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Huang J, Sun M, Wang M, Yu A, Zheng H, Bu C, Zhou J, Zhang Y, Qiao Y, Hu Z. Establishment and characterization of a highly metastatic hepatocellular carcinoma cell line. Bioengineered 2024; 15:2296775. [PMID: 38184822 PMCID: PMC10773622 DOI: 10.1080/21655979.2023.2296775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 12/13/2023] [Indexed: 01/09/2024] Open
Abstract
The prevalence of alcohol-related hepatocellular carcinoma (HCC) has been increasing during the last decade. Cancer research requires cell lines suitable for both in vitro and in vivo assays. However, there is a lack of cell lines with a high in vivo metastatic capacity for this HCC subtype. Herein, a new HCC cell line was established, named HCC-ZJ, using cells from a patient diagnosed with alcohol-related HCC. The karyotype of HCC-ZJ was 46, XY, del (p11.2). Whole-exome sequencing identified several genetic variations in HCC-Z that occur frequently in alcohol-associated HCC, such as mutations in TERT, CTNNB1, ARID1A, CDKN2A, SMARCA2, and HGF. Cell counting kit-8 assays, colony formation assays, and Transwell assays were performed to evaluate the proliferation, migration, and sensitivity to sorafenib and lenvatinib of HCC-Z in vitro. HCC-ZJ showed a robust proliferation rate, a weak foci-forming ability, a strong migration capacity, and a moderate invasion tendency in vitro. Finally, the tumorigenicity and metastatic capacity of HCC-Z were evaluated using a subcutaneous xenograft model, an orthotopic xenograft model, and a tail-veil injection model. HCCZJ exhibited strong tumorigenicity in the subcutaneous xenograft and orthotopic tumor models. Moreover, HCC-ZJ spontaneously formed pulmonary metastases in the orthotopic tumor model. In summary, a new HCC cell line derived from a patient with alcohol-related HCC was established, which showed a high metastatic capacity and could be applied for in vitro and in vivo experiments during pre-clinical research.Highlights• An alcohol-related HCC cell line, HCC-ZJ, was established• HCC-ZJ was applicable for in vitro functional experiment and gene editing• HCC-ZJ was applicable for in vivo tumor growth and spontaneous metastasis models.
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Affiliation(s)
- Jiacheng Huang
- Department of Hepatobiliary and Pancreatic Surgery, The Fourth Affiliated Hospital, International Institutes of Medicine, Zhejiang University School of Medicine, Yiwu, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou, China
| | - Mengqing Sun
- School of Medicine, Zhejiang University, Hangzhou, China
| | - Menglan Wang
- School of Medicine, Zhejiang University, Hangzhou, China
| | - Anning Yu
- Department of Hepatobiliary and Pancreatic Surgery, The Fourth Affiliated Hospital, International Institutes of Medicine, Zhejiang University School of Medicine, Yiwu, China
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou, China
| | - Huilin Zheng
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Chiwen Bu
- Department of General Surgery, People’s Hospital of Guanyun County, Lianyungang, China
| | - Jie Zhou
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yu Zhang
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yiting Qiao
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhenhua Hu
- Department of Hepatobiliary and Pancreatic Surgery, The Fourth Affiliated Hospital, International Institutes of Medicine, Zhejiang University School of Medicine, Yiwu, China
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou, China
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Lin YY, Gao HF, Li H, Hu Q, Du BL, Li S, Xu FP, Cheng MY, Zou JC, Zheng XX, Zhu T, Wang K. Clinical efficacy of tumor organoid-guided cancer therapy for locally advanced unresectable or metastatic breast cancer. Int J Cancer 2024; 155:697-709. [PMID: 38577882 DOI: 10.1002/ijc.34945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 02/27/2024] [Accepted: 03/05/2024] [Indexed: 04/06/2024]
Abstract
Patient-derived organoids (PDOs) may facilitate treatment selection. This retrospective cohort study evaluated the feasibility and clinical benefit of using PDOs to guide personalized treatment in metastatic breast cancer (MBC). Patients diagnosed with MBC were recruited between January 2019 and August 2022. PDOs were established and the efficacy of customized drug panels was determined by measuring cell mortality after drug exposure. Patients receiving organoid-guided treatment (OGT) were matched 1:2 by nearest neighbor propensity scores with patients receiving treatment of physician's choice (TPC). The primary outcome was progression-free survival. Secondary outcomes included objective response rate and disease control rate. Targeted gene sequencing and pathway enrichment analysis were performed. Forty-six PDOs (46 of 51, 90.2%) were generated from 45 MBC patients. PDO drug screening showed an accuracy of 78.4% (95% CI 64.9%-91.9%) in predicting clinical responses. Thirty-six OGT patients were matched to 69 TPC patients. OGT was associated with prolonged median progression-free survival (11.0 months vs. 5.0 months; hazard ratio 0.53 [95% CI 0.33-0.85]; p = .01) and improved disease control (88.9% vs. 63.8%; odd ratio 4.26 [1.44-18.62]) compared with TPC. The objective response rate of both groups was similar. Pathway enrichment analysis in hormone receptor-positive, human epidermal growth factor receptor 2-negative patients demonstrated differentially modulated pathways implicated in DNA repair and transcriptional regulation in those with reduced response to capecitabine/gemcitabine, and pathways associated with cell cycle regulation in those with reduced response to palbociclib. Our study shows that PDO-based functional precision medicine is a feasible and effective strategy for MBC treatment optimization and customization.
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Affiliation(s)
- Ying-Yi Lin
- Shantou University Medical College, Shantou, Guangdong, China
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Hong-Fei Gao
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Hong Li
- Biomedical Laboratory, Jingke BioTech Group, Guangzhou, Guangdong, China
| | - Qiong Hu
- Biomedical Laboratory, Jingke BioTech Group, Guangzhou, Guangdong, China
| | - Bo-le Du
- Biomedical Laboratory, Jingke BioTech Group, Guangzhou, Guangdong, China
| | - Sheng Li
- Biomedical Laboratory, Jingke BioTech Group, Guangzhou, Guangdong, China
| | - Fang-Ping Xu
- Department of Pathology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Min-Yi Cheng
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Jia-Chen Zou
- Guangzhou Medical University, Zhanjiang, Guangdong, China
| | | | - Teng Zhu
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Kun Wang
- Shantou University Medical College, Shantou, Guangdong, China
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
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3
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Pan X, Liu L, Zhang X, Tang X, Qian G, Qiu H, Lin S, Yao H, Dong X, Tan B. FBXO11 variants are associated with intellectual disability and variable clinical manifestation in Chinese affected individuals. J Hum Genet 2024; 69:391-400. [PMID: 38740982 DOI: 10.1038/s10038-024-01255-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 04/01/2024] [Accepted: 04/24/2024] [Indexed: 05/16/2024]
Abstract
F-box protein 11 (FBXO11) is a member of F-Box protein family, which has recently been proved to be associated with intellectual developmental disorder with dysmorphic facies and behavioral abnormalities (IDDFBA, OMIM: 618089). In this study, 12 intellectual disability individuals from 5 Chinese ID families were collected, and whole exome sequencing (WES), sanger sequencing, and RNA sequencing (RNA-seq) were conducted. Almost all the affected individuals presented with mild to severe intellectual disability (12/12), global developmental delay (10/12), speech and language development delay (8/12) associated with a range of alternate features including increased body weight (7/12), short stature (6/12), seizures (3/12), reduced visual acuity (4/12), hypotonia (1/12), and auditory hallucinations and hallucinations (1/12). Distinguishingly, malformation was not observed in all the affected individuals. WES analysis showed 5 novel FBXO11 variants, which include an inframe deletion variant, a missense variant, two frameshift variants, and a partial deletion of FBXO11 (exon 22-23). RNA-seq indicated that exon 22-23 deletion of FBXO11 results in a new mRNA structure. Conservation and protein structure prediction demonstrated deleterious effect of these variants. The DEGs analysis revealed 148 differentially expressed genes shared among 6 affected individuals, which were mainly associated with genes of muscle and immune system. Our research is the first report of FBXO11-associated IDDFBA in Chinese individuals, which expands the genetic and clinical spectrum of this newly identified NDD/ID syndrome.
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Affiliation(s)
- Xin Pan
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400000, China
| | - Li Liu
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400000, China
| | - Xu Zhang
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400000, China
| | - Xianglan Tang
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400000, China
| | - Guanhua Qian
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400000, China
| | - Hao Qiu
- Center for Clinical Genetics and Genomics, DIAN Diagnostics, Hangzhou, 310058, Zhejiang, China
| | - Shuhong Lin
- Center for Clinical Genetics and Genomics, DIAN Diagnostics, Hangzhou, 310058, Zhejiang, China
| | - Hong Yao
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400000, China
| | - Xiaojing Dong
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400000, China
| | - Bo Tan
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400000, China.
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Li M, Yang J, Xiao R, Liu Y, Hu J, Li T, Wu P, Zhang M, Huang Y, Sun Y, Li C. The effect of trisomic chromosomes on spatial genome organization and global transcription in embryonic stem cells. Cell Prolif 2024; 57:e13639. [PMID: 38553796 PMCID: PMC11294443 DOI: 10.1111/cpr.13639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 03/08/2024] [Accepted: 03/14/2024] [Indexed: 08/03/2024] Open
Abstract
Aneuploidy frequently occurs in cancer and developmental diseases such as Down syndrome, with its functional consequences implicated in dosage effects on gene expression and global perturbation of stress response and cell proliferation pathways. However, how aneuploidy affects spatial genome organization remains less understood. In this study, we addressed this question by utilizing the previously established isogenic wild-type (WT) and trisomic mouse embryonic stem cells (mESCs). We employed a combination of Hi-C, RNA-seq, chromosome painting and nascent RNA imaging technologies to compare the spatial genome structures and gene transcription among these cells. We found that trisomy has little effect on spatial genome organization at the level of A/B compartment or topologically associating domain (TAD). Inter-chromosomal interactions are associated with chromosome regions with high gene density, active histone modifications and high transcription levels, which are confirmed by imaging. Imaging also revealed contracted chromosome volume and weakened transcriptional activity for trisomic chromosomes, suggesting potential implications for the transcriptional output of these chromosomes. Our data resources and findings may contribute to a better understanding of the consequences of aneuploidy from the angle of spatial genome organization.
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Affiliation(s)
- Mengfan Li
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijingChina
| | - Junsheng Yang
- State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC)Peking UniversityBeijingChina
| | - Rong Xiao
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Medical GeneticsInstitute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical CollegeBeijingChina
| | - Yunjie Liu
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijingChina
| | - Jiaqi Hu
- School of Health HumanitiesPeking UniversityBeijingChina
| | - Tingting Li
- State Key Laboratory of ProteomicsInstitute of Basic Medical Sciences, National Center of Biomedical AnalysisBeijingChina
| | - Pengze Wu
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijingChina
| | - Meili Zhang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Medical GeneticsInstitute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical CollegeBeijingChina
| | - Yue Huang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Medical GeneticsInstitute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical CollegeBeijingChina
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC)Peking UniversityBeijingChina
| | - Cheng Li
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijingChina
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5
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Hwang HW, Shin HT, An HY, Byun JW. Genomic progression for local invasion of cutaneous squamous cell carcinoma from the superficial to the deep portion. Int J Cancer 2024; 155:532-544. [PMID: 38739001 DOI: 10.1002/ijc.34952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 02/29/2024] [Accepted: 03/19/2024] [Indexed: 05/14/2024]
Abstract
Cutaneous squamous cell carcinoma (cSCC) is the second most common skin cancer. While many treatments exist, our understanding of its genomic progression, especially from the epidermis to the deep dermis, remains limited. This study aims to identify genetic mutations associated with the progression of cSCC into the deep dermis, providing insights into its aggressive behavior and high-risk features. We performed high-depth whole-exome sequencing on 12 cSCC tissues, along with paired normal tissues from six patients, using microdissection techniques. The mutational analysis focused on identifying alterations enriched during cSCC progression. Gene Ontology enrichment analysis, immunohistochemical assays, and external single-cell RNA data were utilized for validation. A total of 8863 non-synonymous somatic mutations were identified in 4092 genes across the superficial and deep portions of cSCCs. Analysis of deep portion mutations revealed a significant correlation with gene ontology biological processes, particularly cell junction organization, and cell-cell adhesion. Clonal mutations in these processes were more prevalent in the deep portions, indicating their impact on the cSCC mutation landscape. Genetic evolution analysis identified 29 causal genes associated with dermal invasion in cSCC. We highlight somatic mutations in cSCC, revealing heterogeneity between superficial and deep regions. Altered genes in cell junction organization and cell-cell adhesion emerged as pivotal in dermal invasion. We identified 29 causal genes primarily in deep tumor regions. Our findings emphasize analyzing multiple tumor regions to capture varied mutational landscapes. These insights advance our understanding of cSCC progression, emphasizing genetic and cellular changes during tumor evolution.
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Affiliation(s)
- Hye Won Hwang
- Department of Dermatology, Inha University School of Medicine, Incheon, Republic of Korea
| | - Hyun-Tae Shin
- Department of Dermatology, Inha University School of Medicine, Incheon, Republic of Korea
- Research Center for Controlling Intercellular Communication (RCIC), Inha University School of Medicine, Incheon, Republic of Korea
| | - Hye Young An
- Department of Dermatology, Inha University School of Medicine, Incheon, Republic of Korea
| | - Ji Won Byun
- Department of Dermatology, Inha University School of Medicine, Incheon, Republic of Korea
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Paineau M, Minio A, Mestre P, Fabre F, Mazet ID, Couture C, Legeai F, Dumartinet T, Cantu D, Delmotte F. Multiple deletions of candidate effector genes lead to the breakdown of partial grapevine resistance to downy mildew. THE NEW PHYTOLOGIST 2024; 243:1490-1505. [PMID: 39021210 DOI: 10.1111/nph.19861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 03/21/2024] [Indexed: 07/20/2024]
Abstract
Grapevine downy mildew, caused by the oomycete Plasmopara viticola (P. viticola, Berk. & M. A. Curtis; Berl. & De Toni), is a global threat to Eurasian wine grapes Vitis vinifera. Although resistant grapevine varieties are becoming more accessible, P. viticola populations are rapidly evolving to overcome these resistances. We aimed to uncover avirulence genes related to Rpv3.1-mediated grapevine resistance. We sequenced the genomes and characterized the development of 136 P. viticola strains on resistant and sensitive grapevine cultivars. A genome-wide association study was conducted to identify genomic variations associated with resistant-breaking phenotypes. We identified a genomic region associated with the breakdown of Rpv3.1 grapevine resistance (avrRpv3.1 locus). A diploid-aware reassembly of the P. viticola INRA-Pv221 genome revealed structural variations in this locus, including a 30 kbp deletion. Virulent P. viticola strains displayed multiple deletions on both haplotypes at the avrRpv3.1 locus. These deletions involve two paralog genes coding for proteins with 800-900 amino acids and signal peptides. These proteins exhibited a structure featuring LWY-fold structural modules, common among oomycete effectors. When transiently expressed, these proteins induced cell death in grapevines carrying Rpv3.1 resistance, confirming their avirulence nature. This discovery sheds light on the genetic mechanisms enabling P. viticola to adapt to grapevine resistance, laying a foundation for developing strategies to manage this destructive crop pathogen.
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Affiliation(s)
- Manon Paineau
- INRAE, Bordeaux Sciences Agro, SAVE, ISVV, F-33340, Villenave d'Ornon, France
- Department of Viticulture and Enology, University of California Davis, Davis, 95616, CA, USA
| | - Andrea Minio
- Department of Viticulture and Enology, University of California Davis, Davis, 95616, CA, USA
| | - Pere Mestre
- INRAE, Université de Strasbourg, SVQV, F-68125, Colmar, France
| | - Frédéric Fabre
- INRAE, Bordeaux Sciences Agro, SAVE, ISVV, F-33340, Villenave d'Ornon, France
| | - Isabelle D Mazet
- INRAE, Bordeaux Sciences Agro, SAVE, ISVV, F-33340, Villenave d'Ornon, France
| | - Carole Couture
- INRAE, Bordeaux Sciences Agro, SAVE, ISVV, F-33340, Villenave d'Ornon, France
| | - Fabrice Legeai
- INRAE, IGEPP, F-35650, Le-Rheu, France
- INRIA, IRISA, GenOuest Core Facility, F-35000, Rennes, France
| | | | - Dario Cantu
- Department of Viticulture and Enology, University of California Davis, Davis, 95616, CA, USA
- Genome Center, University of California Davis, Davis, 95616, CA, USA
| | - François Delmotte
- INRAE, Bordeaux Sciences Agro, SAVE, ISVV, F-33340, Villenave d'Ornon, France
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Barington M, Bak M, Kjartansdóttir KR, Hansen TVO, Birkedal U, Østergaard E, Hove HB. Novel Alu insertion in the ZEB2 gene causing Mowat-Wilson syndrome. Am J Med Genet A 2024; 194:e63581. [PMID: 38600862 DOI: 10.1002/ajmg.a.63581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 02/06/2024] [Accepted: 02/21/2024] [Indexed: 04/12/2024]
Abstract
Alu elements are short, interspersed elements located throughout the genome, playing a role in human diversity, and occasionally causing genetic diseases. Here, we report a novel Alu insertion causing Mowat-Wilson syndrome, a rare neurodevelopmental disorder, in an 8-year-old boy displaying the typical clinical features for Mowat-Wilson syndrome. The variant was not initially detected in genome sequencing data, but through deep phenotyping, which pointed to only one plausible candidate gene, manual inspection of genome sequencing alignment data enabled us to identify a de novo heterozygous Alu insertion in exon 8 of the ZEB2 gene. Nanopore long-read sequencing confirmed the Alu insertion, leading to the formation of a premature stop codon and likely haploinsufficiency of ZEB2. This underscores the importance of deep phenotyping and mobile element insertion analysis in uncovering genetic causes of monogenic disorders as these elements might be overlooked in standard next-generation sequencing protocols.
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Affiliation(s)
- Maria Barington
- Department of Clinical Genetics, Copenhagen University Hospital, Copenhagen, Denmark
| | - Mads Bak
- Department of Clinical Genetics, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Thomas van Overeem Hansen
- Department of Clinical Genetics, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ulf Birkedal
- Department of Clinical Genetics, Copenhagen University Hospital, Copenhagen, Denmark
| | - Elsebet Østergaard
- Department of Clinical Genetics, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Hanne Buciek Hove
- Center for Rare Diseases, Department of Paediatrics and Adolescent Medicine, Copenhagen University Hospital, Copenhagen, Denmark
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8
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Wang J, Sui Z, Huang W, Yu Z, Guo L. Biomimetic hydrogels with mesoscale collagen architecture for patient-derived tumor organoids culture. Bioact Mater 2024; 38:384-398. [PMID: 38764448 PMCID: PMC11101944 DOI: 10.1016/j.bioactmat.2024.04.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 05/21/2024] Open
Abstract
Patient-derived tumor organoids (PDTOs) shows great potential as a preclinical model. However, the current methods for establishing PDTOs primarily focus on modulating local properties, such as sub-micrometer topographies. Nevertheless, they neglect to capture the global millimeter or intermediate mesoscale architecture that have been demonstrated to influence tumor response to therapeutic treatment and tumor progression. In this study, we present a rapid technique for generating collagen bundles with an average length of 90 ± 27 μm and a mean diameter of 5 ± 1.5 μm from tumor tissue debris that underwent mechanical agitation following enzymatic digestion. The collagen bundles were subsequently utilized for the fabrication of biomimetic hydrogels, incorporating microbial transglutaminase (mTG) crosslinked gelatin. These biomimetic hydrogels, referred to as MC-gel, were specifically designed for patient-derived tumor organoids. The lung cancer organoids cultured in MC-gel exhibited larger diameters and higher cell viability compared to those cultured in gels lacking the mesoscale collagen bundle; moreover, their irregular morphology more closely resembled that observed in vivo. The MC-gel-based lung cancer organoids effectively replicated the histology and mutational landscapes observed in the original donor patient's tumor tissue. Additionally, these lung cancer organoids showed a remarkable similarity in their gene expression and drug response across different matrices. This recently developed model holds great potential for investigating the occurrence, progression, metastasis, and management of tumors, thereby offering opportunities for personalized medicine and customized treatment options.
