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Deng S, Lu X, Wang X, Liang B, Xu H, Yang D, Cui G, Yonemura A, Paine H, Zhou Y, Zhang Y, Simile MM, Urigo F, Evert M, Calvisi DF, Green BL, Chen X. Overexpression of TBX3 suppresses tumorigenesis in experimental and human cholangiocarcinoma. Cell Death Dis 2024; 15:441. [PMID: 38909034 PMCID: PMC11193761 DOI: 10.1038/s41419-024-06839-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 06/12/2024] [Accepted: 06/17/2024] [Indexed: 06/24/2024]
Abstract
TBX3 behaves as a tumor suppressor or oncoprotein across cancer. However, TBX3 function remains undetermined in intrahepatic cholangiocarcinoma (iCCA), a deadly primary liver malignancy with few systemic treatment options. This study sought to investigate the impact of TBX3 on iCCA. We found that overexpression of TBX3 strongly inhibited human iCCA cell growth. In the Akt/FBXW7ΔF mouse iCCA model, overexpression of Tbx3 reduced cholangiocarcinogenesis in vivo, while inducible genetic knockout of Tbx3 accelerated iCCA growth. RNA-seq identified MAD2L1 as a downregulated gene in TBX3-overexpressing cells, and ChIP confirmed that TBX3 binds to the MAD2L1 promoter. CRISPR-mediated knockdown of Mad2l1 significantly reduced the growth of two iCCA models in vivo. Finally, we found that TBX3 expression is upregulated in ~20% of human iCCA samples, and its high expression is associated with less proliferation and better survival. MAD2L1 expression is upregulated in most human iCCA samples and negatively correlated with TBX3 expression. Altogether, our findings suggest that overexpression of TBX3 suppresses CCA progression via repressing MAD2L1 expression.
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Affiliation(s)
- Shanshan Deng
- Cancer Biology Program, University of Hawai'i Cancer Center, University of Hawai'i, Honolulu, HI, USA
- Department of Bioengineering and Therapeutic Sciences and Liver Center, University of California, San Francisco, CA, USA
| | - Xinjun Lu
- Department of Biliary-Pancreatic Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xue Wang
- Cancer Biology Program, University of Hawai'i Cancer Center, University of Hawai'i, Honolulu, HI, USA
| | - Binyong Liang
- Department of Bioengineering and Therapeutic Sciences and Liver Center, University of California, San Francisco, CA, USA
| | - Hongwei Xu
- Department of Bioengineering and Therapeutic Sciences and Liver Center, University of California, San Francisco, CA, USA
| | - Doris Yang
- Cancer Biology Program, University of Hawai'i Cancer Center, University of Hawai'i, Honolulu, HI, USA
| | - Guofei Cui
- Cancer Biology Program, University of Hawai'i Cancer Center, University of Hawai'i, Honolulu, HI, USA
- Department of Bioengineering and Therapeutic Sciences and Liver Center, University of California, San Francisco, CA, USA
| | - Andrew Yonemura
- Cancer Biology Program, University of Hawai'i Cancer Center, University of Hawai'i, Honolulu, HI, USA
| | - Honor Paine
- Department of Bioengineering and Therapeutic Sciences and Liver Center, University of California, San Francisco, CA, USA
| | - Yi Zhou
- Department of Bioengineering and Therapeutic Sciences and Liver Center, University of California, San Francisco, CA, USA
| | - Yi Zhang
- School of Pharmacy and Bioengineering, Chongqing University of Technology, 400054, Chongqing, China
| | - Maria Maddalena Simile
- Department of Medicine, Surgery, and Pharmacy, Division of Experimental Pathology and Oncology, University of Sassari, 07100, Sassari, Italy
| | - Francesco Urigo
- Institute of Pathology, University of Regensburg, Regensburg, Germany
| | - Matthias Evert
- Institute of Pathology, University of Regensburg, Regensburg, Germany
| | - Diego F Calvisi
- Institute of Pathology, University of Regensburg, Regensburg, Germany
| | - Benjamin L Green
- Cancer Biology Program, University of Hawai'i Cancer Center, University of Hawai'i, Honolulu, HI, USA.
| | - Xin Chen
- Cancer Biology Program, University of Hawai'i Cancer Center, University of Hawai'i, Honolulu, HI, USA.
- Department of Bioengineering and Therapeutic Sciences and Liver Center, University of California, San Francisco, CA, USA.
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Ala U, Fagoonee S. RNA-binding protein transcripts as potential biomarkers for detecting Primary Sclerosing Cholangitis and for predicting its progression to Cholangiocarcinoma. Front Mol Biosci 2024; 11:1388294. [PMID: 38903178 PMCID: PMC11187294 DOI: 10.3389/fmolb.2024.1388294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 05/13/2024] [Indexed: 06/22/2024] Open
Abstract
Primary Sclerosing Cholangitis (PSC) is a persistent inflammatory liver condition that affects the bile ducts and is commonly diagnosed in young individuals. Despite efforts to incorporate various clinical, biochemical and molecular parameters for diagnosing PSC, it remains challenging, and no biomarkers characteristic of the disease have been identified hitherto. PSC is linked with an uncertain prognosis, and there is a pressing need to explore multiomics databases to establish a new biomarker panel for the early detection of PSC's gradual progression into Cholangiocarcinoma (CCA) and for the development of effective therapeutic interventions. Apart from non-coding RNAs, other components of the Ribonucleoprotein (RNP) complex, such as RNA-Binding Proteins (RBPs), also hold great promise as biomarkers due to their versatile expression in pathological conditions. In the present review, an update on the RBP transcripts that show dysregulated expression in PSC and CCA is provided. Moreover, by utilizing a bioinformatic data mining approach, we give insight into those RBP transcripts that also exhibit differential expression in liver and gall bladder, as well as in body fluids, and are promising as biomarkers for diagnosing and predicting the prognosis of PSC. Expression data were bioinformatically extracted from public repositories usingTCGA Bile Duct Cancer dataset for CCA and specific NCBI GEO datasets for both PSC and CCA; more specifically, RBPs annotations were obtained from RBP World database. Interestingly, our comprehensive analysis shows an elevated expression of the non-canonical RBPs, FANCD2, as well as the microtubule dynamics regulator, ASPM, transcripts in the body fluids of patients with PSC and CCA compared with their respective controls, with the same trend in expression being observed in gall bladder and liver cancer tissues. Consequently, the manipulation of tissue expression of RBP transcripts might be considered as a strategy to mitigate the onset of CCA in PSC patients, and warrants further experimental investigation. The analysis performed herein may be helpful in the identification of non-invasive biomarkers for the early detection of PSC and for predicting its progression into CCA. In conclusion, future clinical research should investigate in more depth the full potential of RBP transcripts as biomarkers for human pathologies.
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Affiliation(s)
- Ugo Ala
- Department of Veterinary Sciences, University of Turin, Turin, Italy
| | - Sharmila Fagoonee
- Institute of Biostructure and Bioimaging (CNR), Molecular Biotechnology Center “Guido Tarone”, Turin, Italy
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Du X, Qi Z, Jiao Y, Wu W, Huang Q, Sun X, Hu S. HK2 promotes migration and invasion of intrahepatic cholangiocarcinoma via enhancing cancer stem-like cells' resistance to anoikis. Cell Signal 2024; 118:111126. [PMID: 38453126 DOI: 10.1016/j.cellsig.2024.111126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/16/2024] [Accepted: 02/29/2024] [Indexed: 03/09/2024]
Abstract
Cancer stem-like cells (CSLCs) and anoikis resistance play crucial roles in the metastasis of cancers. However, it remains unclear whether CSLCs are related to anoikis resistance in intrahepatic cholangiocarcinoma (ICC). Here we identified a group of stemness-related anoikis genes (SRAGs) via bioinformatic analysis of public data. Accordingly, a novel anoikis-related classification was established and it divided ICC into C1 and C2 type. Different type ICC displayed distinct prognosis, molecular as well immune characteristics. Furthermore, we found one key SRAGs via several machine learning algorithms. HK2 was up-regulated in tumor-repopulating cells (TRCs) of ICC, a kind of CSLCs with a potent resistance to anoikis. Its up-regulation may be caused by the activation of MTORC1 signaling in ICC-TRCs. And inhibition of HK2 significantly increased anoikis and decreased migration as well invasion in ICC-TRCs. Our studies provide an insight into the molecular mechanism underlying the resistance of ICC-TRCs to anoikis and enhance the evidences for targeting HK2 in ICC.
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Affiliation(s)
- Xiaojing Du
- Endoscopy Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zhuoran Qi
- Department of Gastroenterology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yunjia Jiao
- Clinical Laboratory, Minhang Hospital, Fudan University, No. 170, Xinsong Road, Shanghai 201199, China
| | - Wenzhi Wu
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Qingke Huang
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Xuecheng Sun
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Sunkuan Hu
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China..
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Plum PS, Hess T, Bertrand D, Morgenstern I, Velazquez Camacho O, Jonas C, Alidousty C, Wagner B, Roessler S, Albrecht T, Becker J, Richartz V, Holz B, Hoppe S, Poh HM, Chia BKH, Chan CX, Pathiraja T, Teo AS, Marquardt JU, Khng A, Heise M, Fei Y, Thieme R, Klein S, Hong JH, Dima SO, Popescu I, Hoppe-Lotichius M, Buettner R, Lautem A, Otto G, Quaas A, Nagarajan N, Rozen S, Teh BT, Goeppert B, Drebber U, Lang H, Tan P, Gockel I, Schumacher J, Hillmer AM. Integrative genomic analyses of European intrahepatic cholangiocarcinoma: Novel ROS1 fusion gene and PBX1 as prognostic marker. Clin Transl Med 2024; 14:e1723. [PMID: 38877653 PMCID: PMC11178519 DOI: 10.1002/ctm2.1723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 04/20/2024] [Accepted: 05/13/2024] [Indexed: 06/16/2024] Open
Abstract
BACKGROUND Cholangiocarcinoma (CCA) is a fatal cancer of the bile duct with a poor prognosis owing to limited therapeutic options. The incidence of intrahepatic CCA (iCCA) is increasing worldwide, and its molecular basis is emerging. Environmental factors may contribute to regional differences in the mutation spectrum of European patients with iCCA, which are underrepresented in systematic genomic and transcriptomic studies of the disease. METHODS We describe an integrated whole-exome sequencing and transcriptomic study of 37 iCCAs patients in Germany. RESULTS We observed as most frequently mutated genes ARID1A (14%), IDH1, BAP1, TP53, KRAS, and ATM in 8% of patients. We identified FGFR2::BICC1 fusions in two tumours, and FGFR2::KCTD1 and TMEM106B::ROS1 as novel fusions with potential therapeutic implications in iCCA and confirmed oncogenic properties of TMEM106B::ROS1 in vitro. Using a data integration framework, we identified PBX1 as a novel central regulatory gene in iCCA. We performed extended screening by targeted sequencing of an additional 40 CCAs. In the joint analysis, IDH1 (13%), BAP1 (10%), TP53 (9%), KRAS (7%), ARID1A (7%), NF1 (5%), and ATM (5%) were the most frequently mutated genes, and we found PBX1 to show copy gain in 20% of the tumours. According to other studies, amplifications of PBX1 tend to occur in European iCCAs in contrast to liver fluke-associated Asian iCCAs. CONCLUSIONS By analyzing an additional European cohort of iCCA patients, we found that PBX1 protein expression was a marker of poor prognosis. Overall, our findings provide insight into key molecular alterations in iCCA, reveal new targetable fusion genes, and suggest that PBX1 is a novel modulator of this disease.
