. Petersburg, Russian Federation
| | - Tatiana Gorodnova
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St. Petersburg, Russian Federation
| | - Matteo Pavone
- Dipartimento Scienze della Salute della Donna e del Bambino, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Roma, Italy
- Dipartimento Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Roma, Italy
| | - Alexandr Ivantsov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St. Petersburg, Russian Federation
| | - Ilya Bizin
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St. Petersburg, Russian Federation
| | - Giovanni Scambia
- Dipartimento Scienze della Salute della Donna e del Bambino, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Roma, Italy
- Dipartimento Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Roma, Italy
| | - Igor Berlev
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St. Petersburg, Russian Federation
| | - Anna Fagotti
- Dipartimento Scienze della Salute della Donna e del Bambino, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Roma, Italy
- Dipartimento Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Roma, Italy
| | - Evgeny Imyanitov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St. Petersburg, Russian Federation
- Department of Medical Genetics, St. Petersburg Pediatric Medical University, St. Petersburg, Russian Federation
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9
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Cheng C, Hong W, Li Y, Xiao X, McKay J, Han Y, Byun J, Peng B, Albanes D, Lam S, Tardon A, Chen C, Bojesen SE, Landi MT, Johansson M, Risch A, Bickeböller H, Wichmann HE, Christiani DC, Rennert G, Arnold S, Goodman G, Field JK, Davies MPA, Shete SS, Le Marchand L, Liu G, Hung RJ, Andrew AS, Kiemeney LA, Zhu M, Shen H, Zienolddiny S, Grankvist K, Johansson M, Cox A, Hong YC, Yuan JM, Lazarus P, Schabath MB, Aldrich MC, Brennan P, Li Y, Gorlova O, Gorlov I, Amos CI. Mosaic Chromosomal Alterations Are Associated With Increased Lung Cancer Risk: Insight From the INTEGRAL-ILCCO Cohort Analysis. J Thorac Oncol 2023; 18:1003-1016. [PMID: 37150255 PMCID: PMC10435278 DOI: 10.1016/j.jtho.2023.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/21/2023] [Accepted: 05/01/2023] [Indexed: 05/09/2023]
Abstract
INTRODUCTION Mosaic chromosomal alterations (mCAs) detected in white blood cells represent a type of clonal hematopoiesis (CH) that is understudied compared with CH-related somatic mutations. A few recent studies indicated their potential link with nonhematological cancers, especially lung cancer. METHODS In this study, we investigated the association between mCAs and lung cancer using the high-density genotyping data from the OncoArray study of INTEGRAL-ILCCO, the largest single genetic study of lung cancer with 18,221 lung cancer cases and 14,825 cancer-free controls. RESULTS We identified a comprehensive list of autosomal mCAs, ChrX mCAs, and mosaic ChrY (mChrY) losses from these samples. Autosomal mCAs were detected in 4.3% of subjects, in addition to ChrX mCAs in 3.6% of females and mChrY losses in 9.6% of males. Multivariable logistic regression analysis indicated that the presence of autosomal mCAs in white blood cells was associated with an increased lung cancer risk after adjusting for key confounding factors, including age, sex, smoking status, and race. This association was mainly driven by a specific type of mCAs: copy-neutral loss of heterozygosity on autosomal chromosomes. The association between autosome copy-neutral loss of heterozygosity and increased risk of lung cancer was further confirmed in two major histologic subtypes, lung adenocarcinoma and squamous cell carcinoma. In addition, we observed a significant increase of ChrX mCAs and mChrY losses in smokers compared with nonsmokers and racial differences in certain types of mCA events. CONCLUSIONS Our study established a link between mCAs in white blood cells and increased risk of lung cancer.
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Affiliation(s)
- Chao Cheng
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas; Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Wei Hong
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas
| | - Yafang Li
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas; Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Xiangjun Xiao
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas
| | - James McKay
- Section of Genetics, International Agency for Research on Cancer, WHO, Lyon, France
| | - Younghun Han
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas; Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Jinyoung Byun
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas; Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Bo Peng
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas; Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Demetrios Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Stephen Lam
- Department of Integrative Oncology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Adonina Tardon
- Public Health Department, University of Oviedo, ISPA and CIBERESP, Asturias, Spain
| | - Chu Chen
- Program in Epidemiology, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Stig E Bojesen
- Department of Clinical Biochemistry, Copenhagen University Hospital, Copenhagen, Denmark; Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Maria T Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Mattias Johansson
- Section of Genetics, International Agency for Research on Cancer, WHO, Lyon, France
| | - Angela Risch
- Thoraxklinik at University Hospital Heidelberg, Heidelberg, Germany; Translational Lung Research Center Heidelberg (TLRC-H), Heidelberg, Germany; University of Salzburg and Cancer Cluster Salzburg, Salzburg, Austria
| | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, Göttingen, Germany
| | - H-Erich Wichmann
- Institute of Medical Statistics and Epidemiology, Technical University Munich, Munich, Germany
| | - David C Christiani
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Gad Rennert
- Clalit National Cancer Control Center at Carmel Medical Center and Technion Faculty of Medicine, Haifa, Israel
| | - Susanne Arnold
- University of Kentucky, Markey Cancer Center, Lexington, Kentucky
| | | | - John K Field
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Michael P A Davies
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Sanjay S Shete
- Department of Biostatistics, The University of Texas M. D. Anderson Cancer Center, Houston, Texas; Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii
| | - Geoffrey Liu
- University Health Network- The Princess Margaret Cancer Centre, Toronto, California
| | - Rayjean J Hung
- Luenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada; Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Angeline S Andrew
- Department of Epidemiology, Dartmouth College, Hanover, New Hampshire; Department of Community and Family Medicine, Dartmouth College, Hanover, New Hampshire
| | | | - Meng Zhu
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | | | - Kjell Grankvist
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | | | - Angela Cox
- Academic Unit of Clinical Oncology University of Sheffield, Weston Park Hospital, Whitham Road, Sheffield, United Kingdom
| | - Yun-Chul Hong
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jian-Min Yuan
- University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center, Pittsburgh, Pennsylvania
| | - Philip Lazarus
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington
| | - Matthew B Schabath
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Melinda C Aldrich
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Paul Brennan
- Section of Genetics, International Agency for Research on Cancer, WHO, Lyon, France
| | - Yong Li
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas; Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Olga Gorlova
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas; Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Ivan Gorlov
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas; Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas; Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas.
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10
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Smukowski Heil C. Loss of Heterozygosity and Its Importance in Evolution. J Mol Evol 2023; 91:369-377. [PMID: 36752826 PMCID: PMC10276065 DOI: 10.1007/s00239-022-10088-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 12/23/2022] [Indexed: 02/09/2023]
Abstract
Loss of heterozygosity (LOH) is a mitotic recombination event that converts heterozygous loci to homozygous loci. This mutation event is widespread in organisms that have asexual reproduction like budding yeasts, and is also an important and frequent mutation event in tumorigenesis. Mutation accumulation studies have demonstrated that LOH occurs at a rate higher than the point mutation rate, and can impact large portions of the genome. Laboratory evolution experiments of heterozygous yeasts have revealed that LOH often unmasks beneficial recessive alleles that can confer large fitness advantages. Here, I highlight advances in understanding dominance, fitness, and phenotypes in laboratory evolved heterozygous yeast strains. I discuss best practices for detecting LOH in intraspecific and interspecific evolved clones and populations. Utilizing heterozygous strain backgrounds in laboratory evolution experiments offers an opportunity to advance our understanding of this important mutation type in shaping adaptation and genome evolution in wild, domesticated, and clinical populations.
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Affiliation(s)
- Caiti Smukowski Heil
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.
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11
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Mixão V, Nunez-Rodriguez JC, Del Olmo V, Ksiezopolska E, Saus E, Boekhout T, Gacser A, Gabaldón T. Evolution of loss of heterozygosity patterns in hybrid genomes of Candida yeast pathogens. BMC Biol 2023; 21:105. [PMID: 37170256 PMCID: PMC10173528 DOI: 10.1186/s12915-023-01608-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 04/27/2023] [Indexed: 05/13/2023] Open
Abstract
BACKGROUND Hybrids are chimeric organisms with highly plastic heterozygous genomes that may confer unique traits enabling the adaptation to new environments. However, most evolutionary theory frameworks predict that the high levels of genetic heterozygosity present in hybrids from divergent parents are likely to result in numerous deleterious epistatic interactions. Under this scenario, selection is expected to favor recombination events resulting in loss of heterozygosity (LOH) affecting genes involved in such negative interactions. Nevertheless, it is so far unknown whether this phenomenon actually drives genomic evolution in natural populations of hybrids. To determine the balance between selection and drift in the evolution of LOH patterns in natural yeast hybrids, we analyzed the genomic sequences from fifty-five hybrid strains of the pathogenic yeasts Candida orthopsilosis and Candida metapsilosis, which derived from at least six distinct natural hybridization events. RESULTS We found that, although LOH patterns in independent hybrid clades share some level of convergence that would not be expected from random occurrence, there is an apparent lack of strong functional selection. Moreover, while mitosis is associated with a limited number of inter-homeologous chromosome recombinations in these genomes, induced DNA breaks seem to increase the LOH rate. We also found that LOH does not accumulate linearly with time in these hybrids. Furthermore, some C. orthopsilosis hybrids present LOH patterns compatible with footprints of meiotic recombination. These meiotic-like patterns are at odds with a lack of evidence of sexual recombination and with our inability to experimentally induce sporulation in these hybrids. CONCLUSIONS Our results suggest that genetic drift is the prevailing force shaping LOH patterns in these hybrid genomes. Moreover, the observed LOH patterns suggest that these are likely not the result of continuous accumulation of sporadic events-as expected by mitotic repair of rare chromosomal breaks-but rather of acute episodes involving many LOH events in a short period of time.
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Affiliation(s)
- Verónica Mixão
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Present address: Genomics and Bioinformatics Unit, Infectious Diseases Department, National Institute of Health Dr. Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal
| | - Juan Carlos Nunez-Rodriguez
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Valentina Del Olmo
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ewa Ksiezopolska
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ester Saus
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Attila Gacser
- Department of Microbiology, University of Szeged, Szeged, Hungary
- MTA-SZTE "Lendület" Mycobiome Research Group, University of Szeged, Szeged, Hungary
| | - Toni Gabaldón
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain.
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- ICREA, Pg. Lluis Companys 23, 08010, Barcelona, Spain.
- Centro de Investigación Biomédica En Red de Enfermedades Infecciosas, Barcelona, Spain.
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12
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Zhang M, Shi B, Zhao M. Cerebral venous thrombosis with hyperhomocysteinemia due to loss of heterozygosity at methylenetetrahydrofolate reductase (MTHFR) locus: a case report. BMC Neurol 2023; 23:154. [PMID: 37076800 PMCID: PMC10114475 DOI: 10.1186/s12883-023-03200-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 04/04/2023] [Indexed: 04/21/2023] Open
Abstract
BACKGROUND Loss of heterozygosity (LOH) at methylenetetrahydrofolate reductase (MTHFR) locus has been reported in tumor tissue. But the mutation was never reported in cerebral venous thrombosis (CVT) with hyperhomocysteinemia (HHcy) before. CASE PRESENTATION A 14-year-old girl was admitted with an intermittent headache and nausea for 2 months. The plasma homocysteine level was 77.2 µmol/L. Lumbar puncture revealed an intracranial pressure > 330 mmH2O. Cerebral MRI and MRV revealed superior sagittal sinus thrombosis. Whole-exome sequencing revealed LOH at Chr1:11836597-11,867,232 affects exons 10-21 of C1orf167, the entire MTHFR, and exons 1-2 of the CLCN6 gene. The normal allele was the c.665 C > T/677 C > T variant in MTHFR. The patient was treated with nadroparin for 2 weeks, followed by oral rivaroxaban. Supplemental folate and vitamins B12 and B6 were prescribed. One month later, she had no headache and the intracranial pressure had decreased to 215 mmH2O. MRI showed shrinkage of the thrombosis in the superior sagittal sinus, the degree of stenosis had significantly decreased. CONCLUSIONS Rare LOH at the MTHFR locus should be analyzed in CVT with HHcy. With anticoagulation treatment, the prognosis was good.
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Affiliation(s)
- Mingjie Zhang
- Department of Neurology, The First Medical Center, Chinese PLA General Hospital, No. 28 Fuxing Road, Beijing, 100853, PR China
| | - Bingxin Shi
- Brain Science Center, Tsinghua University Yuquan Hospital, No. 5 Shijingshan Road, Beijing, 100049, PR China
| | - Mangsuo Zhao
- Brain Science Center, Tsinghua University Yuquan Hospital, No. 5 Shijingshan Road, Beijing, 100049, PR China.
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13
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Seo GT, Minkowitz J, Kapustin DA, Fan J, Minkowitz G, Minkowitz M, Dowling E, Matloob A, Asti D, Dhar M, Shutty C, Brickman A, Urken ML, Brandwein-Weber M, Finkelstein SD. Synchronous thyroid cancer and malignant struma ovarii: concordant mutations and microRNA profile, discordant loss of heterozygosity loci. Diagn Pathol 2023; 18:47. [PMID: 37072862 PMCID: PMC10111709 DOI: 10.1186/s13000-023-01336-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 04/03/2023] [Indexed: 04/20/2023] Open
Abstract
BACKGROUND Struma ovarii is an unusual ovarian teratoma containing predominantly thyroid tissue. Less than 10% of cases undergo malignant transformation in the thyroid tissue and are considered malignant struma ovarii (MSO). MSO have been reported with concurrent thyroid lesions, but molecular data is lacking. CASE PRESENTATION A 42-year-old female developed MSO and synchronous multifocal subcentimeter papillary thyroid carcinoma (PTC). The patient underwent a salpingo-oophrectomy, thyroidectomy, and low-dose radioactive iodine ablation. Both the thyroid subcentimeter PTC and MSO were positive for BRAF V600E mutation, and microRNA expression profiles were similar across all tumor deposits. However, only the malignant component demonstrated extensive loss of heterozygosity (LOH) involving multiple tumor suppressor gene (TSG) chromosomal loci. CONCLUSIONS We present the first reported case of MSO with synchronous multifocal subcentimeter PTC in the thyroid containing concordant BRAF V600E mutations and resulting with discordant LOH findings. This data suggests that loss of expression in tumor suppressor gene(s) may be an important contributor to phenotypic expression of malignancy.
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Affiliation(s)
- Gabriella T Seo
- Thyroid, Head and Neck Cancer (THANC) Foundation, 10 Union Square East, Suite 5B, New York, NY, 10003, USA
| | - Jeremy Minkowitz
- Minkowitz Pathology, 904 49th Street, Brooklyn, NY, 11219, USA
- SUNY Downstate Medical Center, 450 Clarkson Avenue, Brooklyn, NY, 11203, USA
| | - Danielle A Kapustin
- Thyroid, Head and Neck Cancer (THANC) Foundation, 10 Union Square East, Suite 5B, New York, NY, 10003, USA.