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Affiliation(s)
- Jiaxin Wang
- Shenzhen Key Laboratory of Epigenetics and Precision Medicine for Cancers, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academic of Medical Sciences & Peking Union Medical College, Shenzhen, 518116, China
| | - Zhilin Sui
- Shenzhen Key Laboratory of Epigenetics and Precision Medicine for Cancers, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academic of Medical Sciences & Peking Union Medical College, Shenzhen, 518116, China
| | - Wei Huang
- Center for Cell and Gene Circuit Design, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, Guangdong, China
- Department of Biology, Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China
| | - Zhentao Yu
- Shenzhen Key Laboratory of Epigenetics and Precision Medicine for Cancers, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academic of Medical Sciences & Peking Union Medical College, Shenzhen, 518116, China
| | - Ling Guo
- Shenzhen Key Laboratory of Epigenetics and Precision Medicine for Cancers, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academic of Medical Sciences & Peking Union Medical College, Shenzhen, 518116, China
- Department of Biology, Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China
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9
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Qian L, Zhu J, Xue Z, Zhou Y, Xiang N, Xu H, Sun R, Gong W, Cai X, Sun L, Ge W, Liu Y, Su Y, Lin W, Zhan Y, Wang J, Song S, Yi X, Ni M, Zhu Y, Hua Y, Zheng Z, Guo T. Proteomic landscape of epithelial ovarian cancer. Nat Commun 2024; 15:6462. [PMID: 39085232 PMCID: PMC11291745 DOI: 10.1038/s41467-024-50786-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 07/19/2024] [Indexed: 08/02/2024] Open
Abstract
Epithelial ovarian cancer (EOC) is a deadly disease with limited diagnostic biomarkers and therapeutic targets. Here we conduct a comprehensive proteomic profiling of ovarian tissue and plasma samples from 813 patients with different histotypes and therapeutic regimens, covering the expression of 10,715 proteins. We identify eight proteins associated with tumor malignancy in the tissue specimens, which are further validated as potential circulating biomarkers in plasma. Targeted proteomics assays are developed for 12 tissue proteins and 7 blood proteins, and machine learning models are constructed to predict one-year recurrence, which are validated in an independent cohort. These findings contribute to the understanding of EOC pathogenesis and provide potential biomarkers for early detection and monitoring of the disease. Additionally, by integrating mutation analysis with proteomic data, we identify multiple proteins related to DNA damage in recurrent resistant tumors, shedding light on the molecular mechanisms underlying treatment resistance. This study provides a multi-histotype proteomic landscape of EOC, advancing our knowledge for improved diagnosis and treatment strategies.
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Affiliation(s)
- Liujia Qian
- School of Medicine, Westlake University, Hangzhou, Zhejiang Province, China
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, China
| | - Jianqing Zhu
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Zhangzhi Xue
- School of Medicine, Westlake University, Hangzhou, Zhejiang Province, China
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, China
| | - Yan Zhou
- School of Medicine, Westlake University, Hangzhou, Zhejiang Province, China
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, China
| | - Nan Xiang
- School of Medicine, Westlake University, Hangzhou, Zhejiang Province, China
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, China
| | - Hong Xu
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Science, Zhejiang University, Hangzhou, China
| | - Rui Sun
- School of Medicine, Westlake University, Hangzhou, Zhejiang Province, China
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, China
| | - Wangang Gong
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Xue Cai
- School of Medicine, Westlake University, Hangzhou, Zhejiang Province, China
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, China
| | - Lu Sun
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Weigang Ge
- Westlake Omics (Hangzhou) Biotechnology Co., Ltd., Hangzhou, Zhejiang Province, China
| | - Yufeng Liu
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Science, Zhejiang University, Hangzhou, China
| | - Ying Su
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Wangmin Lin
- Westlake Omics (Hangzhou) Biotechnology Co., Ltd., Hangzhou, Zhejiang Province, China
| | - Yuecheng Zhan
- Westlake Omics (Hangzhou) Biotechnology Co., Ltd., Hangzhou, Zhejiang Province, China
| | - Junjian Wang
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Shuang Song
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Science, Zhejiang University, Hangzhou, China
| | - Xiao Yi
- School of Medicine, Westlake University, Hangzhou, Zhejiang Province, China
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, China
| | - Maowei Ni
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Yi Zhu
- School of Medicine, Westlake University, Hangzhou, Zhejiang Province, China.
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China.
- Research Center for Industries of the Future, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, China.
| | - Yuejin Hua
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Science, Zhejiang University, Hangzhou, China.
| | - Zhiguo Zheng
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China.
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China.
| | - Tiannan Guo
- School of Medicine, Westlake University, Hangzhou, Zhejiang Province, China.
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China.
- Research Center for Industries of the Future, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, China.
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10
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Zhou H, Liu Q, Zhang D, Li Q, Cao D, Cheng N, Wan X, Zhang Y, Feng F, Xiang Y, Yang J. Efficacy and safety of an oral combination therapy of niraparib and etoposide in platinum resistant/refractory ovarian cancer: a single arm, prospective, phase II study. Int J Gynecol Cancer 2024:ijgc-2024-005386. [PMID: 39074931 DOI: 10.1136/ijgc-2024-005386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024] Open
Abstract
OBJECTIVE Non-platinum chemotherapy is used in platinum resistant/refractory ovarian cancer patients but offers limited efficacy, especially in those who develop platinum resistance after ≤2 lines of platinum based chemotherapy. This phase II study aimed to evaluate the efficacy and safety of oral niraparib plus etoposide in platinum resistant/refractory ovarian cancer. METHODS Platinum resistant/refractory ovarian cancer patients after ≤2 lines of platinum based chemotherapy, histologically confirmed as non-mucinous epithelial ovarian cancer, regardless of biomarker status, were eligible. Patients received niraparib with a starting dose of 200 mg/100 mg alternate once a day, and oral etoposide of 50 mg once a day, on days 1-20 of 30 days per cycle for a maximum of 6-8 cycles, followed by niraparib until disease progression or intolerable toxicity. The primary endpoint was investigator assessed progression free survival. RESULTS 29 patients were enrolled from 22 May 2020 to 3 February 2023; 26 patients were included in the efficacy analysis set as per protocol. Median progression free survival was 4.2 months (95% confidence interval (CI) 3.9 to 4.4). Overall response rate was 26.9% (95% CI 8.7 to 45.2). Disease control rate was 57.7% (95% CI 37.3 to 78.0). Overall response rate in patients with a BRCA mutation and homologous recombination deficiency was 50% and 41.7%, respectively. Median progression free survival in patients with primary platinum resistance was 4.5 months (95% CI 3.6 to 5.3). 29 patients were included in the safety analysis set, and 8 (28%) patients experienced treatment related adverse events of grade ≥3. There was no treatment related discontinuation. CONCLUSIONS Niraparib combined with etoposide showed evidence of antitumor activity in platinum resistant/refractory ovarian cancer after ≤2 lines of platinum based chemotherapy, particularly in patients with a BRCA mutation, homologous recombination deficiency, or primary platinum resistance. This once-a-day oral combination was a convenient option. TRIAL REGISTRATION NUMBER NCT04217798.
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Affiliation(s)
- Huimei Zhou
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- National Clinical Research Center for Obstetric and Gynecologic Diseases, Beijing, China
| | - Qian Liu
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- National Clinical Research Center for Obstetric and Gynecologic Diseases, Beijing, China
| | - Depu Zhang
- Shandong Cancer Hospital Affiliated to Shandong University, Jinan, China
| | - Qingshui Li
- Shandong Cancer Hospital Affiliated to Shandong University, Jinan, China
| | - Dongyan Cao
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- National Clinical Research Center for Obstetric and Gynecologic Diseases, Beijing, China
| | - Ninghai Cheng
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- National Clinical Research Center for Obstetric and Gynecologic Diseases, Beijing, China
| | - Xirun Wan
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- National Clinical Research Center for Obstetric and Gynecologic Diseases, Beijing, China
| | - Ying Zhang
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- National Clinical Research Center for Obstetric and Gynecologic Diseases, Beijing, China
| | - Fengzhi Feng
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- National Clinical Research Center for Obstetric and Gynecologic Diseases, Beijing, China
| | - Yang Xiang
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- National Clinical Research Center for Obstetric and Gynecologic Diseases, Beijing, China
| | - Jiaxin Yang
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- National Clinical Research Center for Obstetric and Gynecologic Diseases, Beijing, China
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11
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Zhang H, Wang J, Li X, Zhang D, Qi Y, Zhang Q, Luo N, Wang X, Wang T. Distribution of EGFR fusions in 35,023 Chinese patients with solid tumors-the frequency, fusion partners and clinical outcome. World J Surg Oncol 2024; 22:194. [PMID: 39054543 PMCID: PMC11271172 DOI: 10.1186/s12957-024-03463-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 06/30/2024] [Indexed: 07/27/2024] Open
Abstract
BACKGROUND Epidermal growth factor receptor (EGFR) fusions are rare but potentially actionable oncogenic drivers across multiple solid tumors. However, the distribution and molecular characteristics of EGFR fusions in Chinese patients with solid malignancies have not been explored. METHODS Panel-based next-generation sequencing (NGS) data of 35,023 patients with various types of solid tumors was collected and analyzed from the Simcere Diagnostics (Nanjing, China) database. A 9563-patient cohort was derived from The Cancer Genome Atlas (TCGA) to explore the relationship between EGFR fusion status and overall survival (OS). RESULTS In this study, prevalence of functional EGFR fusions was 0.303% (106/35,023) in total across solid tumors, which occur more commonly in gastroesophageal junction cancer (1/61, 1.613%), followed by medulloblastoma (1/66, 1.515%) and glioma (33/2409, 1.370%). Analysis showed a prevalence for fusion partners in different tumor types. The top 3 co-mutant genes with EGFR fusion were TP53 (mutation frequency, MF: 65%), BRCA2 (MF: 43%), and ALK (MF: 41%). Furthermore, patients in the EGFR fusion group had a significantly shorter OS than those in the non-EGFR fusion group (p < 0.0001) in the TCGA cohort, suggesting that EGFR fusion might be a high-risk factor for poor prognosis. CONCLUSIONS Our study is the first retrospective analysis of EGFR fusions in a large-scale solid tumor population, which may provide a reference for future EGFR-TKI clinical trials with EGFR fusions.
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Affiliation(s)
- Haiping Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Julei Wang
- Department of Neurosurgery, Second Affiliated Hospital of Air Force Military Medical University, Xi'an, China
| | - Xiaoxiao Li
- Department of Thoracic Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Dongfeng Zhang
- Department of Thoracic Oncology, Linfen Center Hospital, Linfen, China
| | - Yingxue Qi
- Jiangsu Simcere Diagnostics Co., Ltd, Nanjing Simcere Medical Laboratory Science Co., Ltd, The State Key Laboratory of Neurology and Oncology Drug Development, Nanjing, China
| | - Qin Zhang
- Jiangsu Simcere Diagnostics Co., Ltd, Nanjing Simcere Medical Laboratory Science Co., Ltd, The State Key Laboratory of Neurology and Oncology Drug Development, Nanjing, China
| | - Ningning Luo
- Jiangsu Simcere Diagnostics Co., Ltd, Nanjing Simcere Medical Laboratory Science Co., Ltd, The State Key Laboratory of Neurology and Oncology Drug Development, Nanjing, China
| | - Xiaoou Wang
- Health Education Promotion Department, Shenyang Stomatological Hospital, Shenyang, China
| | - Tuo Wang
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiao Tong University, No. 277, Yanta West Road, Xi'an City, Shanxi Province, China.
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12
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Tandukar B, Deivendran D, Chen L, Cruz-Pacheco N, Sharma H, Xu A, Bandari AK, Chen DB, George C, Marty A, Cho RJ, Cheng J, Saylor D, Gerami P, Arron ST, Bastian BC, Shain AH. Genetic evolution of keratinocytes to cutaneous squamous cell carcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.23.604673. [PMID: 39091884 PMCID: PMC11291049 DOI: 10.1101/2024.07.23.604673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
We performed multi-omic profiling of epidermal keratinocytes, precancerous actinic keratoses, and squamous cell carcinomas to understand the molecular transitions during skin carcinogenesis. Single-cell mutational analyses showed that most keratinocytes in normal skin had lower mutation burdens than melanocytes and fibroblasts, however keratinocytes with TP53 or NOTCH1 mutations had substantially higher mutation burdens, suggesting that these mutations prime keratinocytes for transformation by increasing their mutation rate. Mutational profiling and spatial transcriptomics on squamous cell carcinomas adjacent to actinic keratoses revealed TERT promoter and CDKN2A mutations emerging in actinic keratoses, whereas additional mutations inactivating ARID2 and activating the MAPK-pathway delineated the transition to squamous cell carcinomas. Spatial variation in gene expression patterns was common in both tumor and immune cells, with high expression of checkpoint molecules at the invasive front of tumors. In conclusion, this study documents key events during the evolution of cutaneous squamous cell carcinoma.
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13
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Keahi DL, Sanders MA, Paul MR, Webster ALH, Fang Y, Wiley TF, Shalaby S, Carroll TS, Chandrasekharappa SC, Sandoval-Garcia C, MacMillan ML, Wagner JE, Hatten ME, Smogorzewska A. G-quadruplexes are a source of vulnerability in BRCA2 deficient granule cell progenitors and medulloblastoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.20.604431. [PMID: 39091814 PMCID: PMC11291086 DOI: 10.1101/2024.07.20.604431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Biallelic pathogenic variants in the essential DNA repair gene BRCA2 causes Fanconi anemia, complementation group FA-D1. Patients in this group are highly prone to develop embryonal tumors, most commonly medulloblastoma arising from the cerebellar granule cell progenitors (GCPs). GCPs undergo high proliferation in the postnatal cerebellum under SHH activation, but the type of DNA lesions that require the function of the BRCA2 to prevent tumorigenesis remains unknown. To identify such lesions, we assessed both GCP neurodevelopment and tumor formation using a mouse model with deletion of exons three and four of Brca2 in the central nervous system, coupled with global Trp53 loss. Brca2 Δex3-4 ;Trp53 -/- animals developed SHH subgroup medulloblastomas with complete penetrance. Whole-genome sequencing of the tumors identified structural variants with breakpoints enriched in areas overlapping G-quadruplexes (G4s). Brca2 -deficient GCPs exhibited decreased replication speed in the presence of the G4-stabilizer pyridostatin. Pif1 helicase, which resolves G4s during replication, was highly upregulated in tumors, and Pif1 knockout in primary MB tumor cells resulted in increased genome instability upon pyridostatin treatment. These data suggest that G4s may represent sites prone to replication stalling in highly proliferative GCPs and without BRCA2, G4s become a source of genome instability. Tumor cells upregulate G4-resolving helicases to facilitate rapid proliferation through G4s highlighting PIF1 helicase as a potential therapeutic target for treatment of BRCA2 -deficient medulloblastomas.
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14
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Wang M, Fukushima S, Sheen YS, Ramelyte E, Cruz-Pacheco N, Shi C, Liu S, Banik I, Aquino JD, Sangueza Acosta M, Levesque M, Dummer R, Liau JY, Chu CY, Shain AH, Yeh I, Bastian BC. The genetic evolution of acral melanoma. Nat Commun 2024; 15:6146. [PMID: 39034322 PMCID: PMC11271482 DOI: 10.1038/s41467-024-50233-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 07/02/2024] [Indexed: 07/23/2024] Open
Abstract
Acral melanoma is an aggressive type of melanoma with unknown origins. It is the most common type of melanoma in individuals with dark skin and is notoriously challenging to treat. We examine exome sequencing data of 139 tissue samples, spanning different progression stages, from 37 patients. We find that 78.4% of the melanomas display clustered copy number transitions with focal amplifications, recurring predominantly on chromosomes 5, 11, 12, and 22. These complex genomic aberrations are typically shared across all progression stages of individual patients. TERT activating alterations also arise early, whereas MAP-kinase pathway mutations appear later, an inverted order compared to the canonical evolution. The punctuated formation of complex aberrations and early TERT activation suggest a unique mutational mechanism that initiates acral melanoma. The marked intratumoral heterogeneity, especially concerning MAP-kinase pathway mutations, may partly explain the limited success of therapies for this melanoma subtype.
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Affiliation(s)
- Meng Wang
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Satoshi Fukushima
- Department of Dermatology and Plastic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Yi-Shuan Sheen
- Department of Dermatology, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Egle Ramelyte
- Department of Dermatology, University of Zurich, Zurich, Switzerland
| | - Noel Cruz-Pacheco
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Chenxu Shi
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Shanshan Liu
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Ishani Banik
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Jamie D Aquino
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | | | - Mitchell Levesque
- Department of Dermatology, University of Zurich, Zurich, Switzerland
| | - Reinhard Dummer
- Department of Dermatology, University of Zurich, Zurich, Switzerland
| | - Jau-Yu Liau
- Department of Dermatology, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chia-Yu Chu
- Department of Dermatology, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - A Hunter Shain
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Iwei Yeh
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Boris C Bastian
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA.
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15
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Mortenson KL, Dawes C, Wilson ER, Patchen NE, Johnson HE, Gertz J, Bailey SD, Liu Y, Varley KE, Zhang X. 3D genomic analysis reveals novel enhancer-hijacking caused by complex structural alterations that drive oncogene overexpression. Nat Commun 2024; 15:6130. [PMID: 39033128 PMCID: PMC11271278 DOI: 10.1038/s41467-024-50387-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 07/05/2024] [Indexed: 07/23/2024] Open
Abstract
Cancer genomes are composed of many complex structural alterations on chromosomes and extrachromosomal DNA (ecDNA), making it difficult to identify non-coding enhancer regions that are hijacked to activate oncogene expression. Here, we describe a 3D genomics-based analysis called HAPI (Highly Active Promoter Interactions) to characterize enhancer hijacking. HAPI analysis of HiChIP data from 34 cancer cell lines identified enhancer hijacking events that activate both known and potentially novel oncogenes such as MYC, CCND1, ETV1, CRKL, and ID4. Furthermore, we found enhancer hijacking among multiple oncogenes from different chromosomes, often including MYC, on the same complex amplicons such as ecDNA. We characterized a MYC-ERBB2 chimeric ecDNA, in which ERBB2 heavily hijacks MYC's enhancers. Notably, CRISPRi of the MYC promoter led to increased interaction of ERBB2 with MYC enhancers and elevated ERBB2 expression. Our HAPI analysis tool provides a robust strategy to detect enhancer hijacking and reveals novel insights into oncogene activation.
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Affiliation(s)
- Katelyn L Mortenson
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Courtney Dawes
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Emily R Wilson
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Nathan E Patchen
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Hailey E Johnson
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT, USA
| | - Jason Gertz
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Swneke D Bailey
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Department of Surgery and Human Genetics, McGill University, Montreal, QC, Canada
| | - Yang Liu
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Katherine E Varley
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.
| | - Xiaoyang Zhang
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.