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Affiliation(s)
- Patrick S Plum
- Department of General, Visceral, Cancer and Transplantation Surgery, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
- Institute of Pathology, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
- Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
| | - Timo Hess
- Center for Human Genetics, University Hospital of Marburg, Marburg, Germany
| | - Denis Bertrand
- Computational and Systems Biology, Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore, Singapore, Singapore
| | - Isabelle Morgenstern
- General, Visceral and Transplant Surgery, Johannes Gutenberg University, Mainz, Germany
| | - Oscar Velazquez Camacho
- Institute of Pathology, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Christoph Jonas
- Institute of Pathology, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Christina Alidousty
- Institute of Pathology, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Britta Wagner
- Institute of Pathology, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Stephanie Roessler
- Institute of Pathology, University of Heidelberg, Heidelberg, Germany
- Liver Cancer Center Heidelberg (LCCH), Heidelberg, Germany
| | - Thomas Albrecht
- Institute of Pathology, University of Heidelberg, Heidelberg, Germany
- Liver Cancer Center Heidelberg (LCCH), Heidelberg, Germany
| | - Jessica Becker
- Institute of Human Genetics, University Hospital of Bonn, Bonn, Germany
| | - Vanessa Richartz
- Institute of Pathology, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Barbara Holz
- Institute of Pathology, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Sascha Hoppe
- Institute of Pathology, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Huay Mei Poh
- Cancer Therapeutics and Stratified Oncology, Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore, Singapore, Singapore
| | - Burton Kuan Hui Chia
- Computational and Systems Biology, Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore, Singapore, Singapore
| | - Cheryl Xueli Chan
- Cancer Therapeutics and Stratified Oncology, Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore, Singapore, Singapore
| | - Thushangi Pathiraja
- Cancer Therapeutics and Stratified Oncology, Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore, Singapore, Singapore
| | - Audrey Sm Teo
- Cancer Therapeutics and Stratified Oncology, Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore, Singapore, Singapore
| | - Jens U Marquardt
- I Department of Medicine, Johannes Gutenberg University, Mainz, Germany
- Department of Medicine, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Alexis Khng
- Cancer Therapeutics and Stratified Oncology, Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore, Singapore, Singapore
| | - Michael Heise
- General, Visceral and Transplant Surgery, Johannes Gutenberg University, Mainz, Germany
- Department for General, Visceral and Transplant Surgery, University Hospital Frankfurt, Goethe-University Frankfurt/Main, Frankfurt, Germany
| | - Yao Fei
- Cancer Therapeutics and Stratified Oncology, Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore, Singapore, Singapore
| | - René Thieme
- Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
| | - Sebastian Klein
- Institute of Pathology, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Jing Han Hong
- Duke-NUS Medical School, Cancer and Stem Cell Biology, Singapore, Singapore
- Division of Medical Science, Laboratory of Cancer Epigenome, National Cancer Centre Singapore, Singapore, Singapore
| | - Simona O Dima
- Center of Digestive Diseases and Liver Transplantation, Fundeni Clinical Institute, Bucharest, Romania
| | - Irinel Popescu
- Center of Digestive Diseases and Liver Transplantation, Fundeni Clinical Institute, Bucharest, Romania
| | - Maria Hoppe-Lotichius
- General, Visceral and Transplant Surgery, Johannes Gutenberg University, Mainz, Germany
| | - Reinhard Buettner
- Institute of Pathology, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Anja Lautem
- General, Visceral and Transplant Surgery, Johannes Gutenberg University, Mainz, Germany
| | - Gerd Otto
- Emeritus of the Division of Transplantation Surgery, University Medical Center, Mainz, Germany
| | - Alexander Quaas
- Institute of Pathology, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Niranjan Nagarajan
- Computational and Systems Biology, Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore, Singapore, Singapore
| | - Steve Rozen
- Duke-NUS Medical School, Cancer and Stem Cell Biology, Singapore, Singapore
| | - Bin Tean Teh
- Duke-NUS Medical School, Cancer and Stem Cell Biology, Singapore, Singapore
| | - Benjamin Goeppert
- RKH Klinikum Ludwigsburg, Institute of Pathology and Neuropathology, Ludwigsburg, Germany
- Institute of Tissue Medicine and Pathology, University of Bern, Bern, Switzerland
| | - Uta Drebber
- Institute of Pathology, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Hauke Lang
- General, Visceral and Transplant Surgery, Johannes Gutenberg University, Mainz, Germany
| | - Patrick Tan
- Duke-NUS Medical School, Cancer and Stem Cell Biology, Singapore, Singapore
- Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore, Singapore, Singapore
| | - Ines Gockel
- Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
| | | | - Axel M Hillmer
- Institute of Pathology, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
- Cancer Therapeutics and Stratified Oncology, Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore, Singapore, Singapore
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
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Alexander WB, Wang W, Hill MA, O'Dell MR, Ruffolo LI, Guo B, Jackson KM, Ullman N, Friedland SC, McCall MN, Patel A, Figueroa-Guilliani N, Georger M, Belt BA, Whitney-Miller CL, Linehan DC, Murphy PJ, Hezel AF. Smad4 restricts injury-provoked biliary proliferation and carcinogenesis. Dis Model Mech 2024; 17:dmm050358. [PMID: 38415925 PMCID: PMC10924230 DOI: 10.1242/dmm.050358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 11/10/2023] [Indexed: 02/29/2024] Open
Abstract
Cholangiocarcinoma (CCA) is a deadly and heterogeneous type of cancer characterized by a spectrum of epidemiologic associations as well as genetic and epigenetic alterations. We seek to understand how these features inter-relate in the earliest phase of cancer development and through the course of disease progression. For this, we studied murine models of liver injury integrating the most commonly occurring gene mutations of CCA - including Kras, Tp53, Arid1a and Smad4 - as well as murine hepatobiliary cancer models and derived primary cell lines based on these mutations. Among commonly mutated genes in CCA, we found that Smad4 functions uniquely to restrict reactive cholangiocyte expansion to liver injury through restraint of the proliferative response. Inactivation of Smad4 accelerates carcinogenesis, provoking pre-neoplastic biliary lesions and CCA development in an injury setting. Expression analyses of Smad4-perturbed reactive cholangiocytes and CCA lines demonstrated shared enriched pathways, including cell-cycle regulation, MYC signaling and oxidative phosphorylation, suggesting that Smad4 may act via these mechanisms to regulate cholangiocyte proliferation and progression to CCA. Overall, we showed that TGFβ/SMAD4 signaling serves as a critical barrier restraining cholangiocyte expansion and malignant transformation in states of biliary injury.
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Affiliation(s)
- William B. Alexander
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY 14642, USA
- Department of Medicine, Hematology/Oncology, Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Wenjia Wang
- Department of Medicine, Hematology/Oncology, Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Margaret A. Hill
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY 14642, USA
- Department of Medicine, Hematology/Oncology, Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Michael R. O'Dell
- Department of Medicine, Hematology/Oncology, Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Luis I. Ruffolo
- Department of Surgery, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Bing Guo
- Department of Medicine, Hematology/Oncology, Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Katherine M. Jackson
- Department of Surgery, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Nicholas Ullman
- Department of Surgery, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Scott C. Friedland
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY 14642, USA
- Department of Medicine, Hematology/Oncology, Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Matthew N. McCall
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY 14642, USA
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Ankit Patel
- Department of Surgery, University of Rochester Medical Center, Rochester, NY 14642, USA
| | | | - Mary Georger
- Department of Surgery, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Brian A. Belt
- Department of Surgery, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Christa L. Whitney-Miller
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - David C. Linehan
- Department of Surgery, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Patrick J. Murphy
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Aram F. Hezel
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY 14642, USA
- Department of Medicine, Hematology/Oncology, Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY 14642, USA
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Zhu Y, Koleilat MKI, Roszik J, Kwong MK, Wang Z, Maru DM, Kopetz S, Kwong LN. A Gold Standard-Derived Modular Barcoding Approach to Cancer Transcriptomics. Cancers (Basel) 2024; 16:1886. [PMID: 38791964 PMCID: PMC11120226 DOI: 10.3390/cancers16101886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/22/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
A challenge with studying cancer transcriptomes is in distilling the wealth of information down into manageable portions of information. In this resource, we develop an approach that creates and assembles cancer type-specific gene expression modules into flexible barcodes, allowing for adaptation to a wide variety of uses. Specifically, we propose that modules derived organically from high-quality gold standards such as The Cancer Genome Atlas (TCGA) can accurately capture and describe functionally related genes that are relevant to specific cancer types. We show that such modules can: (1) uncover novel gene relationships and nominate new functional memberships, (2) improve and speed up analysis of smaller or lower-resolution datasets, (3) re-create and expand known cancer subtyping schemes, (4) act as a "decoder" to bridge seemingly disparate established gene signatures, and (5) efficiently apply single-cell RNA sequencing information to other datasets. Moreover, such modules can be used in conjunction with native spreadsheet program commands to create a powerful and rapid approach to hypothesis generation and testing that is readily accessible to non-bioinformaticians. Finally, we provide tools for users to create and interpret their own modules. Overall, the flexible modular nature of the proposed barcoding provides a user-friendly approach to rapidly decoding transcriptome-wide data for research or, potentially, clinical uses.
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Affiliation(s)
- Yan Zhu
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (Y.Z.); (M.K.I.K.)
| | - Mohamad Karim I. Koleilat
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (Y.Z.); (M.K.I.K.)
| | - Jason Roszik
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Man Kam Kwong
- Department of Applied Mathematics, Hong Kong Polytechnic University, Hong Kong, China;
| | - Zhonglin Wang
- Social Science Research Institute, Duke University, Durham, NC 27708, USA;
| | - Dipen M. Maru
- Department of Anatomical Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Lawrence N. Kwong
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (Y.Z.); (M.K.I.K.)
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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7
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Roth GS, Verlingue L, Sarabi M, Blanc JF, Boleslawski E, Boudjema K, Bretagne-Bignon AL, Camus-Duboc M, Coriat R, Créhange G, De Baere T, de la Fouchardière C, Dromain C, Edeline J, Gelli M, Guiu B, Horn S, Laurent-Croise V, Lepage C, Lièvre A, Lopez A, Manfredi S, Meilleroux J, Neuzillet C, Paradis V, Prat F, Ronot M, Rosmorduc O, Cunha AS, Soubrane O, Turpin A, Louvet C, Bouché O, Malka D. Biliary tract cancers: French national clinical practice guidelines for diagnosis, treatments and follow-up (TNCD, SNFGE, FFCD, UNICANCER, GERCOR, SFCD, SFED, AFEF, SFRO, SFP, SFR, ACABi, ACHBPT). Eur J Cancer 2024; 202:114000. [PMID: 38493667 DOI: 10.1016/j.ejca.2024.114000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/28/2024] [Accepted: 03/01/2024] [Indexed: 03/19/2024]
Abstract
INTRODUCTION This document is a summary of the French intergroup guidelines of the management of biliary tract cancers (BTC) (intrahepatic, perihilar and distal cholangiocarcinomas, and gallbladder carcinomas) published in September 2023, available on the website of the French Society of Gastroenterology (SNFGE) (www.tncd.org). METHODS This collaborative work was conducted under the auspices of French medical and surgical societies involved in the management of BTC. Recommendations were graded in three categories (A, B and C) according to the level of scientific evidence until August 2023. RESULTS BTC diagnosis and staging is mainly based on enhanced computed tomography, magnetic resonance imaging and (endoscopic) ultrasound-guided biopsy. Treatment strategy depends on BTC subtype and disease stage. Surgery followed by adjuvant capecitabine is recommended for localised disease. No neoadjuvant treatment is validated to date. Cisplatin-gemcitabine chemotherapy combined to the anti-PD-L1 inhibitor durvalumab is the first-line standard of care for advanced disease. Early systematic tumour molecular profiling is recommended to screen for actionable alterations (IDH1 mutations, FGFR2 rearrangements, HER2 amplification, BRAFV600E mutation, MSI/dMMR status, etc.) and guide subsequent lines of treatment. In the absence of actionable alterations, FOLFOX chemotherapy is the only second-line standard-of-care. No third-line chemotherapy standard is validated to date. CONCLUSION These guidelines are intended to provide a personalised therapeutic strategy for daily clinical practice. Each individual BTC case should be discussed by a multidisciplinary team.
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Affiliation(s)
- Gael S Roth
- Univ. Grenoble Alpes / Hepato-Gastroenterology and Digestive Oncology department, CHU Grenoble Alpes / Institute for Advanced Biosciences, CNRS UMR 5309-INSERM U1209, Grenoble, France
| | - Loic Verlingue
- Medical Oncology Department, Centre Léon Bérard, 28 rue Laennec, Lyon, France
| | - Matthieu Sarabi
- Gastroenterology Department, Hopital privé Jean Mermoz, 69008 Lyon, France
| | | | - Emmanuel Boleslawski
- Univ. Lille, INSERM U1189, CHU Lille, Service de Chirurgie Digestive et Transplantations, Lille, France
| | - Karim Boudjema
- Département de chirurgie viscérale hépatobiliaire, CHU de Rennes, Rennes, France
| | | | - Marine Camus-Duboc
- Endoscopie digestive, Hôpital Saint-Antoine, AP-HP/Sorbonne Université, Paris France
| | - Romain Coriat
- Service de gastroentérologie, d'endoscopie et d'oncologie digestive, Hôpital Cochin, APHP, Paris, France
| | - Gilles Créhange
- Radiation Oncology Department. Paris/Saint-Cloud/Orsay, Institut Curie. PSL Research University, Paris, France
| | - Thierry De Baere
- Département de Radiologie Interventionnelle, Gustave Roussy, 94805 Villejuif, France
| | | | - Clarisse Dromain
- Service de radiodiagnostic et radiologie interventionnelle, Centre Hospitalier Universitaire Vaudois, Switzerland
| | | | - Maximiliano Gelli
- Département de Chirurgie Viscérale, Gustave Roussy, 94805 Villejuif, France
| | - Boris Guiu
- Department of Radiology, St-Eloi University Hospital - Montpellier School of Medicine, Montpellier, France
| | - Samy Horn
- Department of Radiation Oncology, Centre Hospitalier Lyon Sud, Pierre Benite, France
| | - Valérie Laurent-Croise
- Department of Radiology, Centre Hospitalier Universitaire de Nancy, Hôpital de Brabois, 54500 Vandœuvre-lès-Nancy, France
| | - Côme Lepage
- Université de Bourgogne, CHU Dijon-Bourgogne, INSERM U1231. BP 87 900, 14 rue Paul Gaffarel, 21079 Dijon, France
| | - Astrid Lièvre
- Department of Gastroenterology, Rennes University Hospital, University of Rennes 1, INSERM Unité 1242, Rennes, France
| | - Anthony Lopez
- INSERM U1256, NGERE, Faculty of Medicine, University of Lorraine, 54500 Vandœuvre-lès-Nancy, France; Department of Hepatology and Gastroenterology, Nancy University Hospital, University of Lorraine, 54500 Vandœuvre-lès-Nancy, France, NGERE, Faculty of Medicine, University of Lorraine, 54500 Vandœuvre-lès-Nancy, France
| | - Sylvain Manfredi
- Université de Bourgogne, CHU Dijon-Bourgogne, INSERM U1231. BP 87 900, 14 rue Paul Gaffarel, 21079 Dijon, France
| | - Julie Meilleroux
- Pathology and Cytology Department, CHU Toulouse, IUCT Oncopole, Toulouse Cedex 9, France
| | - Cindy Neuzillet
- GI Oncology, Department of Medical Oncology, Institut Curie - Site Saint Cloud, Versailles Saint-Quentin University, Paris Saclay University, Saint-Cloud, France
| | - Valérie Paradis
- Université Paris Cité, APHP.Nord Sce d'Anatomie Pathologique Hôpital Beaujon, Clichy, INSERM UMR 1149, France
| | - Frédéric Prat
- Endoscopie digestive, Hôpital Beaujon, Clichy, France
| | - Maxime Ronot
- Department of Medical Imaging, Beaujon University Hospital, Clichy, France
| | - Olivier Rosmorduc
- AP-HP Hôpital Paul-Brousse, Centre Hépato-Biliaire, INSERM U1193, Université Paris-Saclay, FHU Hépatinov, France
| | - Antonio Sa Cunha
- AP-HP Hôpital Paul-Brousse, Centre Hépato-Biliaire, INSERM U1193, Université Paris-Saclay, FHU Hépatinov, France
| | - Olivier Soubrane
- Department of Digestive Surgery, Institut Mutualiste Montsouris, Paris, France
| | - Anthony Turpin
- Department of Medical Oncology, CNRS UMR9020, Inserm UMR-S 1277-Canther-Cancer Heterogeneity, Plasticity and Resistance to Therapies, University Lille, CHU Lille, Lille; GERCOR, Paris, France
| | - Christophe Louvet
- Department of Medical Oncology, Institute Mutualiste Montsouris, Paris, France
| | - Olivier Bouché
- Gastroenterology and Digestive Oncology Department, Robert-Debré University Hospital, Reims, France
| | - David Malka
- Department of Medical Oncology, Institute Mutualiste Montsouris, Paris, France.
