1
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Nief CA, Hammer PM, Wang A, Charu V, Tanweer A, Litkouhi B, Kidd E, Gentles AJ, Howitt BE. Endometrioid Endometrial RNA Index Predicts Recurrence in Stage I Patients. Clin Cancer Res 2024; 30:2801-2811. [PMID: 38669067 DOI: 10.1158/1078-0432.ccr-23-3158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/13/2024] [Accepted: 04/24/2024] [Indexed: 07/02/2024]
Abstract
PURPOSE Risk prediction with genomic and transcriptomic data has the potential to improve patient outcomes by enabling clinicians to identify patients requiring adjuvant treatment approaches, while sparing low-risk patients from unnecessary interventions. Endometrioid endometrial carcinoma (EEC) is the most common cancer in women in developed countries, and rates of endometrial cancer are increasing. EXPERIMENTAL DESIGN We collected a 105-patient case-control cohort of stage I EEC comprising 45 patients who experienced recurrence less than 6 years after excision, and 60 Fédération Internationale de Gynécologie et d'Obstétrique grade-matched controls without recurrence. We first utilized two RNA-based, previously validated machine learning approaches, namely, EcoTyper and Complexity Index in Sarcoma (CINSARC). We developed Endometrioid Endometrial RNA Index (EERI), which uses RNA expression data from 46 genes to generate a personalized risk score for each patient. EERI was trained on our 105-patient cohort and tested on a publicly available cohort of 263 patients with stage I EEC. RESULTS EERI was able to predict recurrences with 94% accuracy in the training set and 81% accuracy in the test set. In the test set, patients assigned as EERI high-risk were significantly more likely to experience recurrence (30%) than the EERI low-risk group (1%) with a hazard ratio of 9.9 (95% CI, 4.1-23.8; P < 0.001). CONCLUSIONS Tumors with high-risk genetic features may require additional treatment or closer monitoring and are not readily identified using traditional clinicopathologic and molecular features. EERI performs with high sensitivity and modest specificity, which may benefit from further optimization and validation in larger independent cohorts.
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Affiliation(s)
- Corrine A Nief
- Stanford University School of Medicine, Stanford, California
- Department of Pathology, Stanford University, Stanford, California
| | - Phoebe M Hammer
- Department of Pathology, Stanford University, Stanford, California
| | - Aihui Wang
- Department of Pathology, Stanford University, Stanford, California
| | - Vivek Charu
- Department of Pathology, Stanford University, Stanford, California
| | - Amina Tanweer
- Department of Pathology, Stanford University, Stanford, California
| | - Babak Litkouhi
- Department of Biomedical Data Science, Stanford University, Stanford, California
| | - Elizabeth Kidd
- Department of Radiation Oncology, Stanford University, Stanford, California
| | - Andrew J Gentles
- Department of Pathology, Stanford University, Stanford, California
- Department of Gynecologic Oncology, Stanford University, Stanford, California
| | - Brooke E Howitt
- Department of Pathology, Stanford University, Stanford, California
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2
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Liu J, Chai XX, Qiu XR, Sun WJ, Tian YL, Guo WH, Yin DC, Zhang CY. Type X collagen knockdown inactivate ITGB1/PI3K/AKT to suppress chronic unpredictable mild stress-stimulated triple-negative breast cancer progression. Int J Biol Macromol 2024; 273:133074. [PMID: 38866293 DOI: 10.1016/j.ijbiomac.2024.133074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/19/2024] [Accepted: 06/08/2024] [Indexed: 06/14/2024]
Abstract
Triple-negative breast cancer (TNBC) is the most malignant subtype of breast cancer, has a poor prognosis and limited access to efficient targeted treatments. Chronic unpredictable mild stress (CUMS) is highly risk factor for TNBC occurrence and development. Type X collagen (COL10A1), a crucial protein component of the extracellular matrix, ranks second among all aberrantly expressed genes in TNBC, and it is significantly up-regulated under CUMS. Nevertheless, the impact of CUMS and COL10A1 on TNBC, along with the underlying mechanisms are still unclear. In this research, we studied the effect of CUMS-induced norepinephrine (NE) elevation on TNBC, and uncovered that it notably enhanced TNBC cell proliferation, migration, and invasion in vitro, and also fostering tumor growth and lung metastasis in vivo. Additionally, our investigation found that COL10A1 directly interacted with integrin subunit beta 1 (ITGB1), then activates the downstream PI3K/AKT signaling pathway, thereby promoting TNBC growth and metastasis, while it was reversed by knocking down of COL10A1 or ITGB1. Our study demonstrated that the TNBC could respond to CUMS, and advocate for COL10A1 as a pivotal therapeutic target in TNBC treatment.
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Affiliation(s)
- Jie Liu
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710000, Shaanxi, PR China
| | - Xiao-Xia Chai
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710000, Shaanxi, PR China
| | - Xiao-Rong Qiu
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710000, Shaanxi, PR China
| | - Wen-Jun Sun
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710000, Shaanxi, PR China
| | - Yi-Le Tian
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710000, Shaanxi, PR China
| | - Wei-Hong Guo
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710000, Shaanxi, PR China
| | - Da-Chuan Yin
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710000, Shaanxi, PR China.
| | - Chen-Yan Zhang
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710000, Shaanxi, PR China; Research & Development Institute of Northwestern Polytechnical University in Shenzhen, Shenzhen 518063, China.
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3
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Abel J, Jain S, Rajan D, Padigela H, Leidal K, Prakash A, Conway J, Nercessian M, Kirkup C, Javed SA, Biju R, Harguindeguy N, Shenker D, Indorf N, Sanghavi D, Egger R, Trotter B, Gerardin Y, Brosnan-Cashman JA, Dhoot A, Montalto MC, Parmar C, Wapinski I, Khosla A, Drage MG, Yu L, Taylor-Weiner A. AI powered quantification of nuclear morphology in cancers enables prediction of genome instability and prognosis. NPJ Precis Oncol 2024; 8:134. [PMID: 38898127 PMCID: PMC11187064 DOI: 10.1038/s41698-024-00623-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 06/04/2024] [Indexed: 06/21/2024] Open
Abstract
While alterations in nucleus size, shape, and color are ubiquitous in cancer, comprehensive quantification of nuclear morphology across a whole-slide histologic image remains a challenge. Here, we describe the development of a pan-tissue, deep learning-based digital pathology pipeline for exhaustive nucleus detection, segmentation, and classification and the utility of this pipeline for nuclear morphologic biomarker discovery. Manually-collected nucleus annotations were used to train an object detection and segmentation model for identifying nuclei, which was deployed to segment nuclei in H&E-stained slides from the BRCA, LUAD, and PRAD TCGA cohorts. Interpretable features describing the shape, size, color, and texture of each nucleus were extracted from segmented nuclei and compared to measurements of genomic instability, gene expression, and prognosis. The nuclear segmentation and classification model trained herein performed comparably to previously reported models. Features extracted from the model revealed differences sufficient to distinguish between BRCA, LUAD, and PRAD. Furthermore, cancer cell nuclear area was associated with increased aneuploidy score and homologous recombination deficiency. In BRCA, increased fibroblast nuclear area was indicative of poor progression-free and overall survival and was associated with gene expression signatures related to extracellular matrix remodeling and anti-tumor immunity. Thus, we developed a powerful pan-tissue approach for nucleus segmentation and featurization, enabling the construction of predictive models and the identification of features linking nuclear morphology with clinically-relevant prognostic biomarkers across multiple cancer types.
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4
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Liu P, Page D, Ahlquist P, Ong IM, Gitter A. MPAC: a computational framework for inferring cancer pathway activities from multi-omic data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.15.599113. [PMID: 38948762 PMCID: PMC11212914 DOI: 10.1101/2024.06.15.599113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Fully capturing cellular state requires examining genomic, epigenomic, transcriptomic, proteomic, and other assays for a biological sample and comprehensive computational modeling to reason with the complex and sometimes conflicting measurements. Modeling these so-called multi-omic data is especially beneficial in disease analysis, where observations across omic data types may reveal unexpected patient groupings and inform clinical outcomes and treatments. We present Multi-omic Pathway Analysis of Cancer (MPAC), a computational framework that interprets multi-omic data through prior knowledge from biological pathways. MPAC uses network relationships encoded in pathways using a factor graph to infer consensus activity levels for proteins and associated pathway entities from multi-omic data, runs permutation testing to eliminate spurious activity predictions, and groups biological samples by pathway activities to prioritize proteins with potential clinical relevance. Using DNA copy number alteration and RNA-seq data from head and neck squamous cell carcinoma patients from The Cancer Genome Atlas as an example, we demonstrate that MPAC predicts a patient subgroup related to immune responses not identified by analysis with either input omic data type alone. Key proteins identified via this subgroup have pathway activities related to clinical outcome as well as immune cell compositions. Our MPAC R package, available at https://bioconductor.org/packages/MPAC, enables similar multi-omic analyses on new datasets.
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Affiliation(s)
- Peng Liu
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - David Page
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Computer Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Paul Ahlquist
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, Wisconsin, United States of America
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Irene M Ong
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Center for Human Genomics and Precision Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Anthony Gitter
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Computer Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, Wisconsin, United States of America
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5
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Zhang M, Zhang D, Wang Q, Lin G. Construction of a prognostic model for breast cancer based on moonlighting genes. Hum Mol Genet 2024; 33:1023-1035. [PMID: 38491801 DOI: 10.1093/hmg/ddae040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 02/08/2024] [Accepted: 03/05/2024] [Indexed: 03/18/2024] Open
Abstract
Breast cancer (BRCA) is a highly heterogeneous disease, with significant differences in prognosis among patients. Existing biomarkers and prognostic models have limited ability to predict BRCA prognosis. Moonlighting genes regulate tumor progression and are associated with cancer prognosis. This study aimed to construct a moonlighting gene-based prognostic model for BRCA. We obtained differentially expressed genes (DEGs) in BRCA from The Cancer Genome Atlas and intersected them with moonlighting genes from MoonProt to acquire differential moonlighting genes. GO and KEGG results showed main enrichment of these genes in the response of BRCA cells to environmental stimuli and pentose phosphate pathway. Based on moonlighting genes, we conducted drug prediction and validated results through cellular experiments. After ABCB1 knockdown, viability and proliferation of BRCA cells were significantly enhanced. Based on differential moonlighting genes, BRCA was divided into three subgroups, among which cluster2 had the highest survival rate and immunophenoscore and relatively low tumor mutation burden. TP53 had the highest mutation frequency in cluster2 and cluster3, while PIK3CA had a higher mutation frequency in cluster1, with the majority being missense mutations. Subsequently, we established an 11-gene prognostic model in the training set based on DEGs among subgroups using univariate Cox regression, LASSO regression, and multivariable Cox regression analyses. Model prognostic performance was verified in GEO, METABRIC and ICGC validation sets. In summary, this study obtained three BRCA moonlighting gene-related subtypes and constructed an 11-gene prognostic model. The 11-gene BRCA prognostic model has good predictive performance, guiding BRCA prognosis for clinical doctors.
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Affiliation(s)
- Ming Zhang
- Department of the Thyroid and Breast Surgery, Longyan First Hospital Affiliated to Fujian Medical University, No. 105 Jiuyi North Road, Xinluo District, Longyan City, FJ 364000, China
| | - Dejie Zhang
- Department of the Thyroid and Breast Surgery, Longyan First Hospital Affiliated to Fujian Medical University, No. 105 Jiuyi North Road, Xinluo District, Longyan City, FJ 364000, China
| | - Qicai Wang
- Department of the Thyroid and Breast Surgery, Longyan First Hospital Affiliated to Fujian Medical University, No. 105 Jiuyi North Road, Xinluo District, Longyan City, FJ 364000, China
| | - Guoliang Lin
- Department of the Thyroid and Breast Surgery, Longyan First Hospital Affiliated to Fujian Medical University, No. 105 Jiuyi North Road, Xinluo District, Longyan City, FJ 364000, China
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6
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Azuma I, Mizuno T, Kusuhara H. GLDADec: marker-gene guided LDA modeling for bulk gene expression deconvolution. Brief Bioinform 2024; 25:bbae315. [PMID: 38982642 PMCID: PMC11233176 DOI: 10.1093/bib/bbae315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 05/21/2024] [Accepted: 06/14/2024] [Indexed: 07/11/2024] Open
Abstract
Inferring cell type proportions from bulk transcriptome data is crucial in immunology and oncology. Here, we introduce guided LDA deconvolution (GLDADec), a bulk deconvolution method that guides topics using cell type-specific marker gene names to estimate topic distributions for each sample. Through benchmarking using blood-derived datasets, we demonstrate its high estimation performance and robustness. Moreover, we apply GLDADec to heterogeneous tissue bulk data and perform comprehensive cell type analysis in a data-driven manner. We show that GLDADec outperforms existing methods in estimation performance and evaluate its biological interpretability by examining enrichment of biological processes for topics. Finally, we apply GLDADec to The Cancer Genome Atlas tumor samples, enabling subtype stratification and survival analysis based on estimated cell type proportions, thus proving its practical utility in clinical settings. This approach, utilizing marker gene names as partial prior information, can be applied to various scenarios for bulk data deconvolution. GLDADec is available as an open-source Python package at https://github.com/mizuno-group/GLDADec.
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Affiliation(s)
- Iori Azuma
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Bunkyo-ku 113-0033, Japan
| | - Tadahaya Mizuno
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Bunkyo-ku 113-0033, Japan
| | - Hiroyuki Kusuhara
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Bunkyo-ku 113-0033, Japan
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7
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Ruiz-Arenas C, Marín-Goñi I, Wang L, Ochoa I, Pérez-Jurado L, Hernaez M. NetActivity enhances transcriptional signals by combining gene expression into robust gene set activity scores through interpretable autoencoders. Nucleic Acids Res 2024; 52:e44. [PMID: 38597610 PMCID: PMC11109970 DOI: 10.1093/nar/gkae197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 01/23/2024] [Accepted: 03/12/2024] [Indexed: 04/11/2024] Open
Abstract
Grouping gene expression into gene set activity scores (GSAS) provides better biological insights than studying individual genes. However, existing gene set projection methods cannot return representative, robust, and interpretable GSAS. We developed NetActivity, a machine learning framework that generates GSAS based on a sparsely-connected autoencoder, where each neuron in the inner layer represents a gene set. We proposed a three-tier training that yielded representative, robust, and interpretable GSAS. NetActivity model was trained with 1518 GO biological processes terms and KEGG pathways and all GTEx samples. NetActivity generates GSAS robust to the initialization parameters and representative of the original transcriptome, and assigned higher importance to more biologically relevant genes. Moreover, NetActivity returns GSAS with a more consistent definition and higher interpretability than GSVA and hipathia, state-of-the-art gene set projection methods. Finally, NetActivity enables combining bulk RNA-seq and microarray datasets in a meta-analysis of prostate cancer progression, highlighting gene sets related to cell division, key for disease progression. When applied to metastatic prostate cancer, gene sets associated with cancer progression were also altered due to drug resistance, while a classical enrichment analysis identified gene sets irrelevant to the phenotype. NetActivity is publicly available in Bioconductor and GitHub.