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16
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Heczko L, Liška V, Vyčítal O, Fiala O, Šůsová S, Hlaváč V, Souček P. Targeted panel sequencing of pharmacogenes and oncodrivers in colorectal cancer patients reveals genes with prognostic significance. Hum Genomics 2024; 18:83. [PMID: 39030589 PMCID: PMC11264515 DOI: 10.1186/s40246-024-00644-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 06/26/2024] [Indexed: 07/21/2024] Open
Abstract
BACKGROUND Colorectal cancer is still the second leading cause of cancer-related deaths and thus biomarkers allowing prediction of the resistance of patients to therapy and estimating their prognosis are needed. We designed a panel of 558 genes with pharmacogenomics records related to 5-fluorouracil resistance, genes important for sensitivity to other frequently used drugs, major oncodrivers, and actionable genes. We performed a target enrichment sequencing of DNA from tumors and matched blood samples of patients, and compared the results with patient prognosis stratified by systemic adjuvant chemotherapy. RESULTS The median number of detected variants per tumor sample was 18.5 with 4 classified as having a high predicted functional effect and 14.5 moderate effect. APC, TP53, and KRAS were the most frequent mutated genes (64%, 59%, and 42% of mutated samples, respectively) followed by FAT4 (23%), FBXW7, and PIK3CA (16% for both). Patients with advanced stage III had more frequently APC, TP53, or KRAS mutations than those in stages I or II. KRAS mutation counts followed an increasing trend with grade (G1 < G2 < G3). The response to adjuvant therapy was worse in carriers of frameshift mutations in APC or 12D variant in KRAS, but none of these oncodrivers had prognostic value. Carriage of somatic mutations in any of the genes ABCA13, ANK2, COL7A1, NAV3, or UNC80 had prognostic relevance for worse overall survival (OS) of all patients. In contrast, mutations in FLG, GLI3, or UNC80 were prognostic in the same direction for patients untreated, and mutations in COL6A3, LRP1B, NAV3, RYR1, RYR3, TCHH, or TENM4 for patients treated with adjuvant therapy. The first association was externally validated. From all germline variants with high or moderate predicted functional effects (median 326 per patient), > 5% frequency and positive Manhattan plot based on 3-year RFS, rs72753407 in NFACS, rs34621071 in ERBB4, and rs2444274 in RIF1 were significantly associated with RFS, OS or both. CONCLUSIONS The present study identified several putative somatic and germline genetic events with prognostic potential for colorectal cancer that should undergo functional characterization.
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Affiliation(s)
- Lucie Heczko
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, alej Svobody 1655/76, Pilsen, 323 00, Czech Republic
| | - Václav Liška
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, alej Svobody 1655/76, Pilsen, 323 00, Czech Republic
- Department of Surgery, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
| | - Ondřej Vyčítal
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, alej Svobody 1655/76, Pilsen, 323 00, Czech Republic
- Department of Surgery, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
| | - Ondřej Fiala
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, alej Svobody 1655/76, Pilsen, 323 00, Czech Republic
- Department of Oncology and Radiotherapeutics, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
| | - Simona Šůsová
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, alej Svobody 1655/76, Pilsen, 323 00, Czech Republic
- Toxicogenomics Unit, National Institute of Public Health, Prague, Czech Republic
| | - Viktor Hlaváč
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, alej Svobody 1655/76, Pilsen, 323 00, Czech Republic.
- Toxicogenomics Unit, National Institute of Public Health, Prague, Czech Republic.
| | - Pavel Souček
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, alej Svobody 1655/76, Pilsen, 323 00, Czech Republic.
- Toxicogenomics Unit, National Institute of Public Health, Prague, Czech Republic.
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17
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Mendoza RP, Symes E, Wang P, Miller C, Thompson SC, Antic T, Biernacka A. Cytomorphologic and molecular characterization of spindle cell carcinoid tumors of the lung. Cancer Cytopathol 2024. [PMID: 39024046 DOI: 10.1002/cncy.22886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 06/12/2024] [Accepted: 06/13/2024] [Indexed: 07/20/2024]
Abstract
BACKGROUND Spindle cell carcinoid tumor (SCCT) is a rare variant of lung carcinoid tumor consisting predominantly or exclusively of spindle cells. To the authors' knowledge, this is the first study to date investigating the molecular characteristics of SCCTs. METHODS Eighty-five carcinoid tumors initially diagnosed by fine-needle aspiration over a period of 10 years were reviewed. The final diagnostic classification was based on resection specimens. Six SCCTs were identified and characterized based on cytomorphology, and immunohistochemical and molecular features. RESULTS Most patients with SCCT were Caucasian (100.0%), women (83.3%), asymptomatic (66.7%), and nonsmokers (83.3%). The median age at diagnosis was 78.0 years (range, 58.2-80.3 years). A higher proportion of patients who had SCCT were diagnosed with distant metastasis. The smears were cellular and demonstrated clean backgrounds without necrosis or mitotic activity. SCCTs comprised of bipolar-to-elongated cells with finely granular chromatin, inconspicuous nucleoli, scant cytoplasm, and minimal atypia or pleomorphism. The tumor cells sometimes appeared boomerang-shaped and might mimic granulomas or blood vessels. SCCTs showed strong expression for pan-cytokeratin, synaptophysin, chromogranin, and CD56, with weak TTF-1 and a very low Ki-67 proliferation index. All SCCTs had low tumor mutational burden and were microsatellite-stable. One case showed multiple whole-gene losses in chromosome 11, whereas another harbored duplication in ARID1A. Two cases demonstrated gains in chromosomes 17, one of which also showed gains in chromosome 18. None had a single nucleotide mutation. CONCLUSIONS SCCT is a rare subset of lung carcinoid tumors. These tumors harbor unique cytologic, prognostic, and molecular features that may have significant diagnostic and clinical implications.
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Affiliation(s)
- Rachelle P Mendoza
- Department of Pathology, University of Rochester Medical Center, Rochester, New York, USA
| | - Emily Symes
- Department of Pathology, The University of Chicago Medicine, Chicago, Illinois, USA
| | - Peng Wang
- Department of Pathology, The University of Chicago Medicine, Chicago, Illinois, USA
| | - Cole Miller
- Department of Pathology, University of Rochester Medical Center, Rochester, New York, USA
| | - Stephanie C Thompson
- Department of Pathology, University of Rochester Medical Center, Rochester, New York, USA
| | - Tatjana Antic
- Department of Pathology, The University of Chicago Medicine, Chicago, Illinois, USA
| | - Anna Biernacka
- Department of Pathology, The University of Chicago Medicine, Chicago, Illinois, USA
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18
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Bedeir A, Ghani H, Oster C, Crymes A, Ibe I, Yamamoto M, Elliott A, Bryant DA, Oberley MJ, Evans MG. Detection of human papillomavirus (HPV) in malignant melanoma. Ann Diagn Pathol 2024; 73:152361. [PMID: 39032381 DOI: 10.1016/j.anndiagpath.2024.152361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 07/12/2024] [Accepted: 07/15/2024] [Indexed: 07/23/2024]
Abstract
The most common type of melanoma is cutaneous melanoma (CM). The predominant mutational signature is that of ultraviolet radiation (UVR) exposure. The Cancer Genome Atlas (TCGA) molecular classification includes four major subtypes of CM based on common genetic alterations involving the following genes: BRAF, NRAS, and NF1, with a small fraction being "triple" wild-type. The two main signaling pathway abnormalities in CM are the mitogen-activated protein kinase (MAPK) pathway and the phosphoinositol-3-kinase (PI3K) pathway. Other less common types include mucosal melanomas (MM) and uveal melanoma (UM), which have a significantly different genomic landscape. Although few studies reported rare cases with HPV-positive (HPV+) melanoma, the clinicopathological and molecular characteristic of this entity has not been well-described. Among the 2084 melanoma cases queried at our institution, we identified seven patients diagnosed with HPV+ melanoma (prevalence 0.03 %), including five instances of CM and two of MM. The majority of cases were positive for HPV16 (n = 6). Most of the patients were elderly and with advanced disease (n = 6), although this finding may be attributed to the relative frequency of our institution testing advanced-stage tumors. Histologically, most cases showed high degree of pleomorphism and high mitotic count (5 or more mitoses/mm2) (n = 6). UVR signature was present in the CM, but not in the MM cases. Alterations in either MAPK and/or PI3K pathways were detected in the majority of cases (n = 6). The most common genetic abnormalities detected in this study occurred in the TERT promoter (TERTp) (n = 5), a finding that has been reported to be associated with aggressive disease. Our data shows that while HPV+ melanoma is rare, identifying this disease entity could help guide therapy given the demonstrated genomic alterations.
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Affiliation(s)
- Adam Bedeir
- Basis Phoenix High School, Phoenix, AZ, United States of America
| | - Hassan Ghani
- Caris Life Sciences, Phoenix, AZ, United States of America
| | - Cyrus Oster
- Caris Life Sciences, Phoenix, AZ, United States of America
| | - Anthony Crymes
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
| | - Ifegwu Ibe
- University of California Irvine School of Medicine, Irvine, CA, United States of America
| | - Maki Yamamoto
- University of California Irvine School of Medicine, Irvine, CA, United States of America
| | - Andrew Elliott
- Caris Life Sciences, Phoenix, AZ, United States of America
| | - David A Bryant
- Caris Life Sciences, Phoenix, AZ, United States of America
| | | | - Mark G Evans
- Caris Life Sciences, Phoenix, AZ, United States of America.
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19
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Liao X, Schmidt AL, Zhang D, Li P, Wang X, Ko HM, Choi WT, Alpert L, Hao Y, Kovar-Peltz S, Polydorides AD, Wanjari P, Mastro J, Wang P. Clinicopathologic and Molecular Characterization of Inflammatory Bowel Disease-Associated Neuroendocrine Carcinomas and Mixed Neuroendocrine-Non-Neuroendocrine Neoplasms. Mod Pathol 2024:100566. [PMID: 39025404 DOI: 10.1016/j.modpat.2024.100566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 06/27/2024] [Accepted: 07/11/2024] [Indexed: 07/20/2024]
Abstract
The pathogenesis of neuroendocrine carcinoma (NEC) and mixed neuroendocrine-non-neuroendocrine neoplasms (MiNEN) in the gastrointestinal tract remains poorly understood. This study seeks to characterize the clinicopathologic and molecular features of NEC/MiNEN in patients with inflammatory bowel disease (IBD). Eighteen surgically resected IBD-associated intestinal carcinomas with a minimum of 30% neuroendocrine component were collected from 6 academic centers and compared to a control group of 12 IBD-associated carcinomas lacking neuroendocrine differentiation. Both groups exhibited a male predominance and similar age distribution. The NEC/MiNEN group was more likely to have a higher percentage of Crohn's disease (9/18 vs. 1/12, P=0.024), occur in the rectum (9/18 vs. 3/12) and small intestine (4/18 vs. 0/12) (P<0.01), be diagnosed on resection without a preceding biopsy (6/18 vs. 0/12, P=0.057), and have unidentifiable precursor lesions (10/18 vs. 1/12, P=0.018) than the control group. Synchronous carcinoma, advanced tumor stage (pT3 and pT4), and lymph node metastasis occurred at similar rates; however, the NEC/MiNEN group had a higher incidence of angiovascular invasion (14/18 vs. 4/12, P=0.024), distant metastasis (8/18 vs. 1/12, P=0.049), mortality (8/18 vs. 2/12, P=0.058), and worse survival (Kaplan-Meier, P=0.023) than the control group. All tested cases were mismatch repair proficient. A Ki-67 proliferation index ranged from 25% to 100%. Next-generation sequencing in 11 NEC/MiNEN cases revealed low tumor mutational burdens but complex genetic abnormalities commonly involving TP53 (9/11, 82%), FBXW7 (4/11, 36%), and APC (3/11, 27%), with the other genetic alterations randomly occurring in one or two cases. The neuroendocrine component, which shared similar molecular alterations as the non-neuroendocrine component, was subcategorized into intermediate (G3a)- and high-grade (G3b); the higher-grade correlated with more genetic alterations. In conclusion, IBD-associated NEC/MiNEN shows diverse histologic features, variable precursor lesions, intricate genetic abnormalities, and aggressive biologic behavior. The classification and grading of GI-NEC/MiNEN may be refined for better clinical management.
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Affiliation(s)
- Xiaoyan Liao
- University of Rochester Medical Center, Rochester, NY.
| | | | | | - Peizi Li
- Icahn School of Medicine at Mount Sinai, New York, NY
| | - Xintong Wang
- Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Won-Tak Choi
- University of California San Francisco, San Francisco, CA
| | | | - Yansheng Hao
- University of Rochester Medical Center, Rochester, NY
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20
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Fang X, Ma M, Rong W, Lian YY, Wu X, Gao Y, Li HP, Sheng X. Exome sequencing confirms the clinical diagnosis of both joubert syndrome and klinefelter syndrome with keratoconus in a han Chinese family. Front Genet 2024; 15:1417584. [PMID: 39076169 PMCID: PMC11284097 DOI: 10.3389/fgene.2024.1417584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 06/26/2024] [Indexed: 07/31/2024] Open
Abstract
Introduction Joubert syndrome a rare genetic disorder, is characterized by abnormalities in the development of the central nervous system with "molar signs" on magnetic resonance imaging of the brain and accompanied by cerebellar vermis hypoplasia, ataxia, hypotonia, and developmental delay. Keratoconus (KC) is a kind of genetically predisposed eye disease that causes blindness characterized by a dilated thinning of the central or paracentral cornea conically projected forward, highly irregular astigmatism, and severe visual impairment. Klinefelter syndrome is caused by an extra X chromosome in the cells of male patients, and the main phenotype is tall stature and dysplasia with secondary sex characteristics. This study was intended to identify the genetic etiology and determine the clinical diagnosis of one Han Chinese family with specific clinical manifestations of keratoconus and multiorgan involvement. Methods A comprehensive ocular and related general examination was performed on one patient and his asymptomatic parents and brother. Pathogenic genes were tested by exome sequencing. CNV-seq was used to verify the copy number variation, and peripheral blood was cultured for karyotype analysis. The pathogenicity of the identified variant was determined subject to ACMG guidelines. The Gene Expression Omnibus (GEO) dataset of keratoconus-related genes in the NCBI database was obtained to analyze the differentially expressed genes in corneal tissues of the keratoconus group and the normal control group, and analysis of protein-protein interaction networks (PPI) was performed. Results Proband, a 25-year-old male, had sudden loss of vision in the left eye for 1 week. Best corrected visual acuity (BCVA): 0.5 (-1.00DS/-5.00DC*29°) in the right eye, counting fingers/40 cm in the left eye. Slit-lamp microscopy of the right eye showed mild anterior protrusion of the cornea and thinning of the cone-topped cornea. The left eye showed marked thinning of the central region of the cornea, rounded edema in the form of a cone-like bulge, epithelial bullae, edema and turbidity of the stroma, and bulging of the Descemet's membrane. Cranial magnetic resonance imaging (MRI) revealed changes in the midbrain and cerebellum, with a "molar sign" and a "bat-winged" ventriculus quartus cerebri. General check-up: 168 cm in height, decreased muscle tone in all four limbs, knee jerk elicited, negative Babinski sign, abdominal reflexes elicited, finger-to-nose test positive, intentional tremor evident in both hands, positive Romberg's sign, instability of gait, level I intellectual disability, poor adaptive behavior, communication disorders, teeth all dentures, a peculiar face with blepharophimosis, wide inner canthus distance, mild ptosis, severe positive epicanthus, high palatal arches, exotropia, hypotrichosis of beard and face, inconspicuous prominentia laryngea, and short upper and lower limbs. Exome sequencing detected compound heterozygous frameshift variants M1:c.9279dup:p.His3094Thrfs*18 and M2:c.6515_6522del:p.Lys2172Thrfs*37 in the patient's CPLANE1 gene and the presence of duplication-type CNV on the X chromosome. Sanger sequencing showed that the mother and father carried the M1 and M2 variants, respectively, and the younger brother carried the M2 variant, which was a novel variant. CNV-seq analysis showed the presence of a duplication-type CNV Xp22.33-Xq28 (2757837-156030895) of approximately 155 Mb on the X chromosome of the proband, which was a de novo variant and carried by neither of the parents. The two heterozygous frameshift variants and duplication-type CNV were pathogenic according to the ACMG guidelines. Differential expression analysis of keratoconus-related genes showed that CPLANE1 was upregulated in the corneal tissues of keratoconus patients compared with normal controls, and such a difference was statistically significant (p = 0.000515, <0.05). PPI analysis showed that the CPLANE1-NPHP3 complex protein acted as a bridge between cilia and extracellular matrix tissue. According to the genetic test results and clinical phenotype analysis, the family was finally diagnosed with Joubert syndrome combined with Keratoconus and Klinefelter syndrome. Discussion In this study, we report a proband in a Han Chinese family with both Joubert syndrome and X-linked Klinefelter syndrome as well as keratoconus, and the phenotype spectrum of CPLANE1-Joubert syndrome may be expanded accordingly. Meanwhile, the significance of exome sequencing was emphasized in aiding the clinical diagnosis of complex cases, which is difficult to make.
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Affiliation(s)
- Xinhe Fang
- Ningxia Eye Hospital, People’s Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | - Meijiao Ma
- Gansu Aier Ophthalmology and Optometry Hospital, Lanzhou, China
| | - Weining Rong
- Ningxia Eye Hospital, People’s Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | - Yuan-Yuan Lian
- Gansu Aier Ophthalmology and Optometry Hospital, Lanzhou, China
| | - Xueli Wu
- Gansu Aier Ophthalmology and Optometry Hospital, Lanzhou, China
| | - Yongying Gao
- Ningxia Eye Hospital, People’s Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | - Hui-Ping Li
- Ningxia Eye Hospital, People’s Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | - Xunlun Sheng
- Gansu Aier Ophthalmology and Optometry Hospital, Lanzhou, China
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21
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Geng Z, Wafula E, Corbett RJ, Zhang Y, Jin R, Gaonkar KS, Shukla S, Rathi KS, Hill D, Lahiri A, Miller DP, Sickler A, Keith K, Blackden C, Chroni A, Brown MA, Kraya AA, Koschmann CJ, Aldape K, Huang X, Rood BR, Mason JL, Trooskin GR, Abdullaev Z, Wang P, Zhu Y, Farrow BK, Farrel A, Dybas JM, Zhong C, Kuren NV, Zhang B, Santi M, Phul S, Chinwalla AT, Resnick AC, Diskin SJ, Tasian S, Stefankiewicz S, Maris JM, Ennis BM, Lueder MR, Naqvi AS, Coleman N, Ma W, Taylor D, Rokita JL. The Open Pediatric Cancer Project. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.09.599086. [PMID: 39026781 PMCID: PMC11257555 DOI: 10.1101/2024.07.09.599086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Background In 2019, the Open Pediatric Brain Tumor Atlas (OpenPBTA) was created as a global, collaborative open-science initiative to genomically characterize 1,074 pediatric brain tumors and 22 patient-derived cell lines. Here, we extend the OpenPBTA to create the Open Pediatric Cancer (OpenPedCan) Project, a harmonized open-source multi-omic dataset from 6,112 pediatric cancer patients with 7,096 tumor events across more than 100 histologies. Combined with RNA-Seq from the Genotype-Tissue Expression (GTEx) and The Cancer Genome Atlas (TCGA), OpenPedCan contains nearly 48,000 total biospecimens (24,002 tumor and 23,893 normal specimens). Findings We utilized Gabriella Miller Kids First (GMKF) workflows to harmonize WGS, WXS, RNA-seq, and Targeted Sequencing datasets to include somatic SNVs, InDels, CNVs, SVs, RNA expression, fusions, and splice variants. We integrated summarized CPTAC whole cell proteomics and phospho-proteomics data, miRNA-Seq data, and have developed a methylation array harmonization workflow to include m-values, beta-vales, and copy number calls. OpenPedCan contains reproducible, dockerized workflows in GitHub, CAVATICA, and Amazon Web Services (AWS) to deliver harmonized and processed data from over 60 scalable modules which can be leveraged both locally and on AWS. The processed data are released in a versioned manner and accessible through CAVATICA or AWS S3 download (from GitHub), and queryable through PedcBioPortal and the NCI's pediatric Molecular Targets Platform. Notably, we have expanded PBTA molecular subtyping to include methylation information to align with the WHO 2021 Central Nervous System Tumor classifications, allowing us to create research- grade integrated diagnoses for these tumors. Conclusions OpenPedCan data and its reproducible analysis module framework are openly available and can be utilized and/or adapted by researchers to accelerate discovery, validation, and clinical translation.
