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Nath P, Alfarsi LH, El-Ansari R, Masisi BK, Erkan B, Fakroun A, Ellis IO, Rakha EA, Green AR. The amino acid transporter SLC7A11 expression in breast cancer. Cancer Biol Ther 2024; 25:2291855. [PMID: 38073087 PMCID: PMC10761065 DOI: 10.1080/15384047.2023.2291855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 12/02/2023] [Indexed: 12/18/2023] Open
Abstract
Breast cancer (BC), characterized by its diverse molecular profiles and clinical outcomes, presents a significant challenge in the development of effective therapeutic strategies. Metabolic reprogramming, a defining characteristic of cancer, has emerged as a promising target for novel therapies. SLC7A11, an amino acid transporter that facilitates cysteine uptake in exchange for glutamate, plays a crucial role in sustaining the altered metabolism of cancer cells. This study delves into the comprehensive analysis of SLC7A11 at the genomic, transcriptomic, and protein levels in extensive BC datasets to elucidate its potential role in different BC subtypes. SLC7A11 gene copy number and mRNA expression were evaluated using the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) cohort (n = 1,980) and Breast Cancer Gene Expression Miner (n = 4,712). SLC7A11 protein was assessed using immunohistochemistry in a large BC cohort (n = 1,981). Additionally, The Cancer Genome Atlas (TCGA) dataset was used to explore SLC7A11 DNA methylation patterns using MethSurv (n = 782) and association of SLC7A11 mRNA expression with immune infiltrates using TIMER (n = 1,100). High SLC7A11 mRNA and SLC7A11 protein expression were significantly associated with high tumor grade (p ≤ .02), indicating a potential role in cancer progression. Interestingly, SLC7A11 copy number gain was observed in HER2+ tumors (p = .01), suggesting a subtype-specific association. In contrast, SLC7A11 mRNA expression was higher in the basal-like/triple-negative (TN; p < .001) and luminal B tumors (p = .02), highlighting its differential expression across BC subtypes. Notably, high SLC7A11 protein expression was predominantly observed in Estrogen Receptor (ER)-negative and Triple Negative (TN) BC, suggesting a role in these aggressive subtypes. Further analysis revealed that SLC7A11 was positively correlated with other amino acid transporters and enzymes associated with glutamine metabolism, implying a coordinated role in metabolic regulation. Additionally, SLC7A11 gene expression was positively associated with neutrophil and macrophage infiltration, suggesting a potential link between SLC7A11 and tumor immunity. Our findings suggest that SLC7A11 plays a significant role in BC metabolism, demonstrating differential expression across subtypes and associations with poor patient outcomes. Further functional studies are warranted to elucidate the precise mechanisms by which SLC7A11 contributes to BC progression and to explore its potential as a therapeutic target.
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Affiliation(s)
- Preyanka Nath
- Nottingham Breast Cancer Research Centre, Academic Unit of Translational Medical Sciences, School of Medicine, University of Nottingham Biodiscovery Institute, Nottingham, UK
| | - Lutfi H. Alfarsi
- Nottingham Breast Cancer Research Centre, Academic Unit of Translational Medical Sciences, School of Medicine, University of Nottingham Biodiscovery Institute, Nottingham, UK
| | - Rokaya El-Ansari
- Nottingham Breast Cancer Research Centre, Academic Unit of Translational Medical Sciences, School of Medicine, University of Nottingham Biodiscovery Institute, Nottingham, UK
| | - Brendah K. Masisi
- Nottingham Breast Cancer Research Centre, Academic Unit of Translational Medical Sciences, School of Medicine, University of Nottingham Biodiscovery Institute, Nottingham, UK
| | - Busra Erkan
- Nottingham Breast Cancer Research Centre, Academic Unit of Translational Medical Sciences, School of Medicine, University of Nottingham Biodiscovery Institute, Nottingham, UK
| | - Ali Fakroun
- Nottingham Breast Cancer Research Centre, Academic Unit of Translational Medical Sciences, School of Medicine, University of Nottingham Biodiscovery Institute, Nottingham, UK
| | - Ian O. Ellis
- Nottingham Breast Cancer Research Centre, Academic Unit of Translational Medical Sciences, School of Medicine, University of Nottingham Biodiscovery Institute, Nottingham, UK
- Cellular Pathology, Nottingham University Hospitals NHS Trust, Nottingham City Hospital, Nottingham, UK
| | - Emad A. Rakha
- Nottingham Breast Cancer Research Centre, Academic Unit of Translational Medical Sciences, School of Medicine, University of Nottingham Biodiscovery Institute, Nottingham, UK
- Cellular Pathology, Nottingham University Hospitals NHS Trust, Nottingham City Hospital, Nottingham, UK
| | - Andrew R. Green
- Nottingham Breast Cancer Research Centre, Academic Unit of Translational Medical Sciences, School of Medicine, University of Nottingham Biodiscovery Institute, Nottingham, UK
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Wang H, Shen M, Shen X, Liu J, Huang W, Jiang X, Liu H, Zeng S, Nan K, Cai S. An enzyme-free sensing platform for miRNA detection and in situ imaging in clinical samples based on DNAzyme cleavage-triggered catalytic hairpin assembly. Biosens Bioelectron 2024; 256:116279. [PMID: 38608496 DOI: 10.1016/j.bios.2024.116279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/20/2024] [Accepted: 04/08/2024] [Indexed: 04/14/2024]
Abstract
MicroRNA (miRNA) is demonstrated to be associated with the occurrence and development of various diseases including cancer. Currently, most miRNA detection methods are confined to in vitro detection and cannot obtain information on the temporal and spatial expression of miRNA in relevant tissues and cells. In this work, we established a novel enzyme-free method that can be applied to both in vitro detection and in situ imaging of miRNA by integrating DNAzyme and catalytic hairpin assembly (CHA) circuits. This developed CHA-Amplified DNAzyme miRNA (CHAzymi) detection system can realize the quantitively in vitro detection of miR-146b (the biomarker of papillary thyroid carcinoma, PTC) ranging from 25 fmol to 625 fmol. This strategy has also been successfully applied to in situ imaging of miR-146b both in human PTC cell TPC-1 and clinical samples, showing its capacity as an alternative diagnostic method for PTC. Furthermore, this CHAzymi system can be employed as a versatile sensing platform for various miRNAs by revising the relevant sequences. The results imply that this system may expand the modality of miRNA detection and show promise as a novel diagnostic tool in clinical settings, providing valuable insights for effective treatment and management of the disease.
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Affiliation(s)
- Hechen Wang
- State Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Minzhe Shen
- State Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xudan Shen
- State Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jiatong Liu
- State Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Wenwen Huang
- State Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xianfeng Jiang
- Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310020, China
| | - Hui Liu
- Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310020, China
| | - Su Zeng
- State Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Kewang Nan
- State Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China; Department of Gastroenterology Surgery of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China; Jinhua Institute of Zhejiang University, Jinhua, 321299, China.
| | - Sheng Cai
- State Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China; Jinhua Institute of Zhejiang University, Jinhua, 321299, China.
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3
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Yan H, Cao G, Wang J, Zhu X, Dong S, Huang Y, Chao M, Li Y, Gao F, Hua L. An enzymatically activated AND-gate DNA logic circuit for tumor cells recognition via multi-microRNAs detection. Biosens Bioelectron 2024; 256:116278. [PMID: 38608497 DOI: 10.1016/j.bios.2024.116278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 03/26/2024] [Accepted: 04/06/2024] [Indexed: 04/14/2024]
Abstract
The DNA-based logic circuit, constructed to mimic biochemical reaction networks, is highly significant in detecting biomarkers at the molecular level. The differences in the expression levels of microRNAs (miRNAs) within different types of cells provide hope for distinguishing cell subtypes. However, reliance on a single miRNA often leads to unreliable results. Herein, we constructed an enzyme-triggered cascade logic circuit based on the AND gate, which is capable of generating corresponding fluorescence signals in the presence of target miRNAs. The introduction of apurinic/apyrimidinic (AP) sites effectively reduces the likelihood of false signal generation. Amplification of the fluorescence signal relies on the catalytic hairpin assembly and the repetitive reuse of the multicomponent nucleic acid enzyme (MNAzyme). We demonstrated that the logic circuit can not only distinguish cancer cells from normal cells but also identify different types of cancer cells. The programmability of the logic circuits and the simplicity of the assay system allow us to modify the functional sequences to recognize different types of biomarkers, thus providing a reference for the identification of various cell subtypes.
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Affiliation(s)
- Hanrong Yan
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, China
| | - Guojun Cao
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, China; Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Jin Wang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, China
| | - Xu Zhu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, China
| | - Shuqing Dong
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, China
| | - Yuqi Huang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, China
| | - Minghao Chao
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, China
| | - Yuting Li
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, China
| | - Fenglei Gao
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, China.
| | - Lei Hua
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, China; Department of Neurosurgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, China.
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Welsch E, Holzer B, Schuster E, Fabikan H, Weinlinger C, Hauptmann-Repitz E, Illini O, Hochmair MJ, Fischer MB, Weiss E, Zeillinger R, Obermayr E. Prognostic significance of circulating tumor cells and tumor related transcripts in small cell lung cancer: A step further to clinical implementation. Int J Cancer 2024; 154:2189-2199. [PMID: 38353516 DOI: 10.1002/ijc.34886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/05/2024] [Accepted: 01/18/2024] [Indexed: 04/14/2024]
Abstract
Small-cell lung cancer (SCLC) is a fatal disease with limited treatment options. Circulating tumor cells (CTCs) in liquid biopsy samples may serve as predictive and prognostic biomarkers; but the analysis of CTCs is still challenging. By using microfluidic or density gradient CTC enrichment in combination with immunofluorescent (IF) staining or qPCR of CTC-related transcripts, we achieved a 60.8% to 88.0% positivity in SCLC blood samples. Epithelial and neuroendocrine transcripts including the druggable target DLL3 were associated with shorter overall survival (OS), indicating the clinical value of these markers in terms of differential diagnosis and treatment decisions. High CTC counts and the presence of CTC duplets detected by IF staining were prognostic for OS, and thus may serve as indicators of disease progression or therapy failure. In patient samples with high CTC load detected by IF staining, a concordance of the transcripts positivity in circulating free plasma RNA and CTCs was observed. Our data emphasize the role of CTCs and CTC-related transcripts and underline the clinical value of liquid biopsy analysis in SCLC.
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Affiliation(s)
- Eva Welsch
- Molecular Oncology Group, Department of Obstetrics and Gynecology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Barbara Holzer
- Molecular Oncology Group, Department of Obstetrics and Gynecology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Eva Schuster
- Molecular Oncology Group, Department of Obstetrics and Gynecology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Hannah Fabikan
- Department of Respiratory and Critical Care Medicine, Karl Landsteiner Institute of Lung Research and Pulmonary Oncology, Vienna, Austria
| | - Christoph Weinlinger
- Department of Respiratory and Critical Care Medicine, Karl Landsteiner Institute of Lung Research and Pulmonary Oncology, Vienna, Austria
| | - Elisabeth Hauptmann-Repitz
- Department of Respiratory and Critical Care Medicine, Karl Landsteiner Institute of Lung Research and Pulmonary Oncology, Vienna, Austria
| | - Oliver Illini
- Department of Respiratory and Critical Care Medicine, Karl Landsteiner Institute of Lung Research and Pulmonary Oncology, Vienna, Austria
| | - Maximilian J Hochmair
- Department of Respiratory and Critical Care Medicine, Karl Landsteiner Institute of Lung Research and Pulmonary Oncology, Vienna, Austria
| | - Michael B Fischer
- Department of Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Vienna, Austria
| | - Esther Weiss
- OncoLab Diagnostics GmbH, Wiener Neustadt, Austria
| | - Robert Zeillinger
- Molecular Oncology Group, Department of Obstetrics and Gynecology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- OncoLab Diagnostics GmbH, Wiener Neustadt, Austria
| | - Eva Obermayr
- Molecular Oncology Group, Department of Obstetrics and Gynecology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
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Li Y, Liu LE, Han H, Yuan X, Ji J, Xue L, Wu Y, Yang R. A signal-switchable photoelectrochemical biosensor for ultrasensitive detection of long non-coding RNA in cancer cells. Talanta 2024; 273:125878. [PMID: 38492286 DOI: 10.1016/j.talanta.2024.125878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 01/12/2024] [Accepted: 03/04/2024] [Indexed: 03/18/2024]
Abstract
Long non-coding RNA (LncRNA) as an emerging tumor biomarker plays a key factor in the early diagnosis of cancer. Herein, an innovative signal-switchable photoelectrochemical (PEC) biosensor based on ZrO2@CuO bimetallic oxides and T7 Exo-assisted signal amplification is reported for the ultrasensitive and selective detection of lncRNA (HOX gene antisense intergenic RNA, HOTAIR) in cancer cells. Firstly, MOFs-derived TiO2 nanodisks as an excellent photoactive material show an anodic background signal. When target lncRNA exists, the abundant auxiliary DNA1 is freed from T7 Exo-assisted cycle signal amplification, and then competitively hybridizes with auxiliary DNA2 on the electrode. Subsequently, bimetallic MOFs-derived ZrO2@CuO octahedra with a high specific surface area and porous structure are introduced into TiO2 nanodisks-modified biosensor, which appears a cathodic photocurrent and achieves a switchable signal. The developed signal-switchable PEC biosensor shows ultrasensitive detection of lncRNA HOTAIR with a detection limit of 0.12 fM, and can eliminate the false interference. Importantly, the established PEC biosensor has good correlation with RT-qPCR analysis (P < 0.05) for the quantification of lncRNA HOTAIR in cancer cells, which has great potential application for biomarker detection in the early diagnosis of cancer.
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Affiliation(s)
- Yuling Li
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Li-E Liu
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Hangchen Han
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Xinxin Yuan
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Jiangying Ji
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Linsheng Xue
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Yongjun Wu
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Ruiying Yang
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China.
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Moysset I, Castrejon N, Garcia-Herrera A, Castillo P, Marginet M, Teixido C, Podlipnik S, Albero-Gonzalez R, Montironi C, Navarro J, Rovira C, Puig S, Carrera C, Alos L. Restrospective reappraisal of the prognostic classification of spitzoid melanocytic neoplasms after BRAF and NRAS mutation characterisation: a single institution experience. Histopathology 2024; 84:1154-1166. [PMID: 38409889 DOI: 10.1111/his.15160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 02/28/2024]
Abstract
AIMS The current WHO classification of melanocytic tumours excludes neoplasms showing BRAF or NRAS mutations from the Spitz category. This study aimed to review and reclassify atypical melanocytic tumours with spitzoid morphological features diagnosed between 2009 and 2021 in our hospital after expanding the molecular profile, including BRAF and NRAS mutations in all cases. METHODS AND RESULTS A total of 71 neoplasms showing spitzoid features (Spitz-like) and atypia were included. The risk of progression of tumours was first studied by integrating the morphology, immunohistochemistry (p16, Ki67, HMB45 and PRAME) and fluorescence in-situ hybridisation (FISH) results (melanoma multiprobe and 9p21). In a second step, after expanding the molecular study, including BRAF and NRAS mutational status, the neoplasms were finally classified into four subgroups: atypical Spitz tumour (AST, n = 45); BRAF-mutated naevus/low-grade melanocytoma with spitzoid morphology (BAMS, n = 2); Spitz melanoma (SM, n = 14); and BRAF or NRAS mutated melanoma with spitzoid features (MSF, n = 10). Follow-up of patients revealed uneventful results for AST and BAMS. Only one SM presented lymph node metastasis after 134 months. Conversely, patients with MSF showed an unfavourable outcome: three developed lymph node metastases after a mean time of 22 months, with one patient presenting distant metastasis and dying of the disease 64 months from diagnosis. The progression-free survival showed significant differences between the four groups of spitzoid tumours (P < 0.001) and between both melanoma subtypes (P = 0.012). CONCLUSIONS The classification and prognostication of atypical neoplasms with spitzoid features requires the integration of histomorphology with the molecular investigation of tumours, which should include BRAF and NRAS mutational status.
