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He Y, Zhu M, Lai X, Zhang H, Jiang W. The roles of PD-L1 in the various stages of tumor metastasis. Cancer Metastasis Rev 2024:10.1007/s10555-024-10189-4. [PMID: 38733457 DOI: 10.1007/s10555-024-10189-4] [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: 02/06/2024] [Accepted: 05/08/2024] [Indexed: 05/13/2024]
Abstract
The interaction between tumor programmed death ligand 1 (PD-L1) and T-cell programmed cell death 1 (PD-1) has long been acknowledged as a mechanism for evading immune surveillance. Recent studies, however, have unveiled a more nuanced role of tumor-intrinsic PD-L1 in reprograming tumoral phenotypes. Preclinical models emphasize the synchronized effects of both intracellular and extracellular PD-L1 in promoting metastasis, with intricate interactions with the immune system. This review aims to summarize recent findings to elucidate the spatiotemporal heterogeneity of PD-L1 expression and the pro-metastatic roles of PD-L1 in the entire process of tumor metastasis. For example, PD-L1 regulates the epithelial-to-mesenchymal transition (EMT) process, facilitates the survival of circulating tumor cells, and induces the formation of immunosuppressive environments at pre-metastatic niches and metastatic sites. And the complexed and dynamic regulation process of PD-L1 for tumor metastasis is related to the spatiotemporal heterogeneity of PD-L1 expression and functions from tumor primary sites to various metastatic sites. This review extends the current understandings for the roles of PD-L1 in mediating tumor metastasis and provides new insights into therapeutic decisions in clinical practice.
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Affiliation(s)
- Yinjun He
- Department of Colorectal Surgery, First Affiliated Hospital, Zhejiang University Medical School, Hangzhou, 310009, China
- Department of Pathology, Zhejiang University Medical School, Hangzhou, 310058, China
| | - Ming Zhu
- Department of Pathology, Zhejiang University Medical School, Hangzhou, 310058, China
| | - Xuan Lai
- Department of Pathology, Zhejiang University Medical School, Hangzhou, 310058, China
| | - Honghe Zhang
- Department of Pathology, Zhejiang University Medical School, Hangzhou, 310058, China.
| | - Weiqin Jiang
- Department of Colorectal Surgery, First Affiliated Hospital, Zhejiang University Medical School, Hangzhou, 310009, China.
- Department of Pathology, Zhejiang University Medical School, Hangzhou, 310058, China.
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2
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Jin W, Jia J, Si Y, Liu J, Li H, Zhu H, Wu Z, Zuo Y, Yu L. Identification of Key lncRNAs Associated with Immune Infiltration and Prognosis in Gastric Cancer. Biochem Genet 2024:10.1007/s10528-024-10801-w. [PMID: 38658494 DOI: 10.1007/s10528-024-10801-w] [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: 09/20/2023] [Accepted: 04/05/2024] [Indexed: 04/26/2024]
Abstract
Long non-coding RNAs (lncRNAs), as promising novel biomarkers for cancer treatment and prognosis, can function as tumor suppressors and oncogenes in the occurrence and development of many types of cancer, including gastric cancer (GC). However, little is known about the complex regulatory system of lncRNAs in GC. In this study, we systematically analyzed lncRNA and miRNA transcriptomic profiles of GC based on bioinformatics methods and experimental validation. An lncRNA-miRNA interaction network related to GC was constructed, and the nine crucial lncRNAs were identified. These 9 lncRNAs were found to be associated with the prognosis of GC patients by Cox proportional hazards regression analysis. Among them, the expression of lncRNA SNHG14 can affect the survival of GC patients as a potential prognostic marker. Moreover, it was shown that SNHG14 was involved in immune-related pathways and significantly correlated with immune cell infiltration in GC. Meanwhile, we found that SNHG14 affected immune function in many cancers, such as breast cancer and esophageal carcinoma. Such information revealed that SNHG14 may serve as a potential target for cancer immunotherapy. As well, our study could provide practical and theoretical guiding significance for clinical application of non-coding RNAs.
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Affiliation(s)
- Wen Jin
- Clinical Medical Research Center, Inner Mongolia Key Laboratory of Gene Regulation of the Metabolic Disease, Inner Mongolia People's Hospital, Hohhot, 010010, China
| | - Jianchao Jia
- Clinical Medical Research Center, Inner Mongolia Key Laboratory of Gene Regulation of the Metabolic Disease, Inner Mongolia People's Hospital, Hohhot, 010010, China
| | - Yangming Si
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China
| | - Jianli Liu
- School of Water Resource and Environment Engineering, China University of Geosciences, Beijing, 100083, China
| | - Hanshuang Li
- College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Hao Zhu
- Clinical Medical Research Center, Inner Mongolia Key Laboratory of Gene Regulation of the Metabolic Disease, Inner Mongolia People's Hospital, Hohhot, 010010, China
| | - Zhouying Wu
- Clinical Medical Research Center, Inner Mongolia Key Laboratory of Gene Regulation of the Metabolic Disease, Inner Mongolia People's Hospital, Hohhot, 010010, China
| | - Yongchun Zuo
- College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
- Digital College, Inner Mongolia Intelligent Union Big Data Academy, Hohhot, 010010, China.
- Inner Mongolia International Mongolian Hospital, Hohhot, 010065, China.
| | - Lan Yu
- Clinical Medical Research Center, Inner Mongolia Key Laboratory of Gene Regulation of the Metabolic Disease, Inner Mongolia People's Hospital, Hohhot, 010010, China.
- Department of Endocrine and Metabolic Diseases, Inner Mongolia People's Hospital, Hohhot, 010010, China.
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3
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Ray SK, Mukherjee S. Molecular perspectives on systemic priming and concomitant immunity in colorectal carcinoma. J Egypt Natl Canc Inst 2024; 36:7. [PMID: 38462581 DOI: 10.1186/s43046-024-00211-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/15/2024] [Indexed: 03/12/2024] Open
Abstract
The progression of metastasis, a complex systemic disease, is facilitated by interactions between tumor cells and their isolated microenvironments. Over the past few decades, researchers have investigated the metastatic spread of cancer extensively, identifying multiple stages in the process, such as intravasation, extravasation, tumor latency, and the development of micrometastasis and macrometastasis. The premetastatic niche is established in target organs by the accumulation of aberrant immune cells and extracellular matrix proteins. The "seed and soil" idea, which has become widely known and accepted, is being used to this day to guide cancer studies. Changes in the local and systemic immune systems have a major impact on whether an infection spreads or not. The belief that the immune response may play a role in slowing tumor growth and may be beneficial against the metastatic disease underpins the responsiveness shown in the immunological landscape of metastasis. Various hypotheses on the phylogenesis of metastases have been proposed in the past. The primary tumor's secreting factors shape the intratumoral microenvironment and the immune landscape, allowing this progress to be made. Therefore, it is evident that among disseminated tumor cells, there are distinct phenotypes that either carry budding for metastasis or have the ability to obtain this potential or in systemic priming through contact with substantial metastatic niches that have implications for medicinal chemistry. Concurrent immunity signals that the main tumor induces an immune response that may not be strong enough to eradicate the tumor. Immunotherapy's success with some cancer patients shows that it is possible to effectively destroy even advanced-stage tumors by modifying the microenvironment and tumor-immune cell interactions. This review focuses on the metastasome in colorectal carcinoma and the therapeutic implications of site-specific metastasis, systemic priming, tumor spread, and the relationship between the immune system and metastasis.
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Affiliation(s)
- Suman Kumar Ray
- Independent Researcher, Bhopal, Madhya Pradesh, 462020, India
| | - Sukhes Mukherjee
- Department of Biochemistry, All India Institute of Medical Sciences, Bhopal, Madhya Pradesh, 462020, India.
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4
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Gmeiner WH. Recent Advances in Therapeutic Strategies to Improve Colorectal Cancer Treatment. Cancers (Basel) 2024; 16:1029. [PMID: 38473386 PMCID: PMC10930828 DOI: 10.3390/cancers16051029] [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: 01/31/2024] [Revised: 02/24/2024] [Accepted: 02/29/2024] [Indexed: 03/14/2024] Open
Abstract
Colorectal cancer (CRC) is the second-leading cause of cancer-related mortality worldwide. CRC mortality results almost exclusively from metastatic disease (mCRC) for which systemic chemotherapy is often a preferred therapeutic option. Biomarker-based stratification of mCRC enables the use of precision therapy based on individual tumor mutational profiles. Activating mutations in the RAS/RAF/MAPK pathway downstream of EGFR signaling have, until recently, limited the use of EGFR-targeted therapies for mCRC; however, the development of anti-RAS and anti-RAF therapies together with improved strategies to limit compensatory signaling pathways is resulting in improved survival rates in several highly lethal mCRC sub-types (e.g., BRAF-mutant). The use of fluoropyrimidine (FP)-based chemotherapy regimens to treat mCRC continues to evolve contributing to improved long-term survival. Future advances in chemotherapy for mCRC will need to position development relative to the advances made in precision oncology.
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Affiliation(s)
- William H Gmeiner
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
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5
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Tanaka A, Ogawa M, Zhou Y, Namba K, Hendrickson RC, Miele MM, Li Z, Klimstra DS, Buckley PG, Gulcher J, Wang JY, Roehrl MHA. Proteogenomic characterization of primary colorectal cancer and metastatic progression identifies proteome-based subtypes and signatures. Cell Rep 2024; 43:113810. [PMID: 38377004 DOI: 10.1016/j.celrep.2024.113810] [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: 11/20/2022] [Revised: 10/26/2023] [Accepted: 02/01/2024] [Indexed: 02/22/2024] Open
Abstract
Metastatic progression of colorectal adenocarcinoma (CRC) remains poorly understood and poses significant challenges for treatment. To overcome these challenges, we performed multiomics analyses of primary CRC and liver metastases. Genomic alterations, such as structural variants or copy number alterations, were enriched in oncogenes and tumor suppressor genes and increased in metastases. Unsupervised mass spectrometry-based proteomics of 135 primary and 123 metastatic CRCs uncovered distinct proteomic subtypes, three each for primary and metastatic CRCs, respectively. Integrated analyses revealed that hypoxia, stemness, and immune signatures characterize these 6 subtypes. Hypoxic CRC harbors high epithelial-to-mesenchymal transition features and metabolic adaptation. CRC with a stemness signature shows high oncogenic pathway activation and alternative telomere lengthening (ALT) phenotype, especially in metastatic lesions. Tumor microenvironment analysis shows immune evasion via modulation of major histocompatibility complex (MHC) class I/II and antigen processing pathways. This study characterizes both primary and metastatic CRCs and provides a large proteogenomics dataset of metastatic progression.
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Affiliation(s)
- Atsushi Tanaka
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Makiko Ogawa
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yihua Zhou
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; ICU Department, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Kei Namba
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of General Thoracic Surgery and Breast and Endocrinological Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Ronald C Hendrickson
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matthew M Miele
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zhuoning Li
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David S Klimstra
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Paige.AI, New York, NY, USA
| | | | | | | | - Michael H A Roehrl
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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6
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Yang C, Zhang Y, Yan M, Wang J, Wang J, Wang M, Xuan Y, Cheng H, Ma J, Chai C, Li M, Yu Z. Exosomes derived from cancer-associated fibroblasts promote tumorigenesis, metastasis and chemoresistance of colorectal cancer by upregulating circ_0067557 to target Lin28. BMC Cancer 2024; 24:64. [PMID: 38216964 PMCID: PMC10785442 DOI: 10.1186/s12885-023-11791-5] [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: 06/15/2023] [Accepted: 12/22/2023] [Indexed: 01/14/2024] Open
Abstract
BACKGROUND Cancer associated fibroblasts (CAFs) can remodel tumor microenvironment by secreting exosomes. This study aimed to investigate the role of exosomes derived from cancer-associated fibroblasts in colorectal cancer (CRC) progression. METHODS Circular RNA (circRNA) array was used to identify differentially expressed circRNAs in exosomes from normal fibroblasts (NFs) and CAFs, and confirmed one differentially expressed circRNA circ_0067557 by real-time PCR. The effect of circ_0067557 on proliferation, metastasis, chemoresistance and apoptosis was verified by wound heal, tranwell, CCK8, sphere-forming and flow cytometry assay. RESULTS Circ_0067557 expression in exosomes from CAFs was higher than those from NFs. CAF-derived exosomes promoted the proliferation, migration, invasion and chemoresistance of CRC cells while suppressed apoptosis. Silencing of circ_0067557 inhibited malignant phenotypes of CRC cells by targeting Lin28A and Lin28B. Moreover, CAF-derived exosomes enhanced the growth of CRC xenograft tumors. CONCLUSION Circ_0067557/Lin28A and Lin28B signal axis may be a potential therapy target for CRC.
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Affiliation(s)
- Cheng Yang
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, 150086, Harbin, China
| | - Yan Zhang
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, 150086, Harbin, China
| | - Mingze Yan
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, 150086, Harbin, China
| | - Jiahao Wang
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, 150086, Harbin, China
| | - Jiaming Wang
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, 150086, Harbin, China
| | - Muhong Wang
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, 150086, Harbin, China
| | - Yuhong Xuan
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, 150086, Harbin, China
| | - Haiyue Cheng
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, 150086, Harbin, China
| | - Jiaao Ma
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, 150086, Harbin, China
| | - Cuicui Chai
- Digestive Disease Center, The Seventh Affiliated Hospital of Sun Yat-sen University, 518107, Shenzhen, China
| | - Mingzhe Li
- Digestive Disease Center, The Seventh Affiliated Hospital of Sun Yat-sen University, 518107, Shenzhen, China.
| | - Zhiwei Yu
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, 150086, Harbin, China.
- Digestive Disease Center, The Seventh Affiliated Hospital of Sun Yat-sen University, 518107, Shenzhen, China.
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7
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Meyer M, Parpoulas C, Barthélémy T, Becker JP, Charoentong P, Lyu Y, Börsig S, Bulbuc N, Tessmer C, Weinacht L, Ibberson D, Schmidt P, Pipkorn R, Eichmüller SB, Steinberger P, Lindner K, Poschke I, Platten M, Fröhling S, Riemer AB, Hassel JC, Roberti MP, Jäger D, Zörnig I, Momburg F. MediMer: a versatile do-it-yourself peptide-receptive MHC class I multimer platform for tumor neoantigen-specific T cell detection. Front Immunol 2024; 14:1294565. [PMID: 38239352 PMCID: PMC10794645 DOI: 10.3389/fimmu.2023.1294565] [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: 09/14/2023] [Accepted: 11/28/2023] [Indexed: 01/22/2024] Open
Abstract
Peptide-loaded MHC class I (pMHC-I) multimers have revolutionized our capabilities to monitor disease-associated T cell responses with high sensitivity and specificity. To improve the discovery of T cell receptors (TCR) targeting neoantigens of individual tumor patients with recombinant MHC molecules, we developed a peptide-loadable MHC class I platform termed MediMer. MediMers are based on soluble disulfide-stabilized β2-microglobulin/heavy chain ectodomain single-chain dimers (dsSCD) that can be easily produced in large quantities in eukaryotic cells and tailored to individual patients' HLA allotypes with only little hands-on time. Upon transient expression in CHO-S cells together with ER-targeted BirA biotin ligase, biotinylated dsSCD are purified from the cell supernatant and are ready to use. We show that CHO-produced dsSCD are free of endogenous peptide ligands. Empty dsSCD from more than 30 different HLA-A,B,C allotypes, that were produced and validated so far, can be loaded with synthetic peptides matching the known binding criteria of the respective allotypes, and stored at low temperature without loss of binding activity. We demonstrate the usability of peptide-loaded dsSCD multimers for the detection of human antigen-specific T cells with comparable sensitivities as multimers generated with peptide-tethered β2m-HLA heavy chain single-chain trimers (SCT) and wild-type peptide-MHC-I complexes prior formed in small-scale refolding reactions. Using allotype-specific, fluorophore-labeled competitor peptides, we present a novel dsSCD-based peptide binding assay capable of interrogating large libraries of in silico predicted neoepitope peptides by flow cytometry in a high-throughput and rapid format. We discovered rare T cell populations with specificity for tumor neoepitopes and epitopes from shared tumor-associated antigens in peripheral blood of a melanoma patient including a so far unreported HLA-C*08:02-restricted NY-ESO-1-specific CD8+ T cell population. Two representative TCR of this T cell population, which could be of potential value for a broader spectrum of patients, were identified by dsSCD-guided single-cell sequencing and were validated by cognate pMHC-I multimer staining and functional responses to autologous peptide-pulsed antigen presenting cells. By deploying the technically accessible dsSCD MHC-I MediMer platform, we hope to significantly improve success rates for the discovery of personalized neoepitope-specific TCR in the future by being able to also cover rare HLA allotypes.