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Affiliation(s)
- Zhuangzhuang Geng
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Eric Wafula
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Ryan J Corbett
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Yuanchao Zhang
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Run Jin
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Krutika S Gaonkar
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Sangeeta Shukla
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Komal S Rathi
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Dave Hill
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Aditya Lahiri
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Daniel P Miller
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Alex Sickler
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Kelsey Keith
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Christopher Blackden
- Center for Data- Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Antonia Chroni
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Miguel A Brown
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Adam A Kraya
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Carl J Koschmann
- Department of Pediatrics, University of Michigan Health, Ann Arbor, MI, 48105, USA; Pediatric Hematology Oncology, Mott Children's Hospital, Ann Arbor, MI, 48109, USA
| | - Kenneth Aldape
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Xiaoyan Huang
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Brian R Rood
- Children's National Research Institute, Washington, D.C.; George Washington University School of Medicine and Health Sciences, Washington, D.C., 20052, USA
| | - Jennifer L Mason
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Gerri R Trooskin
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Zied Abdullaev
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yuankun Zhu
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Bailey K Farrow
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Alvin Farrel
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA · Funded by NCI/NIH Contract No. 75N91019D00024, Task Order No. 75N91020F00003
| | - Joseph M Dybas
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Chuwei Zhong
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Nicholas Van Kuren
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Bo Zhang
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Mariarita Santi
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Saksham Phul
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Asif T Chinwalla
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Adam C Resnick
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA · Funded by Children's Brain Tumor Network; NIH 3P30 CA016520- 44S5, U2C HL138346-03, U24 CA220457-03; NCI/NIH Contract No. 75N91019D00024, Task Order No. 75N91020F00003; Children's Hospital of Philadelphia Division of Neurosurgery
| | - Sharon J Diskin
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Department of Pediatrics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sarah Tasian
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Department of Pediatrics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Stephanie Stefankiewicz
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - John M Maris
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Department of Pediatrics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Brian M Ennis
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Matthew R Lueder
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Ammar S Naqvi
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Noel Coleman
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Weiping Ma
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Deanne Taylor
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Department of Pediatrics, University of Pennsylvania Perelman Medical School, Philadelphia, PA, 19104, USA · Funded by NCI/NIH Contract No. 75N91019D00024, Task Order No. 75N91020F00003
| | - Jo Lynne Rokita
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA · Funded by NCI/NIH Contract No. 75N91019D00024, Task Order No. 75N91020F00003
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22
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Zhang H, Liu B, Cheng J, Li Z, Jia M, Li M, Zhao L, Wang L, Xi Y. Characterization and integrated analysis of extrachromosomal DNA amplification in hematological malignancies. Neoplasia 2024; 56:101025. [PMID: 38996538 DOI: 10.1016/j.neo.2024.101025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 07/03/2024] [Indexed: 07/14/2024]
Abstract
The study of extrachromosomal DNA (ecDNA), an element existing beyond classical chromosomes, contributes to creating a more comprehensive map of the cancer genome. In hematological malignancies, research on ecDNA has lacked comprehensive investigation into its frequency, structure, function, and mechanisms of formation. We re-analyzed WGS data from 208 hematological cancer samples across 11 types, focusing on ecDNA characteristics. Amplification of ecDNA was observed in 7 of these cancer types, with no instances found in normal blood cells. Patients with leukemia carrying ecDNA showed a low induction therapy remission rate (<30 %), a high relapse rate (75 %) among those who achieved complete remission, and a significantly lower survival rate compared to the general leukemia population, even those with complex chromosomal karyotypes. Among the 55 identified ecDNA amplicons, 268 genes were detected, of which 38 are known cancer-related genes exhibiting significantly increased copy numbers. By integrating RNA-Seq data, we discovered that the increased copy number, resulting in a higher amount of available DNA templates, indeed leads to the elevated expression of genes encoded on ecDNA. Additionally, through the integration of H3K4me3/H3K27ac chromatin immunoprecipitation sequencing, assay for transposase-accessible chromatin with sequencing, and high-throughput chromosome conformation capture data, we identified that ecDNA amplifications can also facilitate efficient, copy number-independent amplification of oncogenes. This process is linked to active histone modifications, improved chromatin accessibility, and enhancer hijacking, all of which are effects of ecDNA amplification. Mechanistically, chromothripsis and dysfunction of the DNA repair pathway can, to some extent, explain the origin of ecDNA.
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Affiliation(s)
- Hao Zhang
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China
| | - Bei Liu
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China
| | - Juan Cheng
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China
| | - Zijian Li
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China
| | - Mingfeng Jia
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China
| | - Ming Li
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China
| | - Long Zhao
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China
| | - Lina Wang
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China
| | - Yaming Xi
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China.
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23
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Wang X, Wu X, Tan B, Zhu L, Zhang Y, Lin L, Xiao Y, Sun A, Wan X, Liu S, Liu Y, Ta N, Zhang H, Song J, Li T, Zhou L, Yin J, Ye L, Lu H, Hong J, Cheng H, Wang P, Li W, Chen J, Zhang J, Luo J, Huang M, Guo L, Pan X, Jin Y, Ye W, Dai L, Zhu J, Sun L, Zheng B, Li D, He Y, Liu M, Wu H, Du B, Xu H. Allogeneic CD19-targeted CAR-T therapy in patients with severe myositis and systemic sclerosis. Cell 2024:S0092-8674(24)00701-3. [PMID: 39013470 DOI: 10.1016/j.cell.2024.06.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 04/28/2024] [Accepted: 06/20/2024] [Indexed: 07/18/2024]
Abstract
Allogeneic chimeric antigen receptor (CAR)-T cells hold great promise for expanding the accessibility of CAR-T therapy, whereas the risks of allograft rejection have hampered its application. Here, we genetically engineered healthy-donor-derived, CD19-targeting CAR-T cells using CRISPR-Cas9 to address the issue of immune rejection and treated one patient with refractory immune-mediated necrotizing myopathy and two patients with diffuse cutaneous systemic sclerosis with these cells. This study was registered at ClinicalTrials.gov (NCT05859997). The infused cells persisted for over 3 months, achieving complete B cell depletion within 2 weeks of treatment. During the 6-month follow-up, we observed deep remission without cytokine release syndrome or other serious adverse events in all three patients, primarily shown by the significant improvement in the clinical response index scores for the two diseases, respectively, and supported by the observations of reversal of inflammation and fibrosis. Our results demonstrate the high safety and promising immune modulatory effect of the off-the-shelf CAR-T cells in treating severe refractory autoimmune diseases.
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Affiliation(s)
- Xiaobing Wang
- Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, Naval Medical University, Shanghai 200003, China; National Key Laboratory for Immunity and Inflammation, Shanghai, China
| | - Xin Wu
- Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, Naval Medical University, Shanghai 200003, China; National Key Laboratory for Immunity and Inflammation, Shanghai, China
| | - Binghe Tan
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences, East China Normal University, Shanghai 200241, China; BRL Medicine Inc., Shanghai 201109, China
| | - Liang Zhu
- Department of Rheumatology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Yi Zhang
- Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, Naval Medical University, Shanghai 200003, China
| | - Li Lin
- Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, Naval Medical University, Shanghai 200003, China; National Key Laboratory for Immunity and Inflammation, Shanghai, China
| | - Yi Xiao
- Department of Radiology, Shanghai Changzheng Hospital, Naval Medical University, Shanghai 200003, China
| | - An Sun
- Department of Radiology, Shanghai Changzheng Hospital, Naval Medical University, Shanghai 200003, China
| | - Xinyi Wan
- Department of Radiology, Shanghai Changzheng Hospital, Naval Medical University, Shanghai 200003, China
| | - Shiyuan Liu
- Department of Radiology, Shanghai Changzheng Hospital, Naval Medical University, Shanghai 200003, China
| | - Yanfang Liu
- National Key Laboratory for Immunity and Inflammation, Shanghai, China; Department of Pathology, Shanghai Changhai Hospital, Naval Medical University, Shanghai 200082, China
| | - Na Ta
- Department of Pathology, Shanghai Changhai Hospital, Naval Medical University, Shanghai 200082, China
| | - Hang Zhang
- Department of Ultrasound, Shanghai Changzheng Hospital, Naval Medical University, Shanghai 200003, China
| | - Jialin Song
- Department of Ultrasound, Shanghai Changzheng Hospital, Naval Medical University, Shanghai 200003, China
| | - Ting Li
- Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, Naval Medical University, Shanghai 200003, China
| | - Ling Zhou
- Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, Naval Medical University, Shanghai 200003, China
| | - Jian Yin
- Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, Naval Medical University, Shanghai 200003, China
| | - Lingying Ye
- Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, Naval Medical University, Shanghai 200003, China
| | - Hongjuan Lu
- Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, Naval Medical University, Shanghai 200003, China
| | - Jinwei Hong
- Department of Rheumatology, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou 325035, China
| | - Hui Cheng
- Department of Rheumatology, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou 325035, China
| | - Ping Wang
- Department of Rheumatology, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou 325035, China
| | - Weiqing Li
- Department of Pathology, Shanghai Changzheng Hospital, Naval Medical University, Shanghai 200003, China
| | - Jianfeng Chen
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jin Zhang
- Department of Rheumatology and Clinical Immunology, Ningbo Medical Center Lihuili Hospital, Ningbo, Zhejiang 315040, China
| | - Jing Luo
- School of Medicine, Tsinghua University, Beijing 100084, China
| | - Miaozhen Huang
- School of Medicine, Tsinghua University, Beijing 100084, China
| | - Lehang Guo
- Department of Medical Ultrasound, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200072, China
| | - Xiaoming Pan
- Department of Cardiology, Shanghai Changzheng Hospital, Naval Medical University, Shanghai 200003, China
| | - Yi Jin
- Department of Dermatology, Shanghai Changzheng Hospital, Naval Medical University, Shanghai Key Laboratory of Medical Mycology, Shanghai 200082, China
| | - Wenjing Ye
- Department of Rheumatology and Immunology, Shanghai Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Lie Dai
- Department of Rheumatology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Jian Zhu
- Department of Rheumatology and Immunology, The First Medical Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Lingyun Sun
- Department of Rheumatology and Immunology, The Affiliated Drum Tower Hospital, Nanjing University Medical School, Nanjing 210008, China
| | - Biao Zheng
- BRL Medicine Inc., Shanghai 201109, China
| | - Dali Li
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences, East China Normal University, Shanghai 200241, China; BRL Medicine Inc., Shanghai 201109, China
| | - Yanran He
- Committee on Cancer Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Mingyao Liu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences, East China Normal University, Shanghai 200241, China; BRL Medicine Inc., Shanghai 201109, China.
| | - Huaxiang Wu
- Department of Rheumatology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China.
| | - Bing Du
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences, East China Normal University, Shanghai 200241, China; BRL Medicine Inc., Shanghai 201109, China.
| | - Huji Xu
- Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, Naval Medical University, Shanghai 200003, China; National Key Laboratory for Immunity and Inflammation, Shanghai, China; School of Medicine, Tsinghua University, Beijing 100084, China; Peking-Tsinghua Center for Life Sciences, Tsinghua University, Beijing 100084, China.
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24
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Mulet-Lazaro R, van Herk S, Nuetzel M, Sijs-Szabo A, Díaz N, Kelly K, Erpelinck-Verschueren C, Schwarzfischer-Pfeilschifter L, Stanewsky H, Ackermann U, Glatz D, Raithel J, Fischer A, Pohl S, Rijneveld A, Vaquerizas JM, Thiede C, Plass C, Wouters BJ, Delwel R, Rehli M, Gebhard C. Epigenetic alterations affecting hematopoietic regulatory networks as drivers of mixed myeloid/lymphoid leukemia. Nat Commun 2024; 15:5693. [PMID: 38972954 PMCID: PMC11228033 DOI: 10.1038/s41467-024-49811-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 06/19/2024] [Indexed: 07/09/2024] Open
Abstract
Leukemias with ambiguous lineage comprise several loosely defined entities, often without a clear mechanistic basis. Here, we extensively profile the epigenome and transcriptome of a subgroup of such leukemias with CpG Island Methylator Phenotype. These leukemias exhibit comparable hybrid myeloid/lymphoid epigenetic landscapes, yet heterogeneous genetic alterations, suggesting they are defined by their shared epigenetic profile rather than common genetic lesions. Gene expression enrichment reveals similarity with early T-cell precursor acute lymphoblastic leukemia and a lymphoid progenitor cell of origin. In line with this, integration of differential DNA methylation and gene expression shows widespread silencing of myeloid transcription factors. Moreover, binding sites for hematopoietic transcription factors, including CEBPA, SPI1 and LEF1, are uniquely inaccessible in these leukemias. Hypermethylation also results in loss of CTCF binding, accompanied by changes in chromatin interactions involving key transcription factors. In conclusion, epigenetic dysregulation, and not genetic lesions, explains the mixed phenotype of this group of leukemias with ambiguous lineage. The data collected here constitute a useful and comprehensive epigenomic reference for subsequent studies of acute myeloid leukemias, T-cell acute lymphoblastic leukemias and mixed-phenotype leukemias.
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Affiliation(s)
- Roger Mulet-Lazaro
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Stanley van Herk
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Margit Nuetzel
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Aniko Sijs-Szabo
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Noelia Díaz
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany
- Renewable Marine Resources Department, Institute of Marine Sciences (ICM-CSIC), Barcelona, Spain
| | - Katherine Kelly
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Claudia Erpelinck-Verschueren
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | | | - Hanna Stanewsky
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Ute Ackermann
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Dagmar Glatz
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Johanna Raithel
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Alexander Fischer
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Sandra Pohl
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
- Department of Conservative Dentistry and Periodontology, University Hospital Regensburg, Regensburg, Germany
| | - Anita Rijneveld
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Juan M Vaquerizas
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany
- MRC London Institute of Medical Sciences, London, United Kingdom
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital 8 Campus, London, United Kingdom
| | - Christian Thiede
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus, Dresden, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bas J Wouters
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands.
- Oncode Institute, Utrecht, the Netherlands.
| | - Ruud Delwel
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands.
- Oncode Institute, Utrecht, the Netherlands.
| | - Michael Rehli
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany.
- Leibniz Institute for Immunotherapy (LIT), Regensburg, Germany.
| | - Claudia Gebhard
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany.
- Leibniz Institute for Immunotherapy (LIT), Regensburg, Germany.
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25
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Um JH, Zheng Y, Mao Q, Nam C, Zhao H, Koh YW, Shin SJ, Park YM, Lin DC. Genomic and single-cell characterization of patient-derived tumor organoid models of head and neck squamous cell carcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.28.601068. [PMID: 39005427 PMCID: PMC11244938 DOI: 10.1101/2024.06.28.601068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Head and Neck Squamous Cell Carcinoma (HNSCC) remains a significant health burden due to tumor heterogeneity and treatment resistance, emphasizing the need for improved biological understanding and tailored therapies. This study enrolled 31 HNSCC patients for the establishment of patient-derived tumor organoids (PDOs), which faithfully maintained genomic features and histopathological traits of primary tumors. Long-term culture preserved key characteristics, affirming PDOs as robust representative models. PDOs demonstrated predictive capability for cisplatin treatment responses, correlating ex vivo drug sensitivity with patient outcomes. Bulk and single-cell RNA sequencing unveiled molecular subtypes and intratumor heterogeneity (ITH) in PDOs, paralleling patient tumors. Notably, a hybrid epithelial-mesenchymal transition (hEMT)-like ITH program is associated with cisplatin resistance and poor patient survival. Functional analyses identified amphiregulin (AREG) as a potential regulator of the hybrid epithelial/mesenchymal state. Moreover, AREG contributes to cisplatin resistance via EGFR pathway activation, corroborated by clinical samples. In summary, HNSCC PDOs serve as reliable and versatile models, offer predictive insights into ITH programs and treatment responses, and uncover potential therapeutic targets for personalized medicine.
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Affiliation(s)
- Jung Hyun Um
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Korea
| | - Yueyuan Zheng
- Clinical Big Data Research Center, Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, P.R. China
| | - Qiong Mao
- Clinical Big Data Research Center, Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, P.R. China
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, Guangzhou Medical University, Guangzhou, 510120, P.R. China
| | - Chehyun Nam
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, USA
| | - Hua Zhao
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, USA
| | - Yoon Woo Koh
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Korea
| | - Su-Jin Shin
- Department of Pathology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Young Min Park
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Korea
| | - De-Chen Lin
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, USA
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26
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Nakazawa MS, Silverman IM, Rimkunas V, Veloso A, Glodzik D, Johnson A, Ohsumi TK, Patel SR, Conley AP, Roland CL, Soliman PT, Beird HC, Wu CC, Ingram DR, Lazcano R, Song D, Wani KM, Lazar AJ, Yap TA, Wang WL, Livingston JA. Loss of the DNA Repair Gene RNase H2 Identifies a Unique Subset of DDR-Deficient Leiomyosarcomas. Mol Cancer Ther 2024; 23:1057-1065. [PMID: 38561019 DOI: 10.1158/1535-7163.mct-23-0761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 01/26/2024] [Accepted: 03/29/2024] [Indexed: 04/04/2024]
Abstract
Targeting the DNA damage response (DDR) pathway is an emerging therapeutic approach for leiomyosarcoma (LMS), and loss of RNase H2, a DDR pathway member, is a potentially actionable alteration for DDR-targeted treatments. Therefore, we designed a protein- and genomic-based RNase H2 screening assay to determine its prevalence and prognostic significance. Using a selective RNase H2 antibody on a pan-tumor microarray (TMA), RNase H2 loss was more common in LMS (11.5%, 9/78) than across all tumors (3.8%, 32/843). In a separate LMS cohort, RNase H2 deficiency was confirmed in uterine LMS (U-LMS, 21%, 23/108) and soft-tissue LMS (ST-LMS; 30%, 39/102). In the TCGA database, RNASEH2B homozygous deletions (HomDels) were found in 6% (5/80) of LMS cases, with a higher proportion in U-LMS (15%; 4/27) compared with ST-LMS (2%; 1/53). Using the SNiPDx targeted-NGS sequencing assay to detect biallelic loss of function in select DDR-related genes, we found RNASEH2B HomDels in 54% (19/35) of U-LMS cases with RNase H2 loss by IHC, and 7% (3/43) HomDels in RNase H2 intact cases. No RNASEH2B HomDels were detected in ST-LMS. In U-LMS patient cohort (n = 109), no significant overall survival difference was seen in patients with RNase H2 loss versus intact, or RNASEH2B HomDel (n = 12) versus Non-HomDel (n = 37). The overall diagnostic accuracy, sensitivity, and specificity of RNase H2 IHC for detecting RNA-SEH2B HomDels in U-LMS was 76%, 93%, and 71%, respectively, and it is being developed for future predictive biomarker driven clinical trials targeting DDR in U-LMS.