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Affiliation(s)
- Irene Moysset
- Department of Pathology, Consorci Sanitari Integral, Barcelona, Spain
- University of Barcelona, Barcelona, Spain
| | - Natalia Castrejon
- Department of Pathology, Hospital Clinic of Barcelona, Barcelona, Spain
| | - Adriana Garcia-Herrera
- University of Barcelona, Barcelona, Spain
- Department of Pathology, Hospital Clinic of Barcelona, Barcelona, Spain
- August Pi I Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Paola Castillo
- University of Barcelona, Barcelona, Spain
- Department of Pathology, Hospital Clinic of Barcelona, Barcelona, Spain
- August Pi I Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Marta Marginet
- Department of Pathology, Hospital Clinic of Barcelona, Barcelona, Spain
| | - Cristina Teixido
- University of Barcelona, Barcelona, Spain
- Department of Pathology, Hospital Clinic of Barcelona, Barcelona, Spain
- August Pi I Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
- Molecular Biology Core, Hospital Clinic Barcelona, Barcelona, Spain
| | | | - Raquel Albero-Gonzalez
- University of Barcelona, Barcelona, Spain
- Department of Pathology, Hospital Clinic of Barcelona, Barcelona, Spain
- August Pi I Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Carla Montironi
- Department of Pathology, Hospital Clinic of Barcelona, Barcelona, Spain
- Molecular Biology Core, Hospital Clinic Barcelona, Barcelona, Spain
| | - Judit Navarro
- Department of Pathology, Hospital Clinic of Barcelona, Barcelona, Spain
| | - Carlota Rovira
- Department of Pathology, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Susana Puig
- University of Barcelona, Barcelona, Spain
- August Pi I Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
- Department of Dermatology, Hospital Clínic of Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Cristina Carrera
- University of Barcelona, Barcelona, Spain
- August Pi I Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
- Department of Dermatology, Hospital Clínic of Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Llucia Alos
- University of Barcelona, Barcelona, Spain
- Department of Pathology, Hospital Clinic of Barcelona, Barcelona, Spain
- August Pi I Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
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Mata DA, Lee JK, Shanmugam V, Marcus CB, Schrock AB, Williams EA, Ritterhouse LL, Hickman RA, Janovitz T, Patel NR, Kroger BR, Ross JS, Mirza KM, Oxnard GR, Vergilio JA, Elvin JA, Benhamida JK, Decker B, Xu ML. Liquid biopsy-based circulating tumour (ct)DNA analysis of a spectrum of myeloid and lymphoid malignancies yields clinically actionable results. Histopathology 2024; 84:1224-1237. [PMID: 38422618 DOI: 10.1111/his.15168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 02/14/2024] [Accepted: 02/15/2024] [Indexed: 03/02/2024]
Abstract
AIMS Liquid biopsy (LBx)-based next-generation sequencing (NGS) of circulating tumour DNA (ctDNA) can facilitate molecular profiling of haematopoietic neoplasms (HNs), particularly when tissue-based NGS is infeasible. METHODS AND RESULTS We studied HN LBx samples tested with FoundationOne Liquid CDx, FoundationOne Liquid, or FoundationACT between July 2016 and March 2022. We identified 271 samples: 89 non-Hodgkin lymphoma (NHL), 43 plasma-cell neoplasm (PCN), 41 histiocytoses, 27 myelodysplastic syndrome (MDS), 25 diffuse large B-cell lymphoma (DLBCL), 22 myeloproliferative neoplasm (MPN), 14 Hodgkin lymphoma (HL), and 10 acute myeloid leukaemia (AML). Among 73.4% with detectable pathogenic alterations, median maximum somatic allele frequency (MSAF) was 16.6%, with AML (36.2%), MDS (19.7%), and MPN (44.5%) having higher MSAFs than DLBCL (3.9%), NHL (8.4%), HL (1.5%), PCN (2.8%), and histiocytoses (1.8%) (P = 0.001). LBx detected characteristic alterations across HNs, including in TP53, KRAS, MYD88, and BTK in NHLs; TP53, KRAS, NRAS, and BRAF in PCNs; IGH in DLBCL; TP53, ATM, and PDCD1LG2 in HL; BRAF and MAP2K1 in histiocytoses; TP53, SF3B1, DNMT3A, TET2, and ASXL1 in MDS; JAK2 in MPNs; and FLT3, IDH2, and NPM1 in AML. Among 24 samples, the positive percent agreement by LBx was 75.7% for variants present in paired buffy coat, marrow, or tissues. Also, 75.0% of pairs exhibited alterations only present on LBx. These were predominantly subclonal (clonal fraction of 3.8%), reflecting the analytical sensitivity of LBx. CONCLUSION These data demonstrate that LBx can detect relevant genomic alterations across HNs, including at low clonal fractions, suggesting a potential clinical utility for identifying residual or emerging therapy-resistant clones that may be undetectable in site-specific tissue biopsies.
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Affiliation(s)
| | | | - Vignesh Shanmugam
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Erik A Williams
- Foundation Medicine, Inc., Cambridge, MA, USA
- Department of Pathology and Laboratory Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | | | | | | | - Benjamin R Kroger
- Division of Hematology/Oncology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jeffrey S Ross
- Foundation Medicine, Inc., Cambridge, MA, USA
- Departments of Pathology, Urology, and Medicine (Oncology), State University of New York Upstate Medical University, Syracuse, New York, USA
| | - Kamran M Mirza
- Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA
| | | | | | | | - Jamal K Benhamida
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Mina L Xu
- Department of Pathology, Yale New-Haven Hospital, Yale School of Medicine, New Haven, CT, USA
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8
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Padhye BD, Nawaz U, Hains PG, Reddel RR, Robinson PJ, Zhong Q, Poulos RC. Proteomic insights into paediatric cancer: Unravelling molecular signatures and therapeutic opportunities. Pediatr Blood Cancer 2024; 71:e30980. [PMID: 38556739 DOI: 10.1002/pbc.30980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 03/13/2024] [Accepted: 03/14/2024] [Indexed: 04/02/2024]
Abstract
Survival rates in some paediatric cancers have improved greatly over recent decades, in part due to the identification of diagnostic, prognostic and predictive molecular signatures, and the development of risk-directed therapies. However, other paediatric cancers have proved difficult to treat, and there is an urgent need to identify novel biomarkers that reveal therapeutic opportunities. The proteome is the total set of expressed proteins present in a cell or tissue at a point in time, and is vastly more dynamic than the genome. Proteomics holds significant promise for cancer research, as proteins are ultimately responsible for cellular phenotype and are the target of most anticancer drugs. Here, we review the discoveries, opportunities and challenges of proteomic analyses in paediatric cancer, with a focus on mass spectrometry (MS)-based approaches. Accelerating incorporation of proteomics into paediatric precision medicine has the potential to improve survival and quality of life for children with cancer.
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Affiliation(s)
- Bhavna D Padhye
- Cancer Centre for Children, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
- Kids Research, Children's Cancer Research Unit, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Urwah Nawaz
- ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
| | - Peter G Hains
- ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
| | - Roger R Reddel
- ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
| | - Phillip J Robinson
- ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
| | - Qing Zhong
- ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
| | - Rebecca C Poulos
- ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
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Huang X, Huang J, Zhou X, Zhang C, Ding X, Wong PJC, Wang Y, Zhang R. Whole-exome sequencing has revealed novel genetic characteristics in intracranial germ cell tumours in the Chinese. Histopathology 2024; 84:1199-1211. [PMID: 38409885 DOI: 10.1111/his.15155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 12/02/2023] [Accepted: 01/26/2024] [Indexed: 02/28/2024]
Abstract
AIMS Intracranial germ cell tumour (IGCT) is a type of rare central nervous system tumour that mainly occurs in children and adolescents, with great variation in its incidence rate and molecular characteristics in patients from different populations. The genetic alterations of IGCT in the Chinese population are still unknown. METHODS AND RESULTS In this study, 47 patients were enrolled and their tumour specimens were analysed by whole-exome sequencing (WES). We found that KIT was the most significantly mutated gene (15/47, 32%), which mainly occurred in the germinoma group (13/20, 65%), and less frequently in NGGCT (2/27, 7%). Copy number variations (CNVs) of FGF6 and TFE3 only appeared in NGGCT patients (P = 0.003 and 0.032, respectively), while CNVs of CXCR4, RAC2, PDGFA, and FEV only appeared in germinoma patients (P = 0.004 of CXCR4 and P = 0.027 for the last three genes). Compared with a previous Japanese cohort, the somatic mutation rates of RELN and SYNE1 were higher in the Chinese. Prognostic analysis showed that the NF1 mutation was associated with shorter overall survival and progression-free survival in IGCT patients. Clonal evolution analysis revealed an early branched evolutionary pattern in two IGCT patients who underwent changes in the histological subtype or degree of differentiation during disease surveillance. CONCLUSION This study indicated that Chinese IGCT patients may have distinct genetic characteristics and identified several possible genetic alterations that have the potential to become prognostic biomarkers of NGGCT patients.
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Affiliation(s)
- Xiang Huang
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Neurosurgical Institute of Fudan University, Shanghai, China
- Shanghai Clinical Medical Center of Neurosurgery, Shanghai, China
- National Center for Neurological Disorders, Shanghai, China
| | - Jianhan Huang
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Neurosurgical Institute of Fudan University, Shanghai, China
| | - Xiaoyu Zhou
- GenomiCare Biotechnology (Shanghai) Co. Ltd, Shanghai, China
| | - Chao Zhang
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Neurosurgical Institute of Fudan University, Shanghai, China
- Shanghai Clinical Medical Center of Neurosurgery, Shanghai, China
- National Center for Neurological Disorders, Shanghai, China
| | - Xinghua Ding
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Neurosurgical Institute of Fudan University, Shanghai, China
- Shanghai Clinical Medical Center of Neurosurgery, Shanghai, China
- National Center for Neurological Disorders, Shanghai, China
| | - Peter Jih Cheng Wong
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Neurosurgical Institute of Fudan University, Shanghai, China
| | - Yang Wang
- Department of Radiotherapy, Huashan Hospital, Fudan University, Shanghai, China
| | - Rong Zhang
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Neurosurgical Institute of Fudan University, Shanghai, China
- Shanghai Clinical Medical Center of Neurosurgery, Shanghai, China
- National Center for Neurological Disorders, Shanghai, China
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10
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Svanøe AA, Humlevik ROC, Knutsvik G, Sæle AKM, Askeland C, Ingebriktsen LM, Hugaas U, Kvamme AB, Tegnander AF, Krüger K, Davidsen B, Hoivik EA, Aas T, Stefansson IM, Akslen LA, Wik E. Age-related phenotypes in breast cancer: A population-based study. Int J Cancer 2024; 154:2014-2024. [PMID: 38319154 DOI: 10.1002/ijc.34863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 12/21/2023] [Accepted: 01/05/2024] [Indexed: 02/07/2024]
Abstract
Breast cancer in young (<40 years) is associated with a higher frequency of aggressive tumor types and poor prognosis. It remains unclear if there is an underlying age-related biology that contributes to the unfavorable outcome. We aim to investigate the relationship between age and breast cancer biology, with emphasis on proliferation. Clinico-pathologic information, immunohistochemical markers and follow-up data were obtained for all patients aged <50 (Bergen cohort-1; n = 355, not part of a breast screening program) and compared to previously obtained information on patients aged 50 to 69 years (Bergen cohort-2; n = 540), who participated in the Norwegian Breast Cancer Screening Program. Young breast cancer patients presented more aggressive tumor features such as hormone receptor negativity, HER2 positivity, lymph-node metastasis, the HER2-enriched and triple-negative subtypes and shorter survival. Age <40 was significantly associated with higher proliferation (by Ki67). Ki67 showed weaker prognostic value in young patients. We point to aggressive phenotypes and increased tumor cell proliferation in breast cancer of the young. Hence, tumors of young breast cancer patients may present unique biological features, also when accounting for screen/interval differences, that may open for new clinical opportunities, stratifying treatment by age.
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Affiliation(s)
- Amalie A Svanøe
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Rasmus O C Humlevik
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Gøril Knutsvik
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Anna K M Sæle
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Cecilie Askeland
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Lise M Ingebriktsen
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Ulrikke Hugaas
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Amalie B Kvamme
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Amalie F Tegnander
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Kristi Krüger
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | | | - Erling A Hoivik
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Turid Aas
- Department of Surgery, Haukeland University Hospital, Bergen, Norway
| | - Ingunn M Stefansson
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Lars A Akslen
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Elisabeth Wik
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Department of Pathology, Haukeland University Hospital, Bergen, Norway
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11
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Xue Y, Zhao G, Song L, Qiao L, Huang C, Wang K, Wang T. The signature of cancer methylation markers in maternal plasma: Factors influencing the development and application of cancer liquid biopsy assay. Gene 2024; 906:148261. [PMID: 38342253 DOI: 10.1016/j.gene.2024.148261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/17/2024] [Accepted: 02/06/2024] [Indexed: 02/13/2024]
Abstract
BACKGROUND DNA methylation is highly correlated with cancer and embryo development, and plasma-based methylation markers have been widely used for cancer early detection. However, whether the commonly used cancer methylation markers cause "false positives" in the plasma of pregnant women has not been comprehensively evaluated. METHODS We conducted a case-control study from February 2021 to March 2023, which included 138 pregnant women and 44 control women. Plasma cell-free DNA (cfDNA) was isolated and bisulfite-converted, and then the methylation levels of eight methylated markers related to gastrointestinal cancer (SEPT9, SDC2, C9orf50, KCNQ5, CLIP4, TFPI2, ELMO1 and ZNF582) and three markers related to lung cancer (SHOX2, RASSF1A and PTGER4) were analyzed. RESULTS When comparing the plasma of pregnant women to that of control women, SEPT9, CLIP4, ZNF582, SHOX2, RASSF1A and PTGER showed significantly higher levels of methylation (p < 0.05). These positive signals originate from the placenta/fetus rather than the mother. We found no discernible difference in DNA methylation levels between fetal cfDNA fractions of < 10 % and ≥ 10 % in pregnant women (p > 0.05), while CLIP4 and PTGER4 showed high methylation levels in the assisted fertilization group compared to the natural fertilization group (p < 0.05). CONCLUSION Our study shows that cancer and fetus/placenta exhibit similar DNA methylation patterns, and some gastrointestinal cancer and lung cancer-related methylation markers also show positives in maternal plasma. This is an important consideration in the design and application of plasma-based cancer liquid biopsy assays.
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Affiliation(s)
- Ying Xue
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu 215000, China
| | - Guodong Zhao
- ZJUT Yinhu Research Institute of Innovation and Entrepreneurship Fuyang District, Hangzhou, Zhejiang 311400, China; Zhejiang University Kunshan Biotechnology Laboratory, Zhejiang University Kunshan Innovation Institute, Kunshan, Jiangsu 215300, China; Suzhou VersaBio Technologies Co. Ltd., Kunshan, Jiangsu 215300, China.
| | - Lishuang Song
- Suzhou VersaBio Technologies Co. Ltd., Kunshan, Jiangsu 215300, China
| | - Longwei Qiao
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu 215000, China
| | - Chao Huang
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu 215000, China
| | - Kai Wang
- Suzhou VersaBio Technologies Co. Ltd., Kunshan, Jiangsu 215300, China
| | - Ting Wang
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu 215000, China.
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12
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Hui Z, Wang B, Liu Z, Wei J, Gan J, Landstrom M, Mu Y, Zang G. TGFβ-induced EN1 promotes tumor budding of adenoid cystic carcinoma in patient-derived organoid model. Int J Cancer 2024; 154:1814-1827. [PMID: 38282121 DOI: 10.1002/ijc.34856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 11/23/2023] [Accepted: 12/20/2023] [Indexed: 01/30/2024]
Abstract
Adenoid cystic carcinoma (ACC) and basal cell adenoma (BCA) share many histological characteristics and often need a differential diagnosis in clinical pathology. Recently, we found homeobox protein engrailed-1 (EN1) was a potential diagnostic marker for ACC in an organoids library of salivary gland tumors (SGTs). Here we aim to confirm EN1 as a differential diagnostic marker for ACC, and further investigate the regulatory mechanism and biological function of EN1 in tumor progression. The transcriptional analysis, quantitative polymerase chain reaction, Western blot and immunohistochemistry staining were performed and revealed that EN1 was specifically and highly expressed in ACC, and accurately differentiated ACC from BCA. Furthermore, TGFβ signaling pathway was found associated with ACC, and the regulation of EN1 through TGFβ was detected in the human ACC cell lines and patient-derived organoids (PDOs). TGFβ-induced EN1 was important in promoting tumor budding in the PDOs model. Interestingly, a high level of EN1 and TGFβ1 in the budding tips was observed in ACC clinical samples, and the expression of EN1 and TGFβ1 in ACC was significantly associated with the clinical stage. In summary, our study verified EN1 is a good diagnostic marker to differentiate ACC from BCA. TGFβ-induced EN1 facilitates the tumor budding of ACC, which might be an important mechanism related to the malignant phenotype of ACC.
