1
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Sato M, Kato T, Tezen Y, Hayashi T, Matsui T, Kobayashi K, Sekigawa K, Tajiri R, Mitsui H. Traditional serrated adenoma with superficially serrated adenoma: A case treated with endoscopic submucosal dissection with detailed endoscopic observation and pathological study. DEN OPEN 2024; 4:e247. [PMID: 37273517 PMCID: PMC10235794 DOI: 10.1002/deo2.247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/10/2023] [Accepted: 05/12/2023] [Indexed: 06/06/2023]
Abstract
A new subtype of serrated lesions, superficially serrated adenoma (SuSA), has been proposed as a lesion that histopathologically exhibits the morphological features of both conventional adenomas and serrated lesions and is difficult to classify as either one. SuSA has been elucidated to be a precursor lesion of KRAS-type traditional serrated adenoma. It has also been reported that SuSA may have malignant potential. We report a case treated with endoscopic submucosal dissection and detailed observation. Endoscopy revealed a raised lesion with a two-tier raised appearance in the sigmoid colon: a tall pinecone-like reddish structure and flattened whitish elevation on white light imaging. Magnifying narrow-band imaging revealed conspicuous blood vessels in the pinecone-like structure and slightly dilated reticular vessels in the flattened area. Crystal violet staining showed that the pinecone-like structure had a type IVH pit pattern and the flattened area had a stellate to slightly elongated type IIIH pit pattern diagnosed based on Kudo's classification and other pit pattern classification systems. Ki67-positive cells were distributed in the basal and middle layers of the gland in the flattened elevated area. Genetic analysis results were positive for KRAS mutation and negative for BRAF mutation. Histopathological examination revealed a traditional serrated adenoma in the pinecone-like structure and SuSA in the adjacent flattened elevated area.
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Affiliation(s)
- Momoka Sato
- Department of GastroenterologyTokyo Teishin HospitalTokyoJapan
| | - Tomoji Kato
- Department of GastroenterologyTokyo Teishin HospitalTokyoJapan
| | - Yu Tezen
- Department of GastroenterologyTokyo Teishin HospitalTokyoJapan
| | - Takeshi Hayashi
- Department of GastroenterologyTokyo Teishin HospitalTokyoJapan
| | - Toru Matsui
- Department of GastroenterologyTokyo Teishin HospitalTokyoJapan
| | | | | | | | - Hiroshi Mitsui
- Department of GastroenterologyTokyo Teishin HospitalTokyoJapan
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2
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Wang JD, Xu GS, Hu XL, Li WQ, Yao N, Han FZ, Zhang Y, Qu J. The histologic features, molecular features, detection and management of serrated polyps: a review. Front Oncol 2024; 14:1356250. [PMID: 38515581 PMCID: PMC10955069 DOI: 10.3389/fonc.2024.1356250] [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: 12/15/2023] [Accepted: 02/21/2024] [Indexed: 03/23/2024] Open
Abstract
The serrated pathway to colorectal cancers (CRCs) is a significant pathway encompassing five distinct types of lesions, namely hyperplastic polyps (HPs), sessile serrated lesions (SSLs), sessile serrated lesions with dysplasia (SSL-Ds), traditional serrated adenomas (TSAs), and serrated adenoma unclassified. In contrast to the conventional adenoma-carcinoma pathway, the serrated pathway primarily involves two mechanisms: BRAF/KRAS mutations and CpG island methylator phenotype (CIMP). HPs are the most prevalent non-malignant lesions, while SSLs play a crucial role as precursors to CRCs, On the other hand, traditional serrated adenomas (TSAs) are the least frequently encountered subtype, also serving as precursors to CRCs. It is crucial to differentiate these lesions based on their unique morphological characteristics observed in histology and colonoscopy, as the identification and management of these serrated lesions significantly impact colorectal cancer screening programs. The management of these lesions necessitates the crucial steps of removing premalignant lesions and implementing regular surveillance. This article provides a comprehensive summary of the epidemiology, histologic features, molecular features, and detection methods for various serrated polyps, along with recommendations for their management and surveillance.