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Affiliation(s)
- Carlos Ruiz-Arenas
- Computational Biology Program, CIMA University of Navarra, idiSNA, Pamplona 31008, Spain
- Department MELIS, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Irene Marín-Goñi
- Computational Biology Program, CIMA University of Navarra, idiSNA, Pamplona 31008, Spain
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Liewei Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Idoia Ochoa
- Department of Electrical and Electronics Engineering, Tecnun, University of Navarra, Donostia, Spain
- Institute for Data Science and Artificial Inteligence (DATAI), University of Navarra, Pamplona 31008, Spain
| | - Luis A Pérez-Jurado
- Department MELIS, Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
- Genetics Service, Hospital del Mar & Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Mikel Hernaez
- Computational Biology Program, CIMA University of Navarra, idiSNA, Pamplona 31008, Spain
- Institute for Data Science and Artificial Inteligence (DATAI), University of Navarra, Pamplona 31008, Spain
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8
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Nicu AT, Ionel IP, Stoica I, Burlibasa L, Jinga V. Recent Advancements in Research on DNA Methylation and Testicular Germ Cell Tumors: Unveiling the Intricate Relationship. Biomedicines 2024; 12:1041. [PMID: 38791003 PMCID: PMC11117643 DOI: 10.3390/biomedicines12051041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 04/30/2024] [Accepted: 05/02/2024] [Indexed: 05/26/2024] Open
Abstract
Testicular germ cell tumors (TGCTs) are the most common type of testicular cancer, with a particularly high incidence in the 15-45-year age category. Although highly treatable, resistance to therapy sometimes occurs, with devastating consequences for the patients. Additionally, the young age at diagnosis and the treatment itself pose a great threat to patients' fertility. Despite extensive research concerning genetic and environmental risk factors, little is known about TGCT etiology. However, epigenetics has recently come into the spotlight as a major factor in TGCT initiation, progression, and even resistance to treatment. As such, recent studies have been focusing on epigenetic mechanisms, which have revealed their potential in the development of novel, non-invasive biomarkers. As the most studied epigenetic mechanism, DNA methylation was the first revelation in this particular field, and it continues to be a main target of investigations as research into its association with TGCT has contributed to a better understanding of this type of cancer and constantly reveals novel aspects that can be exploited through clinical applications. In addition to biomarker development, DNA methylation holds potential for developing novel treatments based on DNA methyltransferase inhibitors (DNMTis) and may even be of interest for fertility management in cancer survivors. This manuscript is structured as a literature review, which comprehensively explores the pivotal role of DNA methylation in the pathogenesis, progression, and treatment resistance of TGCTs.
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Affiliation(s)
- Alina-Teodora Nicu
- Genetics Department, Faculty of Biology, University of Bucharest, 030018 Bucharest, Romania; (A.-T.N.); (I.S.)
| | - Ileana Paula Ionel
- Department of Specific Disciplines, Faculty of Midwifery and Nursing, University of Medicine and Pharmacy “Carol Davila”, 050474 Bucharest, Romania
| | - Ileana Stoica
- Genetics Department, Faculty of Biology, University of Bucharest, 030018 Bucharest, Romania; (A.-T.N.); (I.S.)
| | - Liliana Burlibasa
- Genetics Department, Faculty of Biology, University of Bucharest, 030018 Bucharest, Romania; (A.-T.N.); (I.S.)
| | - Viorel Jinga
- Department of Urology, Faculty of Medicine, University of Medicine and Pharmacy “Carol Davila”, 050474 Bucharest, Romania;
- The Academy of Romanian Scientists, 050044 Bucharest, Romania
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9
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Zhang Q, Luo Y, Qian B, Cao X, Xu C, Guo K, Wan R, Jiang Y, Wang T, Mei Z, Liu J, Lv C. A systematic pan-cancer analysis identifies LDHA as a novel predictor for immunological, prognostic, and immunotherapy resistance. Aging (Albany NY) 2024; 16:8000-8018. [PMID: 38709280 PMCID: PMC11132014 DOI: 10.18632/aging.205800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 03/18/2024] [Indexed: 05/07/2024]
Abstract
Lactate dehydrogenase A (LDHA), a critical enzyme involved in glycolysis, is broadly involved multiple biological functions in human cancers. It is reported that LDHA can impact tumor immune surveillance and induce the transformation of tumor-associated macrophages, highlighting its unnoticed function of LDHA in immune system. However, in human cancers, the role of LDHA in prognosis and immunotherapy hasn't been investigated. In this study, we analyzed the expression pattern and prognostic value of LDHA in pan-cancer and explored its association between tumor microenvironment (TME), immune infiltration subtype, stemness scores, tumor mutation burden (TMB), and immunotherapy resistance. We found that LDHA expression is tumor heterogeneous and that its high expression is associated with poor prognosis in multiple human cancers. In addition, LDHA expression was positively correlated with the presence of mononuclear/macrophage cells, and also promoted the infiltration of a range of immune cells. Genomic alteration of LDHA was common in different types of cancer, while with prognostic value in pan-cancers. Pan-cancer analysis revealed that the significant correlations existed between LDHA expression and tumor microenvironment (including stromal cells and immune cells) as well as stemness scores (DNAss and RNAss) across cancer types. Drug sensitivity analysis also revealed that LDHA was able to predict response to chemotherapy and immunotherapy. Furthermore, it was confirmed that knockdown of LDHA reduced proliferation and migration ability of lung cancer cells. Taken together, LDHA could serve as a prognostic biomarker and a potential immunotherapy marker.
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Affiliation(s)
- Qiqi Zhang
- The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, P.R. China
- Southwest Medical University, Luzhou, P.R. China
| | - Yuanning Luo
- The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, P.R. China
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, P.R. China
| | - Bingshuo Qian
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, P.R. China
- School of Pharmacy, Henan University, Kaifeng, P.R. China
| | - Xiuhua Cao
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Luzhou, P.R. China
| | - Caijun Xu
- Southwest Medical University, Luzhou, P.R. China
| | - Kan Guo
- The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, P.R. China
- Southwest Medical University, Luzhou, P.R. China
| | - Runlan Wan
- The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, P.R. China
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, P.R. China
| | - Yaling Jiang
- Southwest Medical University, Luzhou, P.R. China
| | - Tiecheng Wang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, P.R. China
| | - Zhiqiang Mei
- The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, P.R. China
- Southwest Medical University, Luzhou, P.R. China
| | - Jinbiao Liu
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, P.R. China
| | - Chaoxiang Lv
- The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, P.R. China
- Southwest Medical University, Luzhou, P.R. China
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, P.R. China
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10
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Gupta A, Singh MS, Singh B. Deciphering the functional role of clinical mutations in ABCB1, ABCC1, and ABCG2 ABC transporters in endometrial cancer. Front Pharmacol 2024; 15:1380371. [PMID: 38766631 PMCID: PMC11100334 DOI: 10.3389/fphar.2024.1380371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 03/28/2024] [Indexed: 05/22/2024] Open
Abstract
ATP-binding cassette transporters represent a superfamily of dynamic membrane-based proteins with diverse yet common functions such as use of ATP hydrolysis to efflux substrates across cellular membranes. Three major transporters-P-glycoprotein (P-gp or ABCB1), multidrug resistance protein 1 (MRP1 or ABCC1), and breast cancer resistance protein (BCRP or ABCG2) are notoriously involved in therapy resistance in cancer patients. Despite exhaustive individual characterizations of each of these transporters, there is a lack of understanding in terms of the functional role of mutations in substrate binding and efflux, leading to drug resistance. We analyzed clinical variations reported in endometrial cancers for these transporters. For ABCB1, the majority of key mutations were present in the membrane-facing region, followed by the drug transport channel and ATP-binding regions. Similarly, for ABCG2, the majority of key mutations were located in the membrane-facing region, followed by the ATP-binding region and drug transport channel, thus highlighting the importance of membrane-mediated drug recruitment and efflux in ABCB1 and ABCG2. On the other hand, for ABCC1, the majority of key mutations were present in the inactive nucleotide-binding domain, followed by the drug transport channel and membrane-facing regions, highlighting the importance of the inactive nucleotide-binding domain in facilitating indirect drug efflux in ABCC1. The identified key mutations in endometrial cancer and mapped common mutations present across different types of cancers in ABCB1, ABCC1, and ABCG2 will facilitate the design and discovery of inhibitors targeting unexplored structural regions of these transporters and re-engineering of these transporters to tackle chemoresistance.
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Affiliation(s)
- Aayushi Gupta
- Centre for Life Sciences, Mahindra University, Hyderabad, India
| | - Manu Smriti Singh
- Centre for Life Sciences, Mahindra University, Hyderabad, India
- Interdisciplinary Centre for Nanosensors and Nanomedicine, Mahindra University, Hyderabad, India
| | - Bipin Singh
- Centre for Life Sciences, Mahindra University, Hyderabad, India
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11
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Buisseret L, Bareche Y, Venet D, Girard E, Gombos A, Emonts P, Majjaj S, Rouas G, Serra M, Debien V, Agostinetto E, Garaud S, Willard-Gallo K, Larsimont D, Stagg J, Rothé F, Sotiriou C. The long and winding road to biomarkers for immunotherapy: a retrospective analysis of samples from patients with triple-negative breast cancer treated with pembrolizumab. ESMO Open 2024; 9:102964. [PMID: 38703428 PMCID: PMC11087916 DOI: 10.1016/j.esmoop.2024.102964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Immune checkpoint blockade (ICB) in combination with chemotherapy improves outcome of patients with triple-negative breast cancer (TNBC) in metastatic and early settings. The identification of predictive biomarkers able to guide treatment decisions is challenging and currently limited to programmed death-ligand 1 (PD-L1) expression and high tumor mutational burden (TMB) in the advanced setting, with several limitations. MATERIALS AND METHODS We carried out a retrospective analysis of clinical-pathological and molecular characteristics of tumor samples from 11 patients with advanced TNBC treated with single-agent pembrolizumab participating in two early-phase clinical trials: KEYNOTE-012 and KEYNOTE-086. Clinical, imaging, pathological [i.e. tumor-infiltrating lymphocytes (TILs), PD-L1 status], RNA sequencing, and whole-exome sequencing data were analyzed. We compared our results with publicly available transcriptomic data from TNBC cohorts from TCGA and METABRIC. RESULTS Response to pembrolizumab was heterogeneous: two patients experienced exceptional long-lasting responses, six rapid progressions, and three relatively slower disease progression. Neither PD-L1 nor stromal TILs were significantly associated with response to treatment. Increased TMB values were observed in tumor samples from exceptional responders compared to the rest of the cohort (P = 3.4 × 10-4). Tumors from exceptional responders were enriched in adaptive and innate immune cell signatures. Expression of regulatory T-cell markers (FOXP3, CCR4, CCR8, TIGIT) was mainly observed in tumors from responders except for glycoprotein-A repetitions predominant (GARP), which was overexpressed in tumors from rapid progressors. GARP RNA expression in primary breast tumors from the public dataset was significantly associated with a worse prognosis. CONCLUSIONS The wide spectrum of clinical responses to ICB supports that TNBC is a heterogeneous disease. Tumors with high TMB respond better to ICB. However, the optimal cut-off of 10 mutations (mut)/megabase (Mb) may not reflect the complexity of all tumor subtypes, despite its approval as a tumor-agnostic biomarker. Further studies are required to better elucidate the relevance of the tumor microenvironment and its components as potential predictive biomarkers in the context of ICB.
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Affiliation(s)
- L Buisseret
- Breast Cancer Translational Research Laboratory J-C Heuson, Université Libre de Bruxelles (ULB), Hôpital Universitaire de Bruxelles (HUB), Institut Jules Bordet, Brussels; Medical Oncology Department, Université Libre de Bruxelles (ULB), Hôpital Universitaire de Bruxelles (HUB), Institut Jules Bordet, Brussels, Belgium.
| | - Y Bareche
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montréal; Faculty of Pharmacy, Université de Montréal, Montréal, Canada
| | - D Venet
- Breast Cancer Translational Research Laboratory J-C Heuson, Université Libre de Bruxelles (ULB), Hôpital Universitaire de Bruxelles (HUB), Institut Jules Bordet, Brussels
| | - E Girard
- Breast Cancer Translational Research Laboratory J-C Heuson, Université Libre de Bruxelles (ULB), Hôpital Universitaire de Bruxelles (HUB), Institut Jules Bordet, Brussels; Centre Oscar Lambret, Lille, France
| | - A Gombos
- Medical Oncology Department, Université Libre de Bruxelles (ULB), Hôpital Universitaire de Bruxelles (HUB), Institut Jules Bordet, Brussels, Belgium
| | - P Emonts
- Radiology Department, Université Libre de Bruxelles (ULB), Hôpital Universitaire de Bruxelles (HUB), Institut Jules Bordet, Brussels
| | - S Majjaj
- Breast Cancer Translational Research Laboratory J-C Heuson, Université Libre de Bruxelles (ULB), Hôpital Universitaire de Bruxelles (HUB), Institut Jules Bordet, Brussels
| | - G Rouas
- Breast Cancer Translational Research Laboratory J-C Heuson, Université Libre de Bruxelles (ULB), Hôpital Universitaire de Bruxelles (HUB), Institut Jules Bordet, Brussels
| | - M Serra
- Breast Cancer Translational Research Laboratory J-C Heuson, Université Libre de Bruxelles (ULB), Hôpital Universitaire de Bruxelles (HUB), Institut Jules Bordet, Brussels
| | - V Debien
- Academic Trials Promoting Team, Université Libre de Bruxelles (ULB), Hôpital Universitaire de Bruxelles (HUB), Institut Jules Bordet, Brussels
| | - E Agostinetto
- Academic Trials Promoting Team, Université Libre de Bruxelles (ULB), Hôpital Universitaire de Bruxelles (HUB), Institut Jules Bordet, Brussels
| | - S Garaud
- Molecular Immunology Unit, Université Libre de Bruxelles (ULB), Hôpital Universitaire de Bruxelles (HUB), Institut Jules Bordet, Brussels
| | - K Willard-Gallo
- Molecular Immunology Unit, Université Libre de Bruxelles (ULB), Hôpital Universitaire de Bruxelles (HUB), Institut Jules Bordet, Brussels
| | - D Larsimont
- Pathology Department, Université Libre de Bruxelles (ULB), Hôpital Universitaire de Bruxelles (HUB), Institut Jules Bordet, Brussels, Belgium
| | - J Stagg
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montréal; Faculty of Pharmacy, Université de Montréal, Montréal, Canada
| | - F Rothé
- Breast Cancer Translational Research Laboratory J-C Heuson, Université Libre de Bruxelles (ULB), Hôpital Universitaire de Bruxelles (HUB), Institut Jules Bordet, Brussels
| | - C Sotiriou
- Breast Cancer Translational Research Laboratory J-C Heuson, Université Libre de Bruxelles (ULB), Hôpital Universitaire de Bruxelles (HUB), Institut Jules Bordet, Brussels
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12
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Watson EV, Lee JJK, Gulhan DC, Melloni GEM, Venev SV, Magesh RY, Frederick A, Chiba K, Wooten EC, Naxerova K, Dekker J, Park PJ, Elledge SJ. Chromosome evolution screens recapitulate tissue-specific tumor aneuploidy patterns. Nat Genet 2024; 56:900-912. [PMID: 38388848 PMCID: PMC11096114 DOI: 10.1038/s41588-024-01665-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 01/16/2024] [Indexed: 02/24/2024]
Abstract
Whole chromosome and arm-level copy number alterations occur at high frequencies in tumors, but their selective advantages, if any, are poorly understood. Here, utilizing unbiased whole chromosome genetic screens combined with in vitro evolution to generate arm- and subarm-level events, we iteratively selected the fittest karyotypes from aneuploidized human renal and mammary epithelial cells. Proliferation-based karyotype selection in these epithelial lines modeled tissue-specific tumor aneuploidy patterns in patient cohorts in the absence of driver mutations. Hi-C-based translocation mapping revealed that arm-level events usually emerged in multiples of two via centromeric translocations and occurred more frequently in tetraploids than diploids, contributing to the increased diversity in evolving tetraploid populations. Isogenic clonal lineages enabled elucidation of pro-tumorigenic mechanisms associated with common copy number alterations, revealing Notch signaling potentiation as a driver of 1q gain in breast cancer. We propose that intrinsic, tissue-specific proliferative effects underlie tumor copy number patterns in cancer.