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Affiliation(s)
- Marten Meyer
- Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Clinical Cooperation Unit Applied Tumor Immunity, DKFZ, Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
| | - Christina Parpoulas
- Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Titouan Barthélémy
- Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jonas P. Becker
- Division of Immunotherapy and Immunoprevention, DKFZ, Heidelberg, Germany
- German Center for Infection Research (DZIF) Partner Site Heidelberg, Heidelberg, Germany
| | - Pornpimol Charoentong
- Clinical Cooperation Unit Applied Tumor Immunity, DKFZ, Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
- Center for Quantitative Analysis of Molecular and Cellular Biosystems (Bioquant), Heidelberg University, Heidelberg, Germany
| | - Yanhong Lyu
- Clinical Cooperation Unit Applied Tumor Immunity, DKFZ, Heidelberg, Germany
| | - Selina Börsig
- Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
| | - Nadja Bulbuc
- Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Claudia Tessmer
- Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Clinical Cooperation Unit Applied Tumor Immunity, DKFZ, Heidelberg, Germany
| | - Lisa Weinacht
- Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David Ibberson
- Deep Sequencing Core Facility, Heidelberg University, Heidelberg, Germany
| | - Patrick Schmidt
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
- GMP and T Cell Therapy, DKFZ, Heidelberg, Germany
| | | | | | - Peter Steinberger
- Division of Immune Receptors and T Cell Activation, Center for Pathophysiology, Infectiology, Medical University of Vienna, Vienna, Austria
| | - Katharina Lindner
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, DKFZ, Heidelberg, Germany
- Immune Monitoring Unit, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Isabel Poschke
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, DKFZ, Heidelberg, Germany
- Immune Monitoring Unit, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Michael Platten
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, DKFZ, Heidelberg, Germany
- Immune Monitoring Unit, NCT Heidelberg and DKFZ, Heidelberg, Germany
- German Cancer Consortium (DKTK), DKFZ, Core Center, Heidelberg, Germany
- Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neuroscience (MCTN), Heidelberg University, Mannheim, Germany
- DKFZ Hector Cancer Institute at the University Medical Center, Mannheim, Germany
- Helmholtz Institute for Translational Oncology, Mainz (HI-TRON Mainz), Mainz, Germany
| | - Stefan Fröhling
- German Cancer Consortium (DKTK), DKFZ, Core Center, Heidelberg, Germany
- Division of Translational Medical Oncology, NCT Heidelberg and DKFZ, Heidelberg, Germany
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Angelika B. Riemer
- Division of Immunotherapy and Immunoprevention, DKFZ, Heidelberg, Germany
- German Center for Infection Research (DZIF) Partner Site Heidelberg, Heidelberg, Germany
| | - Jessica C. Hassel
- Section of DermatoOncology, Department of Dermatology and NCT, Heidelberg University Hospital, Heidelberg, Germany
| | - Maria Paula Roberti
- Clinical Cooperation Unit Applied Tumor Immunity, DKFZ, Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
| | - Dirk Jäger
- Clinical Cooperation Unit Applied Tumor Immunity, DKFZ, Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
| | - Inka Zörnig
- Clinical Cooperation Unit Applied Tumor Immunity, DKFZ, Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
| | - Frank Momburg
- Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
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8
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Matsuoka T, Yashiro M. Current status and perspectives of genetic testing in gastrointestinal cancer (Review). Oncol Lett 2024; 27:21. [PMID: 38058469 PMCID: PMC10696628 DOI: 10.3892/ol.2023.14155] [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: 06/22/2023] [Accepted: 10/30/2023] [Indexed: 12/08/2023] Open
Abstract
Genetic testing has become widespread in daily medical care for gastrointestinal (GI) cancers. However, unlike breast cancer and non-small cell lung cancer, in which personalized medicine targeting various driver genes is standardized, the incidence of targeted gene abnormalities in GI cancers is low. Nevertheless, such abnormalities may be linked to therapeutic agents and the further development of therapeutic agents for personalized medicine for GI cancers is desired. A liquid biopsy is of great benefit in offering clinical decision support, in applications such as GI cancer screening, surgical interventions, monitoring disease status and enhancing patient survival outcomes, all of which would contribute to personalized medicine. Germline genetic testing is required for several types of GI cancer, which shows clinical indications of hereditary predisposition. The increasing use of multigene panel testing has redefined gene-cancer associations, and consequently the estimate of cancer risk that vary from low to high penetrance. Comprehensive genetic testing can enable the detection of novel treatment targets and the discovery of undefined multiple diagnostic/predictive markers, which may enhance the molecular-level understanding of GI cancers. Genetic testing can also aid the design of more appropriate and adequate genomic-driven therapies for patients who may benefit from other standardized therapeutic methods.
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Affiliation(s)
- Tasuku Matsuoka
- Department of Molecular Oncology and Therapeutics, Osaka Metropolitan University Graduate School of Medicine, Osaka 5458585, Japan
| | - Masakazu Yashiro
- Department of Molecular Oncology and Therapeutics, Osaka Metropolitan University Graduate School of Medicine, Osaka 5458585, Japan
- Institute of Medical Genetics, Osaka Metropolitan University, Osaka 5458585, Japan
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9
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Abbastabar M, Allgayer H, Sepidarkish M, Sadeghi F, Ghasemi M, Pour-bagher R, Parsian H. Expression Status of Rap1 Pathway-Related Genes in Liver Metastases Compared with Corresponding Primary Colorectal Cancer. Cancers (Basel) 2023; 16:171. [PMID: 38201598 PMCID: PMC10778515 DOI: 10.3390/cancers16010171] [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: 11/20/2023] [Revised: 12/21/2023] [Accepted: 12/26/2023] [Indexed: 01/12/2024] Open
Abstract
Understanding molecular networks of CRLM is an ongoing area of research. In this study, paired CRC tissue and adjacent noncancerous tissue from 15 non-metastatic CRC patients and paired CRC tissue and matched liver metastatic tissues from 15 CRLM patients along with their adjacent noncancerous tissues were evaluated. We assessed Rap1 pathway-related genes including NRAS, FGF-1, NGF, and KDR expression by qRT-PCR and their protein status by Western blot. In CRLM patients, NRAS, FGF1, and KDR mRNA and protein were expressed at higher levels in metastatic than in CRC primary tumor and adjacent noncancerous tissue (p < 0.05). In non-metastatic patients, NRAS, FGF1, KDR, and NGF gene expression did not differ between CRC primary tumor-and adjacent noncancerous tissue (p > 0.05). ROC curve analysis showed a reasonable diagnostic accuracy of NRAS, FGF1, KDR, and FGF for the discrimination of metastatic patients from non- metastatic ones on analysis of their primary tumors. The data suggest that further functional studies on Rap1-related genes' role in CRLM are needed. In conclusion, the present data broaden our knowledge about specific molecular characteristics of CRLM. An increased understanding of the molecular features of metastasis has the potential to create more successful treatment, or prevention, of metastasis, especially in multimodal primary tumor treatment.
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Affiliation(s)
- Maryam Abbastabar
- Student Research Committee, Babol University of Medical Sciences, Babol 47176-47745, Iran;
- Department of Clinical Biochemistry, School of Medicine, Babol University of Medical Sciences, Babol 47176-47745, Iran
| | - Heike Allgayer
- Department of Experimental Surgery-Cancer Metastasis, Medical Faculty Mannheim, Ruprecht-Karls-University Heidelberg, 68167 Mannheim, Germany;
| | - Mahdi Sepidarkish
- Department of Biostatistics and Epidemiology, School of Public Health, Babol University of Medical Sciences, Babol 47176-47745, Iran;
| | - Farzin Sadeghi
- Cellular & Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Ganjafrooz Street, Babol 47176-47745, Iran; (F.S.); (R.P.-b.)
| | - Maryam Ghasemi
- Department of Pathology, Immunogenetics Research Center, Mazandaran University of Medical Sciences, Sari 48175-866, Iran;
| | - Roghayeh Pour-bagher
- Cellular & Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Ganjafrooz Street, Babol 47176-47745, Iran; (F.S.); (R.P.-b.)
| | - Hadi Parsian
- Cellular & Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Ganjafrooz Street, Babol 47176-47745, Iran; (F.S.); (R.P.-b.)
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Patil N, Abdelrahim OG, Leupold JH, Allgayer H. JAK1 Is a Novel Target of Tumor- and Invasion-Suppressive microRNA 494-5p in Colorectal Cancer. Cancers (Basel) 2023; 16:24. [PMID: 38201452 PMCID: PMC10778350 DOI: 10.3390/cancers16010024] [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: 11/27/2023] [Revised: 12/12/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
MiR-494-5p expression has been suggested to be associated with colorectal cancer (CRC) and its metastases in our previous studies. However, functional investigations on the molecule-mediating actions of this miR in CRC are lacking. In silico analysis in the present study revealed a putative binding sequence within the 3'UTR of JAK1. Overexpression of miR-494-5p in cultured CRC significantly reduced the luciferase activity of a reporter plasmid containing the wild-type JAK1-3'UTR, which was abolished by seed sequence mutation. Furthermore, the overexpression of miR-494-5p in CRC cell lines led to a significant reduction in JAK1 expression, proliferation, in vitro migration, and invasion. These effects were abolished by co-transfection with a specific double-stranded RNA that inhibits endogenous miR-494-5p. Moreover, IL-4-induced migration, invasion, and phosphorylation of JAK1, STAT6, and AKT proteins were reduced after an overexpression of this miR, suggesting that this miR affects one of the most essential pathways in CRC. A Kaplan-Meier plotter analysis revealed that patients with high JAK1 expression show reduced survival. Together, these data suggest that miR-494-5p physically inhibits the expression of JAK1 at the translational level as well as in migration and invasion, supporting the hypothesis of miR-494-5p as an early tumor suppressor and inhibitor of early steps of metastasis in CRC.
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Affiliation(s)
| | | | | | - Heike Allgayer
- Correspondence: ; Tel.: +49-(0)621-383-71630 or +49-(0)621-383-71635; Fax: +49-(0)621-383-71631
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11
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Jiang Z, Ju YJ, Ali A, Chung PED, Wang DY, Liu JC, Li H, Vorobieva I, Mwewa E, Ghanbari-Azarnier R, Shrestha M, Ben-David Y, Zacksenhaus E. Thinking (Metastasis) outside the (Primary Tumor) Box. Cancers (Basel) 2023; 15:5315. [PMID: 38001575 PMCID: PMC10670606 DOI: 10.3390/cancers15225315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
The metastasis of tumor cells into vital organs is a major cause of death from diverse types of malignancies [...].
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Affiliation(s)
- Zhe Jiang
- Toronto General Research Institute—University Health Network, 101 College Street, Max Bell Research Centre, Suite 5R406, Toronto, ON M5G 1L7, Canada (Y.-J.J.); (A.A.); (D.-Y.W.); (H.L.); (E.M.); (R.G.-A.); (M.S.)
| | - Young-Jun Ju
- Toronto General Research Institute—University Health Network, 101 College Street, Max Bell Research Centre, Suite 5R406, Toronto, ON M5G 1L7, Canada (Y.-J.J.); (A.A.); (D.-Y.W.); (H.L.); (E.M.); (R.G.-A.); (M.S.)
| | - Amjad Ali
- Toronto General Research Institute—University Health Network, 101 College Street, Max Bell Research Centre, Suite 5R406, Toronto, ON M5G 1L7, Canada (Y.-J.J.); (A.A.); (D.-Y.W.); (H.L.); (E.M.); (R.G.-A.); (M.S.)
| | - Philip E. D. Chung
- Toronto General Research Institute—University Health Network, 101 College Street, Max Bell Research Centre, Suite 5R406, Toronto, ON M5G 1L7, Canada (Y.-J.J.); (A.A.); (D.-Y.W.); (H.L.); (E.M.); (R.G.-A.); (M.S.)
- Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Dong-Yu Wang
- Toronto General Research Institute—University Health Network, 101 College Street, Max Bell Research Centre, Suite 5R406, Toronto, ON M5G 1L7, Canada (Y.-J.J.); (A.A.); (D.-Y.W.); (H.L.); (E.M.); (R.G.-A.); (M.S.)
| | - Jeff C. Liu
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada;
| | - Huiqin Li
- Toronto General Research Institute—University Health Network, 101 College Street, Max Bell Research Centre, Suite 5R406, Toronto, ON M5G 1L7, Canada (Y.-J.J.); (A.A.); (D.-Y.W.); (H.L.); (E.M.); (R.G.-A.); (M.S.)
| | - Ioulia Vorobieva
- Toronto General Research Institute—University Health Network, 101 College Street, Max Bell Research Centre, Suite 5R406, Toronto, ON M5G 1L7, Canada (Y.-J.J.); (A.A.); (D.-Y.W.); (H.L.); (E.M.); (R.G.-A.); (M.S.)
- Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Ethel Mwewa
- Toronto General Research Institute—University Health Network, 101 College Street, Max Bell Research Centre, Suite 5R406, Toronto, ON M5G 1L7, Canada (Y.-J.J.); (A.A.); (D.-Y.W.); (H.L.); (E.M.); (R.G.-A.); (M.S.)
| | - Ronak Ghanbari-Azarnier
- Toronto General Research Institute—University Health Network, 101 College Street, Max Bell Research Centre, Suite 5R406, Toronto, ON M5G 1L7, Canada (Y.-J.J.); (A.A.); (D.-Y.W.); (H.L.); (E.M.); (R.G.-A.); (M.S.)
- Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Mariusz Shrestha
- Toronto General Research Institute—University Health Network, 101 College Street, Max Bell Research Centre, Suite 5R406, Toronto, ON M5G 1L7, Canada (Y.-J.J.); (A.A.); (D.-Y.W.); (H.L.); (E.M.); (R.G.-A.); (M.S.)
- Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Yaacov Ben-David
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550025, China;
- The Natural Products Research Center of Guizhou Province, Guiyang 550014, China
| | - Eldad Zacksenhaus
- Toronto General Research Institute—University Health Network, 101 College Street, Max Bell Research Centre, Suite 5R406, Toronto, ON M5G 1L7, Canada (Y.-J.J.); (A.A.); (D.-Y.W.); (H.L.); (E.M.); (R.G.-A.); (M.S.)
- Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Medicine, University of Toronto, Toronto, ON M5S 3H2, Canada
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12
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Zhou H, Hao X, Zhang P, He S. Noncoding RNA mutations in cancer. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1812. [PMID: 37544928 DOI: 10.1002/wrna.1812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 07/14/2023] [Accepted: 07/17/2023] [Indexed: 08/08/2023]
Abstract
Cancer is driven by both germline and somatic genetic changes. Efforts have been devoted to characterizing essential genetic variations in cancer initiation and development. Most attention has been given to mutations in protein-coding genes and associated regulatory elements such as promoters and enhancers. The development of sequencing technologies and in silico and experimental methods has allowed further exploration of cancer predisposition variants and important somatic mutations in noncoding RNAs, mainly for long noncoding RNAs and microRNAs. Association studies including GWAS have revealed hereditary variations including SNPs and indels in lncRNA or miRNA genes and regulatory regions. These mutations altered RNA secondary structures, expression levels, and target recognition and then conferred cancer predisposition to carriers. Whole-exome/genome sequencing comparing cancer and normal tissues has revealed important somatic mutations in noncoding RNA genes. Mutation hotspots and somatic copy number alterations have been identified in various tumor-associated noncoding RNAs. Increasing focus and effort have been devoted to studying the noncoding region of the genome. The complex genetic network of cancer initiation is being unveiled. This article is categorized under: RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Honghong Zhou
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xinpei Hao
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Peng Zhang
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Shunmin He
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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13
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Liu G, Bu C, Guo G, Zhang Z, Sheng Z, Deng K, Wu S, Xu S, Bu Y, Gao Y, Wang M, Liu G, Kong L, Li T, Li M, Bu X. Molecular and clonal evolution in vivo reveal a common pathway of distant relapse gliomas. iScience 2023; 26:107528. [PMID: 37649695 PMCID: PMC10462858 DOI: 10.1016/j.isci.2023.107528] [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: 10/06/2022] [Revised: 06/18/2023] [Accepted: 07/28/2023] [Indexed: 09/01/2023] Open
Abstract
The evolutionary trajectories of genomic alterations underlying distant recurrence in glioma remain largely unknown. To elucidate glioma evolution, we analyzed the evolutionary trajectories of matched pairs of primary tumors and relapse tumors or tumor in situ fluid (TISF) based on deep whole-genome sequencing data (ctDNA). We found that MMR gene mutations occurred in the late stage in IDH-mutant glioma during gene evolution, which activates multiple signaling pathways and significantly increases distant recurrence potential. The proneural subtype characterized by PDGFRA amplification was likely prone to hypermutation and distant recurrence following treatment. The classical and mesenchymal subtypes tended to progress locally through subclonal reconstruction, trunk genes transformation, and convergence evolution. EGFR and NOTCH signaling pathways and CDNK2A mutation play an important role in promoting tumor local progression. Glioma subtypes displayed distinct preferred evolutionary patterns. ClinicalTrials.gov, NCT05512325.