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Affiliation(s)
- Zhixuan Hui
- Liaoning Provincial Key Laboratory of Oral Disease, School and Hospital of Stomatology, China Medical University, Shenyang City, China
| | - Bo Wang
- Liaoning Provincial Key Laboratory of Oral Disease, School and Hospital of Stomatology, China Medical University, Shenyang City, China
| | - Zhengyan Liu
- Liaoning Provincial Key Laboratory of Oral Disease, School and Hospital of Stomatology, China Medical University, Shenyang City, China
| | - Jinhui Wei
- Liaoning Provincial Key Laboratory of Oral Disease, School and Hospital of Stomatology, China Medical University, Shenyang City, China
| | - Jiaxing Gan
- Liaoning Provincial Key Laboratory of Oral Disease, School and Hospital of Stomatology, China Medical University, Shenyang City, China
| | - Marene Landstrom
- Department of Medical Bioscience, Building 6M, Umeå University, Umeå, Sweden
| | - Yabing Mu
- Department of Medical Bioscience, Building 6M, Umeå University, Umeå, Sweden
| | - Guangxiang Zang
- Liaoning Provincial Key Laboratory of Oral Disease, School and Hospital of Stomatology, China Medical University, Shenyang City, China
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13
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Rohani Z, Sazegar H, Rahimi E. Unlocking the potential of Escherichia coli K-12: A novel approach for malignancy reduction in colorectal cancer through gene expression modulation. Gene 2024; 906:148266. [PMID: 38342251 DOI: 10.1016/j.gene.2024.148266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 01/28/2024] [Accepted: 02/06/2024] [Indexed: 02/13/2024]
Abstract
Studies have noted the association between Escherichia coli K-12 (E. coli K-12) and the reduction of malignancy in colorectal cancer (CRC). However, the molecular mechanisms underlying this relationship have not been thoroughly explored. The aim of this study was to identify the genes influenced by E. coli K-12 and their connection to CRC. We identified the genes affected by E. coli K-12 using the GSE50040 dataset. Additionally, we investigated the relationship between the expression of genes affected by E. coli K-12 and CRC using the cancer genome atlas data. The association between the expression of E. coli K-12-affected genes and patient prognosis was investigated using clinical data. Pathways related to CRC and E. coli K-12-related genes were analyzed using the Enrichr tool. Furthermore, we employed a protein-protein interaction (PPI) network to identify hub genes associated with both E. coli K-12 and CRC. To validate our findings, we conducted RT-qPCR analysis on CRC samples and adjacent normal tissue. The results of GSE50040 showed that E. coli K-12 could change the expression of many genes related to CRC in colorectal cell lines. The results showed that E. coli K-12 reduces the expression of several genes linked to the main pathways used by cancer cells, such as the metastasis, WNT, cell proliferation pathway, and mTORC1. It was demonstrated that elevated BGN, FJX1, and LZTS1 expression is linked to a bad prognosis in patients and that E. coli K-12 may be able to lower this expression. Also, based on the PPI network, genes such as KLF4 and CXCL3 were identified as hub genes related to genes affected by E. coli K-12. When KLF4 and CXCL3 expression levels in cancer samples were compared to nearby normal tissue, a significant change in these genes' expression levels was found in CRC. Our findings demonstrated the potential relationship between oncogene genes and genes impacted by E. coli K-12. Also, our findings demonstrated that E. coli K-12 may regulate the expression of genes linked to a high death rate. In summary, the results of this study suggest that E. coli K-12 can be regarded as a significant probiotic with the potential to mitigate the risk of CRC development.
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Affiliation(s)
- Zeinab Rohani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Hossein Sazegar
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| | - Ebrahim Rahimi
- Department of Food Hygiene, Faculty of Veterinary Medicine, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
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14
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Qiu H, Jiang B, Chen Y, Lin Z, Zheng W, Cao X. Featured lncRNA-based signature for discriminating prognosis and progression of hepatocellular carcinoma. J Appl Genet 2024; 65:355-366. [PMID: 38347289 DOI: 10.1007/s13353-024-00836-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/16/2024] [Accepted: 01/20/2024] [Indexed: 02/20/2024]
Abstract
Long non-coding RNAs (lncRNAs) have been implicated in carcinogenesis and progression of hepatocellular carcinoma (HCC). This study aimed to identify a robust lncRNA signature for predicting the survival of HCC patients. We performed an integrated analysis of the lncRNA expression profiling in The Cancer Genome Atlas (TCGA)-liver hepatocellular carcinoma database to identify the prognosis-related lncRNA for the HCC. The HCC cohort was randomly divided into a training set (n = 250) and a testing set (n = 113). Following a two-step screening, we identified an 18-lncRNA signature risk score. The high-risk subgroups had significantly shorter survival time than the low-risk group in both the training set (P < 0.0001) and the testing set (P = 0.005). Stratification analysis revealed that the prognostic value of the lncRNA-based signature was independent of the tumor stage and pathologic stage. The area under the receiver operating characteristic curve (AUROC) of the 18-lncRNA signature risk score was 0.826 (95%CI, 0.764-0.888), 0.817 (95%CI, 0.759-0.876), and 0.799 (95%CI, 0.731-0.867) for 1-year, 3-year, and 5-year follow-up, respectively. Bioinformatics analyses indicated that the 18 lncRNA might mediate cell cycle, DNA replication processes, and canonical cancer-related pathways, in which MCM3AP-AS1 was a potential target for HCC. In conclusion, the 18-lncRNA signature was a robust predictive biomarker for the prognosis and progression of HCC.
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Affiliation(s)
- Huiyuan Qiu
- Medical School of Nantong University, Nantong, 226001, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Bo Jiang
- Department of Gastroenterology, Suqian First People's Hospital, Suqian, Jiangsu, China
| | - Yinqi Chen
- Medical School of Nantong University, Nantong, 226001, China
| | - Zhaoyi Lin
- Medical School of Nantong University, Nantong, 226001, China
| | - Wenjie Zheng
- Medical School of Nantong University, Nantong, 226001, China.
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China.
| | - Xiaolei Cao
- Medical School of Nantong University, Nantong, 226001, China.
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15
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Sorscher S, Gor P. Interpreting quantitative RNA expression prognostic and predictive results generated from synchronous rather than solitary breast cancers. Biomarkers 2024; 29:115-117. [PMID: 38444305 DOI: 10.1080/1354750x.2024.2324871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 02/25/2024] [Indexed: 03/07/2024]
Affiliation(s)
| | - Priya Gor
- Penn Hematology/Oncology Voorhees, Voorhees, NJ, USA
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16
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Rong C, Liang C, Shen J, Zhang Y, Wang Q, Yang F, Chen Y, Luo Y, Gu M, Gao P, Xia Y, Duan S. CLLU1 as an emerging biomarker in chronic lymphoid leukemia. Hum Cell 2024; 37:625-632. [PMID: 38507118 DOI: 10.1007/s13577-024-01051-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 02/26/2024] [Indexed: 03/22/2024]
Abstract
CLLU1, a disease-specific gene associated with chronic lymphoid leukemia (CLL), is located on chromosome 12q22. Previous studies considered CLLU1 to be a non-coding RNA; however, recent research has discovered that its coding sequence region possesses the potential to encode a short peptide similar to interleukin-4. Remarkably, abnormally elevated expression of CLLU1 has only been detected in chronic lymphoid leukemia among all hematological cancers. High CLLU1 expression often indicates more malignant pathological features and an unfavorable prognosis for patients. Importantly, the expression level of CLLU1 remains unaffected by the passage of time or therapeutic interventions, thus rendering it a novel prognostic marker. This article provides a comprehensive summary of relevant research findings on CLLU1 in the context of CLL prognosis and clinical applications, aiming to guide subsequent theoretical and clinical investigations in this field.
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MESH Headings
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Neoplasm Proteins/genetics
- RNA, Long Noncoding/genetics
- Biomarkers, Tumor/genetics
- Genes, Neoplasm
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Affiliation(s)
- Chunmeng Rong
- Department of Hematology, Yuyao People's Hospital of Zhejiang Province, Ningbo, Zhejiang, China
| | - Chenhao Liang
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Jinze Shen
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Yuhua Zhang
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Qurui Wang
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Fang Yang
- Department of Hematology, Yuyao People's Hospital of Zhejiang Province, Ningbo, Zhejiang, China
| | - Yalu Chen
- Department of Hematology, Yuyao People's Hospital of Zhejiang Province, Ningbo, Zhejiang, China
| | - Yuqing Luo
- Department of Hematology, Yuyao People's Hospital of Zhejiang Province, Ningbo, Zhejiang, China
| | - Meier Gu
- Department of Hematology, Yuyao People's Hospital of Zhejiang Province, Ningbo, Zhejiang, China
| | - Panpan Gao
- Department of Hematology, Yuyao People's Hospital of Zhejiang Province, Ningbo, Zhejiang, China
| | - Yongming Xia
- Department of Hematology, Yuyao People's Hospital of Zhejiang Province, Ningbo, Zhejiang, China.
| | - Shiwei Duan
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China.
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17
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BinHumaid FS, Goel A, Gordon NS, Abbotts B, Cheng KK, Zeegers MP, James ND, Altaweel WM, Seyam RM, Meyer BF, Arnold R, Ward DG, Bryan RT. Circulating Tumour DNA Detection By The Urine-Informed Analysis Of Archival Serum Samples From Muscle-Invasive Bladder Cancer Patients. Eur Urol 2024; 85:508-509. [PMID: 38302315 DOI: 10.1016/j.eururo.2024.01.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 12/22/2023] [Accepted: 01/11/2024] [Indexed: 02/03/2024]
Affiliation(s)
- Faisal S BinHumaid
- Bladder Cancer Research Centre, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK; Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Anshita Goel
- Bladder Cancer Research Centre, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Naheema S Gordon
- Bladder Cancer Research Centre, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Ben Abbotts
- Bladder Cancer Research Centre, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - K K Cheng
- Institute of Applied Health Sciences, University of Birmingham, Birmingham, UK
| | | | | | - Waleed M Altaweel
- Department of Urology, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Raouf M Seyam
- Department of Urology, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Brian F Meyer
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Roland Arnold
- Bladder Cancer Research Centre, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Douglas G Ward
- Bladder Cancer Research Centre, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Richard T Bryan
- Bladder Cancer Research Centre, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK.
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18
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Li M, Xie S, Hou T, Shao T, Kuang J, Liu C, Qu Y, Lu C, Liu J, Liu X, Zhu L, Zhu L. Circulating Tumor DNA Profiling Approach Based on In Silico Background Elimination Guides Chemotherapy in Nasopharyngeal Carcinoma. Clin Pharmacol Ther 2024; 115:993-1006. [PMID: 38037868 DOI: 10.1002/cpt.3125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 11/17/2023] [Indexed: 12/02/2023]
Abstract
Circulating tumor DNA (ctDNA) analysis increasingly provides a promising minimally invasive alternative to tissue biopsies in precision oncology. However, there are no ctDNA analysis approaches available in nasopharyngeal carcinoma (NPC) and current methods of ctDNA mutation profiling have limited resolution because of the high background noise and false-positive rate caused by benign variants in plasma cell-free DNA (cfDNA), majorly generated during clonal hematopoiesis. Although personalized parallel white blood cell genome sequencing suppresses the noise of clonal hematopoiesis variances, the system cost and complexity restrict its extensive application in clinical settings. We developed Matched WBC Genome sequencing Independent CtDNA profiling (MaGIC) approaches, which synergically integrated a ctDNA capturing panel for a hybrid capture cfDNA deep sequencing, in silico background elimination, and a reliable readout measurement. We profiled the ctDNAs of 80 plasma samples from 40 patients with NPC before and during chemotherapy by MaGICs. In addition, the public cfDNA sequencing data and The Cancer Genome Atlas project data were analyzed by MaGICs to evaluate their application in other scenarios of patient classification. The MaGIC version-2 has the ability to predict the chemosensitivity of patients with NPC with high accuracy by utilizing a single sample of liquid biopsy from each patient prior to a standardized treatment regimen. Moreover, both versions of MaGICs are of ideal performance in the diagnosis of patients with prostate cancer by liquid biopsy and prognosis prediction of multiple cancers by tissue biopsy. This study has the potential to enhance the sensitivity and expand the application scope of ctDNA detection, independently of other paired genome sequencing methods. As a result, it might further increase the clinical utilization of liquid biopsy based on ctDNA.
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Affiliation(s)
- Ming Li
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, China
- Jiuquan Satellite Launch Centre, Jiuquan, China
| | - Sisi Xie
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, China
| | - Tao Hou
- Department of Oncology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Tong Shao
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, China
| | - Jingyu Kuang
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, China
| | - Chuanyang Liu
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, China
| | - Ying Qu
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, China
| | - Chenyu Lu
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, China
| | - Jiali Liu
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, China
| | - Xianling Liu
- Department of Oncology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Lingyun Zhu
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, China
| | - Lvyun Zhu
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, China
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19
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Song HH, Park H, Cho D, Bang HI, Oh HJ, Kim J. Optimization of a Protocol for Isolating Cell-free DNA From Cerebrospinal Fluid. Ann Lab Med 2024; 44:294-298. [PMID: 38151854 PMCID: PMC10813833 DOI: 10.3343/alm.2023.0267] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 11/01/2023] [Accepted: 12/08/2023] [Indexed: 12/29/2023] Open
Abstract
A standardized protocol for the isolation of cell-free DNA (cfDNA) from cerebrospinal fluid (CSF) is lacking. Therefore, we established a cfDNA isolation protocol optimized for clinical CSF specimens, integrating acceptable modifications and using artificial CSF generated from remnant CSF spiked with reference cell-free tumor DNA (ctDNA). We compared the isolation yields of in vitro diagnostic (IVD)-certified column-based (CB) and magnetic bead-based (MB) isolation. Furthermore, we modified both methods, including pre- and post-elution steps. To confirm ctDNA integrity and quantify the variant allele frequency after isolation, we performed droplet digital PCR (ddPCR) targeting IDH1 R132C in the reference ctDNA. MB isolation had a higher yield than CB isolation (P<0.0001), and post-isolation vacuum increased the final concentration in both methods, with little effect on cfDNA integrity. Our study provides a protocol to maximize CSF-ctDNA concentrations in IVD testing and future studies.
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Affiliation(s)
- Ho Hyun Song
- Department of Interdisciplinary Program in Biomedical Science, Graduate School, Soonchunhyang University, Asan, Korea
| | - Hyeran Park
- Department of Neurosurgery, Soonchunhyang University Seoul Hospital, Seoul, Korea
| | - Doohwan Cho
- Department of Laboratory Medicine, Soonchunhyang University Seoul Hospital, Seoul, Korea
| | - Hae In Bang
- Department of Laboratory Medicine, Soonchunhyang University Seoul Hospital, Seoul, Korea
| | - Hyuk-Jin Oh
- Department of Neurosurgery, Soonchunhyang University Cheonan Hospital, Cheonan, Korea
| | - Jieun Kim
- Department of Laboratory Medicine, Soonchunhyang University Seoul Hospital, Seoul, Korea
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20
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Hatthakarnkul P, Pennel K, Alexander P, van Wyk H, Roseweir A, Inthagard J, Hay J, Andersen D, Maka N, Park J, Roxburgh C, Thuwajit C, McMillan D, Edwards J. Histopathological tumour microenvironment score independently predicts outcome in primary operable colorectal cancer. J Pathol Clin Res 2024; 10:e12374. [PMID: 38650367 PMCID: PMC11035902 DOI: 10.1002/2056-4538.12374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 02/20/2024] [Accepted: 03/26/2024] [Indexed: 04/25/2024]
Abstract
Colorectal cancer (CRC) is a heterogenous malignancy and research is focused on identifying novel ways to subtype patients. In this study, a novel classification system, tumour microenvironment score (TMS), was devised based on Klintrup-Mäkinen grade (KMG), tumour stroma percentage (TSP), and tumour budding. TMS was performed using a haematoxylin and eosin (H&E)-stained section from retrospective CRC discovery and validation cohorts (n = 1,030, n = 787). TMS0 patients had high KMG, TMS1 were low for KMG, TSP, and budding, TMS2 were high for budding, or TSP and TMS3 were high for TSP and budding. Scores were assessed for association with survival and clinicopathological characteristics. Mutational landscaping and Templated Oligo-Sequencing (TempO-Seq) profiling were performed to establish differences in the underlying biology of TMS. TMS was independently prognostic in both cohorts (p < 0.001, p < 0.001), with TMS3 predictive of the shortest survival times. TMS3 was associated with adverse clinical features including sidedness, local and distant recurrence, higher T stage, higher N stage, and presence of margin involvement. Gene set enrichment analysis of TempO-Seq data showed higher expression of genes associated with hallmarks of cancer pathways including epithelial to mesenchymal transition (p < 0.001), IL2 STAT5 signalling (p = 0.007), and angiogenesis (p = 0.017) in TMS3. Additionally, enrichment of immunosuppressive immune signatures was associated with TMS3 classification. In conclusion, TMS represents a novel and clinically relevant method for subtyping CRC patients from a single H&E-stained tumour section.