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Affiliation(s)
- Emma V Watson
- Department of Genetics, Harvard Medical School and Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jake June-Koo Lee
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Doga C Gulhan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Giorgio E M Melloni
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Sergey V Venev
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Rayna Y Magesh
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Abdulrazak Frederick
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Kunitoshi Chiba
- Department of Genetics, Harvard Medical School and Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
| | - Eric C Wooten
- Department of Genetics, Harvard Medical School and Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
| | - Kamila Naxerova
- Department of Genetics, Harvard Medical School and Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Center for Systems Biology and Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Job Dekker
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Stephen J Elledge
- Department of Genetics, Harvard Medical School and Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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13
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Gremke N, Rodepeter FR, Teply-Szymanski J, Griewing S, Boekhoff J, Stroh A, Tarawneh TS, Riera-Knorrenschild J, Balser C, Hattesohl A, Middeke M, Ross P, Litmeyer AS, Romey M, Stiewe T, Wündisch T, Neubauer A, Denkert C, Wagner U, Mack EKM. NGS-Guided Precision Oncology in Breast Cancer and Gynecological Tumors-A Retrospective Molecular Tumor Board Analysis. Cancers (Basel) 2024; 16:1561. [PMID: 38672643 PMCID: PMC11048446 DOI: 10.3390/cancers16081561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/13/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Background: Precision oncology treatments are being applied more commonly in breast and gynecological oncology through the implementation of Molecular Tumor Boards (MTBs), but real-world clinical outcome data remain limited. Methods: A retrospective analysis was conducted in patients with breast cancer (BC) and gynecological malignancies referred to our center's MTB from 2018 to 2023. The analysis covered patient characteristics, next-generation sequencing (NGS) results, MTB recommendations, therapy received, and clinical outcomes. Results: Sixty-three patients (77.8%) had metastatic disease, and forty-four patients (54.3%) had previously undergone three or more lines of systemic treatment. Personalized treatment recommendations were provided to 50 patients (63.3%), while 29 (36.7%) had no actionable target. Ultimately, 23 patients (29.1%) underwent molecular-matched treatment (MMT). Commonly altered genes in patients with pan-gyn tumors (BC and gynecological malignancies) included TP53 (n = 42/81, 51.9%), PIK3CA (n = 18/81, 22.2%), BRCA1/2 (n = 10/81, 12.3%), and ARID1A (n = 9/81, 11.1%). Patients treated with MMT showed significantly prolonged progression-free survival (median PFS 5.5 vs. 3.5 months, p = 0.0014). Of all patients who underwent molecular profiling, 13.6% experienced a major clinical benefit (PFSr ≥ 1.3 and PR/SD ≥ 6 months) through precision oncology. Conclusions: NGS-guided precision oncology demonstrated improved clinical outcomes in a subgroup of patients with gynecological and breast cancers.
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Affiliation(s)
- Niklas Gremke
- Department of Gynecology, Gynecological Endocrinology and Oncology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (S.G.); (J.B.); (A.S.); (U.W.)
- Institute of Molecular Oncology, Philipps-University, 35043 Marburg, Germany;
| | - Fiona R. Rodepeter
- Institute of Pathology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (F.R.R.); (J.T.-S.); (A.H.); (A.-S.L.); (M.R.); (C.D.)
| | - Julia Teply-Szymanski
- Institute of Pathology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (F.R.R.); (J.T.-S.); (A.H.); (A.-S.L.); (M.R.); (C.D.)
| | - Sebastian Griewing
- Department of Gynecology, Gynecological Endocrinology and Oncology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (S.G.); (J.B.); (A.S.); (U.W.)
| | - Jelena Boekhoff
- Department of Gynecology, Gynecological Endocrinology and Oncology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (S.G.); (J.B.); (A.S.); (U.W.)
| | - Alina Stroh
- Department of Gynecology, Gynecological Endocrinology and Oncology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (S.G.); (J.B.); (A.S.); (U.W.)
- Institute of Molecular Oncology, Philipps-University, 35043 Marburg, Germany;
| | - Thomas S. Tarawneh
- Department of Hematology, Oncology and Immunology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (T.S.T.); (J.R.-K.); (P.R.); (A.N.); (E.K.M.M.)
| | - Jorge Riera-Knorrenschild
- Department of Hematology, Oncology and Immunology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (T.S.T.); (J.R.-K.); (P.R.); (A.N.); (E.K.M.M.)
| | - Christina Balser
- Practice for Internal Medicine, Hematology and Internal Oncology, 35043 Marburg, Germany;
| | - Akira Hattesohl
- Institute of Pathology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (F.R.R.); (J.T.-S.); (A.H.); (A.-S.L.); (M.R.); (C.D.)
| | - Martin Middeke
- Comprehensive Cancer Center Marburg, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (M.M.); (T.W.)
| | - Petra Ross
- Department of Hematology, Oncology and Immunology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (T.S.T.); (J.R.-K.); (P.R.); (A.N.); (E.K.M.M.)
| | - Anne-Sophie Litmeyer
- Institute of Pathology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (F.R.R.); (J.T.-S.); (A.H.); (A.-S.L.); (M.R.); (C.D.)
| | - Marcel Romey
- Institute of Pathology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (F.R.R.); (J.T.-S.); (A.H.); (A.-S.L.); (M.R.); (C.D.)
| | - Thorsten Stiewe
- Institute of Molecular Oncology, Philipps-University, 35043 Marburg, Germany;
| | - Thomas Wündisch
- Comprehensive Cancer Center Marburg, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (M.M.); (T.W.)
| | - Andreas Neubauer
- Department of Hematology, Oncology and Immunology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (T.S.T.); (J.R.-K.); (P.R.); (A.N.); (E.K.M.M.)
| | - Carsten Denkert
- Institute of Pathology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (F.R.R.); (J.T.-S.); (A.H.); (A.-S.L.); (M.R.); (C.D.)
| | - Uwe Wagner
- Department of Gynecology, Gynecological Endocrinology and Oncology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (S.G.); (J.B.); (A.S.); (U.W.)
| | - Elisabeth K. M. Mack
- Department of Hematology, Oncology and Immunology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (T.S.T.); (J.R.-K.); (P.R.); (A.N.); (E.K.M.M.)
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14
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Wasson MCD, Venkatesh J, Cahill HF, McLean ME, Dean CA, Marcato P. LncRNAs exhibit subtype-specific expression, survival associations, and cancer-promoting effects in breast cancer. Gene 2024; 901:148165. [PMID: 38219875 DOI: 10.1016/j.gene.2024.148165] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 12/25/2023] [Accepted: 01/11/2024] [Indexed: 01/16/2024]
Abstract
Long non-coding RNAs (lncRNAs) play important roles in cancer progression, influencing processes such as invasion, metastasis, and drug resistance. Their reported cell type-dependent expression patterns suggest the potential for specialized functions in specific contexts. In breast cancer, lncRNA expression has been associated with different subtypes, highlighting their relevance in disease heterogeneity. However, our understanding of lncRNA function within breast cancer subtypes remains limited, warranting further investigation. We conducted a comprehensive analysis using the TANRIC dataset derived from the TCGA-BRCA cohort, profiling the expression, patient survival associations and immune cell type correlations of 12,727 lncRNAs across subtypes. Our findings revealed subtype-specific associations of lncRNAs with patient survival, tumor infiltrating lymphocytes and other immune cells. Targeting of lncRNAs exhibiting subtype-specific survival associations and expression in a panel of breast cancer cells demonstrated a selective reduction in cell proliferation within their associated subtype, supporting subtype-specific functions of certain lncRNAs. Characterization of HER2 + -specific lncRNA LINC01269 and TNBC-specific lncRNA AL078604.2 showed nuclear localization and altered expression of hundreds of genes enriched in cancer-promoting processes, including apoptosis, cell proliferation and immune cell regulation. This work emphasizes the importance of considering the heterogeneity of breast cancer subtypes and the need for subtype-specific analyses to fully uncover the relevance and potential impact of lncRNAs. Collectively, these findings demonstrate the contribution of lncRNAs to the distinct molecular, prognostic, and cellular composition of breast cancer subtypes.
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Affiliation(s)
| | | | - Hannah F Cahill
- Department of Pathology, Dalhousie University, Halifax, NS B3H4R2, Canada
| | - Meghan E McLean
- Department of Pathology, Dalhousie University, Halifax, NS B3H4R2, Canada
| | - Cheryl A Dean
- Department of Pathology, Dalhousie University, Halifax, NS B3H4R2, Canada
| | - Paola Marcato
- Department of Pathology, Dalhousie University, Halifax, NS B3H4R2, Canada; Department of Microbiology & Immunology, Dalhousie University, Halifax, NS B3H4R2, Canada; Nova Scotia Health Authority, Halifax, NS B3H1V8, Canada.
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15
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Ito T, Saito A, Kamikawa Y, Nakazawa N, Imaizumi K. AIbZIP/CREB3L4 Promotes Cell Proliferation via the SKP2-p27 Axis in Luminal Androgen Receptor Subtype Triple-Negative Breast Cancer. Mol Cancer Res 2024; 22:373-385. [PMID: 38236913 PMCID: PMC10985479 DOI: 10.1158/1541-7786.mcr-23-0629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 12/05/2023] [Accepted: 01/16/2024] [Indexed: 04/04/2024]
Abstract
Breast cancer ranks first in incidence and fifth in cancer-related deaths among all types of cancer globally. Among breast cancer, triple-negative breast cancer (TNBC) has few known therapeutic targets and a poor prognosis. Therefore, new therapeutic targets and strategies against TNBC are required. We found that androgen-induced basic leucine zipper (AIbZIP), also known as cyclic AMP-responsive element-binding protein 3-like protein 4 (CREB3L4), which is encoded by Creb3l4, is highly upregulated in a particular subtype of TNBC, luminal androgen receptor (LAR) subtype. We analyzed the function of AIbZIP through depletion of AIbZIP by siRNA knockdown in LAR subtype TNBC cell lines, MFM223 and MDAMB453. In AIbZIP-depleted cells, the proliferation ratios of cells were greatly suppressed. Moreover, G1-S transition was inhibited in AIbZIP-depleted cells. We comprehensively analyzed the expression levels of proteins that regulate G1-S transition and found that p27 was specifically upregulated in AIbZIP-depleted cells. Furthermore, we identified that this p27 downregulation was caused by protein degradation modulated by the ubiquitin-proteasome system via F-box protein S-phase kinase-associated protein 2 (SKP2) upregulation. Our findings demonstrate that AIbZIP is a novel p27-SKP2 pathway-regulating factor and a potential molecule that contributes to LAR subtype TNBC progression. IMPLICATIONS This research shows a new mechanism for the proliferation of LAR subtype TNBC regulated by AIbZIP, that may provide novel insight into the LAR subtype TNBC progression and the molecular mechanisms involved in cell proliferation.
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Affiliation(s)
- Taichi Ito
- Department of Biochemistry, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Atsushi Saito
- Department of Biochemistry, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Yasunao Kamikawa
- Department of Biochemistry, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Nayuta Nakazawa
- Department of Biochemistry, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Kazunori Imaizumi
- Department of Biochemistry, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
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16
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Marin AG, Filipescu A, Petca A. The Role of Obesity in the Etiology and Carcinogenesis of Endometrial Cancer. Cureus 2024; 16:e59219. [PMID: 38807790 PMCID: PMC11132319 DOI: 10.7759/cureus.59219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2024] [Indexed: 05/30/2024] Open
Abstract
Endometrial cancer, the most common gynecological malignancy, presents a complex public health challenge. While its incidence rises alongside the obesity epidemic, a well-established risk factor for endometrial cancer development, the impact of obesity on survival after diagnosis remains unclear. This review aims to explore the complex relationship between obesity and endometrial cancer's development and survival rates, examining evidence from both epidemiological and clinical studies. It also aims to explore the proposed biological mechanisms by which excess adipose tissue promotes carcinogenesis and contributes to endometrial cancer progression and its negative effects on treatment outcomes. Furthermore, we analyzed the impact of body mass index, inflammation, hormonal imbalances, and their potential effects on endometrial cancer survival rates.
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Affiliation(s)
| | - Alexandru Filipescu
- Obstetrics and Gynaecology, Elias Emergency University Hospital, Bucharest, ROU
| | - Aida Petca
- Obstetrics and Gynaecology, Carol Davila University of Medicine and Pharmacy, Bucharest, ROU
- Obstetrics and Gynaecology, Elias Emergency University Hospital, Bucharest, ROU
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17
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Ding C, Dai DY, Luo ZK, Wang GY, Dong Z, Qin GJ, Du XJ, Ma J. Evaluation of a novel model incorporating serological indicators into the conventional TNM staging system for nasopharyngeal carcinoma. Oral Oncol 2024; 151:106725. [PMID: 38430711 DOI: 10.1016/j.oraloncology.2024.106725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 03/05/2024]
Abstract
BACKGROUND Non-anatomical factors significantly affect treatment guidance and prognostic prediction in nasopharyngeal carcinoma (NPC) patients. Here, we developed a novel survival model by combining conventional TNM staging and serological indicators. METHODS We retrospectively enrolled 10,914 eligible patients with nonmetastatic NPC over 2009-2017 and randomly divided them into training (n = 7672) and validation (n = 3242) cohorts. The new staging system was constructed based on T category, N category, and pretreatment serological markers by using recursive partitioning analysis (RPA). RESULTS In multivariate Cox analysis, pretreatment cell-free Epstein-Barr virus (cfEBV) DNA levels of >2000 copies/mL [HROS (95 % CI) = 1.78 (1.57-2.02)], elevated lactate dehydrogenase (LDH) levels [HROS (95 % CI) = 1.64 (1.41-1.92)], and C-reactive protein-to-albumin ratio (CAR) of >0.04 [HROS (95 % CI) = 1.20 (1.07-1.34)] were associated with negative prognosis (all P < 0.05). Through RPA, we stratified patients into four risk groups: RPA I (n = 3209), RPA II (n = 2063), RPA III (n = 1263), and RPA IV (n = 1137), with 5-year overall survival (OS) rates of 93.2 %, 86.0 %, 80.6 %, and 71.9 % (all P < 0.001), respectively. Compared with the TNM staging system (eighth edition), RPA risk grouping demonstrated higher prognostic prediction efficacy in the training [area under the curve (AUC) = 0.661 vs. 0.631, P < 0.001] and validation (AUC = 0.687 vs. 0.654, P = 0.001) cohorts. Furthermore, our model could distinguish sensitive patients suitable for induction chemotherapy well. CONCLUSION Our novel RPA staging model outperformed the current TNM staging system in prognostic prediction and clinical decision-making. We recommend incorporating cfEBV DNA, LDH, and CAR into the TNM staging system.
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Affiliation(s)
- Cong Ding
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China
| | - Dong-Yu Dai
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China
| | - Zi-Kang Luo
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China
| | - Gao-Yuan Wang
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China
| | - Zhe Dong
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China
| | - Guan-Jie Qin
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China
| | - Xiao-Jing Du
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China
| | - Jun Ma
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China.
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Li Y, Yang S, Qi L, Li Y, Wang X. Identification of a Group of Therapeutic Targets and Prognostic Biomarker for Triple Negative Breast Cancer. Adv Ther 2024; 41:1621-1636. [PMID: 38421558 DOI: 10.1007/s12325-024-02806-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/29/2024] [Indexed: 03/02/2024]
Abstract
INTRODUCTION Triple-negative breast cancer (TNBC) is a highly heterogeneous disease. Mining differentially expressed genes of TNBC is helpful to explore new therapeutic targets. This study aimed to investigate diagnostic biomarker genes in TNBC compared to normal tissue. Additionally, we explored the functions and prognostic value of these key genes as well as potential targeted drugs that could affect these genes. METHODS Differential gene expression analysis was conducted using the R software with data from the Gene Expression Omnibus (GEO) database. Then, the identified differentially expressed genes (DEGs) were used to construct a protein-protein interaction (PPI) network using the Search Tool for the Retrieval of Interacting Genes (STRING) database and Cytoscape software. The mRNA expression levels of key genes were analyzed using the UALCAN database with data from The Cancer Genome Atlas (TCGA). Enrichment and survival analyses were performed using R software. In addition, potential compounds showing sensitivity to key genes were identified by gene set cancer analysis (GSCA). RESULTS Compared with normal tissues, a total of 203 DEGs were upregulated in TNBC. These DEGs participated in various biological processes including nuclear division, microtubule binding, cell cycle, and the p53 signaling pathway. Through the PPI network analysis, ten key genes were identified, among which four genes showed significant correlation with poor progression-free interval (PFI) in patients with TNBC. Moreover, the four survival-related genes were found to act as sensitive therapeutic targets. CONCLUSION The identified four key genes were considered new biomarkers for diagnosis and prognosis and also potential therapeutic targets for TNBC.
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Affiliation(s)
- Yan Li
- Phase I Clinical Trial Center, Beijing Shijitan Hospital, Capital Medical University, No. 10 Tieyi Road, Haidian District, Beijing, 100038, China
| | - Shengjie Yang
- Phase I Clinical Trial Center, Beijing Shijitan Hospital, Capital Medical University, No. 10 Tieyi Road, Haidian District, Beijing, 100038, China
| | - Lu Qi
- Phase I Clinical Trial Center, Beijing Shijitan Hospital, Capital Medical University, No. 10 Tieyi Road, Haidian District, Beijing, 100038, China
| | - Yinjuan Li
- Phase I Clinical Trial Center, Beijing Shijitan Hospital, Capital Medical University, No. 10 Tieyi Road, Haidian District, Beijing, 100038, China
| | - Xinghe Wang
- Phase I Clinical Trial Center, Beijing Shijitan Hospital, Capital Medical University, No. 10 Tieyi Road, Haidian District, Beijing, 100038, China.