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Affiliation(s)
- Jin-Dong Wang
- Department of General Surgery, Peking University Aerospace School of Clinical Medicine, Beijing, China
| | - Guo-Shuai Xu
- Department of General Surgery, Aerospace Center Hospital, Beijing, China
| | - Xin-Long Hu
- Department of General Surgery, Aerospace Center Hospital, Beijing, China
| | - Wen-Qiang Li
- Department of General Surgery, Aerospace Center Hospital, Beijing, China
| | - Nan Yao
- Department of General Surgery, Aerospace Center Hospital, Beijing, China
| | - Fu-Zhou Han
- Department of General Surgery, Aerospace Center Hospital, Beijing, China
| | - Yin Zhang
- Department of General Surgery, Aerospace Center Hospital, Beijing, China
| | - Jun Qu
- Department of General Surgery, Aerospace Center Hospital, Beijing, China
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3
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Ter Steege EJ, Doornbos LW, Haughton PD, van Diest PJ, Hilkens J, Derksen PWB, Bakker ERM. R-spondin-3 promotes proliferation and invasion of breast cancer cells independently of Wnt signaling. Cancer Lett 2023; 568:216301. [PMID: 37406727 DOI: 10.1016/j.canlet.2023.216301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 06/27/2023] [Accepted: 07/02/2023] [Indexed: 07/07/2023]
Abstract
We recently identified R-spondin-3 (RSPO3) as a novel driver of breast cancer associating with reduced patient survival, expanding its clinical value as potential therapeutic target that had been recognized mostly for colorectal cancer so far. (Pre)clinical studies exploring RSPO3 targeting in colorectal cancer approach this indirectly with Wnt inhibitors, or directly with anti-RSPO3 antibodies. Here, we address the clinical relevance of RSPO3 in breast cancer and provide insight in the oncogenic activities of RSPO3. Utilizing the RSPO3 breast cancer mouse model, we show that RSPO3 drives the aberrant expansion of luminal progenitor cells expressing cancer stem cell marker CD61, inducing proliferative, poorly differentiated and invasive tumors. Complementary studies with tumor organoids and human breast cancer cell lines demonstrate that RSPO3 consistently promotes the proliferation and invasion of breast cancer cells. Importantly, RSPO3 exerts these oncogenic effects independently of Wnt signaling, rejecting the therapeutic value of Wnt inhibitors in RSPO3-driven breast cancer. Instead, direct RSPO3 targeting effectively inhibited RSPO3-driven growth of breast cancer cells. Conclusively, our data indicate that RSPO3 exerts unfavorable oncogenic effects in breast cancer, enhancing proliferation and malignancy in a Wnt-independent fashion, proposing RSPO3 itself as a valuable therapeutic target in breast cancer.
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Affiliation(s)
- Eline J Ter Steege
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Loes W Doornbos
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Peter D Haughton
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Paul J van Diest
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - John Hilkens
- Department of Molecular Genetics, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Patrick W B Derksen
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands.
| | - Elvira R M Bakker
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands; Department of Molecular Genetics, Netherlands Cancer Institute, Amsterdam, the Netherlands.