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Affiliation(s)
- Michael S Nakazawa
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | | | | | | | | | - Shreyaskumar R Patel
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Anthony P Conley
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Christina L Roland
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Pamela T Soliman
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hannah C Beird
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chia-Chin Wu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Davis R Ingram
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rossana Lazcano
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Dawon Song
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Khalida M Wani
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Alexander J Lazar
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Timothy A Yap
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Wei-Lien Wang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - J Andrew Livingston
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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27
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Purshouse K, Pollard SM, Bickmore WA. Imaging extrachromosomal DNA (ecDNA) in cancer. Histochem Cell Biol 2024; 162:53-64. [PMID: 38625562 PMCID: PMC7616135 DOI: 10.1007/s00418-024-02280-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/19/2024] [Indexed: 04/17/2024]
Abstract
Extrachromosomal DNA (ecDNA) are circular regions of DNA that are found in many cancers. They are an important means of oncogene amplification, and correlate with treatment resistance and poor prognosis. Consequently, there is great interest in exploring and targeting ecDNA vulnerabilities as potential new therapeutic targets for cancer treatment. However, the biological significance of ecDNA and their associated regulatory control remains unclear. Light microscopy has been a central tool in the identification and characterisation of ecDNA. In this review we describe the different cellular models available to study ecDNA, and the imaging tools used to characterise ecDNA and their regulation. The insights gained from quantitative imaging are discussed in comparison with genome sequencing and computational approaches. We suggest that there is a crucial need for ongoing innovation using imaging if we are to achieve a full understanding of the dynamic regulation and organisation of ecDNA and their role in tumourigenesis.
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Affiliation(s)
- Karin Purshouse
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Centre for Regenerative Medicine, Institute for Regeneration and Repair & Cancer Research UK Scotland Centre, University of Edinburgh, Edinburgh, UK
- Edinburgh Cancer Research UK Centre, University of Edinburgh, Edinburgh, UK
| | - Steven M Pollard
- Centre for Regenerative Medicine, Institute for Regeneration and Repair & Cancer Research UK Scotland Centre, University of Edinburgh, Edinburgh, UK
- Edinburgh Cancer Research UK Centre, University of Edinburgh, Edinburgh, UK
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
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28
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Palathingal Bava E, Sanfrancesco JM, Alkashash A, Favazza L, Aldilami A, Williamson SR, Cheng L, Idrees MT, Al-Obaidy KI. Acquired cystic disease associated renal cell carcinoma: A clinicopathologic and molecular study of 31 tumors. Hum Pathol 2024; 149:48-54. [PMID: 38862094 DOI: 10.1016/j.humpath.2024.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/31/2024] [Accepted: 06/08/2024] [Indexed: 06/13/2024]
Abstract
Acquired cystic disease associated renal cell carcinomas (ACD-RCC) are rare and their molecular and histopathological characteristics are still being explored. We therefore investigated the clinicopathologic and molecular characteristics of 31 tumors. The patients were predominantly male (n = 30), with tumors mainly left-sided (n = 17), unifocal (n = 19), and unilateral (n = 29) and a mean tumor size of 25 mm (range, 3-65 mm). Microscopically, several histologic patterns were present, including pure classic sieve-like (n = 4), and varied proportions of mixed classic sieve-like with papillary (n = 23), tubulocystic (n = 9), compact tubular (n = 4) and solid (n = 1) patterns. Calcium-oxalate crystals were seen in all tumors. Molecular analysis of 9 tumors using next generation sequencing showed alterations in SMARCB1 in 3 tumors (1 with frameshift deletion and 2 with copy number loss in chromosome 22 involving SMARCB1 region), however, INI1 stain was retained in all. Nonrecurrent genetic alterations in SETD2, NF1, NOTCH4, BRCA2 and CANT1 genes were also seen. Additionally, MTOR p.Pro351Ser was identified in one tumor. Copy number analysis showed gains in chromosome 16 (n = 5), 17 (n = 2) and 8 (n = 2) as well as loss in chromosome 22 (n = 2). In summary, ACD-RCC is a recognized subtype of kidney tumors, with several histological architectural patterns. Our molecular data identifies genetic alterations in chromatin modifying genes (SMARCB1 and SETD2), which may suggest a role of such genes in ACD-RCC development.
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Affiliation(s)
- Ejas Palathingal Bava
- Department of Pathology and Laboratory Medicine, Henry Ford Health, Detroit, MI, USA.
| | | | - Ahmed Alkashash
- Department of Pathology and Laboratory Medicine, Indiana University, Indianapolis, IN, USA.
| | - Laura Favazza
- Department of Pathology and Laboratory Medicine, Henry Ford Health, Detroit, MI, USA.
| | - Akram Aldilami
- Department of Neurology, Henry Ford Health, Detroit, MI, USA.
| | - Sean R Williamson
- Pathology and Laboratory Medicine Institute, The Cleveland Clinic, Cleveland, OH, USA.
| | - Liang Cheng
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School of Brown University, Providence, RI, USA.
| | - Mohammed T Idrees
- Department of Pathology and Laboratory Medicine, Indiana University, Indianapolis, IN, USA.
| | - Khaleel I Al-Obaidy
- Department of Pathology and Laboratory Medicine, Henry Ford Health, Detroit, MI, USA; Department of Medicine, College of Human Medicine, Michigan State University, East Lansing, MI, USA.
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29
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Schupp PG, Shelton SJ, Brody DJ, Eliscu R, Johnson BE, Mazor T, Kelley KW, Potts MB, McDermott MW, Huang EJ, Lim DA, Pieper RO, Berger MS, Costello JF, Phillips JJ, Oldham MC. Deconstructing Intratumoral Heterogeneity through Multiomic and Multiscale Analysis of Serial Sections. Cancers (Basel) 2024; 16:2429. [PMID: 39001492 PMCID: PMC11240479 DOI: 10.3390/cancers16132429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Revised: 06/27/2024] [Accepted: 06/28/2024] [Indexed: 07/16/2024] Open
Abstract
Tumors may contain billions of cells, including distinct malignant clones and nonmalignant cell types. Clarifying the evolutionary histories, prevalence, and defining molecular features of these cells is essential for improving clinical outcomes, since intratumoral heterogeneity provides fuel for acquired resistance to targeted therapies. Here we present a statistically motivated strategy for deconstructing intratumoral heterogeneity through multiomic and multiscale analysis of serial tumor sections (MOMA). By combining deep sampling of IDH-mutant astrocytomas with integrative analysis of single-nucleotide variants, copy-number variants, and gene expression, we reconstruct and validate the phylogenies, spatial distributions, and transcriptional profiles of distinct malignant clones. By genotyping nuclei analyzed by single-nucleus RNA-seq for truncal mutations, we further show that commonly used algorithms for identifying cancer cells from single-cell transcriptomes may be inaccurate. We also demonstrate that correlating gene expression with tumor purity in bulk samples can reveal optimal markers of malignant cells and use this approach to identify a core set of genes that are consistently expressed by astrocytoma truncal clones, including AKR1C3, whose expression is associated with poor outcomes in several types of cancer. In summary, MOMA provides a robust and flexible strategy for precisely deconstructing intratumoral heterogeneity and clarifying the core molecular properties of distinct cellular populations in solid tumors.
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Affiliation(s)
- Patrick G. Schupp
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Samuel J. Shelton
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
| | - Daniel J. Brody
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
| | - Rebecca Eliscu
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
| | - Brett E. Johnson
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
| | - Tali Mazor
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kevin W. Kelley
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94143, USA
- Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Matthew B. Potts
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
| | - Michael W. McDermott
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
| | - Eric J. Huang
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA;
| | - Daniel A. Lim
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
| | - Russell O. Pieper
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
| | - Mitchel S. Berger
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
| | - Joseph F. Costello
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
| | - Joanna J. Phillips
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA;
| | - Michael C. Oldham
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
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Wang Q, Wang D, Qin T, Zhang X, Lin X, Chen J, Chen W, Zhao L, Huang W, Lin Z, Li J, Dongye M, Wu X, Wang X, Li X, Lin Y, Tan H, Liu Y, Lin H, Chen W. Early Diagnosis of Syndromic Congenital Cataracts in a Large Cohort of Congenital Cataracts. Am J Ophthalmol 2024; 263:206-213. [PMID: 38184101 DOI: 10.1016/j.ajo.2023.10.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 10/20/2023] [Accepted: 10/25/2023] [Indexed: 01/08/2024]
Abstract
PURPOSE To explore the factors related to the diagnosis yield of syndromic congenital cataracts and describe the phenotype-genotype correlation in congenital cataract patients. DESIGN Prospective cohort study. METHODS Setting: the participants from underwent clinical examinations between 2021 and 2022. Facial and anterior eye segment photographs, pre- and postoperative ocular parameters, and medical and family histories were recorded. Bioinformatics analysis was performed using whole-exome sequencing data. Statistical and correlation analyses were performed using the basic characteristics, deep phenotype, and genotype data. PARTICIPANTS 115 patients with unrelated congenital cataract. INTERVENTIONS performing clinical examinations, whole-exome sequencing, and bioinformatics analysis for all participants. MAIN OUTCOMES AND MEASURES factors related to the genetic diagnosis yield of syndromic congenital cataracts. RESULTS Bilaterally asymmetrical cataracts were identified to be associated with syndromic congenital cataracts. The overall genetic diagnostic yield in the cohort was 72.2%. In total, 34.8% of the probands were early diagnosed with various syndromes with the help of genetic information. A phenotype-genotype correlation was detected for some genes and deep phenotypes. CONCLUSIONS We highlight the importance of screening syndromic diseases in the patients with asymmetrical congenital cataracts. Application of whole-exome sequencing helps provide early diagnosis and treatment for the patients with syndromic congenital cataracts. This study also achieved a high genetic diagnostic yield, expanded the genotypic spectrum, and found phenotype-genotype correlations. A comprehensive analysis of cataract symmetricity, family history, and deep phenotypes makes the genotype prediction of some congenital cataract patients possible.
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Affiliation(s)
- Qiwei Wang
- From the State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Guangzhou, Guangdong Province, China
| | - Dongni Wang
- From the State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Guangzhou, Guangdong Province, China
| | - Tingfeng Qin
- From the State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Guangzhou, Guangdong Province, China
| | - Xulin Zhang
- From the State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Guangzhou, Guangdong Province, China
| | - Xiaoshan Lin
- From the State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Guangzhou, Guangdong Province, China
| | - Jingjing Chen
- From the State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Guangzhou, Guangdong Province, China
| | - Wan Chen
- From the State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Guangzhou, Guangdong Province, China
| | - Lanqin Zhao
- From the State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Guangzhou, Guangdong Province, China
| | - Weiming Huang
- From the State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Guangzhou, Guangdong Province, China
| | - Zhuoling Lin
- From the State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Guangzhou, Guangdong Province, China
| | - Jing Li
- From the State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Guangzhou, Guangdong Province, China
| | - Meimei Dongye
- From the State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Guangzhou, Guangdong Province, China
| | - Xiaohang Wu
- From the State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Guangzhou, Guangdong Province, China
| | - Xun Wang
- From the State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Guangzhou, Guangdong Province, China
| | - Xiaoyan Li
- From the State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Guangzhou, Guangdong Province, China
| | - Yongbin Lin
- From the State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Guangzhou, Guangdong Province, China
| | - Haowen Tan
- From the State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Guangzhou, Guangdong Province, China
| | - Yizhi Liu
- From the State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Guangzhou, Guangdong Province, China
| | - Haotian Lin
- From the State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Guangzhou, Guangdong Province, China.
| | - Weirong Chen
- From the State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Guangzhou, Guangdong Province, China.
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Devins KM, Ordulu Z, Mendoza RP, Croce S, Haridas R, Wanjari P, Pinto A, Oliva E, Bennett JA. Uterine Inflammatory Myofibroblastic Tumors: p16 as a Surrogate for CDKN2A Deletion and Predictor of Aggressive Behavior. Am J Surg Pathol 2024; 48:813-824. [PMID: 38630911 DOI: 10.1097/pas.0000000000002220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Uterine inflammatory myofibroblastic tumors (IMTs) are rare mesenchymal neoplasms of uncertain malignant potential. Aside from the recently described risk stratification score, which has not been validated by other studies, and rare reports of aberrant p16 expression in malignant tumors, there are no criteria to reliably predict behavior. Herein, we evaluated the clinicopathologic features and p16 expression patterns in 30 IMTs, with genomic profiling performed in a subset (13 malignant, 3 benign). Fifteen patients had malignant IMTs, defined by extrauterine disease at diagnosis (n=5) or recurrence (n=10; median: 24 mo). Patients ranged from 8 to 65 (median: 51) years and tumors from 6 to 22 (median: 12.5) cm. In primary tumors (n=13), infiltrative borders were noted in 10, moderate/severe cytologic atypia in 9, tumor cell necrosis in 7, and lymphovascular invasion in 6, while mitoses ranged from 0 to 21 (median: 7) per 10 high-power fields. In contrast, 15 patients with benign IMTs ranged from 28 to 65 (median: 44) years, with follow-up of 18 to 114 (median: 41) months. Tumors ranged from 1.9 to 8.5 (median: 5.5) cm, 2 demonstrated infiltrative borders, and 1 had moderate cytologic atypia. No other high-risk histologic features were observed. Application of the previously described clinicopathologic risk stratification score in all primary IMTs with complete data (n=18) classified 8 as high-risk (all malignant), 8 as intermediate-risk (3 malignant, 5 benign), and 2 as low-risk (benign). p16 was aberrant in all malignant IMTs, with <1% expression noted in 10, overexpression (>90%) in 4, and subclonal loss in 1; all benign tumors had patchy staining (20% to 80%; median 50%). Molecular analysis detected CDKN2A deletions in 8 of 9 tumors with <1% p16 expression, while the other harbored a TERT promoter mutation. TERT promoter mutations were also identified in 2 of 3 IMTs with p16 overexpression. Neither of these alterations was detected in the 3 sequenced benign IMTs. Thus, we recommend performing p16 on all uterine IMTs, which, combined with the risk stratification score, is a promising and cost-effective tool for predicting CDKN2A status and outcome in these patients. It may be particularly useful for tumors with incomplete information for risk stratification (ie, morcellated tumors) and for further stratifying intermediate-risk IMTs when sequencing is unavailable.
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Affiliation(s)
- Kyle M Devins
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Zehra Ordulu
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL
| | - Rachelle P Mendoza
- Department of Pathology and Laboratory Medicine, University of Rochester, Rochester, NY
| | - Sabrina Croce
- Department of Biopathology, Institut Bergonie, Bordeaux, France
| | | | | | - Andre Pinto
- Department of Pathology, University of Miami, Miami, FL
| | - Esther Oliva
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
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Guo W, Lu T, Song Y, Li A, Feng X, Han D, Cao Y, Sun D, Gong X, Li C, Jin R, Du H, Chen K, Xiang J, Hang J, Chen G, Li H. Lymph node metastasis in early invasive lung adenocarcinoma: Prediction model establishment and validation based on genomic profiling and clinicopathologic characteristics. Cancer Med 2024; 13:e70039. [PMID: 39046176 PMCID: PMC11267562 DOI: 10.1002/cam4.70039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 06/22/2024] [Accepted: 07/12/2024] [Indexed: 07/25/2024] Open
Abstract
BACKGROUND The presence of lymph node (LN) metastasis directly affects the treatment strategy for lung adenocarcinoma (LUAD). Next-generation sequencing (NGS) has been widely used in patients with advanced LUAD to identify targeted genes, while early detection of pathologic LN metastasis using NGS has not been assessed. METHODS Clinicopathologic features and molecular characteristics of 224 patients from Ruijin Hospital were analyzed to detect factors associated with LN metastases. Another 140 patients from Huashan Hospital were set as a test cohort. RESULTS Twenty-four out of 224 patients were found to have lymph node metastases (10.7%). Pathologic LN-positive tumors showed higher mutant allele tumor heterogeneity (p < 0.05), higher tumor mutation burden (p < 0.001), as well as more frequent KEAP1 (p = 0.001), STK11 (p = 0.004), KRAS (p = 0.007), CTNNB1 (p = 0.017), TP53, and ARID2 mutations (both p = 0.02); whereas low frequency of EGFR mutation (p = 0.005). A predictive nomogram involving male sex, solid tumor morphology, higher T stage, EGFR wild-type, and TP53, STK11, CDKN2A, KEAP1, ARID2, KRAS, SDHA, SPEN, CTNNB1, DICER1 mutations showed outstanding efficiency in both the training cohort (AUC = 0.819) and the test cohort (AUC = 0.780). CONCLUSION This study suggests that the integration of genomic profiling and clinical features identifies early-invasive LUAD patients at higher risk of LN metastasis. Improved identification of LN metastasis is beneficial for the optimization of the patient's therapy decisions.
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Affiliation(s)
- Wei Guo
- Department of Thoracic SurgeryRuijin Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Tong Lu
- Department of Thoracic SurgeryRuijin Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Yang Song
- Department of Thoracic SurgeryHuashan Hospital, Fudan UniversityShanghaiChina
| | - Anqi Li
- Department of PathologyRuijin Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Xijia Feng
- Department of Thoracic SurgeryRuijin Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Dingpei Han
- Department of Thoracic SurgeryRuijin Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Yuqin Cao
- Department of Thoracic SurgeryRuijin Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Debin Sun
- Genecast Biotechnology Co., LtdWuxiChina
| | | | - Chengqiang Li
- Department of Thoracic SurgeryRuijin Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Runsen Jin
- Department of Thoracic SurgeryRuijin Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Hailei Du
- Department of Thoracic SurgeryRuijin Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Kai Chen
- Department of Thoracic SurgeryRuijin Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Jie Xiang
- Department of Thoracic SurgeryRuijin Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Junbiao Hang
- Department of Thoracic SurgeryRuijin Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Gang Chen
- Department of Thoracic SurgeryHuashan Hospital, Fudan UniversityShanghaiChina
| | - Hecheng Li
- Department of Thoracic SurgeryRuijin Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
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Zhang L, Fang K, Ren H, Fan S, Wang J, Guan H. Comparison of the diagnostic significance of cerebrospinal fluid metagenomic next-generation sequencing copy number variation analysis and cytology in leptomeningeal malignancy. BMC Neurol 2024; 24:223. [PMID: 38943096 PMCID: PMC11212224 DOI: 10.1186/s12883-024-03655-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 04/26/2024] [Indexed: 07/01/2024] Open
Abstract
BACKGROUND Diagnosis and monitoring of leptomeningeal malignancy remain challenging, and are usually based on neurological, radiological, cerebrospinal fluid (CSF) and pathological findings. This study aimed to investigate the diagnostic performance of CSF metagenomic next-generation sequencing (mNGS) and chromosome copy number variations (CNVs) analysis in the detection of leptomeningeal malignancy. METHODS Of the 51 patients included in the study, 34 patients were diagnosed with leptomeningeal malignancies, and 17 patients were diagnosed with central nervous system (CNS) inflammatory diseases. The Sayk's spontaneous cell sedimentation technique was employed for CSF cytology. And a well-designed approach utilizing the CSF mNGS-CNVs technique was explored for early diagnosis of leptomeningeal malignancy. RESULTS In the tumor group, 28 patients were positive for CSF cytology, and 24 patients were positive for CSF mNGS-CNVs. Sensitivity and specificity of CSF cytology were 82.35% (95% CI: 66.83-92.61%) and 94.12% (95% CI: 69.24-99.69%). In comparison, sensitivity and specificity of CSF mNGS-CNV were 70.59% (95% CI: 52.33-84.29%) and 100% (95% CI: 77.08-100%). There was no significant difference in diagnostic consistency between CSF cytology and mNGS-CNVs (p = 0.18, kappa = 0.650). CONCLUSIONS CSF mNGS-CNVs tend to have higher specificity compared with traditional cytology and can be used as a complementary diagnostic method for patients with leptomeningeal malignancies.