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19
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Hu Z, Wu Z, Liu W, Ning Y, Liu J, Ding W, Fan J, Cai S, Li Q, Li W, Yang X, Dou Y, Wang W, Peng W, Lu F, Zhuang X, Qin T, Kang X, Feng C, Xu Z, Lv Q, Wang Q, Wang C, Wang X, Wang Z, Wang J, Jiang J, Wang B, Mills GB, Ma D, Gao Q, Li K, Chen G, Chen X, Sun C. Proteogenomic insights into early-onset endometrioid endometrial carcinoma: predictors for fertility-sparing therapy response. Nat Genet 2024; 56:637-651. [PMID: 38565644 DOI: 10.1038/s41588-024-01703-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 03/05/2024] [Indexed: 04/04/2024]
Abstract
Endometrial carcinoma remains a public health concern with a growing incidence, particularly in younger women. Preserving fertility is a crucial consideration in the management of early-onset endometrioid endometrial carcinoma (EEEC), particularly in patients under 40 who maintain both reproductive desire and capacity. To illuminate the molecular characteristics of EEEC, we undertook a large-scale multi-omics study of 215 patients with endometrial carcinoma, including 81 with EEEC. We reveal an unexpected association between exposome-related mutational signature and EEEC, characterized by specific CTNNB1 and SIGLEC10 hotspot mutations and disruption of downstream pathways. Interestingly, SIGLEC10Q144K mutation in EEECs resulted in aberrant SIGLEC-10 protein expression and promoted progestin resistance by interacting with estrogen receptor alpha. We also identified potential protein biomarkers for progestin response in fertility-sparing treatment for EEEC. Collectively, our study establishes a proteogenomic resource of EEECs, uncovering the interactions between exposome and genomic susceptibilities that contribute to the development of primary prevention and early detection strategies for EEECs.
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Affiliation(s)
- Zhe Hu
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Zimeng Wu
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Wei Liu
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, P. R. China
| | - Yan Ning
- Department of Pathology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, P. R. China
| | - Jingbo Liu
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Wencheng Ding
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Junpeng Fan
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Shuyan Cai
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, P. R. China
| | - Qinlan Li
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Wenting Li
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Xiaohang Yang
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Yingyu Dou
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Wei Wang
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Wenju Peng
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Funian Lu
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Xucui Zhuang
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Tianyu Qin
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Xiaoyan Kang
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Chenzhao Feng
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Zhiying Xu
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, P. R. China
| | - Qiaoying Lv
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, P. R. China
| | - Qian Wang
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, P. R. China
| | - Chao Wang
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, P. R. China
| | - Xinyu Wang
- The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, P. R. China
| | - Zhiqi Wang
- Department of Obstetrics and Gynecology, Peking University People's Hospital; Peking University People's Hospital, Xicheng District, Beijing, P. R. China
| | - Jianliu Wang
- Department of Obstetrics and Gynecology, Peking University People's Hospital; Peking University People's Hospital, Xicheng District, Beijing, P. R. China
| | - Jie Jiang
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, P. R. China
| | - Beibei Wang
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | | | - Ding Ma
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Qinglei Gao
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China.
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China.
| | - Kezhen Li
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China.
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China.
| | - Gang Chen
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China.
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China.
| | - Xiaojun Chen
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, P. R. China.
| | - Chaoyang Sun
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China.
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China.
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20
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Wang X, Jiang Y, Sun Y. Revealing genomic heterogeneity and commonality: A penalized integrative analysis approach accounting for the adjacency structure of measurements. Genet Epidemiol 2024; 48:114-140. [PMID: 38317326 DOI: 10.1002/gepi.22549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 12/18/2023] [Accepted: 01/08/2024] [Indexed: 02/07/2024]
Abstract
Advancements in high-throughput genomic technologies have revolutionized the field of disease biomarker identification by providing large-scale genomic data. There is an increasing focus on understanding the relationships among diverse patient groups with distinct disease subtypes and characteristics. Complex diseases exhibit both heterogeneity and shared genomic factors, making it essential to investigate these patterns to accurately detect markers and comprehensively understand the diseases. Integrative analysis has emerged as a promising approach to address this challenge. However, existing studies have been limited by ignoring the adjacency structure of genomic measurements, such as single nucleotide polymorphisms (SNPs) and DNA methylations. In this study, we propose a structured integrative analysis method that incorporates a spline type penalty to accommodate this adjacency structure. We utilize a fused lasso type penalty to identify both heterogeneity and commonality across the groups. Extensive simulations demonstrate its superiority compared to several direct competing methods. The analysis of The Cancer Genome Atlas melanoma data with DNA methylation measurements and GENEVA diabetes data with SNP measurements exhibit that the proposed analysis lead to meaningful findings with better prediction performance and higher selection stability.
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Affiliation(s)
- Xindi Wang
- Center for Applied Statistics, School of Statistics, Renmin University of China, Beijing, China
| | - Yu Jiang
- School of Public Health, The University of Memphis, Memphis, Tennessee, USA
| | - Yifan Sun
- Center for Applied Statistics, School of Statistics, Renmin University of China, Beijing, China
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21
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Al-Danakh A, Safi M, Jian Y, Yang L, Zhu X, Chen Q, Yang K, Wang S, Zhang J, Yang D. Aging-related biomarker discovery in the era of immune checkpoint inhibitors for cancer patients. Front Immunol 2024; 15:1348189. [PMID: 38590525 PMCID: PMC11000233 DOI: 10.3389/fimmu.2024.1348189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 01/29/2024] [Indexed: 04/10/2024] Open
Abstract
Older patients with cancer, particularly those over 75 years of age, often experience poorer clinical outcomes compared to younger patients. This can be attributed to age-related comorbidities, weakened immune function, and reduced tolerance to treatment-related adverse effects. In the immune checkpoint inhibitors (ICI) era, age has emerged as an influential factor impacting the discovery of predictive biomarkers for ICI treatment. These age-linked changes in the immune system can influence the composition and functionality of tumor-infiltrating immune cells (TIICs) that play a crucial role in the cancer response. Older patients may have lower levels of TIICs infiltration due to age-related immune senescence particularly T cell function, which can limit the effectivity of cancer immunotherapies. Furthermore, age-related immune dysregulation increases the exhaustion of immune cells, characterized by the dysregulation of ICI-related biomarkers and a dampened response to ICI. Our review aims to provide a comprehensive understanding of the mechanisms that contribute to the impact of age on ICI-related biomarkers and ICI response. Understanding these mechanisms will facilitate the development of treatment approaches tailored to elderly individuals with cancer.
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Affiliation(s)
- Abdullah Al-Danakh
- Department of Urology, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Mohammed Safi
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Yuli Jian
- Department of Biochemistry and Molecular Biology, Institute of Glycobiology, Dalian Medical University, Dalian, China
| | - Linlin Yang
- Department of Urology, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Xinqing Zhu
- Department of Urology, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Qiwei Chen
- Department of Urology, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Kangkang Yang
- Institute for Genome Engineered Animal Models of Human Diseases, National Center of Genetically Engineered Animal Models for International Research, Dalian Medical University, Dalian, Liaoning, China
| | - Shujing Wang
- Department of Biochemistry and Molecular Biology, Institute of Glycobiology, Dalian Medical University, Dalian, China
| | - Jianjun Zhang
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Deyong Yang
- Department of Urology, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
- Department of Surgery, Healinghands Clinic, Dalian, Liaoning, China
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22
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Yashar WM, Estabrook J, Holly HD, Somers J, Nikolova O, Babur Ö, Braun TP, Demir E. Predicting transcription factor activity using prior biological information. iScience 2024; 27:109124. [PMID: 38455978 PMCID: PMC10918219 DOI: 10.1016/j.isci.2024.109124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/20/2023] [Accepted: 01/31/2024] [Indexed: 03/09/2024] Open
Abstract
Dysregulation of normal transcription factor activity is a common driver of disease. Therefore, the detection of aberrant transcription factor activity is important to understand disease pathogenesis. We have developed Priori, a method to predict transcription factor activity from RNA sequencing data. Priori has two key advantages over existing methods. First, Priori utilizes literature-supported regulatory information to identify transcription factor-target gene relationships. It then applies linear models to determine the impact of transcription factor regulation on the expression of its target genes. Second, results from a third-party benchmarking pipeline reveals that Priori detects aberrant activity from 124 single-gene perturbation experiments with higher sensitivity and specificity than 11 other methods. We applied Priori and other top-performing methods to predict transcription factor activity from two large primary patient datasets. Our work demonstrates that Priori uniquely discovered significant determinants of survival in breast cancer and identified mediators of drug response in leukemia.
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Affiliation(s)
- William M. Yashar
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Division of Oncologic Sciences, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Joseph Estabrook
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Molecular and Medical Genetics, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
- Cancer Early Detection Advanced Research Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Hannah D. Holly
- Department of Molecular and Medical Genetics, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
- Cancer Early Detection Advanced Research Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Julia Somers
- Department of Molecular and Medical Genetics, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
- Cancer Early Detection Advanced Research Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Olga Nikolova
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Division of Oncologic Sciences, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Özgün Babur
- Computer Science Department, University of Massachusetts, Boston, MA 02125, USA
| | - Theodore P. Braun
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Division of Oncologic Sciences, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Emek Demir
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Division of Oncologic Sciences, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Molecular and Medical Genetics, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
- Pacific Northwest National Laboratories, Richland, WA 99354, USA
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23
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Arslan S, Schmidt J, Bass C, Mehrotra D, Geraldes A, Singhal S, Hense J, Li X, Raharja-Liu P, Maiques O, Kather JN, Pandya P. A systematic pan-cancer study on deep learning-based prediction of multi-omic biomarkers from routine pathology images. COMMUNICATIONS MEDICINE 2024; 4:48. [PMID: 38491101 PMCID: PMC10942985 DOI: 10.1038/s43856-024-00471-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 02/29/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND The objective of this comprehensive pan-cancer study is to evaluate the potential of deep learning (DL) for molecular profiling of multi-omic biomarkers directly from hematoxylin and eosin (H&E)-stained whole slide images. METHODS A total of 12,093 DL models predicting 4031 multi-omic biomarkers across 32 cancer types were trained and validated. The study included a broad range of genetic, transcriptomic, and proteomic biomarkers, as well as established prognostic markers, molecular subtypes, and clinical outcomes. RESULTS Here we show that 50% of the models achieve an area under the curve (AUC) of 0.644 or higher. The observed AUC for 25% of the models is at least 0.719 and exceeds 0.834 for the top 5%. Molecular profiling with image-based histomorphological features is generally considered feasible for most of the investigated biomarkers and across different cancer types. The performance appears to be independent of tumor purity, sample size, and class ratio (prevalence), suggesting a degree of inherent predictability in histomorphology. CONCLUSIONS The results demonstrate that DL holds promise to predict a wide range of biomarkers across the omics spectrum using only H&E-stained histological slides of solid tumors. This paves the way for accelerating diagnosis and developing more precise treatments for cancer patients.
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Affiliation(s)
| | | | | | - Debapriya Mehrotra
- Panakeia Technologies, London, UK
- Department of Pathology, Barking, Havering and Redbridge University NHS Trust, Romford, UK
| | | | - Shikha Singhal
- Panakeia Technologies, London, UK
- Department of Pathology, The Royal Wolverhampton NHS Trust, Wolverhampton, UK
| | | | - Xiusi Li
- Panakeia Technologies, London, UK
| | | | - Oscar Maiques
- Cytoskeleton and Cancer Metastasis Group, Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
- Cancer Biomarkers & Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, John Vane Science Building, London, UK
| | - Jakob Nikolas Kather
- Medical Oncology, National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
- Else Kroener Fresenius Center for Digital Health, Medical Faculty Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
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Ding Y, Zhou Q, Ding B, Zhang Y, Shen Y. Transcriptome analysis reveals the clinical significance of CXCL13 in Pan-Gyn tumors. J Cancer Res Clin Oncol 2024; 150:116. [PMID: 38459390 PMCID: PMC10923744 DOI: 10.1007/s00432-024-05619-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 01/09/2024] [Indexed: 03/10/2024]
Abstract
BACKGROUND Gynecologic and breast tumors (Pan-Gyn) exhibit similar characteristics, and the role of CXCL13 in anti-tumor immunity and it's potential as a biomarker for immune checkpoint blockade (ICB) therapy have been gradually revealed. However, the precise role of CXCL13 in Pan-Gyn remains unclear, lacking a systematic analysis. METHODS We analyzed 2497 Pan-Gyn samples from the TCGA database, categorizing them into high and low CXCL13 expression groups. Validation was conducted using tumor expression datasets sourced from the GEO database. Correlation between CXCL13 and tumor immune microenvironment (TIME) was evaluated using multiple algorithms. Finally, we established nomograms for 3-year and 5-year mortality. RESULTS High expression of CXCL13 in Pan-Gyn correlates with a favorable clinical prognosis, increased immune cell infiltration, and reduced intra-tumor heterogeneity. Model was assessed using the C-index [BRCA: 0.763 (0.732-0.794), UCEC: 0.821 (0.793-0.849), CESC: 0.736 (0.684-0.788), and OV: 0.728 (0.707-0.749)], showing decent prediction of discrimination and calibration. CONCLUSION Overall, this study provides comprehensive insights into the commonalities and differences of CXCL13 in Pan-Gyn, potentially opening new avenues for personalized treatment.
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Affiliation(s)
- Yue Ding
- Zhongda Hospital Southeast University, Nanjing, China
| | - Quan Zhou
- Zhongda Hospital Southeast University, Nanjing, China
| | - Bo Ding
- Zhongda Hospital Southeast University, Nanjing, China
| | - Yang Zhang
- Department of Obstetrics and Gynecology, First People's Hospital of Lianyungang, No. 6 East Zhenhua Road, Haizhou, Lianyungang, China
| | - Yang Shen
- Zhongda Hospital Southeast University, Nanjing, China.
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25
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Rodriguez I, Rossi NM, Keskus AG, Xie Y, Ahmad T, Bryant A, Lou H, Paredes JG, Milano R, Rao N, Tulsyan S, Boland JF, Luo W, Liu J, O'Hanlon T, Bess J, Mukhina V, Gaykalova D, Yuki Y, Malik L, Billingsley KJ, Blauwendraat C, Carrington M, Yeager M, Mirabello L, Kolmogorov M, Dean M. Insights into the mechanisms and structure of breakage-fusion-bridge cycles in cervical cancer using long-read sequencing. Am J Hum Genet 2024; 111:544-561. [PMID: 38307027 PMCID: PMC10940022 DOI: 10.1016/j.ajhg.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 12/20/2023] [Accepted: 01/04/2024] [Indexed: 02/04/2024] Open
Abstract
Cervical cancer is caused by human papillomavirus (HPV) infection, has few approved targeted therapeutics, and is the most common cause of cancer death in low-resource countries. We characterized 19 cervical and four head and neck cancer cell lines using long-read DNA and RNA sequencing and identified the HPV types, HPV integration sites, chromosomal alterations, and cancer driver mutations. Structural variation analysis revealed telomeric deletions associated with DNA inversions resulting from breakage-fusion-bridge (BFB) cycles. BFB is a common mechanism of chromosomal alterations in cancer, and our study applies long-read sequencing to this important chromosomal rearrangement type. Analysis of the inversion sites revealed staggered ends consistent with exonuclease digestion of the DNA after breakage. Some BFB events are complex, involving inter- or intra-chromosomal insertions or rearrangements. None of the BFB breakpoints had telomere sequences added to resolve the dicentric chromosomes, and only one BFB breakpoint showed chromothripsis. Five cell lines have a chromosomal region 11q BFB event, with YAP1-BIRC3-BIRC2 amplification. Indeed, YAP1 amplification is associated with a 10-year-earlier age of diagnosis of cervical cancer and is three times more common in African American women. This suggests that individuals with cervical cancer and YAP1-BIRC3-BIRC2 amplification, especially those of African ancestry, might benefit from targeted therapy. In summary, we uncovered valuable insights into the mechanisms and consequences of BFB cycles in cervical cancer using long-read sequencing.