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4
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ter Steege EJ, Boer M, Timmer NC, Ammerlaan CME, Song J, Derksen PWB, Hilkens J, Bakker ERM. R-spondin-3 is an oncogenic driver of poorly differentiated invasive breast cancer. J Pathol 2022; 258:289-299. [PMID: 36106661 PMCID: PMC9825844 DOI: 10.1002/path.5999] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/28/2022] [Accepted: 08/05/2022] [Indexed: 01/11/2023]
Abstract
R-spondins (RSPOs) are influential signaling molecules that promote the Wnt/β-catenin pathway and self-renewal of stem cells. Currently, RSPOs are emerging as clinically relevant oncogenes, being linked to cancer development in multiple organs. Although this has instigated the rapid development and testing of therapeutic antibodies targeting RSPOs, functional evidence that RSPO causally drives cancer has focused primarily on the intestinal tract. Here, we assess the oncogenic capacity of RSPO in breast cancer in a direct fashion by generating and characterizing a novel mouse model with conditional Rspo3 expression in the mammary gland. We also address the prevalence of RSPO gene alterations in breast cancer patients. We found that a quarter of breast cancer patients harbor RSPO2/RSPO3 copy number amplifications, which are associated with lack of steroid hormone receptor expression and reduced patient survival. Foremost, we demonstrate the causal oncogenic capacity of RSPO3 in the breast, as conditional Rspo3 overexpression consistently drives the development of mammary adenocarcinomas in our novel Rspo3 breast cancer model. RSPO3-driven mammary tumors typically show poor differentiation, areas of epithelial-to-mesenchymal transition, and metastatic potential. Given the reported interplay in the Wnt/β-catenin pathway, we comparatively analyzed RSPO3-driven mouse mammary tumors versus classical WNT1-driven analogues. This revealed that RSPO3-driven tumors are distinct, as the poorly differentiated tumor morphology and metastatic potential were observed in RSPO3-driven tumorigenesis exclusively, further substantiated by differentiating gene expression profiles. Co-expression of Rspo3 and Wnt1 transduced mammary tumors with a mixed phenotype harboring morphological features characteristic of both transgenes. In summary, we report that a quarter of breast cancer patients harbor RSPO2/RSPO3 copy number gains, and these patients have a worse prognosis, whilst providing in vivo evidence that RSPO3 drives poorly differentiated invasive breast cancer in mice. Herewith, we establish RSPO3 as a driver of breast cancer with clinical relevance, proposing RSPO3 as a novel candidate target for therapy in breast cancer. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Eline J ter Steege
- Department of PathologyUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Mandy Boer
- Department of Molecular GeneticsThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Nikki C Timmer
- Department of Molecular GeneticsThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Carola ME Ammerlaan
- Department of Molecular GeneticsThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Ji‐Ying Song
- Department of Experimental Animal PathologyThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Patrick WB Derksen
- Department of PathologyUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - John Hilkens
- Department of Molecular GeneticsThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Elvira RM Bakker
- Department of PathologyUniversity Medical Center UtrechtUtrechtThe Netherlands,Department of Molecular GeneticsThe Netherlands Cancer InstituteAmsterdamThe Netherlands
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5
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Hashimoto T, Takayanagi D, Yonemaru J, Naka T, Nagashima K, Yatabe Y, Shida D, Hamamoto R, Kleeman SO, Leedham SJ, Maughan T, Takashima A, Shiraishi K, Sekine S. Clinicopathological and molecular characteristics of RSPO fusion-positive colorectal cancer. Br J Cancer 2022; 127:1043-1050. [PMID: 35715628 PMCID: PMC9470590 DOI: 10.1038/s41416-022-01880-w] [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: 10/21/2021] [Revised: 05/26/2022] [Accepted: 06/01/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND RSPO fusions that lead to WNT pathway activation are potential therapeutic targets in colorectal cancer (CRC), but their clinicopathological significance remains unclear. METHODS We screened 1019 CRCs for RSPO fusions using multiplex reverse transcription-PCR. The RSPO fusion-positive tumours were subjected to whole-exome sequencing (WES). RESULTS Our analysis identified 29 CRCs with RSPO fusions (2.8%), consisting of five with an EIF3E-RSPO2 fusion and 24 with PTPRK-RSPO3 fusions. The patients were 17 women and 12 men. Thirteen tumours (45%) were right-sided. Histologically, approximately half of the tumours (13/29, 45%) had a focal or extensive mucinous component that was significantly more frequent than the RSPO fusion-negative tumours (13%; P = 8.1 × 10-7). Four tumours (14%) were mismatch repair-deficient. WES identified KRAS, BRAF, and NRAS mutations in a total of 27 tumours (93%). In contrast, pathogenic mutations in major WNT pathway genes, such as APC, CTNNB1 and RNF43, were absent. RSPO fusion status did not have a statistically significant influence on the overall or recurrence-free survival. These clinicopathological and genetic features were also confirmed in a pooled analysis of previous studies. CONCLUSION RSPO fusion-positive CRCs constitute a rare subgroup of CRCs with several characteristic clinicopathological and genetic features.