- Department of Otolaryngology-Head and Neck Surgery, Icahn School of Medicine at Mount Sinai, 10 Union Square East, Suite 5B, New York, NY, 10003, USA.
| | - Jun Fan
- Department of Pathology, Mount Sinai West Medical Center, 1000 10th Avenue, New York, NY, 10019, USA
| | | | | | - Eric Dowling
- Department of Otolaryngology-Head and Neck Surgery, Icahn School of Medicine at Mount Sinai, 10 Union Square East, Suite 5B, New York, NY, 10003, USA
| | - Ammar Matloob
- Department of Pathology, Mount Sinai West Medical Center, 1000 10th Avenue, New York, NY, 10019, USA
| | - Divya Asti
- Department of Hematology and Medical Oncology, Northwell Health Staten Island University Hospital, 475 Seaview Avenue, Staten Island, NY, 10305, USA
| | - Meekoo Dhar
- Department of Hematology and Medical Oncology, Northwell Health Staten Island University Hospital, 475 Seaview Avenue, Staten Island, NY, 10305, USA
| | | | - Alan Brickman
- ParCare Community Health Network, 6010 Bay Parkway, Brooklyn, NY, 11204, USA
| | - Mark L Urken
- Thyroid, Head and Neck Cancer (THANC) Foundation, 10 Union Square East, Suite 5B, New York, NY, 10003, USA
- Department of Otolaryngology-Head and Neck Surgery, Icahn School of Medicine at Mount Sinai, 10 Union Square East, Suite 5B, New York, NY, 10003, USA
| | - Margaret Brandwein-Weber
- Department of Pathology, Mount Sinai West Medical Center, 1000 10th Avenue, New York, NY, 10019, USA
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Anno M, Izawa S, Fujioka Y, Matsuzawa K, Saito K, Hikita K, Makishima K, Nosaka K, Takenaka A, Usui T, Yamamoto K. Retroperitoneal paraganglioma with loss of heterozygosity of the von Hippel-Lindau gene: a case report and review of the literature. Endocr J 2022; 69:1137-1147. [PMID: 35466127 DOI: 10.1507/endocrj.ej21-0611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Von Hippel-Lindau (VHL) disease is an autosomal dominant disease related to germline mutations in VHL. In VHL disease, pheochromocytoma develops in 10%-20% of patients because of germline mutations and loss of heterozygosity of VHL. However, the rate of paraganglioma associated with VHL is low compared with that of pheochromocytoma, and the reason is unknown. In this study, we performed germline and somatic mutation analyses of retroperitoneal paraganglioma that developed in a patient with clinically diagnosed VHL disease and investigated the tumorigenic mechanism of paraganglioma. The patient was a 25-year-old woman who was considered to have VHL disease on the basis of her family history. She was referred to our clinic to investigate a tumor at the bifurcation of the common iliac artery. The tumor was diagnosed as retroperitoneal paraganglioma by clinical evaluations. A left renal cell carcinoma was also suspected. Polymerase chain reaction direct sequencing analysis and polymorphic microsatellite analysis within the VHL locus suggested that loss of heterozygosity of VHL was associated with paraganglioma and renal cell carcinoma. Multiplex ligation-dependent probe amplification analysis showed a loss of the copy number of VHL exons in paraganglioma. These results suggest that VHL disease contributes to the development of paraganglioma. A literature review showed no reported common missense variants involved in the progression of paraganglioma. The loss of heterozygosity of VHL can be a tumorigenic mechanism of retroperitoneal paraganglioma in VHL disease. However, the low rate of paraganglioma compared with pheochromocytoma is not explained by their genetic background alone.
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Affiliation(s)
- Mari Anno
- Division of Endocrinology and Metabolism, Tottori University Faculty of Medicine, Yonago 683-8504, Japan
| | - Shoichiro Izawa
- Division of Endocrinology and Metabolism, Tottori University Faculty of Medicine, Yonago 683-8504, Japan
| | - Yohei Fujioka
- Division of Endocrinology and Metabolism, Tottori University Faculty of Medicine, Yonago 683-8504, Japan
| | - Kazuhiko Matsuzawa
- Division of Endocrinology and Metabolism, Tottori University Faculty of Medicine, Yonago 683-8504, Japan
| | - Kohei Saito
- Center for Diabetes, Endocrinology and Metabolism, Shizuoka Prefectural Hospital, Shizuoka 420-8527, Japan
| | - Katsuya Hikita
- Division of Urology, Tottori University Faculty of Medicine, Yonago 683-8504, Japan
| | - Karen Makishima
- Division of Pathology, Tottori University Faculty of Medicine, Yonago 683-8504, Japan
| | - Kanae Nosaka
- Division of Pathology, Tottori University Faculty of Medicine, Yonago 683-8504, Japan
| | - Atsushi Takenaka
- Division of Urology, Tottori University Faculty of Medicine, Yonago 683-8504, Japan
| | - Takeshi Usui
- Research Support Center, Shizuoka Prefectural Hospital, Shizuoka 420-8527, Japan
- Shizuoka Graduate University of Public Health, Shizuoka 420-0881, Japan
| | - Kazuhiro Yamamoto
- Division of Endocrinology and Metabolism, Tottori University Faculty of Medicine, Yonago 683-8504, Japan
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15
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Sait H, Sharma L, Dabadghao P, Phadke SR. Congenital Hyperinsulinemia of Infancy: Role of Molecular Testing in Management and Genetic Counseling. Indian J Pediatr 2022; 89:395-398. [PMID: 35182381 DOI: 10.1007/s12098-021-04014-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 09/30/2021] [Indexed: 11/28/2022]
Abstract
Congenital hyperinsulinemia (CHI) is a genetically and clinically heterogenous disorder. In addition to the standard care of management of the proband, genetic counseling regarding the risk of recurrence in the future siblings is an important part in the management of the disorder. The counseling needs identification of accurate etiology and is challenging due to the complexity of the molecular mechanisms of CHI. This case highlights the importance of molecular testing which not only helped in planning the management of the proband with CHI but also helped in providing genetic counseling for which the family had consulted the medical genetics department.
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Affiliation(s)
- Haseena Sait
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, 226014, India
| | - Lokesh Sharma
- Department of Endocrinology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Preeti Dabadghao
- Department of Endocrinology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Shubha R Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, 226014, India.
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16
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Iyevleva AG, Aleksakhina SN, Sokolenko AP, Baskina SV, Venina AR, Anisimova EI, Bizin IV, Ivantsov AO, Belysheva YV, Chernyakova AP, Togo AV, Imyanitov EN. Somatic loss of the remaining allele occurs approximately in half of CHEK2-driven breast cancers and is accompanied by a border-line increase of chromosomal instability. Breast Cancer Res Treat 2022; 192:283-291. [PMID: 35020107 DOI: 10.1007/s10549-022-06517-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 01/03/2022] [Indexed: 02/06/2023]
Abstract
PURPOSE Germline mutations in CHEK2 gene represent the second most frequent cause of hereditary breast cancer (BC) after BRCA1/2 lesions. This study aimed to identify the molecular characteristics of CHEK2-driven BCs. METHODS Loss of heterozygosity (LOH) for the remaining CHEK2 allele was examined in 50 CHEK2-driven BCs using allele-specific PCR assays for the germline mutations and analysis of surrounding single-nucleotide polymorphisms (SNPs). Paired tumor and normal DNA samples from 25 cases were subjected to next-generation sequencing analysis. RESULTS CHEK2 LOH was detected in 28/50 (56%) BCs. LOH involved the wild-type allele in 24 BCs, mutant CHEK2 copy was deleted in 3 carcinomas, while in one case the origin of the deleted allele could not be identified. Somatic PIK3CA and TP53 mutations were present in 13/25 (52%) and 4/25 (16%) tumors, respectively. Genomic features of homologous recombination deficiency (HRD), including the HRD score ≥ 42, the predominance of BRCA-related mutational signature 3, and the high proportion of long (≥ 5 bp) indels, were observed only in 1/20 (5%) BC analyzed for chromosomal instability. Tumors with the deleted wild-type CHEK2 allele differed from LOH-negative cases by elevated HRD scores (median 23 vs. 7, p = 0.010) and higher numbers of chromosomal segments affected by copy number aberrations (p = 0.008). CONCLUSION Somatic loss of the wild-type CHEK2 allele is observed in approximately half of CHEK2-driven BCs. Tumors without CHEK2 LOH are chromosomally stable. BCs with LOH demonstrate some signs of chromosomal instability; however, its degree is significantly lower as compared to BRCA1/2-associated cancers.
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Affiliation(s)
- Aglaya G Iyevleva
- N.N. Petrov Institute of Oncology, Leningradskaya str. 68, Pesochny, Saint Petersburg, Russia, 197758.
| | - Svetlana N Aleksakhina
- N.N. Petrov Institute of Oncology, Leningradskaya str. 68, Pesochny, Saint Petersburg, Russia, 197758
| | - Anna P Sokolenko
- N.N. Petrov Institute of Oncology, Leningradskaya str. 68, Pesochny, Saint Petersburg, Russia, 197758
| | - Sofia V Baskina
- N.N. Petrov Institute of Oncology, Leningradskaya str. 68, Pesochny, Saint Petersburg, Russia, 197758
| | - Aigul R Venina
- N.N. Petrov Institute of Oncology, Leningradskaya str. 68, Pesochny, Saint Petersburg, Russia, 197758
| | | | - Ilya V Bizin
- N.N. Petrov Institute of Oncology, Leningradskaya str. 68, Pesochny, Saint Petersburg, Russia, 197758
| | - Alexandr O Ivantsov
- N.N. Petrov Institute of Oncology, Leningradskaya str. 68, Pesochny, Saint Petersburg, Russia, 197758
| | - Yana V Belysheva
- N.N. Petrov Institute of Oncology, Leningradskaya str. 68, Pesochny, Saint Petersburg, Russia, 197758
| | - Alexandra P Chernyakova
- N.N. Petrov Institute of Oncology, Leningradskaya str. 68, Pesochny, Saint Petersburg, Russia, 197758
| | - Alexandr V Togo
- N.N. Petrov Institute of Oncology, Leningradskaya str. 68, Pesochny, Saint Petersburg, Russia, 197758
| | - Evgeny N Imyanitov
- N.N. Petrov Institute of Oncology, Leningradskaya str. 68, Pesochny, Saint Petersburg, Russia, 197758.,St.-Petersburg State Pediatric Medical University, Saint Petersburg, Russia, 194100.,I.I. Mechnikov North-Western Medical University, Saint Petersburg, Russia, 191015
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17
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Abstract
A central question in neuroscience is how 100 billion neurons come together to build the human brain. The wiring, morphology, survival, and death of each neuron are controlled by genes that encode intrinsic and extrinsic factors. Determining the function of these genes at a high spatiotemporal resolution is a critical step toward understanding brain development and function. Moreover, an increasing number of somatic mutations are being discovered in many brain disorders. However, neurons are embedded in complex networks, making it difficult to distinguish cell-autonomous from non-cell-autonomous function of any given gene in the brain. Here, I describe MADM (mosaic analysis with double markers), a genetic method that allows for labeling and manipulating gene function at the single-cell level within the mouse brain. I present mouse breeding schemes to employ MADM analysis and important considerations for experimental design. This powerful system can be adapted to make fundamental neuroscience discoveries by targeting genetically defined cell types in the mouse brain with high spatiotemporal resolution.
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Affiliation(s)
- Wei-Hsiang Huang
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Montréal, QC, Canada.
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18
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Islam S, Dutta P, Sahay O, Gopalakrishnan K, Roy Muhury S, Parameshwar P, Shetty P, Santra MK. Feedback-regulated transcriptional repression of FBXO31 by c-Myc triggers ovarian cancer tumorigenesis. Int J Cancer 2021; 150:1512-1524. [PMID: 34706096 DOI: 10.1002/ijc.33854] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 07/30/2021] [Accepted: 09/02/2021] [Indexed: 11/08/2022]
Abstract
FBXO31, a member of F-box protein family, has been shown to play an important role in preventing tumorigenesis by preserving genomic stability during cell proliferations as well as upon genotoxic stresses. Inactivation of FBXO31 due to loss of heterozygosity is associated with various cancers, including ovarian cancer, one of the deadliest forms of gynecological cancers. However, the role and regulation of FBXO31 in ovarian cancer remained elusive. Here, using biochemical and molecular biology techniques, we show that c-Myc suppresses the mRNA levels of FBXO31 in ovarian cancer cell lines and mouse model. Chromatin immunoprecipitation experiment showed that c-Myc is recruited to the promoter region of FBXO31 and prevents FBXO31 mRNA synthesis. In contrast, FBXO31 maintains the c-Myc expression at an optimum through proteasome pathway. FBXO31 interacts with and facilitates the polyubiquitination of c-Myc through the SCF complex and thereby inhibits ovarian cancer growth both in vitro and in vivo. Moreover, FBXO31-mediated proteasomal degradation of c-Myc is unique. Unlike other negative regulators, FBXO31 recognizes c-Myc in phosphorylation independent manner to direct its degradation. Further, expression levels analysis revealed that c-Myc and FBXO31 share a converse correlation of expression in ovarian cancer cell lines and patient samples. We observed an increase in the expression levels of c-Myc with a concomitant decrease in the levels of FBXO31 in higher grades of ovarian cancer patient samples. In conclusion, our study demonstrated that oncogene c-Myc impairs the tumor-suppressive functions of FBXO31 to promote ovarian cancer progression, and therefore c-Myc-FBXO31 axis can be explored to develop better cancer therapy. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Sehbanul Islam
- National Centre for Cell Science, NCCS Complex, Ganeshkhind Road, Pune, Maharashtra, India.,Department of Biotechnology, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Parul Dutta
- National Centre for Cell Science, NCCS Complex, Ganeshkhind Road, Pune, Maharashtra, India.,Department of Biotechnology, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Osheen Sahay
- National Centre for Cell Science, NCCS Complex, Ganeshkhind Road, Pune, Maharashtra, India.,Department of Biotechnology, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - K Gopalakrishnan
- National Centre for Cell Science, NCCS Complex, Ganeshkhind Road, Pune, Maharashtra, India
| | - Sushrita Roy Muhury
- National Centre for Cell Science, NCCS Complex, Ganeshkhind Road, Pune, Maharashtra, India
| | - Parinitha Parameshwar
- Department of Pathology, SDM College of Medical Sciences & Hospital, Sattur, Dharwad, India
| | - Praveenkumar Shetty
- K. S. Hegde Medical Academy, NITTE (Deemed to be University), University Enclave, Medical Sciences Complex, Dheralakatte, Mangalore, India
| | - Manas Kumar Santra
- National Centre for Cell Science, NCCS Complex, Ganeshkhind Road, Pune, Maharashtra, India
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19
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Huo X, Feng D, Zhang S, Li Z, Li X, Li C, Guo M, Wang J, Zhang Z, Lu Q, Du X, Bai Z, Chen Z. Characterization and clinical evaluation of microsatellite instability and loss of heterozygosity within tumor-related genes in colorectal cancer. BMC Med Genomics 2021; 14:235. [PMID: 34563193 PMCID: PMC8466986 DOI: 10.1186/s12920-021-01051-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 08/05/2021] [Indexed: 11/30/2022] Open
Abstract
Background Microsatellite instability (MSI) is a biomarker for better outcomes in colorectal cancer (CRC). However, this conclusion is controversial. In addition, MSs can be a useful marker for loss of heterozygosity (LOH) of genes, but this finding has not been well studied. Here, we aimed to clarify the predictive value of MSI/LOH within tumor-related genes in CRC. Methods We detected MSI/LOH of MSs in tumor-related genes and the Bethesda (B5) panel by STR scanning and cloning/sequencing. We further analyzed the relationship between MSI/LOH status and clinical features or outcomes by Pearson’s Chi-square test, Fisher’s exact test and the Kaplan–Meier method. Results The findings indicated that the MSI rates of B5 loci were all higher than those of loci in tumor-related genes. Interestingly, MSI/LOH of 2 loci in the B5 panel and 12 loci in tumor-related genes were associated with poorer outcomes, while MSI/LOH of the B5 panel failed to predict outcomes in CRC. MSI of BAT25, MSI/LOH of BAT26 and MSI of the B5 panel showed closer relationships with mucinous carcinoma. In addition, LOH-H of the B5 panel was associated with increased lymphatic metastasis. Conclusions In summary, MSI/LOH of certain loci or the whole panel of B5 is related to clinical features, and several loci within tumor-related genes showed prognostic value in the outcomes of CRC. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-021-01051-5.