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Affiliation(s)
- Isabel Rodriguez
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Nicole M Rossi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Ayse G Keskus
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Yi Xie
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Tanveer Ahmad
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Asher Bryant
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Hong Lou
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Jesica Godinez Paredes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Rose Milano
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Nina Rao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA; Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Sonam Tulsyan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Joseph F Boland
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Wen Luo
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Jia Liu
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Tim O'Hanlon
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Jazmyn Bess
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Vera Mukhina
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medical Center, Baltimore, MD, USA
| | - Daria Gaykalova
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA; Marlene & Stewart Greenebaum Comprehensive Cancer Center, University of Maryland Medical System, Baltimore, MD, USA; Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Yuko Yuki
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Laksh Malik
- Center for Alzheimer's and Related Dementias, National Institute on Aging, Bethesda, MD, USA
| | | | - Cornelis Blauwendraat
- Center for Alzheimer's and Related Dementias, National Institute on Aging, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Mary Carrington
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Meredith Yeager
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Mikhail Kolmogorov
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA.
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Ding X, Li X, Jiang Y, Li Y, Li H, Shang L, Feng G, Zhang H, Xu Z, Yang L, Li B, Zhao RC. RGS20 promotes non-small cell lung carcinoma proliferation via autophagy activation and inhibition of the PKA-Hippo signaling pathway. Cancer Cell Int 2024; 24:93. [PMID: 38431606 PMCID: PMC10909273 DOI: 10.1186/s12935-024-03282-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 02/24/2024] [Indexed: 03/05/2024] Open
Abstract
BACKGROUND Novel therapeutic targets are urgently needed for treating drug-resistant non-small cell lung cancer (NSCLC) and overcoming drug resistance to molecular-targeted therapies. Regulator of G protein signaling 20 (RGS20) is identified as an upregulated factor in many cancers, yet its specific role and the mechanism through which RGS20 functions in NSCLC remain unclear. Our study aimed to identify the role of RGS20 in NSCLC prognosis and delineate associated cellular and molecular pathways. METHODS Immunohistochemistry and lung cancer tissue microarray were used to verify the expression of RGS20 between NSCLC patients. CCK8 and cell cloning were conducted to determine the proliferation ability of H1299 and Anip973 cells in vitro. Furthermore, Transcriptome sequencing was performed to show enrichment genes and pathways. Immunofluorescence was used to detect the translocation changes of YAP to nucleus. Western blotting demonstrated different expressions of autophagy and the Hippo-PKA signal pathway. In vitro and in vivo experiments verified whether overexpression of RGS20 affect the proliferation and autophagy of NSCLC through regulating the Hippo pathway. RESULTS The higher RGS20 expression was found to be significantly correlated with a poorer five-year survival rate. Further, RGS20 accelerated cell proliferation by increasing autophagy. Transcriptomic sequencing suggested the involvement of the Hippo signaling pathway in the action of RGS20 in NSCLC. RGS20 activation reduced YAP phosphorylation and facilitated its nuclear translocation. Remarkably, inhibiting Hippo signaling with GA-017 promoted cell proliferation and activated autophagy in RGS20 knock-down cells. However, forskolin, a GPCR activator, increased YAP phosphorylation and reversed the promoting effect of RGS20 in RGS20-overexpressing cells. Lastly, in vivo experiments further confirmed role of RGS20 in aggravating tumorigenicity, as its overexpression increased NSCLC cell proliferation. CONCLUSION Our findings indicate that RGS20 drives NSCLC cell proliferation by triggering autophagy via the inhibition of PKA-Hippo signaling. These insights support the role of RGS20 as a promising novel molecular marker and a target for future targeted therapies in lung cancer treatment.
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Affiliation(s)
- Xiaoyan Ding
- School of Basic Medicine, Institute of Stem Cell and Regenerative Medicine, Qingdao University, Qingdao, China
| | - Xiaoxia Li
- School of Basic Medicine, Institute of Stem Cell and Regenerative Medicine, Qingdao University, Qingdao, China
| | - Yanxia Jiang
- Department of Pathology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yujun Li
- Department of Pathology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Hong Li
- Department of Pathology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Lipeng Shang
- School of Basic Medicine, Institute of Stem Cell and Regenerative Medicine, Qingdao University, Qingdao, China
| | - Guilin Feng
- School of Basic Medicine, Institute of Stem Cell and Regenerative Medicine, Qingdao University, Qingdao, China
| | - Huhu Zhang
- School of Basic Medicine, Institute of Stem Cell and Regenerative Medicine, Qingdao University, Qingdao, China
| | - Ziyuan Xu
- School of Basic Medicine, Institute of Stem Cell and Regenerative Medicine, Qingdao University, Qingdao, China
| | - Lina Yang
- School of Basic Medicine, Institute of Stem Cell and Regenerative Medicine, Qingdao University, Qingdao, China.
| | - Bing Li
- School of Basic Medicine, Institute of Stem Cell and Regenerative Medicine, Qingdao University, Qingdao, China.
| | - Robert Chunhua Zhao
- School of Basic Medicine, Institute of Stem Cell and Regenerative Medicine, Qingdao University, Qingdao, China.
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China.
- School of Life Sciences, Shanghai University, Shanghai, China.
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27
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Takahashi K, Yachida N, Tamura R, Adachi S, Kondo S, Abé T, Umezu H, Nyuzuki H, Okuda S, Nakaoka H, Yoshihara K. Clonal origin and genomic diversity in Lynch syndrome-associated endometrial cancer with multiple synchronous tumors: Identification of the pathogenicity of MLH1 p.L582H. Genes Chromosomes Cancer 2024; 63:e23231. [PMID: 38459936 DOI: 10.1002/gcc.23231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/06/2024] [Accepted: 02/20/2024] [Indexed: 03/11/2024] Open
Abstract
Lynch syndrome-associated endometrial cancer patients often present multiple synchronous tumors and this assessment can affect treatment strategies. We present a case of a 27-year-old woman with tumors in the uterine corpus, cervix, and ovaries who was diagnosed with endometrial cancer and exhibited cervical invasion and ovarian metastasis. Her family history suggested Lynch syndrome, and genetic testing identified a variant of uncertain significance, MLH1 p.L582H. We conducted immunohistochemical staining, microsatellite instability analysis, and Sanger sequencing for Lynch syndrome-associated cancers in three generations of the family and identified consistent MLH1 loss. Whole-exome sequencing for the corpus, cervical, and ovarian tumors of the proband identified a copy-neutral loss of heterozygosity (LOH) occurring at the MLH1 position in all tumors. This indicated that the germline variant and the copy-neutral LOH led to biallelic loss of MLH1 and was the cause of cancer initiation. All tumors shared a portion of somatic mutations with high mutant allele frequencies, suggesting a common clonal origin. There were no mutations shared only between the cervix and ovary samples. The profiles of mutant allele frequencies shared between the corpus and cervix or ovary indicated that two different subclones originating from the corpus independently metastasized to the cervix or ovary. Additionally, all tumors presented unique mutations in endometrial cancer-associated genes such as ARID1A and PIK3CA. In conclusion, we demonstrated clonal origin and genomic diversity in a Lynch syndrome-associated endometrial cancer, suggesting the importance of evaluating multiple sites in Lynch syndrome patients with synchronous tumors.
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Affiliation(s)
- Kotaro Takahashi
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
- Department of Cancer Genome Research, Sasaki Institute, Tokyo, Japan
| | - Nozomi Yachida
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Ryo Tamura
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Sosuke Adachi
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Shuhei Kondo
- Division of Pathology, Niigata University Medical and Dental Hospital, Niigata, Japan
| | - Tatsuya Abé
- Division of Oral Pathology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
- Division of Molecular and Diagnostic Pathology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Hajime Umezu
- Division of Pathology, Niigata University Medical and Dental Hospital, Niigata, Japan
| | - Hiromi Nyuzuki
- Department of Pediatrics, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Shujiro Okuda
- Division of bioinformatics, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Hirofumi Nakaoka
- Department of Cancer Genome Research, Sasaki Institute, Tokyo, Japan
| | - Kosuke Yoshihara
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
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Chai H, Lin S, Lin J, He M, Yang Y, OuYang Y, Zhao H. An uncertainty-based interpretable deep learning framework for predicting breast cancer outcome. BMC Bioinformatics 2024; 25:88. [PMID: 38418940 PMCID: PMC10902951 DOI: 10.1186/s12859-024-05716-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 02/21/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND Predicting outcome of breast cancer is important for selecting appropriate treatments and prolonging the survival periods of patients. Recently, different deep learning-based methods have been carefully designed for cancer outcome prediction. However, the application of these methods is still challenged by interpretability. In this study, we proposed a novel multitask deep neural network called UISNet to predict the outcome of breast cancer. The UISNet is able to interpret the importance of features for the prediction model via an uncertainty-based integrated gradients algorithm. UISNet improved the prediction by introducing prior biological pathway knowledge and utilizing patient heterogeneity information. RESULTS The model was tested in seven public datasets of breast cancer, and showed better performance (average C-index = 0.691) than the state-of-the-art methods (average C-index = 0.650, ranged from 0.619 to 0.677). Importantly, the UISNet identified 20 genes as associated with breast cancer, among which 11 have been proven to be associated with breast cancer by previous studies, and others are novel findings of this study. CONCLUSIONS Our proposed method is accurate and robust in predicting breast cancer outcomes, and it is an effective way to identify breast cancer-associated genes. The method codes are available at: https://github.com/chh171/UISNet .
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Affiliation(s)
- Hua Chai
- School of Mathematics and Big Data, Foshan University, Foshan, 528000, China
| | - Siyin Lin
- School of Data and Computer Science, Sun Yat-Sen University, Guangzhou, 510000, China
| | - Junqi Lin
- School of Mathematics and Big Data, Foshan University, Foshan, 528000, China
| | - Minfan He
- School of Mathematics and Big Data, Foshan University, Foshan, 528000, China
| | - Yuedong Yang
- School of Data and Computer Science, Sun Yat-Sen University, Guangzhou, 510000, China
| | - Yongzhong OuYang
- School of Mathematics and Big Data, Foshan University, Foshan, 528000, China.
| | - Huiying Zhao
- Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510000, China.
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29
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Gardi N, Chaubal R, Parab P, Pachakar S, Kulkarni S, Shet T, Joshi S, Kembhavi Y, Chandrani P, Quist J, Kowtal P, Grigoriadis A, Sarin R, Govindarajan R, Gupta S. Natural History of Germline BRCA1 Mutated and BRCA Wild-type Triple-negative Breast Cancer. CANCER RESEARCH COMMUNICATIONS 2024; 4:404-417. [PMID: 38315150 PMCID: PMC10865976 DOI: 10.1158/2767-9764.crc-23-0277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/09/2023] [Accepted: 01/26/2024] [Indexed: 02/07/2024]
Abstract
We report a deep next-generation sequencing analysis of 13 sequentially obtained tumor samples, eight sequentially obtained circulating tumor DNA (ctDNA) samples and three germline DNA samples over the life history of 3 patients with triple-negative breast cancer (TNBC), 2 of whom had germline pathogenic BRCA1 mutation, to unravel tumor evolution. Tumor tissue from all timepoints and germline DNA was subjected to whole-exome sequencing (WES), custom amplicon deep sequencing (30,000X) of a WES-derived somatic mutation panel, and SNP arrays for copy-number variation (CNV), while whole transcriptome sequencing (RNA-seq) was performed only on somatic tumor.There was enrichment of homologous recombination deficiency signature in all tumors and widespread CNV, which remained largely stable over time. Somatic tumor mutation numbers varied between patients and within each patient (range: 70-216, one outlier). There was minimal mutational overlap between patients with TP53 being the sole commonly mutated gene, but there was substantial overlap in sequential samples in each patient. Each patient's tumor contained a founding ("stem") clone at diagnosis, which persisted over time, from which all other clones ("subclone") were derived ("branching evolution"), which contained mutations in well-characterized cancer-related genes like PDGFRB, ARID2, TP53 (Patient_02), TP53, BRAF, BRIP1, CSF3R (Patient_04), and TP53, APC, EZH2 (Patient_07). Including stem and subclones, tumors from all patients were polyclonal at diagnosis and during disease progression. ctDNA recapitulated most tissue-derived stem clonal and subclonal mutations while detecting some additional subclonal mutations. RNA-seq revealed a stable basal-like pattern, with most highly expressed variants belonging to stem clone. SIGNIFICANCE In germline BRCA1 mutated and BRCA wild-type patients, TNBC shows a branching evolutionary pattern of mutations with a single founding clone, are polyclonal throughout their disease course, and have widespread copy-number aberrations. This evolutionary pattern may be associated with treatment resistance or sensitivity and could be therapeutically exploited.
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Affiliation(s)
- Nilesh Gardi
- Department of Medical Oncology, Tata Memorial Centre, Mumbai
- Clinician Scientist Laboratory, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai
- Homi Bhabha National Institute, Mumbai
| | - Rohan Chaubal
- Clinician Scientist Laboratory, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai
- Homi Bhabha National Institute, Mumbai
- Department of Surgical Oncology, Tata Memorial Centre, Mumbai
| | - Pallavi Parab
- Department of Medical Oncology, Tata Memorial Centre, Mumbai
- Homi Bhabha National Institute, Mumbai
| | - Sunil Pachakar
- Department of Medical Oncology, Tata Memorial Centre, Mumbai
- Clinician Scientist Laboratory, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai
- Homi Bhabha National Institute, Mumbai
| | - Suyash Kulkarni
- Homi Bhabha National Institute, Mumbai
- Department of Radiodiagnosis, Tata Memorial Centre, Mumbai
| | - Tanuja Shet
- Homi Bhabha National Institute, Mumbai
- Department of Pathology, Tata Memorial Centre, Mumbai
| | - Shalaka Joshi
- Homi Bhabha National Institute, Mumbai
- Department of Surgical Oncology, Tata Memorial Centre, Mumbai
| | - Yogesh Kembhavi
- Department of Medical Oncology, Tata Memorial Centre, Mumbai
- Homi Bhabha National Institute, Mumbai
| | - Pratik Chandrani
- Department of Medical Oncology, Tata Memorial Centre, Mumbai
- Homi Bhabha National Institute, Mumbai
| | - Jelmar Quist
- Cancer Bioinformatics, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
- School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
- Breast Cancer Now Unit, School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Pradnya Kowtal
- Homi Bhabha National Institute, Mumbai
- DNA sequencing Facility, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai
| | - Anita Grigoriadis
- Cancer Bioinformatics, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
- School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
- Breast Cancer Now Unit, School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Rajiv Sarin
- Homi Bhabha National Institute, Mumbai
- Department of Radiation Oncology, Tata Memorial Centre, Mumbai
| | | | - Sudeep Gupta
- Department of Medical Oncology, Tata Memorial Centre, Mumbai
- Clinician Scientist Laboratory, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai
- Homi Bhabha National Institute, Mumbai
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30
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Mahieu CI, Mancini AG, Vikram EP, Planells-Palop V, Joseph NM, Tward AD. ORAOV1, CCND1, and MIR548K Are the Driver Oncogenes of the 11q13 Amplicon in Squamous Cell Carcinoma. Mol Cancer Res 2024; 22:152-168. [PMID: 37930255 PMCID: PMC10831340 DOI: 10.1158/1541-7786.mcr-23-0746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 09/29/2023] [Accepted: 11/02/2023] [Indexed: 11/07/2023]
Abstract
11q13 amplification is a frequent event in human cancer and in particular in squamous cell carcinomas (SCC). Despite almost invariably spanning 10 genes, it is unclear which genetic components of the amplicon are the key driver events in SCC. A combination of computational, in vitro, ex vivo, and in vivo models leveraging efficient primary human keratinocyte genome editing by Cas9-RNP electroporation, identified ORAOV1, CCND1, and MIR548K as the critical drivers of the amplicon in head and neck SCC. CCND1 amplification drives the cell cycle in a CDK4/6/RB1-independent fashion and may confer a novel dependency on RRM2. MIR548K contributes to epithelial-mesenchymal transition. Finally, we identify ORAOV1 as an oncogene that acts likely via its ability to modulate reactive oxygen species. Thus, the 11q13 amplicon drives SCC through at least three independent genetic elements and suggests therapeutic targets for this morbid and lethal disease. IMPLICATIONS This work demonstrates novel mechanisms and ways to target these mechanisms underlying the most common amplification in squamous cell carcinoma, one of the most prevalent and deadly forms of human cancer.