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Affiliation(s)
- Guanzheng Liu
- Department of Neurosurgery, Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou 450003, China
- Juha International Central Laboratory of Neurosurgery, Henan Provincial People’s Hospital, Zhengzhou 450003, China
| | - Chaojie Bu
- Department of Neurosurgery, Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou 450003, China
- Juha International Central Laboratory of Neurosurgery, Henan Provincial People’s Hospital, Zhengzhou 450003, China
| | - Guangzhong Guo
- Department of Neurosurgery, Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou 450003, China
- Juha International Central Laboratory of Neurosurgery, Henan Provincial People’s Hospital, Zhengzhou 450003, China
| | - Zhiyue Zhang
- Department of Neurosurgery, Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou 450003, China
- Juha International Central Laboratory of Neurosurgery, Henan Provincial People’s Hospital, Zhengzhou 450003, China
| | - Zhiyuan Sheng
- Department of Neurosurgery, Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou 450003, China
- Juha International Central Laboratory of Neurosurgery, Henan Provincial People’s Hospital, Zhengzhou 450003, China
| | - Kaiyuan Deng
- Department of Neurosurgery, Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou 450003, China
- Juha International Central Laboratory of Neurosurgery, Henan Provincial People’s Hospital, Zhengzhou 450003, China
| | - Shuang Wu
- Department of Neurosurgery, Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou 450003, China
- Juha International Central Laboratory of Neurosurgery, Henan Provincial People’s Hospital, Zhengzhou 450003, China
| | - Sensen Xu
- Department of Neurosurgery, Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou 450003, China
- Juha International Central Laboratory of Neurosurgery, Henan Provincial People’s Hospital, Zhengzhou 450003, China
| | - Yage Bu
- Department of Neurosurgery, Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou 450003, China
- Juha International Central Laboratory of Neurosurgery, Henan Provincial People’s Hospital, Zhengzhou 450003, China
| | - Yushuai Gao
- Department of Neurosurgery, Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou 450003, China
- Juha International Central Laboratory of Neurosurgery, Henan Provincial People’s Hospital, Zhengzhou 450003, China
| | - Meiyun Wang
- Department of Radiology, Henan Provincial People’s Hospital, Zhengzhou 450003, China
| | - Gang Liu
- Department of Center for Clinical Single Cell Biomedicine, Clinical Research Center, Department of Oncology, Henan Provincial People’s Hospital, Zhengzhou University People’s Hospital, Zhengzhou 450003, China
| | - Lingfei Kong
- Department of Pathology, Henan Provincial People’s Hospital, Zhengzhou 450003, China
| | - Tianxiao Li
- Department of Neurosurgery, Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou 450003, China
- Juha International Central Laboratory of Neurosurgery, Henan Provincial People’s Hospital, Zhengzhou 450003, China
| | - Ming Li
- Department of Neurosurgery, Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou 450003, China
- Juha International Central Laboratory of Neurosurgery, Henan Provincial People’s Hospital, Zhengzhou 450003, China
| | - Xingyao Bu
- Department of Neurosurgery, Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou 450003, China
- Juha International Central Laboratory of Neurosurgery, Henan Provincial People’s Hospital, Zhengzhou 450003, China
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14
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Guo XW, Lei RE, Zhou QN, Zhang G, Hu BL, Liang YX. Tumor microenvironment characterization in colorectal cancer to identify prognostic and immunotherapy genes signature. BMC Cancer 2023; 23:773. [PMID: 37596528 PMCID: PMC10436413 DOI: 10.1186/s12885-023-11277-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 08/08/2023] [Indexed: 08/20/2023] Open
Abstract
BACKGROUND The tumor microenvironment (TME) plays a crucial role in tumorigenesis, progression, and therapeutic response in many cancers. This study aimed to comprehensively investigate the role of TME in colorectal cancer (CRC) by generating a TMEscore based on gene expression. METHODS The TME patterns of CRC datasets were investigated, and the TMEscores were calculated. An unsupervised clustering method was used to divide samples into clusters. The associations between TMEscores and clinical features, prognosis, immune score, gene mutations, and immune checkpoint inhibitors were analyzed. A TME signature was constructed using the TMEscore-related genes. The results were validated using external and clinical cohorts. RESULTS The TME pattern landscape was for CRC was examined using 960 samples, and then the TMEscore pattern of CRC datasets was evaluated. Two TMEscore clusters were identified, and the high TMEscore cluster was associated with early-stage CRC and better prognosis in patients with CRC when compared with the low TMEscore clusters. The high TMEscore cluster indicated elevated tumor cell scores and tumor gene mutation burden, and decreased tumor purity, when compared with the low TMEscore cluster. Patients with high TMEscore were more likely to respond to immune checkpoint therapy than those with low TMEscore. A TME signature was constructed using the TMEscore-related genes superimposing the results of two machine learning methods (LASSO and XGBoost algorithms), and a TMEscore-related four-gene signature was established, which had a high predictive value for discriminating patients from different TMEscore clusters. The prognostic value of the TMEscore was validated in two independent cohorts, and the expression of TME signature genes was verified in four external cohorts and clinical samples. CONCLUSION Our study provides a comprehensive description of TME characteristics in CRC and demonstrates that the TMEscore is a reliable prognostic biomarker and predictive indicator for patients with CRC undergoing immunotherapy.
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Affiliation(s)
- Xian-Wen Guo
- Department of Gastroenterology, The People's Hospital of Guangxi Zhuang Autonomous Region, No.6 Tao-Yuan Road, Nanning, 530021, Guangxi, China
| | - Rong-E Lei
- Department of Gastroenterology, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Qing-Nan Zhou
- Department of Gastroenterology, The People's Hospital of Guangxi Zhuang Autonomous Region, No.6 Tao-Yuan Road, Nanning, 530021, Guangxi, China
| | - Guo Zhang
- Department of Gastroenterology, The People's Hospital of Guangxi Zhuang Autonomous Region, No.6 Tao-Yuan Road, Nanning, 530021, Guangxi, China
| | - Bang-Li Hu
- Department of Research, Guangxi Medical University Cancer Hospital, No.71 Hedi Road, Nanning, 530021, Guangxi, China.
| | - Yun-Xiao Liang
- Department of Gastroenterology, The People's Hospital of Guangxi Zhuang Autonomous Region, No.6 Tao-Yuan Road, Nanning, 530021, Guangxi, China.
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15
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Zhou H, Liu H, Li J, Wang J, Fu X, Li Y, Mao S, Du J. Postoperative circulating tumor DNA detection and CBLB mutations are prognostic biomarkers for gastric cancer. Genes Genomics 2023; 45:1037-1046. [PMID: 37306927 PMCID: PMC10349697 DOI: 10.1007/s13258-023-01412-7] [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: 12/14/2022] [Accepted: 05/30/2023] [Indexed: 06/13/2023]
Abstract
BACKGROUND Several studies have demonstrated that circulating tumor DNA (ctDNA) can be used to predict the postoperative recurrence of several cancers. However, there are few studies on the use of ctDNA as a prognosis tool for gastric cancer (GC) patients. OBJECTIVE This study aims to determine whether ctDNA could be used as a prognostic biomarker in GC patients through multigene-panel sequencing. METHODS Using next-generation sequencing (NGS) Multigene Panels, the mutational signatures associated with the prognosis of GC patients were identified. We calculated the survival probability with Kaplan-Meier and used the Log-rank test to compare survival curves between ctDNA-positive and ctDNA-negative groups. Potential application of radiology combined with tumor plasma biomarker analysis of ctDNA in GC patients was carried out. RESULTS Disease progression is more likely in ctDNA-positive patients as characterized clinically by a generally higher T stage and a poorer therapeutic response (P < 0.05). ctDNA-positive patients also had worse overall-survival (OS: P = 0.203) and progression-free survival (PFS: P = 0.037). The combined analysis of ctDNA, radiological, and serum biomarkers in four patients indicated that ctDNA monitoring can be a good complement to radiological and plasma tumor markers for GC patients. Kaplan-Meier analysis using a cohort of GC patients in the TCGA database showed that patients with CBLB mutations had shorter OS and PFS than wild-type patients (OS: P = 0.0036; PFS: P = 0.0027). CONCLUSIONS This study confirmed the utility and feasibility of ctDNA in the prognosis monitoring of gastric cancer.
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Affiliation(s)
- Hekai Zhou
- Research Center for Clinical and Translational Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital, and the 6th Affiliated Hospital of Shenzhen University Medical School, Guangdong, 518052, Shenzhen, China
| | - Houcong Liu
- Research Center for Clinical and Translational Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital, and the 6th Affiliated Hospital of Shenzhen University Medical School, Guangdong, 518052, Shenzhen, China
| | - Jun Li
- HaploX Biotechnology Co., Ltd., Shenzhen, 518057, Guangdong, China
| | - Jidong Wang
- Research Center for Clinical and Translational Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital, and the 6th Affiliated Hospital of Shenzhen University Medical School, Guangdong, 518052, Shenzhen, China
| | - Xiaohong Fu
- Department of Oncology, Huazhong University of Science and Technology Union Shenzhen Hospital, and the 6th Affiliated Hospital of Shenzhen University Medical School, Guangdong, 518052, Shenzhen, China
| | - Yingqiang Li
- HaploX Biotechnology Co., Ltd., Shenzhen, 518057, Guangdong, China
| | - Shaolong Mao
- HaploX Biotechnology Co., Ltd., Shenzhen, 518057, Guangdong, China
| | - Jihui Du
- Research Center for Clinical and Translational Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital, and the 6th Affiliated Hospital of Shenzhen University Medical School, Guangdong, 518052, Shenzhen, China.
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16
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Liu G, Bu C, Guo G, Zhang Z, Sheng Z, Deng K, Wu S, Xu S, Bu Y, Gao Y, Wang M, Liu G, Kong L, Li T, Li M, Bu X. Genomic alterations of oligodendrogliomas at distant recurrence. Cancer Med 2023; 12:17171-17183. [PMID: 37533228 PMCID: PMC10501240 DOI: 10.1002/cam4.6327] [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: 01/18/2023] [Revised: 06/19/2023] [Accepted: 06/28/2023] [Indexed: 08/04/2023] Open
Abstract
BACKGROUND Oligodendroglioma is known for its relatively better prognosis and responsiveness to radiotherapy and chemotherapy. However, little is known about the evolution of genetic changes as oligodendroglioma progresses. METHODS In this study, we evaluated gene evolution invivo during tumor progression based on deep whole-genome sequencing data (ctDNA). We analyzed longitudinal genomic data from six patients during tumor evolution, of which five patients developed distant recurrence. RESULTS Whole-exome sequencing demonstrated that the rate of shared mutations between the primary and recurrent samples was relatively low. In two cases, even well-known major driver mutations in CIC and FUBP1 that were detected in primary tumors were not detected in the relapse samples. Among these cases, two patients had a conversion from the IDH mutation in the originating state to the IDH1 wild state during the process of gene evolution under chemotherapy treatment, indicating that the cell phenotype and genetic characteristics of oligodendroglioma may change during tumor evolution. Two patients received long-term temozolomide (TMZ) treatment before the operation, and we found that recurrence tumors harbored mutations in the PI3K/AKT and Sonic hedgehog (SHh) signaling pathways. Hypermutation occurred with mutations in MMR genes in one patient, contributing to the rapid progression of the tumor. CONCLUSION Oligodendroglioma displayed great spatial and temporal heterogeneity during tumor evolution. The PI3K/AKT and SHh signaling pathways may play an important role in promoting treatment resistance and distant relapse during oligodendroglioma evolution. In addition, there was a tendency to increase the degree of tumor malignancy during evolution. Distant recurrence may be a later event duringoligodendroglioma progression. CLINICALTRIALS gov, Identifier: NCT05512325.
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Affiliation(s)
- Guanzheng Liu
- Department of NeurosurgeryZhengzhou University People's Hospital, Henan Provincial People's HospitalZhengzhouChina
- Juha International Central Laboratory of NeurosurgeryHenan Provincial People's HospitalZhengzhouChina
| | - Chaojie Bu
- Department of NeurosurgeryZhengzhou University People's Hospital, Henan Provincial People's HospitalZhengzhouChina
- Juha International Central Laboratory of NeurosurgeryHenan Provincial People's HospitalZhengzhouChina
| | - Guangzhong Guo
- Department of NeurosurgeryZhengzhou University People's Hospital, Henan Provincial People's HospitalZhengzhouChina
- Juha International Central Laboratory of NeurosurgeryHenan Provincial People's HospitalZhengzhouChina
| | - Zhiyue Zhang
- Department of NeurosurgeryZhengzhou University People's Hospital, Henan Provincial People's HospitalZhengzhouChina
- Juha International Central Laboratory of NeurosurgeryHenan Provincial People's HospitalZhengzhouChina
| | - Zhiyuan Sheng
- Department of NeurosurgeryZhengzhou University People's Hospital, Henan Provincial People's HospitalZhengzhouChina
- Juha International Central Laboratory of NeurosurgeryHenan Provincial People's HospitalZhengzhouChina
| | - Kaiyuan Deng
- Department of NeurosurgeryZhengzhou University People's Hospital, Henan Provincial People's HospitalZhengzhouChina
- Juha International Central Laboratory of NeurosurgeryHenan Provincial People's HospitalZhengzhouChina
| | - Shuang Wu
- Department of NeurosurgeryZhengzhou University People's Hospital, Henan Provincial People's HospitalZhengzhouChina
- Juha International Central Laboratory of NeurosurgeryHenan Provincial People's HospitalZhengzhouChina
| | - Sensen Xu
- Department of NeurosurgeryZhengzhou University People's Hospital, Henan Provincial People's HospitalZhengzhouChina
- Juha International Central Laboratory of NeurosurgeryHenan Provincial People's HospitalZhengzhouChina
| | - Yage Bu
- Department of NeurosurgeryZhengzhou University People's Hospital, Henan Provincial People's HospitalZhengzhouChina
- Juha International Central Laboratory of NeurosurgeryHenan Provincial People's HospitalZhengzhouChina
| | - Yushuai Gao
- Department of NeurosurgeryZhengzhou University People's Hospital, Henan Provincial People's HospitalZhengzhouChina
- Juha International Central Laboratory of NeurosurgeryHenan Provincial People's HospitalZhengzhouChina
| | - Meiyun Wang
- Department of RadiologyHenan Provincial People's HospitalZhengzhouChina
| | - Gang Liu
- Department of Center for Clinical Single Cell Biomedicine, Department of Oncology, Clinical Research Center, Henan Provincial People's HospitalZhengzhou University People's HospitalZhengzhouChina
| | - Lingfei Kong
- Department of PathologyHenan Provincial People's HospitalZhengzhouChina
| | - Tianxiao Li
- Department of NeurosurgeryZhengzhou University People's Hospital, Henan Provincial People's HospitalZhengzhouChina
- Juha International Central Laboratory of NeurosurgeryHenan Provincial People's HospitalZhengzhouChina
| | - Ming Li
- Department of NeurosurgeryZhengzhou University People's Hospital, Henan Provincial People's HospitalZhengzhouChina
- Juha International Central Laboratory of NeurosurgeryHenan Provincial People's HospitalZhengzhouChina
| | - Xingyao Bu
- Department of NeurosurgeryZhengzhou University People's Hospital, Henan Provincial People's HospitalZhengzhouChina
- Juha International Central Laboratory of NeurosurgeryHenan Provincial People's HospitalZhengzhouChina
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17
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Jiang Z, Ju Y, Ali A, Chung PED, Skowron P, Wang DY, Shrestha M, Li H, Liu JC, Vorobieva I, Ghanbari-Azarnier R, Mwewa E, Koritzinsky M, Ben-David Y, Woodgett JR, Perou CM, Dupuy A, Bader GD, Egan SE, Taylor MD, Zacksenhaus E. Distinct shared and compartment-enriched oncogenic networks drive primary versus metastatic breast cancer. Nat Commun 2023; 14:4313. [PMID: 37463901 PMCID: PMC10354065 DOI: 10.1038/s41467-023-39935-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 06/16/2023] [Indexed: 07/20/2023] Open
Abstract
Metastatic breast-cancer is a major cause of death in women worldwide, yet the relationship between oncogenic drivers that promote metastatic versus primary cancer is still contentious. To elucidate this relationship in treatment-naive animals, we hereby describe mammary-specific transposon-mutagenesis screens in female mice together with loss-of-function Rb, which is frequently inactivated in breast-cancer. We report gene-centric common insertion-sites (gCIS) that are enriched in primary-tumors, in metastases or shared by both compartments. Shared-gCIS comprise a major MET-RAS network, whereas metastasis-gCIS form three additional hubs: Rho-signaling, Ubiquitination and RNA-processing. Pathway analysis of four clinical cohorts with paired primary-tumors and metastases reveals similar organization in human breast-cancer with subtype-specific shared-drivers (e.g. RB1-loss, TP53-loss, high MET, RAS, ER), primary-enriched (EGFR, TGFβ and STAT3) and metastasis-enriched (RHO, PI3K) oncogenic signaling. Inhibitors of RB1-deficiency or MET plus RHO-signaling cooperate to block cell migration and drive tumor cell-death. Thus, targeting shared- and metastasis- but not primary-enriched derivers offers a rational avenue to prevent metastatic breast-cancer.