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Affiliation(s)
- Phimmada Hatthakarnkul
- School of Cancer SciencesUniversity of GlasgowGlasgowUK
- Biomedical Science Program, Faculty of Medicine Siriraj HospitalMahidol UniversityBangkokThailand
| | | | - Peter Alexander
- School of Cancer SciencesUniversity of GlasgowGlasgowUK
- Academic Unit of SurgeryUniversity of GlasgowUK
| | | | | | | | - Jennifer Hay
- Glasgow Tissue Research FacilityQueen Elizabeth University HospitalGlasgowUK
| | - Ditte Andersen
- Bioclavis LtdQueen Elizabeth University HospitalGlasgowUK
| | - Noori Maka
- Department of PathologyQueen Elizabeth HospitalGlasgowUK
| | - James Park
- Department of SurgeryQueen Elizabeth University HospitalGlasgowUK
| | - Campbell Roxburgh
- School of Cancer SciencesUniversity of GlasgowGlasgowUK
- Academic Unit of SurgeryUniversity of GlasgowUK
| | - Chanitra Thuwajit
- Biomedical Science Program, Faculty of Medicine Siriraj HospitalMahidol UniversityBangkokThailand
| | - Donald McMillan
- School of Cancer SciencesUniversity of GlasgowGlasgowUK
- Academic Unit of SurgeryUniversity of GlasgowUK
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21
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Wang X, Gao Y, Wang H, Gong X, Bao P. Tumor markers for lipid metabolism-related genes: Based on small cell lung cancer and bronchial asthma dual analysis. Environ Toxicol 2024; 39:2855-2868. [PMID: 38293814 DOI: 10.1002/tox.24152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/09/2024] [Accepted: 01/17/2024] [Indexed: 02/01/2024]
Abstract
Numerous studies have elucidated the intricate relationship between bronchial asthma and small cell lung cancer (SCLC), as well as the role lipid metabolism genes play in transitioning from bronchial asthma to SCLC. Despite this, the predictive power of single gene biomarkers remains insufficient and necessitates the development of more accurate prognostic models. In our study, we downloaded and preprocessed scRNA-seq of SCLC from the GEO database GSE164404 and severe asthma scRNA-seq from GSE145013 using the Seurat package. Using the MSigDB database and geneCard database, we selected lipid metabolism-related genes and performed scRNA-seq data analysis from the gene expression GEO database, aiming to uncover potential links between immune signaling pathways in bronchial asthma and SCLC. Our investigations yielded differentially expressed genes based on the scRNA-seq dataset related to lipid metabolism. We executed differential gene analysis, gene ontology, and Kyoto Encyclopedia of Genes and Genomes analyses. In-depth GSEA pathway activation analysis, crucial target gene predictions via protein-protein interactions, and key cluster gene evaluations for differential and diagnostic ROC values correlation analysis confirmed that key cluster genes are significant predictors for the progression of bronchial asthma to SCLC. To validate our findings, we performed wet laboratory experiments using real-time quantitative PCR to assess the expression of these relevant genes in SCLC cell lines. In conclusion, this research proposes a novel lipid metabolism-related gene marker that can offer comprehensive insights into the pathogenesis of bronchial asthma leading to SCLC. Although this study does not directly focus on senescence-associated molecular alterations, our findings in the lipid metabolism genes associated with inflammation and cancer progression offer valuable insights for further research targeting senescence-related changes in treating inflammatory diseases.
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Affiliation(s)
- Xiaobin Wang
- Department of Thoracic Surgery, Tangdu Hospital of Air Force Medical University, China
| | - Yang Gao
- Department of Thoracic Surgery, Tangdu Hospital of Air Force Medical University, China
| | - Haiqiang Wang
- Department of Thoracic Surgery, Tangdu Hospital of Air Force Medical University, China
| | - Xiaokang Gong
- Department of Thoracic Surgery, Tangdu Hospital of Air Force Medical University, China
| | - Peilong Bao
- Department of Thoracic Surgery, Tangdu Hospital of Air Force Medical University, China
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22
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Fu Y, Wang C, Wu Z, Zhang X, Liu Y, Wang X, Liu F, Chen Y, Zhang Y, Zhao H, Wang Q. Discovery of the potential biomarkers for early diagnosis of endometrial cancer via integrating metabolomics and transcriptomics. Comput Biol Med 2024; 173:108327. [PMID: 38552279 DOI: 10.1016/j.compbiomed.2024.108327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/07/2024] [Accepted: 03/17/2024] [Indexed: 04/17/2024]
Abstract
Endometrial cancer (EC) is one of the most common malignant tumors in women, and the increasing incidence and mortality pose a serious threat to the public health. Early diagnosis of EC could prolong the survival period and optimize the survivorship, greatly alleviating patients' suffering and social medical pressure. In this study, we collected urine and serum samples from the recruited patients, analyzed the samples using LC-MS approach, and identified the differential metabolites through metabolomic analysis. Then, the differentially expressed genes were identified through the systematic transcriptomic analysis of EC-related dataset from Gene Expression Omnibus (GEO), followed by network profiling of metabolic-reaction-enzyme-gene. In this experiment, a total of 83 differential metabolites and 19 hub genes were discovered, of which 10 different metabolites and 3 hub genes were further evaluated as more potential biomarkers based on network analysis. According to the KEGG enrichment analysis, the potential biomarkers and gene-encoded proteins were found to be involved in the arginine and proline metabolism, histidine metabolism, and pyrimidine metabolism, which was of significance for the early diagnosis of EC. In particular, the combination of metabolites (histamine, 1-methylhistamine, and methylimidazole acetaldehyde) as well as the combination of RRM2, TYMS and TK1 exerted more accurate discrimination abilities between EC and healthy groups, providing more criteria for the early diagnosis of EC.
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Affiliation(s)
- Yan Fu
- School of Pharmacy, Hebei Medical University, Shijiazhuang, 050017, China; Core Facilities and Centers, Hebei Medical University, Shijiazhuang, 050017, China
| | - Chengzhao Wang
- College of Basic Medicine, Hebei Medical University, Shijiazhuang, 050017, China
| | - Zhimin Wu
- School of Pharmacy, Hebei Medical University, Shijiazhuang, 050017, China
| | - Xiaoguang Zhang
- Core Facilities and Centers, Hebei Medical University, Shijiazhuang, 050017, China; College of Basic Medicine, Hebei Medical University, Shijiazhuang, 050017, China
| | - Yan Liu
- School of Pharmacy, Hebei Medical University, Shijiazhuang, 050017, China
| | - Xu Wang
- School of Pharmacy, Hebei Medical University, Shijiazhuang, 050017, China
| | - Fangfang Liu
- School of Pharmacy, Hebei Medical University, Shijiazhuang, 050017, China
| | - Yujuan Chen
- School of Pharmacy, Hebei Medical University, Shijiazhuang, 050017, China
| | - Yang Zhang
- School of Pharmacy, Hebei Medical University, Shijiazhuang, 050017, China.
| | - Huanhuan Zhao
- Department of Obstetrics and Gynecology, The Fourth Hospital of Hebei Medical University, 050011, China.
| | - Qiao Wang
- School of Pharmacy, Hebei Medical University, Shijiazhuang, 050017, China.
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23
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Rickles-Young M, Tinoco G, Tsuji J, Pollock S, Haynam M, Lefebvre H, Glover K, Owen DH, Collier KA, Ha G, Adalsteinsson VA, Cibulskis C, Lennon NJ, Stover DG. Assay Validation of Cell-Free DNA Shallow Whole-Genome Sequencing to Determine Tumor Fraction in Advanced Cancers. J Mol Diagn 2024; 26:413-422. [PMID: 38490303 DOI: 10.1016/j.jmoldx.2024.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 09/21/2023] [Accepted: 01/18/2024] [Indexed: 03/17/2024] Open
Abstract
Blood-based liquid biopsy is increasingly used in clinical care of patients with cancer, and fraction of tumor-derived DNA in circulation (tumor fraction; TFx) has demonstrated clinical validity across multiple cancer types. To determine TFx, shallow whole-genome sequencing of cell-free DNA (cfDNA) can be performed from a single blood sample, using an established computational pipeline (ichorCNA), without prior knowledge of tumor mutations, in a highly cost-effective manner. We describe assay validation of this approach to facilitate broad clinical application, including evaluation of assay sensitivity, precision, repeatability, reproducibility, pre-analytic factors, and DNA quality/quantity. Sensitivity to detect TFx of 3% (lower limit of detection) was 97.2% to 100% at 1× and 0.1× mean sequencing depth, respectively. Precision was demonstrated on distinct sequencing instruments (HiSeqX and NovaSeq) with no observable differences. The assay achieved prespecified 95% agreement of TFx across replicates of the same specimen (repeatability) and duplicate samples in different batches (reproducibility). Comparison of samples collected in EDTA and Streck tubes from single venipuncture in 23 patients demonstrated that EDTA or Streck tubes were comparable if processed within 8 hours. On the basis of a range of DNA inputs (1 to 50 ng), 20 ng cfDNA is the preferred input, with 5 ng minimum acceptable. Overall, this shallow whole-genome sequencing of cfDNA and ichorCNA approach offers sensitive, precise, and reproducible quantitation of TFx, facilitating assay application in clinical cancer care.
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Affiliation(s)
- Micah Rickles-Young
- Genomics Platform, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Gabriel Tinoco
- Division of Medical Oncology, The Ohio State University College of Medicine, Columbus, Ohio; Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Junko Tsuji
- Genomics Platform, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Sam Pollock
- Genomics Platform, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Marcy Haynam
- Ohio State University Comprehensive Cancer Center, Columbus, Ohio; Stefanie Spielman Comprehensive Breast Center, Columbus, Ohio
| | - Heather Lefebvre
- Ohio State University Comprehensive Cancer Center, Columbus, Ohio; Stefanie Spielman Comprehensive Breast Center, Columbus, Ohio
| | - Kristyn Glover
- Ohio State University Comprehensive Cancer Center, Columbus, Ohio; Stefanie Spielman Comprehensive Breast Center, Columbus, Ohio
| | - Dwight H Owen
- Division of Medical Oncology, The Ohio State University College of Medicine, Columbus, Ohio; Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Katharine A Collier
- Division of Medical Oncology, The Ohio State University College of Medicine, Columbus, Ohio; Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Gavin Ha
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Viktor A Adalsteinsson
- Genomics Platform, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Carrie Cibulskis
- Genomics Platform, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Niall J Lennon
- Genomics Platform, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts.
| | - Daniel G Stover
- Division of Medical Oncology, The Ohio State University College of Medicine, Columbus, Ohio; Ohio State University Comprehensive Cancer Center, Columbus, Ohio; Stefanie Spielman Comprehensive Breast Center, Columbus, Ohio.
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24
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Monjé N, Dragomir MP, Sinn BV, Hoffmann I, Makhmut A, Simon T, Kunze CA, Ihlow J, Schmitt WD, Pohl J, Piwonski I, Marchenko S, Keunecke C, Calina TG, Tiso F, Kulbe H, Kreuzinger C, Cacsire Castillo-Tong D, Sehouli J, Braicu EI, Denkert C, Darb-Esfahani S, Kübler K, Capper D, Coscia F, Morkel M, Horst D, Sers C, Taube ET. AHRR and SFRP2 in primary versus recurrent high-grade serous ovarian carcinoma and their prognostic implication. Br J Cancer 2024; 130:1249-1260. [PMID: 38361045 PMCID: PMC11014847 DOI: 10.1038/s41416-023-02550-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 12/03/2023] [Accepted: 12/11/2023] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND The aim of this study was to analyse transcriptomic differences between primary and recurrent high-grade serous ovarian carcinoma (HGSOC) to identify prognostic biomarkers. METHODS We analysed 19 paired primary and recurrent HGSOC samples using targeted RNA sequencing. We selected the best candidates using in silico survival and pathway analysis and validated the biomarkers using immunohistochemistry on a cohort of 44 paired samples, an additional cohort of 504 primary HGSOCs and explored their function. RESULTS We identified 233 differential expressed genes. Twenty-three showed a significant prognostic value for PFS and OS in silico. Seven markers (AHRR, COL5A2, FABP4, HMGCS2, ITGA5, SFRP2 and WNT9B) were chosen for validation at the protein level. AHRR expression was higher in primary tumours (p < 0.0001) and correlated with better patient survival (p < 0.05). Stromal SFRP2 expression was higher in recurrent samples (p = 0.009) and protein expression in primary tumours was associated with worse patient survival (p = 0.022). In multivariate analysis, tumour AHRR and SFRP2 remained independent prognostic markers. In vitro studies supported the anti-tumorigenic role of AHRR and the oncogenic function of SFRP2. CONCLUSIONS Our results underline the relevance of AHRR and SFRP2 proteins in aryl-hydrocarbon receptor and Wnt-signalling, respectively, and might lead to establishing them as biomarkers in HGSOC.
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Affiliation(s)
- Nanna Monjé
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
| | - Mihnea P Dragomir
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Bruno V Sinn
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
| | - Inga Hoffmann
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
| | - Anuar Makhmut
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Spatial Proteomics Group, Berlin, Germany
| | - Tincy Simon
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
| | - Catarina A Kunze
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
| | - Jana Ihlow
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Wolfgang D Schmitt
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
| | - Jonathan Pohl
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
| | - Iris Piwonski
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
| | - Sofya Marchenko
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
| | - Carlotta Keunecke
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department for Gynecology with the Center for Oncologic Surgery Charité Campus Virchow-Klinikum, Charitéplatz 1, 10117, Berlin, Germany
| | | | - Francesca Tiso
- Center of Functional Genomics, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
- Department of Hematology, Oncology and Cancer Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Hindenburgdamm 30, 12203, Berlin, Germany
| | - Hagen Kulbe
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department for Gynecology with the Center for Oncologic Surgery Charité Campus Virchow-Klinikum, Charitéplatz 1, 10117, Berlin, Germany
| | - Caroline Kreuzinger
- Translational Gynecology Group, Department of Obstetrics and Gynecology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Dan Cacsire Castillo-Tong
- Translational Gynecology Group, Department of Obstetrics and Gynecology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Jalid Sehouli
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department for Gynecology with the Center for Oncologic Surgery Charité Campus Virchow-Klinikum, Charitéplatz 1, 10117, Berlin, Germany
| | - Elena I Braicu
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department for Gynecology with the Center for Oncologic Surgery Charité Campus Virchow-Klinikum, Charitéplatz 1, 10117, Berlin, Germany
| | - Carsten Denkert
- Institute of Pathology, University Hospital Gießen and Marburg, Marburg, Germany
| | - Silvia Darb-Esfahani
- Institute of Pathology, Berlin-Spandau, Stadtrandstraße 555, 13589, Berlin, Germany
| | - Kirsten Kübler
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Center of Functional Genomics, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
- Department of Hematology, Oncology and Cancer Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Hindenburgdamm 30, 12203, Berlin, Germany
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School Teaching Hospital, Charlestown, MA, USA
| | - David Capper
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Fabian Coscia
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Spatial Proteomics Group, Berlin, Germany
| | - Markus Morkel
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - David Horst
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Christine Sers
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Eliane T Taube
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany.