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8
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Lee SH, Song SY. Recent Advancement in Diagnosis of Biliary Tract Cancer through Pathological and Molecular Classifications. Cancers (Basel) 2024; 16:1761. [PMID: 38730713 PMCID: PMC11083053 DOI: 10.3390/cancers16091761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/24/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024] Open
Abstract
Biliary tract cancers (BTCs), including intrahepatic, perihilar, and distal cholangiocarcinomas, as well as gallbladder cancer, are a diverse group of cancers that exhibit unique molecular characteristics in each of their anatomic and pathological subtypes. The pathological classification of BTCs compromises distinct growth patterns, including mass forming, periductal infiltrating, and intraductal growing types, which can be identified through gross examination. The small-duct and large-duct types of intrahepatic cholangiocarcinoma have been recently introduced into the WHO classification. The presentation of typical clinical symptoms, as well as the extensive utilization of radiological, endoscopic, and molecular diagnostic methods, is thoroughly detailed in the description. To overcome the limitations of traditional tissue acquisition methods, new diagnostic modalities are being explored. The treatment landscape is also rapidly evolving owing to the emergence of distinct subgroups with unique molecular alterations and corresponding targeted therapies. Furthermore, we emphasize the crucial aspects of diagnosing BTC in practical clinical settings.
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Affiliation(s)
- Sang-Hoon Lee
- Department of Internal Medicine, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul 05030, Republic of Korea;
| | - Si Young Song
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03772, Republic of Korea
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9
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Lewinska M, Zhuravleva E, Satriano L, Martinez MB, Bhatt DK, Oliveira DVNP, Antoku Y, Keggenhoff FL, Castven D, Marquardt JU, Matter MS, Erler JT, Oliveira RC, Aldana BI, Al-Abdulla R, Perugorria MJ, Calvisi DF, Perez LA, Rodrigues PM, Labiano I, Banales JM, Andersen JB. Fibroblast-Derived Lysyl Oxidase Increases Oxidative Phosphorylation and Stemness in Cholangiocarcinoma. Gastroenterology 2024; 166:886-901.e7. [PMID: 38096955 DOI: 10.1053/j.gastro.2023.11.302] [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: 02/27/2023] [Revised: 10/24/2023] [Accepted: 11/20/2023] [Indexed: 12/31/2023]
Abstract
BACKGROUND & AIMS Metabolic and transcriptional programs respond to extracellular matrix-derived cues in complex environments, such as the tumor microenvironment. Here, we demonstrate how lysyl oxidase (LOX), a known factor in collagen crosslinking, contributes to the development and progression of cholangiocarcinoma (CCA). METHODS Transcriptomes of 209 human CCA tumors, 143 surrounding tissues, and single-cell data from 30 patients were analyzed. The recombinant protein and a small molecule inhibitor of the LOX activity were used on primary patient-derived CCA cultures to establish the role of LOX in migration, proliferation, colony formation, metabolic fitness, and the LOX interactome. The oncogenic role of LOX was further investigated by RNAscope and in vivo using the AKT/NICD genetically engineered murine CCA model. RESULTS We traced LOX expression to hepatic stellate cells and specifically hepatic stellate cell-derived inflammatory cancer-associated fibroblasts and found that cancer-associated fibroblast-driven LOX increases oxidative phosphorylation and metabolic fitness of CCA, and regulates mitochondrial function through transcription factor A, mitochondrial. Inhibiting LOX activity in vivo impedes CCA development and progression. Our work highlights that LOX alters tumor microenvironment-directed transcriptional reprogramming of CCA cells by facilitating the expression of the oxidative phosphorylation pathway and by increasing stemness and mobility. CONCLUSIONS Increased LOX is driven by stromal inflammatory cancer-associated fibroblasts and correlates with diminished survival of patients with CCA. Modulating the LOX activity can serve as a novel tumor microenvironment-directed therapeutic strategy in bile duct pathologies.
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Affiliation(s)
- Monika Lewinska
- Department of Health and Medical Sciences, Biotech Research and Innovation Center, University of Copenhagen, Copenhagen, Denmark
| | - Ekaterina Zhuravleva
- Department of Health and Medical Sciences, Biotech Research and Innovation Center, University of Copenhagen, Copenhagen, Denmark
| | - Letizia Satriano
- Department of Health and Medical Sciences, Biotech Research and Innovation Center, University of Copenhagen, Copenhagen, Denmark
| | - Marta B Martinez
- Department of Health and Medical Sciences, Biotech Research and Innovation Center, University of Copenhagen, Copenhagen, Denmark
| | - Deepak K Bhatt
- Department of Health and Medical Sciences, Biotech Research and Innovation Center, University of Copenhagen, Copenhagen, Denmark
| | - Douglas V N P Oliveira
- Department of Health and Medical Sciences, Biotech Research and Innovation Center, University of Copenhagen, Copenhagen, Denmark
| | - Yasuko Antoku
- Department of Health and Medical Sciences, Biotech Research and Innovation Center, University of Copenhagen, Copenhagen, Denmark
| | - Friederike L Keggenhoff
- Universitatsklinikum Schleswig-Holstein, Medizinische Klinik I, Campus Lubeck, Lubeck, Germany
| | - Darko Castven
- Universitatsklinikum Schleswig-Holstein, Medizinische Klinik I, Campus Lubeck, Lubeck, Germany
| | - Jens U Marquardt
- Universitatsklinikum Schleswig-Holstein, Medizinische Klinik I, Campus Lubeck, Lubeck, Germany
| | - Matthias S Matter
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Janine T Erler
- Department of Health and Medical Sciences, Biotech Research and Innovation Center, University of Copenhagen, Copenhagen, Denmark
| | - Rui C Oliveira
- Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Blanca I Aldana
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ruba Al-Abdulla
- Experimental Hepatology and Drug Targeting, Instituto de Investigación Biomédica de Salamanca, University of Salamanca, Salamanca, Spain
| | - Maria J Perugorria
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute, Donostia University Hospital, University of the Basque Country, San Sebastian, Spain; National Institute for the Study of Liver and Gastrointestinal Diseases, Centro de Investigacion Biomedica en Red de Enfermedades Hepaticas y Digestivas, Instituto de Salud Carlos III, Madrid, Spain; Department of Medicine, Faculty of Medicine and Nursing, University of the Basque Country (Universidad del País Vasco/Euskal Herriko Unibertsitatea), Leioa, Spain
| | - Diego F Calvisi
- University of Regensburg, Institute of Pathology, Regensburg, Germany
| | - Luis Arnes Perez
- Department of Health and Medical Sciences, Biotech Research and Innovation Center, University of Copenhagen, Copenhagen, Denmark
| | - Pedro M Rodrigues
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute, Donostia University Hospital, University of the Basque Country, San Sebastian, Spain; National Institute for the Study of Liver and Gastrointestinal Diseases, Centro de Investigacion Biomedica en Red de Enfermedades Hepaticas y Digestivas, Instituto de Salud Carlos III, Madrid, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Ibone Labiano
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute, Donostia University Hospital, University of the Basque Country, San Sebastian, Spain
| | - Jesus M Banales
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute, Donostia University Hospital, University of the Basque Country, San Sebastian, Spain; National Institute for the Study of Liver and Gastrointestinal Diseases, Centro de Investigacion Biomedica en Red de Enfermedades Hepaticas y Digestivas, Instituto de Salud Carlos III, Madrid, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain; Department of Biochemistry and Genetics, School of Sciences, University of Navarra, Pamplona, Spain
| | - Jesper B Andersen
- Department of Health and Medical Sciences, Biotech Research and Innovation Center, University of Copenhagen, Copenhagen, Denmark.
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10
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Heumann P, Albert A, Gülow K, Tümen D, Müller M, Kandulski A. Current and Future Therapeutic Targets for Directed Molecular Therapies in Cholangiocarcinoma. Cancers (Basel) 2024; 16:1690. [PMID: 38730642 PMCID: PMC11083102 DOI: 10.3390/cancers16091690] [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: 03/25/2024] [Revised: 04/17/2024] [Accepted: 04/21/2024] [Indexed: 05/13/2024] Open
Abstract
We conducted a comprehensive review of the current literature of published data, clinical trials (MEDLINE; ncbi.pubmed.com), congress contributions (asco.org; esmo.org), and active recruiting clinical trains (clinicaltrial.gov) on targeted therapies in cholangiocarcinoma. Palliative treatment regimens were analyzed as well as preoperative and perioperative treatment options. We summarized the current knowledge for each mutation and molecular pathway that is or has been under clinical evaluation and discussed the results on the background of current treatment guidelines. We established and recommended targeted treatment options that already exist for second-line settings, including IDH-, BRAF-, and NTRK-mutated tumors, as well as for FGFR2 fusion, HER2/neu-overexpression, and microsatellite instable tumors. Other options for targeted treatment include EGFR- or VEGF-dependent pathways, which are known to be overexpressed or dysregulated in this cancer type and are currently under clinical investigation. Targeted therapy in CCA is a hallmark of individualized medicine as these therapies aim to specifically block pathways that promote cancer cell growth and survival, leading to tumor shrinkage and improved patient outcomes based on the molecular profile of the tumor.
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Affiliation(s)
- Philipp Heumann
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology, and Infectious Diseases University Hospital Regensburg Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany
| | | | | | | | | | - Arne Kandulski
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology, and Infectious Diseases University Hospital Regensburg Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany
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11
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Cui Z, Li C, Liu W, Sun M, Deng S, Cao J, Yang H, Chen P. Scutellarin activates IDH1 to exert antitumor effects in hepatocellular carcinoma progression. Cell Death Dis 2024; 15:267. [PMID: 38622131 PMCID: PMC11018852 DOI: 10.1038/s41419-024-06625-6] [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: 12/22/2023] [Revised: 03/14/2024] [Accepted: 03/19/2024] [Indexed: 04/17/2024]
Abstract
Isochlorate dehydrogenase 1 (IDH1) is an important metabolic enzyme for the production of α-ketoglutarate (α-KG), which has antitumor effects and is considered to have potential antitumor effects. The activation of IDH1 as a pathway for the development of anticancer drugs has not been attempted. We demonstrated that IDH1 can limit glycolysis in hepatocellular carcinoma (HCC) cells to activate the tumor immune microenvironment. In addition, through proteomic microarray analysis, we identified a natural small molecule, scutellarin (Scu), which activates IDH1 and inhibits the growth of HCC cells. By selectively modifying Cys297, Scu promotes IDH1 active dimer formation and increases α-KG production, leading to ubiquitination and degradation of HIF1a. The loss of HIF1a further leads to the inhibition of glycolysis in HCC cells. The activation of IDH1 by Scu can significantly increase the level of α-KG in tumor tissue, downregulate the HIF1a signaling pathway, and activate the tumor immune microenvironment in vivo. This study demonstrated the inhibitory effect of IDH1-α-KG-HIF1a on the growth of HCC cells and evaluated the inhibitory effect of Scu, the first IDH1 small molecule agonist, which provides a reference for cancer immunotherapy involving activated IDH1.
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Affiliation(s)
- Zhao Cui
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, 100700, Beijing, China
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Caifeng Li
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Wei Liu
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Mo Sun
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Shiwen Deng
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Junxian Cao
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Hongjun Yang
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, 100700, Beijing, China.
| | - Peng Chen
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, 100700, Beijing, China.
- Robot Intelligent Laboratory of Traditional Chinese Medicine, Experimental Research Center, China Academy of Chinese Medical Sciences & MEGAROBO, Beijing, China.