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Affiliation(s)
- Taiki Hashimoto
- Division of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan
| | - Daisuke Takayanagi
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Junpei Yonemaru
- Division of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan
| | - Tomoaki Naka
- Division of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan
| | - Kengo Nagashima
- Biostatistics Unit, Clinical and Translational Research Center, Keio University Hospital, Tokyo, Japan
| | - Yasushi Yatabe
- Division of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan.,Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo, Japan
| | - Dai Shida
- Division of Colorectal Surgery, National Cancer Center Hospital, Tokyo, Japan.,Division of Frontier Surgery, The Institute of Medical Science, Tokyo, Japan
| | - Ryuji Hamamoto
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, Japan
| | | | - Simon J Leedham
- Intestinal Stem Cell Biology Lab, Welcome Trust Centre Human Genetics, University of Oxford, Oxford, UK
| | | | - Atsuo Takashima
- Division of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Kouya Shiraishi
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Shigeki Sekine
- Division of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan. .,Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo, Japan.
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6
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Ascension AM, Arauzo-Bravo MJ. BigMPI4py: Python Module for Parallelization of Big Data Objects Discloses Germ Layer Specific DNA Demethylation Motifs. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:1507-1522. [PMID: 33301409 DOI: 10.1109/tcbb.2020.3043979] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Parallelization in Python integrates Message Passing Interface via the mpi4py module. Since mpi4py does not support parallelization of objects greater than 231 bytes, we developed BigMPI4py, a Python module that wraps mpi4py, supporting object sizes beyond this boundary. BigMPI4py automatically determines the optimal object distribution strategy, and uses vectorized methods, achieving higher parallelization efficiency. BigMPI4py facilitates the implementation of Python for Big Data applications in multicore workstations and High Performance Computer systems. We use BigMPI4py to speed-up the search for germ line specific de novo DNA methylated/unmethylated motifs from the 59 whole genome bisulfite sequencing DNA methylation samples from 27 human tissues of the ENCODE project. We developed a parallel implementation of the Kruskall-Wallis test to find CpGs with differential methylation across germ layers. The parallel evaluation of the significance of 55 million CpG achieved a 22x speedup with 25 cores allowing us an efficient identification of a set of hypermethylated genes in ectoderm and mesoderm-related tissues, and another set in endoderm-related tissues and finally, the discovery of germ layer specific DNA demethylation motifs. Our results point out that DNA methylation signal provide a higher degree of information for the demethylated state than for the methylated state. BigMPI4py is available at https://https://www.arauzolab.org/tools/bigmpi4py and https://gitlab.com/alexmascension/bigmpi4py and the Jupyter Notebook with WGBS analysis at https://gitlab.com/alexmascension/wgbs-analysis.