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Affiliation(s)
- Céline I. Mahieu
- Department of Otolaryngology, Head and Neck Surgery, University of California San Francisco, San Francisco, Calfornia
| | | | - Ellee P. Vikram
- Department of Otolaryngology, Head and Neck Surgery, University of California San Francisco, San Francisco, Calfornia
| | - Vicente Planells-Palop
- Department of Otolaryngology, Head and Neck Surgery, University of California San Francisco, San Francisco, Calfornia
| | - Nancy M. Joseph
- Department of Pathology, University of California San Francisco, San Francisco, California
| | - Aaron D. Tward
- Department of Otolaryngology, Head and Neck Surgery, University of California San Francisco, San Francisco, Calfornia
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31
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Bagger MM, Sjölund J, Kim J, Kohler KT, Villadsen R, Jafari A, Kassem M, Pietras K, Rønnov-Jessen L, Petersen OW. Evidence of steady-state fibroblast subtypes in the normal human breast as cells-of-origin for perturbed-state fibroblasts in breast cancer. Breast Cancer Res 2024; 26:11. [PMID: 38229104 PMCID: PMC10790388 DOI: 10.1186/s13058-024-01763-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 01/02/2024] [Indexed: 01/18/2024] Open
Abstract
BACKGROUND Human breast cancer most frequently originates within a well-defined anatomical structure referred to as the terminal duct lobular unit (TDLU). This structure is endowed with its very own lobular fibroblasts representing one out of two steady-state fibroblast subtypes-the other being interlobular fibroblasts. While cancer-associated fibroblasts (CAFs) are increasingly appreciated as covering a spectrum of perturbed states, we lack a coherent understanding of their relationship-if any-with the steady-state fibroblast subtypes. To address this, we here established two autologous CAF lines representing inflammatory CAFs (iCAFs) and myofibroblast CAFs (myCAFs) and compared them with already established interlobular- and lobular fibroblasts with respect to their origin and impact on tumor formation. METHODS Primary breast tumor-derived CAFs were transduced to express human telomerase reverse transcriptase (hTERT) and sorted into CD105low and CD105high populations using fluorescence-activated cell sorting (FACS). The two populations were tested for differentiation similarities to iCAF and myCAF states through transcriptome-wide RNA-Sequencing (RNA-Seq) including comparison to an available iCAF-myCAF cell state atlas. Inference of origin in interlobular and lobular fibroblasts relied on RNA-Seq profiles, immunocytochemistry and growth characteristics. Osteogenic differentiation and bone formation assays in culture and in vivo were employed to gauge for origin in bone marrow-derived mesenchymal stem cells (bMSCs). Functional characteristics were assessed with respect to contractility in culture and interaction with tumor cells in mouse xenografts. The cells' gene expression signatures were tested for association with clinical outcome of breast cancer patients using survival data from The Cancer Genome Atlas database. RESULTS We demonstrate that iCAFs have properties in common with interlobular fibroblasts while myCAFs and lobular fibroblasts are related. None of the CAFs qualify as bMSCs as revealed by lack of critical performance in bone formation assays. Functionally, myCAFs and lobular fibroblasts are almost equally tumor promoting as opposed to iCAFs and interlobular fibroblasts. A myCAF gene signature is found to associate with poor breast cancer-specific survival. CONCLUSIONS We propose that iCAFs and myCAFs originate in interlobular and lobular fibroblasts, respectively, and more importantly, that the tumor-promoting properties of lobular fibroblasts render the TDLU an epicenter for breast cancer evolution.
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Affiliation(s)
- Mikkel Morsing Bagger
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University Cancer Centre, Lund University, Lund, Sweden.
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark.
| | - Jonas Sjölund
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University Cancer Centre, Lund University, Lund, Sweden
| | - Jiyoung Kim
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | | | - René Villadsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Abbas Jafari
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Moustapha Kassem
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
- Laboratory of Molecular Endocrinology, KMEB, Department of Endocrinology, Odense University Hospital and University of Southern Denmark, Odense, Denmark
| | - Kristian Pietras
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University Cancer Centre, Lund University, Lund, Sweden
| | - Lone Rønnov-Jessen
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ole William Petersen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
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32
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Zengin T, Masud BA, Önal-Süzek T. TCGAnalyzeR: An Online Pan-Cancer Tool for Integrative Visualization of Molecular and Clinical Data of Cancer Patients for Cohort and Associated Gene Discovery. Cancers (Basel) 2024; 16:345. [PMID: 38254834 PMCID: PMC10814871 DOI: 10.3390/cancers16020345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/08/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
For humans, the parallel processing capability of visual recognition allows for faster comprehension of complex scenes and patterns. This is essential, especially for clinicians interpreting big data for whom the visualization tools play an even more vital role in transforming raw big data into clinical decision making by managing the inherent complexity and monitoring patterns interactively in real time. The Cancer Genome Atlas (TCGA) database's size and data variety challenge the effective utilization of this valuable resource by clinicians and biologists. We re-analyzed the five molecular data types, i.e., mutation, transcriptome profile, copy number variation, miRNA, and methylation data, of ~11,000 cancer patients with all 33 cancer types and integrated the existing TCGA patient cohorts from the literature into a free and efficient web application: TCGAnalyzeR. TCGAnalyzeR provides an integrative visualization of pre-analyzed TCGA data with several novel modules: (i) simple nucleotide variations with driver prediction; (ii) recurrent copy number alterations; (iii) differential expression in tumor versus normal, with pathway and the survival analysis; (iv) TCGA clinical data including metastasis and survival analysis; (v) external subcohorts from the literature, curatedTCGAData, and BiocOncoTK R packages; (vi) internal patient clusters determined using an iClusterPlus R package or signature-based expression analysis of five molecular data types. TCGAnalyzeR integrated the multi-omics, pan-cancer TCGA with ~120 subcohorts from the literature along with clipboard panels, thus allowing users to create their own subcohorts, compare against existing external subcohorts (MSI, Immune, PAM50, Triple Negative, IDH1, miRNA, metastasis, etc.) along with our internal patient clusters, and visualize cohort-centric or gene-centric results interactively using TCGAnalyzeR.
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Affiliation(s)
- Talip Zengin
- Department of Molecular Biology and Genetics, Mugla Sitki Kocman University, Mugla 48000, Türkiye;
| | - Başak Abak Masud
- Department of Bioinformatics, Mugla Sitki Kocman University, Mugla 48000, Türkiye;
| | - Tuğba Önal-Süzek
- Department of Bioinformatics, Mugla Sitki Kocman University, Mugla 48000, Türkiye;
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Jin J, Li J, Liu Y, Shi Q, Zhang B, Ji Y, Hu P. Thyroid Hormone Changes Correlate to Combined Breast Cancer with Primary Thyroid Cancer. BREAST CANCER (DOVE MEDICAL PRESS) 2024; 16:15-22. [PMID: 38223235 PMCID: PMC10787567 DOI: 10.2147/bctt.s442707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 12/21/2023] [Indexed: 01/16/2024]
Abstract
Background Breast cancer and thyroid cancer are two prevalent malignancies in women, and a potential association between the two diseases has been suggested. Methods This retrospective case-control study was conducted involving 97 patients with breast cancer and thyroid cancer (BC-TC group) and 97 age-matched patients with breast cancer alone (BC group). Thyroid hormone levels, including triiodothyronine (T3), thyroxine (T4), free triiodothyronine (FT3), free thyroxine (FT4) and thyroid-stimulating hormone (TSH), were analyzed in healthy controls, BC patients, and BC-TC patients. Results BC-TC patients exhibited a higher rate of estrogen receptor (ER) and progesterone receptor (PR) positivity compared to BC patients. Serum T3 levels were significantly decreased in BC and BC-TC patients compared to healthy controls. However, there was no significant difference in T3 levels between BC and BC-TC patients. Serum TSH levels were significantly higher in BC-TC patients compared to BC patients. Conclusion ER positivity, PR positivity, and serum TSH levels greater than 4.45 mU/L were independent risk factors for primary thyroid cancer in breast cancer patients.
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Affiliation(s)
- Jian Jin
- Thyroid and Breast Surgery Department, Cangzhou Central Hospital, Cangzhou, Hebei, 061000, People’s Republic of China
| | - Jie Li
- Thyroid and Breast Surgery Department, Cangzhou Central Hospital, Cangzhou, Hebei, 061000, People’s Republic of China
| | - Yonghong Liu
- Thyroid and Breast Surgery Department, Cangzhou Central Hospital, Cangzhou, Hebei, 061000, People’s Republic of China
| | - Qingfeng Shi
- Thyroid and Breast Surgery Department, Cangzhou Central Hospital, Cangzhou, Hebei, 061000, People’s Republic of China
| | - Bo Zhang
- Thyroid and Breast Surgery Department, Cangzhou Central Hospital, Cangzhou, Hebei, 061000, People’s Republic of China
| | - Yanting Ji
- Thyroid and Breast Surgery Department, Cangzhou Central Hospital, Cangzhou, Hebei, 061000, People’s Republic of China
| | - Pengfei Hu
- Thyroid and Breast Surgery Department, Cangzhou Central Hospital, Cangzhou, Hebei, 061000, People’s Republic of China
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Amgad M, Hodge JM, Elsebaie MAT, Bodelon C, Puvanesarajah S, Gutman DA, Siziopikou KP, Goldstein JA, Gaudet MM, Teras LR, Cooper LAD. A population-level digital histologic biomarker for enhanced prognosis of invasive breast cancer. Nat Med 2024; 30:85-97. [PMID: 38012314 DOI: 10.1038/s41591-023-02643-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 10/13/2023] [Indexed: 11/29/2023]
Abstract
Breast cancer is a heterogeneous disease with variable survival outcomes. Pathologists grade the microscopic appearance of breast tissue using the Nottingham criteria, which are qualitative and do not account for noncancerous elements within the tumor microenvironment. Here we present the Histomic Prognostic Signature (HiPS), a comprehensive, interpretable scoring of the survival risk incurred by breast tumor microenvironment morphology. HiPS uses deep learning to accurately map cellular and tissue structures to measure epithelial, stromal, immune, and spatial interaction features. It was developed using a population-level cohort from the Cancer Prevention Study-II and validated using data from three independent cohorts, including the Prostate, Lung, Colorectal, and Ovarian Cancer trial, Cancer Prevention Study-3, and The Cancer Genome Atlas. HiPS consistently outperformed pathologists in predicting survival outcomes, independent of tumor-node-metastasis stage and pertinent variables. This was largely driven by stromal and immune features. In conclusion, HiPS is a robustly validated biomarker to support pathologists and improve patient prognosis.
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Affiliation(s)
- Mohamed Amgad
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - James M Hodge
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Maha A T Elsebaie
- Department of Medicine, John H. Stroger, Jr. Hospital of Cook County, Chicago, IL, USA
| | - Clara Bodelon
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | | | - David A Gutman
- Department of Pathology, Emory University School of Medicine, Atlanta, GA, USA
| | - Kalliopi P Siziopikou
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Jeffery A Goldstein
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Mia M Gaudet
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Lauren R Teras
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Lee A D Cooper
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
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Anaya J, Sidhom JW, Mahmood F, Baras AS. Multiple-instance learning of somatic mutations for the classification of tumour type and the prediction of microsatellite status. Nat Biomed Eng 2024; 8:57-67. [PMID: 37919367 PMCID: PMC10805698 DOI: 10.1038/s41551-023-01120-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 09/30/2023] [Indexed: 11/04/2023]
Abstract
Large-scale genomic data are well suited to analysis by deep learning algorithms. However, for many genomic datasets, labels are at the level of the sample rather than for individual genomic measures. Machine learning models leveraging these datasets generate predictions by using statically encoded measures that are then aggregated at the sample level. Here we show that a single weakly supervised end-to-end multiple-instance-learning model with multi-headed attention can be trained to encode and aggregate the local sequence context or genomic position of somatic mutations, hence allowing for the modelling of the importance of individual measures for sample-level classification and thus providing enhanced explainability. The model solves synthetic tasks that conventional models fail at, and achieves best-in-class performance for the classification of tumour type and for predicting microsatellite status. By improving the performance of tasks that require aggregate information from genomic datasets, multiple-instance deep learning may generate biological insight.
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Affiliation(s)
- Jordan Anaya
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - John-William Sidhom
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Faisal Mahmood
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cancer Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Data Science Initiative, Harvard University, Cambridge, MA, USA
| | - Alexander S Baras
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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Linder H, Zhang Y, Wang Y, Ouyang Z. Integrative pathway analysis with gene expression, miRNA, methylation and copy number variation for breast cancer subtypes. Stat Appl Genet Mol Biol 2024; 23:sagmb-2019-0050. [PMID: 38363177 DOI: 10.1515/sagmb-2019-0050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 01/27/2024] [Indexed: 02/17/2024]
Abstract
Developments in biotechnologies enable multi-platform data collection for functional genomic units apart from the gene. Profiling of non-coding microRNAs (miRNAs) is a valuable tool for understanding the molecular profile of the cell, both for canonical functions and malignant behavior due to complex diseases. We propose a graphical mixed-effects statistical model incorporating miRNA-gene target relationships. We implement an integrative pathway analysis that leverages measurements of miRNA activity for joint analysis with multimodal observations of gene activity including gene expression, methylation, and copy number variation. We apply our analysis to a breast cancer dataset, and consider differential activity in signaling pathways across breast tumor subtypes. We offer discussion of specific signaling pathways and the effect of miRNA integration, as well as publish an interactive data visualization to give public access to the results of our analysis.
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Affiliation(s)
- Henry Linder
- Department of Statistics, University of Connecticut, Storrs, CT, 06269, USA
| | - Yuping Zhang
- Department of Statistics, University of Connecticut, Storrs, CT, 06269, USA
| | - Yunqi Wang
- Department of Statistics, University of Connecticut, Storrs, CT, 06269, USA
| | - Zhengqing Ouyang
- Department of Biostatistics and Epidemiology, University of Massachusetts, Amherst, MA, 01003, USA
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Yang C, Wang Z, Zhang S, Li X, Wang X, Liu J, Li R, Zeng S. MVNMDA: A Multi-View Network Combing Semantic and Global Features for Predicting miRNA-Disease Association. Molecules 2023; 29:230. [PMID: 38202814 PMCID: PMC10780172 DOI: 10.3390/molecules29010230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 12/23/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
A growing body of experimental evidence suggests that microRNAs (miRNAs) are closely associated with specific human diseases and play critical roles in their development and progression. Therefore, identifying miRNA related to specific diseases is of great significance for disease screening and treatment. In the early stages, the identification of associations between miRNAs and diseases demanded laborious and time-consuming biological experiments that often carried a substantial risk of failure. With the exponential growth in the number of potential miRNA-disease association combinations, traditional biological experimental methods face difficulties in processing massive amounts of data. Hence, developing more efficient computational methods to predict possible miRNA-disease associations and prioritize them is particularly necessary. In recent years, numerous deep learning-based computational methods have been developed and have demonstrated excellent performance. However, most of these methods rely on external databases or tools to compute various auxiliary information. Unfortunately, these external databases or tools often cover only a limited portion of miRNAs and diseases, resulting in many miRNAs and diseases being unable to match with these computational methods. Therefore, there are certain limitations associated with the practical application of these methods. To overcome the above limitations, this study proposes a multi-view computational model called MVNMDA, which predicts potential miRNA-disease associations by integrating features of miRNA and diseases from local views, global views, and semantic views. Specifically, MVNMDA utilizes known association information to construct node initial features. Then, multiple networks are constructed based on known association to extract low-dimensional feature embedding of all nodes. Finally, a cascaded attention classifier is proposed to fuse features from coarse to fine, suppressing noise within the features and making precise predictions. To validate the effectiveness of the proposed method, extensive experiments were conducted on the HMDD v2.0 and HMDD v3.2 datasets. The experimental results demonstrate that MVNMDA achieves better performance compared to other computational methods. Additionally, the case study results further demonstrate the reliable predictive performance of MVNMDA.