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12
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Bekric D, Kiesslich T, Ocker M, Winklmayr M, Ritter M, Dobias H, Beyreis M, Neureiter D, Mayr C. The efficacy of ferroptosis-inducing compounds IKE and RSL3 correlates with the expression of ferroptotic pathway regulators CD71 and SLC7A11 in biliary tract cancer cells. PLoS One 2024; 19:e0302050. [PMID: 38603713 PMCID: PMC11008848 DOI: 10.1371/journal.pone.0302050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 03/27/2024] [Indexed: 04/13/2024] Open
Abstract
INTRODUCTION Biliary tract cancer (BTC) is a lethal disease with a bad overall survivability, partly arising from inadequate therapeutic alternatives, detection at a belated stage, and a resistance to common therapeutic approaches. Ferroptosis is a form of programmed cell death that depends on reactive oxygen species (ROS) and iron, causing excessive peroxidation of polyunsaturated fatty acids (PUFAs). Therefore, the objective of this investigation is, whether ferroptosis can be induced in BTC in vitro and whether this induction is dependent on specific molecular markers. METHODS The study conducted resazurin assay and IC25/50 calculation to explore the possible cytotoxic outcomes of different classes of ferroptosis-inducing substances (FINs) on a comprehensive in vitro model of 11 BTC cell lines. Combinatory treatments with different cell death inhibitors were performed to evaluate the magnitude of ferroptosis induction. To ascertain whether ferroptotic cell death occurred, liperfluo and iron assay kits were employed to evaluate lipid ROS and intracellular iron abundance. Potential biomarkers of ferroptosis sensitivity were then assessed via western blot analysis, a rtPCR panel and functional assay kits. RESULTS The study found that different FINs reduced cell viability in a cell line-dependent manner. In addition, we measured increased lipid ROS and intracellular Fe2+ levels upon exposure to FINs in BTC cells. Combining FINs with inhibitors of ferroptosis, necroptosis or apoptosis suggests the occurrence of ferroptotic events in BTC cell lines CCC-5, HuH-28 and KKU-055. Furthermore, we found that BTC cells display a heterogeneous profile regarding different molecular genes/markers of ferroptosis. Subsequent analysis revealed that sensitivity of BTC cells towards IKE and RSL3 positively correlated with CD71 and SLC7A11 protein expression. CONCLUSION Our results demonstrate that induction of ferroptosis is a promising approach to inhibit BTC cell growth and that the sensitivity of BTC cells towards ferroptosis induction might be dependent on molecular markers such as CD71 and SLC7A11.
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Affiliation(s)
- Dino Bekric
- Center of Physiology, Pathophysiology and Biophysics, Institute of Physiology and Pathophysiology Salzburg, Paracelsus Medical University, Salzburg, Austria
- Cancer Cluster Salzburg, Salzburg, Austria
| | - Tobias Kiesslich
- Center of Physiology, Pathophysiology and Biophysics, Institute of Physiology and Pathophysiology Salzburg, Paracelsus Medical University, Salzburg, Austria
- Department of Internal Medicine I, University Clinics Salzburg, Paracelsus Medical University, Salzburg, Austria
| | - Matthias Ocker
- Division of Hematology, Oncology, and Cancer Immunology, Medical Department, Charité University Medicine Berlin, Berlin, Germany
- Tacalyx GmbH, Berlin, Germany
| | - Martina Winklmayr
- Ludwig Boltzmann Institute for Arthritis und Rehabilitation, Paracelsus Medical University, Salzburg, Austria
| | - Markus Ritter
- Center of Physiology, Pathophysiology and Biophysics, Institute of Physiology and Pathophysiology Salzburg, Paracelsus Medical University, Salzburg, Austria
- Ludwig Boltzmann Institute for Arthritis und Rehabilitation, Paracelsus Medical University, Salzburg, Austria
- Gastein Research Institute, Paracelsus Medical University, Salzburg, Austria
- Kathmandu Medical School of Medical Sciences, Dhulikhel, Nepal
| | - Heidemarie Dobias
- Center of Physiology, Pathophysiology and Biophysics, Institute of Physiology and Pathophysiology Salzburg, Paracelsus Medical University, Salzburg, Austria
| | - Marlena Beyreis
- Center of Physiology, Pathophysiology and Biophysics, Institute of Physiology and Pathophysiology Salzburg, Paracelsus Medical University, Salzburg, Austria
| | - Daniel Neureiter
- Cancer Cluster Salzburg, Salzburg, Austria
- Institute of Pathology, University Clinics Salzburg, Paracelsus Medical University, Salzburg, Austria
| | - Christian Mayr
- Center of Physiology, Pathophysiology and Biophysics, Institute of Physiology and Pathophysiology Salzburg, Paracelsus Medical University, Salzburg, Austria
- Department of Internal Medicine I, University Clinics Salzburg, Paracelsus Medical University, Salzburg, Austria
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13
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Cottrell S, Wang R, Wei GW. PLPCA: Persistent Laplacian-Enhanced PCA for Microarray Data Analysis. J Chem Inf Model 2024; 64:2405-2420. [PMID: 37738663 PMCID: PMC10999748 DOI: 10.1021/acs.jcim.3c01023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Over the years, Principal Component Analysis (PCA) has served as the baseline approach for dimensionality reduction in gene expression data analysis. Its primary objective is to identify a subset of disease-causing genes from a vast pool of thousands of genes. However, PCA possesses inherent limitations that hinder its interpretability, introduce class ambiguity, and fail to capture complex geometric structures in the data. Although these limitations have been partially addressed in the literature by incorporating various regularizers, such as graph Laplacian regularization, existing PCA based methods still face challenges related to multiscale analysis and capturing higher-order interactions in the data. To address these challenges, we propose a novel approach called Persistent Laplacian-enhanced Principal Component Analysis (PLPCA). PLPCA amalgamates the advantages of earlier regularized PCA methods with persistent spectral graph theory, specifically persistent Laplacians derived from algebraic topology. In contrast to graph Laplacians, persistent Laplacians enable multiscale analysis through filtration and can incorporate higher-order simplicial complexes to capture higher-order interactions in the data. We evaluate and validate the performance of PLPCA using ten benchmark microarray data sets that exhibit a wide range of dimensions and data imbalance ratios. Our extensive studies over these data sets demonstrate that PLPCA provides up to 12% improvement to the current state-of-the-art PCA models on five evaluation metrics for classification tasks after dimensionality reduction.
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Affiliation(s)
- Sean Cottrell
- Department of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Rui Wang
- Department of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Guo-Wei Wei
- Department of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
- Department of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
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14
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Achurra P, Fernandes E, O'Kane G, Grant R, Cattral M, Sapisochin G. Liver transplantation for intrahepatic cholangiocarcinoma: who, when and how. Curr Opin Organ Transplant 2024; 29:161-171. [PMID: 38258823 DOI: 10.1097/mot.0000000000001136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
PURPOSE OF REVIEW Using transplant oncology principles, selected patients with intrahepatic cholangiocarcinoma (iCCA) may achieve long-term survival after liver transplantation. Strategies for identifying and managing these patients are discussed in this review. RECENT FINDINGS Unlike initial reports, several modern series have reported positive outcomes after liver transplantation for iCCA. The main challenges are in identifying the appropriate candidates and graft scarcity. Tumor burden and response to neoadjuvant therapies have been successfully used to identify favorable biology in unresectable cases. New molecular biomarkers will probably predict this response in the future. Also, new technologies and better strategies have been used to increase graft availability for these patients without affecting the liver waitlist. SUMMARY Liver transplantation for the management of patients with unresectable iCCA is currently a reality under strict research protocols. Who is a candidate for transplantation, when to use neoadjuvant and locoregional therapies, and how to increase graft availability are the main topics of this review.
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Affiliation(s)
- Pablo Achurra
- Department of Abdominal Transplant and HPB Surgical Oncology, Toronto General Hospital, University of Toronto
- Department of Digestive Surgery, Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - Eduardo Fernandes
- Department of Surgery and Abdominal Organ Transplantation - São Lucas Hospital Copacabana, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Grainne O'Kane
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Robert Grant
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Mark Cattral
- Department of Abdominal Transplant and HPB Surgical Oncology, Toronto General Hospital, University of Toronto
| | - Gonzalo Sapisochin
- Department of Abdominal Transplant and HPB Surgical Oncology, Toronto General Hospital, University of Toronto
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15
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Kacar Z, Slud E, Levy D, Candia J, Budhu A, Forgues M, Wu X, Raziuddin A, Tran B, Shetty J, Pomyen Y, Chaisaingmongkol J, Rabibhadana S, Pupacdi B, Bhudhisawasdi V, Lertprasertsuke N, Auewarakul C, Sangrajrang S, Mahidol C, Ruchirawat M, Wang XW. Characterization of tumor evolution by functional clonality and phylogenetics in hepatocellular carcinoma. Commun Biol 2024; 7:383. [PMID: 38553628 DOI: 10.1038/s42003-024-06040-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 03/11/2024] [Indexed: 04/02/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is a molecularly heterogeneous solid malignancy, and its fitness may be shaped by how its tumor cells evolve. However, ability to monitor tumor cell evolution is hampered by the presence of numerous passenger mutations that do not provide any biological consequences. Here we develop a strategy to determine the tumor clonality of three independent HCC cohorts of 524 patients with diverse etiologies and race/ethnicity by utilizing somatic mutations in cancer driver genes. We identify two main types of tumor evolution, i.e., linear, and non-linear models where non-linear type could be further divided into classes, which we call shallow branching and deep branching. We find that linear evolving HCC is less aggressive than other types. GTF2IRD2B mutations are enriched in HCC with linear evolution, while TP53 mutations are the most frequent genetic alterations in HCC with non-linear models. Furthermore, we observe significant B cell enrichment in linear trees compared to non-linear trees suggesting the need for further research to uncover potential variations in immune cell types within genomically determined phylogeny types. These results hint at the possibility that tumor cells and their microenvironment may collectively influence the tumor evolution process.
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Affiliation(s)
- Zeynep Kacar
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
- Department of Mathematics, University of Maryland, College Park, MD, 20742, USA
| | - Eric Slud
- Department of Mathematics, University of Maryland, College Park, MD, 20742, USA
| | - Doron Levy
- Department of Mathematics, University of Maryland, College Park, MD, 20742, USA
| | - Julián Candia
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, 21224, USA
| | - Anuradha Budhu
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
- Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Marshonna Forgues
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Xiaolin Wu
- Cancer Research Technology Program, Frederick, MD, 21702, USA
| | - Arati Raziuddin
- Cancer Research Technology Program, Frederick, MD, 21702, USA
| | - Bao Tran
- Cancer Research Technology Program, Frederick, MD, 21702, USA
| | - Jyoti Shetty
- Cancer Research Technology Program, Frederick, MD, 21702, USA
| | - Yotsawat Pomyen
- Laboratory of Chemical Carcinogenesis, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | | | - Siritida Rabibhadana
- Laboratory of Chemical Carcinogenesis, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Benjarath Pupacdi
- Laboratory of Chemical Carcinogenesis, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | | | | | - Chirayu Auewarakul
- Princess Srisavangavadhana College of Medicine, Chulabhorn Royal Academy, Bangkok, 10210, Thailand
| | | | - Chulabhorn Mahidol
- Laboratory of Chemical Carcinogenesis, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Mathuros Ruchirawat
- Laboratory of Chemical Carcinogenesis, Chulabhorn Research Institute, Bangkok, 10210, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok, Thailand
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA.
- Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA.
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16
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Gopal P, Robert ME, Zhang X. Cholangiocarcinoma: Pathologic and Molecular Classification in the Era of Precision Medicine. Arch Pathol Lab Med 2024; 148:359-370. [PMID: 37327187 DOI: 10.5858/arpa.2022-0537-ra] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
CONTEXT.— Cholangiocarcinoma (CCA) is a heterogeneous cancer of the bile duct, and its diagnosis is often challenging. OBJECTIVE.— To provide insights into state-of-the-art approaches for the diagnosis of CCA. DATA SOURCES.— Literature review via PubMed search and authors' experiences. CONCLUSIONS.— CCA can be categorized as intrahepatic or extrahepatic. Intrahepatic CCA is further classified into small-duct-type and large-duct-type, whereas extrahepatic CCA is classified into distal and perihilar according to site of origin within the extrahepatic biliary tree. Tumor growth patterns include mass forming, periductal infiltrating, and intraductal tumors. The clinical diagnosis of CCA is challenging and usually occurs at an advanced tumor stage. Pathologic diagnosis is made difficult by tumor inaccessibility and challenges in distinguishing CCA from metastatic adenocarcinoma to the liver. Immunohistochemical stains can assist in differentiating CCA from other malignancies, such as hepatocellular carcinoma, but no distinctive CCA-specific immunohistochemical profile has been identified. Recent advances in next-generation sequencing-based high-throughput assays have identified distinct genomic profiles of CCA subtypes, including genomic alterations that are susceptible to targeted therapies or immune checkpoint inhibitors. Detailed histopathologic and molecular evaluations of CCA by pathologists are critical for correct diagnosis, subclassification, therapeutic decision-making, and prognostication. The first step toward achieving these goals is to acquire a detailed understanding of the histologic and genetic subtypes of this heterogeneous tumor group. Here, we review state-of-the-art approaches that should be applied to establish a diagnosis of CCA, including clinical presentation, histopathology, staging, and the practical use of genetic testing methodologies.