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Affiliation(s)
- Zhe Jiang
- Toronto General Research Institute - University Health Network, 101 College Street, Max Bell Research Centre, suite 5R406, Toronto, ON, M5G 1L7, Canada
| | - YoungJun Ju
- Toronto General Research Institute - University Health Network, 101 College Street, Max Bell Research Centre, suite 5R406, Toronto, ON, M5G 1L7, Canada
| | - Amjad Ali
- Toronto General Research Institute - University Health Network, 101 College Street, Max Bell Research Centre, suite 5R406, Toronto, ON, M5G 1L7, Canada
| | - Philip E D Chung
- Toronto General Research Institute - University Health Network, 101 College Street, Max Bell Research Centre, suite 5R406, Toronto, ON, M5G 1L7, Canada
- Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Patryk Skowron
- Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada
- Program in Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Dong-Yu Wang
- Toronto General Research Institute - University Health Network, 101 College Street, Max Bell Research Centre, suite 5R406, Toronto, ON, M5G 1L7, Canada
| | - Mariusz Shrestha
- Toronto General Research Institute - University Health Network, 101 College Street, Max Bell Research Centre, suite 5R406, Toronto, ON, M5G 1L7, Canada
- Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Huiqin Li
- Toronto General Research Institute - University Health Network, 101 College Street, Max Bell Research Centre, suite 5R406, Toronto, ON, M5G 1L7, Canada
| | - Jeff C Liu
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Ioulia Vorobieva
- Toronto General Research Institute - University Health Network, 101 College Street, Max Bell Research Centre, suite 5R406, Toronto, ON, M5G 1L7, Canada
- Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Ronak Ghanbari-Azarnier
- Toronto General Research Institute - University Health Network, 101 College Street, Max Bell Research Centre, suite 5R406, Toronto, ON, M5G 1L7, Canada
- Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Ethel Mwewa
- Toronto General Research Institute - University Health Network, 101 College Street, Max Bell Research Centre, suite 5R406, Toronto, ON, M5G 1L7, Canada
| | | | - Yaacov Ben-David
- The Key laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, Guizhou, 550014, China
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550025, China
| | - James R Woodgett
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON, Canada
| | - Charles M Perou
- Lineberger Comprehensive Cancer Center, Departments of Genetics and Pathology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Adam Dupuy
- Department of Pathology, Carver College of Medicine, The University of Iowa, Iowa City, Iowa, 52242, USA
| | - Gary D Bader
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Sean E Egan
- Program in Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Michael D Taylor
- Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada
- Program in Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Eldad Zacksenhaus
- Toronto General Research Institute - University Health Network, 101 College Street, Max Bell Research Centre, suite 5R406, Toronto, ON, M5G 1L7, Canada.
- Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada.
- Department of Medicine, University of Toronto, Toronto, ON, Canada.
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18
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Liu QL, Zhou H, Zhou ZG, Chen HN. Colorectal cancer liver metastasis: genomic evolution and crosstalk with the liver microenvironment. Cancer Metastasis Rev 2023; 42:575-587. [PMID: 37061644 DOI: 10.1007/s10555-023-10107-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/10/2023] [Indexed: 04/17/2023]
Abstract
Colorectal cancer (CRC) patients frequently develop liver metastases, which are the major cause of cancer-related mortality. The molecular basis and management of colorectal liver metastases (CRLMs) remain a challenging clinical issue. Recent genomic evidence has demonstrated the liver tropism of CRC and the presence of a stricter evolutionary bottleneck in the liver as a target organ compared to lymph nodes. This bottleneck challenging CRC cells in the liver is organ-specific and requires adaptation not only at the genetic level, but also at the phenotypic level to crosstalk with the hepatic microenvironment. Here, we highlight the emerging evidence on the clonal evolution of CRLM and review recent insights into the molecular mechanisms orchestrating the bidirectional interactions between metastatic CRC cells and the unique liver microenvironment.
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Affiliation(s)
- Qiu-Luo Liu
- Department of General Surgery, Colorectal Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
| | - Huijie Zhou
- Department of Oncology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Zong-Guang Zhou
- Department of General Surgery, Colorectal Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
| | - Hai-Ning Chen
- Department of General Surgery, Colorectal Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China.
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19
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Yang G, Yu XR, Weisenberger DJ, Lu T, Liang G. A Multi-Omics Overview of Colorectal Cancer to Address Mechanisms of Disease, Metastasis, Patient Disparities and Outcomes. Cancers (Basel) 2023; 15:cancers15112934. [PMID: 37296894 DOI: 10.3390/cancers15112934] [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: 04/09/2023] [Revised: 05/16/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
Human colorectal cancer (CRC) is one of the most common malignancies in men and women across the globe, albeit CRC incidence and mortality shows a substantial racial and ethnic disparity, with the highest burden in African American patients. Even with effective screening tools such as colonoscopy and diagnostic detection assays, CRC remains a substantial health burden. In addition, primary tumors located in the proximal (right) or distal (left) sides of the colorectum have been shown to be unique tumor types that require unique treatment schema. Distal metastases in the liver and other organ systems are the major causes of mortality in CRC patients. Characterizing genomic, epigenomic, transcriptomic and proteomic (multi-omics) alterations has led to a better understanding of primary tumor biology, resulting in targeted therapeutic advancements. In this regard, molecular-based CRC subgroups have been developed that show correlations with patient outcomes. Molecular characterization of CRC metastases has highlighted similarities and differences between metastases and primary tumors; however, our understanding as to how to improve patient outcomes based on metastasis biology is lagging and remains a major obstacle to improving CRC patient outcomes. In this review, we will summarize the multi-omics features of primary CRC tumors and their metastases across racial and ethnic groups, the differences in proximal and distal tumor biology, molecular-based CRC subgroups, treatment strategies and challenges for improving patient outcomes.
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Affiliation(s)
- Guang Yang
- School of Sciences, China Pharmaceutical University, Nanjing 211121, China
- China Grand Enterprises, Beijing 100101, China
| | - Xi Richard Yu
- China Grand Enterprises, Beijing 100101, China
- Huadong Medicine Co., Ltd., Hangzhou 310011, China
| | - Daniel J Weisenberger
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- USC Institute of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Tao Lu
- School of Sciences, China Pharmaceutical University, Nanjing 211121, China
- State Key Laboratory of Natural Sciences, China Pharmaceutical University, Nanjing 211121, China
| | - Gangning Liang
- USC Institute of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
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20
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Hlaváč V, Červenková L, Šůsová S, Holý P, Liška V, Vyčítal O, Šorejs O, Fiala O, Daum O, Souček P. Exome Sequencing of Paired Colorectal Carcinomas and Synchronous Liver Metastases for Prognosis and Therapy Prediction. JCO Precis Oncol 2023; 7:e2200557. [PMID: 37141551 DOI: 10.1200/po.22.00557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023] Open
Abstract
PURPOSE Analysis of somatic variant profiles in retrospectively collected pairs of primary tumors and synchronous liver metastases from surgically treated patients with colorectal carcinomas. Mutational profiles were compared between groups of patients stratified by response to chemotherapy and survival. PATIENTS AND METHODS The study used whole-exome sequencing of tumor sample pairs from 20 patients diagnosed and treated at a single center. The Cancer Genome Atlas COAD-READ data set (n = 380) was used for validation in silico, where possible. RESULTS The most frequently altered oncodrivers were APC (55% in primaries and 60% in metastases), TP53 (50/45), TRIP11 (30/5), FAT4 (20/25), and KRAS (15/25). Harboring variants with a high or moderate predicted functional effect in KRAS in primary tumors was significantly associated with poor relapse-free survival in both our sample set and the validation data set. We found a number of additional prognostic associations, including mutational load, alterations in individual genes, oncodriver pathways, and single base substitution (SBS) signatures in primary tissues, which were not confirmed by validation. Altered ATM, DNAH11, and MUC5AC, or a higher share of SBS24 signature in metastases seemed to represent poor prognostic factors, but because of a lack of suitable validation data sets, these results must be treated with extreme caution. No gene or profile was significantly associated with response to chemotherapy. CONCLUSION Taken together, we report subtle differences in exome mutational profiles between paired primary tumors and synchronous liver metastases and a distinct prognostic relevance of KRAS in primary tumors. Although the general scarcity of primary tumor-synchronous metastasis sample pairs with high-quality clinical data makes robust validation difficult, this study provides potentially valuable data for utilization in precision oncology and could serve as a springboard for larger studies.
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Affiliation(s)
- Viktor Hlaváč
- Laboratory of Pharmacogenomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Lenka Červenková
- Laboratory of Translational Cancer Genomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
- Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Simona Šůsová
- Laboratory of Pharmacogenomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Petr Holý
- Laboratory of Pharmacogenomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
- Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Václav Liška
- Laboratory of Translational Cancer Genomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
- Department of Surgery, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
| | - Ondřej Vyčítal
- Laboratory of Translational Cancer Genomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
- Department of Surgery, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
| | - Ondřej Šorejs
- Laboratory of Translational Cancer Genomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
- Department of Oncology and Radiotherapeutics, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
| | - Ondřej Fiala
- Laboratory of Translational Cancer Genomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
- Department of Oncology and Radiotherapeutics, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
| | - Ondřej Daum
- Department of Pathology, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
| | - Pavel Souček
- Laboratory of Pharmacogenomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
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21
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Park J, Paramasivam N. PyOncoPrint: a python package for plotting OncoPrints. Genomics Inform 2023; 21:e14. [PMID: 37037472 PMCID: PMC10085746 DOI: 10.5808/gi.22079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 03/10/2023] [Indexed: 04/03/2023] Open
Abstract
OncoPrint, the plot to visualize an overview of genetic variants in sequencing data, has been widely used in the field of cancer genomics. However, still, there have been no Python libraries capable to generate OncoPrint yet, a big hassle to plot OncoPrints within Python-based genetic variants analysis pipelines. This paper introduces a new Python package PyOncoPrint, which can be easily used to plot OncoPrints in Python. The package is based on the existing widely used scientific plotting library Matplotlib, the resulting plots are easy to be adjusted for various needs.
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Affiliation(s)
- Jeongbin Park
- School of Biomedical Convergence Engineering, Pusan National University, Busan 50612, Korea
- *Corresponding author E-mail:
| | - Nagarajan Paramasivam
- Computational Oncology, Molecular Precision Oncology Program, National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
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22
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Abbes S, Baldi S, Sellami H, Amedei A, Keskes L. Molecular methods for colorectal cancer screening: Progress with next-generation sequencing evolution. World J Gastrointest Oncol 2023; 15:425-442. [PMID: 37009313 PMCID: PMC10052664 DOI: 10.4251/wjgo.v15.i3.425] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/02/2023] [Accepted: 02/15/2023] [Indexed: 03/14/2023] Open
Abstract
Currently, colorectal cancer (CRC) represents the third most common malignancy and the second most deadly cancer worldwide, with a higher incidence in developed countries. Like other solid tumors, CRC is a heterogeneous genomic disease in which various alterations, such as point mutations, genomic rearrangements, gene fusions or chromosomal copy number alterations, can contribute to the disease development. However, because of its orderly natural history, easily accessible onset location and high lifetime incidence, CRC is ideally suited for preventive intervention, but the many screening efforts of the last decades have been compromised by performance limitations and low penetrance of the standard screening tools. The advent of next-generation sequencing (NGS) has both facilitated the identification of previously unrecognized CRC features such as its relationship with gut microbial pathogens and revolutionized the speed and throughput of cataloguing CRC-related genomic alterations. Hence, in this review, we summarized the several diagnostic tools used for CRC screening in the past and the present, focusing on recent NGS approaches and their revolutionary role in the identification of novel genomic CRC characteristics, the advancement of understanding the CRC carcinogenesis and the screening of clinically actionable targets for personalized medicine.
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Affiliation(s)
- Salma Abbes
- Laboratory of Parasitic and Fungal Molecular Biology, University of Sfax, Sfax 3029, Tunisia
| | - Simone Baldi
- Department of Experimental and Clinical Medicine, University of Florence, Florence 50134, Italy
| | - Hayet Sellami
- Drosophila Research Unit-Parasitology and Mycologie Laboratory, University of Sfax, Sfax 3029, Tunisia
| | - Amedeo Amedei
- Department of Experimental and Clinical Medicine, University of Florence, Florence 50134, Italy
- SOD of Interdisciplinary Internal Medicine, Careggi University Hospital, Florence 50134, Italy
| | - Leila Keskes
- Laboratory of Human Molecular Genetic, University of Sfax, Sfax 3029, Tunisia
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23
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Wei M, Su J, Zhang J, Liu S, Ma J, Meng XP. Construction of a DDR-related signature for predicting of prognosis in metastatic colorectal carcinoma. Front Oncol 2023; 13:1043160. [PMID: 36816926 PMCID: PMC9931195 DOI: 10.3389/fonc.2023.1043160] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 01/20/2023] [Indexed: 02/04/2023] Open
Abstract
Background Colorectal cancer (CRC) is the third most prevalent malignancy and the one of most lethal cancer. Metastatic CRC (mCRC) is the third most common cause of cancer deaths worldwide. DNA damage response (DDR) genes are closely associated with the tumorigenesis and development of CRC. In this study, we aimed to construct a DDR-related gene signature for predicting the prognosis of mCRC patients. Methods The gene expression and corresponding clinical information data of CRC/mCRC patients were obtained from Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases. A prognostic model was obtained and termed DDRScore by the multivariate Cox proportional hazards regression in the patients with mCRC. The Kaplan-Meier (K-M) and Receiver Operating Characteristic (ROC) curves were employed to validate the predictive ability of the prognostic model. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were performed for patients between the high-DDRscore and low-DDRscore groups. Results We constructed a prognostic model consisting of four DDR-related genes (EME2, MSH4, MLH3, and SPO11). Survival analysis showed that patients in the high-DDRscore group had a significantly worse OS than those in the low-DDRscore group. The area under the curve (AUC) value of the ROC curve of the predictive model is 0.763 in the training cohort GSE72970, 0.659 in the stage III/IV colorectal cancer (CRC) patients from The Cancer Genome Atlas (TCGA) data portal, and 0.639 in another validation cohort GSE39582, respectively. GSEA functional analysis revealed that the most significantly enriched pathways focused on nucleotide excision repair, base excision repair, homologous recombination, cytokine receptor interaction, chemokine signal pathway, cell adhesion molecules cams, ECM-receptor interaction, and focal adhesion. Conclusion The DDRscore was identified as an independent prognostic and therapy response predictor, and the DDR-related genes may be potential diagnosis or prognosis biomarkers for mCRC patients.
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Affiliation(s)
- Maohua Wei
- Department of General Surgery, Dalian Medical University, Dalian, China
| | - Junyan Su
- Department of Scientific Research Projects, ChosenMed Technology Co. Ltd., Beijing, China
| | - Jiali Zhang
- Department of Scientific Research Projects, ChosenMed Technology Co. Ltd., Beijing, China
| | - Siyao Liu
- Department of Scientific Research Projects, ChosenMed Technology Co. Ltd., Beijing, China
| | - Jia Ma
- Department of Gastroenterology, The Fourth Affiliated Hospital of China Medical University, Shenyang, China,*Correspondence: Xiang peng Meng, ; Jia Ma,
| | - Xiang peng Meng
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China,*Correspondence: Xiang peng Meng, ; Jia Ma,
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24
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Vergara IA, Aivazian K, Carlino MS, Guminski AD, Maher NG, Shannon KF, Ch'ng S, Saw RPM, Long GV, Wilmott JS, Scolyer RA. Genomic Profiling of Metastatic Basal cell Carcinoma Reveals Candidate Drivers of Disease and Therapeutic Targets. Mod Pathol 2023; 36:100099. [PMID: 36788083 DOI: 10.1016/j.modpat.2023.100099] [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: 10/26/2022] [Revised: 11/30/2022] [Accepted: 12/26/2022] [Indexed: 01/11/2023]
Abstract
Basal cell carcinomas (BCCs) are human beings' most common malignant tumors. Most are easily managed by surgery or topical therapies, and metastasis is rare. Although BCCs can become locally advanced, metastatic BCCs are very uncommon and may be biologically distinct. We assessed the clinicopathologic characteristics of 17 patients with metastatic BCC and pursued whole-exome sequencing of tumor and germline DNA from 8 patients. Genomic profiling revealed aberrant activation of Hedgehog signaling and alterations in GLI transcriptional regulators and Notch and Hippo signaling. Matched local recurrences of primary BCCs and metastases from 3 patients provided evidence of a clonal origin in all cases. Mutations associated with YAP inhibition were found exclusively in 2 hematogenously-spread lung metastases, and metastatic BCCs were enriched for mutations in the YAP/TAZ-binding domain of TEAD genes. Accordingly, YAP/TAZ nuclear localization was associated with metastatic types and Hippo mutations, suggesting an enhanced oncogenic role in hematogenously-spread metastases. Mutations in RET, HGF, and phosphatidylinositol 3‑kinase (PI3K)/protein kinase B (AKT) signaling were enriched compared with a cohort of low clinical-risk BCCs. Our results implicate Hippo and PI3K/AKT dysregulation in metastatic progression of BCCs, making these potential therapeutic targets in metastatic disease. The common clonal origin of matched recurrent and metastatic BCCs suggests that molecular profiling can assist in determining the nature/origin of poorly differentiated metastatic tumors of uncertain type. Genes and pathways enriched for mutations in this cohort are candidate drivers of metastasis and can be used to identify patients at high risk of metastasis who may benefit from aggressive local treatment and careful clinical follow-up.