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Affiliation(s)
- Xueyun Huo
- School of Basic Medical Sciences, Capital Medical University, Beijing Key Laboratory of Cancer Invasion & Metastasis Research, Beijing, 100069, China
| | - Dandan Feng
- School of Basic Medical Sciences, Capital Medical University, Beijing Key Laboratory of Cancer Invasion & Metastasis Research, Beijing, 100069, China
| | - Shuangyue Zhang
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical Collage, Beijing, 100021 , China
| | - Zhenkun Li
- School of Basic Medical Sciences, Capital Medical University, Beijing Key Laboratory of Cancer Invasion & Metastasis Research, Beijing, 100069, China
| | - Xiaohong Li
- School of Basic Medical Sciences, Capital Medical University, Beijing Key Laboratory of Cancer Invasion & Metastasis Research, Beijing, 100069, China
| | - Changlong Li
- School of Basic Medical Sciences, Capital Medical University, Beijing Key Laboratory of Cancer Invasion & Metastasis Research, Beijing, 100069, China
| | - Meng Guo
- School of Basic Medical Sciences, Capital Medical University, Beijing Key Laboratory of Cancer Invasion & Metastasis Research, Beijing, 100069, China
| | - Jin Wang
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing Key Laboratory of Cancer Invasion & Metastasis Research & National Clinical Research Center for Digestive Diseases, Beijing, 100050, China
| | - Zhongtao Zhang
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing Key Laboratory of Cancer Invasion & Metastasis Research & National Clinical Research Center for Digestive Diseases, Beijing, 100050, China
| | - Qingxian Lu
- Department of Ophthalmology and Visual Sciences, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Xiaoyan Du
- School of Basic Medical Sciences, Capital Medical University, Beijing Key Laboratory of Cancer Invasion & Metastasis Research, Beijing, 100069, China
| | - Zhigang Bai
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing Key Laboratory of Cancer Invasion & Metastasis Research & National Clinical Research Center for Digestive Diseases, Beijing, 100050, China.
| | - Zhenwen Chen
- School of Basic Medical Sciences, Capital Medical University, Beijing Key Laboratory of Cancer Invasion & Metastasis Research, Beijing, 100069, China.
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20
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Awadalla A, Harraz AM, Abol-Enein H, Laymon M, Ahmed AE, Abdel-Rahim M, Zekri AN, Shokeir AA. Prognostic influence of microsatellite alterations of muscle-invasive bladder cancer treated with radical cystectomy. Urol Oncol 2021:S1078-1439(21)00385-9. [PMID: 34538725 DOI: 10.1016/j.urolonc.2021.08.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/30/2021] [Accepted: 08/19/2021] [Indexed: 11/22/2022]
Abstract
OBJECTIVE To examine the prognostic effect of microsatellite instability (MSI) and loss of heterozygosity (LOH) on cancer-specific survival (CSS) in patients with muscle-invasive bladder cancer (MIBC). PATIENTS AND METHODS The liquid nitrogen-preserved specimens of 220 patients between March 2009 and December 2012 were analyzed for the presence of MSI and LOH in 12 loci (ACTBP2, D16S310, D16S476, D18S51, D4S243, D9S162, D9S171, D9S747, FGA, INF-α, MBP, MJD) using polymerase chain reaction. MSI was defined as MSI-stable, MSI-Low, or MSI-High if instability was detected in 0, 1, or 2 or more of the examined markers, respectively. The association between MSI-High and LOH and CSS was analyzed using uni- and multivariate analyses and the degree of agreement between tumor and urine samples were determined. RESULTS MSI were found in 1030 (39%) and 1148 (43.5%) in tumor and urine specimens, respectively (Kappa = 0.77). On the other hand, LOH was found in 163 (6.2%) of tumor tissues and 44 (1.7%) in urine specimens (Kappa = 0.34). Microsatellite alterations were significantly associated with worse CSS at 1- and 5-year in tumor tissue (95% and 83.7% vs. 65.8% and 3.5%, respectively; P < 0.001) and in urine sample (90% and 64% vs. 46.5% and 9.3%, respectively; P < 0.001). MSI and/or LOH was an independent predictor of CSS (HR: 9.8; 95%CI: 5.1-18.9; P < 0.001). CONCLUSIONS Microsatellite alterations were potentially an independent predictor of CSS in patients with MIBC. The agreement was good between tumor and urine MSI but weak for LOH.
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21
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Shi X, Li P, Hu R, Han W, Gao S. Pretransplant HLA mistyping in diagnostic sample of a T-ALL patient due to loss of heterozygosity in the major histocompatibility complex. Transpl Immunol 2021; 69:101463. [PMID: 34492296 DOI: 10.1016/j.trim.2021.101463] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 09/02/2021] [Accepted: 09/02/2021] [Indexed: 11/29/2022]
Abstract
PURPOSE The degree of HLA compatibility between donor and recipient in hematopoietic stem cell transplantation is critical. In this report, we describe an acute lymphoblastic leukemia case with loss of heterozygosity (LOH) encompassing the entire HLA. METHODS HLA molecular typing was performed on peripheral blood (PB) and buccal swabs (BS). Chromosomal microarray analysis (CMA) was performed using a whole genome platform. RESULTS Typing results on PB sample collected during blast crisis demonstrated homozygosity at the-B,-C,-DR, and -DP loci. A BS sample demonstrated heterozygosity at the above loci. A subsequent PB sample drawn after count recovery confirmed heterozygosity. The CMA performed on PB samples collected during blast crisis revealed a large terminal region of copy-neutral LOH involving chromosome region 6p25.3p21.31, spanning approximately 33.32 Mb. The results of the CMA assay on sample collected after count recovery did not demonstrate LOH. CONCLUSIONS LOH at the HLA gene locus may significantly influence the donor search resulting in mistakenly choosing homozygous donors. We recommend confirming the HLA typing of recipients with hematological malignancies when homozygosity is detected at any locus by using BS samples, or alternatively from PB when remission is achieved.
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Affiliation(s)
- XiuMin Shi
- Department of Hematology, The First Hospital of Jilin University, Changchun, China
| | - PeiTong Li
- Department of Hematology, The First Hospital of Jilin University, Changchun, China
| | - RuiPing Hu
- Department of Hematology, The First Hospital of Jilin University, Changchun, China
| | - Wei Han
- Department of Hematology, The First Hospital of Jilin University, Changchun, China
| | - SuJun Gao
- Department of Hematology, The First Hospital of Jilin University, Changchun, China.
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22
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Moretto R, Elliott A, Zhang J, Arai H, Germani MM, Conca V, Xiu J, Stafford P, Oberley M, Abraham J, Spetzler D, Rossini D, Antoniotti C, Marshall J, Shields A, Lopes G, Lonardi S, Pietrantonio F, Tomasello G, Passardi A, Tamburini E, Santini D, Aprile G, Masi G, Falcone A, Lenz HJ, Korn M, Cremolini C. Homologous Recombination Deficiency Alterations in Colorectal Cancer: Clinical, Molecular, and Prognostic Implications. J Natl Cancer Inst 2021; 114:271-279. [PMID: 34469533 DOI: 10.1093/jnci/djab169] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/10/2021] [Accepted: 07/27/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Tumors with homologous recombination (HR) deficiency (HRD) show high sensitivity to platinum salts and PARP-inhibitors in several malignancies. In colorectal cancer (CRC), the role of HRD alterations is mostly unknown. METHODS Next generation sequencing, whole transcriptome sequencing and whole exome sequencing were conducted using CRC samples submitted to a commercial Clinical Laboratory Improvement Amendments (CLIA) certified laboratory. Tumors with pathogenic/presumed pathogenic mutations in 33 genes involved in the HR pathway were considered HRD, the others HR proficient (HRP). Furthermore, tumor samples from patients enrolled in the phase III TRIBE2 study comparing upfront FOLFOXIRI/bevacizumab versus FOLFOX/bevacizumab were analyzed with next generation sequencing. The analyses were separately conducted in microsatellite stable/proficient mismatch repair (MSS/pMMR) and microsatellite instable-high/deficient mismatch repair (MSI-H/dMMR) groups. All statistical tests were 2-sided. RESULTS Of 9321 CRC tumors, 1270 (13.6%) and 8051 (86.4%) were HRD and HRP, respectively. HRD tumors were more frequent among MSI-H/dMMR than MSS/pMMR tumors (73.4% vs 9.5%, p and q < 0.001). In MSS/pMMR group, HRD tumors were more frequently tumor mutational burden high (8.1% vs 2.2% P and q < 0.001) and PD-L1 positive (5.0% vs 2.4%, P and q = 0.001), enriched in all immune cell and fibroblast populations, and genomic loss of heterozygosity-high (16.2% vs 9.5%, P = .03). In the TRIBE2 study, patients with MSS/pMMR and HRD tumors (10.7%) showed longer overall survival compared to MSS/pMMR and HRP ones (40.2 vs 23.8 months; hazard ratio = 0.66; 95% confidence interval = 0.45-0.98, P = .04). Consistent results were reported in the multivariable model (hazard ratio = 0.67; 95% confidence ratio = 0.45-1.02, P = .07). No interaction effect was evident between HR groups and treatment arm. CONCLUSIONS HRD tumors are a distinctive subgroup of MSS/pMMR CRCs with specific molecular and prognostic characteristics. The potential efficacy of agents targeting the HR system and immune check-point inhibitors in this subgroup is worth of clinical investigation.
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Affiliation(s)
- Roberto Moretto
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy
| | - Andrew Elliott
- Clinical & Translational Research, Medical Affairs, Caris Life Sciences, Phoenix, AZ, USA
| | - Jian Zhang
- Clinical & Translational Research, Medical Affairs, Caris Life Sciences, Phoenix, AZ, USA
| | - Hiroyuki Arai
- Division of Medical Oncology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Marco Maria Germani
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy.,Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Veronica Conca
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy.,Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Joanne Xiu
- Clinical & Translational Research, Medical Affairs, Caris Life Sciences, Phoenix, AZ, USA
| | - Phillip Stafford
- Clinical & Translational Research, Medical Affairs, Caris Life Sciences, Phoenix, AZ, USA
| | - Matthew Oberley
- Clinical & Translational Research, Medical Affairs, Caris Life Sciences, Phoenix, AZ, USA
| | - Jim Abraham
- Clinical & Translational Research, Medical Affairs, Caris Life Sciences, Phoenix, AZ, USA
| | - David Spetzler
- Clinical & Translational Research, Medical Affairs, Caris Life Sciences, Phoenix, AZ, USA
| | - Daniele Rossini
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy.,Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Carlotta Antoniotti
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy.,Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - John Marshall
- Division of Hematology/Oncology, Ruesch Center for The Cure of Gastrointestinal Cancers, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, D.C, ., USA
| | - Anthony Shields
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, USA
| | - Gilberto Lopes
- Division of Medical Oncology, Department of Medicine, Miller School of Medicine, University of Miami, Sylvester Comprehensive Cancer Center, Miami, FL, USA
| | - Sara Lonardi
- Early Phase Clinical Trial Unit, Department of Oncology, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy.,Medical Oncology Unit 1, Department of Oncology, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Filippo Pietrantonio
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.,Oncology and Hemato-oncology Department, University of Milan, Milan, Italy
| | - Gianluca Tomasello
- Oncology Unit, Oncology Department, ASST of Cremona, Cremona, Italy.,UOC Medical Oncology, IRCCS Foundation Ca' Granda Maggiore Hospital Policlinic, Milan, Italy
| | - Alessandro Passardi
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Emiliano Tamburini
- Department of Oncology and Palliative Care, Cardinale G Panico, Tricase City Hospital, Tricase, Italy
| | - Daniele Santini
- Department of Medical Oncology, University Campus Biomedico, Rome, Italy
| | - Giuseppe Aprile
- Department of Oncology, San Bortolo General Hospital, Vicenza, Italy
| | - Gianluca Masi
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy.,Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Alfredo Falcone
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy.,Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Heinz-Josef Lenz
- Division of Medical Oncology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Michael Korn
- Clinical & Translational Research, Medical Affairs, Caris Life Sciences, Phoenix, AZ, USA
| | - Chiara Cremolini
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy.,Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
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23
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Sorscher S, Ramkissoon S. Rapid Progression of Metastatic Pancreatic Adenocarcinoma During Platinum-Based Therapy in a Patient Harboring a Pathogenic BRCA2 Germline Variant. Oncologist 2021; 26:916-918. [PMID: 34309133 DOI: 10.1002/onco.13912] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 07/20/2021] [Indexed: 12/24/2022] Open
Abstract
Familial pancreatic adenocarcinoma (PDAC) is most commonly related to inheritance of a pathogenic BRCA variant (J Med Genet 2005;42:711-719). The National Comprehensive Cancer Network recommends germline testing for patients diagnosed with PDAC and recommends platinum-based chemotherapy as the preferred initial systemic therapy for patients harboring a pathogenic BRCA germline variant with PDAC (https://www.nccn.org/guidelines/guidelines-detail?category=1&id=1455). PDACs related to pathogenic BRCA germline variants typically demonstrate BRCA loss of heterozygosity (LOH), which results in ineffective DNA damage repair due to a lack of normal BRCA gene product activity. By causing DNA damage, platinum-based therapies have been shown to be highly effective therapies (Cancer Cell 2010;18:499-509, Gen Med 2015;17:569). In contrast, platinum-based therapies would be predicted to be significantly less effective for PDACs in patients with pathogenic BRCA germline variants who have cancers that lack BRCA LOH. Poly (ADP-ribose) polymerase 1 (PARP) is also key to effective DNA repair. The Food and Drug Administration has approved PARP inhibitors for patients carrying germline pathogenic BRCA variants and metastatic breast cancer or ovarian cancer (Ann Oncol 2019;30:558-566, J Clin Oncol 2015;33:244-250). PARP inhibitors would again be expected to be far less effective in patients who carry pathogenic BRCA germline variants with breast and ovarian cancers (those that lack BRCA LOH) than in those with BRCA-related breast and ovarian cancers (which typically demonstrate BRCA LOH), because PARP is involved in DNA repair. Here, we present a patient harboring a pathogenic BRCA germline variant whose PDAC grew rapidly during platinum-based therapy and lacked BRCA LOH and therefore was not likely BRCA related. Given the molecular fingerprint of BRCA-related PDAC in patients with pathogenic BRCA germline variants and the mechanism of action of platinum-based therapies and PARP inhibitors, this case underscores the importance of future studies aimed at determining whether the lack of BRCA LOH in PDACs in pathogenic BRCA germline variant carriers is a biomarker of less responsiveness to platinum-based chemotherapy and PARP inhibitors. KEY POINTS: Platinum-based therapy or Poly (ADP-ribose) polymerase 1 (PARP) inhibitor therapies are highly effective systemic therapy options for most patients with pancreatic adenocarcinoma who carry a germline pathogenic BRCA variant. In the case presented here, a patient carrying a germline pathogenic BRCA variant saw rapid progression of his pancreatic adenocarcinoma while on platinum-based therapy. Next-generation sequencing confirmed that his pancreatic cancer was likely not related to BRCA loss of heterozygosity (LOH). Studies are needed to determine, in patients who harbor germline pathogenic BRCA variants, whether similar cancers (i.e., those that lack BRCA LOH) are less responsive to platinum-based or PARP inhibitor therapies than are those more common BRCA-related cancers (i.e., those that demonstrate LOH).