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7
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Mizuguchi Y, Tanaka Y, Cho H, Sekiguchi M, Takamaru H, Yamada M, Sakamoto T, Matsuda T, Hashimoto T, Sekine S, Saito Y. Endoscopic features of isolated and traditional serrated adenoma-associated superficially serrated adenomas of the colorectum. Dig Endosc 2022; 34:153-162. [PMID: 33871900 DOI: 10.1111/den.13992] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 04/11/2021] [Indexed: 02/08/2023]
Abstract
BACKGROUND AND AIM Superficially serrated adenoma (SuSA) is a recently proposed subtype of colorectal serrated lesions. It is characterized by distinct clinicopathological and molecular features, including mixed serrated and adenomatous histology and frequent genetic alterations involving KRAS and RSPO. This study aimed to characterize the endoscopic features of isolated and traditional serrated adenoma (TSA)-associated SuSAs. METHODS We retrospectively evaluated the endoscopic findings of 25 isolated SuSAs and 21 TSA-associated SuSAs that were histologically and molecularly characterized. RESULTS SuSAs appeared as a sessile polyp or slightly elevated lesion located mostly in the sigmoid colon and rectum (88%). The size was between 3 and 20 mm (median, 6 mm). Most of them exhibited KRAS mutations (96%) and RSPO fusions/overexpression (92%). Endoscopically, many lesions had a whitish color (84%), a distinct border (96%), an irregular border (76%), and a lobulated surface (72%). However, diminutive lesions exhibited overlapping features with hyperplastic polyps. On narrow-band imaging, vessel patterns were invisible or appeared as lacy microvessels in most lesions (80%). Chromoendoscopy invariably showed stellar or elongated/branched stellar pits, indicating a serrated microarchitecture. Most TSA-associated SuSAs typically presented as polyps with a two-tier raised appearance, consisting of whitish lower and reddish higher components corresponding to a SuSA and a TSA, respectively. CONCLUSIONS SuSAs exhibit several characteristic endoscopic features on white-light and image-enhanced endoscopy. Diminutive lesions exhibit endoscopic features overlapping with hyperplastic polyps. Nonetheless, the endoscopic diagnosis of larger and TSA-associated SuSAs may be feasible.
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Affiliation(s)
- Yasuhiko Mizuguchi
- Endoscopy Division, National Cancer Center Hospital, Tokyo, Japan.,Division of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan
| | - Yusaku Tanaka
- Endoscopy Division, National Cancer Center Hospital, Tokyo, Japan.,Division of Gastroenterology, Keiyu Hospital, Kanagawa, Japan
| | - Hourin Cho
- Endoscopy Division, National Cancer Center Hospital, Tokyo, Japan
| | - Masau Sekiguchi
- Endoscopy Division, National Cancer Center Hospital, Tokyo, Japan.,Cancer Screening Center, National Cancer Center Hospital, Tokyo, Japan
| | | | - Masayoshi Yamada
- Endoscopy Division, National Cancer Center Hospital, Tokyo, Japan
| | - Taku Sakamoto
- Endoscopy Division, National Cancer Center Hospital, Tokyo, Japan
| | - Takahisa Matsuda
- Endoscopy Division, National Cancer Center Hospital, Tokyo, Japan.,Cancer Screening Center, National Cancer Center Hospital, Tokyo, Japan
| | - Taiki Hashimoto
- Division of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan
| | - Shigeki Sekine
- Division of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan.,Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo, Japan
| | - Yutaka Saito
- Endoscopy Division, National Cancer Center Hospital, Tokyo, Japan
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8
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Ter Steege EJ, Bakker ERM. The role of R-spondin proteins in cancer biology. Oncogene 2021; 40:6469-6478. [PMID: 34663878 PMCID: PMC8616751 DOI: 10.1038/s41388-021-02059-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/23/2021] [Accepted: 10/01/2021] [Indexed: 02/07/2023]
Abstract
R-spondin (RSPO) proteins constitute a family of four secreted glycoproteins (RSPO1-4) that have appeared as multipotent signaling ligands. The best-known molecular function of RSPOs lie within their capacity to agonize the Wnt/β-catenin signaling pathway. As RSPOs act upon cognate receptors LGR4/5/6 that are typically expressed by stem cells and progenitor cells, RSPO proteins importantly potentiate Wnt/β-catenin signaling especially within these proliferative stem cell compartments. Since multiple organs express LGR4/5/6 receptors and RSPO ligands within their stem cell niches, RSPOs can exert an influential role in stem cell regulation throughout the body. Inherently, over the last decade a multitude of reports implicated the deregulation of RSPOs in cancer development. First, RSPO2 and RSPO3 gene fusions with concomitant enhanced expression have been identified in colon cancer patients, and proposed as an alternative driver of Wnt/β-catenin hyperactivation that earmarks cancer in the colorectal tract. Moreover, the causal oncogenic capacity of RSPO3 overactivation has been demonstrated in the mouse intestine. As a paradigm organ in this field, most of current knowledge about RSPOs in cancer is derived from studies in the intestinal tract. However, RSPO gene fusions as well as enhanced RSPO expression have been reported in multiple additional cancer types, affecting different organs that involve divergent stem cell hierarchies. Importantly, the emerging oncogenic role of RSPO and its potential clinical utility as a therapeutic target have been recognized and investigated in preclinical and clinical settings. This review provides a survey of current knowledge on the role of RSPOs in cancer biology, addressing the different organs implicated, and of efforts made to explore intervention opportunities in cancer cases with RSPO overrepresentation, including the potential utilization of RSPO as novel therapeutic target itself.