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25
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Wang H, Jin H, Zhao S. Expression and clinical significance of RHCG in endometrial cancer. Histol Histopathol 2024; 39:611-621. [PMID: 37732703 DOI: 10.14670/hh-18-663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Endometrial cancer (EC) is the most common gynecological cancer. Rhesus family, C glycoprotein (RHCG) has been evidenced to be involved in the occurrence and development of various tumors. This study aimed to investigate the expression and clinical significance of RHCG in EC. Bioinformatics analysis was based on the RNAseq counts data from TCGA database, and the prognosis analysis was performed using the Kaplan-Meier method; 4 cases of endometrioid adenocarcinomas samples and 4 cases of normal proliferative endometrium were collected for qPCR and western blot; immunohistochemistry analysis was employed to assess the expression of RHCG in a tissue microarray; the correlation between RHCG and clinicopathological factors was analyzed through Mann-Whitney U test. The lentiviral interference vector was further constructed. The results demonstrated that RHCG was highly expressed in EC tissues, and RHCG was an independent factor affecting the overall survival of patients. Additionally, the expression of RHCG was related to FIGO stage and tumor infiltrate. After interfering with shRHCG, the proliferation activity of EC cells decreased, the migration ability of cells decreased, the apoptosis of cells increased, and the tumor outgrowth was arrested. In summary, RHCG promotes the malignant proliferation and migration of EC, and makes the cells have anti-apoptotic activity. Our study provides a theoretical basis for RHCG to become a potential therapeutic target for EC in the future.
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Affiliation(s)
- Huifang Wang
- Department of Gynecology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei Province, PR China
- Department of Gynecology, The First Hospital of Qinhuangdao, Qinhuangdao, Hebei Province, PR China
| | - Haihong Jin
- Department of Gynecology, The First Hospital of Qinhuangdao, Qinhuangdao, Hebei Province, PR China
| | - Sufen Zhao
- Department of Gynecology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei Province, PR China.
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Huang P, Wen F, Li Y, Li Q. The tale of SOX2: Focusing on lncRNA regulation in cancer progression and therapy. Life Sci 2024; 344:122576. [PMID: 38492918 DOI: 10.1016/j.lfs.2024.122576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 03/06/2024] [Accepted: 03/13/2024] [Indexed: 03/18/2024]
Abstract
Long non-coding RNAs (lncRNAs) have emerged as influential contributors to diverse cellular processes, which regulate gene function and expression via multiple mechanistic pathways. Therefore, it is essential to exploit the structures and interactions of lncRNAs to comprehend their mechanistic functions within cells. A growing body of evidence has revealed that deregulated lncRNAs are involved in multiple regulations of malignant events including cell proliferation, growth, invasion, and metabolism. SRY-related high mobility group box (SOX)2, a well-recognized member of the SOX family, is commonly overexpressed in various types of cancer, contributing to tumor progression and maintenance of stemness. Emerging studies have shown that lncRNAs interact with SOX2 to remarkably contribute to carcinogenesis and disease states. This review elaborates on the crosstalk between the intricate and complicated functions of lncRNAs and SOX2 in the context of malignant diseases. We elucidate distinct molecular mechanisms that contribute to the onset/advancement of cancer, indicating that lncRNAs/SOX2 axes hold immense promise for potential therapeutic targets. Furthermore, we delve into the modalities of emerging feasible treatment options for targeting lncRNAs, highlighting the limitations of such therapies and providing novel insights into further ameliorations of targeted strategies of lncRNAs to promote the clinical implications. Translating current discoveries into clinical applications could ultimately boost improved survival and prognosis of cancer patients.
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Affiliation(s)
- Peng Huang
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Feng Wen
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - YiShan Li
- Thoracic Oncology Ward, Cancer Center, West China Hospital, Sichuan University, West China School of Nursing, Chengdu, Sichuan 610041, China
| | - Qiu Li
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.
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von Koskull A, Hagström J, Haglund C, Kaprio T, Böckelman C. High-tissue FRMD6 expression predicts better outcomes among colorectal cancer patients. Biomarkers 2024; 29:127-133. [PMID: 38385211 DOI: 10.1080/1354750x.2024.2321916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 02/17/2024] [Indexed: 02/23/2024]
Abstract
INTRODUCTION Colorectal cancer (CRC) is the second most common cause of cancer-related deaths. The hippo pathway works as a regulator of organ growth and is often a target for mutations in cancer. Ferm domain containing protein 6 (FRMD6) is an activator of the hippo pathway. This study aimed to explore the role of FRMD6 in CRC and to determine how well it works as a prognostic factor among CRC patients. METHODS The tumor expression of FRMD6 was evaluated using immunohistochemistry in 538 colorectal patients operated on at Helsinki University Hospital. We assessed FRMD6 expression with clinicopathological parameters and the impact of FRMD6 expression on survival. RESULTS Patients with a high FRMD6 expression exhibited a better prognosis (univariable hazard ratio [HR] 0.58, 95% confidence interval [CI] 0.41-0.81), with a 5-year disease-specific survival (DSS) of 66.3%. By contrast, patients with a low FRMD6 expression had a 5-year DSS of 52.8%. A high FRMD6 expression level served as an independent predictor for better survival in the Cox multivariable survival analysis (HR 0.53, 95% CI 0.33-0.86). DISCUSSION To our knowledge, this is the first study to show that a high FRMD6 expression is an independent marker for a better prognosis in CRC and could help determine the prognosis for CRC patients.
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Affiliation(s)
- Arthur von Koskull
- Department of Surgery, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Jaana Hagström
- Translational Cancer Medicine Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Oral Pathology and Radiology, University of Turku, Turku, Finland
| | - Caj Haglund
- Department of Surgery, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Translational Cancer Medicine Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Tuomas Kaprio
- Department of Surgery, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Translational Cancer Medicine Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Camilla Böckelman
- Department of Surgery, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Translational Cancer Medicine Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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Schlieben LD, Carta MG, Moskalev EA, Stöhr R, Metzler M, Besendörfer M, Meidenbauer N, Semrau S, Janka R, Grützmann R, Wiemann S, Hartmann A, Agaimy A, Haller F, Ferrazzi F. Machine Learning-Supported Diagnosis of Small Blue Round Cell Sarcomas Using Targeted RNA Sequencing. J Mol Diagn 2024; 26:387-398. [PMID: 38395409 DOI: 10.1016/j.jmoldx.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 01/25/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Small blue round cell sarcomas (SBRCSs) are a heterogeneous group of tumors with overlapping morphologic features but markedly varying prognosis. They are characterized by distinct chromosomal alterations, particularly rearrangements leading to gene fusions, whose detection currently represents the most reliable diagnostic marker. Ewing sarcomas are the most common SBRCSs, defined by gene fusions involving EWSR1 and transcription factors of the ETS family, and the most frequent non-EWSR1-rearranged SBRCSs harbor a CIC rearrangement. Unfortunately, currently the identification of CIC::DUX4 translocation events, the most common CIC rearrangement, is challenging. Here, we present a machine-learning approach to support SBRCS diagnosis that relies on gene expression profiles measured via targeted sequencing. The analyses on a curated cohort of 69 soft-tissue tumors showed markedly distinct expression patterns for SBRCS subgroups. A random forest classifier trained on Ewing sarcoma and CIC-rearranged cases predicted probabilities of being CIC-rearranged >0.9 for CIC-rearranged-like sarcomas and <0.6 for other SBRCSs. Testing on a retrospective cohort of 1335 routine diagnostic cases identified 15 candidate CIC-rearranged tumors with a probability >0.75, all of which were supported by expert histopathologic reassessment. Furthermore, the multigene random forest classifier appeared advantageous over using high ETV4 expression alone, previously proposed as a surrogate to identify CIC rearrangement. Taken together, the expression-based classifier can offer valuable support for SBRCS pathologic diagnosis.
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Affiliation(s)
- Lea D Schlieben
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany; Bavarian Cancer Research Center, Erlangen, Germany
| | - Maria Giulia Carta
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany; Bavarian Cancer Research Center, Erlangen, Germany
| | - Evgeny A Moskalev
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany; Bavarian Cancer Research Center, Erlangen, Germany
| | - Robert Stöhr
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany; Bavarian Cancer Research Center, Erlangen, Germany
| | - Markus Metzler
- Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany; Bavarian Cancer Research Center, Erlangen, Germany; Department of Pediatrics, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Manuel Besendörfer
- Department of Pediatric Surgery, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Norbert Meidenbauer
- Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany; Bavarian Cancer Research Center, Erlangen, Germany; Department of Internal Medicine 5-Hematology and Oncology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Sabine Semrau
- Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany; Bavarian Cancer Research Center, Erlangen, Germany; Department of Radiation Oncology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Rolf Janka
- Department of Radiology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Robert Grützmann
- Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany; Bavarian Cancer Research Center, Erlangen, Germany; Department of Pediatric Surgery, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Department of Surgery, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Stefan Wiemann
- Division of Molecular Genome Analysis, German Cancer Research Center, Heidelberg, Germany
| | - Arndt Hartmann
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany; Bavarian Cancer Research Center, Erlangen, Germany
| | - Abbas Agaimy
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany; Bavarian Cancer Research Center, Erlangen, Germany
| | - Florian Haller
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany; Bavarian Cancer Research Center, Erlangen, Germany
| | - Fulvia Ferrazzi
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany; Bavarian Cancer Research Center, Erlangen, Germany; Department of Nephropathology, Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.
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George B, Kudryashova O, Kravets A, Thalji S, Malarkannan S, Kurzrock R, Chernyavskaya E, Gusakova M, Kravchenko D, Tychinin D, Savin E, Alekseeva L, Butusova A, Bagaev A, Shin N, Brown JH, Sethi I, Wang D, Taylor B, McFall T, Kamgar M, Hall WA, Erickson B, Christians KK, Evans DB, Tsai S. Transcriptomic-Based Microenvironment Classification Reveals Precision Medicine Strategies for Pancreatic Ductal Adenocarcinoma. Gastroenterology 2024; 166:859-871.e3. [PMID: 38280684 DOI: 10.1053/j.gastro.2024.01.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 12/11/2023] [Accepted: 01/18/2024] [Indexed: 01/29/2024]
Abstract
BACKGROUND & AIMS The complex tumor microenvironment (TME) of pancreatic ductal adenocarcinoma (PDAC) has hindered the development of reliable predictive biomarkers for targeted therapy and immunomodulatory strategies. A comprehensive characterization of the TME is necessary to advance precision therapeutics in PDAC. METHODS A transcriptomic profiling platform for TME classification based on functional gene signatures was applied to 14 publicly available PDAC datasets (n = 1657) and validated in a clinically annotated independent cohort of patients with PDAC (n = 79). Four distinct subtypes were identified using unsupervised clustering and assessed to evaluate predictive and prognostic utility. RESULTS TME classification using transcriptomic profiling identified 4 biologically distinct subtypes based on their TME immune composition: immune enriched (IE); immune enriched, fibrotic (IE/F); fibrotic (F); and immune depleted (D). The IE and IE/F subtypes demonstrated a more favorable prognosis and potential for response to immunotherapy compared with the F and D subtypes. Most lung metastases and liver metastases were subtypes IE and D, respectively, indicating the role of clonal phenotype and immune milieu in developing personalized therapeutic strategies. In addition, distinct TMEs with potential therapeutic implications were identified in treatment-naive primary tumors compared with tumors that underwent neoadjuvant therapy. CONCLUSIONS This novel approach defines a distinct subgroup of PADC patients that may benefit from immunotherapeutic strategies based on their TME subtype and provides a framework to select patients for prospective clinical trials investigating precision immunotherapy in PDAC. Further, the predictive utility and real-world clinical applicability espoused by this transcriptomic-based TME classification approach will accelerate the advancement of precision medicine in PDAC.
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Affiliation(s)
- Ben George
- LaBahn Pancreatic Cancer Program, Division of Hematology and Oncology, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin.
| | | | | | - Samih Thalji
- LaBahn Pancreatic Cancer Program, Department of Surgery, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | - Subramaniam Malarkannan
- Versiti Blood Research Institute, Department of Medicine, Microbiology & Molecular Genetics, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | - Razelle Kurzrock
- Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Division of Hematology and Oncology, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | | | | | | | | | - Egor Savin
- BostonGene Corporation, Waltham, Massachusetts
| | | | | | | | - Nara Shin
- BostonGene Corporation, Waltham, Massachusetts
| | | | - Isha Sethi
- BostonGene Corporation, Waltham, Massachusetts
| | - Dandan Wang
- Versiti Blood Research Institute, Department of Medicine, Microbiology & Molecular Genetics, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | - Bradley Taylor
- Clinical and Translational Science Institute, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | - Thomas McFall
- LaBahn Pancreatic Cancer Program, Department of Biochemistry, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | - Mandana Kamgar
- LaBahn Pancreatic Cancer Program, Division of Hematology and Oncology, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | - William A Hall
- LaBahn Pancreatic Cancer Program, Department of Radiation Oncology, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | - Beth Erickson
- LaBahn Pancreatic Cancer Program, Department of Radiation Oncology, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | - Kathleen K Christians
- LaBahn Pancreatic Cancer Program, Department of Surgery, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | - Douglas B Evans
- LaBahn Pancreatic Cancer Program, Department of Surgery, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | - Susan Tsai
- LaBahn Pancreatic Cancer Program, Department of Surgery, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
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Ando Y, Goggins M. ASO Author Reflections: Using a CA19-9 Tumor Marker Gene Test to Assess Outcome after Pancreatic Cancer Surgery. Ann Surg Oncol 2024; 31:2961-2962. [PMID: 38280960 DOI: 10.1245/s10434-024-14974-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 01/11/2024] [Indexed: 01/29/2024]
Affiliation(s)
- Yohei Ando
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Michael Goggins
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD, USA.
- Department of Medicine, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD, USA.
- Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD, USA.
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31
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Xu J, Wang Y, Li X, Zheng M, Li Y, Zhang W. Clinical value assessment for serum hsa_tsr013526 in the diagnosis of gastric carcinoma. Environ Toxicol 2024; 39:2753-2767. [PMID: 38251933 DOI: 10.1002/tox.24146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/29/2023] [Accepted: 01/06/2024] [Indexed: 01/23/2024]
Abstract
Gastric carcinoma (GC) is a malignant tumor that is detrimental to human health. Transfer RNA-derived small RNAs are a newly identified class of noncoding small RNAs with specific biological functions that are aberrantly expressed in cancer. The aim of this study was to investigate the potential of hsa_tsr013526 as a biomarker for GC. Quantitative real-time fluorescence polymerase chain reaction was used to detect the expression level of hsa_tsr013526. The molecular characteristics of hsa_tsr013526 were verified by agarose gel electrophoresis, Sanger sequencing, and separation of nuclear and cytoplasmic RNA fractions. By testing the receiver operating characteristic (ROC) curves, the diagnostic efficiency of GC using hsa_tsr013526 was determined. Finally, we predicted the downstream of hsa_tsr013526 using functional assays and bioinformatics analysis. Serum expression of hsa_tsr013526 was higher in GC patients than in healthy donors. Serum expression showed differential changes in GC patients, gastritis patients, and healthy donors. Chi-squared tests showed that high expression of hsa_tsr013526 was significantly correlated with T stage, lymphatic metastasis, and tumor node metastasis stage. ROC curve analysis indicated that GC patients could be discriminated from healthy donors or gastritis patients based on their serum levels of hsa_tsr013526. Furthermore, hsa_tsr013526 expression was significantly reduced in postoperative GC patients (p = .0016). High expression of hsa_tsr013526 promotes gastric cancer cell proliferation, invasion, and migration. Serum hsa_tsr013526 was stable and specific, and could be used for dynamic monitoring of GC patients. Therefore, hsa_tsr013526 may be a new biomarker for the diagnosis and postoperative monitoring of GC patients.
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Affiliation(s)
- Jing Xu
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
- Medical School, Nantong University, Nantong, China
| | - Yue Wang
- Basic Medicine School, Xuzhou Medical University, Xuzhou, China
| | - Xian Li
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Ming Zheng
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Yang Li
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
- Medical School, Nantong University, Nantong, China
| | - Weiwei Zhang
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
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Churg A, Naso JR. Correspondence: SPARC, HEG1, and the Diagnosis of Epithelioid Mesothelioma. Am J Surg Pathol 2024; 48:632. [PMID: 38223954 DOI: 10.1097/pas.0000000000002178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Affiliation(s)
- Andrew Churg
- Department of Pathology, Vancouver General Hospital Vancouver, BC, Canada
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Zhang W, Zhao Y, Jia Y, Bai Y. Prognostic value of long noncoding RNA LINC00924 in lung adenocarcinoma and its regulatory effect on tumor progression. Histol Histopathol 2024; 39:595-602. [PMID: 37358073 DOI: 10.14670/hh-18-642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2023]
Abstract
PURPOSE Long non-coding RNAs (lncRNAs) have been used in the study of tumor biomarkers in recent years. However, the prognostic role of lncRNA LINC00924 (LINC00924) in lung adenocarcinoma (LUAD) has not yet been concluded. Therefore, this study investigates the prognostic value of LINC00924 in LUAD and its regulatory effect on tumor progression. PATIENTS AND METHODS The LUAD tissues and adjacent normal tissues of 128 subjects were extracted, and the expressions of LINC00924 and miR-196a-5p in tissues and cells were detected by RT-qPCR. The prognostic value of LINC00924 in LUAD patients was obtained by Kaplan-Meier analysis and multivariate Cox regression test. The cell counting kit-8 (CCK-8) and Transwell assay were used to detect the effect of overexpression LINC00924 on LUAD cells. RESULTS In LUAD tissues and cells, LINC00924 expression was down-regulated and miR-196a-5p expression was up-regulated compared with the normal control group. High expression of LINC00924 inhibited the proliferation level, migration ability and invasion situation of LUAD cells, which was more conducive to the survival and prognosis of LUAD patients. Bioinformatics studies indicated that overexpression of LINC00924 inhibited the development of LUAD by targeting miR-196a-5p, while miR-196a-5p mimic effectively weakened the inhibition. CONCLUSION LINC00924 sponges of miR-196a-5p may be considered as a potential prognostic biomarker for LUAD.