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Affiliation(s)
- Steven Sorscher
- Department of Internal Medicine, Oncology Division, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Shakti Ramkissoon
- Pathology and Diagnostic Medicine, Foundation Medicine, Inc, Cambridge, Massachusetts, USA
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Sharma A, Jain M, Halder A, Kaushal S. Identification of genomic imbalances (CNVs as well as LOH) in sertoli cell only syndrome cases through cytoscan microarray. Gene 2021; 801:145851. [PMID: 34274474 DOI: 10.1016/j.gene.2021.145851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 06/01/2021] [Accepted: 07/13/2021] [Indexed: 10/20/2022]
Abstract
Sertoli cell only syndrome (SCOS) is characterized by complete absence of germ cells in seminiferous tubules of testis. SCOS is multifactorial but genetic factors play a major role in pathogenesis of the disorder with idiopathic origin. Genetic factors majorly include sex chromosomal aneuploidy and Yq Microdeletion. But a large number of cases are still idiopathic. The study aimed to evaluate the genomic imbalances (CNVs and LOH) in idiopathic SCOS patients. The study is based on 28 apparent idiopathic SCOS cases and 10 controls. Molecular cytogenetic techniques viz., FISH, STS-Multiplex PCR and Affymetrix cytoscan microarray (750 K) were used. The microarray screened whole genomic imbalances in DNA from peripheral blood of 25 cases (excluded Klinefelter syndrome patients) and testicular FNAC sample of 2 cases. High FSH and low Inhibin B were observed in cases as compared to control controls groups. Four cases of sex chromosomal abnormality (i.e., three non-mosaic 47, XXY males and one non-mosaic 46, XX male) as well as four cases of Yq microdeletion (i.e., three cases with AZFc deletion and one case with complete AZFa, b and c deletion) were identified. Microarray detected unbalanced translocation of two segments of Y-chromosome i.e., Yp11.31-p11.2 (~4.o mb region, involving SRY) and Yp11.2 (~2.5 mb region) on X-chromosome in XX male. Also, loss of segment on same X-chromosome involving PAR1 region was identified. We have identified both autosomal and sex chromosomal CNVs (recurrent as well as private) involving candidate genes like SYCE1, ZFPM2, SRPK1, DAZ1, BPY2, HSFY1, VCY1 etc. All these CNVs are possibly associated with SCOS pathogenesis. CNVs identified in cases were already reported as pathogenic variant in clinical database DECIPHER. Microarray also detected many LOH (all autosomal, >3.0 mb size) that covered genes with spermatogenesis related function. The mechanism of action of LOH in pathogenesis of SCOS still remains unravelled. CNVs and LOH related to spermatogenesis identified from two different sample types (blood vs. testicular tissue) were discordant. This study should be extended for larger cohort of patients.
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Affiliation(s)
- Aiyush Sharma
- Department of Reproductive Biology, All India Institute of Medical Sciences, New Delhi, India
| | - Manish Jain
- Department of Reproductive Biology, All India Institute of Medical Sciences, New Delhi, India.
| | - Ashutosh Halder
- Department of Reproductive Biology, All India Institute of Medical Sciences, New Delhi, India
| | - Seema Kaushal
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
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Ripamonti CB, Bossi P, Manoukian S, Locati L, Colombo M, Carcangiu ML, Vingiani A, Licitra L, Radice P. Malignant salivary gland tumours in families with breast cancer susceptibility. Virchows Arch 2021; 479:221-226. [PMID: 34100114 DOI: 10.1007/s00428-021-03105-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 03/26/2021] [Accepted: 04/19/2021] [Indexed: 11/26/2022]
Abstract
Salivary gland cancers (SGCs) are rare malignancies with highly heterogeneous histological features. Patients affected with SGCs are at increased risk of secondary malignancies, including breast cancer (BC). Previous studies enlightened a possible link between SGCs and hereditary predisposition to BC. Here, we searched for SGC-affected patients in 1796 high-risk BC families recruited at the Genetic Unit of the Istituto Nazionale dei Tumori of Milan, 516 of which carried pathogenic variants in BRCA1 and/or BRCA2, the main genetic risk factors for BC. We detected five families with an individual affected with SGC, including two male patients, one carrying a constitutional mutation in BRCA1 and the other in BRCA2. Loss of heterozygosity of BRCA wild-type alleles was assessed in the patients' tumour DNA. We conclude that our observations support the hypothesis that genetic factors associated with BC susceptibility might play a role also in at least a subset of SGCs.
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Affiliation(s)
- Carla B Ripamonti
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Research Department, Fondazione IRCCS Istituto Nazionale Dei Tumori, Via Amadeo 42, 20133, Milan, Italy.
| | - Paolo Bossi
- Unit of Head and Neck Cancers, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale Dei Tumori, Via Venezian 1, 20133, Milan, Italy
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Medical Oncology and Hematology Fondazione, IRCCS Istituto Nazionale Dei Tumori, Via Venezian 1, 20133, Milan, Italy
| | - Laura Locati
- Unit of Head and Neck Cancers, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale Dei Tumori, Via Venezian 1, 20133, Milan, Italy
| | - Mara Colombo
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Research Department, Fondazione IRCCS Istituto Nazionale Dei Tumori, Via Amadeo 42, 20133, Milan, Italy
| | - Maria L Carcangiu
- Unit of Anatomic Pathology 1, Department of Pathology, Fondazione IRCCS Istituto Nazionale Dei Tumori, Via Venezian 1, 20133, Milan, Italy
| | - Andrea Vingiani
- Unit of Anatomic Pathology 2, Department of Pathology, Fondazione IRCCS Istituto Nazionale Dei Tumori, Via Venezian 1, 20133, Milan, Italy
| | - Lisa Licitra
- Unit of Head and Neck Cancers, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale Dei Tumori, Via Venezian 1, 20133, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Research Department, Fondazione IRCCS Istituto Nazionale Dei Tumori, Via Amadeo 42, 20133, Milan, Italy
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Suzuki M, Kondo A, Ogino I, Akiyama O, Fujita N, Shimizu Y, Arai H. A case of solitary subependymal giant cell astrocytoma with histopathological anaplasia and TSC2 gene alteration. Childs Nerv Syst 2021; 37:1357-1362. [PMID: 32725466 DOI: 10.1007/s00381-020-04839-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 07/24/2020] [Indexed: 11/24/2022]
Abstract
We report a case of subependymal giant cell astrocytoma (SEGA) with anaplastic histological features in a 3-year-old girl. She had no clinical manifestations of tuberous sclerosis complex (TSC) and no relevant family history. A few cases have been reported in which patients with SEGA had no other clinical manifestations of TSC (solitary SEGA). Genetic analysis using a blood sample from the patient showed no germline alterations in TSC1 or TSC2 genes, while the tumor tissue exhibited loss of heterozygosity (LOH) in TSC2. SEGAs are benign, slowly growing tumors that rarely have significant mitotic activity. However, histopathological examination in the present case revealed high mitotic activity and necrosis besides the typical large plump cells arranged in sheets. This may be the first genetically proven case of a solitary SEGA with histopathological anaplastic features. In this report, we reviewed solitary SEGAs and histopathological malignancy in SEGA.
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Affiliation(s)
- Mario Suzuki
- Department of Neurosurgery, Juntendo University Faculty of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, Japan
| | - Akihide Kondo
- Department of Neurosurgery, Juntendo University Faculty of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, Japan.
| | - Ikuko Ogino
- Department of Neurosurgery, Juntendo University Faculty of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, Japan
| | - Osamu Akiyama
- Department of Neurosurgery, Juntendo University Faculty of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, Japan
| | - Naohide Fujita
- Department of Neurosurgery, Juntendo University Faculty of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, Japan
| | - Yuzaburo Shimizu
- Department of Neurosurgery, Juntendo University Faculty of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, Japan
| | - Hajime Arai
- Department of Neurosurgery, Juntendo University Faculty of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, Japan
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Sugimoto R, Habano W, Yanagawa N, Akasaka R, Toya Y, Sasaki A, Matsumoto T, Sugai T. Molecular alterations in gastric cancer and the surrounding intestinal metaplastic mucosa: an analysis of isolated glands. Gastric Cancer 2021; 24:382-91. [PMID: 33141339 DOI: 10.1007/s10120-020-01130-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 10/11/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Intestinal metaplasias (IMs) are generally regarded as pre-neoplastic gastric lesions. However, molecular alterations including genetic and epigenetic changes occurring in individual IM glands are not well defined. AIMS We sought to identify DNA methylation status, microsatellite instability (MSI) and allelic imbalance (AI) occurring in individual IM glands and non-IM glands within the same mucosa. METHODS We divided examined isolated gland obtained from GC into 4 components: isolated cancer, antral isolated intestinal metaplastic tissue, antral isolated non-metaplastic gland and isolated non-metaplastic gland derived from the greater curvature of the most distant gastric body without mucosal atrophy. We examined AI and microsatellite instability statuses using PCR-based microsatellite analysis. Next, the DNA methylation status (high methylation epigenome [HME], intermediate methylation epigenome [IME], and low methylation epigenome [LME]) was investigated. DNA methylation analysis of CDKN2A, mir34-b/c and MLHI genes was also performed. RESULTS Although antral isolated IM glands were characterized by IME, isolated non-IM glands showed LME. In isolated cancer glands, HME was frequently found, compared with isolated non-IM glands. DNA methylation of mir34-b/c was common in isolated cancer and IM glands, whereas DNA methylation of CDKN2A was a rare event in isolated samples. The MLH1 gene was not methylated in isolated non-IM glands. Although multiple AIs were frequently found in isolated cancer glands, a few AIs were detected in isolated IM glands. CONCLUSIONS We suggest that the DNA methylation status and the status of the mir34-b/c gene among isolated samples of IMs and isolated non-IM glands have an impact on IM development.
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Blondal T, Gamba C, Møller Jagd L, Su L, Demirov D, Guo S, Johnston CM, Riising EM, Wu X, Mikkelsen MJ, Szabova L, Mouritzen P. Verification of CRISPR editing and finding transgenic inserts by Xdrop indirect sequence capture followed by short- and long-read sequencing. Methods 2021; 191:68-77. [PMID: 33582298 DOI: 10.1016/j.ymeth.2021.02.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 11/12/2020] [Accepted: 02/02/2021] [Indexed: 01/02/2023] Open
Abstract
Validation of CRISPR-Cas9 editing typically explores the immediate vicinity of the gene editing site and distal off-target sequences, which has led to the conclusion that CRISPR-Cas9 editing is very specific. However, an increasing number of studies suggest that on-target unintended editing events like deletions and insertions are relatively frequent but unfortunately often missed in the validation of CRISPR-Cas9 editing. The deletions may be several kilobases-long and only affect one allele. The gold standard in molecular validation of gene editing is direct sequencing of relatively short PCR amplicons. This approach allows the detection of small editing events but fails in detecting large rearrangements, in particular when only one allele is affected. Detection of large rearrangements requires that an extended region is analyzed and the characterization of events may benefit from long-read sequencing. Here we implemented Xdrop™, a new microfluidic technology that allows targeted enrichment of long regions (~100 kb) using just a single standard PCR primer set. Sequencing of the enriched CRISPR-Cas9 gene-edited region in four cell lines on long- and short-read sequencing platforms unravelled unknown and unintended genome editing events. The analysis revealed accidental kilobases-large insertions in three of the cell lines, which remained undetected using standard procedures. We also applied the targeted enrichment approach to identify the integration site of a transgene in a mouse line. The results demonstrate the potential of this technology in gene editing validation as well as in more classic transgenics.