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Affiliation(s)
- Le Zhang
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Kechi Fang
- CAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing, 100101, China
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haitao Ren
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Siyuan Fan
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Jing Wang
- CAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing, 100101, China.
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Hongzhi Guan
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
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Razavi-Mohseni M, Huang W, Guo YA, Shigaki D, Ho SWT, Tan P, Skanderup AJ, Beer MA. Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer. Genome Res 2024; 34:680-695. [PMID: 38777607 PMCID: PMC11216402 DOI: 10.1101/gr.278565.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 05/13/2024] [Indexed: 05/25/2024]
Abstract
Gastric cancer (GC) is the fifth most common cancer worldwide and is a heterogeneous disease. Among GC subtypes, the mesenchymal phenotype (Mes-like) is more invasive than the epithelial phenotype (Epi-like). Although gene expression of the epithelial-to-mesenchymal transition (EMT) has been studied, the regulatory landscape shaping this process is not fully understood. Here we use ATAC-seq and RNA-seq data from a compendium of GC cell lines and primary tumors to detect drivers of regulatory state changes and their transcriptional responses. Using the ATAC-seq data, we developed a machine learning approach to determine the transcription factors (TFs) regulating the subtypes of GC. We identified TFs driving the mesenchymal (RUNX2, ZEB1, SNAI2, AP-1 dimer) and the epithelial (GATA4, GATA6, KLF5, HNF4A, FOXA2, GRHL2) states in GC. We identified DNA copy number alterations associated with dysregulation of these TFs, specifically deletion of GATA4 and amplification of MAPK9 Comparisons with bulk and single-cell RNA-seq data sets identified activation toward fibroblast-like epigenomic and expression signatures in Mes-like GC. The activation of this mesenchymal fibrotic program is associated with differentially accessible DNA cis-regulatory elements flanking upregulated mesenchymal genes. These findings establish a map of TF activity in GC and highlight the role of copy number driven alterations in shaping epigenomic regulatory programs as potential drivers of GC heterogeneity and progression.
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Affiliation(s)
- Milad Razavi-Mohseni
- Department of Biomedical Engineering and McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - Weitai Huang
- Laboratory of Computational Cancer Genomics, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore 138672
| | - Yu A Guo
- Laboratory of Computational Cancer Genomics, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore 138672
| | - Dustin Shigaki
- Department of Biomedical Engineering and McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - Shamaine Wei Ting Ho
- Laboratory of Cancer Epigenetic Regulation, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore 138672
| | - Patrick Tan
- Laboratory of Cancer Epigenetic Regulation, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore 138672
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore 169857
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593
| | - Anders J Skanderup
- Laboratory of Computational Cancer Genomics, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore 138672
| | - Michael A Beer
- Department of Biomedical Engineering and McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA;
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35
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Li M, Wang L, Li A, Wang B, Yang X, Zhang Y, Chen C, Sun F, Zhu Z, Ye L. Integrated analyses reveal unexpected complex inversion and recombination in RH genes. Blood Adv 2024; 8:3154-3165. [PMID: 38551808 PMCID: PMC11222952 DOI: 10.1182/bloodadvances.2023012147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/28/2024] [Indexed: 06/15/2024] Open
Abstract
ABSTRACT Phenotype D-- is associated with severe hemolytic transfusion reactions and hemolytic disease of the fetus and newborn. It is typically caused by defective RHCE genes. In this study, we identified a D-- phenotype proband and verified Rh phenotypes of other 6 family members. However, inconsistent results between the phenotypic analysis and Sanger sequencing revealed intact RHCE exons with no mutations in the D-- proband, but the protein was not expressed. Subsequent whole-genome sequencing by Oxford Nanopore Technologies of the proband revealed an inversion with ambiguous breakpoints in intron 2 and intron 7 and copy number variation loss in the RHCE gene region. Given that the RHCE gene is highly homologous to the RHD gene, we conducted a comprehensive analysis using Pacific Biosciences long-read target sequencing, Bionano optical genome mapping, and targeted next-generation sequencing. Our findings revealed that the proband had 2 novel recombinant RHCE haplotypes, RHCE∗Ce(1-2)-D(3-10) and RHCE∗Ce(1-2)-D(3-10)-Ce(10-8)-Ce(3-10), with clear-cut breakpoints identified. Furthermore, the RH haplotypes of the family members were identified and verified. In summary, we made, to our knowledge, a novel discovery of hereditary large inversion and recombination events occurring between the RHD and RHCE genes, leading to a lack of RhCE expression. This highlights the advantages of using integrated genetic analyses and also provides new insights into RH genotyping.
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Affiliation(s)
- Minghao Li
- Immunohematology Laboratory, Shanghai Institute of Blood Transfusion, Shanghai Blood Centre, Shanghai, China
| | - Liping Wang
- Blood Transfusion Department, Weifang People’s Hospital, Shandong, China
| | - Aijing Li
- Immunohematology Laboratory, Shanghai Institute of Blood Transfusion, Shanghai Blood Centre, Shanghai, China
| | - Bo Wang
- Xi’an Haorui Genomics Technology Company Limited, Chang’an District, Xi’an, Shaanxi, China
| | - Xiaohong Yang
- Xi’an Haorui Genomics Technology Company Limited, Chang’an District, Xi’an, Shaanxi, China
| | - Yue Zhang
- Xi’an Haorui Genomics Technology Company Limited, Chang’an District, Xi’an, Shaanxi, China
| | - Chaoqiong Chen
- Xi’an Haorui Genomics Technology Company Limited, Chang’an District, Xi’an, Shaanxi, China
| | - Futing Sun
- Blood Transfusion Department, Weifang People’s Hospital, Shandong, China
| | - Ziyan Zhu
- Immunohematology Laboratory, Shanghai Institute of Blood Transfusion, Shanghai Blood Centre, Shanghai, China
| | - Luyi Ye
- Immunohematology Laboratory, Shanghai Institute of Blood Transfusion, Shanghai Blood Centre, Shanghai, China
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36
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Mortenson KL, Dawes C, Wilson ER, Patchen NE, Johnson HE, Gertz J, Bailey SD, Liu Y, Varley KE, Zhang X. 3D genomic analysis reveals novel enhancer-hijacking caused by complex structural alterations that drive oncogene overexpression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.23.576965. [PMID: 38328209 PMCID: PMC10849656 DOI: 10.1101/2024.01.23.576965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Cancer genomes are composed of many complex structural alterations on chromosomes and extrachromosomal DNA (ecDNA), making it difficult to identify non-coding enhancer regions that are hijacked to activate oncogene expression. Here, we describe a 3D genomics-based analysis called HAPI (Highly Active Promoter Interactions) to characterize enhancer hijacking. HAPI analysis of HiChIP data from 34 cancer cell lines identified enhancer hijacking events that activate both known and potentially novel oncogenes such as MYC, CCND1 , ETV1 , CRKL , and ID4 . Furthermore, we found enhancer hijacking among multiple oncogenes from different chromosomes, often including MYC , on the same complex amplicons such as ecDNA. We characterized a MYC - ERBB2 chimeric ecDNA, in which ERBB2 heavily hijacks MYC 's enhancers. Notably, CRISPRi of the MYC promoter led to increased interaction of ERBB2 with MYC enhancers and elevated ERBB2 expression. Our HAPI analysis tool provides a robust strategy to detect enhancer hijacking and reveals novel insights into oncogene activation.
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37
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Li Y, Van Alsten SC, Lee DN, Kim T, Calhoun BC, Perou CM, Wobker SE, Marron JS, Hoadley KA, Troester MA. Visual Intratumor Heterogeneity and Breast Tumor Progression. Cancers (Basel) 2024; 16:2294. [PMID: 39001357 PMCID: PMC11240824 DOI: 10.3390/cancers16132294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 06/13/2024] [Accepted: 06/18/2024] [Indexed: 07/16/2024] Open
Abstract
High intratumoral heterogeneity is thought to be a poor prognostic indicator. However, the source of heterogeneity may also be important, as genomic heterogeneity is not always reflected in histologic or 'visual' heterogeneity. We aimed to develop a predictor of histologic heterogeneity and evaluate its association with outcomes and molecular heterogeneity. We used VGG16 to train an image classifier to identify unique, patient-specific visual features in 1655 breast tumors (5907 core images) from the Carolina Breast Cancer Study (CBCS). Extracted features for images, as well as the epithelial and stromal image components, were hierarchically clustered, and visual heterogeneity was defined as a greater distance between images from the same patient. We assessed the association between visual heterogeneity, clinical features, and DNA-based molecular heterogeneity using generalized linear models, and we used Cox models to estimate the association between visual heterogeneity and tumor recurrence. Basal-like and ER-negative tumors were more likely to have low visual heterogeneity, as were the tumors from younger and Black women. Less heterogeneous tumors had a higher risk of recurrence (hazard ratio = 1.62, 95% confidence interval = 1.22-2.16), and were more likely to come from patients whose tumors were comprised of only one subclone or had a TP53 mutation. Associations were similar regardless of whether the image was based on stroma, epithelium, or both. Histologic heterogeneity adds complementary information to commonly used molecular indicators, with low heterogeneity predicting worse outcomes. Future work integrating multiple sources of heterogeneity may provide a more comprehensive understanding of tumor progression.
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Affiliation(s)
- Yao Li
- Department of Statistics and Operations Research, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sarah C Van Alsten
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Dong Neuck Lee
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Taebin Kim
- Department of Statistics and Operations Research, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Benjamin C Calhoun
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Charles M Perou
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sara E Wobker
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - J S Marron
- Department of Statistics and Operations Research, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Katherine A Hoadley
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Melissa A Troester
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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38
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Masood D, Ren L, Nguyen C, Brundu FG, Zheng L, Zhao Y, Jaeger E, Li Y, Cha SW, Halpern A, Truong S, Virata M, Yan C, Chen Q, Pang A, Alberto R, Xiao C, Yang Z, Chen W, Wang C, Cross F, Catreux S, Shi L, Beaver JA, Xiao W, Meerzaman DM. Evaluation of somatic copy number variation detection by NGS technologies and bioinformatics tools on a hyper-diploid cancer genome. Genome Biol 2024; 25:163. [PMID: 38902799 PMCID: PMC11188507 DOI: 10.1186/s13059-024-03294-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/29/2024] [Indexed: 06/22/2024] Open
Abstract
BACKGROUND Copy number variation (CNV) is a key genetic characteristic for cancer diagnostics and can be used as a biomarker for the selection of therapeutic treatments. Using data sets established in our previous study, we benchmark the performance of cancer CNV calling by six most recent and commonly used software tools on their detection accuracy, sensitivity, and reproducibility. In comparison to other orthogonal methods, such as microarray and Bionano, we also explore the consistency of CNV calling across different technologies on a challenging genome. RESULTS While consistent results are observed for copy gain, loss, and loss of heterozygosity (LOH) calls across sequencing centers, CNV callers, and different technologies, variation of CNV calls are mostly affected by the determination of genome ploidy. Using consensus results from six CNV callers and confirmation from three orthogonal methods, we establish a high confident CNV call set for the reference cancer cell line (HCC1395). CONCLUSIONS NGS technologies and current bioinformatics tools can offer reliable results for detection of copy gain, loss, and LOH. However, when working with a hyper-diploid genome, some software tools can call excessive copy gain or loss due to inaccurate assessment of genome ploidy. With performance matrices on various experimental conditions, this study raises awareness within the cancer research community for the selection of sequencing platforms, sample preparation, sequencing coverage, and the choice of CNV detection tools.
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Affiliation(s)
- Daniall Masood
- Office of Oncologic Diseases, Office of New Drug, Center for Drug Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, 20993, USA
| | - Luyao Ren
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Cu Nguyen
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics and Information Technology (CBIIT), National Cancer Institute, Rockville, MD, USA
| | | | - Lily Zheng
- Office of Oncologic Diseases, Office of New Drug, Center for Drug Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, 20993, USA
| | - Yongmei Zhao
- Sequencing Facility Bioinformatics Group, Biomedical Informatics and Data Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | - Yong Li
- Illumina Inc., San Diego, CA, USA
| | | | | | | | | | - Chunhua Yan
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics and Information Technology (CBIIT), National Cancer Institute, Rockville, MD, USA
| | - Qingrong Chen
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics and Information Technology (CBIIT), National Cancer Institute, Rockville, MD, USA
| | - Andy Pang
- Bionano Genomics, San Diego, CA, 20892, USA
| | | | - Chunlin Xiao
- National Center for Biotechnology Information, National Librarssy of Medicine, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Zhaowei Yang
- Center for Genomics, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Wanqiu Chen
- Center for Genomics, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Charles Wang
- Center for Genomics, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Frank Cross
- Office of Oncologic Diseases, Office of New Drug, Center for Drug Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, 20993, USA
| | | | - Leming Shi
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Julia A Beaver
- Office of Oncologic Diseases, Office of New Drug, Center for Drug Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, 20993, USA
- Oncology Center of Excellence, Food and Drug Administration, Silver Spring, MD, USA
| | - Wenming Xiao
- Office of Oncologic Diseases, Office of New Drug, Center for Drug Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, 20993, USA.
| | - Daoud M Meerzaman
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics and Information Technology (CBIIT), National Cancer Institute, Rockville, MD, USA.
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39
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Henon C, Vibert J, Eychenne T, Gruel N, Colmet-Daage L, Ngo C, Garrido M, Dorvault N, Marques Da Costa ME, Marty V, Signolle N, Marchais A, Herbel N, Kawai-Kawachi A, Lenormand M, Astier C, Chabanon R, Verret B, Bahleda R, Le Cesne A, Mechta-Grigoriou F, Faron M, Honoré C, Delattre O, Waterfall JJ, Watson S, Postel-Vinay S. Single-cell multiomics profiling reveals heterogeneous transcriptional programs and microenvironment in DSRCTs. Cell Rep Med 2024; 5:101582. [PMID: 38781959 PMCID: PMC11228554 DOI: 10.1016/j.xcrm.2024.101582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 02/28/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024]
Abstract
Desmoplastic small round cell tumor (DSRCT) is a rare, aggressive sarcoma driven by the EWSR1::WT1 chimeric transcription factor. Despite this unique oncogenic driver, DSRCT displays a polyphenotypic differentiation of unknown causality. Using single-cell multi-omics on 12 samples from five patients, we find that DSRCT tumor cells cluster into consistent subpopulations with partially overlapping lineage- and metabolism-related transcriptional programs. In vitro modeling shows that high EWSR1::WT1 DNA-binding activity associates with most lineage-related states, in contrast to glycolytic and profibrotic states. Single-cell chromatin accessibility analysis suggests that EWSR1::WT1 binding site variability may drive distinct lineage-related transcriptional programs, supporting some level of cell-intrinsic plasticity. Spatial transcriptomics reveals that glycolytic and profibrotic states specifically localize within hypoxic niches at the periphery of tumor cell islets, suggesting an additional role of tumor cell-extrinsic microenvironmental cues. We finally identify a single-cell transcriptomics-derived epithelial signature associated with improved patient survival, highlighting the clinical relevance of our findings.
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Affiliation(s)
- Clémence Henon
- ATIP-Avenir INSERM and ERC StG Group, Equipe labellisée ARC Recherche Fondamentale, INSERM U981, Gustave Roussy, Paris Saclay University, Villejuif, France; Department of Medical Oncology, Gustave Roussy, Villejuif, France; Drug Development Department, DITEP, Gustave Roussy, Villejuif, France
| | - Julien Vibert
- INSERM U830, Équipe labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France; INSERM U830, Integrative Functional Genomics of Cancer Lab, PSL Research University, Institut Curie Research Center, Paris, France; Department of Translational Research, PSL Research University, Institut Curie Research Center, Paris, France
| | - Thomas Eychenne
- ATIP-Avenir INSERM and ERC StG Group, Equipe labellisée ARC Recherche Fondamentale, INSERM U981, Gustave Roussy, Paris Saclay University, Villejuif, France
| | - Nadège Gruel
- INSERM U830, Équipe labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France; Department of Translational Research, PSL Research University, Institut Curie Research Center, Paris, France
| | - Léo Colmet-Daage
- ATIP-Avenir INSERM and ERC StG Group, Equipe labellisée ARC Recherche Fondamentale, INSERM U981, Gustave Roussy, Paris Saclay University, Villejuif, France
| | - Carine Ngo
- ATIP-Avenir INSERM and ERC StG Group, Equipe labellisée ARC Recherche Fondamentale, INSERM U981, Gustave Roussy, Paris Saclay University, Villejuif, France; Department of Pathology, Gustave Roussy, Villejuif, France
| | - Marlène Garrido
- ATIP-Avenir INSERM and ERC StG Group, Equipe labellisée ARC Recherche Fondamentale, INSERM U981, Gustave Roussy, Paris Saclay University, Villejuif, France
| | - Nicolas Dorvault
- ATIP-Avenir INSERM and ERC StG Group, Equipe labellisée ARC Recherche Fondamentale, INSERM U981, Gustave Roussy, Paris Saclay University, Villejuif, France
| | - Maria Eugenia Marques Da Costa
- INSERM U1015, Gustave Roussy, Paris Saclay University, Villejuif, France; Department of Pediatric and Adolescent Oncology, Gustave Roussy, Villejuif, France
| | - Virginie Marty
- Experimental and Translational Pathology Platform (PETRA), AMMICa, INSERM US23/UAR3655, Gustave Roussy, Villejuif, France
| | - Nicolas Signolle
- Experimental and Translational Pathology Platform (PETRA), AMMICa, INSERM US23/UAR3655, Gustave Roussy, Villejuif, France
| | - Antonin Marchais
- INSERM U1015, Gustave Roussy, Paris Saclay University, Villejuif, France; Department of Pediatric and Adolescent Oncology, Gustave Roussy, Villejuif, France
| | - Noé Herbel
- ATIP-Avenir INSERM and ERC StG Group, Equipe labellisée ARC Recherche Fondamentale, INSERM U981, Gustave Roussy, Paris Saclay University, Villejuif, France
| | - Asuka Kawai-Kawachi
- ATIP-Avenir INSERM and ERC StG Group, Equipe labellisée ARC Recherche Fondamentale, INSERM U981, Gustave Roussy, Paris Saclay University, Villejuif, France
| | - Madison Lenormand
- ATIP-Avenir INSERM and ERC StG Group, Equipe labellisée ARC Recherche Fondamentale, INSERM U981, Gustave Roussy, Paris Saclay University, Villejuif, France
| | - Clémence Astier
- ATIP-Avenir INSERM and ERC StG Group, Equipe labellisée ARC Recherche Fondamentale, INSERM U981, Gustave Roussy, Paris Saclay University, Villejuif, France
| | - Roman Chabanon
- ATIP-Avenir INSERM and ERC StG Group, Equipe labellisée ARC Recherche Fondamentale, INSERM U981, Gustave Roussy, Paris Saclay University, Villejuif, France
| | - Benjamin Verret
- Department of Medical Oncology, Gustave Roussy, Villejuif, France; Breast Cancer Translational Research Group, INSERM U981, Gustave Roussy, Villejuif, France
| | - Rastislav Bahleda
- Drug Development Department, DITEP, Gustave Roussy, Villejuif, France
| | - Axel Le Cesne
- Department of Medical Oncology, Gustave Roussy, Villejuif, France; International Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - Fatima Mechta-Grigoriou
- INSERM U830, Equipe labellisée LNCC, Stress et Cancer, PSL Research University, Institut Curie Research Center, Paris, France
| | | | | | - Olivier Delattre
- INSERM U830, Équipe labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Joshua J Waterfall
- INSERM U830, Integrative Functional Genomics of Cancer Lab, PSL Research University, Institut Curie Research Center, Paris, France; Department of Translational Research, PSL Research University, Institut Curie Research Center, Paris, France
| | - Sarah Watson
- INSERM U830, Équipe labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France; Department of Translational Research, PSL Research University, Institut Curie Research Center, Paris, France
| | - Sophie Postel-Vinay
- ATIP-Avenir INSERM and ERC StG Group, Equipe labellisée ARC Recherche Fondamentale, INSERM U981, Gustave Roussy, Paris Saclay University, Villejuif, France; Drug Development Department, DITEP, Gustave Roussy, Villejuif, France; University College of London, Cancer Institute, London, UK.