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Affiliation(s)
| | - Zhen Wang
- School of Electronic Infomation, Xijing University, Xi’an 710123, China; (C.Y.); (S.Z.); (X.L.); (X.W.); (J.L.); (R.L.); (S.Z.)
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Shen S, Liu X, Guo Q, Liang Q, Wu J, Guan G, Zou C, Zhu C, Yan Z, Liu T, Chen L, Cheng P, Cheng W, Wu A. Tumor microenvironment remodeling plus immunotherapy could be used in mesenchymal-like tumor with high tumor residual and drug resistant rate. Commun Biol 2023; 6:1281. [PMID: 38110614 PMCID: PMC10728080 DOI: 10.1038/s42003-023-05667-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 12/04/2023] [Indexed: 12/20/2023] Open
Abstract
Epithelial-mesenchymal transition (EMT) is a common process during tumor progression and is always related to residual tumor, drug resistance and immune suppression. However, considering the heterogeneity in EMT process, there is still a need to establish robust EMT classification system with reasonable molecular, biological and clinical implications to investigate whether these unfavorable survival factors are common or unique in different individuals. In our work, we classify tumors with four EMT status, that is, EMTlow, EMTmid, EMThigh-NOS (Not Otherwise Specified), and EMThigh-AKT (AKT pathway overactivation) subtypes. We find that EMThigh-NOS subtype is driven by intrinsic somatic alterations. While, EMThigh-AKT subtype is maintained by extrinsic cellular interplay between tumor cells and macrophages in an AKT-dependent manner. EMThigh-AKT subtype is both unresectable and drug resistant while EMThigh-NOS subtype can be treated with cell cycle related drugs. Importantly, AKT activation in EMThigh-AKT not only enhances EMT process, but also contributes to the immunosuppressive microenvironment. By remodeling tumor immune-microenvironment by AKT inhibition, EMThigh-AKT can be treated by immune checkpoint blockade therapies. Meanwhile, we develop TumorMT website ( http://tumormt.neuroscience.org.cn/ ) to apply this EMT classification and provide reasonable therapeutic guidance.
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Affiliation(s)
- Shuai Shen
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Xing Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Qing Guo
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Qingyu Liang
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Jianqi Wu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Gefei Guan
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Cunyi Zou
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Chen Zhu
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Zihao Yan
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Tianqi Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Ling Chen
- Department of Neurosurgery, Chinese People's Liberation Army of China (PLA) General Hospital, Medical School of Chinese PLA, Institute of Neurosurgery of Chinese PLA, Beijing, China
| | - Peng Cheng
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, China.
| | - Wen Cheng
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China.
| | - Anhua Wu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China.
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Duan L, Liu R, Cui X, Zhang Q, Cao D, Chen M, Zhang A. Identification of UBFD1 as a prognostic biomarker and molecular target among estrogen receptor-positive breast cancer. Biochem Biophys Res Commun 2023; 686:149171. [PMID: 37922573 DOI: 10.1016/j.bbrc.2023.149171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 10/19/2023] [Accepted: 10/26/2023] [Indexed: 11/07/2023]
Abstract
Estrogen receptor (ER)-positive breast cancer (BRCA) is the most commonly diagnosed molecular subtype of BRCA. It is routinely treated with endocrine therapy; however, some patients relapse after therapy and develop drug resistance, resulting in treatment failure. In the present study, we identified markers of ER-positive BRCA and evaluated their putative function in immune infiltration as well as their clinicopathological significance. The ubiquitin family domain containing 1 (UBFD1) protein was associated with the prognosis of ER-positive BRCA patients. Its expression was higher in ER-positive BRCA tissues compared with adjacent nontumor tissues. Patients with higher UBFD1 expression had a poorer prognosis. UBFD1 is an independent risk factor for ER-positive BRCA patients and its function was primarily associated with hormone activity and inflammation. Taken together, UBFD1 is a potential prognostic biomarker and candidate target of ER-positive BRCA.
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Affiliation(s)
- Lian Duan
- Basic Laboratory, Suining Central Hospital, Suining, China
| | - Rui Liu
- Department of Breast and Thyroid Surgery, Suining Central Hospital, Suining, China
| | - Xiaoyue Cui
- Basic Laboratory, Suining Central Hospital, Suining, China
| | - Qiaoling Zhang
- Basic Laboratory, Suining Central Hospital, Suining, China; Key Laboratory of Metabolic Diseases, Suining Central Hospital, Suining, China
| | - Dan Cao
- Basic Laboratory, Suining Central Hospital, Suining, China; Key Laboratory of Metabolic Diseases, Suining Central Hospital, Suining, China
| | - Maoshan Chen
- Department of Breast and Thyroid Surgery, Suining Central Hospital, Suining, China.
| | - Aijie Zhang
- Basic Laboratory, Suining Central Hospital, Suining, China; Key Laboratory of Metabolic Diseases, Suining Central Hospital, Suining, China.
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Vahdatinia M, Derakhshan F, Da Cruz Paula A, Dopeso H, Marra A, Gazzo AM, Brown D, Selenica P, Ross DS, Razavi P, Zhang H, Weigelt B, Wen HY, Brogi E, Reis-Filho JS, Pareja F. KIT genetic alterations in breast cancer. J Clin Pathol 2023; 77:40-45. [PMID: 36323507 PMCID: PMC10151428 DOI: 10.1136/jcp-2022-208611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 10/12/2022] [Indexed: 01/19/2023]
Abstract
AIMS Activating somatic mutations or gene amplification of KIT result in constitutive activation of its receptor tyrosine kinase, which is targetable in various solid tumours. Here, we sought to investigate the presence of KIT genetic alterations in breast cancer (BC) and characterise the histological and genomic features of these tumours. METHODS A retrospective analysis of 5,575 BCs previously subjected to targeted sequencing using the FDA-authorised Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Targets (MSK-IMPACT) assay was performed to identify BCs with KIT alterations. A histological assessment of KIT-altered BCs was conducted, and their repertoire of genetic alterations was compared with that of BCs lacking KIT genetic alterations, matched for age, histological type, oestrogen receptor/HER2 status and sample type. RESULTS We identified 18 BCs (0.32%), including 9 primary and 9 metastatic BCs, with oncogenic/likely oncogenic genetic alterations affecting KIT, including activating somatic mutations (n=4) or gene amplification (n=14). All KIT-altered BCs were of high histological grade, although no distinctive histological features were observed. When compared with BCs lacking KIT genetic alterations, no distinctive genetic features were identified. In two metastatic KIT-altered BCs in which the matched primary BC had also been analysed by MSK-IMPACT, the KIT mutations were found to be restricted to the metastatic samples, suggesting that they were late events in the evolution of these cancers. CONCLUSIONS KIT genetic alterations are vanishingly rare in BC. KIT-altered BCs are of high grade but lack distinctive histological features. Genetic alterations in KIT might be late events in the evolution and/or progression of BC.
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Affiliation(s)
- Mahsa Vahdatinia
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Fatemeh Derakhshan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Arnaud Da Cruz Paula
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Higinio Dopeso
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Antonio Marra
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Andrea M Gazzo
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - David Brown
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Pier Selenica
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Dara S Ross
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Pedram Razavi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Hong Zhang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Hannah Y Wen
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Edi Brogi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jorge S Reis-Filho
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Fresia Pareja
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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Pedernera E, Morales-Vásquez F, Gómora MJ, Almaraz MA, Mena E, Pérez-Montiel D, Rendon E, López-Basave H, Maldonado-Cubas J, Méndez C. 17β-hydroxysteroid dehydrogenase type 1 improves survival in serous epithelial ovarian tumors. Endocr Connect 2023; 12:e230315. [PMID: 37924640 PMCID: PMC10762561 DOI: 10.1530/ec-23-0315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 10/26/2023] [Indexed: 11/06/2023]
Abstract
The incidence of ovarian cancer has been epidemiologically related to female reproductive events and hormone replacement therapy after menopause. This highlights the importance of evaluating the role of sexual steroid hormones in ovarian cancer by the expression of enzymes related to steroid hormone biosynthesis in the tumor cells. This study was aimed to evaluate the presence of 17β-hydroxysteroid dehydrogenase type 1 (17β-HSD1), aromatase and estrogen receptor alpha (ERα) in the tumor cells and their association with the overall survival in 111 patients diagnosed with primary ovarian tumors. Positive immunoreactivity for 17β-HSD1 was observed in 74% of the tumors. In the same samples, aromatase and ERα revealed 66% and 47% positivity, respectively. No association was observed of 17β-HSD1 expression with the histological subtypes and clinical stages of the tumor. The overall survival of patients was improved in 17β-HSD1-positive group in Kaplan-Meier analysis (P = 0.028), and 17β-HSD1 expression had a protective effect from multivariate proportional regression evaluation (HR = 0.44; 95% CI 0.24-0.9; P = 0.040). The improved survival was observed in serous epithelial tumors but not in nonserous ovarian tumors. The expression of 17β-HSD1 in the cells of the serous epithelial ovarian tumors was associated with an improved overall survival, whereas aromatase and ERα were not related to a better survival. The evaluation of hazard risk factors demonstrated that age and clinical stage showed worse prognosis, and 17β-HSD1 expression displayed a protective effect with a better survival outcome in patients of epithelial ovarian tumors.
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Affiliation(s)
- Enrique Pedernera
- Universidad Nacional Autónoma de México, Facultad de Medicina, Departamento de Embriología y Genética, Ciudad de México, México
| | | | - María J Gómora
- Universidad Nacional Autónoma de México, Facultad de Medicina, Departamento de Embriología y Genética, Ciudad de México, México
| | - Miguel A Almaraz
- Universidad Nacional Autónoma de México, Facultad de Medicina, Departamento de Embriología y Genética, Ciudad de México, México
| | - Esteban Mena
- Universidad Nacional Autónoma de México, Facultad de Medicina, Secretaría General, Ciudad de México, México
- Universidad La Salle, Posgrado de la Facultad de Ciencias Químicas, Ciudad de México, México
| | | | - Elizabeth Rendon
- Hospital Militar de Especialidades de la Mujer y Neonatología. Ciudad de México, México
| | | | - Juan Maldonado-Cubas
- Universidad La Salle, Posgrado de la Facultad de Ciencias Químicas, Ciudad de México, México
| | - Carmen Méndez
- Universidad Nacional Autónoma de México, Facultad de Medicina, Departamento de Embriología y Genética, Ciudad de México, México
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Wang Y, Armendariz D, Wang L, Zhao H, Xie S, Hon GC. Enhancer regulatory networks globally connect non-coding breast cancer loci to cancer genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.20.567880. [PMID: 38045327 PMCID: PMC10690208 DOI: 10.1101/2023.11.20.567880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Genetic studies have associated thousands of enhancers with breast cancer. However, the vast majority have not been functionally characterized. Thus, it remains unclear how variant-associated enhancers contribute to cancer. Here, we perform single-cell CRISPRi screens of 3,512 regulatory elements associated with breast cancer to measure the impact of these regions on transcriptional phenotypes. Analysis of >500,000 single-cell transcriptomes in two breast cancer cell lines shows that perturbation of variant-associated enhancers disrupts breast cancer gene programs. We observe variant-associated enhancers that directly or indirectly regulate the expression of cancer genes. We also find one-to-multiple and multiple-to-one network motifs where enhancers indirectly regulate cancer genes. Notably, multiple variant-associated enhancers indirectly regulate TP53. Comparative studies illustrate sub-type specific functions between enhancers in ER+ and ER- cells. Finally, we developed the pySpade package to facilitate analysis of single-cell enhancer screens. Overall, we demonstrate that enhancers form regulatory networks that link cancer genes in the genome, providing a more comprehensive understanding of the contribution of enhancers to breast cancer development.
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Affiliation(s)
- Yihan Wang
- Cecil H. and Ida Green Center for Reproductive Biology Sciences
| | | | - Lei Wang
- Cecil H. and Ida Green Center for Reproductive Biology Sciences
| | - Huan Zhao
- Cecil H. and Ida Green Center for Reproductive Biology Sciences
| | - Shiqi Xie
- Cecil H. and Ida Green Center for Reproductive Biology Sciences
- Current address: Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Gary C Hon
- Cecil H. and Ida Green Center for Reproductive Biology Sciences
- Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390
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Huang H, Pan Y, Huang J, Zhang C, Liao Y, Du Q, Qin S, Chen Y, Tan H, Chen M, Xu M, Xia M, Liu Y, Li J, Liu T, Zou Q, Zhou Y, Yuan L, Wang W, Liang Y, Pan CY, Liu J, Yao S. Patient-derived organoids as personalized avatars and a potential immunotherapy model in cervical cancer. iScience 2023; 26:108198. [PMID: 38026204 PMCID: PMC10679865 DOI: 10.1016/j.isci.2023.108198] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/05/2023] [Accepted: 10/10/2023] [Indexed: 12/01/2023] Open
Abstract
Cervical cancer remains a significant health issue in developing countries. However, finding a preclinical model that accurately reproduces tumor characteristics is challenging. Therefore, we established a patient-derived organoids (PDOs) biobank containing 67 cases of heterogeneous cervical cancer that mimic the histopathological and genomic characteristics of parental tumors. The in vitro response of the organoids indicated their ability to capture the radiological heterogeneity of the patients. To model individual responses to adoptive T cell therapy (ACT), we expanded tumor-infiltrating lymphocytes (TILs) ex vivo and co-cultured them with paired organoids. The PDOs-TILs co-culture system demonstrates clear responses that correspond to established immunotherapy efficiency markers like the proportion of CTLs. This study supports the potential of the PDOs platform to guide treatment in prospective interventional trials in cervical cancer.
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Affiliation(s)
- Hua Huang
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Yuwen Pan
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Jiaming Huang
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Chunyu Zhang
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Yuandong Liao
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Qiqiao Du
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Shuhang Qin
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Yili Chen
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Hao Tan
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Ming Chen
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Manman Xu
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Meng Xia
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Yunyun Liu
- Sun Yat-Sen Memorial Hospital of Sun Yat-sen University, Guangzhou 510120, China
| | - Jie Li
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Tianyu Liu
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Qiaojian Zou
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Yijia Zhou
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Li Yuan
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Wei Wang
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Yanchun Liang
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Chao yun Pan
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Junxiu Liu
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Shuzhong Yao
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
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Wei J, Yu W, Wu L, Chen Z, Huang G, Hu M, Du H. Intercellular Molecular Crosstalk Networks within Invasive and Immunosuppressive Tumor Microenvironment Subtypes Associated with Clinical Outcomes in Four Cancer Types. Biomedicines 2023; 11:3057. [PMID: 38002057 PMCID: PMC10669098 DOI: 10.3390/biomedicines11113057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Heterogeneity is a critical basis for understanding how the tumor microenvironment (TME) contributes to tumor progression. However, an understanding of the specific characteristics and functions of TME subtypes (subTMEs) in the progression of cancer is required for further investigations into single-cell resolutions. Here, we analyzed single-cell RNA sequencing data of 250 clinical samples with more than 200,000 cells analyzed in each cancer datum. Based on the construction of an intercellular infiltration model and unsupervised clustering analysis, four, three, three, and four subTMEs were revealed in breast, colorectal, esophageal, and pancreatic cancer, respectively. Among the subTMEs, the immune-suppressive subTME (subTME-IS) and matrix remodeling with malignant cells subTME (subTME-MRM) were highly enriched in tumors, whereas the immune cell infiltration subTME (subTME-ICI) and precancerous state of epithelial cells subTME (subTME-PSE) were less in tumors, compared with paracancerous tissues. We detected and compared genes encoding cytokines, chemokines, cytotoxic mediators, PD1, and PD-L1. The results showed that these genes were specifically overexpressed in different cell types, and, compared with normal tissues, they were upregulated in tumor-derived cells. In addition, compared with other subTMEs, the expression levels of PDCD1 and TGFB1 were higher in subTME-IS. The Cox proportional risk regression model was further constructed to identify possible prognostic markers in each subTME across four cancer types. Cell-cell interaction analysis revealed the distinguishing features in molecular pairs among different subTMEs. Notably, ligand-receptor gene pairs, including COL1A1-SDC1, COL6A2-SDC1, COL6A3-SDC1, and COL4A1-ITGA2 between stromal and tumor cells, associated with tumor invasion phenotypes, poor patient prognoses, and tumor advanced progression, were revealed in subTME-MRM. C5AR1-RPS19, LGALS9-HAVCR2, and SPP1-PTGER4 between macrophages and CD8+ T cells, associated with CD8+ T-cell dysfunction, immunosuppressive status, and tumor advanced progression, were revealed in subTME-IS. The spatial co-location information of cellular and molecular interactions was further verified by spatial transcriptome data from colorectal cancer clinical samples. Overall, our study revealed the heterogeneity within the TME, highlighting the potential pro-invasion and pro-immunosuppressive functions and cellular infiltration characteristics of specific subTMEs, and also identified the key cellular and molecular interactions that might be associated with the survival, invasion, immune escape, and classification of cancer patients across four cancer types.