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Affiliation(s)
- Ismael A Vergara
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia; Charles Perkin Centre, The University of Sydney, Sydney, NSW, Australia
| | - Karina Aivazian
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia; Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, NSW, Australia
| | - Matteo S Carlino
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia; Department of Medicine, Blacktown Hospital, Blacktown, New South Wales, Australia; Department of Medicine, Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney, New South Wales, Australia
| | - Alexander D Guminski
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia; Royal North Shore and Mater Hospitals, Sydney, NSW, Australia
| | - Nigel G Maher
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia; Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, NSW, Australia
| | - Kerwin F Shannon
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia; Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Sydney Ch'ng
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia; Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Robyn P M Saw
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia; Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Georgina V Long
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia; Charles Perkin Centre, The University of Sydney, Sydney, NSW, Australia; Royal North Shore and Mater Hospitals, Sydney, NSW, Australia
| | - James S Wilmott
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia; Charles Perkin Centre, The University of Sydney, Sydney, NSW, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia; Charles Perkin Centre, The University of Sydney, Sydney, NSW, Australia; Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, NSW, Australia.
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25
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Fyta M. Functionalized electrodes embedded in nanopores: read-out enhancement? Chem Asian J 2023; 18:e202200916. [PMID: 36372991 PMCID: PMC10107472 DOI: 10.1002/asia.202200916] [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: 09/02/2022] [Revised: 11/12/2022] [Accepted: 11/12/2022] [Indexed: 11/16/2022]
Abstract
In this review, functionalized nanogaps embedded in nanopores are discussed in view of their high biosensitivity in detecting biomolecules, their length, type, and sequence. Specific focus is given on nanoelectrodes functionalized with tiny nanometer-sized diamond-like particles offering vast functionalization possibilities for gold junction electrodes. This choice of the functionalization, in turn, offers nucleotide-specific binding possibilities improving the detection signals arising from such functionalized electrodes potentially embedded in a nanopore. The review sheds light onto the use and enhancement of the tunnelling recognition in functionalized nanogaps towards sensing DNA nucleotides and mutation detection, providing important input for a practical realization.
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Affiliation(s)
- Maria Fyta
- Computational Biotechnology, RWTH-Aachen University, Worringerweg 3, 52072, Aachen, Germany
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26
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Shen M, Kang Y. Cancer fitness genes: emerging therapeutic targets for metastasis. Trends Cancer 2023; 9:69-82. [PMID: 36184492 DOI: 10.1016/j.trecan.2022.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/25/2022] [Accepted: 08/30/2022] [Indexed: 12/31/2022]
Abstract
Development of cancer therapeutics has traditionally focused on targeting driver oncogenes. Such an approach is limited by toxicity to normal tissues and treatment resistance. A class of 'cancer fitness genes' with crucial roles in metastasis have been identified. Elevated or altered activities of these genes do not directly cause cancer; instead, they relieve the stresses that tumor cells encounter and help them adapt to a changing microenvironment, thus facilitating tumor progression and metastasis. Importantly, as normal cells do not experience high levels of stress under physiological conditions, targeting cancer fitness genes is less likely to cause toxicity to noncancerous tissues. Here, we summarize the key features and function of cancer fitness genes and discuss their therapeutic potential.
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Affiliation(s)
- Minhong Shen
- Department of Pharmacology, Wayne State University School of Medicine, Michigan, MI, USA; Department of Oncology, Wayne State University School of Medicine and Tumor Biology and Microenvironment Research Program, Barbara Ann Karmanos Cancer Institute, Michigan, MI, USA.
| | - Yibin Kang
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA; Ludwig Institute for Cancer Research Princeton Branch, Princeton, NJ, USA.
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27
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Regulation of Metastatic Tumor Dormancy and Emerging Opportunities for Therapeutic Intervention. Int J Mol Sci 2022; 23:ijms232213931. [PMID: 36430404 PMCID: PMC9698240 DOI: 10.3390/ijms232213931] [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: 09/30/2022] [Revised: 10/26/2022] [Accepted: 11/02/2022] [Indexed: 11/16/2022] Open
Abstract
Cancer recurrence and metastasis, following successful treatment, constitutes a critical threat in clinical oncology and are the leading causes of death amongst cancer patients. This phenomenon is largely attributed to metastatic tumor dormancy, a rate-limiting stage during cancer progression, in which disseminated cancer cells remain in a viable, yet not proliferating state for a prolonged period. Dormant cancer cells are characterized by their entry into cell cycle arrest and survival in a quiescence state to adapt to their new microenvironment through the acquisition of mutations and epigenetic modifications, rendering them resistant to anti-cancer treatment and immune surveillance. Under favorable conditions, disseminated dormant tumor cells 're-awake', resume their proliferation and thus colonize distant sites. Due to their rarity, detection of dormant cells using current diagnostic tools is challenging and, thus, therapeutic targets are hard to be identified. Therefore, unraveling the underlying mechanisms required for keeping disseminating tumor cells dormant, along with signals that stimulate their "re-awakening" are crucial for the discovery of novel pharmacological treatments. In this review, we shed light into the main mechanisms that control dormancy induction and escape as well as emerging therapeutic strategies for the eradication of metastatic dormant cells, including dormancy maintenance, direct targeting of dormant cells and re-awakening dormant cells. Studies on the ability of the metastatic cancer cells to cease proliferation and survive in a quiescent state before re-initiating proliferation and colonization years after successful treatment, will pave the way toward developing innovative therapeutic strategies against dormancy-mediated metastatic outgrowth.
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Mo S, Tang P, Luo W, Zhang L, Li Y, Hu X, Ma X, Chen Y, Bao Y, He X, Fu G, Xu X, Rao X, Li X, Guan R, Chen S, Deng Y, Lv T, Mu P, Zheng Q, Wang S, Liu F, Li Y, Sheng W, Huang D, Hu C, Gao J, Zhang Z, Cai S, Clevers H, Peng J, Hua G. Patient-Derived Organoids from Colorectal Cancer with Paired Liver Metastasis Reveal Tumor Heterogeneity and Predict Response to Chemotherapy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2204097. [PMID: 36058001 PMCID: PMC9631073 DOI: 10.1002/advs.202204097] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/18/2022] [Indexed: 05/19/2023]
Abstract
There is no effective method to predict chemotherapy response and postoperative prognosis of colorectal cancer liver metastasis (CRLM) patients. Patient-derived organoid (PDO) has become an important preclinical model. Herein, a living biobank with 50 CRLM organoids derived from primary tumors and paired liver metastatic lesions is successfully constructed. CRLM PDOs from the multiomics levels (histopathology, genome, transcriptome and single-cell sequencing) are comprehensively analyzed and confirmed that this organoid platform for CRLM could capture intra- and interpatient heterogeneity. The chemosensitivity data in vitro reveal the potential value of clinical application for PDOs to predict chemotherapy response (FOLFOX or FOLFIRI) and clinical prognosis of CRLM patients. Taken together, CRLM PDOs can be utilized to deliver a potential application for personalized medicine.
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29
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Chang H, Jin L, Xie P, Zhang B, Yu M, Li H, Liu S, Yan J, Zhou B, Li X, Xu Y, Xiao Y, Ye Q, Guo L. Complement C5 is a novel biomarker for liver metastasis of colorectal cancer. J Gastrointest Oncol 2022; 13:2351-2365. [PMID: 36388659 PMCID: PMC9660033 DOI: 10.21037/jgo-22-829] [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: 07/25/2022] [Accepted: 09/30/2022] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the most prominent malignant diseases, with a high incidence and a dismal prognosis. Metastasis to the liver is the leading cause of death in CRC patients. This study aimed to identify accurate metastatic biomarkers of CRC and investigate the potential molecular mechanisms of liver metastasis of colorectal cancer (LMCRC). METHODS Three independent datasets were screened and downloaded from the Gene Expression Omnibus (GEO) database. The GEO2R tool was used to identify differentially expressed genes (DEGs) in CRC tissues and liver metastases. Next, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted using the Database for Annotation, Visualization, and Integrated Discovery (DAVID). Furthermore, the protein-protein interactions (PPIs) of the DEGs were analyzed using the Search Tool for the Retrieval of Interacting Genes (STRING) database, Cytoscape, and Molecular Complex Detection (MCODE). Next, the expression levels and Kaplan-Meier survival analysis of the target gene between normal colon and CRC tissues were performed by UALCAN. The expression of the target gene in tissues and cell lines was verified by quantitative reverse transcription-polymerase chain reaction (qRT-PCR), western blot, and immunohistochemistry (IHC) assay. The impact of the target gene on the proliferation, invasion, and migration ability of COAD cells was explored in vitro. RESULTS A total of 92 common DEGs were found in the three independent datasets. GO/KEGG enrichment analysis showed that the DEGs were mainly involved in 14 different pathways. The protein-protein interaction (PPI) network revealed that complement 5 (C5), the upstream gene of C8A in the complement system, was associated with C8 and other key hub genes. Meanwhile, the online UALCAN resource showed that C5 was up-regulated and facilitated malignant progression in COAD samples. Next, we confirmed that C5 remarkably increased and promoted cell proliferation, migration, and invasion in CRC cell lines, SW620 and SW480. The IHC assay showed C5 was also highly expressed in a majority of LMCRC tissues compared with paired CRC tissues. CONCLUSIONS The findings of our integrated bioinformatics study suggest that complement C5 might serve as a potential therapeutic target in patients with CRC.
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Affiliation(s)
- Hulin Chang
- Department of Hepatobiliary Surgery, Shaanxi Provincial People’s Hospital, Xi’an, China
| | - Lei Jin
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Peiyi Xie
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Bo Zhang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Mincheng Yu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Hui Li
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China;,Shanghai Medical College and Zhongshan Hospital Immunotherapy Technology Transfer Center, Shanghai, China
| | - Shuang Liu
- Department of Neurosurgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jiuliang Yan
- Department of Pancreatic Surgery, Shanghai General Hospital and Shanghai Key Laboratory of Pancreatic Disease, Institute of Pancreatic Disease, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Binghai Zhou
- Department of Hepatobiliary and Pancreatic Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiaoqiang Li
- Department of Thoracic Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Yongfeng Xu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Yongsheng Xiao
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Qinghai Ye
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Lei Guo
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
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30
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Ding RF, Zhang Y, Wu LY, You P, Fang ZX, Li ZY, Zhang ZY, Ji ZL. Discovering Innate Driver Variants for Risk Assessment of Early Colorectal Cancer Metastasis. Front Oncol 2022; 12:898117. [PMID: 35795065 PMCID: PMC9252167 DOI: 10.3389/fonc.2022.898117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/16/2022] [Indexed: 11/23/2022] Open
Abstract
Metastasis is the main fatal cause of colorectal cancer (CRC). Although enormous efforts have been made to date to identify biomarkers associated with metastasis, there is still a huge gap to translate these efforts into effective clinical applications due to the poor consistency of biomarkers in dealing with the genetic heterogeneity of CRCs. In this study, a small cohort of eight CRC patients was recruited, from whom we collected cancer, paracancer, and normal tissues simultaneously and performed whole-exome sequencing. Given the exomes, a novel statistical parameter LIP was introduced to quantitatively measure the local invasion power for every somatic and germline mutation, whereby we affirmed that the innate germline mutations instead of somatic mutations might serve as the major driving force in promoting local invasion. Furthermore, via bioinformatic analyses of big data derived from the public zone, we identified ten potential driver variants that likely urged the local invasion of tumor cells into nearby tissue. Of them, six corresponding genes were new to CRC metastasis. In addition, a metastasis resister variant was also identified. Based on these eleven variants, we constructed a logistic regression model for rapid risk assessment of early metastasis, which was also deployed as an online server, AmetaRisk (http://www.bio-add.org/AmetaRisk). In summary, we made a valuable attempt in this study to exome-wide explore the genetic driving force to local invasion, which provides new insights into the mechanistic understanding of metastasis. Furthermore, the risk assessment model can assist in prioritizing therapeutic regimens in clinics and discovering new drug targets, and thus substantially increase the survival rate of CRC patients.
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Affiliation(s)
- Ruo-Fan Ding
- State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yun Zhang
- State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, China
| | - Lv-Ying Wu
- State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, China
| | - Pan You
- Department of Clinical Laboratory, Xiamen Xianyue Hospital, Xiamen, China
- Department of Clinical Laboratory, Zhongshan Hospital , affiliated to Xiamen University, Xiamen, China
- *Correspondence: Zhi-Liang Ji, ; Pan You,
| | - Zan-Xi Fang
- Department of Clinical Laboratory, Zhongshan Hospital , affiliated to Xiamen University, Xiamen, China
| | - Zhi-Yuan Li
- Department of Clinical Laboratory, Zhongshan Hospital , affiliated to Xiamen University, Xiamen, China
| | - Zhong-Ying Zhang
- Department of Clinical Laboratory, Zhongshan Hospital , affiliated to Xiamen University, Xiamen, China
| | - Zhi-Liang Ji
- State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, China
- *Correspondence: Zhi-Liang Ji, ; Pan You,
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31
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Li D, Jiang S, Zhou X, Si C, Shao P, Jiang Q, Zhu L, Shen L, Meng Q, Yin JC, Shao Y, Sun Y, Yang L. FBXW7 and Its Downstream NOTCH Pathway Could be Potential Indicators of Organ-Free Metastasis in Colorectal Cancer. Front Oncol 2022; 11:783564. [PMID: 35712679 PMCID: PMC9197223 DOI: 10.3389/fonc.2021.783564] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 12/07/2021] [Indexed: 01/01/2023] Open
Abstract
Colorectal cancer (CRC) is one of the leading causes of cancer-related deaths globally. Metastasis is associated with a poor prognosis, yet the underlying molecular mechanism(s) remained largely unknown. In this study, a total of 85 CRC patients were included and the primary tumor lesions were evaluated by next-generation sequencing using a targeted panel for genetic aberrations. Patients were sub-divided according to their metastasis pattern into the non-organ metastases (Non-OM) and organ metastases (OM) groups. By comparing the genetic differences between the two groups, we found that mutations in FBXW7 and alterations in its downstream NOTCH signaling pathway were more common in the Non-OM group. Moreover, correlation analysis suggested that FBXW7 mutations were independent of other somatic alterations. The negative associations of alterations in FBXW7 and its downstream NOTCH signaling pathway with CRC organ metastasis were validated in a cohort of 230 patients in the TCGA CRC dataset. Thus, we speculated that the genomic alterations of FBXW7/NOTCH axis might be an independent negative indicator of CRC organ metastases.
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Affiliation(s)
- Dongzheng Li
- Division of Colorectal Surgery, Department of General Surgery, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
| | - Shiye Jiang
- Division of Colorectal Surgery, Department of General Surgery, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
| | - Xin Zhou
- Division of Colorectal Surgery, Department of General Surgery, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
| | - Chengshuai Si
- Division of Colorectal Surgery, Department of General Surgery, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
| | - Peng Shao
- Division of Colorectal Surgery, Department of General Surgery, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
| | - Qian Jiang
- Division of Colorectal Surgery, Department of General Surgery, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
| | - Liuqing Zhu
- Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Lu Shen
- Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Qi Meng
- Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Jiani C Yin
- Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Yang Shao
- Nanjing Geneseeq Technology Inc., Nanjing, China.,School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yueming Sun
- Division of Colorectal Surgery, Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China & The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China
| | - Liu Yang
- Division of Colorectal Surgery, Department of General Surgery, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
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32
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Alves JM, Prado-López S, Tomás L, Valecha M, Estévez-Gómez N, Alvariño P, Geisel D, Modest DP, Sauer IM, Pratschke J, Raschzok N, Sers C, Mamlouk S, Posada D. Clonality and timing of relapsing colorectal cancer metastasis revealed through whole-genome single-cell sequencing. Cancer Lett 2022; 543:215767. [PMID: 35688262 DOI: 10.1016/j.canlet.2022.215767] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/26/2022] [Accepted: 05/29/2022] [Indexed: 11/02/2022]
Abstract
Recurrence of tumor cells following local and systemic therapy is a significant hurdle in cancer. Most patients with metastatic colorectal cancer (mCRC) will relapse, despite resection of the metastatic lesions. A better understanding of the evolutionary history of recurrent lesions is required to identify the spatial and temporal patterns of metastatic progression and expose the genetic and evolutionary determinants of therapeutic resistance. With this goal in mind, here we leveraged a unique single-cell whole-genome sequencing dataset from recurrent hepatic lesions of an mCRC patient. Our phylogenetic analysis confirms that the treatment induced a severe demographic bottleneck in the liver metastasis but also that a previously diverged lineage survived this surgery, possibly after migration to a different site in the liver. This lineage evolved very slowly for two years under adjuvant drug therapy and diversified again in a very short period. We identified several non-silent mutations specific to this lineage and inferred a substantial contribution of chemotherapy to the overall, genome-wide mutational burden. All in all, our study suggests that mCRC subclones can migrate locally and evade resection, keep evolving despite rounds of chemotherapy, and re-expand explosively.