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40
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Hatakeyama K, Muramatsu K, Nagashima T, Ichida H, Kawanishi Y, Fukumura R, Ohshima K, Shimoda Y, Ohnami S, Ohnami S, Maruyama K, Naruoka A, Kenmotsu H, Urakami K, Akiyama Y, Sugino T, Yamaguchi K. Tumor cell enrichment by tissue suspension improves sensitivity to copy number variation in diffuse gastric cancer with low tumor content. Sci Rep 2024; 14:13699. [PMID: 38871991 DOI: 10.1038/s41598-024-64541-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 06/10/2024] [Indexed: 06/15/2024] Open
Abstract
The detection of copy number variations (CNVs) and somatic mutations in cancer is important for the selection of specific drugs for patients with cancer. In cancers with sporadic tumor cells, low tumor content prevents the accurate detection of somatic alterations using targeted sequencing. To efficiently identify CNVs, we performed tumor cell enrichment using tissue suspensions of formalin-fixed paraffin-embedded (FFPE) tissue sections with low tumor cell content. Tumor-enriched and residual fractions were separated from FFPE tissue suspensions of intestinal and diffuse-type gastric cancers containing sporadic tumor cells, and targeted sequencing was performed on 225 cancer-related genes. Sequencing of a targeted panel of cancer-related genes using tumor-enriched fractions increased the number of detectable CNVs and the copy number of amplified genes. Furthermore, CNV analysis using the normal cell-enriched residual fraction as a reference for CNV scoring allowed targeted sequencing to detect CNV characteristics of diffuse-type gastric cancer with low tumor content. Our approach improves the CNV detection rate in targeted sequencing with tumor enrichment and the accuracy of CNV detection in archival samples without paired blood.
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Affiliation(s)
- Keiichi Hatakeyama
- Cancer Multiomics Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan.
| | - Koji Muramatsu
- Division of Pathology, Shizuoka Cancer Center, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Takeshi Nagashima
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
- SRL Inc., Shinjuku-ku, Tokyo, 163-0409, Japan
| | - Hiroyuki Ichida
- SRL and Shizuoka Cancer Center Collaborative Laboratories Inc., Sunto-gun, Shizuoka, 411-8777, Japan
| | - Yuichi Kawanishi
- SRL and Shizuoka Cancer Center Collaborative Laboratories Inc., Sunto-gun, Shizuoka, 411-8777, Japan
| | - Ryutaro Fukumura
- SRL and Shizuoka Cancer Center Collaborative Laboratories Inc., Sunto-gun, Shizuoka, 411-8777, Japan
| | - Keiichi Ohshima
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Yuji Shimoda
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Sumiko Ohnami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Shumpei Ohnami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Koji Maruyama
- Experimental Animal Facility, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Akane Naruoka
- Drug Discovery and Development Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Hirotsugu Kenmotsu
- Division of Thoracic Oncology, Shizuoka Cancer Center, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Kenichi Urakami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Yasuto Akiyama
- Immunotheraphy Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Takashi Sugino
- Division of Pathology, Shizuoka Cancer Center, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Ken Yamaguchi
- Shizuoka Cancer Center, Sunto-gun, Shizuoka, 411-8777, Japan
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41
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Choi Y, Choi SA, Koh EJ, Yun I, Park S, Jeon S, Kim Y, Park S, Woo D, Phi JH, Park SH, Kim DS, Kim SH, Choi JW, Lee JW, Jung TY, Bhak J, Lee S, Kim SK. Comprehensive multiomics analysis reveals distinct differences between pediatric choroid plexus papilloma and carcinoma. Acta Neuropathol Commun 2024; 12:93. [PMID: 38867333 PMCID: PMC11167863 DOI: 10.1186/s40478-024-01814-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 06/02/2024] [Indexed: 06/14/2024] Open
Abstract
Choroid plexus tumors (CPTs) are intraventricular tumors derived from the choroid plexus epithelium and occur frequently in children. The aim of this study was to investigate the genomic and epigenomic characteristics of CPT and identify the differences between choroid plexus papilloma (CPP) and choroid plexus carcinoma (CPC). We conducted multiomics analyses of 20 CPT patients including CPP and CPC. Multiomics analysis included whole-genome sequencing, whole-transcriptome sequencing, and methylation sequencing. Mutually exclusive TP53 and EPHA7 point mutations, coupled with the amplification of chromosome 1, were exclusively identified in CPC. In contrast, amplification of chromosome 9 was specific to CPP. Differential gene expression analysis uncovered a significant overexpression of genes related to cell cycle regulation and epithelial-mesenchymal transition pathways in CPC compared to CPP. Overexpression of genes associated with tumor metastasis and progression was observed in the CPC subgroup with leptomeningeal dissemination. Furthermore, methylation profiling unveiled hypomethylation in major repeat regions, including long interspersed nuclear elements, short interspersed nuclear elements, long terminal repeats, and retrotransposons in CPC compared to CPP, implying that the loss of epigenetic silencing of transposable elements may play a role in tumorigenesis of CPC. Finally, the differential expression of AK1, regulated by both genomic and epigenomic factors, emerged as a potential contributing factor to the histological difference of CPP against CPC. Our results suggest pronounced genomic and epigenomic disparities between CPP and CPC, providing insights into the pathogenesis of CPT at the molecular level.
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Affiliation(s)
- Yeonsong Choi
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Korean Genomics Center, UNIST, Ulsan, Republic of Korea
| | - Seung Ah Choi
- Division of Pediatric Neurosurgery, Seoul National University Children's Hospital, Seoul, Republic of Korea
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Eun Jung Koh
- Division of Pediatric Neurosurgery, Seoul National University Children's Hospital, Seoul, Republic of Korea
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ilsun Yun
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Korean Genomics Center, UNIST, Ulsan, Republic of Korea
| | - Suhyun Park
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Korean Genomics Center, UNIST, Ulsan, Republic of Korea
| | | | | | - Sangbeen Park
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Donggeon Woo
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Ji Hoon Phi
- Division of Pediatric Neurosurgery, Seoul National University Children's Hospital, Seoul, Republic of Korea
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
- Neuroscience Research Institute, Seoul National University Medical Research Center, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sung-Hye Park
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Dong-Seok Kim
- Department of Pediatric Neurosurgery, Severance Children's Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Se Hoon Kim
- Department of Pathology, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jung Won Choi
- Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Ji Won Lee
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Tae-Young Jung
- Department of Neurosurgery, Chonnam National University Medical School and Hwasun Hospital, Hwasun, Republic of Korea
| | - Jong Bhak
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Korean Genomics Center, UNIST, Ulsan, Republic of Korea
- Clinomics Inc., Ulsan, Republic of Korea
| | - Semin Lee
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea.
- Korean Genomics Center, UNIST, Ulsan, Republic of Korea.
| | - Seung-Ki Kim
- Division of Pediatric Neurosurgery, Seoul National University Children's Hospital, Seoul, Republic of Korea.
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea.
- Neuroscience Research Institute, Seoul National University Medical Research Center, Seoul National University College of Medicine, Seoul, Republic of Korea.
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Liang X, Xu J, Jiang Y, Yan Y, Wu H, Dai J, Cui Y, Zhang C, Chen W, Zhang Z, Guo R. Concomitant genomic features stratify prognosis to patients with advanced EGFR mutant lung cancer. Mol Carcinog 2024. [PMID: 38860603 DOI: 10.1002/mc.23750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 04/23/2024] [Accepted: 05/13/2024] [Indexed: 06/12/2024]
Abstract
This study aimed to explore the clinical significance of genomics features including tumor mutation burden (TMB) and copy number alteration (CNA) for advanced EGFR mutant lung cancer. We retrospectively identified 1378 patients with advanced EGFR mutant lung cancer and next-generation sequencing tests from three cohorts. Multiple co-occurring genomics alternations occurred in a large proportion (97%) of patients with advanced EGFR mutant lung cancers. Both TMB and CNA were predictive biomarkers for these patients. A joint analysis of TMB and CNA found that patients with high TMB and high CNA showed worse responses to EGFR-TKIs and predicted worse outcomes. TMBhighCNAhigh, as a high-risk genomic feature, showed predictive ability in most of the subgroups based on clinical characteristics. These patients had larger numbers of metastatic sites, and higher rates of EGFR copy number amplification, TP53 mutations, and cell-cycle gene alterations, which showed more potential survival gain from combination treatment. Furthermore, a nomogram based on genomic features and clinical features was developed to distinguish prognosis. Genomic features could stratify prognosis and guide clinical treatment for patients with advanced EGFR mutant lung cancer.
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Affiliation(s)
- Xiao Liang
- Department of Medical Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Department of Medical Oncology, The Affiliated Jiangyin Hospital of Nantong University, Jiangyin, China
| | - Jiali Xu
- Department of Medical Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yuqin Jiang
- Department of Medical Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yuqian Yan
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Hongshuai Wu
- Department of Central Laboratory, Wuxi Key Laboratory of Biomaterials for Clinical Application, Key Laboratory for Multidisciplinary Intersection of Radiotherapy and Immunology for Gastrointestinal Tumor, Jiangyin Clinical College of Xuzhou Medical University, Jiangyin, China
| | - Jiali Dai
- Department of Medical Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yanan Cui
- Department of Medical Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chen Zhang
- Department of Medical Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wei Chen
- Department of Radiotherapy, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institue of Cancer Research, Nanjing, Jiangsu, China
| | - Zhihong Zhang
- Department of Pathology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Renhua Guo
- Department of Medical Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Liu H, Gao J, Feng M, Cheng J, Tang Y, Cao Q, Zhao Z, Meng Z, Zhang J, Zhang G, Zhang C, Zhao M, Yan Y, Wang Y, Xue R, Zhang N, Li H. Integrative molecular and spatial analysis reveals evolutionary dynamics and tumor-immune interplay of in situ and invasive acral melanoma. Cancer Cell 2024; 42:1067-1085.e11. [PMID: 38759655 DOI: 10.1016/j.ccell.2024.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 03/21/2024] [Accepted: 04/26/2024] [Indexed: 05/19/2024]
Abstract
In acral melanoma (AM), progression from in situ (AMis) to invasive AM (iAM) leads to significantly reduced survival. However, evolutionary dynamics during this process remain elusive. Here, we report integrative molecular and spatial characterization of 147 AMs using genomics, bulk and single-cell transcriptomics, and spatial transcriptomics and proteomics. Vertical invasion from AMis to iAM displays an early and monoclonal seeding pattern. The subsequent regional expansion of iAM exhibits two distinct patterns, clonal expansion and subclonal diversification. Notably, molecular subtyping reveals an aggressive iAM subset featured with subclonal diversification, increased epithelial-mesenchymal transition (EMT), and spatial enrichment of APOE+/CD163+ macrophages. In vitro and ex vivo experiments further demonstrate that APOE+CD163+ macrophages promote tumor EMT via IGF1-IGF1R interaction. Adnexal involvement can predict AMis with higher invasive potential whereas APOE and CD163 serve as prognostic biomarkers for iAM. Altogether, our results provide implications for the early detection and treatment of AM.
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MESH Headings
- Humans
- Melanoma/genetics
- Melanoma/immunology
- Melanoma/pathology
- Epithelial-Mesenchymal Transition/genetics
- Skin Neoplasms/genetics
- Skin Neoplasms/immunology
- Skin Neoplasms/pathology
- Antigens, Differentiation, Myelomonocytic/metabolism
- Antigens, Differentiation, Myelomonocytic/genetics
- Antigens, CD/metabolism
- Antigens, CD/genetics
- Neoplasm Invasiveness
- Apolipoproteins E/genetics
- Macrophages/immunology
- Macrophages/metabolism
- Male
- Female
- Receptor, IGF Type 1/genetics
- Receptor, IGF Type 1/metabolism
- Tumor Microenvironment/immunology
- Tumor Microenvironment/genetics
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Gene Expression Regulation, Neoplastic
- Spatial Analysis
- Middle Aged
- Prognosis
- Disease Progression
- Aged
- Receptors, Cell Surface
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Affiliation(s)
- Hengkang Liu
- Peking University-Yunnan Baiyao International Medical Research Center, Peking University First Hospital, Beijing 100191, China; School of Basic Medical Sciences, International Cancer Institute, Peking University, Beijing 100191, China
| | - Jiawen Gao
- National Clinical Research Center for Skin and Immune Diseases, NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Peking University First Hospital, Beijing 100034, China; Institute of Photomedicine and Department of Phototherapy at Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai 200443, China
| | - Mei Feng
- Peking University-Yunnan Baiyao International Medical Research Center, Peking University First Hospital, Beijing 100191, China
| | - Jinghui Cheng
- Peking University-Yunnan Baiyao International Medical Research Center, Peking University First Hospital, Beijing 100191, China
| | - Yuchen Tang
- National Clinical Research Center for Skin and Immune Diseases, NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Peking University First Hospital, Beijing 100034, China
| | - Qi Cao
- Peking University-Yunnan Baiyao International Medical Research Center, Peking University First Hospital, Beijing 100191, China
| | - Ziji Zhao
- Peking University-Yunnan Baiyao International Medical Research Center, Peking University First Hospital, Beijing 100191, China
| | - Ziqiao Meng
- Peking University-Yunnan Baiyao International Medical Research Center, Peking University First Hospital, Beijing 100191, China
| | - Jiarui Zhang
- National Clinical Research Center for Skin and Immune Diseases, NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Peking University First Hospital, Beijing 100034, China
| | - Guohong Zhang
- National Clinical Research Center for Skin and Immune Diseases, NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Peking University First Hospital, Beijing 100034, China
| | - Chong Zhang
- National Clinical Research Center for Skin and Immune Diseases, NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Peking University First Hospital, Beijing 100034, China
| | - Mingming Zhao
- National Clinical Research Center for Skin and Immune Diseases, NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Peking University First Hospital, Beijing 100034, China
| | - Yicen Yan
- National Clinical Research Center for Skin and Immune Diseases, NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Peking University First Hospital, Beijing 100034, China
| | - Yang Wang
- National Clinical Research Center for Skin and Immune Diseases, NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Peking University First Hospital, Beijing 100034, China
| | - Ruidong Xue
- Peking University-Yunnan Baiyao International Medical Research Center, Peking University First Hospital, Beijing 100191, China; School of Basic Medical Sciences, International Cancer Institute, Peking University, Beijing 100191, China.
| | - Ning Zhang
- Peking University-Yunnan Baiyao International Medical Research Center, Peking University First Hospital, Beijing 100191, China; School of Basic Medical Sciences, International Cancer Institute, Peking University, Beijing 100191, China; Yunnan Baiyao Group, Kunming 650500, China.
| | - Hang Li
- Peking University-Yunnan Baiyao International Medical Research Center, Peking University First Hospital, Beijing 100191, China; National Clinical Research Center for Skin and Immune Diseases, NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Peking University First Hospital, Beijing 100034, China; Yunnan Baiyao Group, Kunming 650500, China.
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Gerami P, Tandukar B, Deivendran D, Olivares S, Chen L, Tang J, Tan T, Sharma H, Bandari AK, Cruz-Pacheco N, Chang D, Marty A, Olshen A, Murad NF, Song J, Lee J, Yeh I, Hunter Shain A. Molecular effects of indoor tanning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597225. [PMID: 38895302 PMCID: PMC11185634 DOI: 10.1101/2024.06.04.597225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Background Tanning bed users have a significantly increased risk of melanoma, but it remains unclear how indoor tanning drives melanomagenesis. Tanning bed radiation is often thought of as a substitute for natural UV radiation despite differences in the maximum doses, UV content, body sites exposed, and patterns of melanoma that arise. Methods To better understand the epidemiologic trends and etiology of melanoma associated with tanning bed use, we described the patterns of melanoma in patients with quantifiable tanning bed usage and performed exome sequencing of 182 melanocytes from normal skin of a subset of these patients. Results Tanning bed users were more likely than non-users to have melanoma on body sites with low cumulative levels of sun damage and were more likely to have multiple melanomas. The melanocytes in normal appearing skin from tanning bed users had higher mutation burdens, a higher proportion of melanocytes with pathogenic mutations, and distinct mutational signatures. These differences were most prominent over body sites that experience comparatively less exposure to natural sunlight. Conclusions We conclude that tanning bed radiation induces melanoma by increasing the mutation burden of melanocytes and by mutagenizing a broader field of melanocytes than are typically exposed to natural sunlight. The unique signatures of mutations in skin cells of tanning users may be attributable to the distinct spectra of radiation emitted from solariums.
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Affiliation(s)
- Pedram Gerami
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Bishal Tandukar
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Delahny Deivendran
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Shantel Olivares
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Limin Chen
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Jessica Tang
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Tuyet Tan
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- School of Medicine, University of California, San Diego, San Diego, CA, USA
| | - Harsh Sharma
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Aravind K Bandari
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Noel Cruz-Pacheco
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Darwin Chang
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Department of Immunology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Annika Marty
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - Adam Olshen
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Natalia Faraj Murad
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Jing Song
- Division of Biostatistics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Jungwha Lee
- Division of Biostatistics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Iwei Yeh
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - A Hunter Shain
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
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Takahashi N, Pongor L, Agrawal SP, Shtumpf M, Rajapakse VN, Shafiei A, Schultz CW, Kim S, Roame D, Carter P, Vilimas R, Nichols S, Desai P, Figg WD, Bagheri M, Teif VB, Thomas A. Genomic alterations and transcriptional phenotypes in circulating tumor DNA and matched metastatic tumor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.02.597054. [PMID: 38895436 PMCID: PMC11185519 DOI: 10.1101/2024.06.02.597054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Background Profiling circulating cell-free DNA (cfDNA) has become a fundamental practice in cancer medicine, but the effectiveness of cfDNA at elucidating tumor-derived molecular features has not been systematically compared to standard single-lesion tumor biopsies in prospective cohorts of patients. The use of plasma instead of tissue to guide therapy is particularly attractive for patients with small cell lung cancer (SCLC), a cancer whose aggressive clinical course making it exceedingly challenging to obtain tumor biopsies. Methods Here, a prospective cohort of 49 plasma samples obtained before, during, and after treatment from 20 patients with recurrent SCLC, we study cfDNA low pass whole genome (0.1X coverage) and exome (130X) sequencing in comparison with time-point matched tumor, characterized using exome and transcriptome sequencing. Results Direct comparison of cfDNA versus tumor biopsy reveals that cfDNA not only mirrors the mutation and copy number landscape of the corresponding tumor but also identifies clinically relevant resistance mechanisms and cancer driver alterations not found in matched tumor biopsies. Longitudinal cfDNA analysis reliably tracks tumor response, progression, and clonal evolution. Genomic sequencing coverage of plasma DNA fragments around transcription start sites shows distinct treatment-related changes and captures the expression of key transcription factors such as NEUROD1 and REST in the corresponding SCLC tumors, allowing prediction of SCLC neuroendocrine phenotypes and treatment responses. Conclusions These findings have important implications for non-invasive stratification and subtype-specific therapies for patients with SCLC, now treated as a single disease.