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Affiliation(s)
| | | | | | - Ling Su
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Dimiter Demirov
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Shuang Guo
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | | | - Xiaolin Wu
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | - Ludmila Szabova
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research at the National Cancer Institute-Frederick, Frederick, MD, USA
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Abstract
DNA break lesions pose a serious threat to the integrity of the genome. Eukaryotic cells can repair these lesions using the homologous recombination pathway that guides the repair reaction by using a homologous DNA template. The budding yeast Saccharomyces cerevisiae is an excellent model system with which to study this repair mechanism and the resulting patterns of genomic change resulting from it. In this chapter, we describe an approach that utilizes whole-genome sequencing data to support the analysis of tracts of loss-of-heterozygosity (LOH) that can arise from mitotic recombination in the context of the entire diploid yeast genome. The workflow and the discussion in this chapter are intended to enable classically trained molecular biologists and geneticists with limited experience in computational methods to conceptually understand and execute the steps of genome-wide LOH analysis as well as to adapt and apply them to their own specific studies and experimental models.
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Affiliation(s)
- Lydia R Heasley
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Nadia M V Sampaio
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
- Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, USA
| | - Juan Lucas Argueso
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA.
- Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, USA.
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30
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Ross JS, Sokol ES, Moch H, Mileshkin L, Baciarello G, Losa F, Beringer A, Thomas M, Elvin JA, Ngo N, Jin DX, Krämer A. Comprehensive Genomic Profiling of Carcinoma of Unknown Primary Origin: Retrospective Molecular Classification Considering the CUPISCO Study Design. Oncologist 2020; 26:e394-e402. [PMID: 33219618 PMCID: PMC7930409 DOI: 10.1002/onco.13597] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/28/2020] [Indexed: 11/20/2022] Open
Abstract
Background Carcinoma of unknown primary origin (CUP) accounts for 2%–5% of newly diagnosed advanced malignancies, with chemotherapy as the standard of care. CUPISCO (NCT03498521) is an ongoing randomized trial using comprehensive genomic profiling (CGP) to assign patients with CUP to targeted or immunotherapy treatment arms based on genomic profiling. We performed a retrospective analysis of CUP cases referred for CGP to determine how many were potentially eligible for enrollment into an experimental CUPISCO arm. Materials and Methods Centrally reviewed adenocarcinoma and undifferentiated CUP specimens in the FoundationCore database were analyzed using the hybrid capture‐based FoundationOne CDx assay (mean coverage, >600×). Presence of genomic alterations, microsatellite instability (MSI), tumor mutational burden (TMB), genomic loss of heterozygosity (gLOH), and programmed death‐ligand 1 (PD‐L1) positivity were determined. Results A total of 96 of 303 patients (31.7%) could be matched to an experimental CUPISCO arm. Key genomic alterations included ERBB2 (7.3%), PIK3CA (6.3%), NF1 (5.6%), NF2 (4.6%), BRAF (4.3%), IDH1 (3.3%), PTEN, FGFR2, EGFR (3.6% each), MET (4.3%), CDK6 (3.0%), FBXW7, CDK4 (2.3% each), IDH2, RET, ROS1, NTRK (1.0% each), and ALK (0.7%). Median TMB was 3.75 mutations per megabase of DNA; 34 patients (11.6%) had a TMB ≥16 mutations per megabase. Three patients (1%) had high MSI, and 42 (14%) displayed high PD‐L1 expression (tumor proportion score ≥50%). gLOH could be assessed in 199 of 303 specimens; 19.6% had a score of >16%. Conclusions Thirty‐two percent of patients would have been eligible for targeted therapy in CUPISCO. Future studies, including additional biomarkers such as PD‐L1 positivity and gLOH, may identify a greater proportion potentially benefiting from CGP‐informed treatment. Clinical trial identification number. NCT03498521 Implications for Practice The findings of this retrospective analysis of carcinoma of unknown primary origin (CUP) cases validate the experimental treatment arms being used in the CUPISCO study (NCT03498521), an ongoing randomized trial using comprehensive genomic profiling to assign patients with CUP to targeted or immunotherapy treatment arms based on the presence of pathogenic genomic alterations. The findings also suggest that future studies including additional biomarkers and treatment arms, such as programmed death‐ligand 1 positivity and genomic loss of heterozygosity, may identify a greater proportion of patients with CUP potentially benefiting from comprehensive genomic profiling‐informed treatment. This article focuses on the ability of comprehensive genomic profiling to identify potentially targetable genetic alterations in cancers of unknown primary, based on the inclusion criteria for the CUPISCO clinical trial and aiming for more effective therapeutic options for patients.
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Affiliation(s)
- Jeffrey S Ross
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA.,SUNY Upstate Medical University, Syracuse, New York, New York, USA
| | - Ethan S Sokol
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA
| | - Holger Moch
- University of Zurich and University Hospital Zurich, Zurich, Switzerland
| | - Linda Mileshkin
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | | | - Ferran Losa
- Hospital de Sant Joan Despí Moisès Broggi, Barcelona, Spain
| | | | | | - Julia A Elvin
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA
| | - Nhu Ngo
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA
| | - Dexter X Jin
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA
| | - Alwin Krämer
- German Cancer Research Center (DKFZ) and University of Heidelberg, Heidelberg, Germany
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Tsutsumi M, Miura H, Inagaki H, Shinkai Y, Kato A, Kato T, Hamada-Tsutsumi S, Tanaka M, Kudo K, Yoshikawa T, Kurahashi H. An aggressive systemic mastocytosis preceded by ovarian dysgerminoma. BMC Cancer 2020; 20:1162. [PMID: 33246418 PMCID: PMC7693501 DOI: 10.1186/s12885-020-07653-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 11/17/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Aggressive systemic mastocytosis (ASM) is a rare malignant disease characterized by disordered mast cell accumulation in various organs. We here describe a female ASM patient with a previous history of ovarian dysgerminoma. METHODS Molecular cytogenomic analyses were performed to elucidate an etiological link between the ASM and dysgerminoma of the patient. RESULTS This patient was affected by ovarian dysgerminoma which was treated by chemotherapy and surgical resection. Having subsequently been in complete remission for 2 years, she developed symptoms of ASM. A somatic D816A mutation in the KIT gene was detected in her bone marrow, which facilitated the diagnosis of ASM. Unexpectedly, this KIT D816A variant was also detected in the prior ovarian dysgerminoma sample. Whole-exome sequencing allowed us to identify a somatic nonsense mutation of the TP53 gene in the bone marrow, but not in the dysgerminoma. Microarray analysis of the patient's bone marrow revealed a copy-number-neutral loss of heterozygosity at the TP53 locus, suggestive of the homozygous nonsense mutation in the TP53 gene. In addition, the loss of heterozygosity at the TP53 locus was also detected in the dysgerminoma. CONCLUSIONS These results indicated that either the mast cells causing the ASM in this case had originated from the preceding ovarian dysgerminoma as a clonal evolution of a residual tumor cell, which acquired the TP53 mutation, or that both tumors developed from a common cancer stem cell carrying the KIT D816A variation.
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Affiliation(s)
- Makiko Tsutsumi
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Hiroki Miura
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Japan
| | - Hidehito Inagaki
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Yasuko Shinkai
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Asuka Kato
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
- ITOCHU Collaborative Research-Molecular Targeted Cancer Treatment for Next Generation, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Takema Kato
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Susumu Hamada-Tsutsumi
- Department of Virology and Liver Unit, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Makito Tanaka
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Japan
| | - Kazuko Kudo
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Japan
| | - Tetsushi Yoshikawa
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Japan
| | - Hiroki Kurahashi
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan.
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Ma Q, Wang J, Qi J, Peng D, Guan B, Zhang J, Li Z, Zhang H, Li T, Shi Y, Li X, Zhou L, Chen K, Ci W. Increased chromosomal instability characterizes metastatic renal cell carcinoma. Transl Oncol 2020; 14:100929. [PMID: 33157517 PMCID: PMC7649528 DOI: 10.1016/j.tranon.2020.100929] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 12/16/2022] Open
Abstract
The clonal origin and parallel evolution of the metastatic lesions and primary tumour. The evolutionary branches of primary and metastatic clones diverge early in the development of the tumour. Increased genome instability and specific enriched somatic copy number alteration (SCNAs) in metastatic lesions compared to primary tumour. LOH at 14q, loss of 14q32.31 and gain of 6p22.2 are highly selected events during metastatic evolution.
The evolutionary trajectories of treatment-naïve metastatic tumour are largely unknown. Such knowledge is crucial for cancer prevention and therapeutic interventions. Herein, we performed whole genome or exome sequencing of 19 tumour specimens and 8 matched normal kidney tissues from 8 clear cell renal cell carcinoma (ccRCC) patients. The clonal origin and parallel evolution of the metastatic lesions and primary tumour is identified in all 8 patients. But the evolutionary branches of primary and metastatic clones diverge early in the development of the tumour. More importantly, larger scale genomic aberrations including somatic copy number alteration (SCNA) or loss of heterozygosity (LOH) differentiate the metastasis lesions from primary tumour. Based on it, we identify that LOH at 14q, loss of 14q32.31 and gain of 6p22.2 are highly selected events during metastatic evolution. Further functional validations of multiple genes within the SCNA regions indicated that these selected events interact to drive metastatic risk with potential therapeutic relevance. Collectively, we described increased genome instability in metastatic ccRCC and validated it via molecular biology, providing an evolution pattern which may facilitate the translation of basic finding.
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Affiliation(s)
- Qin Ma
- Department of Urology, Peking University First Hospital, Beijing 100034, China; Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jilu Wang
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Qi
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ding Peng
- Department of Urology, Peking University First Hospital, Beijing 100034, China; Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Bao Guan
- Department of Urology, Peking University First Hospital, Beijing 100034, China; Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; Institute of Urology, Peking University, Beijing 100034, China; National Urological Cancer Centre, Beijing 100034, China
| | - Jianye Zhang
- Department of Urology, Peking University First Hospital, Beijing 100034, China; Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; Institute of Urology, Peking University, Beijing 100034, China; National Urological Cancer Centre, Beijing 100034, China
| | - Zhongwu Li
- Department of Pathology, Peking University School of Oncology, 100142 Beijing, China
| | - Hongxian Zhang
- Department of Urology, School of Life Sciences, Third Hospital, Peking University, Beijing 100083, China
| | - Ting Li
- Department of Urology, Peking University First Hospital, Beijing 100034, China; Institute of Urology, Peking University, Beijing 100034, China; National Urological Cancer Centre, Beijing 100034, China
| | - Yue Shi
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuesong Li
- Department of Urology, Peking University First Hospital, Beijing 100034, China; Institute of Urology, Peking University, Beijing 100034, China; National Urological Cancer Centre, Beijing 100034, China.
| | - Liqun Zhou
- Department of Urology, Peking University First Hospital, Beijing 100034, China; Institute of Urology, Peking University, Beijing 100034, China; National Urological Cancer Centre, Beijing 100034, China.
| | - Ke Chen
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Weimin Ci
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute of Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
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Ura A, Saito T, Motoi T, Takagi T, Suehara Y, Kurihara T, Sano K, Sasa K, Hayashi T, Yao T. A case of primary distal-type epithelioid sarcoma of the lumbar vertebra with a review of literature. Virchows Arch 2020; 479:393-400. [PMID: 33103211 DOI: 10.1007/s00428-020-02955-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/15/2020] [Accepted: 10/19/2020] [Indexed: 10/23/2022]
Abstract
Epithelioid sarcoma (EpS) is a rare malignant neoplasm that accounts for < 1% of adult soft tissue sarcomas. Primary EpS of the bone is extremely rare and only a few cases have been reported to date. We report a case of primary distal-type EpS of the lumbar vertebra. A 30-year-old man without any history of malignant tumors had complained of lumbago for 3 months before visiting the hospital. Magnetic resonance imaging (MRI) of the lumbar spine showed a high signal intensity on the fat-suppressed T2-weighted image (WI) and a low signal on the T1WI at the L1 vertebral body. The tumor protruded toward the anterior components. Systemic radiological examination revealed no other lesion. A biopsy revealed a primary malignant tumor with epithelioid features. After chemotherapy, total en bloc spondylectomy was performed. Macroscopically, the tumor replaced the entire L1 with necrosis. Histologically, the tumor showed nodules of epithelioid cells that were strongly positive for epithelial markers, but a lack of INI1 expression. Central necrosis in the tumor nodule was also observed. This tumor showed loss of heterozygosity at the SMARCB1 locus but without the SMARCB1 mutation. The result of Foundation One ®CDx showed no actionable mutations. Seven months after surgery, a subcutaneous metastasis to the left cheek and bilateral lung metastasis with pleural dissemination were observed on radiological examination. A final diagnosis of distal-type EpS was made based on these findings. The patient died of the disease 8 months after surgery.
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Affiliation(s)
- Ayako Ura
- Department of Human Pathology, School of Medicine, Juntendo University, 2-1-1, Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Tsuyoshi Saito
- Department of Human Pathology, School of Medicine, Juntendo University, 2-1-1, Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan.
| | - Toru Motoi
- Department of Diagnostic Pathology, Tokyo Metropolitan Cancer and Infectious Disease Center Komagome Hospital, 3-18-22, Honkomagome, Bunkyo-ku, Tokyo, 113-8677, Japan
| | - Tatsuya Takagi
- Department of Orthopaedic Surgery, School of Medicine, Juntendo University, 2-1-1, Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Yoshiyuki Suehara
- Department of Orthopaedic Surgery, School of Medicine, Juntendo University, 2-1-1, Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Taisei Kurihara
- Department of Human Pathology, School of Medicine, Juntendo University, 2-1-1, Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan.,Department of Orthopaedic Surgery, School of Medicine, Juntendo University, 2-1-1, Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Kei Sano
- Department of Human Pathology, School of Medicine, Juntendo University, 2-1-1, Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan.,Department of Orthopaedic Surgery, School of Medicine, Juntendo University, 2-1-1, Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Keita Sasa
- Department of Human Pathology, School of Medicine, Juntendo University, 2-1-1, Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan.,Department of Orthopaedic Surgery, School of Medicine, Juntendo University, 2-1-1, Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Takuo Hayashi
- Department of Human Pathology, School of Medicine, Juntendo University, 2-1-1, Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Takashi Yao
- Department of Human Pathology, School of Medicine, Juntendo University, 2-1-1, Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
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Sharma A, Halder A, Kaushal S, Jain M. Intra-individual Genomic Variation Analysis in Tissues (Blood vs. Testis) Through SNP Microarray: A Case Report of Two Patients with Idiopathic Sertoli Cell Only Syndrome (SCOS). J Reprod Infertil 2020; 21:308-311. [PMID: 33209739 PMCID: PMC7648869 DOI: 10.18502/jri.v21i4.4325] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Background: Inflammatory responses within the peritoneal cavity may result in endometrial dysfunction in women with endometriosis. The true causes of this disease remain poorly understood. It is hypothesized that downstream toll-like receptors (TLRs) inflammatory cytokines in response to pathogens may be associated with endometriosis. So, this study was aimed at evaluating the expression of TLRs signaling and endometriosis-associated inflammatory responses. Methods: Totally, 20 infertile endometriosis patients and 20 normal women undergoing controlled ovarian stimulation were enrolled. The cellular pellet and supernatant were obtained by centrifugation of follicular fluid (FF). Evaluation of TLRs and their signaling pathway gene expression was performed on cellular pellets using quantitative-PCR. The supernatant was used for determination of cytokine protein expression by ELISA. The results are expressed as mean±SEM and a p<0.05 was considered statistically significant. Results: Quantitative-PCR analysis suggested that TLR1, 5, 6, 7, 8, 10, MYD88, NF-ĸB, IL-10 and TGF-β genes expression significantly increased in patients compared to the control group (p<0.05). TLR3, 9, INF-β genes expression was significantly lower in endometriosis than control group (p<0.05). There was no significant difference in the expression of TLR2, TLR4, TIRAP, TRIF, TRAM, and IRF3 between two groups. Also, significant increase in the levels of IL-6, IL-8 and MIF protein in FF of endometriosis group was detected in comparison with normal women (p<0.05). Conclusion: The expression of TLR downstream signaling in the follicular cells can initiate inflammatory responses and changes in the FF cytokine profile which in turn may induce endometriosis and infertility disorder.