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Affiliation(s)
- Wenlong Zhang
- Department of Oncology and Hematology, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Yanan Zhao
- Department of Oncology and Hematology, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Yuanyuan Jia
- Department of Oncology and Hematology, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Yuansong Bai
- Department of Oncology and Hematology, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China.
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Imoto K, Yamamoto H, Ohkawa C, Shimada N, Ikuzawa R, Takeda H, Ohhara T, Kojima Y, Furuya N, Motoyoshi A, Migita O, Kuga A, Keira T, Wakamatsu H, Sato T, Oike N, Koike J, Yamano Y, Sunakawa Y. An approach for improvement of the accuracy of cancer gene panel testing. Int J Clin Oncol 2024; 29:571-581. [PMID: 38472663 DOI: 10.1007/s10147-024-02483-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 01/22/2024] [Indexed: 03/14/2024]
Abstract
BACKGROUND Tissue-based comprehensive genomic profiling (CGP) is increasingly being employed for genotype-directed therapies in patients with advanced cancer. However, tissue availability may limit their potential applications. In Japan, the cost of cancer gene panel tests is covered by public insurance for patients diagnosed with advanced solid tumors once in their lifetime. Therefore, it is essential to improve the success rate (reportability) and accuracy of CGP tests. The purpose of this study was to identify the factors associated with efficient and accurate CGP testing using relevant information obtained from real-world data. METHODS This study included 159 samples analyzed using tumor-only panel FoundationOne® CDx cancer genome profiling (F1CDx) and 85 samples analyzed using matched-pair panel OncoGuide™ NCC Oncopanel system (NCCOP) at St. Marianna University Hospital. Sample characteristics (fixation conditions, storage period, histology, tumor cell ratio, and genomic tumor cell content), CGP performance, and quality control status were evaluated across all 244 tested samples. RESULTS In 237/244 samples (97.1%), CGP testing results were successfully obtained [F1CDx, 99.4% (158/159) and NCCOP, 92.9% (79/85)]. An increased number of fibroblasts, inflammatory cells, and necrotic tumor cells, long-term storage, and/or prolonged fixation of tissue sections were involved in the unreported results and/or qualified CGP results. In addition, a negative correlation between median insert size values and ΔΔCq was observed in the NCCOP system. CONCLUSION We identified various factors associated with efficient and accurate CGP testing using relevant information obtained from real-world data, suggesting that thorough selection and preparation of tissue sections could optimize CGP and maximize useful information.
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Affiliation(s)
- Kiyomi Imoto
- Center for Genomic Medicine, St. Marianna University Hospital, Kawasaki, Japan
| | - Hiroyuki Yamamoto
- Department of Bioinformatics, St. Marianna University Graduate School of Medicine, 2-16-1 Sugao, Miyamae-ku, Kawasaki, Kanagawa, 216-8511, Japan.
- Department of Gastroenterology, St. Marianna University School of Medicine, Kawasaki, Japan.
| | - Chie Ohkawa
- Department of Pathology, St. Marianna University Hospital, Kawasaki, Japan
| | - Naoki Shimada
- Department of Pathology, St. Marianna University Hospital, Kawasaki, Japan
| | - Ryo Ikuzawa
- Department of Pathology, St. Marianna University Hospital, Kawasaki, Japan
| | - Hiroyuki Takeda
- Department of Clinical Oncology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Tatsuru Ohhara
- Department of Obstetrics and Gynecology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Yasuyuki Kojima
- Department of Breast and Endocrine Surgery, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Naoki Furuya
- Department of Respiratory Medicine, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Ai Motoyoshi
- Center for Genomic Medicine, St. Marianna University Hospital, Kawasaki, Japan
- Department of Breast and Endocrine Surgery, St. Marianna University School of Medicine, Kawasaki, Japan
- Department of Clinical Genetics, St. Marianna University Hospital, Kawasaki, Japan
| | - Ohsuke Migita
- Department of Clinical Genetics, St. Marianna University Hospital, Kawasaki, Japan
| | - Asami Kuga
- Department of Clinical Genetics, St. Marianna University Hospital, Kawasaki, Japan
| | - Takayuki Keira
- Department of Pharmacy, St. Marianna University Hospital, Kawasaki, Japan
| | | | - Tomoo Sato
- Center for Genomic Medicine, St. Marianna University Hospital, Kawasaki, Japan
| | - Nobuyuki Oike
- Department of Pathology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Junki Koike
- Department of Pathology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Yoshihisa Yamano
- Center for Genomic Medicine, St. Marianna University Hospital, Kawasaki, Japan
- Department of Neurology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Yu Sunakawa
- Center for Genomic Medicine, St. Marianna University Hospital, Kawasaki, Japan
- Department of Clinical Oncology, St. Marianna University School of Medicine, Kawasaki, Japan
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Thakore VP, Patel KD, Vora HH, Patel PS, Jain NK. Up-regulation of extracellular-matrix and inflammation related genes in oral squamous cell carcinoma. Arch Oral Biol 2024; 161:105925. [PMID: 38442470 DOI: 10.1016/j.archoralbio.2024.105925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 02/16/2024] [Accepted: 02/18/2024] [Indexed: 03/07/2024]
Abstract
OBJECTIVE Oral squamous cell carcinoma (OSCC) is the most prevalent malignancy with late-presentation, site-specific heterogeneity, and high-propensity for recurrence/metastasis that has shown rise in mortality. Lately, research emphasize on dynamic interactions between tumor-cells and extracellular-matrix components within tumor-microenvironment that promote tissue integrity loss and carcinogenesis. Therefore, OSCC clinical-management is still challenging. DESIGN Present study validated clinical utility of a 13 gene-panel in two chief sub-sites of OSCC: Buccal mucosa squamous cell carcinoma (BMSCC) (N = 50) and Tongue squamous cell carcinoma (TSCC) (N = 52) using qRT-PCR. Principal component analysis and binary logistic regression analysis were applied to acquire definite multi gene models. Protein expression analysis was employed using the Human Protein Atlas, UALCAN and TIMER 2.0 databases to explore potential correlation between immune cells and gene-panels. RESULTS Significant up-regulation of CXCL8, CXCL10, FN1, GBP1, IFIT3, ISG15, MMP1, MMP3, MMP10, PLAU, SERPINE1 and SPP1 except OASL was observed in OSCC tissue in comparison of absolute normal controls. Although, this gene-panel could potentially discriminate OSCC tissues from absolute normal controls as solitarily diagnostic and/or predictive biomarkers, models generated also showed substantial discriminating efficacy. Eight-genes were found to be significantly associated with poor-prognosis on clinico-pathological association. Protein-expression confirmed overexpression of gene-panel and added advantage of being secretory-protein. Importantly, up-regulated genes in our study showed significant relation with immune-cells infiltration suggesting their contribution in immune-escape. CONCLUSION Thus, we propose that the 13 gene-panel could pave the way to effective and personalized clinical-management of OSCC in terms of diagnostic and prognostic measures and thereby as therapeutic targets.
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Affiliation(s)
- Vaidehi P Thakore
- Life Science Department, School of Science, Gujarat University, Ahmedabad 380009, Gujarat, India; Cancer Biology Department, The Gujarat Cancer & Research Institute, Civil, Ahmedabad, Gujarat, India
| | - Kinjal D Patel
- Cancer Biology Department, The Gujarat Cancer & Research Institute, Civil, Ahmedabad, Gujarat, India
| | - Hemangini H Vora
- Cancer Biology Department, The Gujarat Cancer & Research Institute, Civil, Ahmedabad, Gujarat, India
| | - Prabhudas S Patel
- Cancer Biology Department, The Gujarat Cancer & Research Institute, Civil, Ahmedabad, Gujarat, India
| | - Nayan K Jain
- Life Science Department, School of Science, Gujarat University, Ahmedabad 380009, Gujarat, India.
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Ando Y, Dbouk M, Blackford AL, Yoshida T, Saba H, Abou Diwan E, Yoshida K, Sokoll L, Eshleman JR, Burkhart R, He J, Goggins M. Using a CA19-9 Tumor Marker Gene Test to Assess Outcome After Pancreatic Cancer Surgery. Ann Surg Oncol 2024; 31:2902-2912. [PMID: 38319515 DOI: 10.1245/s10434-024-14942-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 12/29/2023] [Indexed: 02/07/2024]
Abstract
BACKGROUND Cancer antigen 19-9 (CA19-9) is widely used as a marker of pancreatic cancer tumor burden and response to therapy. Synthesis of CA19-9 and its circulating levels are determined by variants encoding the fucosyltransferases, FUT2 and FUT3. Individuals can be grouped into one of four functional FUT groups (FUT3-null, FUT-low, FUT-intermediate, FUT-high), each with its own CA19-9 reference range based on its predicted capacity to produce CA19-9. The authors hypothesized that a FUT variant-based CA19-9 tumor marker gene test could improve the prognostic performance of CA19-9. METHODS Preoperative and pre-treatment CA19-9 levels were measured, and FUT variants were determined in 449 patients who underwent surgery for pancreatic ductal adenocarcinoma (PDAC) at Johns Hopkins Hospital between 2010 and 2020, including 270 patients who underwent neoadjuvant therapy. Factors associated with recurrence-free and overall survival were determined in Cox proportional hazards models. RESULTS Higher preoperative CA19-9 levels were associated with recurrence and mortality for patients in the higher-FUT groups (FUT-intermediate, FUT-high for mortality, with adjustment for other prognostic factors; hazard ratio [HR], 1.34 and 1.58, respectively; P < 0.001), but not for those in the lower-FUT groups (FUT3-null, FUT-low). As a tumor marker, CA19-9 levels of 100 U/ml or lower after neoadjuvant therapy and normalization of CA19-9 based on FUT group were more sensitive but less specific predictors of evidence for a major pathologic response to therapy (little/no residual tumor) and of early recurrence (within 6 months). CONCLUSION Among patients undergoing pancreatic cancer resection, a CA19-9 tumor marker gene test modestly improved the prognostic performance of CA19-9.
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Affiliation(s)
- Yohei Ando
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Mohamad Dbouk
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Amanda L Blackford
- Department of Medicine, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Takeichi Yoshida
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Helena Saba
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Elizabeth Abou Diwan
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Kanako Yoshida
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Lori Sokoll
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - James R Eshleman
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD, USA
- Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Richard Burkhart
- Department of Surgery, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Jin He
- Department of Surgery, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Michael Goggins
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD, USA.
- Department of Medicine, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD, USA.
- Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD, USA.
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Doytcheva K, Storozuk T, Tjota M, Antic T. Oncocytoma-Like Angiomyolipoma of the Kidney: A Closer Look into the Clinicopathologic, Immunohistochemical, and Molecular Characteristics of a Rare Entity with Review of the Literature. Int J Surg Pathol 2024; 32:625-631. [PMID: 37487196 DOI: 10.1177/10668969231186925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Introduction. Angiomyolipoma (AML) is a mesenchymal neoplasm that belongs to the perivascular epithelioid cell tumor family (PEComa). AMLs can be subtyped into several patterns dependent on cell type, morphology, and tissue composition. One of the patterns, oncocytoma-like AML is a rare entity with only three cases published in the literature. Case presentation. We present a case of a previously healthy 29-year-old woman who underwent a left partial nephrectomy secondary to a 4.6 cm heterogeneous renal neoplasm. Gross examination demonstrated a well-circumscribed renal mass. Modified Giemsa stain preparation showed oncocytic cells in syncytial pattern with ample granular cytoplasm and round nuclei with prominent nucleoli. Histology assessment showed an oncocytic neoplasm with interspersed adipose tissue. The tumor exhibited tubular architecture with the tubules lined by eosinophilic epithelioid cells with nuclear atypia and prominent nucleoli. Thick blood vessels with emanating epithelioid cells were present. High-grade histology features were not identified. The tumor cells were positive for HMB-45 and SMA and negative for PAX8, keratins, KIT, and vimentin. A diagnosis of oncocytoma-like AML was rendered. Next-generation sequencing (NGS) and RNA fusion were performed. NGS revealed no pathogenic variants and RNA fusion identified no rearrangements. Chromosomal copy number alterations were present in the long arm of chromosome 1 (1p) and chromosome 22. Conclusions. We describe and discuss the clinical, cytomorphologic, histologic, and molecular findings of oncocytoma-like AML, a rare renal neoplasm, and provide a review of the literature.
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Affiliation(s)
| | - Tanner Storozuk
- Department of Pathology, The University of Chicago, Chicago, IL, USA
| | - Melissa Tjota
- Department of Pathology, The University of Chicago, Chicago, IL, USA
| | - Tatjana Antic
- Department of Pathology, The University of Chicago, Chicago, IL, USA
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Kikuchi Y, Shimada H, Yamasaki F, Yamashita T, Araki K, Horimoto K, Yajima S, Yashiro M, Yokoi K, Cho H, Ehira T, Nakahara K, Yasuda H, Isobe K, Hayashida T, Hatakeyama S, Akakura K, Aoki D, Nomura H, Tada Y, Yoshimatsu Y, Miyachi H, Takebayashi C, Hanamura I, Takahashi H. Clinical practice guidelines for molecular tumor marker, 2nd edition review part 2. Int J Clin Oncol 2024; 29:512-534. [PMID: 38493447 DOI: 10.1007/s10147-024-02497-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 02/21/2024] [Indexed: 03/19/2024]
Abstract
In recent years, rapid advancement in gene/protein analysis technology has resulted in target molecule identification that may be useful in cancer treatment. Therefore, "Clinical Practice Guidelines for Molecular Tumor Marker, Second Edition" was published in Japan in September 2021. These guidelines were established to align the clinical usefulness of external diagnostic products with the evaluation criteria of the Pharmaceuticals and Medical Devices Agency. The guidelines were scoped for each tumor, and a clinical questionnaire was developed based on a serious clinical problem. This guideline was based on a careful review of the evidence obtained through a literature search, and recommendations were identified following the recommended grades of the Medical Information Network Distribution Services (Minds). Therefore, this guideline can be a tool for cancer treatment in clinical practice. We have already reported the review portion of "Clinical Practice Guidelines for Molecular Tumor Marker, Second Edition" as Part 1. Here, we present the English version of each part of the Clinical Practice Guidelines for Molecular Tumor Marker, Second Edition.
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Affiliation(s)
| | - Hideaki Shimada
- Department of Clinical Oncology, Toho University, Tokyo, Japan.