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Affiliation(s)
- Nobuyuki Takahashi
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, USA
- Medical Oncology Branch, Center Hospital, National Center for Global Health and Medicine, Tokyo, Japan
- Department of Medical Oncology, National Cancer Center East Hospital, Kashiwa, Japan
| | - Lorinc Pongor
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, USA
| | | | - Mariya Shtumpf
- School of Life Sciences, University of Essex, Colchester, UK
| | - Vinodh N Rajapakse
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, USA
| | - Ahmad Shafiei
- Department of Radiology and Imaging Sciences, Center for Cancer Research, National Cancer Institute, Bethesda, USA
| | - Christopher W Schultz
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, USA
| | - Sehyun Kim
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, USA
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Diana Roame
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, USA
| | - Paula Carter
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, USA
| | - Rasa Vilimas
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, USA
| | - Samantha Nichols
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, USA
| | - Parth Desai
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, USA
| | - William Douglas Figg
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, USA
| | - Mohammad Bagheri
- Department of Radiology and Imaging Sciences, Center for Cancer Research, National Cancer Institute, Bethesda, USA
| | - Vladimir B Teif
- School of Life Sciences, University of Essex, Colchester, UK
| | - Anish Thomas
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, USA
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Lim BY, Guo Z, Lim JQ, Ko TK, Lee ECY, Kannan B, Lee JY, Lim AH, Li Z, Ng CCY, Busmanis I, Chan JY. Whole genome sequencing of HER2-positive metastatic extramammary Paget's disease: a case report. Orphanet J Rare Dis 2024; 19:223. [PMID: 38831459 PMCID: PMC11149212 DOI: 10.1186/s13023-024-03169-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 03/30/2024] [Indexed: 06/05/2024] Open
Abstract
BACKGROUND Extramammary Paget's disease (EMPD) is a rare cancer that occurs within the epithelium of the skin, arising predominantly in areas with high apocrine gland concentration such as the vulva, scrotum, penis and perianal regions. Here, we aim to integrate clinicopathological data with genomic analysis of aggressive, rapidly-progressing de novo metastatic EMPD responding to HER2-directed treatment in combination with other agents, to attain a more comprehensive understanding of the disease landscape. METHODS Immunohistochemical staining on the scrotal wall tumor and bone marrow metastasis demonstrated HER2 overexpression. Whole genome sequencing of the tumor and matched blood was performed. RESULTS Notable copy number gains (log2FC > 0.9) on chromosomes 7 and 8 were detected (n = 81), with 92.6% of these unique genes specifically located on chromosome 8. Prominent cancer-associated genes include ZNF703, HOOK3, DDHD2, LSM1, NSD3, ADAM9, BRF2, KAT6A and FGFR1. Interestingly, ERBB2 gene did not exhibit high copy number gain (log2FC = 0.4) although 90% of tumor cells stained HER2-positive. Enrichment in pathways associated with transforming growth factor-beta (TGFβ) (FDR = 0.0376, Enrichment Ratio = 8.12) and fibroblast growth factor receptor (FGFR1) signaling (FDR = 0.0082, Enrichment Ratio = 2.3) was detected. Amplicon structure analysis revealed that this was a simple-linear amplification event. CONCLUSION Whole genome sequencing revealed the underlying copy number variation landscape in HER2-positive metastatic EMPD. The presence of alternative signalling pathways and genetic variants suggests potential interactions with HER2 signalling, which possibly contributed to the HER2 overexpression and observed response to HER2-directed therapy combined with other agents in a comprehensive treatment regimen.
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Affiliation(s)
- Boon Yee Lim
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore
| | - Zexi Guo
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore
| | - Jing Quan Lim
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Tun Kiat Ko
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore
| | | | - Bavani Kannan
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore
| | - Jing Yi Lee
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore
| | - Abner Herbert Lim
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore
| | - Zhimei Li
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore
| | | | - Inny Busmanis
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore
| | - Jason Yongsheng Chan
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore.
- Duke-NUS Medical School, Singapore, Singapore.
- Divison of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore.
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Du J, Li L, Fu D. Whole-exome-based single nucleotide variants and copy number analysis for prenatal diagnosis of compound heterozygosity of SMPD4. Psychiatr Genet 2024; 34:74-80. [PMID: 38690959 DOI: 10.1097/ypg.0000000000000369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
BACKGROUND Biallelic loss-of-function variants in SMPD4 cause a rare and severe neurodevelopmental disorder. These variants have been identified in a group of children with neurodevelopmental disorders with microcephaly, arthrogryposis, and structural brain anomalies. SMPD4 encodes a sphingomyelinase that hydrolyzes sphingomyelin into ceramide at neutral pH and can thereby affect membrane lipid homeostasis. SMPD4 localizes to the membranes of the endoplasmic reticulum and nuclear envelope and interacts with nuclear pore complexes. MATERIALS AND METHODS For the efficient prenatal diagnosis of rare and undiagnosed diseases, the parallel detection of copy number variants (CNVs) and single nucleotide variants using whole-exome analysis is required. A physical examination of the parents was performed. Karyotype and whole-exome analysis were performed for the fetus and the parents. RESULTS A fetus with microcephaly and arthrogryposis; biallelic null variants (c.387-1G>A; Chr2[GRCh38]: g.130142742_130202459del) were detected by whole-exome sequencing (WES). We have reported for the first time the biallelic loss-of-function mutations in SMPD4 in patients born to unrelated parents in China. CONCLUSION WES could replace chromosomal microarray analysis and copy number variation sequencing as a more cost-effective genetic test for detecting CNVs and diagnosing highly heterogeneous conditions.
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Affiliation(s)
| | - Lin Li
- Department of Ultrasound, Renmin Hospital, Hubei University of Medicine, Shiyan, People's Republic of China
| | - Dinghu Fu
- Department of Ultrasound, Renmin Hospital, Hubei University of Medicine, Shiyan, People's Republic of China
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Molinet J, Navarrete JP, Villarroel CA, Villarreal P, Sandoval FI, Nespolo RF, Stelkens R, Cubillos FA. Wild Patagonian yeast improve the evolutionary potential of novel interspecific hybrid strains for lager brewing. PLoS Genet 2024; 20:e1011154. [PMID: 38900713 PMCID: PMC11189258 DOI: 10.1371/journal.pgen.1011154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 05/17/2024] [Indexed: 06/22/2024] Open
Abstract
Lager yeasts are limited to a few strains worldwide, imposing restrictions on flavour and aroma diversity and hindering our understanding of the complex evolutionary mechanisms during yeast domestication. The recent finding of diverse S. eubayanus lineages from Patagonia offers potential for generating new lager yeasts with different flavour profiles. Here, we leverage the natural genetic diversity of S. eubayanus and expand the lager yeast repertoire by including three distinct Patagonian S. eubayanus lineages. We used experimental evolution and selection on desirable traits to enhance the fermentation profiles of novel S. cerevisiae x S. eubayanus hybrids. Our analyses reveal an intricate interplay of pre-existing diversity, selection on species-specific mitochondria, de-novo mutations, and gene copy variations in sugar metabolism genes, resulting in high ethanol production and unique aroma profiles. Hybrids with S. eubayanus mitochondria exhibited greater evolutionary potential and superior fitness post-evolution, analogous to commercial lager hybrids. Using genome-wide screens of the parental subgenomes, we identified genetic changes in IRA2, IMA1, and MALX genes that influence maltose metabolism, and increase glycolytic flux and sugar consumption in the evolved hybrids. Functional validation and transcriptome analyses confirmed increased maltose-related gene expression, influencing greater maltotriose consumption in evolved hybrids. This study demonstrates the potential for generating industrially viable lager yeast hybrids from wild Patagonian strains. Our hybridization, evolution, and mitochondrial selection approach produced hybrids with high fermentation capacity and expands lager beer brewing options.
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Affiliation(s)
- Jennifer Molinet
- ANID-Millennium Science Initiative-Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Juan P. Navarrete
- ANID-Millennium Science Initiative-Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Carlos A. Villarroel
- ANID-Millennium Science Initiative-Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Centro de Biotecnología de los Recursos Naturales (CENBio), Facultad de Ciencias Agrarias y Forestales, Universidad Católica del Maule, Talca, Chile
| | - Pablo Villarreal
- ANID-Millennium Science Initiative-Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Felipe I. Sandoval
- ANID-Millennium Science Initiative-Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Roberto F. Nespolo
- ANID-Millennium Science Initiative-Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- ANID-Millennium Nucleus of Patagonian Limit of Life (LiLi), Valdivia, Chile
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - Rike Stelkens
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Francisco A. Cubillos
- ANID-Millennium Science Initiative-Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
- ANID-Millennium Nucleus of Patagonian Limit of Life (LiLi), Valdivia, Chile
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49
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Fukuda H, Arai K, Mizuno H, Nishito Y, Motoi N, Arai Y, Hiraoka N, Shibata T, Sonobe Y, Kayukawa Y, Hashimoto E, Takahashi M, Fujii E, Maruyama T, Kuwabara K, Nishizawa T, Mizoguchi Y, Yoshida Y, Watanabe S, Yamashita M, Kitano S, Sakamoto H, Nagata Y, Mitsumori R, Ozaki K, Niida S, Kanai Y, Hirayama A, Soga T, Tsukada K, Yabuki N, Shimada M, Kitazawa T, Natori O, Sawada N, Kato A, Yoshida T, Yasuda K, Ochiai A, Tsunoda H, Aoki K. Molecular subtypes of lung adenocarcinoma present distinct immune tumor microenvironments. Cancer Sci 2024; 115:1763-1777. [PMID: 38527308 PMCID: PMC11145114 DOI: 10.1111/cas.16154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 01/31/2024] [Accepted: 03/04/2024] [Indexed: 03/27/2024] Open
Abstract
Overcoming resistance to immune checkpoint inhibitors is an important issue in patients with non-small-cell lung cancer (NSCLC). Transcriptome analysis shows that adenocarcinoma can be divided into three molecular subtypes: terminal respiratory unit (TRU), proximal proliferative (PP), and proximal inflammatory (PI), and squamous cell carcinoma (LUSQ) into four. However, the immunological characteristics of these subtypes are not fully understood. In this study, we investigated the immune landscape of NSCLC tissues in molecular subtypes using a multi-omics dataset, including tumor-infiltrating leukocytes (TILs) analyzed using flow cytometry, RNA sequences, whole exome sequences, metabolomic analysis, and clinicopathologic findings. In the PI subtype, the number of TILs increased and the immune response in the tumor microenvironment (TME) was activated, as indicated by high levels of tertiary lymphoid structures, and high cytotoxic marker levels. Patient prognosis was worse in the PP subtype than in other adenocarcinoma subtypes. Glucose transporter 1 (GLUT1) expression levels were upregulated and lactate accumulated in the TME of the PP subtype. This could lead to the formation of an immunosuppressive TME, including the inactivation of antigen-presenting cells. The TRU subtype had low biological malignancy and "cold" tumor-immune phenotypes. Squamous cell carcinoma (LUSQ) did not show distinct immunological characteristics in its respective subtypes. Elucidation of the immune characteristics of molecular subtypes could lead to the development of personalized immune therapy for lung cancer. Immune checkpoint inhibitors could be an effective treatment for the PI subtype. Glycolysis is a potential target for converting an immunosuppressive TME into an antitumorigenic TME in the PP subtype.
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Affiliation(s)
- Hironori Fukuda
- Department of Immune MedicineNational Cancer Center Research InstituteTokyoJapan
- Department of UrologyTokyo Women's Medical UniversityTokyoJapan
| | - Kosuke Arai
- Department of Immune MedicineNational Cancer Center Research InstituteTokyoJapan
- Department of HematologyGraduate School of Medical and Dental Sciences, Tokyo Medical and Dental UniversityTokyoJapan
| | - Hideaki Mizuno
- Chugai Life Science Park YokohamaChugai Pharmaceutical Co. LtdYokohamaJapan
| | - Yukari Nishito
- Chugai Life Science Park YokohamaChugai Pharmaceutical Co. LtdYokohamaJapan
| | - Noriko Motoi
- Department of Diagnostic PathologyNational Cancer Center HospitalTokyoJapan
| | - Yasuhito Arai
- Division of Cancer GenomicsNational Cancer Center Research InstituteTokyoJapan
| | - Nobuyoshi Hiraoka
- Department of Analytical PathologyNational Cancer Center Research InstituteTokyoJapan
| | - Tatsuhiro Shibata
- Division of Cancer GenomicsNational Cancer Center Research InstituteTokyoJapan
| | - Yukiko Sonobe
- Chugai Life Science Park YokohamaChugai Pharmaceutical Co. LtdYokohamaJapan
| | - Yoko Kayukawa
- Chugai Life Science Park YokohamaChugai Pharmaceutical Co. LtdYokohamaJapan
| | - Eri Hashimoto
- Chugai Life Science Park YokohamaChugai Pharmaceutical Co. LtdYokohamaJapan
| | - Mina Takahashi
- Chugai Life Science Park YokohamaChugai Pharmaceutical Co. LtdYokohamaJapan
| | - Etsuko Fujii
- Chugai Life Science Park YokohamaChugai Pharmaceutical Co. LtdYokohamaJapan
| | - Toru Maruyama
- Chugai Life Science Park YokohamaChugai Pharmaceutical Co. LtdYokohamaJapan
| | - Kenta Kuwabara
- Chugai Life Science Park YokohamaChugai Pharmaceutical Co. LtdYokohamaJapan
| | - Takashi Nishizawa
- Chugai Life Science Park YokohamaChugai Pharmaceutical Co. LtdYokohamaJapan
| | - Yukihiro Mizoguchi
- Department of Immune MedicineNational Cancer Center Research InstituteTokyoJapan
| | - Yukihiro Yoshida
- Department of Thoracic SurgeryNational Cancer Center HospitalTokyoJapan
| | | | - Makiko Yamashita
- Advanced Medical Development CenterCancer Research Hospital, Japanese Foundation for Cancer ResearchTokyoJapan
| | - Shigehisa Kitano
- Advanced Medical Development CenterCancer Research Hospital, Japanese Foundation for Cancer ResearchTokyoJapan
| | - Hiromi Sakamoto
- Department of Clinical GenomicsNational Cancer Center Research InstituteTokyoJapan
| | - Yuki Nagata
- Medical Genome CenterResearch Institute, National Center for Geriatrics and GerontologyObuJapan
- Bioresource Research Center, Graduate School of Medical and Dental ScienceTokyo Medical and Dental UniversityTokyoJapan
| | - Risa Mitsumori
- Medical Genome CenterResearch Institute, National Center for Geriatrics and GerontologyObuJapan
| | - Kouichi Ozaki
- Medical Genome CenterResearch Institute, National Center for Geriatrics and GerontologyObuJapan
| | - Shumpei Niida
- Medical Genome CenterResearch Institute, National Center for Geriatrics and GerontologyObuJapan
| | - Yae Kanai
- Department of Pathology, School of MedicineKeio UniversityTokyoJapan
| | | | - Tomoyoshi Soga
- Institute for Advanced BiosciencesKeio UniversityYamagataJapan
| | - Keisuke Tsukada
- Chugai Life Science Park YokohamaChugai Pharmaceutical Co. LtdYokohamaJapan
| | - Nami Yabuki
- Chugai Life Science Park YokohamaChugai Pharmaceutical Co. LtdYokohamaJapan
| | - Mei Shimada
- Chugai Life Science Park YokohamaChugai Pharmaceutical Co. LtdYokohamaJapan
| | - Takehisa Kitazawa
- Chugai Life Science Park YokohamaChugai Pharmaceutical Co. LtdYokohamaJapan
| | - Osamu Natori
- Chugai Life Science Park YokohamaChugai Pharmaceutical Co. LtdYokohamaJapan
| | - Noriaki Sawada
- Chugai Life Science Park YokohamaChugai Pharmaceutical Co. LtdYokohamaJapan
| | - Atsuhiko Kato
- Chugai Life Science Park YokohamaChugai Pharmaceutical Co. LtdYokohamaJapan
| | - Teruhiko Yoshida
- Department of Genetic Medicine and ServicesNational Cancer Center HospitalTokyoJapan
| | - Kazuki Yasuda
- Department of Metabolic Disorder, Diabetes Research Center, Research InstituteNational Center for Global Health and MedicineTokyoJapan
| | - Atsushi Ochiai
- Exploratory Oncology Research and Clinical Trial CenterNational Cancer CenterChibaJapan
| | - Hiroyuki Tsunoda
- Chugai Life Science Park YokohamaChugai Pharmaceutical Co. LtdYokohamaJapan
| | - Kazunori Aoki
- Department of Immune MedicineNational Cancer Center Research InstituteTokyoJapan
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50
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Prendeville S, Kaur H, Ansari S, Al Qa'qa' S, Stockley TL, Lajkosz K, van der Kwast T, Cheung CC, Selvarajah S. Somatic Tumor Testing in Prostate Cancer: Experience of a Tertiary Care Center Including Pathologist-Driven Reflex Testing of Localized Tumors at Diagnosis. Mod Pathol 2024; 37:100489. [PMID: 38588883 DOI: 10.1016/j.modpat.2024.100489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 02/17/2024] [Accepted: 03/15/2024] [Indexed: 04/10/2024]
Abstract
Somatic tumor testing in prostate cancer (PCa) can guide treatment options by identifying clinically actionable variants in DNA damage repair genes, including acquired variants not detected using germline testing alone. Guidelines currently recommend performing somatic tumor testing in metastatic PCa, whereas there is no consensus on the role of testing in regional disease, and the optimal testing strategy is only evolving. This study evaluates the frequency, distribution, and pathologic correlates of somatic DNA damage repair mutations in metastatic and localized PCa following the implementation of pathologist-driven reflex testing at diagnosis. A cohort of 516 PCa samples were sequenced using a custom next-generation sequencing panel including homologous recombination repair and mismatch repair genes. Variants were classified based on the Association for Molecular Pathology/American Society of Clinical Oncology/College of American Pathologists guidelines. In total, 183 (35.5%) patients had at least one variant, which is as follows: 72 of 516 (13.9%) patients had at least 1 tier I or tier II variant, whereas 111 of 516 (21.5%) patients had a tier III variant. Tier I/II variant(s) were identified in 27% (12/44) of metastatic biopsy samples and 13% (61/472) of primary samples. Overall, 12% (62/516) of patients had at least 1 tier I/II variant in a homologous recombination repair gene, whereas 2.9% (10/516) had at least 1 tier I/II variant in a mismatch repair gene. The presence of a tier I/II variant was not significantly associated with the grade group (GG) or presence of intraductal/cribriform carcinoma in the primary tumor. Among the 309 reflex-tested hormone-naive primary tumors, tier I/II variants were identified in 10% (31/309) of cases, which is as follows: 9.2% (9/98) GG2; 9% (9/100) GG3; 9.1% (4/44) GG4; and 13.4% (9/67) GG5 cases. Our findings confirm the use of somatic tumor testing in detecting variants of clinical significance in PCa and provide insights that can inform the design of testing strategies. Pathologist-initiated reflex testing streamlines the availability of the results for clinical decision-making; however, pathologic parameters such as GG and the presence of intraductal/cribriform carcinoma may not be reliable to guide patient selection.
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Affiliation(s)
- Susan Prendeville
- Division of Anatomic Pathology, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
| | - Harpreet Kaur
- Division of Genome Diagnostics, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | - Shervin Ansari
- Division of Genome Diagnostics, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | - Shifaa' Al Qa'qa'
- Division of Anatomic Pathology, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada; Department of Pathology and Forensic Medicine, Faculty of Medicine, Al-Balqa Applied University, Al-Salt, Jordan
| | - Tracy L Stockley
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada; Division of Genome Diagnostics, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | - Katherine Lajkosz
- Department of Biostatistics, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Theodorus van der Kwast
- Division of Anatomic Pathology, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Carol C Cheung
- Division of Anatomic Pathology, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Shamini Selvarajah
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada; Division of Genome Diagnostics, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
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