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Affiliation(s)
- Purva Gopal
- From the Department of Pathology, UT Southwestern Medical Center, Dallas, Texas (Gopal)
| | - Marie E Robert
- the Department of Pathology, Yale University School of Medicine, New Haven, Connecticut (Robert, Zhang)
| | - Xuchen Zhang
- the Department of Pathology, Yale University School of Medicine, New Haven, Connecticut (Robert, Zhang)
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17
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Park DD, Xu G, Park SS, Haigh NE, Phoomak C, Wongkham S, Maverakis E, Lebrilla CB. Combined analysis of secreted proteins and glycosylation identifies prognostic features in cholangiocarcinoma. J Cell Physiol 2024; 239:e31147. [PMID: 37921263 PMCID: PMC10939962 DOI: 10.1002/jcp.31147] [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: 05/07/2023] [Revised: 09/05/2023] [Accepted: 10/16/2023] [Indexed: 11/04/2023]
Abstract
Secreted proteins are overexpressed in cholangiocarcinoma (CCA) and actively involved in promoting metastatic spread. Many of these proteins possess one or more sites of glycosylation and their various glycoforms have potential utility as prognostic or diagnostic biomarkers. To evaluate the effects of secretome glycosylation on patient outcome, we elucidated the glycosylation patterns of proteins secreted by parental and metastatic CCA cells using liquid chromatography-mass spectrometry. Our analysis showed that the secretome of CCA cells was dominated by fucosylated and fucosialylated glycoforms. Based on the glycan and protein profiles, we evaluated the combined prognostic significance of glycosyltransferases and secretory proteins. Significantly, genes encoding fucosyltransferases and sialyltransferases showed favorable prognostic effects when combined with secretory protein-coding gene expression, particularly thrombospondin-1. Combining these measures may provide improved risk assessment for CCA and be used to indicate stages of disease progression.
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Affiliation(s)
| | - Gege Xu
- Department of Chemistry, University of California, Davis, CA, 95616 USA
| | - Simon S. Park
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215 USA
| | - Nathan E. Haigh
- Department of Dermatology, University of California, Davis School of Medicine, Sacramento, CA, 95817 USA
| | - Chatchai Phoomak
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Thailand
| | - Sopit Wongkham
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Thailand
| | - Emanual Maverakis
- Department of Dermatology, University of California, Davis School of Medicine, Sacramento, CA, 95817 USA
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18
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Hissong E, Al Assaad M, Bal M, Reed KA, Fornelli A, Levine MF, Gundem G, Semaan A, Orr CE, Sakhadeo U, Manohar J, Sigouros M, Wilkes D, Sboner A, Montgomery EA, Graham RP, Medina-Martínez JS, Robine N, Fang JM, Choi EYK, Westerhoff M, Delgado-de la Mora J, Caudell P, Yantiss RK, Papaemmanuil E, Elemento O, Sigel C, Jessurun J, Mosquera JM. NIPBL::NACC1 Fusion Hepatic Carcinoma. Am J Surg Pathol 2024; 48:183-193. [PMID: 38047392 DOI: 10.1097/pas.0000000000002159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Several reports describing a rare primary liver tumor with histologic features reminiscent of follicular thyroid neoplasms have been published under a variety of descriptive terms including thyroid-like, solid tubulocystic, and cholangioblastic cholangiocarcinoma. Although these tumors are considered to represent histologic variants, they lack classic features of cholangiocarcinoma and have unique characteristics, namely immunoreactivity for inhibin and NIPBL::NACC1 fusions. The purpose of this study is to present clinicopathologic and molecular data for a large series of these tumors to better understand their pathogenesis. We identified 11 hepatic tumors with these features. Immunohistochemical and NACC1 and NIPBL fluorescence in situ hybridization assays were performed on all cases. Four cases had available material for whole-genome sequencing (WGS) analysis. Most patients were adult women (mean age: 42 y) who presented with abdominal pain and large hepatic masses (mean size: 14 cm). Ten patients had no known liver disease. Of the patients with follow-up information, 3/9 (33%) pursued aggressive behavior. All tumors were composed of bland cuboidal cells with follicular and solid/trabecular growth patterns in various combinations, were immunoreactive for inhibin, showed albumin mRNA by in situ hybridization, and harbored the NIPBL::NACC1 fusion by fluorescence in situ hybridization. WGS corroborated the presence of the fusion in all 4 tested cases, high tumor mutational burden in 2 cases, and over 30 structural variants per case in 3 sequenced tumors. The cases lacked mutations typical of conventional intrahepatic cholangiocarcinoma. In this report, we describe the largest series of primary inhibin-positive hepatic neoplasms harboring a NIPBL::NACC1 fusion and the first WGS analysis of these tumors. We propose to name this neoplasm NIPBL:NACC1 fusion hepatic carcinoma.
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Affiliation(s)
- Erika Hissong
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine
| | - Majd Al Assaad
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian
| | - Munita Bal
- Department of Pathology, Tata Memorial Centre, Mumbai, Maharashtra, India
| | - Katelyn A Reed
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Adele Fornelli
- U.O. Anatomia Patologica, Ospedale Maggiore, Bologna, Italy
| | | | | | - Alissa Semaan
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian
| | - Christine E Orr
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine
| | - Uma Sakhadeo
- Department of Pathology, Tata Memorial Centre, Mumbai, Maharashtra, India
| | - Jyothi Manohar
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian
| | - Michael Sigouros
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian
| | - David Wilkes
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian
| | - Andrea Sboner
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine
- Institute for Computational Biomedicine, Weill Cornell Medicine
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian
| | - Elizabeth A Montgomery
- Department of Pathology and Laboratory Medicine, University of Miami Hospital (UMH), Miami, FL
| | - Rondell P Graham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | | | | | - Jiayun M Fang
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | | | | | - Jesús Delgado-de la Mora
- National Institute of Medical Sciences and Nutrition, Salvador Zubiran, Mexico City, CDMX, Mexico
| | | | - Rhonda K Yantiss
- Department of Pathology and Laboratory Medicine, University of Miami Hospital (UMH), Miami, FL
| | | | - Olivier Elemento
- Institute for Computational Biomedicine, Weill Cornell Medicine
- Department of Physiology and Biophysics, Weill Cornell Medicine
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian
| | - Carlie Sigel
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - José Jessurun
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine
| | - Juan Miguel Mosquera
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian
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19
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Longerich T, Stenzinger A, Schirmacher P. Molecular diagnostics of hepatobiliary and pancreatic neoplasias. Virchows Arch 2024; 484:263-272. [PMID: 38429607 PMCID: PMC10948571 DOI: 10.1007/s00428-024-03744-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 03/03/2024]
Abstract
Neoplasias of the hepatopancreatobiliary tract are growing in numbers, have the poorest prognosis of all major cancer entities, and thus represent a rising clinical problem. Their molecular diagnostic has dramatically improved, contributing to tumor subtyping, definition of malignancy, and uncovering cases with hereditary predisposition. Most of all, predictive molecular testing allows to identify cases amenable to treatment with the rising number of approved targeted drugs, immune-oncological treatment, and clinical trials. In this review, the current state of molecular testing and its contribution to clinical decision-making are outlined.
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Affiliation(s)
- T Longerich
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69118, Heidelberg, Germany
| | - A Stenzinger
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69118, Heidelberg, Germany
| | - P Schirmacher
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69118, Heidelberg, Germany.
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20
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Liu W, Wang H, Zhao Q, Tao C, Qu W, Hou Y, Huang R, Sun Z, Zhu G, Jiang X, Fang Y, Gao J, Wu X, Yang Z, Ping R, Chen J, Yang R, Chu T, Zhou J, Fan J, Tang Z, Yang D, Shi Y. Multiomics analysis reveals metabolic subtypes and identifies diacylglycerol kinase α (DGKA) as a potential therapeutic target for intrahepatic cholangiocarcinoma. Cancer Commun (Lond) 2024; 44:226-250. [PMID: 38143235 PMCID: PMC10876206 DOI: 10.1002/cac2.12513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 11/23/2023] [Accepted: 12/14/2023] [Indexed: 12/26/2023] Open
Abstract
BACKGROUND Intrahepatic cholangiocarcinoma (iCCA) is a highly heterogeneous and lethal hepatobiliary tumor with few therapeutic strategies. The metabolic reprogramming of tumor cells plays an essential role in the development of tumors, while the metabolic molecular classification of iCCA is largely unknown. Here, we performed an integrated multiomics analysis and metabolic classification to depict differences in metabolic characteristics of iCCA patients, hoping to provide a novel perspective to understand and treat iCCA. METHODS We performed integrated multiomics analysis in 116 iCCA samples, including whole-exome sequencing, bulk RNA-sequencing and proteome analysis. Based on the non-negative matrix factorization method and the protein abundance of metabolic genes in human genome-scale metabolic models, the metabolic subtype of iCCA was determined. Survival and prognostic gene analyses were used to compare overall survival (OS) differences between metabolic subtypes. Cell proliferation analysis, 5-ethynyl-2'-deoxyuridine (EdU) assay, colony formation assay, RNA-sequencing and Western blotting were performed to investigate the molecular mechanisms of diacylglycerol kinase α (DGKA) in iCCA cells. RESULTS Three metabolic subtypes (S1-S3) with subtype-specific biomarkers of iCCA were identified. These metabolic subtypes presented with distinct prognoses, metabolic features, immune microenvironments, and genetic alterations. The S2 subtype with the worst survival showed the activation of some special metabolic processes, immune-suppressed microenvironment and Kirsten rat sarcoma viral oncogene homolog (KRAS)/AT-rich interactive domain 1A (ARID1A) mutations. Among the S2 subtype-specific upregulated proteins, DGKA was further identified as a potential drug target for iCCA, which promoted cell proliferation by enhancing phosphatidic acid (PA) metabolism and activating mitogen-activated protein kinase (MAPK) signaling. CONCLUSION Via multiomics analyses, we identified three metabolic subtypes of iCCA, revealing that the S2 subtype exhibited the poorest survival outcomes. We further identified DGKA as a potential target for the S2 subtype.
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Affiliation(s)
- Weiren Liu
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Huqiang Wang
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsBeijingP. R. China
| | - Qianfu Zhao
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Chenyang Tao
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Weifeng Qu
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Yushan Hou
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsBeijingP. R. China
| | - Run Huang
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Zimei Sun
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsBeijingP. R. China
| | - Guiqi Zhu
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Xifei Jiang
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Yuan Fang
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Jun Gao
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Xiaoling Wu
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Zhixiang Yang
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsBeijingP. R. China
| | - Rongyu Ping
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsBeijingP. R. China
| | - Jiafeng Chen
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Rui Yang
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Tianhao Chu
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Jian Zhou
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Jia Fan
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Zheng Tang
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Dong Yang
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsBeijingP. R. China
| | - Yinghong Shi
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
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21
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Zhu Y, Zhang D, Shukla P, Jung YH, Malgulwar PB, Chagani S, Colic M, Benjamin S, Copland JA, Tan L, Lorenzi PL, Javle M, Huse JT, Roszik J, Hart T, Kwong LN. CRISPR screening identifies BET and mTOR inhibitor synergy in cholangiocarcinoma through serine glycine one carbon. JCI Insight 2024; 9:e174220. [PMID: 38060314 PMCID: PMC10906219 DOI: 10.1172/jci.insight.174220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 12/05/2023] [Indexed: 01/24/2024] Open
Abstract
Patients with cholangiocarcinoma have poor clinical outcomes due to late diagnoses, poor prognoses, and limited treatment strategies. To identify drug combinations for this disease, we have conducted a genome-wide CRISPR screen anchored on the bromodomain and extraterminal domain (BET) PROTAC degrader ARV825, from which we identified anticancer synergy when combined with genetic ablation of members of the mTOR pathway. This combination effect was validated using multiple pharmacological BET and mTOR inhibitors, accompanied by increased levels of apoptosis and cell cycle arrest. In a xenograft model, combined BET degradation and mTOR inhibition induced tumor regression. Mechanistically, the 2 inhibitor classes converged on H3K27ac-marked epigenetic suppression of the serine glycine one carbon (SGOC) metabolism pathway, including the key enzymes PHGDH and PSAT1. Knockdown of PSAT1 was sufficient to replicate synergy with single-agent inhibition of either BET or mTOR. Our results tie together epigenetic regulation, metabolism, and apoptosis induction as key therapeutic targets for further exploration in this underserved disease.
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Affiliation(s)
- Yan Zhu
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Dengyong Zhang
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of general surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China
| | - Pooja Shukla
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Young-Ho Jung
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Prit Benny Malgulwar
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sharmeen Chagani
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Medina Colic
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sarah Benjamin
- Department of Natural Sciences, Rice University, Houston, Texas, USA
| | - John A. Copland
- Department of Cancer Biology, Mayo Clinic Jacksonville, Florida, USA
| | - Lin Tan
- Metabolomics Core Facility, Department of Bioinformatics & Computational Biology
| | - Philip L. Lorenzi
- Metabolomics Core Facility, Department of Bioinformatics & Computational Biology
| | | | - Jason T. Huse
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jason Roszik
- Department of Melanoma Medical Oncology-Research, Division of Cancer Medicine
- Department of Genomic Medicine, Division of Cancer Medicine, and
| | - Traver Hart
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Lawrence N. Kwong
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Genomic Medicine, Division of Cancer Medicine, and
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22
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Fan Z, Zou X, Wang G, Liu Y, Jiang Y, Wang H, Zhang P, Wei F, Du X, Wang M, Sun X, Ji B, Hu X, Chen L, Zhou P, Wang D, Bai J, Xiao X, Zuo L, Xia X, Yi X, Lv G. A transcriptome based molecular classification scheme for cholangiocarcinoma and subtype-derived prognostic biomarker. Nat Commun 2024; 15:484. [PMID: 38212331 PMCID: PMC10784309 DOI: 10.1038/s41467-024-44748-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 12/15/2023] [Indexed: 01/13/2024] Open
Abstract
Previous studies on the molecular classification of cholangiocarcinoma (CCA) focused on certain anatomical sites, and disregarded tissue contamination biases in transcriptomic profiles. We aim to provide universal molecular classification scheme and prognostic biomarker of CCAs across anatomical locations. Comprehensive bioinformatics analysis is performed on transcriptomic data from 438 CCA cases across various anatomical locations. After excluding CCA tumors showing normal tissue expression patterns, we identify two universal molecular subtypes across anatomical subtypes, explore the molecular, clinical, and microenvironmental features of each class. Subsequently, a 30-gene classifier and a biomarker (called "CORE-37") are developed to predict the molecular subtype of CCA and prognosis, respectively. Two subtypes display distinct molecular characteristics and survival outcomes. Key findings are validated in external cohorts regardless of the stage and anatomical location. Our study provides a CCA classification scheme that complements the conventional anatomy-based classification and presents a promising prognostic biomarker for clinical application.