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Affiliation(s)
- Aiyush Sharma
- Department of Reproductive Biology, All India Institute of Medical Sciences, New Delhi, India
| | - Ashutosh Halder
- Department of Reproductive Biology, All India Institute of Medical Sciences, New Delhi, India
| | - Seema Kaushal
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Manish Jain
- Department of Reproductive Biology, All India Institute of Medical Sciences, New Delhi, India
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Ma Y, Li Y, Ling S, Li X, Kong B, Hu M, Huang P. Loss of heterozygosity for Kras G12D promotes REDD1-dependent, non-canonical glutamine metabolism in pancreatic ductal adenocarcinoma. Biochem Biophys Res Commun 2020; 526:880-888. [PMID: 32279996 DOI: 10.1016/j.bbrc.2020.03.137] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 03/24/2020] [Indexed: 12/22/2022]
Abstract
Pancreatic cancer is associated with high mortality, and pancreatic ductal adenocarcinoma (PDAC) is its most common subtype. The rapid growth of PDAC is dependent on the non-canonical pathway of glutamine (Gln) utilization, and loss of heterozygosity for KrasG12D (KrasG12D-LOH) frequently observed in PDAC is associated with an aggressive and invasive phenotype. However, it remains unclear whether KrasG12D-LOH contributes to non-canonical Gln metabolism in PDAC. Here, we showed that KrasG12D-LOH leads to a substantial increase in non-canonical Gln metabolism in PDAC cells. Importantly, we observed elevated expression of regulated in DNA damage and development 1 (REDD1), which is activated in response to hypoxia and nutrient deprivation, in KrasG12D-LOH PDAC, and that REDD1 knockdown efficiently repressed KrasG12D-LOH-regulated Gln metabolism and suppressed proliferation, migration, and invasion of KrasG12D-LOH PDAC cells. These data provide evidence that REDD1 is a downstream target of KrasG12D-LOH and is involved in promoting non-canonical Gln metabolism in PDAC.
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Affiliation(s)
- Yu Ma
- School of Medicine, Southeast University, Nanjing, 210009, China
| | - Yuan Li
- School of Medicine, Southeast University, Nanjing, 210009, China
| | - Sunkai Ling
- School of Medicine, Southeast University, Nanjing, 210009, China
| | - Xiaoxue Li
- School of Medicine, Southeast University, Nanjing, 210009, China
| | - Bo Kong
- Department of Surgery, Klinikumrechts der Isar, School of Medicine, Technical University of Munich (TUM), Munich, 81675, Germany
| | - Mingyue Hu
- School of Medicine, Southeast University, Nanjing, 210009, China; Department of Gastroenterology, Southeast University, Dingjiaqiao 87, Gulou District, Nanjing, 210009, China.
| | - Peilin Huang
- School of Medicine, Southeast University, Nanjing, 210009, China.
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Ni VI, Ivantsov AO, Kotkova MA, Baskina SV, Ponomareva EV, Orlova RV, Topuzov EE, Kryukov KK, Shelekhova KV, Aleksakhina SN, Sokolenko AP, Imyanitov EN. Small fraction of testicular cancer cases may be causatively related to CHEK2 inactivating germ-line mutations: evidence for somatic loss of the remaining CHEK2 allele in the tumor tissue. Fam Cancer 2020; 20:49-53. [PMID: 32451744 DOI: 10.1007/s10689-020-00190-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
A recent study suggested a role of CHEK2 loss-of-function germ-line pathogenic variants in the predisposition to testicular cancer (TC) (AlDubayan et al. JAMA Oncol 5:514-522, 2019). We attempted to validate this finding relying on the high population frequency of recurrent CHEK2 pathogenic variants in Slavic populations. CHEK2 pathogenic alleles (c.1100delC (p.Thr367Metfs); del5395 [del ex9-10]; IVS2 + 1G > A [c.444 + 1G > A]) were detected in 7/280 (2.5%) TC patients vs. 3/424 (0.7%) healthy men and 6/1007 (0.6%) healthy women [OR 4.0 (95% CI 1.5-11), p = 0.009 for pooled control groups]. Somatic CHEK2 loss-of-heterozygosity (LOH) was detected in 4 out of 6 tumors available for analysis; strikingly all these instances of LOH involved inactivation of the wild-type allele. The CHEK2 c.470T > C (p.Ile157Thr) variant was detected in 21/280 (7.5%) affected vs. 22/424 (5.2%) non-affected men [OR 1.5 (95% CI 0.8-2.7), p = 0.3]. Somatic CHEK2 LOH was revealed only in 6 out of 21 tumors obtained from CHEK2 c.470T > C (p.Ile157Thr) carriers, with the C-allele lost in two cases and T-allele deleted in four tumors. The results of comparison of allele frequencies in TC patients versus population controls coupled with the data on CHEK2 LOH status in tumor tissues support the association of CHEK2 pathogenic variants with TC risk.
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Affiliation(s)
- Valeriya I Ni
- N.N. Petrov Institute of Oncology, Leningradskaya, 68, Pesochny-2, St.-Petersburg, Russia, 197758
| | - Alexandr O Ivantsov
- N.N. Petrov Institute of Oncology, Leningradskaya, 68, Pesochny-2, St.-Petersburg, Russia, 197758
- St.-Petersburg Pediatric Medical University, St.-Petersburg, Russia, 194100
| | - Mariya A Kotkova
- N.N. Petrov Institute of Oncology, Leningradskaya, 68, Pesochny-2, St.-Petersburg, Russia, 197758
| | - Sofia V Baskina
- N.N. Petrov Institute of Oncology, Leningradskaya, 68, Pesochny-2, St.-Petersburg, Russia, 197758
| | | | | | | | | | | | - Svetlana N Aleksakhina
- N.N. Petrov Institute of Oncology, Leningradskaya, 68, Pesochny-2, St.-Petersburg, Russia, 197758
| | - Anna P Sokolenko
- N.N. Petrov Institute of Oncology, Leningradskaya, 68, Pesochny-2, St.-Petersburg, Russia, 197758
- St.-Petersburg Pediatric Medical University, St.-Petersburg, Russia, 194100
| | - Evgeny N Imyanitov
- N.N. Petrov Institute of Oncology, Leningradskaya, 68, Pesochny-2, St.-Petersburg, Russia, 197758.
- St.-Petersburg Pediatric Medical University, St.-Petersburg, Russia, 194100.
- City Cancer Center, St.-Petersburg, Russia, 197758.
- I.I. Mechnikov North-Western Medical University, St.-Petersburg, Russia, 191015.
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Liu YJ, Houldsworth J, Emmadi R, Dyer L, Wolff DJ. Assessing Genomic Copy Number Alterations as Best Practice for Renal Cell Neoplasia: An Evidence-Based Review from the Cancer Genomics Consortium Workgroup. Cancer Genet 2020; 244:40-54. [PMID: 32434132 DOI: 10.1016/j.cancergen.2020.04.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 04/06/2020] [Accepted: 04/07/2020] [Indexed: 02/05/2023]
Abstract
Renal cell neoplasia are heterogeneous with diverse histology, genetic alterations, and clinical behavior that are diagnosed mostly on morphologic features. The Renal Cell Neoplasia Workgroup of the Cancer Genomics Consortium systematically evaluated peer-reviewed literature on genomic studies of renal cell carcinoma (RCC), including clear cell RCC, papillary RCC, chromophobe RCC, and the translocation RCC involving TFE3, TFEB and MITF rearrangements, as well as benign oncocytoma, which together comprise about 95% of all renal cell neoplasia. The Workgroup curated recurrent copy number alterations (CNAs), copy-neutral loss-of-heterozygosity (cnLOH), rearrangements, and mutations, found in each subtype and assigned clinical relevance according to established criteria. In clear cell RCC, loss of 3p has a disease-initiating role and most likely also in progression with mutations detected in VHL and other genes mapped to this arm, and loss of 9p and/or 14q has well-substantiated prognostic utility. Gain of chromosomes 7 and 17 are hallmark CNAs of papillary RCC, but patterns of other CNAs as detected by chromosomal microarray analysis (CMA) afford sub-classification into Type 1 and 2 with prognostic value, and for further sub-stratification of Type 2. Inherent chromosome loss in chromophobe RCC as detected by CMA is useful for distinguishing the eosinophilic variant from benign oncocytoma which in contrast exhibits few CNAs or rearranged CCND1, but share mitochondrial DNA mutations. In morphologically atypical RCCs, rearrangement of TFE3 and TFEB should be considered in the differential diagnosis, portending an aggressive RCC subtype. Overall, this evidence-based review provides a validated role for assessment of CNAs in renal cell neoplasia in the clinical setting to assist in renal cell neoplasm diagnosis and sub-classification within subtypes that is integral to the management of patients, from small incidentally found renal masses to larger surgically resected specimens, and simultaneously identify the presence of key alterations portending outcome in malignant RCC subtypes.
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Affiliation(s)
- Yajuan J Liu
- Departments of Pathology and Laboratory Medicine, University of Washington School of Medicine, 1959 NE Pacific Street, Seattle, WA 98195.
| | - Jane Houldsworth
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, The Mount Sinai Health System, 1 Gustave Levy Place, New York, NY 10029.
| | - Rajyasree Emmadi
- Department of Pathology, University of Illinois at Chicago, 840 S. Wood Street, Chicago, IL 60612
| | - Lisa Dyer
- Department of Pediatrics, Division of Human Genetics, University of Cincinnati, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave, MLC 4006, Cincinnati, OH 45229-3039
| | - Daynna J Wolff
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, 165 Ashley Avenue, MSC 908, Charleston, SC 29425
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Quevedo R, Spreafico A, Bruce J, Danesh A, El Ghamrasni S, Giesler A, Hanna Y, Have C, Li T, Yang SYC, Zhang T, Asa SL, Haibe-Kains B, Krzyzanowska M, Smith AC, Singh S, Siu LL, Pugh TJ. Centromeric cohesion failure invokes a conserved choreography of chromosomal mis-segregations in pancreatic neuroendocrine tumor. Genome Med 2020; 12:38. [PMID: 32345369 PMCID: PMC7189550 DOI: 10.1186/s13073-020-00730-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 03/10/2020] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Pancreatic neuroendocrine tumors (PANETs) are rare, slow growing cancers that often present with local and distant metastasis upon detection. PANETS contain distinct karyotypes, epigenetic dysregulation, and recurrent mutations in MEN1, ATRX, and DAXX (MAD+); however, the molecular basis of disease progression remains uncharacterized. METHODS We evaluated associations between aneuploidy and the MAD+ mutational state of 532 PANETs from 11 published genomic studies and 19 new cases using a combination of exome, targeted panel, shallow WGS, or RNA-seq. We mapped the molecular timing of MAD+ PANET progression using cellular fractions corrected for inferred tumor content. RESULTS In 287 PANETs with mutational data, MAD+ tumors always exhibited a highly recurrent signature of loss of heterozygosity (LOH) and copy-number alterations affecting 11 chromosomes, typically followed by genome doubling upon metastasis. These LOH chromosomes substantially overlap with those that undergo non-random mis-segregation due to ectopic CENP-A localization to flanking centromeric regions in DAXX-depleted cell lines. Using expression data from 122 PANETs, we found decreased gene expression in the regions immediately adjacent to the centromere in MAD+ PANETs. Using 43 PANETs from AACR GENIE, we inferred this signature to be preceded by mutations in MEN1, ATRX, and DAXX. We conducted a meta-analysis on 226 PANETs from 8 CGH studies to show an association of this signature with metastatic incidence. Our study shows that MAD+ tumors are a genetically diverse and aggressive subtype of PANETs that display extensive chromosomal loss after MAD+ mutation, which is followed by genome doubling. CONCLUSIONS We propose an evolutionary model for a subset of aggressive PANETs that is initiated by mutation of MEN1, ATRX, and DAXX, resulting in defects in centromere cohesion from ectopic CENP-A deposition that leads to selective loss of chromosomes and the LOH phenotype seen in late-stage metastatic PANETs. These insights aid in disease risk stratification and nominate potential therapeutic vulnerabilities to treat this disease.
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Affiliation(s)
- Rene Quevedo
- Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Suite 5-718, Toronto, Ontario, M5G 2M9, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Anna Spreafico
- Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Suite 5-718, Toronto, Ontario, M5G 2M9, Canada.,Division of Medical Oncology and Hematology, University of Toronto, Toronto, Ontario, Canada
| | - Jeff Bruce
- Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Suite 5-718, Toronto, Ontario, M5G 2M9, Canada
| | - Arnavaz Danesh
- Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Suite 5-718, Toronto, Ontario, M5G 2M9, Canada
| | - Samah El Ghamrasni
- Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Suite 5-718, Toronto, Ontario, M5G 2M9, Canada
| | - Amanda Giesler
- Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Suite 5-718, Toronto, Ontario, M5G 2M9, Canada
| | - Youstina Hanna
- Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Suite 5-718, Toronto, Ontario, M5G 2M9, Canada
| | - Cherry Have
- Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | - Tiantian Li
- Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Suite 5-718, Toronto, Ontario, M5G 2M9, Canada
| | - S Y Cindy Yang
- Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Suite 5-718, Toronto, Ontario, M5G 2M9, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Tong Zhang
- Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Suite 5-718, Toronto, Ontario, M5G 2M9, Canada.,Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | - Sylvia L Asa
- Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Suite 5-718, Toronto, Ontario, M5G 2M9, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.,Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Monika Krzyzanowska
- Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Suite 5-718, Toronto, Ontario, M5G 2M9, Canada
| | - Adam C Smith
- Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Simron Singh
- Susan Leslie Clinic for Neuroendocrine Cancer, Sunnybrook Odette Cancer Center, Toronto, Ontario, Canada
| | - Lillian L Siu
- Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Suite 5-718, Toronto, Ontario, M5G 2M9, Canada. .,Division of Medical Oncology and Hematology, University of Toronto, Toronto, Ontario, Canada.
| | - Trevor J Pugh
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada. .,Ontario Institute for Cancer Research, Toronto, Ontario, Canada. .,Princess Margaret Cancer Centre, University Health Network, 101 College Street, TMDT, Room 9-305, Toronto, Ontario, M5G 1L7, Canada.