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Affiliation(s)
- Eline J Ter Steege
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Elvira R M Bakker
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands.
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9
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Mathkar PP, Chen X, Sulovari A, Li D. Characterization of Hepatitis B Virus Integrations Identified in Hepatocellular Carcinoma Genomes. Viruses 2021; 13:v13020245. [PMID: 33557409 PMCID: PMC7915589 DOI: 10.3390/v13020245] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/31/2021] [Accepted: 02/02/2021] [Indexed: 12/19/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a leading cause of cancer-related mortality. Almost half of HCC cases are associated with hepatitis B virus (HBV) infections, which often lead to HBV sequence integrations in the human genome. Accurate identification of HBV integration sites at a single nucleotide resolution is critical for developing a better understanding of the cancer genome landscape and of the disease itself. Here, we performed further analyses and characterization of HBV integrations identified by our recently reported VIcaller platform in recurrent or known HCC genes (such as TERT, MLL4, and CCNE1) as well as non-recurrent cancer-related genes (such as CSMD2, NKD2, and RHOU). Our pathway enrichment analysis revealed multiple pathways involving the alcohol dehydrogenase 4 gene, such as the metabolism pathways of retinol, tyrosine, and fatty acid. Further analysis of the HBV integration sites revealed distinct patterns involving the integration upper breakpoints, integrated genome lengths, and integration allele fractions between tumor and normal tissues. Our analysis also implies that the VIcaller method has diagnostic potential through discovering novel clonal integrations in cancer-related genes. In conclusion, although VIcaller is a hypothesis free virome-wide approach, it can still be applied to accurately identify genome-wide integration events of a specific candidate virus and their integration allele fractions.
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Affiliation(s)
- Pranav P. Mathkar
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA; (P.P.M.); (A.S.)
| | - Xun Chen
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA; (P.P.M.); (A.S.)
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto 606-8501, Japan
- Correspondence: (X.C.); (D.L.)
| | - Arvis Sulovari
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA; (P.P.M.); (A.S.)
- Cajal Neuroscience Inc., Seattle, WA 98102, USA
| | - Dawei Li
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA; (P.P.M.); (A.S.)
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL 33431, USA
- Correspondence: (X.C.); (D.L.)
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10
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Lund JB, Li S, Baumbach J, Christensen K, Li W, Mohammadnejad A, Pattie A, Marioni RE, Deary IJ, Tan Q. Weighted Gene Coregulation Network Analysis of Promoter DNA Methylation on All-Cause Mortality in Old-Aged Birth Cohorts Finds Modules of High-Risk Associated Biomarkers. J Gerontol A Biol Sci Med Sci 2020; 75:2249-2257. [PMID: 32154558 DOI: 10.1093/gerona/glaa066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Indexed: 02/07/2023] Open
Abstract
Overall or all-cause mortality is a key measure of health in a population. Multiple epigenome-wide association studies have been conducted on all-cause mortality with limited significant findings and low replication. To elucidate the coregulated DNA methylation patterns associated with all-cause mortality, we conducted a weighted DNA methylation coregulation network analysis on whole-blood samples of 1,425 older individuals from the Lothian Birth Cohorts of 1921 and 1936. Our network-based analysis defined coregulated DNA methylation patterns in gene promoters into clusters or modules whose correlation with all-cause mortality was assessed by survival analysis. We found two significant modules or gene clusters associated with all-cause mortality in LBC1921 based on their eigengenes; one negatively correlated (p = 8.14E-03, 698 genes) and one positively correlated (p = 4.26E-02, 1,431 genes) with the risk of death. The two modules were replicated in LBC1936 with the same directions of correlation (p = 6.35E-02 and p = 3.64E-02, respectively). Furthermore, the modules revealed 32 genes associated with all-cause mortality (FDR < 0.05) linked to various diseases, including cancer and diabetes. Additionally, we performed pathway analysis and found 22 pathways (FDR < 0.05), including a pathway for taste transduction, which has been shown to be associated with poor prognosis in acutely hospitalized patients, and several pathways were linked to different types of cancer. The results from our network analysis show that DNA methylation of multiple genes could have been coregulated in an association with the overall risk of death. The identified epigenetic markers might help with our understanding of the molecular basis of all-cause mortality and general health.