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Affiliation(s)
- Joao M Alves
- CINBIO, Universidade de Vigo, 36310, Vigo, Spain; Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Spain
| | - Sonia Prado-López
- CINBIO, Universidade de Vigo, 36310, Vigo, Spain; Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Spain
| | - Laura Tomás
- CINBIO, Universidade de Vigo, 36310, Vigo, Spain; Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Spain
| | - Monica Valecha
- CINBIO, Universidade de Vigo, 36310, Vigo, Spain; Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Spain
| | - Nuria Estévez-Gómez
- CINBIO, Universidade de Vigo, 36310, Vigo, Spain; Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Spain
| | - Pilar Alvariño
- CINBIO, Universidade de Vigo, 36310, Vigo, Spain; Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Spain
| | - Dominik Geisel
- Department of Radiology, Campus Virchow-Klinikum, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Germany
| | - Dominik Paul Modest
- Department of Hematology, Oncology, and Cancer Immunology, Campus Charité Mitte, Campus Virchow-Klinikum, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Igor M Sauer
- Department of Surgery, Campus Charité Mitte, Campus Virchow-Klinikum, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu, Berlin, Germany
| | - Johann Pratschke
- Department of Surgery, Campus Charité Mitte, Campus Virchow-Klinikum, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu, Berlin, Germany
| | - Nathanael Raschzok
- Department of Surgery, Campus Charité Mitte, Campus Virchow-Klinikum, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu, Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Academy, Clinician Scientist Program, Berlin, Germany
| | - Christine Sers
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany; German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Soulafa Mamlouk
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany; German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - David Posada
- CINBIO, Universidade de Vigo, 36310, Vigo, Spain; Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Spain; Department of Biochemistry, Genetics, and Immunology, Universidade de Vigo, 36310, Vigo, Spain.
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33
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The genomic and transcriptional landscape of primary central nervous system lymphoma. Nat Commun 2022; 13:2558. [PMID: 35538064 PMCID: PMC9091224 DOI: 10.1038/s41467-022-30050-y] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 04/12/2022] [Indexed: 02/07/2023] Open
Abstract
Primary lymphomas of the central nervous system (PCNSL) are mainly diffuse large B-cell lymphomas (DLBCLs) confined to the central nervous system (CNS). Molecular drivers of PCNSL have not been fully elucidated. Here, we profile and compare the whole-genome and transcriptome landscape of 51 CNS lymphomas (CNSL) to 39 follicular lymphoma and 36 DLBCL cases outside the CNS. We find recurrent mutations in JAK-STAT, NFkB, and B-cell receptor signaling pathways, including hallmark mutations in MYD88 L265P (67%) and CD79B (63%), and CDKN2A deletions (83%). PCNSLs exhibit significantly more focal deletions of HLA-D (6p21) locus as a potential mechanism of immune evasion. Mutational signatures correlating with DNA replication and mitosis are significantly enriched in PCNSL. TERT gene expression is significantly higher in PCNSL compared to activated B-cell (ABC)-DLBCL. Transcriptome analysis clearly distinguishes PCNSL and systemic DLBCL into distinct molecular subtypes. Epstein-Barr virus (EBV)+ CNSL cases lack recurrent mutational hotspots apart from IG and HLA-DRB loci. We show that PCNSL can be clearly distinguished from DLBCL, having distinct expression profiles, IG expression and translocation patterns, as well as specific combinations of genetic alterations.
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34
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Fu A, Yao B, Dong T, Chen Y, Yao J, Liu Y, Li H, Bai H, Liu X, Zhang Y, Wang C, Guo Y, Li N, Cai S. Tumor-resident intracellular microbiota promotes metastatic colonization in breast cancer. Cell 2022; 185:1356-1372.e26. [PMID: 35395179 DOI: 10.1016/j.cell.2022.02.027] [Citation(s) in RCA: 264] [Impact Index Per Article: 132.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/10/2022] [Accepted: 02/24/2022] [Indexed: 12/12/2022]
Abstract
Tumor-resident intracellular microbiota is an emerging tumor component that has been documented for a variety of cancer types with unclear biological functions. Here, we explored the functional significance of these intratumor bacteria, primarily using a murine spontaneous breast-tumor model MMTV-PyMT. We found that depletion of intratumor bacteria significantly reduced lung metastasis without affecting primary tumor growth. During metastatic colonization, intratumor bacteria carried by circulating tumor cells promoted host-cell survival by enhancing resistance to fluid shear stress by reorganizing actin cytoskeleton. We further showed that intratumor administration of selected bacteria strains isolated from tumor-resident microbiota promoted metastasis in two murine tumor models with significantly different levels of metastasis potential. Our findings suggest that tumor-resident microbiota, albeit at low biomass, play an important role in promoting cancer metastasis, intervention of which might therefore be worth exploring for advancing oncology care.
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Affiliation(s)
- Aikun Fu
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Bingqing Yao
- School of Life Sciences, Fudan University, Shanghai, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Tingting Dong
- School of Life Sciences, Fudan University, Shanghai, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Yongyi Chen
- Department of Clinical Laboratory, Zhejiang Cancer Hospital, Hangzhou, Zhejiang Province, 310000, China
| | - Jia Yao
- Department of Breast Surgery, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Yu Liu
- Department of Breast Surgery, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Hang Li
- Westlake University High-Performance Computing Center, Westlake University, Hangzhou, Zhejiang, China
| | - Huiru Bai
- School of Life Sciences, Fudan University, Shanghai, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Xiaoqin Liu
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; School of Life Sciences, Fudan University, Shanghai, China
| | - Yue Zhang
- School of Life Sciences, Fudan University, Shanghai, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Chunhui Wang
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Westlake Disease Modeling lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
| | - Yajing Guo
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Nan Li
- Westlake University High-Performance Computing Center, Westlake University, Hangzhou, Zhejiang, China
| | - Shang Cai
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Westlake Disease Modeling lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China.
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35
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Siraj S, Masoodi T, Siraj AK, Azam S, Qadri Z, Parvathareddy SK, Bu R, Siddiqui KS, Al-Sobhi SS, AlDawish M, Al-Kuraya KS. APOBEC SBS13 Mutational Signature-A Novel Predictor of Radioactive Iodine Refractory Papillary Thyroid Carcinoma. Cancers (Basel) 2022; 14:cancers14061584. [PMID: 35326735 PMCID: PMC8946015 DOI: 10.3390/cancers14061584] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/03/2022] [Accepted: 03/15/2022] [Indexed: 02/04/2023] Open
Abstract
Standard surgery followed by radioactive iodine (131I, RAI) therapy are not curative for 5−20% of papillary thyroid carcinoma (PTC) patients with RAI refractory disease. Early predictors indicating therapeutic response to RAI therapy in PTC are yet to be elucidated. Whole-exome sequencing was performed (at median depth 198x) on 66 RAI-refractory and 92 RAI-avid PTCs with patient-matched germline. RAI-refractory tumors were significantly associated with distinct aggressive clinicopathological features, including positive surgical margins (p = 0.016) and the presence of lymph node metastases at primary diagnosis (p = 0.012); higher nonsilent tumor mutation burden (p = 0.011); TERT promoter (TERTp) mutation (p < 0.0001); and the enrichment of the APOBEC-related single-base substitution (SBS) COSMIC mutational signatures 2 (p = 0.030) and 13 (p < 0.001). Notably, SBS13 (odds ratio [OR] 30.4, 95% confidence intervals [CI] 1.43−647.22) and TERTp mutation (OR 41.3, 95% CI 4.35−391.60) were revealed to be independent predictors of RAI refractoriness in PTC (p = 0.029 and 0.001, respectively). Although SBS13 and TERTp mutations alone highly predicted RAI refractoriness, when combined, they significantly increased the likelihood of predicting RAI refractoriness in PTC. This study highlights the APOBEC SBS13 mutational signature as a novel independent predictor of RAI refractoriness in a distinct subgroup of PTC.
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Affiliation(s)
- Sarah Siraj
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.K.P.); (R.B.)
| | - Tariq Masoodi
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.K.P.); (R.B.)
| | - Abdul K. Siraj
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.K.P.); (R.B.)
| | - Saud Azam
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.K.P.); (R.B.)
| | - Zeeshan Qadri
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.K.P.); (R.B.)
| | - Sandeep K. Parvathareddy
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.K.P.); (R.B.)
| | - Rong Bu
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.K.P.); (R.B.)
| | - Khawar S. Siddiqui
- Department of Pediatric Hematology-Oncology, King Faisal Specialist Hospital and Research Center, P.O. Box 3354, Riyadh 11211, Saudi Arabia;
| | - Saif S. Al-Sobhi
- Department of Surgery, King Faisal Specialist Hospital and Research Center, P.O. Box 3354, Riyadh 11211, Saudi Arabia;
| | - Mohammed AlDawish
- Department of Endocrinology and Diabetes, Prince Sultan Military Medical City, P.O. Box 261370, Riyadh 11342, Saudi Arabia;
| | - Khawla S. Al-Kuraya
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.K.P.); (R.B.)
- Correspondence: ; Tel.: +966-112-055-2167
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Zhang Y, Sun L, Li H, Ai L, Ma Q, Qiao X, Yang J, Zhang H, Ou X, Wang Y, Chen G, Xue J, Zhu X, Zhao Y, Yang Y, Liu C. Binding blockade between TLN1 and integrin β1 represses triple-negative breast cancer. eLife 2022; 11:68481. [PMID: 35285795 PMCID: PMC8937232 DOI: 10.7554/elife.68481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 03/07/2022] [Indexed: 12/21/2022] Open
Abstract
Background: Integrin family are known as key gears in focal adhesion for triple-negative breast cancer (TNBC) metastasis. However, the integrin independent factor TLN1 remains vague in TNBC. Methods: Bioinformatics analysis was performed based on TCGA database and Shengjing Hospital cohort. Western blot and RT-PCR were used to detect the expression of TLN1 and integrin pathway in cells. A small-molecule C67399 was screened for blocking TLN1 and integrin β1 through a novel computational screening approach by targeting the protein-protein binding interface. Drug pharmacodynamics were determined through xenograft assay. Results: Upregulation of TLN1 in TNBC samples correlates with metastasis and worse prognosis. Silencing TLN1 in TNBC cells significantly attenuated the migration of tumour cells through interfering the dynamic formation of focal adhesion with integrin β1, thus regulating FAK-AKT signal pathway and epithelial-mesenchymal transformation. Targeting the binding between TLN1 and integrin β1 by C67399 could repress metastasis of TNBC. Conclusions: TLN1 overexpression contributes to TNBC metastasis and C67399 targeting TLN1 may hold promise for TNBC treatment. Funding: This study was supported by grants from the National Natural Science Foundation of China (No. 81872159, 81902607, 81874301), Liaoning Colleges Innovative Talent Support Program (Name: Cancer Stem Cell Origin and Biological Behaviour), Outstanding Scientific Fund of Shengjing Hospital (201803), and Outstanding Young Scholars of Liaoning Province (2019-YQ-10).
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Affiliation(s)
- Yixiao Zhang
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, China.,Cancer Stem Cell and Translational Medicine Laboratory, Shengjing Hospital of China Medical University, Shenyang, China
| | - Lisha Sun
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, China.,Cancer Stem Cell and Translational Medicine Laboratory, Shengjing Hospital of China Medical University, Shenyang, China.,Innovative Cancer Drug Research and Development Engineering Center of Liaoning Province, Shenyang, China
| | - Haonan Li
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Liping Ai
- Cancer Stem Cell and Translational Medicine Laboratory, Shengjing Hospital of China Medical University, Shenyang, China
| | - Qingtian Ma
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, China.,Cancer Stem Cell and Translational Medicine Laboratory, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xinbo Qiao
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, China.,Cancer Stem Cell and Translational Medicine Laboratory, Shengjing Hospital of China Medical University, Shenyang, China
| | - Jie Yang
- Cancer Stem Cell and Translational Medicine Laboratory, Shengjing Hospital of China Medical University, Shenyang, China
| | - Hao Zhang
- Cancer Stem Cell and Translational Medicine Laboratory, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xunyan Ou
- Cancer Stem Cell and Translational Medicine Laboratory, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yining Wang
- Cancer Stem Cell and Translational Medicine Laboratory, Shengjing Hospital of China Medical University, Shenyang, China
| | - Guanglei Chen
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, China.,Cancer Stem Cell and Translational Medicine Laboratory, Shengjing Hospital of China Medical University, Shenyang, China
| | - Jinqi Xue
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, China.,Cancer Stem Cell and Translational Medicine Laboratory, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xudong Zhu
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, China.,Cancer Stem Cell and Translational Medicine Laboratory, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yu Zhao
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Yongliang Yang
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, China.,School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Caigang Liu
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, China.,Cancer Stem Cell and Translational Medicine Laboratory, Shengjing Hospital of China Medical University, Shenyang, China.,Innovative Cancer Drug Research and Development Engineering Center of Liaoning Province, Shenyang, China
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ErbB4 Is a Potential Key Regulator of the Pathways Activated by NTRK-Fusions in Thyroid Cancer. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12052506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
NTRK gene fusions are drivers of tumorigenesis events that specific Trk-inhibitors can target. Current knowledge of the downstream pathways activated has been previously limited to the pathways of regulator proteins phosphorylated directly by Trk receptors. Here, we aimed to detect genes whose expression is increased in response to the activation of these pathways. We identified and analyzed differentially expressed genes in thyroid cancer samples with NTRK1 or NTRK3 gene fusions, and without any NTRK fusions, versus normal thyroid gland tissues, using data from the Cancer Genome Atlas, the DESeq2 tool, and the Genome Enhancer and geneXplain platforms. Searching for the genes activated only in samples with an NTRK fusion as opposed to those without NTRK fusions, we identified 29 genes involved in nervous system development, including AUTS2, DTNA, ERBB4, FLRT2, FLRT3, RPH3A, and SCN4A. We found that genes regulating the expression of the upregulated genes (i.e., upstream regulators) were enriched in the “signaling by ERBB4” pathway. ERBB4 was also one of three genes encoding master regulators whose expression was increased only in samples with an NTRK fusion. Moreover, the algorithm searching for positive feedback loops for gene promoters and transcription factors (a so-called “walking pathways” algorithm) identified the ErbB4 protein as the key master regulator. ERBB4 upregulation (p-value = 0.004) was confirmed in an independent sample of ETV6-NTRK3-positive FFPE specimens. Thus, ErbB4 is the potential key regulator of the pathways activated by NTRK gene fusions in thyroid cancer. These results are preliminary and require additional biochemical validation.
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Viganò L, Jayakody Arachchige VS, Fiz F. Is precision medicine for colorectal liver metastases still a utopia? New perspectives by modern biomarkers, radiomics, and artificial intelligence. World J Gastroenterol 2022; 28:608-623. [PMID: 35317421 PMCID: PMC8900542 DOI: 10.3748/wjg.v28.i6.608] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/29/2021] [Accepted: 01/20/2022] [Indexed: 02/06/2023] Open
Abstract
The management of patients with liver metastases from colorectal cancer is still debated. Several therapeutic options and treatment strategies are available for an extremely heterogeneous clinical scenario. Adequate prediction of patients’ outcomes and of the effectiveness of chemotherapy and loco-regional treatments are crucial to reach a precision medicine approach. This has been an unmet need for a long time, but recent studies have opened new perspectives. New morphological biomarkers have been identified. The dynamic evaluation of the metastases across a time interval, with or without chemotherapy, provided a reliable assessment of the tumor biology. Genetics have been explored and, thanks to their strong association with prognosis, have the potential to drive treatment planning. The liver-tumor interface has been identified as one of the main determinants of tumor progression, and its components, in particular the immune infiltrate, are the focus of major research. Image mining and analyses provided new insights on tumor biology and are expected to have a relevant impact on clinical practice. Artificial intelligence is a further step forward. The present paper depicts the evolution of clinical decision-making for patients affected by colorectal liver metastases, facing modern biomarkers and innovative opportunities that will characterize the evolution of clinical research and practice in the next few years.