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Pan Y, Feng C, Wang H, Lee M, Tang Z, Lin Z. Ichthyosis with confetti caused by new and recurrent mutations in KRT10 associated with varying degrees of keratin 10 mis-localization. J Dermatol Sci 2020; 98:35-40. [PMID: 32113649 DOI: 10.1016/j.jdermsci.2020.02.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 02/01/2020] [Accepted: 02/18/2020] [Indexed: 11/21/2022]
Abstract
BACKGROUND Ichthyosis with confetti (IWC) is an extremely rare autosomal-dominant genodermatosis characterized by erythroderma with numerous confetti-like pale spots. IWC is caused by mutations in KRT10 (IWC-I) or KRT1 (IWC-II) which affect their tail domains. In IWC-I, the mutations lead to replacement of glycine/serine-rich keratin 10 (K10) tail with arginine- or alanine-rich frameshift motifs, causing K10 mis-localization which might trigger loss of the mutant KRT10 allele via mitotic recombination, leading to genetic reversion. OBJECTIVE To investigate mutations in five IWC-I patients and their functional consequences. METHODS We performed Sanger sequencing of KRT1 and KRT10 in peripheral blood samples of five patients, with highly polymorphic KRT10 SNPs genotyped to confirm loss-of-heterozygosity in the epidermis of pale spots. K10 expression pattern was examined in both patient skin biopsies and HaCaT cells overexpressing mutant KRT10-enhanced green fluorescence protein fusion. RESULTS Four novel and one recurrent KRT10 mutations were identified in patient peripheral blood samples but not in the corresponding pale spot epidermis. Two of the mutations, c.1696_1699dupCACA and c.1676dupG, affected residues close to K10 carboxyl terminus and encoded only 3 and 6 arginine residues, which were far fewer than reported previously. Interestingly, imaging analyses for K10 in HaCaT cells overexpressing either of these two mutations and in the corresponding patients' affected skin, showed a remarkably lower level of K10 mis-localization compared to that of other mutations reported in this study. CONCLUSIONS Our findings suggest that the number of arginine residues in the mutant tail may correlate with the level of K10 mis-localization in IWC-I keratinocytes. These results expand the genotypic and phenotypic spectrum of IWC-I.
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Guo X, Chen Y, Moore MM, Mei N. Detection of Loss of Heterozygosity in Tk-Deficient Mutants from L5178Y Tk +/--3.7.2C Mouse Lymphoma Cells. Methods Mol Biol 2020; 2102:251-270. [PMID: 31989560 DOI: 10.1007/978-1-0716-0223-2_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The mouse lymphoma assay (MLA), a forward mutation assay using the Tk+/--3.7.2C clone of the L5178Y mouse lymphoma cell line and the Thymidine kinase (Tk) gene, has been widely used as an in vitro genetic toxicity assay for more than four decades. The MLA can evaluate the ability of mutagens to induce a wide range of genetic events including both gene mutations and chromosomal mutations and has been recommended as one component of several genotoxicity test batteries. Tk-deficient mutants often exhibit chromosomal abnormalities involving the distal end of chromosome 11 where the Tk gene is located, in mice, and the type of chromosome alteration can be analyzed using a loss of heterozygosity (LOH) approach. LOH has been considered an important event in human tumorigenesis and can result from any of the following several mechanisms: large deletions, mitotic recombination, and chromosome loss. In this chapter, the authors describe the procedures for the detection of LOH in the Tk mutants from the MLA, and apply LOH analysis for understanding the types of genetic damage that is induced by individual chemicals.
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Affiliation(s)
- Xiaoqing Guo
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Jefferson, AR, USA
| | - Ying Chen
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Jefferson, AR, USA
| | | | - Nan Mei
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA.
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Nomura T. Recombination-induced revertant mosaicism in ichthyosis with confetti and loricrin keratoderma. J Dermatol Sci 2019; 97:94-100. [PMID: 31928837 DOI: 10.1016/j.jdermsci.2019.12.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 12/26/2019] [Accepted: 12/26/2019] [Indexed: 01/23/2023]
Abstract
Revertant mosaicism refers to a condition in which a pathogenic germline mutation is spontaneously corrected in somatic cells, resulting in the presence of two or more cell populations with different genotypes in an organism arising from a single fertilized egg. If the revertant cells are clonally expanded due to a survival advantage over the surrounding mutant cells, patients benefit from this self-healing phenomenon which leads to the development of milder-than-expected clinical phenotypes; in genetic skin diseases, patients with revertant mosaicism present with small islands of healthy skin. To date, revertant mosaicism has been reported in ∼50 genetic diseases involving the skin, blood, liver, muscle, and brain. In this review, I briefly summarize current knowledge on revertant mosaicism in two particular skin diseases, ichthyosis with confetti (IWC) and loricrin keratoderma (LK), both of which develop numerous revertant skin patches. Notably, homologous recombination (HR) is the only mechanism underlying the reversion of pathogenic mutations in IWC and LK, and this was identified following the analysis of ∼50 revertant epidermis samples. All the samples showed long-tract loss of heterozygosity (LOH) that originated at regions centromeric to pathogenic mutations and extended to the telomere of the mutation-harboring chromosomes. Elucidating the molecular mechanisms underlying revertant mosaicism in IWC and LK-especially how mutant proteins induce long-tract LOH-would potentially expand the possibility of manipulating HR to induce the reversion of disease-causing mutations and help devising novel therapies not only for IWC and LK but also for other intractable genetic diseases.
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Affiliation(s)
- Toshifumi Nomura
- Department of Dermatology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan.
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Sunpaweravong S, Bunbanjerdsuk S, Pongrujikorn T, Naktang C, Sunpaweravong P, Nitiruangjaras A, Dechaphankul T, Jinawath N. Clonal relationship of synchronous head and neck cancer and esophageal cancer assessed by single nucleotide polymorphism-based loss of heterozygosity analysis. BMC Cancer 2019; 19:1174. [PMID: 31795956 PMCID: PMC6889604 DOI: 10.1186/s12885-019-6394-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 11/22/2019] [Indexed: 12/27/2022] Open
Abstract
Background The prognoses of head and neck squamous cell carcinoma (HNSCC) and esophageal squamous cell carcinoma (ESCC) are poor, especially when both tumors occur at the same time. We examined the clonal relatedness of HNSCCs with synchronous ESCCs to confirm whether the second tumors were metastasis or separate second primary malignancies (SPMs) using loss of heterozygosity (LOH) analysis. Methods Twenty-one pairs of formalin-fixed paraffin-embedded tissue from HNSCC patients with synchronous esophageal cancer were analyzed by single nucleotide polymorphism (SNP) array using the Illumina HumanCytoSNP FFPE-12 BeadChip (San Diego, CA), which contains approximately 300,000 probes. LOH was identified using Nexus Copy Number software (El Segundo, CA). Results Comparing the LOH pattern between HNSCC and paired ESCC, we found that 20 out of 21 paired tissues had a high number of discordant LOHs (LOH identified solely in the primary HNSCC but not in synchronous ESCC at the same genomic location) and a low number of concordant LOHs (LOH at the same genomic location in both HNSCC and ESCC). Only one case fell into the undetermined category. Therefore, these 20 ESCCs were classified as SPMs or second field tumors (SFTs). Moreover, the HNSCC patients with molecularly confirmed esophageal SPM had significantly poorer survival than the other patients. Conclusions We propose the use of a genome-wide SNP array as a tool to differentiate metastatic tumors from SPM/SFT. The SNP array offers genome-wide LOH information that earlier microsatellite analysis studies lack. The ability to accurately identify SPM should contribute to a better treatment plan and follow-up care of these patients.
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Affiliation(s)
- Somkiat Sunpaweravong
- Department of Surgery, Faculty of Medicine, Prince of Songkla University, Songkhla, 90110, Thailand.
| | - Sacarin Bunbanjerdsuk
- Program in Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand.,Medical Genetics Center, Medical Life Sciences Institute, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Tanjitti Pongrujikorn
- Program in Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand
| | - Chaiwat Naktang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Patrapim Sunpaweravong
- Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Anupong Nitiruangjaras
- Department of Pathology, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Tanadech Dechaphankul
- Department of Otolaryngology, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Natini Jinawath
- Program in Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand. .,Integrative Computational BioScience Center (ICBS), Mahidol University, Nakhon Prathom, Thailand.
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De Sousa SMC, Wang PPS, Santoreneos S, Shen A, Yates CJ, Babic M, Eshraghi L, Feng J, Koszyca B, Roberts-Thomson S, Schreiber AW, Torpy DJ, Scott HS. The Genomic Landscape of Sporadic Prolactinomas. Endocr Pathol 2019; 30:318-328. [PMID: 31473917 DOI: 10.1007/s12022-019-09587-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Somatic GNAS and USP8 mutations have been implicated in sporadic somatotrophinomas and corticotrophinomas, respectively. However, no genes are known to be recurrently mutated in sporadic prolactinomas. The prevalence of copy number variants (CNV), which is emerging as a mechanism of tumorigenesis in sporadic pituitary adenomas in general, is also unclear in prolactinomas. To characterize the genetic events underpinning sporadic prolactinomas, we performed whole exome sequencing of paired tumor and germline DNA from 12 prolactinoma patients. We observed recurrent large-scale CNV, most commonly in the form of copy number gains. We also identified sequence variants of interest in 15 genes. This included the DRD2, PRL, TMEM67, and MLH3 genes with plausible links to prolactinoma formation. Of the 15 genes of interest, CNV was seen at the gene locus in the corresponding tumor in 10 cases, and pituitary expression of eight genes was in the top 10% of tissues. However, none of our shortlisted somatic variants appeared to be classical driver mutations as no variant was found in more than one tumor. Future directions of research include mechanistic studies to investigate how CNV may contribute to prolactinoma formation, larger studies of relevant prolactinoma subsets according to clinical characteristics, and additional genetic investigations for aberrations not captured by whole exome sequencing.
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Affiliation(s)
- Sunita M C De Sousa
- Endocrine and Metabolic Unit, Royal Adelaide Hospital, Adelaide, Australia.
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, an SA Pathology and University of South Australia Alliance, Adelaide, Australia.
- School of Medicine, University of Adelaide, Adelaide, Australia.
| | - Paul P S Wang
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, an SA Pathology and University of South Australia Alliance, Adelaide, Australia
| | | | - Angeline Shen
- Department of Diabetes and Endocrinology, Royal Melbourne Hospital, Melbourne, Australia
- Department of Medicine, University of Melbourne, Melbourne, Australia
| | - Christopher J Yates
- Department of Diabetes and Endocrinology, Royal Melbourne Hospital, Melbourne, Australia
- Department of Medicine, University of Melbourne, Melbourne, Australia
| | - Milena Babic
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, an SA Pathology and University of South Australia Alliance, Adelaide, Australia
| | - Leila Eshraghi
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, an SA Pathology and University of South Australia Alliance, Adelaide, Australia
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, an SA Pathology and University of South Australia Alliance, Adelaide, Australia
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia
| | - Jinghua Feng
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, an SA Pathology and University of South Australia Alliance, Adelaide, Australia
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia
| | - Barbara Koszyca
- Department of Anatomical Pathology, Royal Adelaide Hospital, Adelaide, Australia
| | | | - Andreas W Schreiber
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, an SA Pathology and University of South Australia Alliance, Adelaide, Australia
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia
- School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - David J Torpy
- Endocrine and Metabolic Unit, Royal Adelaide Hospital, Adelaide, Australia
- School of Medicine, University of Adelaide, Adelaide, Australia
| | - Hamish S Scott
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, an SA Pathology and University of South Australia Alliance, Adelaide, Australia
- School of Medicine, University of Adelaide, Adelaide, Australia
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, an SA Pathology and University of South Australia Alliance, Adelaide, Australia
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia
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Chaves FN, Bezerra TMM, Moraes DC, Costa SFDS, Silva PGB, Alves APNN, Costa FWG, Bernardes VF, Pereira KMA. Loss of heterozygosity and immunoexpression of PTEN in oral epithelial dysplasia and squamous cell carcinoma. Exp Mol Pathol 2019; 112:104341. [PMID: 31730755 DOI: 10.1016/j.yexmp.2019.104341] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 09/28/2019] [Accepted: 11/11/2019] [Indexed: 12/25/2022]
Abstract
INTRODUCTION Oral epithelial dysplasia (OED) is a risk factor for developing subsequent oral squamous cell carcinoma (OSCC). Loss of heterozygosity (LOH) profiles have been validated as risk predictors of malignant transformation of OED. It is still unclear if Phosphatase and tensin homologue deleted on chromosome 10 (PTEN) allelic loss also occurs in initial stage malignant lesions and if the allelic loss is involved as one of the mechanisms of oral carcinogenesis. Thus, this study objective investigate LOH of PTEN gene and the immunohistochemical expression of the protein in OED and OSCC samples. MATERIAL AND METHODS Formalin-fixed paraffin-embedded samples of 19 OEDs and 16 OSCCs were included to immunohistochemistry and LOH analysis. Two polymorphic microsatellite markers (AFMA086WG9 and D10S1765) located in chromosome 10 were used in this study for LOH analysis. For immunohistochemical analysis, 5 random fields with 400× magnification were evaluated quantitatively and qualitatively in epithelial and neoplastic cells. RESULTS AFMA086WG9 marker only demonstrated LOH in OEDs cases (10.5%). D10S1765 marker demonstrated LOH in 57.2% of OEDs and 50% of OSCCs. Higher nuclear immunostaining was detected in cases of OSCCs when compared to OEDs (p < .001) and there was strong cytoplasmic immunoexpression in OSCCs (p < .045). CONCLUSIONS We provide evidence that the allelic loss of PTEN is present in premalignant oral lesions and OSCCs, however the LOH of PTEN does not seems to influence its protein expression.