- Department of Surgery, Toho University, Tokyo, Japan.
| | - Fumiyuki Yamasaki
- Department of Neurosurgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Taku Yamashita
- Department of Otorhinolaryngology-Head and Neck Surgery, Kitasato University School of Medicine, Kanagawa, Japan
| | - Koji Araki
- Department of Otorhinolaryngology-Head and Neck Surgery, National Defense Medical College, Saitama, Japan
| | - Kohei Horimoto
- Department of Dermatology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | | | - Masakazu Yashiro
- Department of Molecular Oncology and Therapeutics, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
| | - Keigo Yokoi
- Department of Lower Gastrointestinal Surgery, Kitasato University School of Medicine, Kanagawa, Japan
| | - Haruhiko Cho
- Department of Surgery, Tokyo Metropolitan Komagome Hospital, Tokyo, Japan
| | - Takuya Ehira
- Department of Gastroenterology, St. Marianna University School of Medicine, Kanagawa, Japan
| | - Kazunari Nakahara
- Department of Gastroenterology, St. Marianna University School of Medicine, Kanagawa, Japan
| | - Hiroshi Yasuda
- Department of Gastroenterology, St. Marianna University School of Medicine, Kanagawa, Japan
| | - Kazutoshi Isobe
- Division of Respiratory Medicine, Department of Internal Medicine (Omori), Toho University, Tokyo, Japan
| | - Tetsu Hayashida
- Department of Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Shingo Hatakeyama
- Department of Urology, Hirosaki University Graduate School of Medicine, Aomori, Japan
| | | | - Daisuke Aoki
- International University of Health and Welfare Graduate School, Tokyo, Japan
| | - Hiroyuki Nomura
- Department of Obstetrics and Gynecology, School of Medicine, Fujita Health University, Aichi, Japan
| | - Yuji Tada
- Department of Pulmonology, School of Medicine, International University of Health and Welfare, Chiba, Japan
| | - Yuki Yoshimatsu
- Department of Patient-Derived Cancer Model, Tochigi Cancer Center Research Institute, Tochigi, Japan
| | - Hayato Miyachi
- Faculty of Clinical Laboratory Sciences, Nitobe Bunka College, Tokyo, Japan
| | - Chiaki Takebayashi
- Division of Hematology and Oncology, Department of Internal Medicine (Omori), Toho University, Tokyo, Japan
| | - Ichiro Hanamura
- Division of Hematology, Department of Internal Medicine, Aichi Medical University, Aichi, Japan
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Ye JH, Yu J, Huang MY, Mo YM. The correlation study between TOP2A gene expression in circulating tumor cells and chemotherapeutic drug resistance of patients with breast cancer. Breast Cancer 2024; 31:417-425. [PMID: 38561479 DOI: 10.1007/s12282-024-01553-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 02/11/2024] [Indexed: 04/04/2024]
Abstract
BACKGROUND Patients with breast cancer (BC) at advanced stages have poor outcomes because of high rate of recurrence and metastasis. Biomarkers for predicting prognosis remain to be explored. This study aimed to evaluate the relationships between circulating tumor cells (CTCs) and outcomes of BC patients. PATIENTS AND METHODS A total of 50 female were enrolled in this study. Their diagnoses were determined by clinical characteristics, image data, and clinical pathology. CTC subtypes and TOP2A gene expression on CTCs were detected by CanPatrol™ technology and triple color in situ RNA hybridization (RNA-ISH), which divided into epithelial CTCs (eCTCs), mesenchymal CTCs (MCTCs), and hybrid CTCs (HCTCs) based on their surface markers. Hormone receptor, including estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER-2) expression, was measured by immunohistochemistry (IHC) method before treatment. The risk factors for predicting recurrence and metastasis were calculated by COX risk regression model. The progression-free survival (PFS) of patients was determined using Kaplan-Meier survival curve. RESULTS The patients with a large tumor size (≥ 3 cm) and advanced tumor node metastasis (TNM) stages had high total CTCs (TCTCs) (P < 0.05). These patients also had high TOP2A expression level. COX risk regression analysis indicated that TOP2A expression levels in TCTCs, ER + , HER-2 + , and TNM stages were critical risk factors for recurrence and metastasis of patients (P < 0.05). The PFS of patients with ≥ 5 TCTCs, ≥ 3 HCTCs, and positive TOP2A expression in ≥ 3 TCTCs was significantly longer than that in patient with < 5 TCTCs, < 3 HCTCs, and TOP2A expression in < 3 TCTCs (P < 0.05). In contrast, the PFS of patients with positive hormone receptors (ER + , PR + , HER-2 +) also was dramatically lived longer than that in patients with negative hormone receptor expression. CONCLUSIONS High TCTC, HCTCs, and positive TOP2A gene expression on CTCs were critical biomarkers for predicting outcomes of BC patients. Positive hormone receptor expression in BC patients has significant favor PFS.
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MESH Headings
- Humans
- Female
- Neoplastic Cells, Circulating/metabolism
- Neoplastic Cells, Circulating/pathology
- Breast Neoplasms/pathology
- Breast Neoplasms/genetics
- Breast Neoplasms/drug therapy
- DNA Topoisomerases, Type II/genetics
- DNA Topoisomerases, Type II/metabolism
- Middle Aged
- Drug Resistance, Neoplasm/genetics
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Adult
- Aged
- Receptor, ErbB-2/metabolism
- Prognosis
- Receptors, Estrogen/metabolism
- Poly-ADP-Ribose Binding Proteins/genetics
- Poly-ADP-Ribose Binding Proteins/metabolism
- Neoplasm Recurrence, Local/pathology
- Neoplasm Recurrence, Local/genetics
- Receptors, Progesterone/metabolism
- Gene Expression Regulation, Neoplastic
- Progression-Free Survival
- Kaplan-Meier Estimate
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Affiliation(s)
- Jin-Hui Ye
- Department of Breast Disease, The First People's Hospital of Zhaoqing, Zhaoqing, 526021, Guangdong, China
| | - Jian Yu
- Department of Breast Disease, The First People's Hospital of Zhaoqing, Zhaoqing, 526021, Guangdong, China
| | - Ming-Ying Huang
- Department of Breast Disease, The First People's Hospital of Zhaoqing, Zhaoqing, 526021, Guangdong, China.
| | - Yue-Mei Mo
- Department of Breast Disease, The First People's Hospital of Zhaoqing, Zhaoqing, 526021, Guangdong, China.
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Mehanna H, Alemany L, von Buchwald C. Advances in testing for human papillomavirus -mediated head and neck cancer. Curr Opin Oncol 2024; 36:143-146. [PMID: 38506408 PMCID: PMC10990024 DOI: 10.1097/cco.0000000000001029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
PURPOSE OF REVIEW New evidence has recently emerged regarding the utility and benefits of dual p16 INKa (p16) and Human papillomavirus (HPV) status testing when determining the diagnosis and prognosis of patients with oropharyngeal cancer. RECENT FINDINGS HPV RNA polymerase chain reaction (PCR) is the most accurate diagnostic test. The other assays (HPV DNA PCR, HPV DNA/RNA in-situ hybridization (ISH) and p16) applied to formalin fixed tumour tissue have varying but high sensitivities and specificities. Dual p16 and HPV testing identifies discordant (p16+/HPV- or p16-/HPV+) results in 9.2% of cases, who have significantly poorer prognoses than p16+/HPV+, particularly in smokers. The proportion of discordant cases varies by region, and appears to be highest in regions with lowest attributable (p16+/HPV+) fractions. Dual testing improves prognostication for oropharyngeal cancer cases by identifying discordant cases and improving the prognostic power of the Tumour Node Metastasis (TNM) classification, especially in regions with high discordant rates. SUMMARY Dual testing is essential when considering patients for clinical trials of treatment de-escalation, and may be important when counselling patients on prognosis, especially in regions with high discordant rates and in smokers.
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Affiliation(s)
- Hisham Mehanna
- Institute of Head and Neck Studies and Education (InHANSE), University of Birmingham, Birmingham, UK
| | - Laia Alemany
- Consortium for Biomedical Research in Epidemiology and Public Health—CIBERESP, Carlos III Institute of Health, Av. De Monforte de Lemos 5, 28029 Madrid, Spain
- Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO), Institut d’Investigació Biomedica de Bellvitge (IDIBELL), L’Hospitalet de Llobregat, Barcelona, Spain
| | - Christian von Buchwald
- Department of Otolaryngology, Head and Neck Surgery and Audiology, Copenhagen University Hospital – Rigshospitalet, Copenhagen, Denmark
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Warrick J. Molecular Subtypes of Bladder Cancer: Component Signatures and Potential Value in Clinical Decision-making. Adv Anat Pathol 2024; 31:178-187. [PMID: 38231156 DOI: 10.1097/pap.0000000000000430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
Bladder cancer may be classified into "molecular subtypes" based on gene expression. These are associated with treatment response and patient outcomes. The gene expression signatures that define these subtypes are diverse, including signatures of epithelial differentiation, stromal involvement, cell cycle activity, and immune cell infiltration. Multiple different systems are described. While earlier studies considered molecular subtypes to be intrinsic properties of cancer, recent data have shown molecular subtypes change as tumors progress and evolve, and often differ between histologically distinct regions of a tumor. The data also indicate that some signatures that define molecular subtypes may be treated as independent continuous variables, rather than categorical subtypes, and these individual signatures may be more clinically informative. This review describes molecular subtypes of urothelial carcinoma, including histologic subtypes and tumors with divergent differentiation, and explores potential future uses in patient management.
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Affiliation(s)
- Joshua Warrick
- Departments of Pathology and Urology, Penn State College of Medicine, Hershey, PA
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Tsuchida Y, Niikura N, Chishima T, Mizuno M, Kawate T, Fuchikami H, Miyoshi Y, Sakai T, Kotani H, Kondo N, Hayashi N. Correlation between postoperative treatment selection and prognosis determined using the Oncotype DX® test data: a retrospective multicenter study in Japan. Breast Cancer 2024; 31:401-408. [PMID: 38451415 DOI: 10.1007/s12282-024-01548-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 01/21/2024] [Indexed: 03/08/2024]
Abstract
PURPOSE Oncotype DX® is a frequently used multigene assay for hormone receptor-positive breast cancers. However, limited evidence is available regarding its application in Japan owing to the lack of insurance coverage. Therefore, we conducted this large-scale, retrospective study by collecting data from nine Japanese institutes and assessed postoperative treatment choice and prognosis by using Oncotype DX®. METHODS Six hundred thirty-two patients who underwent breast surgery and whose recurrence score (RS) data were available were included. They were divided into RS 0-25 and RS ≥ 26 groups. The groups were compared in terms of clinicopathological factors, treatment options, and prognosis. RESULTS After the median follow-up period of 10.1 years, the disease-free survival (DFS) rates were significantly better in the RS 0-25 group (p = 0.02). Per the recurrent event type, there was no significant intergroup difference in locoregional recurrence (p = 0.139). However, a trend toward better distant DFS was observed in the RS 0-25 group (p = 0.08). Overall survival was also significantly better in this group (p = 0.027). Considering chemotherapy use, DFS worsened among chemotherapy-treated patients with an RS of 0-25 and those with an RS ≥ 26 who did not receive chemotherapy (p < 0.001). Seven (1.35%) chemotherapy-treated patients with an RS of 0-25 showed disease recurrence. CONCLUSIONS This study presents the largest database-derived prognostic data in Japanese patients, utilizing the Oncotype DX® treatment selection. Further studies are needed to determine the impact on treatment choice, considering the clinical risk, and the need for additional postoperative treatment.
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Affiliation(s)
- Yasue Tsuchida
- Department of Breast Surgical Oncology, St. Luke's International Hospital, Tokyo, Japan
| | - Naoki Niikura
- Department of Breast Oncology, Tokai University School of Medicine, Kanagawa, Japan
| | - Takashi Chishima
- Department of Breast Surgery, Yokohama Rosai Hospital, Kanagawa, Japan
- Division of Breast Surgical Oncology, Department of Surgery, Showa University Northern Yokohama Hospital, Kanagawa, Japan
| | - Mari Mizuno
- Department of Breast Oncology, Tokai University School of Medicine, Kanagawa, Japan
| | - Takahiko Kawate
- Department of Breast Oncology and Surgery, Tokyo Medical University, Tokyo, Japan
| | - Hiromi Fuchikami
- Department of Breast Oncology, Tokyo-West Tokushukai Hospital, Tokyo, Japan
| | - Yasuo Miyoshi
- Division of Breast and Endocrine Surgery, Department of Surgery, Hyogo College of Medicine, Hyogo, Japan
| | - Takehiko Sakai
- Department of Breast Oncology Center, Cancer Institute Hospital of JFCR, Tokyo, Japan
| | - Haruru Kotani
- Department of Breast Oncology, Aichi Cancer Center Hospital, Aichi, Japan
| | - Naoto Kondo
- Department of Breast Surgery, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Naoki Hayashi
- Division of Breast Surgical Oncology, Department of Surgery, Showa University School of Medicine, 1-5-8, Hatanodai, Shinahawa-ku, Tokyo, 142-8666, Japan.
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Walker M, Mayr EM, Koppermann ML, Terron A, Wagner Y, Kling C, Pfarr N. [Molecular pathological analysis through the ages]. Pathologie (Heidelb) 2024; 45:173-179. [PMID: 38619582 DOI: 10.1007/s00292-024-01326-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/18/2024] [Indexed: 04/16/2024]
Abstract
BACKGROUND Molecular pathological examinations of tumor samples encompass a wide range of diagnostic analyses. Especially in recent years, numerous new biomarkers have come to the forefront-the analysis of which is crucial for therapy decisions. OBJECTIVES Within the field of molecular pathology, the demands of next generation sequencing (NGS)-based requirements have experienced massive growth in recent years. To meet this demand, methods are constantly being adapted and further developed. The following sections aim to illuminate how this trend arises and which analyses are gaining importance. METHODS The article provides an overview of the essential nucleic acid-based analysis techniques in the field of massive parallel sequencing. Terms such as DNA- and RNA-based techniques, as well as the associated analysis methods, are described, particularly with regard to their use in routine molecular pathological diagnostics. RESULTS The breadth of genomic sequencing has been steadily growing in recent years, particularly due to the increasing relevance of personalized medicine, along with the rising approvals of targeted therapeutics. This necessitates, among other things, the analysis of new biomarkers. The diagnostics as part of interdisciplinary molecular tumor boards (MTB) are now based on large gene panels (> 1 megabase). Furthermore, through the "Modellvorhaben Genomsequenzierung" § 64e, whole exome or whole genome sequencing has been made available for oncological patients. Given these developments, it is evident that future analyses will require the integration of additional omics fields, such as whole transcriptome analysis, epigenomics, and proteomics. CONCLUSION The challenges of personalized medicine along with the necessity of simultaneously assessing numerous new biomarkers require the implementation and execution of new techniques in molecular pathology whose complexity is steadily increasing.
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Affiliation(s)
- Maria Walker
- Institut für Pathologie, Technische Universität München, Trogerstr. 18, 81675, München, Deutschland
| | - Eva-Maria Mayr
- Institut für Pathologie, Technische Universität München, Trogerstr. 18, 81675, München, Deutschland
| | - Mai-Lan Koppermann
- Institut für Pathologie, Technische Universität München, Trogerstr. 18, 81675, München, Deutschland
| | - Ana Terron
- Institut für Pathologie, Technische Universität München, Trogerstr. 18, 81675, München, Deutschland
| | - Yoko Wagner
- Institut für Pathologie, Technische Universität München, Trogerstr. 18, 81675, München, Deutschland
| | - Charlotte Kling
- Institut für Pathologie, Technische Universität München, Trogerstr. 18, 81675, München, Deutschland
- Deutsches Konsortium für Translationale Krebsforschung (DKTK), Heidelberg, Deutschland
| | - Nicole Pfarr
- Institut für Pathologie, Technische Universität München, Trogerstr. 18, 81675, München, Deutschland.
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Zhang LQ, Liang YC, Wang JX, Zhang J, La T, Li QZ. Unlocking the potential: A novel prognostic index signature for acute myeloid leukemia. Comput Biol Med 2024; 173:108396. [PMID: 38574529 DOI: 10.1016/j.compbiomed.2024.108396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/12/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024]
Abstract
Acute myeloid leukemia (AML) is an aggressive malignancy characterized by challenges in treatment, including drug resistance and frequent relapse. Recent research highlights the crucial roles of tumor microenvironment (TME) in assisting tumor cell immune escape and promoting tumor aggressiveness. This study delves into the interplay between AML and TME. Through the exploration of potential driver genes, we constructed an AML prognostic index (AMLPI). Cross-platform data and multi-dimensional internal and external validations confirmed that the AMLPI outperforms existing models in terms of areas under the receiver operating characteristic curves, concordance index values, and net benefits. High AMLPIs in AML patients were indicative of unfavorable prognostic outcomes. Immune analyses revealed that the high-AMLPI samples exhibit higher expression of HLA-family genes and immune checkpoint genes (including PD1 and CTLA4), along with lower T cell infiltration and higher macrophage infiltration. Genetic variation analyses revealed that the high-AMLPI samples associate with adverse variation events, including TP53 mutations, secondary NPM1 co-mutations, and copy number deletions. Biological interpretation indicated that ALDH2 and SPATS2L contribute significantly to AML patient survival, and their abnormal expression correlates with DNA methylation at cg12142865 and cg11912272. Drug response analyses revealed that different AMLPI samples tend to have different clinical selections, with low-AMLPI samples being more likely to benefit from immunotherapy. Finally, to facilitate broader access to our findings, a user-friendly and publicly accessible webserver was established and available at http://bioinfor.imu.edu.cn/amlpi. This server provides tools including TME-related AML driver genes mining, AMLPI construction, multi-dimensional validations, AML patients risk assessment, and figures drawing.