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Affiliation(s)
- Luca Viganò
- Department of Hepatobiliary and General Surgery, IRCCS Humanitas Research Hospital, Rozzano 20089, MI, Italy
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele 20072, MI, Italy
| | - Visala S Jayakody Arachchige
- Department of Hepatobiliary and General Surgery, IRCCS Humanitas Research Hospital, Rozzano 20089, MI, Italy
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele 20072, MI, Italy
| | - Francesco Fiz
- Nuclear Medicine, IRCCS Humanitas Research Hospital, Rozzano 20089, MI, Italy
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Al-Joufi FA, Setia A, Salem-Bekhit MM, Sahu RK, Alqahtani FY, Widyowati R, Aleanizy FS. Molecular Pathogenesis of Colorectal Cancer with an Emphasis on Recent Advances in Biomarkers, as Well as Nanotechnology-Based Diagnostic and Therapeutic Approaches. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:169. [PMID: 35010119 PMCID: PMC8746463 DOI: 10.3390/nano12010169] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/22/2021] [Accepted: 12/24/2021] [Indexed: 02/06/2023]
Abstract
Colorectal cancer (CRC) is a serious disease that affects millions of people throughout the world, despite considerable advances in therapy. The formation of colorectal adenomas and invasive adenocarcinomas is the consequence of a succession of genetic and epigenetic changes in the normal colonic epithelium. Genetic and epigenetic processes associated with the onset, development, and metastasis of sporadic CRC have been studied in depth, resulting in identifying biomarkers that might be used to predict behaviour and prognosis beyond staging and influence therapeutic options. A novel biomarker, or a group of biomarkers, must be discovered in order to build an accurate and clinically useful test that may be used as an alternative to conventional methods for the early detection of CRC and to identify prospective new therapeutic intervention targets. To minimise the mortality burden of colorectal cancer, new screening methods with higher accuracy and nano-based diagnostic precision are needed. Cytotoxic medication has negative side effects and is restricted by medication resistance. One of the most promising cancer treatment techniques is the use of nano-based carrier system as a medication delivery mechanism. To deliver cytotoxic medicines, targeted nanoparticles might take advantage of differently expressed molecules on the surface of cancer cells. The use of different compounds as ligands on the surface of nanoparticles to interact with cancer cells, enabling the efficient delivery of antitumor medicines. Formulations based on nanoparticles might aid in early cancer diagnosis and help to overcome the limitations of traditional treatments, including low water solubility, nonspecific biodistribution, and restricted bioavailability. This article addresses about the molecular pathogenesis of CRC and highlights about biomarkers. It also provides conceptual knowledge of nanotechnology-based diagnostic techniques and therapeutic approaches for malignant colorectal cancer.
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Affiliation(s)
- Fakhria A. Al-Joufi
- Department of Pharmacology, College of Pharmacy, Jouf University, Aljouf 72341, Saudi Arabia;
| | - Aseem Setia
- Department of Pharmacy, Shri Rawatpura Sarkar University, Raipur 492015, India
| | - Mounir M. Salem-Bekhit
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (F.Y.A.); (F.S.A.)
- Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhar University, Cairo 11884, Egypt
| | - Ram Kumar Sahu
- Department of Pharmaceutical Science, Assam University (A Central University), Silchar 788011, India
| | - Fulwah Y. Alqahtani
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (F.Y.A.); (F.S.A.)
| | - Retno Widyowati
- Department of Pharmaceutical Science, Faculty of Pharmacy, Universitas Airlangga, Surabaya 60115, Indonesia;
| | - Fadilah Sfouq Aleanizy
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (F.Y.A.); (F.S.A.)
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40
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Nazarian A, Arbeev KG, Yashkin AP, Kulminski AM. Genome-wide analysis of genetic predisposition to common polygenic cancers. J Appl Genet 2022; 63:315-325. [PMID: 34981446 PMCID: PMC8983541 DOI: 10.1007/s13353-021-00679-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 12/13/2021] [Accepted: 12/23/2021] [Indexed: 12/16/2022]
Abstract
Lung, breast, prostate, and colorectal cancers are among the most common and fatal malignancies worldwide. They are mainly caused by multifactorial mechanisms and are genetically heterogeneous. We investigated the genetic architecture of these cancers through genome-wide association, pathway-based, and summary-based transcriptome-/methylome-wide association analyses using three independent cohorts. Our genome-wide association analyses identified the associations of 33 single-nucleotide polymorphisms (SNPs) at P < 5E - 06, of which 32 SNPs were not previously reported and did not have proxy variants within their ± 1 Mb flanking regions. Moreover, other polymorphisms mapped to their closest genes were not previously associated with the same cancers at P < 5E - 06. Our pathway enrichment analyses revealed associations of 32 pathways; mainly related to the immune system, DNA replication/transcription, and chromosomal organization; with the studied cancers. Also, 60 probes were associated with these cancers in our transcriptome-wide and methylome-wide analyses. The ± 1 Mb flanking regions of most probes had not attained P < 5E - 06 in genome-wide association studies. The genes corresponding to the significant probes can be considered as potential targets for further functional studies. Two genes (i.e., CDC14A and PMEL) demonstrated stronger evidence of associations with lung cancer as they had significant probes in both transcriptome-wide and methylome-wide association analyses. The novel cancer-associated SNPs and genes identified here would advance our understanding of the genetic heterogeneity of the common cancers.
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Affiliation(s)
- Alireza Nazarian
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Erwin Mill Building, 2024 W. Main St., Durham, NC, 27705, USA.
| | - Konstantin G Arbeev
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Erwin Mill Building, 2024 W. Main St., Durham, NC, 27705, USA
| | - Arseniy P Yashkin
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Erwin Mill Building, 2024 W. Main St., Durham, NC, 27705, USA
| | - Alexander M Kulminski
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Erwin Mill Building, 2024 W. Main St., Durham, NC, 27705, USA.
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Marongiu L, Landry JJM, Rausch T, Abba ML, Delecluse S, Delecluse H, Allgayer H. Metagenomic analysis of primary colorectal carcinomas and their metastases identifies potential microbial risk factors. Mol Oncol 2021; 15:3363-3384. [PMID: 34328665 PMCID: PMC8637581 DOI: 10.1002/1878-0261.13070] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/09/2021] [Accepted: 07/29/2021] [Indexed: 12/18/2022] Open
Abstract
The paucity of microbiome studies at intestinal tissues has contributed to a yet limited understanding of potential viral and bacterial cofactors of colorectal cancer (CRC) carcinogenesis or progression. We analysed whole-genome sequences of CRC primary tumours, their corresponding metastases and matched normal tissue for sequences of viral, phage and bacterial species. Bacteriome analysis showed Fusobacterium nucleatum, Streptococcus sanguinis, F. Hwasookii, Anaerococcus mediterraneensis and further species enriched in primary CRCs. The primary CRC of one patient was enriched for F. alocis, S. anginosus, Parvimonas micra and Gemella sp. 948. Enrichment of Escherichia coli strains IAI1, SE11, K-12 and M8 was observed in metastases together with coliphages enterobacteria phage φ80 and Escherichia phage VT2φ_272. Virome analysis showed that phages were the most preponderant viral species (46%), the main families being Myoviridae, Siphoviridae and Podoviridae. Primary CRCs were enriched for bacteriophages, showing five phages (Enterobacteria, Bacillus, Proteus, Streptococcus phages) together with their pathogenic hosts in contrast to normal tissues. The most frequently detected, and Blast-confirmed, viruses included human endogenous retrovirus K113, human herpesviruses 7 and 6B, Megavirus chilensis, cytomegalovirus (CMV) and Epstein-Barr virus (EBV), with one patient showing EBV enrichment in primary tumour and metastases. EBV was PCR-validated in 80 pairs of CRC primary tumour and their corresponding normal tissues; in 21 of these pairs (26.3%), it was detectable in primary tumours only. The number of viral species was increased and bacterial species decreased in CRCs compared with normal tissues, and we could discriminate primary CRCs from metastases and normal tissues by applying the Hutcheson t-test on the Shannon indices based on viral and bacterial species. Taken together, our results descriptively support hypotheses on microorganisms as potential (co)risk factors of CRC and extend putative suggestions on critical microbiome species in CRC metastasis.
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Affiliation(s)
- Luigi Marongiu
- Department of Experimental Surgery – Cancer MetastasisMedical Faculty MannheimRuprecht‐Karls University of HeidelbergMannheimGermany
| | | | - Tobias Rausch
- Genomics Core FacilityEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Mohammed L. Abba
- Department of Experimental Surgery – Cancer MetastasisMedical Faculty MannheimRuprecht‐Karls University of HeidelbergMannheimGermany
| | | | | | - Heike Allgayer
- Department of Experimental Surgery – Cancer MetastasisMedical Faculty MannheimRuprecht‐Karls University of HeidelbergMannheimGermany
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Patil N, Abba ML, Zhou C, Chang S, Gaiser T, Leupold JH, Allgayer H. Changes in Methylation across Structural and MicroRNA Genes Relevant for Progression and Metastasis in Colorectal Cancer. Cancers (Basel) 2021; 13:cancers13235951. [PMID: 34885060 DOI: 10.3390/cancers13235951] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 11/24/2021] [Accepted: 11/24/2021] [Indexed: 12/12/2022] Open
Abstract
MiRs are important players in cancer and primarily genetic/transcriptional means of regulating their gene expression are known. However, epigenetic changes modify gene expression significantly. Here, we evaluated genome-wide methylation changes focusing on miR genes from primary CRC and corresponding normal tissues. Differentially methylated CpGs spanning CpG islands, open seas, and north and south shore regions were evaluated, with the largest number of changes observed within open seas and islands. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed several of these miRs to act in important cancer-related pathways, including phosphatidylinositol 3-kinase (PI3K)-protein kinase B (Akt) and mitogen-activated protein kinase (MAPK) pathways. We found 18 miR genes to be significantly differentially methylated, with MIR124-2, MIR124-3, MIR129-2, MIR137, MIR34B, MIR34C, MIR548G, MIR762, and MIR9-3 hypermethylated and MIR1204, MIR17, MIR17HG, MIR18A, MIR19A, MIR19B1, MIR20A, MIR548F5, and MIR548I4 hypomethylated in CRC tumor compared with normal tissue, most of these miRs having been shown to regulate steps of metastasis. Generally, methylation changes were distributed evenly across all chromosomes with predominance for chromosomes 1/2 and protein-coding genes. Interestingly, chromosomes abundantly affected by methylation changes globally were rarely affected by methylation changes within miR genes. Our findings support additional mechanisms of methylation changes affecting (miR) genes that orchestrate CRC progression and metastasis.
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Affiliation(s)
- Nitin Patil
- Department of Experimental Surgery-Cancer Metastasis, Mannheim Medical Faculty, Ruprecht Karls University of Heidelberg, 68167 Mannheim, Germany
| | - Mohammed L Abba
- Department of Experimental Surgery-Cancer Metastasis, Mannheim Medical Faculty, Ruprecht Karls University of Heidelberg, 68167 Mannheim, Germany
| | - Chan Zhou
- Department of Experimental Surgery-Cancer Metastasis, Mannheim Medical Faculty, Ruprecht Karls University of Heidelberg, 68167 Mannheim, Germany
| | - Shujian Chang
- Department of Experimental Surgery-Cancer Metastasis, Mannheim Medical Faculty, Ruprecht Karls University of Heidelberg, 68167 Mannheim, Germany
| | - Timo Gaiser
- Institute of Pathology, Mannheim Medical Faculty, Ruprecht Karls University of Heidelberg, Theodor Kutzer Ufer 1-3, 68167 Mannheim, Germany
| | - Jörg H Leupold
- Department of Experimental Surgery-Cancer Metastasis, Mannheim Medical Faculty, Ruprecht Karls University of Heidelberg, 68167 Mannheim, Germany
| | - Heike Allgayer
- Department of Experimental Surgery-Cancer Metastasis, Mannheim Medical Faculty, Ruprecht Karls University of Heidelberg, 68167 Mannheim, Germany
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Yeoh Y, Low TY, Abu N, Lee PY. Regulation of signal transduction pathways in colorectal cancer: implications for therapeutic resistance. PeerJ 2021; 9:e12338. [PMID: 34733591 PMCID: PMC8544255 DOI: 10.7717/peerj.12338] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 09/28/2021] [Indexed: 12/13/2022] Open
Abstract
Resistance to anti-cancer treatments is a critical and widespread health issue that has brought serious impacts on lives, the economy and public policies. Mounting research has suggested that a selected spectrum of patients with advanced colorectal cancer (CRC) tend to respond poorly to both chemotherapeutic and targeted therapeutic regimens. Drug resistance in tumours can occur in an intrinsic or acquired manner, rendering cancer cells insensitive to the treatment of anti-cancer therapies. Multiple factors have been associated with drug resistance. The most well-established factors are the emergence of cancer stem cell-like properties and overexpression of ABC transporters that mediate drug efflux. Besides, there is emerging evidence that signalling pathways that modulate cell survival and drug metabolism play major roles in the maintenance of multidrug resistance in CRC. This article reviews drug resistance in CRC as a result of alterations in the MAPK, PI3K/PKB, Wnt/β-catenin and Notch pathways.
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Affiliation(s)
- Yeelon Yeoh
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Teck Yew Low
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Nadiah Abu
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Pey Yee Lee
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
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Ma B, Cao L, Li Y. A novel 10-gene immune-related lncRNA signature model for the prognosis of colorectal cancer. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2021; 18:9743-9760. [PMID: 34814366 DOI: 10.3934/mbe.2021477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
BACKGROUND The tumor immune microenvironment of colorectal cancer (CRC) affects tumor development, prognosis and immunotherapy strategies. Recently, immune-related lncRNA were shown to play vital roles in the tumor immune microenvironment. The objective of this study was to identify lncRNAs involved in the immune response, tumorigenesis and progression of CRC and to establish an immune-related lncRNA signature for predicting the prognosis of CRC. METHODS We used data retrieved from the cancer genome atlas (TCGA) dataset to construct a 10-gene immune-related lncRNA pair (IRLP) signature model using a method based on the ranking and comparison of paired gene expression in CRC. The clinical prognosis, immune checkpoints and lncRNA-protein networks were analyzed to evaluate the signature. RESULTS The signature was closely associated with overall survival of CRC patients (p < 0.001 in both of the training and validating cohorts) and the 3-year AUC values for the training and validating cohorts were 0.884 and 0.739, respectively. And, there were positive correlations between the signature and age (p = 0.048), clinical stage (p < 0.01), T stage (p < 0.01), N stage (p < 0.001) and M stage (p < 0.01). In addition, the signature model appeared to be highly relevant to some checkpoints, including CD160, TNFSF15, HHLA2, IDO2 and KIR3DL1. Further, molecular functional analysis and lncRNA-protein networks were applied to understand the molecular mechanisms underlying the carcinogenic effect and progression. CONCLUSION The 10-gene IRLP signature model is an independent prognostic factor for CRC patient and can be utilized for the development of immunotherapy.
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Affiliation(s)
- Bin Ma
- Department of Colorectal Surgery, Liaoning Cancer Hospital & Institute (Cancer Hospital of China Medical University), Shenyang, China
| | - Lianqun Cao
- Department of Colorectal Surgery, Liaoning Cancer Hospital & Institute (Cancer Hospital of China Medical University), Shenyang, China
| | - Yongmin Li
- Department of Colorectal Surgery, Liaoning Cancer Hospital & Institute (Cancer Hospital of China Medical University), Shenyang, China
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45
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Marongiu L, Allgayer H. Viruses in colorectal cancer. Mol Oncol 2021; 16:1423-1450. [PMID: 34514694 PMCID: PMC8978519 DOI: 10.1002/1878-0261.13100] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/15/2021] [Accepted: 09/10/2021] [Indexed: 12/23/2022] Open
Abstract
Increasing evidence suggests that microorganisms might represent at least highly interesting cofactors in colorectal cancer (CRC) oncogenesis and progression. Still, associated mechanisms, specifically in colonocytes and their microenvironmental interactions, are still poorly understood. Although, currently, at least seven viruses are being recognized as human carcinogens, only three of these – Epstein–Barr virus (EBV), human papillomavirus (HPV) and John Cunningham virus (JCV) – have been described, with varying levels of evidence, in CRC. In addition, cytomegalovirus (CMV) has been associated with CRC in some publications, albeit not being a fully acknowledged oncovirus. Moreover, recent microbiome studies set increasing grounds for new hypotheses on bacteriophages as interesting additional modulators in CRC carcinogenesis and progression. The present Review summarizes how particular groups of viruses, including bacteriophages, affect cells and the cellular and microbial microenvironment, thereby putatively contributing to foster CRC. This could be achieved, for example, by promoting several processes – such as DNA damage, chromosomal instability, or molecular aspects of cell proliferation, CRC progression and metastasis – not necessarily by direct infection of epithelial cells only, but also by interaction with the microenvironment of infected cells. In this context, there are striking common features of EBV, CMV, HPV and JCV that are able to promote oncogenesis, in terms of establishing latent infections and affecting p53‐/pRb‐driven, epithelial–mesenchymal transition (EMT)‐/EGFR‐associated and especially Wnt/β‐catenin‐driven pathways. We speculate that, at least in part, such viral impacts on particular pathways might be reflected in lasting (e.g. mutational or further genomic) fingerprints of viruses in cells. Also, the complex interplay between several species within the intestinal microbiome, involving a direct or indirect impact on colorectal and microenvironmental cells but also between, for example, phages and bacterial and viral pathogens, and further novel species certainly might, in part, explain ongoing difficulties to establish unequivocal monocausal links between specific viral infections and CRC.