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Affiliation(s)
- Jesper B Lund
- Epidemiology and Biostatistics, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Shuxia Li
- Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Jan Baumbach
- Experimental Bioinformatics, Department of Informatics, TUM School of Life Sciences Weihenstephan, Germany
| | - Kaare Christensen
- Epidemiology and Biostatistics, Department of Public Health, University of Southern Denmark, Odense, Denmark.,Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Weilong Li
- Epidemiology and Biostatistics, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Afsaneh Mohammadnejad
- Epidemiology and Biostatistics, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Alison Pattie
- Department of Psychology, Centre for Cognitive Aging and Cognitive Epidemiology, University of Edinburgh, UK
| | - Riccardo E Marioni
- Department of Psychology, Centre for Cognitive Aging and Cognitive Epidemiology, University of Edinburgh, UK.,Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, Scotland, UK
| | - Ian J Deary
- Department of Psychology, Centre for Cognitive Aging and Cognitive Epidemiology, University of Edinburgh, UK.,Department of Psychology, University of Edinburgh, UK
| | - Qihua Tan
- Epidemiology and Biostatistics, Department of Public Health, University of Southern Denmark, Odense, Denmark.,Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
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11
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Kim JH, Kang GH. Evolving pathologic concepts of serrated lesions of the colorectum. J Pathol Transl Med 2020; 54:276-289. [PMID: 32580537 PMCID: PMC7385269 DOI: 10.4132/jptm.2020.04.15] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 04/15/2020] [Indexed: 12/12/2022] Open
Abstract
Here, we provide an up-to-date review of the histopathology and molecular pathology of serrated colorectal lesions. First, we introduce the updated contents of the 2019 World Health Organization classification for serrated lesions. The sessile serrated lesion (SSL) is a new diagnostic terminology that replaces sessile serrated adenoma and sessile serrated polyp. The diagnostic criteria for SSL were revised to require only one unequivocal distorted serrated crypt, which is sufficient for diagnosis. Unclassified serrated adenomas have been included as a new category of serrated lesions. Second, we review ongoing issues concerning the morphology of serrated lesions. Minor morphologic variants with distinct molecular features were recently defined, including serrated tubulovillous adenoma, mucin-rich variant of traditional serrated adenoma (TSA), and superficially serrated adenoma. In addition to intestinal dysplasia and serrated dysplasia, minimal deviation dysplasia and not otherwise specified dysplasia were newly suggested as dysplasia subtypes of SSLs. Third, we summarize the molecular features of serrated lesions. The critical determinant of CpG island methylation development in SSLs is patient age. Interestingly, there may be ethnic differences in BRAF/KRAS mutation frequencies in SSLs. The molecular pathogenesis of TSAs is divided into KRAS and BRAF mutation pathways. SSLs with MLH1 methylation can progress into favorable prognostic microsatellite instability-positive (MSI+)/CpG island methylator phenotype-positive (CIMP+) carcinomas, whereas MLH1-unmethylated SSLs and BRAF-mutated TSAs can be precursors of poor-prognostic MSI−/CIMP+ carcinomas. Finally, based on our recent data, we propose an algorithm for stratifying risk subgroups of non-dysplastic SSLs.
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Affiliation(s)
- Jung Ho Kim
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea.,Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Gyeong Hoon Kang
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea.,Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
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