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MESH Headings
- Humans
- Prognosis
- Nucleophosmin
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Leukemia, Myeloid, Acute/therapy
- DNA Methylation
- Tumor Microenvironment
- Aldehyde Dehydrogenase, Mitochondrial/genetics
- Aldehyde Dehydrogenase, Mitochondrial/metabolism
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Affiliation(s)
- Lu-Qiang Zhang
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China.
| | - Yu-Chao Liang
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010070, China.
| | - Jun-Xuan Wang
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China.
| | - Jing Zhang
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China.
| | - Ta La
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China.
| | - Qian-Zhong Li
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China; The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010070, China.
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45
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Repetto F, Sirohi D, Greipp P, Mahlow J. Incidental Detection of TFEB-Amplified Renal Cell Carcinoma by Colocated Gene Amplification of CCND3 (6p21): A Case Report and Review of the Literature. Int J Surg Pathol 2024; 32:551-555. [PMID: 37394760 DOI: 10.1177/10668969231185081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
TFEB-amplified renal cell carcinoma (RCC), which belongs to the MITF family of RCC, is characterized by genomic amplification at the 6p21.1 locus where the TFEB gene is located. The vascular endothelial growth factor A and cyclin D3 genes are also located at this same locus. When tumors lack classic morphologic features, they may be classified as "RCC not otherwise specified (NOS)." However, it is increasingly important to accurately diagnose the RCC subtype to define the patient's individual prognosis and select the subsequent therapeutic modalities, which now include targeted agents. Therefore, knowledge of the diagnostic features of TFEB-altered RCCs, such as t(6;11) RCCs and TFEB-amplified RCCs, is critical for identifying these tumors. Herein, we present an interesting case of TFEB-amplified RCC that was initially diagnosed as RCC NOS on biopsy of a renal tumor in a community practice setting with available molecular findings demonstrating CCND3 amplification. The genetic abnormality was "accidentally" detected due to the amplification of the colocated CCND3 gene at the 6p21 locus of the TFEB gene on a limited genetic sequencing panel. This case highlights the importance of molecular tests in accurately diagnosing RCC and carefully interpreting molecular findings in the context of histomorphologic features.
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Affiliation(s)
- Federico Repetto
- Favaloro University, School of Medicine, Buenos Aires, Argentina
| | - Deepika Sirohi
- University of Utah, Department of Pathology, Salt Lake City, UT, USA
| | - Patricia Greipp
- Mayo Clinic, Laboratory Medicine and Pathology, Rochester, MN, USA
| | - Jonathon Mahlow
- University of Utah, Department of Pathology, Salt Lake City, UT, USA
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Hashimoto T, Nakamura Y, Oki E, Kobayashi S, Yuda J, Shibuki T, Bando H, Yoshino T. Bridging horizons beyond CIRCULATE-Japan: a new paradigm in molecular residual disease detection via whole genome sequencing-based circulating tumor DNA assay. Int J Clin Oncol 2024; 29:495-511. [PMID: 38551727 DOI: 10.1007/s10147-024-02493-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 02/16/2024] [Indexed: 04/26/2024]
Abstract
Circulating tumor DNA (ctDNA) is the fraction of cell-free DNA in patient blood that originates from a tumor. Advances in DNA sequencing technologies and our understanding of the molecular biology of tumors have increased interest in exploiting ctDNA to facilitate detection of molecular residual disease (MRD). Analysis of ctDNA as a promising MRD biomarker of solid malignancies has a central role in precision medicine initiatives exemplified by our CIRCULATE-Japan project involving patients with resectable colorectal cancer. Notably, the project underscores the prognostic significance of the ctDNA status at 4 weeks post-surgery and its correlation to adjuvant therapy efficacy at interim analysis. This substantiates the hypothesis that MRD is a critical prognostic indicator of relapse in patients with colorectal cancer. Despite remarkable advancements, challenges endure, primarily attributable to the exceedingly low ctDNA concentration in peripheral blood, particularly in scenarios involving low tumor shedding and the intrinsic error rates of current sequencing technologies. These complications necessitate more sensitive and sophisticated assays to verify the clinical utility of MRD across all solid tumors. Whole genome sequencing (WGS)-based tumor-informed MRD assays have recently demonstrated the ability to detect ctDNA in the parts-per-million range. This review delineates the current landscape of MRD assays, highlighting WGS-based approaches as the forefront technique in ctDNA analysis. Additionally, it introduces our upcoming endeavor, WGS-based pan-cancer MRD detection via ctDNA, in our forthcoming project, SCRUM-Japan MONSTAR-SCREEN-3.
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Affiliation(s)
- Tadayoshi Hashimoto
- Translational Research Support Office, National Cancer Center Hospital East, Kashiwa, Japan
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, 6-5-1 Kashiwanoha, Kashiwa, Chiba, 277-8577, Japan
| | - Yoshiaki Nakamura
- Translational Research Support Office, National Cancer Center Hospital East, Kashiwa, Japan
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, 6-5-1 Kashiwanoha, Kashiwa, Chiba, 277-8577, Japan
| | - Eiji Oki
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Shin Kobayashi
- Department of Hepatobiliary and Pancreatic Surgery, National Cancer Center Hospital East, Kashiwa, Japan
| | - Junichiro Yuda
- Department of Hematology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Taro Shibuki
- Translational Research Support Office, National Cancer Center Hospital East, Kashiwa, Japan
| | - Hideaki Bando
- Translational Research Support Office, National Cancer Center Hospital East, Kashiwa, Japan
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, 6-5-1 Kashiwanoha, Kashiwa, Chiba, 277-8577, Japan
| | - Takayuki Yoshino
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, 6-5-1 Kashiwanoha, Kashiwa, Chiba, 277-8577, Japan.
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47
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Norsworthy KJ, Lee-Alonzo RJ, Pazdur R. FDA approvals in 2023: biomarker-positive subsets, equipoise and verification of benefit. Nat Rev Clin Oncol 2024; 21:333-334. [PMID: 38383759 DOI: 10.1038/s41571-024-00871-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Affiliation(s)
- Kelly J Norsworthy
- Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA.
| | - Rosa J Lee-Alonzo
- Oncology Center of Excellence, US Food and Drug Administration, Silver Spring, MD, USA
| | - Richard Pazdur
- Oncology Center of Excellence, US Food and Drug Administration, Silver Spring, MD, USA
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48
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Lee JS, Cho EH, Kim B, Hong J, Kim YG, Kim Y, Jang JH, Lee ST, Kong SY, Lee W, Shin S, Song EY. Clinical Practice Guideline for Blood-based Circulating Tumor DNA Assays. Ann Lab Med 2024; 44:195-209. [PMID: 38221747 PMCID: PMC10813828 DOI: 10.3343/alm.2023.0389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/06/2023] [Accepted: 01/06/2024] [Indexed: 01/16/2024] Open
Abstract
Circulating tumor DNA (ctDNA) has emerged as a promising tool for various clinical applications, including early diagnosis, therapeutic target identification, treatment response monitoring, prognosis evaluation, and minimal residual disease detection. Consequently, ctDNA assays have been incorporated into clinical practice. In this review, we offer an in-depth exploration of the clinical implementation of ctDNA assays. Notably, we examined existing evidence related to pre-analytical procedures, analytical components in current technologies, and result interpretation and reporting processes. The primary objective of this guidelines is to provide recommendations for the clinical utilization of ctDNA assays.
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Affiliation(s)
- Jee-Soo Lee
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Eun Hye Cho
- Department of Laboratory Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Boram Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | | | - Young-gon Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Yoonjung Kim
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Ja-Hyun Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
- Dxome Co. Ltd., Seongnam, Korea
| | - Sun-Young Kong
- Department of Laboratory Medicine, National Cancer Center, Goyang, Korea
| | - Woochang Lee
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Saeam Shin
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Eun Young Song
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
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49
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Klubíčková N, Dermawan JK, Mosaieby E, Martínek P, Vaněček T, Hájková V, Ptáková N, Grossmann P, Šteiner P, Švajdler M, Kinkor Z, Michalová K, Szepe P, Plank L, Hederová S, Kolenová A, Spasov NJ, Kosemehmetoglu K, Pažanin L, Špůrková Z, Baník M, Baumruk L, Meyer A, Kalmykova A, Koshyk O, Michal M, Michal M. Comprehensive clinicopathological, molecular, and methylation analysis of mesenchymal tumors with NTRK and other kinase gene aberrations. J Pathol 2024; 263:61-73. [PMID: 38332737 DOI: 10.1002/path.6260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 12/13/2023] [Accepted: 01/04/2024] [Indexed: 02/10/2024]
Abstract
Alterations in kinase genes such as NTRK1/2/3, RET, and BRAF underlie infantile fibrosarcoma (IFS), the emerging entity 'NTRK-rearranged spindle cell neoplasms' included in the latest WHO classification, and a growing set of tumors with overlapping clinical and pathological features. In this study, we conducted a comprehensive clinicopathological and molecular analysis of 22 cases of IFS and other kinase gene-altered spindle cell neoplasms affecting both pediatric and adult patients. Follow-up periods for 16 patients ranged in length from 10 to 130 months (mean 38 months). Six patients were treated with targeted therapy, achieving a partial or complete response in five cases. Overall, three cases recurred and one metastasized. Eight patients were free of disease, five were alive with disease, and two patients died. All cases showed previously reported morphological patterns. Based on the cellularity and level of atypia, cases were divided into three morphological grade groups. S100 protein and CD34 were at least focally positive in 12/22 and 14/22 cases, respectively. Novel PWWP2A::RET, NUMA1::RET, ITSN1::RAF1, and CAPZA2::MET fusions, which we report herein in mesenchymal tumors for the first time, were detected by RNA sequencing. Additionally, the first uterine case with BRAF and EGFR mutations and CD34 and S100 co-expression is described. DNA sequencing performed in 13 cases uncovered very rare additional genetic aberrations. The CNV profiles showed that high-grade tumors demonstrate a significantly higher percentage of copy number gains and losses across the genome compared with low- and intermediate-grade tumors. Unsupervised clustering of the tumors' methylation profiles revealed that in 8/9 cases, the methylation profiles clustered with the IFS methylation class, irrespective of their clinicopathological or molecular features. © 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Natálie Klubíčková
- Department of Pathology, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
- Bioptical Laboratory Ltd, Pilsen, Czech Republic
| | - Josephine K Dermawan
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Elaheh Mosaieby
- Department of Pathology, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
- Bioptical Laboratory Ltd, Pilsen, Czech Republic
| | | | | | | | - Nikola Ptáková
- Bioptical Laboratory Ltd, Pilsen, Czech Republic
- Department of Biology and Medical Genetics, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | | | - Petr Šteiner
- Bioptical Laboratory Ltd, Pilsen, Czech Republic
| | - Marián Švajdler
- Department of Pathology, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
- Bioptical Laboratory Ltd, Pilsen, Czech Republic
| | | | - Květoslava Michalová
- Department of Pathology, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
- Bioptical Laboratory Ltd, Pilsen, Czech Republic
| | - Peter Szepe
- Institute of Pathological Anatomy, Jessenius Faculty of Medicine in Martin, Comenius University, Martin, Slovakia
| | - Lukáš Plank
- Institute of Pathological Anatomy, Jessenius Faculty of Medicine in Martin, Comenius University, Martin, Slovakia
| | - Stanislava Hederová
- Department of Pediatric Hematology and Oncology, National Institute of Children's Diseases and Medical Faculty, Comenius University, Bratislava, Slovakia
| | - Alexandra Kolenová
- Department of Pediatric Hematology and Oncology, National Institute of Children's Diseases and Medical Faculty, Comenius University, Bratislava, Slovakia
| | - Neofit Juriev Spasov
- Department of Pediatrics and Medical Genetics, Oncohematology Unit, Medical University Plovdiv, University Hospital Sveti Georgi, Plovdiv, Bulgaria
| | | | - Leo Pažanin
- Department of Pathology, Sestre Milosrdnice University Hospital Center, Zagreb, Croatia
| | - Zuzana Špůrková
- Department of Pathology, Na Bulovce Hospital, Prague, Czech Republic
| | - Martin Baník
- Department of Pathology, Regional Hospital Karlovy Vary, Karlovy Vary, Czech Republic
| | - Luděk Baumruk
- Department of Pathology, Regional Hospital Příbram, Příbram, Czech Republic
| | - Anders Meyer
- Department of Pathology, University of Kansas, Kansas City, KS, USA
| | | | - Olena Koshyk
- Medical Laboratory CSD Health Care Ltd, Kyiv, Ukraine
| | - Michal Michal
- Department of Pathology, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
- Bioptical Laboratory Ltd, Pilsen, Czech Republic
| | - Michael Michal
- Department of Pathology, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
- Bioptical Laboratory Ltd, Pilsen, Czech Republic
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50
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Gao X, Xu S, Zhu P, Lao IW, Yu L, Wang J. Primary NTRK -rearranged Spindle Cell Neoplasm of the Gastrointestinal Tract: A Clinicopathological and Molecular Analysis of 8 Cases. Am J Surg Pathol 2024; 48:623-631. [PMID: 38525823 DOI: 10.1097/pas.0000000000002202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
NTRK-rearranged spindle cell neoplasm occurs predominantly in the superficial or deep soft tissues of extremities or trunk. Occurrence in the visceral organs is extremely rare. Herein, we describe 8 cases of NTRK-rearranged spindle cell neoplasm that arose primarily in the gastrointestinal tract. Patients included 5 males and 3 females with age at presentation ranging from 6 to 63 years (median: 29.5 years). Tumors occurred in the colon (n=3), small intestine (n=2), rectum (n=2), and stomach (n=1). Tumor size ranged from 3.5 to 9 cm (median: 5 cm). Morphologically, 4 tumors were low-grade, composed of haphazard or intertwining fascicles of spindle cells, with prominent interstitial collagen fibers and ring-like perivascular hyalinization being present in 2 tumors. The other 4 tumors were histologically high-grade sarcomas, consisting of sweeping fascicles of atypical spindle cells showing increased cellularity and brisk mitotic activity. Immunohistochemically, 6/6 cases (100%) showed diffuse and strong cytoplasmic staining of pan-TRK. Variable expression of TrkA, CD34, and S100 was noted in 5/5 (100%), 5/8 (62.5%), and 4/7 (57.1%) cases, respectively. Fluorescence in situ hybridization analysis showed NTRK1 rearrangement (n=7) and NTRK2 rearrangement (n=1). In cases with available materials, RNA sequencing identified LMNA::NTRK1 (n=3), TPM3::NTRK1 (n=2), and STRN::NTRK2 (n=1) fusions. At follow-up (range: 4 to 30 months; median: 12.5 months), 6 of 7 patients who underwent surgery had no evidence of disease at last follow-up. One patient was succumbed to the disease at 12 months despite adjunctive treatment with TRK inhibitor larotrectinib after surgery. One patient was treated with larotrectinib alone. He showed significant response at 7 months after treatment. NTRK-rearranged spindle cell neoplasm represents an exceptionally rare entity in the gastrointestinal tract. The presence of interstitial collagen fibers and ring-like perivascular hyalinization and co-expression of CD34 and S100 are diagnostic clues to low-grade neoplasms. However, high-grade sarcomas pose a considerable diagnostic challenge to pathologists owing to the lack of specific features. The final diagnosis relies on molecular assays. Patients with advanced disease may benefit from TRK inhibitor treatment.
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Affiliation(s)
- Xiaojiao Gao
- Department of Pathology, Fudan University Shanghai Cancer Center
- Department of Pathology, The First People's Hospital of Kunshan, Kunshan, Jiangsu, China
| | - Song Xu
- Department of Pathology, The First People's Hospital of Kunshan, Kunshan, Jiangsu, China
| | - Peipei Zhu
- Department of Pathology, Fudan University Shanghai Cancer Center
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai
| | - I Weng Lao
- Department of Pathology, Fudan University Shanghai Cancer Center
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai
| | - Lin Yu
- Department of Pathology, Fudan University Shanghai Cancer Center
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai
| | - Jian Wang
- Department of Pathology, Fudan University Shanghai Cancer Center
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai
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