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Affiliation(s)
| | | | | | | | | | | | - Hongli Du
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China; (J.W.); (W.Y.); (L.W.); (Z.C.); (G.H.); (M.H.)
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Jiang Y, Wang C, Zhou S. Artificial intelligence-based risk stratification, accurate diagnosis and treatment prediction in gynecologic oncology. Semin Cancer Biol 2023; 96:82-99. [PMID: 37783319 DOI: 10.1016/j.semcancer.2023.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 08/27/2023] [Accepted: 09/25/2023] [Indexed: 10/04/2023]
Abstract
As data-driven science, artificial intelligence (AI) has paved a promising path toward an evolving health system teeming with thrilling opportunities for precision oncology. Notwithstanding the tremendous success of oncological AI in such fields as lung carcinoma, breast tumor and brain malignancy, less attention has been devoted to investigating the influence of AI on gynecologic oncology. Hereby, this review sheds light on the ever-increasing contribution of state-of-the-art AI techniques to the refined risk stratification and whole-course management of patients with gynecologic tumors, in particular, cervical, ovarian and endometrial cancer, centering on information and features extracted from clinical data (electronic health records), cancer imaging including radiological imaging, colposcopic images, cytological and histopathological digital images, and molecular profiling (genomics, transcriptomics, metabolomics and so forth). However, there are still noteworthy challenges beyond performance validation. Thus, this work further describes the limitations and challenges faced in the real-word implementation of AI models, as well as potential solutions to address these issues.
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Affiliation(s)
- Yuting Jiang
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan 610041, China; Department of Pulmonary and Critical Care Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Chengdi Wang
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan 610041, China; Department of Pulmonary and Critical Care Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Shengtao Zhou
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan 610041, China; Department of Pulmonary and Critical Care Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.
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Mei J, Cai Y, Chen L, Wu Y, Liu J, Qian Z, Jiang Y, Zhang P, Xia T, Pan X, Zhang Y. The heterogeneity of tumour immune microenvironment revealing the CRABP2/CD69 signature discriminates distinct clinical outcomes in breast cancer. Br J Cancer 2023; 129:1645-1657. [PMID: 37715025 PMCID: PMC10646008 DOI: 10.1038/s41416-023-02432-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 08/31/2023] [Accepted: 09/06/2023] [Indexed: 09/17/2023] Open
Abstract
BACKGROUND It has been acknowledged that the tumour immune microenvironment (TIME) plays a critical role in determining therapeutic responses and clinical outcomes in breast cancer (BrCa). Thus, the identification of the TIME features is essential for guiding therapy and prognostic assessment for BrCa. METHODS The heterogeneous cellular composition of the TIME in BrCa by single-cell RNA sequencing (scRNA-seq). Two subtype-special genes upregulated in the tumour-rich subtype and the immune-infiltrating subtype were extracted, respectively. The CRABP2/CD69 signature was established based on CRABP2 and CD69 expression, and its predictive values for the clinical outcome and the neoadjuvant chemotherapy (NAT) responses were validated in multiple cohorts. Moreover, the oncogenic role of CRABP2 was explored in BrCa cells. RESULTS Based on the heterogeneous cellular composition of the TIME in BrCa, the BrCa samples could be divided into the tumour-rich subtype and the immune-infiltrating subtype, which exhibited distinct prognosis and chemotherapeutic responses. Next, we extracted CRABP2 as the biomarker for the tumour-rich subtype and CD69 as the biomarker for the immune-infiltrating subtype. Based on the CRABP2/CD69 signature, BrCa samples were re-divided into three subtypes, and the CRABP2highCD69low subtype exhibited the worst prognosis and the lowest chemotherapeutic response, while the CRABP2lowCD69high subtype showed the opposite results. Furthermore, CARBP2 functioned as a novel oncogene in BrCa, which promoted tumour cell proliferation, migration, and invasion, and CRABP2 inhibition triggered the activation of cytotoxic T lymphocytes (CTLs). CONCLUSION The CRABP2/CD69 signature is significantly associated with the TIME features and could effectively predict the clinical outcome. Also, CRABP2 is determined to be a novel oncogene, which could be a therapeutic target in BrCa.
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Affiliation(s)
- Jie Mei
- Wuxi Maternal and Child Health Hospital, Wuxi Medical Center of Nanjing Medical University, 214023, Wuxi, China
- The First Clinical Medical College, Nanjing Medical University, 211166, Nanjing, China
| | - Yun Cai
- Wuxi Maternal and Child Health Hospital, Wuxi Medical Center of Nanjing Medical University, 214023, Wuxi, China
| | - Lingyan Chen
- Wuxi Maternal and Child Health Hospital, Wuxi Medical Center of Nanjing Medical University, 214023, Wuxi, China
| | - Youqing Wu
- School of Artificial Intelligence and Computer Science, Jiangnan University, 214122, Wuxi, China
| | - Jiayu Liu
- Department of Oncology, The Women's Hospital of Jiangnan University, 214023, Wuxi, China
| | - Zhiwen Qian
- Wuxi Maternal and Child Health Hospital, Wuxi Medical Center of Nanjing Medical University, 214023, Wuxi, China
| | - Ying Jiang
- Department of Oncology, The Women's Hospital of Jiangnan University, 214023, Wuxi, China
| | - Ping Zhang
- Department of Breast Surgery, The Women's Hospital of Jiangnan University, 214023, Wuxi, China
| | - Tiansong Xia
- Jiangsu Breast Disease Center, The First Affiliated Hospital of Nanjing Medical University, 210029, Nanjing, China.
| | - Xiang Pan
- School of Artificial Intelligence and Computer Science, Jiangnan University, 214122, Wuxi, China.
| | - Yan Zhang
- Wuxi Maternal and Child Health Hospital, Wuxi Medical Center of Nanjing Medical University, 214023, Wuxi, China.
- Department of Oncology, The Women's Hospital of Jiangnan University, 214023, Wuxi, China.
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Alberghina L. The Warburg Effect Explained: Integration of Enhanced Glycolysis with Heterogeneous Mitochondria to Promote Cancer Cell Proliferation. Int J Mol Sci 2023; 24:15787. [PMID: 37958775 PMCID: PMC10648413 DOI: 10.3390/ijms242115787] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/19/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
The Warburg effect is the long-standing riddle of cancer biology. How does aerobic glycolysis, inefficient in producing ATP, confer a growth advantage to cancer cells? A new evaluation of a large set of literature findings covering the Warburg effect and its yeast counterpart, the Crabtree effect, led to an innovative working hypothesis presented here. It holds that enhanced glycolysis partially inactivates oxidative phosphorylation to induce functional rewiring of a set of TCA cycle enzymes to generate new non-canonical metabolic pathways that sustain faster growth rates. The hypothesis has been structured by constructing two metabolic maps, one for cancer metabolism and the other for the yeast Crabtree effect. New lines of investigation, suggested by these maps, are discussed as instrumental in leading toward a better understanding of cancer biology in order to allow the development of more efficient metabolism-targeted anticancer drugs.
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Affiliation(s)
- Lilia Alberghina
- Centre of Systems Biology, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
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Xiao H, Hu L, Tan Q, Jia J, Xie P, Li J, Wang M. Transcriptional profiles reveal histologic origin and prognosis across 33 The Cancer Genome Atlas tumor types. Transl Cancer Res 2023; 12:2764-2780. [PMID: 37969389 PMCID: PMC10643977 DOI: 10.21037/tcr-23-234] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 08/18/2023] [Indexed: 11/17/2023]
Abstract
Background In recent years, with the development of transcriptome sequencing, the molecular characteristics of tumors are gradually revealed. Because of the complexity of tumor transcriptome, there is a need to look for the molecular signatures which can be used to evaluate the tissue origin and cell stemness of tumors in order to promote the diagnosis and treatment of tumors. Methods Tumor tissue-specific gene sets (TTSGs) consisting of 200 genes were selected using RNA expression data of 9,875 patients from 33 tumor types. t-distributed Stochastic Neighbor Embedding (t-SNE) was used for dimensionality reduction and visualization of TTSGs in each tumor type. To evaluate oncogenic dedifferentiation and loss of cell stemness, Euclidean distance from each sample to a human embryo single-cell RNA-seq dataset (GSE36552) of TTSGs was calculated as TTSGs index indicating dissimilarity of tumors and embryo. TTSGs index was evaluated for prognosis in each tumor type. Two published signature indexes, the mRNA signature index (mRNAsi) and CIBERSORT, were compared to assess the correlation between the TTSGs index with cell stemness and immune microenvironment. Finally, the difference of prognosis, immune microenvironment and radiotherapy outcomes were compared between patients with high and low TTSGs index. Results In this study, all 33 tumor types in The Cancer Genome Atlas (TCGA) were embedded into isolated clusters by t-SNE and confirmed by k-nearest neighbors (kNN) algorithm. Clusters of squamous-cell carcinoma were adjacent to each other revealing similar histologic origin. Basal-like breast cancer was separated from luminal and HER-2-amplified subtypes and closed to squamous-cell carcinoma. TTSGs index was related to overall survival outcomes in cancers derived from liver, thyroid, brain, cervical and kidney. There was a positive correlation between mRNAsi and TTSGs index in pan-kidney and pan-neuronal cancers. Furthermore, cell fractions of M2 macrophages and total leukocytes increased in the group with higher TTSGs index. Patients with higher TTSGs index had longer overall survival time and less radiation therapy resistance compared to patients with lower TTSGs index. Conclusions The signature of TTSGs is related to tumor expression features that distinguish tumors of different histologic origin using t-SNE. The signature also relates to prognosis of certain kinds of tumors.
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Affiliation(s)
- Hui Xiao
- Department of Pathology, The Second Affiliated Hospital, School of Medicine, The Chinese University of Hong Kong, Shenzhen & Longgang District People’s Hospital of Shenzhen, Shenzhen, China
| | - Liang Hu
- Central Laboratory, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City, Shenzhen, China
| | - Qi Tan
- Department of Pathology, The Second Affiliated Hospital, School of Medicine, The Chinese University of Hong Kong, Shenzhen & Longgang District People’s Hospital of Shenzhen, Shenzhen, China
| | - Jinping Jia
- Department of Pathology, The Second Affiliated Hospital, School of Medicine, The Chinese University of Hong Kong, Shenzhen & Longgang District People’s Hospital of Shenzhen, Shenzhen, China
| | - Ping Xie
- Department of Pathology, The Second Affiliated Hospital, School of Medicine, The Chinese University of Hong Kong, Shenzhen & Longgang District People’s Hospital of Shenzhen, Shenzhen, China
| | - Junai Li
- Department of Pathology, The Second Affiliated Hospital, School of Medicine, The Chinese University of Hong Kong, Shenzhen & Longgang District People’s Hospital of Shenzhen, Shenzhen, China
| | - Minghua Wang
- Department of Pathology, The Second Affiliated Hospital, School of Medicine, The Chinese University of Hong Kong, Shenzhen & Longgang District People’s Hospital of Shenzhen, Shenzhen, China
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Abatti LE, Lado-Fernández P, Huynh L, Collado M, Hoffman M, Mitchell J. Epigenetic reprogramming of a distal developmental enhancer cluster drives SOX2 overexpression in breast and lung adenocarcinoma. Nucleic Acids Res 2023; 51:10109-10131. [PMID: 37738673 PMCID: PMC10602899 DOI: 10.1093/nar/gkad734] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/18/2023] [Accepted: 08/24/2023] [Indexed: 09/24/2023] Open
Abstract
Enhancer reprogramming has been proposed as a key source of transcriptional dysregulation during tumorigenesis, but the molecular mechanisms underlying this process remain unclear. Here, we identify an enhancer cluster required for normal development that is aberrantly activated in breast and lung adenocarcinoma. Deletion of the SRR124-134 cluster disrupts expression of the SOX2 oncogene, dysregulates genome-wide transcription and chromatin accessibility and reduces the ability of cancer cells to form colonies in vitro. Analysis of primary tumors reveals a correlation between chromatin accessibility at this cluster and SOX2 overexpression in breast and lung cancer patients. We demonstrate that FOXA1 is an activator and NFIB is a repressor of SRR124-134 activity and SOX2 transcription in cancer cells, revealing a co-opting of the regulatory mechanisms involved in early development. Notably, we show that the conserved SRR124 and SRR134 regions are essential during mouse development, where homozygous deletion results in the lethal failure of esophageal-tracheal separation. These findings provide insights into how developmental enhancers can be reprogrammed during tumorigenesis and underscore the importance of understanding enhancer dynamics during development and disease.
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Affiliation(s)
- Luis E Abatti
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Patricia Lado-Fernández
- Laboratory of Cell Senescence, Cancer and Aging, Health Research Institute of Santiago de Compostela (IDIS), Xerencia de Xestión Integrada de Santiago (XXIS/SERGAS), Santiago de Compostela, Spain
- Department of Physiology and Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Linh Huynh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Manuel Collado
- Laboratory of Cell Senescence, Cancer and Aging, Health Research Institute of Santiago de Compostela (IDIS), Xerencia de Xestión Integrada de Santiago (XXIS/SERGAS), Santiago de Compostela, Spain
| | - Michael M Hoffman
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- Vector Institute for Artificial Intelligence, Toronto, Ontario, Canada
| | - Jennifer A Mitchell
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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Zhang TA, Zhang Q, Zhang J, Zhao R, Shi R, Wei S, Liu S, Zhang Q, Wang H. Identification of the role of endoplasmic reticulum stress genes in endometrial cancer and their association with tumor immunity. BMC Med Genomics 2023; 16:261. [PMID: 37880674 PMCID: PMC10599039 DOI: 10.1186/s12920-023-01679-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 09/30/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND Endometrial cancer (EC) is one of the worldwide gynecological malignancies. Endoplasmic reticulum (ER) stress is the cellular homeostasis disturbance that participates in cancer progression. However, the mechanisms of ER Stress on EC have not been fully elucidated. METHOD The ER Stress-related genes were obtained from Gene Set Enrichment Analysis (GSEA) and GeneCards, and the RNA-seq and clinical data were downloaded from The Cancer Genome Atlas (TCGA). The risk signature was constructed by the Cox regression and the least absolute shrinkage and selection operator (LASSO) analysis. The significance of the risk signature and clinical factors were tested by time-dependent receiver operating characteristic (ROC) curves, and the selected were to build a nomogram. The immunity correlation was particularly analyzed, including the related immune cells, pathways, and immune checkpoints. Functional enrichment, potential chemotherapies, and in vitro validation were also conducted. RESULT An ER Stress-based risk signature, consisting of TRIB3, CREB3L3, XBP1, and PPP1R15A was established. Patients were randomly divided into training and testing groups with 1:1 ratio for subsequent calculation and validation. Based on risk scores, high- and low-risk subgroups were classified, and low-risk subgroup demonstrated better prognosis. The Area Under Curve (AUC) demonstrated a reliable predictive capability of the risk signature. The majority of significantly different immune cells and pathways were enriched more in low-risk subgroup. Similarly, several typical immune checkpoints, expressed higher in low-risk subgroup. Patients of the two subgroups responded differently to chemotherapies. CONCLUSION We established an ER Stress-based risk signature that could effectively predict EC patients' prognosis and their immune correlation.
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Affiliation(s)
- Tang Ansu Zhang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, Hubei, China
| | - Qian Zhang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, Hubei, China
| | - Jun Zhang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, Hubei, China
| | - Rong Zhao
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, Hubei, China
| | - Rui Shi
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, Hubei, China
| | - Sitian Wei
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, Hubei, China
| | - Shuangge Liu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, Hubei, China
| | - Qi Zhang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, Hubei, China.
| | - Hongbo Wang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, Hubei, China.
- Clinical Research Center of Cancer Immunotherapy, Wuhan, 430022, Hubei, China.
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