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Affiliation(s)
- Zhongqi Fan
- Department of Hepatobiliary and Pancreatic Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, China
| | - Xinchen Zou
- Geneplus-Beijing Institute, 9th Floor, No.6 Building, Peking University Medical Industrial Park, Zhongguancun Life Science Park, Beijing, China
| | - Guangyi Wang
- Department of Hepatobiliary and Pancreatic Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, China
| | - Yahui Liu
- Department of Hepatobiliary and Pancreatic Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, China
| | - Yanfang Jiang
- Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
| | - Haoyan Wang
- Geneplus-Beijing Institute, 9th Floor, No.6 Building, Peking University Medical Industrial Park, Zhongguancun Life Science Park, Beijing, China
| | - Ping Zhang
- Department of Hepatobiliary and Pancreatic Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, China
| | - Feng Wei
- Department of Hepatobiliary and Pancreatic Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, China
| | - Xiaohong Du
- Department of Hepatobiliary and Pancreatic Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, China
| | - Meng Wang
- Department of Hepatobiliary and Pancreatic Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, China
| | - Xiaodong Sun
- Department of Hepatobiliary and Pancreatic Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, China
| | - Bai Ji
- Department of Hepatobiliary and Pancreatic Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, China
| | - Xintong Hu
- Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
| | - Liguo Chen
- Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
| | - Peiwen Zhou
- Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
| | - Duo Wang
- Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
| | - Jing Bai
- Geneplus-Beijing Institute, 9th Floor, No.6 Building, Peking University Medical Industrial Park, Zhongguancun Life Science Park, Beijing, China
| | - Xiao Xiao
- Geneplus-Shenzhen, No.14 Zhongxing Road, Pingshan District, Shenzhen, China
| | - Lijiao Zuo
- Geneplus-Beijing Institute, 9th Floor, No.6 Building, Peking University Medical Industrial Park, Zhongguancun Life Science Park, Beijing, China
| | - Xuefeng Xia
- Geneplus-Beijing Institute, 9th Floor, No.6 Building, Peking University Medical Industrial Park, Zhongguancun Life Science Park, Beijing, China
| | - Xin Yi
- Geneplus-Beijing Institute, 9th Floor, No.6 Building, Peking University Medical Industrial Park, Zhongguancun Life Science Park, Beijing, China
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Guoyue Lv
- Department of Hepatobiliary and Pancreatic Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, China.
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23
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Ohyama H, Hirotsu Y, Amemiya K, Mikata R, Amano H, Hirose S, Oyama T, Iimuro Y, Kojima Y, Mochizuki H, Kato N, Omata M. Development of a molecular barcode detection system for pancreaticobiliary malignancies and comparison with next-generation sequencing. Cancer Genet 2024; 280-281:6-12. [PMID: 38113555 DOI: 10.1016/j.cancergen.2023.12.002] [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: 06/18/2023] [Revised: 10/29/2023] [Accepted: 12/07/2023] [Indexed: 12/21/2023]
Abstract
BACKGROUND Obtaining sufficient tumor tissue for genomic profiling is challenging in pancreaticobiliary cancer (PBCA). We determined the utility of molecular barcoding (MB) of liquid biopsies (bile, duodenal fluid, and plasma) for highly sensitive genomic diagnosis and detection of druggable mutations for PBCA. METHODS Two in-house panels of 60 genes (non-MB panel) and 21 genes using MB (MB panel) were used for the genomic analysis of 112 DNA samples from 20 PBCA patients. We measured the yield of DNA and compared the genomic profiles of liquid samples obtained using the non-MB panel and the MB panel. The utility of the panels in detecting druggable mutations was investigated. RESULTS A significantly greater amount of DNA was obtained from bile supernatants and precipitates compared to tumor samples (P < 0.001 and P = 0.001, respectively). The number of mutations per patient was significantly higher using the MB panel than using the non-MB panel (2.8 vs. 1.3, P = 0.002). Tumor-derived mutations were detected more frequently using the MB panel than the non-MB panel (P = 0.023). Five drug-matched mutations were detected in liquid samples. CONCLUSIONS Liquid biopsy with MB may have utility in providing genomic information for the prognosis of patients with PBCA.
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Affiliation(s)
- Hiroshi Ohyama
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba, Japan; Genome Analysis Center, Yamanashi Central Hospital, Yamanashi, Japan; Department of Gastroenterology, Yamanashi Central Hospital, Yamanashi, Japan.
| | - Yosuke Hirotsu
- Genome Analysis Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Kenji Amemiya
- Genome Analysis Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Rintaro Mikata
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hiroyuki Amano
- Department of Gastroenterology, Yamanashi Central Hospital, Yamanashi, Japan
| | - Sumio Hirose
- Department of Gastroenterology, Yamanashi Central Hospital, Yamanashi, Japan
| | - Toshio Oyama
- Department of Pathology, Yamanashi Central Hospital, Yamanashi, Japan
| | - Yuji Iimuro
- Department of Surgery, Yamanashi Central Hospital, Yamanashi, Japan
| | - Yuichiro Kojima
- Department of Gastroenterology, Yamanashi Central Hospital, Yamanashi, Japan
| | - Hitoshi Mochizuki
- Genome Analysis Center, Yamanashi Central Hospital, Yamanashi, Japan; Department of Gastroenterology, Yamanashi Central Hospital, Yamanashi, Japan
| | - Naoya Kato
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Masao Omata
- Genome Analysis Center, Yamanashi Central Hospital, Yamanashi, Japan; Department of Gastroenterology, Yamanashi Central Hospital, Yamanashi, Japan; University of Tokyo, Tokyo, Japan
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24
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Feng F, Xing X, Jiang G, Xu X, Li B, Li Z, Xie Z, Wu Y, Li X, Gao Q, Liu D, Shen Y, Ao J, Zhang D, Chang Y, Jiang X. Genomic and transcriptomic characteristics of 12 novel primary cell lines derived from three patients with cholangiocarcinoma. Genomics 2024; 116:110765. [PMID: 38113975 DOI: 10.1016/j.ygeno.2023.110765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 11/20/2023] [Accepted: 12/14/2023] [Indexed: 12/21/2023]
Abstract
Cholangiocarcinoma (CCA) is an aggressive bile duct malignancy with poor prognosis. To improve our understanding of the biological characteristics of CCA and develop effective therapies, appropriate preclinical models are required. Here, we established and characterized 12 novel patient-derived primary cancer cell (PDPC) models using multi-region sampling. At the genomic level of PDPCs, we observed not only commonly mutated genes, such as TP53, JAK3, and KMT2C, consistent with the reports in CCA, but also specific mutation patterns in each cell line. In addition, specific expression patterns with distinct biological functions and pathways involved were also observed in the PDPCs at the transcriptomic level. Furthermore, the drug-sensitivity results revealed that the PDPCs exhibited different responses to the six commonly used compounds. Our findings indicate that the established PDPCs can serve as novel in vitro reliable models to provide a crucial molecular basis for improving the understanding of tumorigenesis and its treatment.
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Affiliation(s)
- Feiling Feng
- Department of Biliary Tract Surgery I, Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Xianglei Xing
- Department of Biliary Tract Surgery IV, Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Guojuan Jiang
- Department of Clinical and Translational Medicine, 3D Medicines Inc., Shanghai, China
| | - Xiaoya Xu
- Department of Clinical and Translational Medicine, 3D Medicines Inc., Shanghai, China
| | - Bin Li
- Department of Clinical and Translational Medicine, 3D Medicines Inc., Shanghai, China
| | - Zhizhen Li
- Department of Biliary Tract Surgery I, Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Zhenghua Xie
- Department of Clinical and Translational Medicine, 3D Medicines Inc., Shanghai, China
| | - Yue Wu
- Department of Biliary Tract Surgery I, Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Xiaofang Li
- Department of Clinical and Translational Medicine, 3D Medicines Inc., Shanghai, China
| | - Qingxiang Gao
- Department of Biliary Tract Surgery I, Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Dongyu Liu
- Department of Clinical and Translational Medicine, 3D Medicines Inc., Shanghai, China
| | - Yang Shen
- Department of Biliary Tract Surgery I, Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Jianyang Ao
- Department of Biliary Tract Surgery I, Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Dadong Zhang
- Department of Clinical and Translational Medicine, 3D Medicines Inc., Shanghai, China.
| | - Yanxin Chang
- Department of Biliary Tract Surgery II, Eastern Hepatobiliary Surgery Hospital, Shanghai, China.
| | - Xiaoqing Jiang
- Department of Biliary Tract Surgery I, Eastern Hepatobiliary Surgery Hospital, Shanghai, China.
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25
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Hadfield MJ, DeCarli K, Bash K, Sun G, Almhanna K. Current and Emerging Therapeutic Targets for the Treatment of Cholangiocarcinoma: An Updated Review. Int J Mol Sci 2023; 25:543. [PMID: 38203714 PMCID: PMC10779232 DOI: 10.3390/ijms25010543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
Cholangiocarcinoma is a malignancy of the bile ducts that is often associated with late diagnosis, poor overall survival, and limited treatment options. The standard of care therapy for cholangiocarcinoma has been cytotoxic chemotherapy with modest improvements in overall survival with the addition of immune checkpoint inhibitors. The discovery of actionable mutations has led to the advent of targeted therapies against FGFR and IDH-1, which has expanded the treatment landscape for this patient population. Significant efforts have been made in the pre-clinical space to explore novel immunotherapeutic approaches, as well as antibody-drug conjugates. This review provides an overview of the current landscape of treatment options, as well as promising future therapeutic targets.
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Affiliation(s)
- Matthew J. Hadfield
- Division of Hematology/Oncology, Department of Medicine, The Warren Alpert School of Medicine of Brown University, Providence, RI 02806, USA; (M.J.H.); (G.S.)
| | - Kathryn DeCarli
- Division of Hematology/Oncology, Department of Medicine, The Warren Alpert School of Medicine of Brown University, Providence, RI 02806, USA; (M.J.H.); (G.S.)
| | - Kinan Bash
- Department of Graduate Studies, University of New England, Biddeford, ME 04005, USA;
| | - Grace Sun
- Division of Hematology/Oncology, Department of Medicine, The Warren Alpert School of Medicine of Brown University, Providence, RI 02806, USA; (M.J.H.); (G.S.)
| | - Khaldoun Almhanna
- Division of Hematology/Oncology, Department of Medicine, The Warren Alpert School of Medicine of Brown University, Providence, RI 02806, USA; (M.J.H.); (G.S.)
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26
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Andraus W, Tustumi F, de Meira Junior JD, Pinheiro RSN, Waisberg DR, Lopes LD, Arantes RM, Rocha Santos V, de Martino RB, Carneiro D’Albuquerque LA. Molecular Profile of Intrahepatic Cholangiocarcinoma. Int J Mol Sci 2023; 25:461. [PMID: 38203635 PMCID: PMC10778975 DOI: 10.3390/ijms25010461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/23/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
Intrahepatic cholangiocarcinoma (ICC) is a relatively uncommon but highly aggressive primary liver cancer that originates within the liver. The aim of this study is to review the molecular profile of intrahepatic cholangiocarcinoma and its implications for prognostication and decision-making. This comprehensive characterization of ICC tumors sheds light on the disease's underlying biology and offers a foundation for more personalized treatment strategies. This is a narrative review of the prognostic and therapeutic role of the molecular profile of ICC. Knowing the molecular profile of tumors helps determine prognosis and support certain target therapies. The molecular panel in ICC helps to select patients for specific therapies, predict treatment responses, and monitor treatment responses. Precision medicine in ICC can promote improvement in prognosis and reduce unnecessary toxicity and might have a significant role in the management of ICC in the following years. The main mutations in ICC are in tumor protein p53 (TP53), Kirsten rat sarcoma virus (KRAS), isocitrate dehydrogenase 1 (IDH1), and AT-rich interactive domain-containing protein 1A (ARID1A). The rate of mutations varies significantly for each population. Targeting TP53 and KRAS is challenging due to the natural characteristics of these genes. Different stages of clinical studies have shown encouraging results with inhibitors of mutated IDH1 and target therapy for ARID1A downstream effectors. Fibroblast growth factor receptor 2 (FGFR2) fusions are an important target in patients with ICC. Immune checkpoint blockade can be applied to a small percentage of ICC patients. Molecular profiling in ICC represents a groundbreaking approach to understanding and managing this complex liver cancer. As our comprehension of ICC's molecular intricacies continues to expand, so does the potential for offering patients more precise and effective treatments. The integration of molecular profiling into clinical practice signifies the dawn of a new era in ICC care, emphasizing personalized medicine in the ongoing battle against this malignancy.