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Affiliation(s)
- Filipe Nobre Chaves
- School of Dentistry, Federal University of Ceará Campus Sobral, Sobral, Brazil
| | | | - Debora Chaves Moraes
- Department of Surgery, School of Medicine, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Sara Ferreira Dos Santos Costa
- Department of Oral Surgery and Pathology, School of Dentistry, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Paulo Goberlanio Barros Silva
- Department of Dental Clinic, Faculty of Pharmacy, Dentistry and Nursing, Federal University of Ceará, Fortaleza, Brazil
| | | | - Fábio Wildson Gurgel Costa
- Department of Dental Clinic, Faculty of Pharmacy, Dentistry and Nursing, Federal University of Ceará, Fortaleza, Brazil
| | - Vanessa Fátima Bernardes
- Department of Pathology, Biological Sciences Institute, Federal University of Minas Gerais, Belo Horizonte, Brazil
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Pirini F, Tedaldi G, Danesi R, Cangini I, Tumedei MM, Ferrari A, Vitali S, De Maio G, Terragna C, Solli V, Tebaldi M, Puccetti M, Zampiga V, Ravegnani M, Ulivi P, Falcini F, Martinelli G, Calistri D. Identification of a novel large EPCAM-MSH2 duplication, concurrently with LOHs in chromosome 20 and X, in a family with Lynch syndrome. Int J Colorectal Dis 2019; 34:1999-2002. [PMID: 31655866 DOI: 10.1007/s00384-019-03414-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/23/2019] [Indexed: 02/04/2023]
Abstract
BACKGROUND Lynch syndrome (LS) is associated with germline mutations in one of the mismatch repair genes or EPCAM. The majority of the causative alterations are point mutations. Large genomic rearrangements represent only 5-20%. Hypothetically, the allelic imbalance, like the loss of heterozygosity, may be another high penetrance risk factor. CASE PRESENTATION We describe the case of a patient who developed 5 tumors during her lifetime and with a family history characterized by a high frequency of tumors associated with LS. The proband was tested for mutations and copy number alterations with a panel of hereditary cancer genes and by SNP array. She showed a 187 Kb duplication including EPCAM and the first 7 exons of MSH2, plus two loss of heterozygosity (LOHs) in chromosome 20 and one in chromosome X which include many tumor suppressor genes. CONCLUSION We found a novel large EPCAM-MSH2 duplication associated with LS and the presence of LOHs in regions containing numerous tumor suppressors, raising the hypothesis that these alterations could contribute to cancer susceptibility. Our results underline the importance to deepen the knowledge of molecular mechanisms in order to determine the role in cancer predisposition of novel genetic alterations.
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Affiliation(s)
- Francesca Pirini
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via Piero Maroncelli 40, 47014, Meldola, FC, Italy.
| | - Gianluca Tedaldi
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via Piero Maroncelli 40, 47014, Meldola, FC, Italy
| | - Rita Danesi
- Romagna Cancer Registry, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Ilaria Cangini
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via Piero Maroncelli 40, 47014, Meldola, FC, Italy
| | - Maria Maddalena Tumedei
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via Piero Maroncelli 40, 47014, Meldola, FC, Italy
| | - Anna Ferrari
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via Piero Maroncelli 40, 47014, Meldola, FC, Italy
| | - Silvia Vitali
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
| | - Giulia De Maio
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via Piero Maroncelli 40, 47014, Meldola, FC, Italy
| | - Carolina Terragna
- L. & A. Seragnoli Institute of Haematology, Bologna University School of Medicine, Bologna, Italy
| | - Vincenza Solli
- L. & A. Seragnoli Institute of Haematology, Bologna University School of Medicine, Bologna, Italy
| | - Michela Tebaldi
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via Piero Maroncelli 40, 47014, Meldola, FC, Italy
| | | | - Valentina Zampiga
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via Piero Maroncelli 40, 47014, Meldola, FC, Italy
| | - Mila Ravegnani
- Romagna Cancer Registry, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Paola Ulivi
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via Piero Maroncelli 40, 47014, Meldola, FC, Italy
| | - Fabio Falcini
- Romagna Cancer Registry, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Giovanni Martinelli
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Daniele Calistri
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via Piero Maroncelli 40, 47014, Meldola, FC, Italy
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Park JE, Noh OK, Lee Y, Choi HS, Han JW, Hahn SM, Lyu CJ, Lee JW, Yoo KH, Koo HH, Jeong SY, Sung KW. Loss of Heterozygosity at Chromosome 16q Is a Negative Prognostic Factor in Korean Pediatric Patients with Favorable Histology Wilms Tumor: A Report of the Korean Pediatric Hematology Oncology Group (K-PHOG). Cancer Res Treat 2019; 52:438-445. [PMID: 31505910 PMCID: PMC7176966 DOI: 10.4143/crt.2019.313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 09/09/2019] [Indexed: 11/21/2022] Open
Abstract
PURPOSE Loss of heterozygosity (LOH) at chromosomes 1p and 16q is a poor prognostic factor in favorable histology Wilms tumor (FHWT). This study investigated the prevalence of LOH at 1p and 16q and evaluated its prognostic value in Korean children with FHWT. MATERIALS AND METHODS We analyzed 101 FHWT patients who were diagnosed between 1996 and 2016 in Korean Society of Pediatric Hematology Oncology Group hospitals. Using paraffin-embedded kidney tissue samples sent from each center, we reviewed LOH at 1p and 16q in each patient and assessed the prognostic value of LOH status for clinical parameters affecting event-free survival (EFS). RESULTS Of the 101 patients, 12 (11.9%) experienced recurrence; the 3-year EFS was 87.6%. LOH at 1p or 16q was detected in 19 patients (18.8%), with five having LOH at both 1q and 16q. The frequency of LOH at 1p was higher among younger patients (p=0.049), but there was no difference in LOH prevalence according to tumor stage. In the multivariate analysis, LOH at 16q was a significant negative prognostic factor affecting EFS (3-year EFS, 73.7% vs. 91.1%; hazard ratio, 3.95; p=0.037), whereas LOH at 1p was not (p=0.786). CONCLUSION LOH at 16q was a significant negative prognostic factor affecting outcome in Korean pediatric FHWT patients. Due to the small sample size of this study, large-scale multicenter trials are warranted to investigate the prognostic value of LOH at 1p and 16q in Korean children with FHWT.
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Affiliation(s)
- Jun Eun Park
- Department of Pediatrics, Ajou University School of Medicine, Suwon, Korea
| | - O Kyu Noh
- Department of Radiation Oncology, Ajou University School of Medicine, Suwon, Korea
| | - Yonghee Lee
- Department of Pathology, Ajou University School of Medicine, Suwon, Korea
| | - Hyoung Soo Choi
- Department of Pediatrics, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Jung Woo Han
- Department of Pediatric Hematology and Oncology, Yonsei Cancer Center, Yonsei University Health System, Seoul, Korea
| | - Seung Min Hahn
- Department of Pediatric Hematology and Oncology, Yonsei Cancer Center, Yonsei University Health System, Seoul, Korea
| | - Chuhl Joo Lyu
- Department of Pediatric Hematology and Oncology, Yonsei Cancer Center, Yonsei University Health System, Seoul, Korea
| | - Ji Won Lee
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Keon Hee Yoo
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hong Hoe Koo
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Seon-Yong Jeong
- Department of Medical Genetics, Ajou University School of Medicine, Suwon, Korea
| | - Ki Woong Sung
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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Ali MAM, Hassan AM, Saafan MA, Abdelmagid AA. Additive Diagnostic Yield of Homozygosity Regions Identified During Chromosomal microarray Testing in Children with Developmental Delay, Dysmorphic Features or Congenital Anomalies. Biochem Genet 2020; 58:74-101. [PMID: 31273557 DOI: 10.1007/s10528-019-09931-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 06/27/2019] [Indexed: 11/26/2022]
Abstract
Chromosomal microarray (CMA) has emerged as a robust tool for identifying microdeletions and microduplications, termed copy number variants (CNVs). Nevertheless, data regarding its utility in different patient populations with developmental delay (DD), dysmorphic features (DF) and congenital anomalies (CA), is a matter of dense debate. Although regions of homozygosity (ROH) are not diagnostic of a specific condition, they may have pathogenic implications. Certain CNVs and ROH have ethnically specific occurrences and frequencies. We aimed to determine whether CMA testing offers additional diagnostic information over classical cytogenetics for identifying genomic imbalances in a pediatric cohort with idiopathic DD, DF, or CA. One hundred sixty-nine patients were offered cytogenetics and CMA simultaneously for etiological diagnosis of DD (n = 67), DF (n = 52) and CA (n = 50). CMA could identify additional, clinically significant anomalies as compared with cytogenetics. CMA detected 61 CNVs [21 (34.4%) pathogenic CNVs, 37 (60.7%) variants of uncertain clinical significance and 3 (4.9%) benign CNVs] in 44 patients. CMA identified one or more ROH in 116/169 (68.6%) patients. When considering pathogenic CNVs and aneuploidies as positive findings, 9/169 (5.3%) received a genetic diagnosis from cytogenetics, while 25/169 (14.8%) could have a genetic diagnosis from CMA. The identification of ROH was clinically significant in two cases (2/169), thereby, adding 1.2% to the diagnostic yield of CMA (16% vs. 5.3%, p < 0.001). CMA uncovers additional genetic diagnoses over cytogenetics, thereby, offering a much higher diagnostic yield. Our findings convincingly demonstrate the additive diagnostic value of clinically significant ROH identified during CMA testing, highlighting the need for careful clinical interpretation of these ROH.
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Yatagai N, Saito T, Akazawa Y, Hayashi T, Yanai Y, Tsuyama S, Murakami T, Ueyama H, Watanabe S, Nagahara A, Yao T. Frequent loss of heterozygosity of SMAD4 locus and prognostic impacts of SMAD4 immunohistochemistry in gastric adenocarcinoma with enteroblastic differentiation. Hum Pathol 2019; 88:18-26. [PMID: 30946932 DOI: 10.1016/j.humpath.2019.03.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 02/20/2019] [Accepted: 03/14/2019] [Indexed: 12/22/2022]
Abstract
Gastric adenocarcinoma with enteroblastic differentiation (GAED) is a rare variant of gastric adenocarcinoma. Clinicopathologically, GAED is known to be aggressive and is characterized by frequent vascular invasion, lymphatic invasion, and liver metastasis even in early stages. SMAD4 was identified as a frequently deleted gene in GAED by copy number variation analysis in our previous next-generation sequencing study; therefore, we examined the clinicopathological impacts of SMAD4 in 51 cases of GAEDs (early: 17, advanced: 34). We performed Sanger sequencing for SMAD4 mutations and loss of heterozygosity (LOH) analysis of the SMAD4 locus, in addition to immunohistochemistry for SMAD4, to determine its clinicopathological correlations and impacts on survival. The frequency of LOH at the SMAD4 locus was 45.1%, and it was significantly higher in GAED compared to in conventional gastric adenocarcinoma. SMAD4 mutations were not found in any case. Reduced SMAD4 expression was found in 60.8% of cases; it was significantly correlated with advanced stages and lymph node metastasis and showed trends of larger tumor size and lymphatic invasion. Reduced SMAD4 expression in metastatic lymph nodes was found in 21 of 36 cases. Survival analysis revealed that reduced SMAD4 expression significantly affected the patient's overall survival (OS) and recurrence-free survival (RFS), although multivariate analysis showed that only liver metastasis and lymphatic infiltration (Ly+) were independent prognostic factors for OS and RFS. The SMAD4 locus is one of the susceptibility genes in this tumor, although SMAD4 mutation was not detected. Furthermore, the inactivation of SMAD4 appeared to contribute to the aggressiveness of GAED.
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Affiliation(s)
- Noboru Yatagai
- Department of Human Pathology, Juntendo University, Graduate School of Medicine, Tokyo, 113-8421, Japan; Department of Gastroenterology, Juntendo University, Graduate School of Medicine, Tokyo, 113-8421, Japan
| | - Tsuyoshi Saito
- Department of Human Pathology, Juntendo University, Graduate School of Medicine, Tokyo, 113-8421, Japan; Intractable Disease Research Center, Juntendo University, Graduate School of Medicine, Tokyo, 113-8421, Japan.
| | - Yoichi Akazawa
- Department of Human Pathology, Juntendo University, Graduate School of Medicine, Tokyo, 113-8421, Japan; Department of Gastroenterology, Juntendo University, Graduate School of Medicine, Tokyo, 113-8421, Japan
| | - Takuo Hayashi
- Department of Human Pathology, Juntendo University, Graduate School of Medicine, Tokyo, 113-8421, Japan
| | - Yuka Yanai
- Department of Human Pathology, Juntendo University, Graduate School of Medicine, Tokyo, 113-8421, Japan
| | - Sho Tsuyama
- Department of Human Pathology, Juntendo University, Graduate School of Medicine, Tokyo, 113-8421, Japan
| | - Takashi Murakami
- Department of Gastroenterology, Juntendo University, Graduate School of Medicine, Tokyo, 113-8421, Japan
| | - Hiroya Ueyama
- Department of Gastroenterology, Juntendo University, Graduate School of Medicine, Tokyo, 113-8421, Japan
| | - Sumio Watanabe
- Department of Gastroenterology, Juntendo University, Graduate School of Medicine, Tokyo, 113-8421, Japan
| | - Akihito Nagahara
- Department of Gastroenterology, Juntendo University, Graduate School of Medicine, Tokyo, 113-8421, Japan
| | - Takashi Yao
- Department of Human Pathology, Juntendo University, Graduate School of Medicine, Tokyo, 113-8421, Japan
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Abstract
Copy number variants (CNVs) and copy neutral loss of heterozygosity (CN-LOH) represent important types of genomic abnormalities in cancer. Genomic DNA microarray serves as the current gold standard method for detecting genome-wide CNVs and CN-LOH. However, as next-generation sequencing (NGS) is widely used to detect gene variants in clinical testing, the ability of NGS to detect CNVs and CN-LOH has also been demonstrated. This chapter describes a protocol for detecting genome-wide large somatic CNVs and CN-LOH using a single nucleotide polymorphism (SNP) sequencing backbone. When combined with a targeted gene mutation panel, this strategy allows for simultaneous detection of somatic gene mutations and genome-wide CNVs and CN-LOH.
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Affiliation(s)
- Wei Shen
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | | | | | - Todd W Kelley
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Xinjie Xu
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA.
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50
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Abstract
The basis of cancer biology is built upon two fundamental processes that result in uncontrolled cell proliferation and tumor formation: loss of tumor suppressor gene function and gain of oncogene function. Somatic DNA copy number variants (CNVs), which generally range in size from kilobases to entire chromosomes, facilitate gains and losses of chromosomal material incorporating oncogenes and tumor suppressor genes, respectively. In fact, many cancer types are characterized by DNA copy number changes and relatively few single nucleotide mutations (Ciriello et al. Nat Genet 45:1127-1133, 2013). Currently, the optimal method to detect such somatic copy number changes across the cancer genome is whole-genome single nucleotide polymorphism (SNP) microarray analysis.
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Affiliation(s)
- Ross Rowsey
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Iya Znoyko
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Daynna J Wolff
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, USA.
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