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Affiliation(s)
- Luigi Marongiu
- Department of Experimental Surgery - Cancer Metastasis, Medical Faculty Mannheim, Ruprecht-Karls-University of Heidelberg, Mannheim, Germany
| | - Heike Allgayer
- Department of Experimental Surgery - Cancer Metastasis, Medical Faculty Mannheim, Ruprecht-Karls-University of Heidelberg, Mannheim, Germany
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Whole exome and transcriptome sequencing reveal clonal evolution and exhibit immune-related features in metastatic colorectal tumors. Cell Death Discov 2021; 7:222. [PMID: 34453042 PMCID: PMC8397721 DOI: 10.1038/s41420-021-00607-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 07/14/2021] [Accepted: 07/29/2021] [Indexed: 01/05/2023] Open
Abstract
Liver is the most common site where metastatic lesions of colorectal cancer (CRC) arise. Although researches have shown mutations in driver genes, copy number variations (CNV) and alterations in relevant signaling pathways promoted the tumor evolution and immune escape during colorectal liver metastasis (CLM), the underlying mechanism remains largely elusive. Tumor and matched metastatic tissues were collected from 16 patients diagnosed with colorectal cancer and subjected to whole-exome sequencing (WES) and RNA sequencing (RNA-seq) for studying colorectal cancer clonal evolution and immune escape during CLM. Shared somatic mutations between primary and metastatic tissues with a commonly observed subclonal-clonal (S-C) changing pattern indicated a common clonal origin between two lesions. The recurrent mutations with S-C changing pattern included those in KRAS, SYNE1, CACNA1H, PCLO, FBXL2, and DNAH11. The main CNV events underwent clonal-clonal evolution (20q amplification (amp), 17p deletion (del), 18q del and 8p del), subclonal-clonal evolution (8q amp, 13q amp, 8p del) and metastasis-specific evolution (8q amp) during the process of CLM. In addition, we revealed a potential mechanism of tumor cell immune escape by analyzing human leukocytes antigens (HLA) related clonal neoantigens and immune cell components in CLM. Our study proposed a novel liver metastasis-related evolutionary process in colorectal cancer and emphasized the theory of neo-immune escape in colorectal liver metastasis.
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Lang F, Contreras-Gerenas MF, Gelléri M, Neumann J, Kröger O, Sadlo F, Berniak K, Marx A, Cremer C, Wagenknecht HA, Allgayer H. Tackling Tumour Cell Heterogeneity at the Super-Resolution Level in Human Colorectal Cancer Tissue. Cancers (Basel) 2021; 13:cancers13153692. [PMID: 34359592 PMCID: PMC8345115 DOI: 10.3390/cancers13153692] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Tumour cell heterogeneity is the most fundamental problem in cancer diagnosis and therapy. Micro-diagnostic technologies able to differentiate the heterogeneous molecular, especially metastatic, potential of single cells or cell clones already within early primary tumours of carcinoma patients would be of utmost importance. Single molecule localisation microscopy (SMLM) has recently allowed the imaging of subcellular features at the nanoscale. However, the technology has mostly been limited to cultured cell lines only. We introduce a first-in-field approach for quantitative SMLM-analysis of chromatin nanostructure in individual cells in resected, routine-pathology colorectal carcinoma patient tissue sections, illustrating, as a first example, changes in nuclear chromatin nanostructure and microRNA intracellular distribution within carcinoma cells as opposed to normal cells, chromatin accessibility and microRNAs having been shown to be critical in gene regulation and metastasis. We believe this technology to have an enormous potential for future differential diagnosis between individual cells in the tissue context. Abstract Tumour cell heterogeneity, and its early individual diagnosis, is one of the most fundamental problems in cancer diagnosis and therapy. Single molecule localisation microscopy (SMLM) resolves subcellular features but has been limited to cultured cell lines only. Since nuclear chromatin architecture and microRNAs are critical in metastasis, we introduce a first-in-field approach for quantitative SMLM-analysis of chromatin nanostructure in individual cells in resected, routine-pathology colorectal carcinoma (CRC) patient tissue sections. Chromatin density profiles proved to differ for cells in normal and carcinoma colorectal tissues. In tumour sections, nuclear size and chromatin compaction percentages were significantly different in carcinoma versus normal epithelial and other cells of colorectal tissue. SMLM analysis in nuclei from normal colorectal tissue revealed abrupt changes in chromatin density profiles at the nanoscale, features not detected by conventional widefield microscopy. SMLM for microRNAs relevant for metastasis was achieved in colorectal cancer tissue at the nuclear level. Super-resolution microscopy with quantitative image evaluation algorithms provide powerful tools to analyse chromatin nanostructure and microRNAs of individual cells from normal and tumour tissue at the nanoscale. Our new perspectives improve the differential diagnosis of normal and (metastatically relevant) tumour cells at the single-cell level within the heterogeneity of primary tumours of patients.
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Affiliation(s)
- Fabian Lang
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, Campus Süd, 76131 Karlsruhe, Germany; (F.L.); (H.-A.W.)
| | - María F. Contreras-Gerenas
- Department of Experimental Surgery—Cancer Metastasis, Mannheim Medical Faculty, Ruprecht-Karls University of Heidelberg, Ludolf-Krehl-Straße 13-17, 68167 Mannheim, Germany;
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany; (M.G.); (J.N.); (C.C.)
| | - Márton Gelléri
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany; (M.G.); (J.N.); (C.C.)
| | - Jan Neumann
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany; (M.G.); (J.N.); (C.C.)
| | - Ole Kröger
- Interdisciplinary Centre for Scientific Computing (IWR), University Heidelberg, Mathematikon B, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany; (O.K.); (F.S.)
| | - Filip Sadlo
- Interdisciplinary Centre for Scientific Computing (IWR), University Heidelberg, Mathematikon B, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany; (O.K.); (F.S.)
| | - Krzysztof Berniak
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7 Street, 30-387 Krakow, Poland;
| | - Alexander Marx
- Institute of Pathology, Mannheim Medical Faculty, Ruprecht-Karls University of Heidelberg, Theodor-Kutzer-Ufer 1, 68167 Mannheim, Germany;
| | - Christoph Cremer
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany; (M.G.); (J.N.); (C.C.)
- Interdisciplinary Centre for Scientific Computing (IWR), University Heidelberg, Mathematikon B, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany; (O.K.); (F.S.)
- Institute of Pharmacy & Molecular Biotechnology, Ruprecht-Karls University of Heidelberg, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, Campus Süd, 76131 Karlsruhe, Germany; (F.L.); (H.-A.W.)
| | - Heike Allgayer
- Department of Experimental Surgery—Cancer Metastasis, Mannheim Medical Faculty, Ruprecht-Karls University of Heidelberg, Ludolf-Krehl-Straße 13-17, 68167 Mannheim, Germany;
- Correspondence: ; Tel.: +49-(0)621-383-71630/-1406/-71635; Fax: +49-(0)621-383-71631
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Pan R, Lu Q, Ren C, Li H, Zeng F, Tian X, Chen H. Anoctamin 5 promotes osteosarcoma development by increasing degradation of Nel-like proteins 1 and 2. Aging (Albany NY) 2021; 13:17316-17327. [PMID: 34238763 PMCID: PMC8312408 DOI: 10.18632/aging.203212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/20/2021] [Indexed: 11/25/2022]
Abstract
Anoctamin 5 (ANO5) is a member of the Anoctamin (ANO) family of calcium-activated chloride channels. Although ANO5 expression is upregulated in various cancers, its role in osteosarcoma remains largely unknown. In this study, bioinformatics analysis, western blot, and immunohistochemical staining revealed that ANO5 was upregulated in osteosarcoma cell lines and osteosarcoma tissues, and ANO5 expression was positively associated with tumor size, tumor grade, and metastasis. Functional experiments demonstrated that inhibition of ANO5 decreased, while ANO5 overexpression increased, osteosarcoma cell proliferation and mobility in vitro. Immunoprecipitation, western blot, and confocal microscopy experiments showed that ANO5 bound to and promoted the degradation of Nel-like proteins 1 (NELL1) and 2 (NELL2). Moreover, a subcutaneous tumor transplantation model revealed that ANO5 knockdown reduced osteosarcoma cell proliferation and increased NELL1 and NELL2 expression in vivo. Finally, rescue experiments showed that knockdown of NELL1 or NELL2 reversed the inhibitory effects of ANO5 knockdown on osteosarcoma cell proliferation and migration. These results demonstrated that upregulation of ANO5 promoted osteosarcoma development by decreasing the stability of the NELL1 and NELL2 proteins and that ANO5 may be an effective target for the treatment of osteosarcoma.
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Affiliation(s)
- Runsang Pan
- Department of Orthopedics, Guiyang Maternal and Child Health-Care Hospital, Guiyang 550009, Guizhou, China
| | - Qiaoying Lu
- Department of Orthopedics, Guiyang Maternal and Child Health-Care Hospital, Guiyang 550009, Guizhou, China
| | - Chong Ren
- Department of Orthopedics, Guiyang Maternal and Child Health-Care Hospital, Guiyang 550009, Guizhou, China
| | - Hao Li
- Department of Orthopedics, Guiyang Maternal and Child Health-Care Hospital, Guiyang 550009, Guizhou, China
| | - Fanqiang Zeng
- Department of Orthopedics, Guiyang Maternal and Child Health-Care Hospital, Guiyang 550009, Guizhou, China
| | - Xiaobin Tian
- Department of Orthopedics, The Affiliated Hospital of Guizhou Medical University, Guiyang 550009, Guizhou, China
| | - Houping Chen
- Department of Orthopedics, Guiyang Maternal and Child Health-Care Hospital, Guiyang 550009, Guizhou, China
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Yu Z, Song M, Chouchane L, Ma X. Functional Genomic Analysis of Breast Cancer Metastasis: Implications for Diagnosis and Therapy. Cancers (Basel) 2021; 13:cancers13133276. [PMID: 34208889 PMCID: PMC8268362 DOI: 10.3390/cancers13133276] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 06/29/2021] [Accepted: 06/29/2021] [Indexed: 12/11/2022] Open
Abstract
Simple Summary Metastasis remains the greatest cause of fatalities in breast cancer patients world-wide. The process of metastases is highly complex, and the current research efforts in this area are still rather fragmented. The revolution of genomic profiling methods to analyze samples from human and animal models dramatically improved our understanding of breast cancer metastasis. This article summarizes the recent breakthroughs in genomic analyses of breast cancer metastasis and discusses their implications for prognostic and therapeutic applications. Abstract Breast cancer (BC) is one of the most diagnosed cancers worldwide and is the second cause of cancer related death in women. The most frequent cause of BC-related deaths, like many cancers, is metastasis. However, metastasis is a complicated and poorly understood process for which there is a shortage of accurate prognostic indicators and effective treatments. With the rapid and ever-evolving development and application of genomic sequencing technologies, many novel molecules were identified that play previously unappreciated and important roles in the various stages of metastasis. In this review, we summarize current advancements in the functional genomic analysis of BC metastasis and discuss about the potential prognostic and therapeutic implications from the recent genomic findings.
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Affiliation(s)
- Ziqi Yu
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA;
- Correspondence: (Z.Y.); (X.M.)
| | - Mei Song
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA;
| | - Lotfi Chouchane
- Department of Genetic Medicine, Weill Cornell Medicine-Qatar, Qatar Foundation, Doha P.O. Box 24144, Qatar;
| | - Xiaojing Ma
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA;
- Correspondence: (Z.Y.); (X.M.)
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50
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Chen TJ, Tian YF, Chou CL, Chan TC, He HL, Li WS, Tsai HH, Li CF, Lai HY. High SPINK4 Expression Predicts Poor Outcomes among Rectal Cancer Patients Receiving CCRT. ACTA ACUST UNITED AC 2021; 28:2373-2384. [PMID: 34202399 PMCID: PMC8293060 DOI: 10.3390/curroncol28040218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/15/2021] [Accepted: 06/22/2021] [Indexed: 01/21/2023]
Abstract
Background: Patients with rectal cancer can prospectively be favored for neoadjuvant concurrent chemoradiotherapy (CCRT) to downstage before a radical proctectomy, but the risk stratification and clinical outcomes remain disappointing. Methods: From a published rectal cancer transcriptome dataset (GSE35452), we highlighted extracellular matrix (ECM)-linked genes and identified the serine protease inhibitor Kazal-type 4 (SPINK4) gene as the most relevant among the top 10 differentially expressed genes associated with CCRT resistance. We accumulated the cases of 172 rectal cancer patients who received neoadjuvant CCRT followed by surgery and collected tumor specimens for the evaluation of the expression of SPINK4 using immunohistochemistry. Results: The results revealed that high SPINK4 immunoexpression was significantly related to advanced pre-CCRT and post-CCRT tumor status (both p < 0.001), post-CCRT lymph node metastasis (p = 0.001), more vascular and perineurial invasion (p = 0.015 and p = 0.023), and a lower degree of tumor regression (p = 0.001). In univariate analyses, high SPINK4 immunoexpression was remarkably correlated with worse disease-specific survival (DSS) (p < 0.0001), local recurrence-free survival (LRFS) (p = 0.0017), and metastasis-free survival (MeFS) (p < 0.0001). Furthermore, in multivariate analyses, high SPINK4 immunoexpression remained independently prognostic of inferior DSS and MeFS (p = 0.004 and p = 0.002). Conclusion: These results imply that high SPINK4 expression is associated with advanced clinicopathological features and a poor therapeutic response among rectal cancer patients undergoing CCRT, thus validating the prospective prognostic value of SPINK4 for those patients.
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Affiliation(s)
- Tzu-Ju Chen
- Department of Pathology, Chi Mei Medical Center, Tainan 710, Taiwan; (T.-J.C.); (H.-L.H.); (W.-S.L.); (H.-H.T.)
- Department of Medical Technology, Chung Hwa University of Medical Technology, Tainan 717, Taiwan
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung 804, Taiwan
| | - Yu-Feng Tian
- Division of Colon and Rectal Surgery, Department of Surgery, Chi Mei Medical Center, Tainan 710, Taiwan; (Y.-F.T.); (C.-L.C.)
| | - Chia-Lin Chou
- Division of Colon and Rectal Surgery, Department of Surgery, Chi Mei Medical Center, Tainan 710, Taiwan; (Y.-F.T.); (C.-L.C.)
| | - Ti-Chun Chan
- Department of Medical Research, Chi Mei Medical Center, Tainan 710, Taiwan;
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan
| | - Hong-Lin He
- Department of Pathology, Chi Mei Medical Center, Tainan 710, Taiwan; (T.-J.C.); (H.-L.H.); (W.-S.L.); (H.-H.T.)
- Department of Optometry, Chung Hwa University of Medical Technology, Tainan 717, Taiwan
| | - Wan-Shan Li
- Department of Pathology, Chi Mei Medical Center, Tainan 710, Taiwan; (T.-J.C.); (H.-L.H.); (W.-S.L.); (H.-H.T.)
- Department of Medical Technology, Chung Hwa University of Medical Technology, Tainan 717, Taiwan
| | - Hsin-Hwa Tsai
- Department of Pathology, Chi Mei Medical Center, Tainan 710, Taiwan; (T.-J.C.); (H.-L.H.); (W.-S.L.); (H.-H.T.)
- Department of Medical Research, Chi Mei Medical Center, Tainan 710, Taiwan;
| | - Chien-Feng Li
- Department of Pathology, Chi Mei Medical Center, Tainan 710, Taiwan; (T.-J.C.); (H.-L.H.); (W.-S.L.); (H.-H.T.)
- Department of Medical Research, Chi Mei Medical Center, Tainan 710, Taiwan;
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan
- Institute of Precision Medicine, National Sun Yat-Sen University, Kaohsiung 804, Taiwan
- Department of Pathology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Correspondence: (C.-F.L.); (H.-Y.L.)
| | - Hong-Yue Lai
- Department of Pathology, Chi Mei Medical Center, Tainan 710, Taiwan; (T.-J.C.); (H.-L.H.); (W.-S.L.); (H.-H.T.)
- Department of Medical Research, Chi Mei Medical Center, Tainan 710, Taiwan;
- Correspondence: (C.-F.L.); (H.-Y.L.)
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