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Affiliation(s)
| | - Francisco Tustumi
- Department of Gastroenterology, Transplantation Unit, Universidade de São Paulo, São Paulo 05403-000, Brazil
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27
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Zhang X, Zhang Y, Zhang Q, Lu M, Chen Y, Zhang X, Zhang P. Role of AT-rich interaction domain 1A in gastric cancer immunotherapy: Preclinical and clinical perspectives. J Cell Mol Med 2023; 28:e18063. [PMID: 38041544 PMCID: PMC10902580 DOI: 10.1111/jcmm.18063] [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: 09/13/2023] [Revised: 10/31/2023] [Accepted: 11/14/2023] [Indexed: 12/03/2023] Open
Abstract
The application of immune checkpoint inhibitor (ICI) using monoclonal antibodies has brought about a profound transformation in the clinical outcomes for patients grappling with advanced gastric cancer (GC). Nonetheless, despite these achievements, the quest for effective functional biomarkers for ICI therapy remains constrained. Recent research endeavours have shed light on the critical involvement of modified epigenetic regulators in the pathogenesis of gastric tumorigenesis, thus providing a glimpse into potential biomarkers. Among these regulatory factors, AT-rich interaction domain 1A (ARID1A), a pivotal constituent of the switch/sucrose non-fermentable (SWI/SNF) complex, has emerged as a promising candidate. Investigations have unveiled the pivotal role of ARID1A in bridging the gap between genome instability and the reconfiguration of the tumour immune microenvironment, culminating in an enhanced response to ICI within the landscape of gastric cancer treatment. This all-encompassing review aims to dissect the potential of ARID1A as a valuable biomarker for immunotherapeutic approaches in gastric cancer, drawing from insights garnered from both preclinical experimentation and clinical observations.
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Affiliation(s)
- Xuemei Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Youzhi Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- School of Pharmacy, Hubei University of Science and Technology, Xianning, China
| | - Qiaoyun Zhang
- School of Pharmacy, Hubei University of Science and Technology, Xianning, China
| | - Mengyao Lu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuan Chen
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoyu Zhang
- Division of Gastrointestinal Surgery, Department of General Surgery, Huai'an Second People's Hospital, the Affiliated Huai'an Hospital of Xuzhou Medical University, Huaian, China
| | - Peng Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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28
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Bakhshwin A, Lai KK, Ammoun A, Friedman K, El Hag M. Inhibin-Positive "Cholangioblastic" Variant of Intrahepatic Cholangiocarcinoma: Report of 3 New Patients With Review of the Literature. Int J Surg Pathol 2023; 31:1495-1504. [PMID: 37073447 DOI: 10.1177/10668969231157775] [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] [Indexed: 04/20/2023]
Abstract
Cholangiocarcinoma is the second most common primary liver malignant neoplasm. It usually affects older individuals in their seventh decade of life with no gender predilection. Recently, a distinct subtype of cholangiocarcinoma has emerged with 2 proposed names: "cholangioblastic" and "solid tubulocystic." This variant predominantly occurs in younger women who lack the common risk factors for patients diagnosed with cholangiocarcinomas, such as older age and chronic liver disease or cirrhosis. We describe 3 new patients with a cholangioblastic variant of intrahepatic cholangiocarcinoma. At the time of diagnosis, the patients were aged 19-, 46-, and 28-year-old; 2 females and 1 male (the 46-year-old). None of our patients had a history of chronic liver disease or known predisposing factors for liver tumors. Tumor size ranged from 2.3 to 23 cm in greatest dimension. Histological examination of these tumors demonstrated reproducible morphology characterized by trabecular, nested, and multicystic patterns with micro and macro follicles filled with eosinophilic material. The immunohistochemical profile showed that the tumor cells were positive for keratin 7, inhibin, synaptophysin, and albumin in situ hybridization, while negative for HepPar1, arginase, and INSM1. All tumors lacked conventional intrahepatic cholangiocarcinoma/adenocarcinoma morphology. We also review the literature and emphasize that neuroendocrine tumors should be recognized as a major diagnostic pitfall of this variant.
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Affiliation(s)
- Ahmed Bakhshwin
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
- King Abdulaziz University, Jeddah, Saudi Arabia
| | - Keith K Lai
- Contra Costa Pathology Associates, Pleasant Hill, CA, USA
| | - Alwalid Ammoun
- Case Western Reserve University/University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Kenneth Friedman
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Mohamed El Hag
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
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29
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Hiromatsu M, Toshida K, Itoh S, Harada N, Kohashi K, Oda Y, Yoshizumi T. Transferrin Receptor is Associated with Sensitivity to Ferroptosis Inducers in Hepatocellular Carcinoma. Ann Surg Oncol 2023; 30:8675-8689. [PMID: 37548836 DOI: 10.1245/s10434-023-14053-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 06/19/2023] [Indexed: 08/08/2023]
Abstract
PURPOSE Transferrin receptor (TFR), a membrane protein that has a critical role in the transport of iron into cells, is known to be a ferroptosis-related marker. Although TFR is reported to be abundantly expressed in tumor cells, its relationship with ferroptosis inducers in hepatocellular carcinoma (HCC) remains unclear. METHODS The authors performed immunohistochemical staining of TFR and divided 350 HCC patients into two groups according to its expression. They analyzed the association between TFR expression and prognosis or clinicopathologic factors. In addition, the regulation of malignant activity and its effect on the efficacy of ferroptosis inducers were investigated in vitro. RESULTS For this study, 350 patients were divided into TFR-positive (n =180, 51.4%) and TFR-negative (n = 170, 48.6%) groups. The TFR-positive group had more hepatitis B surface antigen (HBs-Ag) (p = 0.0230), higher α-fetoprotein (AFP) levels (p = 0.0023), higher des-gamma-carboxyprothrombin (DCP) levels (p = 0.0327), a larger tumor size (p = 0.0090), greater proportions of Barcelona Clinic Liver Cancer (BCLC) stage B or C (p = 0.0005), poor differentiation (p < 0.0001), and microscopic intrahepatic metastasis (p = 0.0066). In the multivariate analyses, TFR expression was an independent prognostic factor in disease-free survival (p = 0.0315). In vitro, TFRC knockdown decreased cell motility. In addition, TFRC knockdown abolished artesunate (AS)-, lenvatinib-, and sorafenib-induced ferroptosis in HCC cell lines. The study demonstrated that simultaneous treatment of AS with multi-kinase inhibitor augmented the ferroptosis-inducing effects of AS in HCC cell lines. CONCLUSION TFR expression is a poor prognostic factor in HCC, but its expression increases sensitivity to ferroptosis-inducing agents.
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Affiliation(s)
- Maki Hiromatsu
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Katsuya Toshida
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Shinji Itoh
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.
| | - Noboru Harada
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kenichi Kohashi
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshinao Oda
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tomoharu Yoshizumi
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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30
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Li Z, Huang N, Du Q, Huang W, Wang B, Wang B, Shen G, Zhang H, Shi S, Wang L. Role of immunophenotypic characterisation in prognostic subtyping of intrahepatic cholangiocarcinoma. Pathology 2023; 55:979-988. [PMID: 37858435 DOI: 10.1016/j.pathol.2023.07.008] [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: 01/17/2023] [Revised: 06/07/2023] [Accepted: 07/23/2023] [Indexed: 10/21/2023]
Abstract
Intrahepatic cholangiocarcinoma (iCCA) is classified by the 5th WHO classification of tumours of the digestive system as large duct type (LDT) and small duct type (SDT), based on the anatomical location, morphological appearances, immunophenotype, and gene events. We evaluated the subtyping system using real-world data and established a supplementary method using immunohistochemical (IHC) detection. We retrospectively investigated 190 cases of surgically resected iCCA and classified them according to histological evaluations and gene detection. The prognostic value of the IHC markers were evaluated according to the relapse-free survival (RFS) and overall survival (OS). Basic histological classification was insufficient, with 61 cases classified as uncertain. This method showed no prognostic value for RFS or OS. The four-marker IHC detection, including EMA, S100P, N-cadherin, and CRP, which classified 68 cases as LDT, 108 cases as SDT, and 14 cases as uncertain, was highly efficient in subtyping and prognosis. The seven-marker method, including CD56, MUC5AC and MUC6, was consistent with the four-marker method. FGFR2 gene fusion was exclusively detected in 20 cases of SDT iCCA, according to the four- and seven-marker IHC detection. This novel method of iCCA classification exhibited diagnostic, prognostic and therapeutic value in clinical practice.
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Affiliation(s)
- Zhuo Li
- Department of Pathology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ning Huang
- Department of Hepatobiliary Surgery, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qiang Du
- Department of Pathology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wenting Huang
- Department of Pathology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Department of Pathology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Bingzhi Wang
- Department of Pathology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bingning Wang
- Department of Pathology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Guihua Shen
- Department of Pathology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Haifeng Zhang
- Department of Pathology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Susheng Shi
- Department of Pathology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Liming Wang
- Department of Hepatobiliary Surgery, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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31
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Peng A, Lin X, Yang Q, Sun Y, Chen R, Liu B, Yu X. ΔNp63α facilitates proliferation and migration, and modulates the chromatin landscape in intrahepatic cholangiocarcinoma cells. Cell Death Dis 2023; 14:777. [PMID: 38012140 PMCID: PMC10682000 DOI: 10.1038/s41419-023-06309-7] [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: 05/12/2023] [Revised: 11/10/2023] [Accepted: 11/14/2023] [Indexed: 11/29/2023]
Abstract
p63 plays a crucial role in epithelia-originating tumours; however, its role in intrahepatic cholangiocarcinoma (iCCA) has not been completely explored. Our study revealed the oncogenic properties of p63 in iCCA and identified the major expressed isoform as ΔNp63α. We collected iCCA clinical data from The Cancer Genome Atlas database and analyzed p63 expression in iCCA tissue samples. We further established genetically modified iCCA cell lines in which p63 was overexpressed or knocked down to study the protein function/function of p63 in iCCA. We found that cells overexpressing p63, but not p63 knockdown counterparts, displayed increased proliferation, migration, and invasion. Transcriptome analysis showed that p63 altered the iCCA transcriptome, particularly by affecting cell adhesion-related genes. Moreover, chromatin accessibility decreased at p63 target sites when p63 binding was lost and increased when p63 binding was gained. The majority of the p63 bound sites were located in the distal intergenic regions and showed strong enhancer marks; however, active histone modifications around the Transcription Start Site changed as p63 expression changed. We also detected an interaction between p63 and the chromatin structural protein YY1. Taken together, our results suggest an oncogenic role for p63 in iCCA.
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Affiliation(s)
- Anghui Peng
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China
- Zhuhai Interventional Medical Center, Zhuhai Precision Medical Center, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China
| | - Xiaowen Lin
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China
- Zhuhai Interventional Medical Center, Zhuhai Precision Medical Center, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China
| | - Quanli Yang
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China
| | - Yihao Sun
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China
- Zhuhai Interventional Medical Center, Zhuhai Precision Medical Center, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China
| | - Ruiyan Chen
- Department of Dermatology, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China
| | - Bing Liu
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China.
- Zhuhai Interventional Medical Center, Zhuhai Precision Medical Center, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China.
| | - Xinyang Yu
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China.
- Zhuhai Interventional Medical Center, Zhuhai Precision Medical Center, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China.
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32
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Zhou PY, Zhou C, Gan W, Tang Z, Sun BY, Huang JL, Liu G, Liu WR, Tian MX, Jiang XF, Wang H, Tao CY, Fang Y, Qu WF, Huang R, Zhu GQ, Huang C, Fu XT, Ding ZB, Gao Q, Zhou J, Shi YH, Yi Y, Fan J, Qiu SJ. Single-cell and spatial architecture of primary liver cancer. Commun Biol 2023; 6:1181. [PMID: 37985711 PMCID: PMC10661180 DOI: 10.1038/s42003-023-05455-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 10/12/2023] [Indexed: 11/22/2023] Open
Abstract
Primary liver cancer (PLC) poses a leading threat to human health, and its treatment options are limited. Meanwhile, the investigation of homogeneity and heterogeneity among PLCs remains challenging. Here, using single-cell RNA sequencing, spatial transcriptomic and bulk multi-omics, we elaborated a molecular architecture of 3 PLC types, namely hepatocellular carcinoma (HCC), intrahepatic cholangiocarcinoma (ICC) and combined hepatocellular-cholangiocarcinoma (CHC). Taking a high-resolution perspective, our observations revealed that CHC cells exhibit internally discordant phenotypes, whereas ICC and HCC exhibit distinct tumor-specific features. Specifically, ICC was found to be the primary source of cancer-associated fibroblasts, while HCC exhibited disrupted metabolism and greater individual heterogeneity of T cells. We further revealed a diversity of intermediate-state cells residing in the tumor-peritumor junctional zone, including a congregation of CPE+ intermediate-state endothelial cells (ECs), which harbored the molecular characteristics of tumor-associated ECs and normal ECs. This architecture offers insights into molecular characteristics of PLC microenvironment, and hints that the tumor-peritumor junctional zone could serve as a targeted region for precise therapeutical strategies.
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Affiliation(s)
- Pei-Yun Zhou
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China.
- Shanghai Cancer Center, Fudan University, Shanghai, 200032, China.
| | - Cheng Zhou
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Wei Gan
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Zheng Tang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Bao-Ye Sun
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Jin-Long Huang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Gao Liu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Wei-Ren Liu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Meng-Xin Tian
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Xi-Fei Jiang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Han Wang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Chen-Yang Tao
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Yuan Fang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Wei-Feng Qu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Run Huang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Gui-Qi Zhu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Cheng Huang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Xiu-Tao Fu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Zhen-Bin Ding
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Qiang Gao
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Jian Zhou
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Ying-Hong Shi
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Yong Yi
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China.
| | - Jia Fan
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China.
| | - Shuang-Jian Qiu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China.
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Kikuchi AT, Umetsu S, Joseph N, Kakar S. Genomic Analysis in the Categorization of Poorly Differentiated Primary Liver Carcinomas. Am J Surg Pathol 2023; 47:1207-1218. [PMID: 37661782 DOI: 10.1097/pas.0000000000002116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
A subset of primary liver carcinomas (PLCs) cannot be classified as hepatocellular carcinoma (HCC) or intrahepatic cholangiocarcinoma (iCCA) based on morphology and immunohistochemistry (IHC). This includes tumors with morphology suggestive of HCC but lacking hepatocellular marker expression, tumors with ambiguous morphology characterized by co-expression of hepatocellular and cholangiocytic markers, and undifferentiated pleomorphic carcinomas with no discernible line of differentiation on morphology or IHC. This study examines the role of genomic analysis in the categorization of these tumors. Genomic analysis was performed on 16 PLCs that could not be definitely classified as HCC or iCCA based on morphology and IHC using a capture-based next-generation sequencing assay (n=15) or single gene mutational analysis (n=1). Genomic alterations in TERT promoter were seen in 9/16 cases (56%) and strongly favored HCC. Genomic alterations favoring iCCA were seen in 5/16 cases (31%) and included mutations in IDH1 , PBRM1 , BAP1 , and ERBB2 , as well as FGFR2 fusion. Genomic changes were helpful in classifying 14/16 (87%) PLCs. Though not specific, these genomic alterations can provide valuable diagnostic clues in selected morphologically and immunohistochemically unclassifiable cases. Given the important differences in management between HCC and iCCA, routine use of genomic analysis in diagnostically challenging settings should be considered.
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Affiliation(s)
- Alexander T Kikuchi
- Department of Pathology, University of California San Francisco, San Francisco, CA
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Ahn KS, Kang KJ, Kim YH, Kim TS, Cho KB, Kim HS, Baek WK, Suh SI, Han JY. Diagnostic Role of Bile Pigment Components in Biliary Tract Cancer. Biomol Ther (Seoul) 2023; 31:674-681. [PMID: 37558633 PMCID: PMC10616509 DOI: 10.4062/biomolther.2023.010] [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: 01/11/2023] [Revised: 06/08/2023] [Accepted: 07/04/2023] [Indexed: 08/11/2023] Open
Abstract
Bile pigment, bilirubin, and biliverdin concentrations may change as a results of biliary tract cancer (BTC) altering the mechanisms of radical oxidation and heme breakdown. We explored whether changes in bile pigment components could help distinguish BTC from benign biliary illness by evaluating alterations in patients with BTC. We collected bile fluid from 15 patients with a common bile duct stone (CBD group) and 63 individuals with BTC (BTC group). We examined the bile fluid's bilirubin, biliverdin reductase (BVR), heme oxygenase (HO-1), and bacterial taxonomic abundance. Serum bilirubin levels had no impact on the amounts of bile HO-1, BVR, or bilirubin. In comparison to the control group, the BTC group had considerably higher amounts of HO-1, BVR, and bilirubin in the bile. The areas under the curve for the receiver operating characteristic curve analyses of the BVR and HO-1 were 0.832 (p<0.001) and 0.891 (p<0.001), respectively. Firmicutes was the most prevalent phylum in both CBD and BTC, according to a taxonomic abundance analysis, however the Firmicutes/Bacteroidetes ratio was substantially greater in the BTC group than in the CBD group. The findings of this study showed that, regardless of the existence of obstructive jaundice, biliary carcinogenesis impacts heme degradation and bile pigmentation, and that the bile pigment components HO-1, BVR, and bilirubin in bile fluid have a diagnostic significance in BTC. In tissue biopsies for the diagnosis of BTC, particularly for distinguishing BTC from benign biliary strictures, bile pigment components can be used as additional biomarkers.
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Affiliation(s)
- Keun Soo Ahn
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Keimyung University Dongsan Medical Center, Daegu 42601, Republic of Korea
| | - Koo Jeong Kang
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Keimyung University Dongsan Medical Center, Daegu 42601, Republic of Korea
| | - Yong Hoon Kim
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Keimyung University Dongsan Medical Center, Daegu 42601, Republic of Korea
| | - Tae-Seok Kim
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Keimyung University Dongsan Medical Center, Daegu 42601, Republic of Korea
| | - Kwang Bum Cho
- Division of Gaestroenterology, Department of Internal Medicine, Keimyung University Dongsan Medical Center, Daegu 42601, Republic of Korea
| | - Hye Soon Kim
- Division of Endocrinology, Department of Internal Medicine, Keimyung University Dongsan Medical Center, Daegu 42601, Republic of Korea
| | - Won-Ki Baek
- Department of Microbiology, Keimyung University School of Medicine, Daegu 42601, Republic of Korea
| | - Seong-Il Suh
- Department of Microbiology, Keimyung University School of Medicine, Daegu 42601, Republic of Korea
| | - Jin-Yi Han
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Keimyung University Dongsan Medical Center, Daegu 42601, Republic of Korea
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Du X, Zhang X, Qi Z, Zeng Z, Xu Y, Yu Z, Cao X, Xia J. HELLS modulates the stemness of intrahepatic cholangiocarcinoma through promoting senescence-associated secretory phenotype. Comput Struct Biotechnol J 2023; 21:5174-5185. [PMID: 37920816 PMCID: PMC10618119 DOI: 10.1016/j.csbj.2023.09.020] [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: 05/11/2023] [Revised: 09/17/2023] [Accepted: 09/17/2023] [Indexed: 11/04/2023] Open
Abstract
The senescence-associated secretory phenotype (SASP) is closely associated with the tumorigenesis and progression of intrahepatic cholangiocarcinoma (ICC). However, it remains unclear its relation to stemness of ICC. In the study, the stemness indices of ICC were calculated using one-class linear regression (OCLR) and single-sample gene set enrichment analysis (ssGSEA) algorithms. A total of 14 senescence-related stemness genes (SRSGs) were identified using Pearson correlation analysis in ICC. Subsequently, a SRSGs-related classification was established using a consensus clustering for ICC. Different types of ICC exhibit distinct prognosis, immunity, metabolisms, and oncogenic signatures. Additionally, we constructed a risk score model for ICC using principal component analysis (PCA). The risk score was positively correlated with stemness, immune infiltration, metabolisms and oncogenic signatures, but negatively with prognosis in ICC. Patients with a high risk score may respond well to immunotherapy. Furthermore, we employed 3D fibrin gels to select tumor-repopulating cells (TRC) with stemness features. We found that HELLS, belonging to the 14 SRSGs, was up-regulated in ICC-TRC. And silencing HELLS significantly reduced the colony size, inhibited migration and invasion, and attenuated SASP in ICC-TRC. In summary, we provided a novel classification and risk score for ICC and uncovered a molecular mechanism via which CSLCs could obtain an active SASP.
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Affiliation(s)
- Xiaojing Du
- Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Endoscopy Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xingxing Zhang
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
- Department of Gastroenterology, Shanghai University of Medicine & Health Sciences Affiliated Sixth People’s Hospital South Campus, Shanghai 201499, China
| | - Zhuoran Qi
- Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Department of Gastroenterology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Ziyi Zeng
- Royal Prince Alfred Hospital, 50 Missenden Rd, Camperdown, NSW 2050, Australia
| | - Ye Xu
- Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Zhijie Yu
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
- Wenzhou Key Laboratory of Hematology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Xin Cao
- Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jinglin Xia
- Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
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Shirakami Y, Kato J, Ohnishi M, Taguchi D, Maeda T, Ideta T, Kubota M, Sakai H, Tomita H, Tanaka T, Shimizu M. A Novel Mouse Model of Intrahepatic Cholangiocarcinoma Induced by Azoxymethane. Int J Mol Sci 2023; 24:14581. [PMID: 37834032 PMCID: PMC10572168 DOI: 10.3390/ijms241914581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/20/2023] [Accepted: 09/24/2023] [Indexed: 10/15/2023] Open
Abstract
Cholangiocarcinoma is the second most common primary cancer of the liver and has a poor prognosis. Various animal models, including carcinogen-induced and genetically engineered rodent models, have been established to clarify the mechanisms underlying cholangiocarcinoma development. In the present study, we developed a novel mouse model of malignant lesions in the biliary ducts induced by the administration of the carcinogen azoxymethane to obese C57BLKS/J-db/db mice. A histopathological analysis revealed that the biliary tract lesions in the liver appeared to be an intrahepatic cholangiocarcinoma with higher tumor incidence, shorter experimental duration, and a markedly increased incidence in obese mice. Molecular markers analyzed using a microarray and a qPCR indicated that the cancerous lesions originated from the cholangiocytes and developed in the inflamed livers. These findings indicated that this is a novel mouse model of intrahepatic cholangiocarcinoma in the context of steatohepatitis. This model can be used to provide a better understanding of the pathogenic mechanisms of cholangiocarcinoma and to develop novel therapeutic strategies for this malignancy.
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Affiliation(s)
- Yohei Shirakami
- Department of Gastroenterology, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan; (J.K.); (M.O.); (D.T.); (T.M.); (T.I.); (M.K.); (H.S.); (M.S.)
| | - Junichi Kato
- Department of Gastroenterology, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan; (J.K.); (M.O.); (D.T.); (T.M.); (T.I.); (M.K.); (H.S.); (M.S.)
| | - Masaya Ohnishi
- Department of Gastroenterology, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan; (J.K.); (M.O.); (D.T.); (T.M.); (T.I.); (M.K.); (H.S.); (M.S.)
| | - Daisuke Taguchi
- Department of Gastroenterology, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan; (J.K.); (M.O.); (D.T.); (T.M.); (T.I.); (M.K.); (H.S.); (M.S.)
| | - Toshihide Maeda
- Department of Gastroenterology, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan; (J.K.); (M.O.); (D.T.); (T.M.); (T.I.); (M.K.); (H.S.); (M.S.)
| | - Takayasu Ideta
- Department of Gastroenterology, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan; (J.K.); (M.O.); (D.T.); (T.M.); (T.I.); (M.K.); (H.S.); (M.S.)
| | - Masaya Kubota
- Department of Gastroenterology, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan; (J.K.); (M.O.); (D.T.); (T.M.); (T.I.); (M.K.); (H.S.); (M.S.)
| | - Hiroyasu Sakai
- Department of Gastroenterology, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan; (J.K.); (M.O.); (D.T.); (T.M.); (T.I.); (M.K.); (H.S.); (M.S.)
| | - Hiroyuki Tomita
- Department of Tumor Pathology, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan;
| | - Takuji Tanaka
- Department of Pathological Diagnosis, Gifu Municipal Hospital, Gifu 500-8513, Japan;
| | - Masahito Shimizu
- Department of Gastroenterology, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan; (J.K.); (M.O.); (D.T.); (T.M.); (T.I.); (M.K.); (H.S.); (M.S.)
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Koay EJ, Javle M, Belknap M, Derasari S, Roach M, Ludmir EB. What Role Does Radiotherapy Play in the Molecular Era for Intrahepatic Cholangiocarcinoma? Cancer J 2023; 29:272-278. [PMID: 37796645 DOI: 10.1097/ppo.0000000000000685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
ABSTRACT Intrahepatic cholangiocarcinoma is a rare disease, yet with rising incidence globally. Most patients are not eligible for potentially curative surgical resection, and many patients with unresectable disease die within 12 months of diagnosis, primarily due to liver failure from the primary tumor. Recent prospective and retrospective studies indicate that local control of the primary tumor can be achieved with hypofractionated radiotherapy in patients with unresectable disease, translating into prolonged survival of these patients. During the time that these encouraging reports for radiotherapy have been published, numerous concurrent studies have also shown that intrahepatic cholangiocarcinoma is a molecularly diverse disease with multiple targetable genetic alterations and a complex tumor microenvironment. These biological insights have translated into new drug approvals for subsets of patients. We review the current knowledge about the biology and targeted treatment of intrahepatic cholangiocarcinoma and describe these developments in the context of modern radiotherapy.
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Affiliation(s)
- Eugene J Koay
- From the University of Texas MD Anderson Cancer Center, Houston, TX
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Tang Z, Yang Y, Chen W, Liang T. Epigenetic deregulation of MLF1 drives intrahepatic cholangiocarcinoma progression through EGFR/AKT and Wnt/β-catenin signaling. Hepatol Commun 2023; 7:e0204. [PMID: 37486965 PMCID: PMC10368384 DOI: 10.1097/hc9.0000000000000204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/02/2023] [Indexed: 07/26/2023] Open
Abstract
BACKGROUND Intrahepatic cholangiocarcinoma (iCCA) is an aggressive malignancy with multiple etiologies and is largely refractory to current treatment strategies. Myeloid leukemia factor 1 (MLF1) is associated with human cancer progression. Nevertheless, the function of MLF1 in iCCA remains unknown. METHODS We performed expression analyses of MLF1 in human iCCA. In vitro and in vivo experiments were conducted to investigate the role of MLF1 in iCCA progression. The upstream regulatory mechanism of MLF1 upregulation in iCCA was deciphered by luciferase and DNA methylation analyses. RESULTS MLF1 was significantly upregulated in clinical iCCA tissue specimens and human iCCA cell lines. MLF1 was positively correlated with KRT19 and MUC1 expression and epithelial-mesenchymal transition (EMT) gene set enrichment score in clinical iCCA. High MLF1 expression was independently associated with worse prognoses in iCCA patients after curative resection. In addition, experimental knockdown of MLF1 attenuated, while overexpression of MLF1 promoted the proliferation, invasiveness, and growth of iCCA cells in vitro and in vivo. Mechanically, MLF1 comodulated EGFR/AKT and Wnt/β-catenin signalings through regulating EGFR, AKT, WNT3, and p-GSK3β expression. Promoter CpG sites' hypermethylation-induced downregulation of miR-29c-3p contributed to MLF1 upregulation in iCCA patients. The upregulation of DNA methyltransferase (DNMT)1, 3A, and 3B downregulated miR-29c-3p by dictating promoter DNA methylation pattern. MiR-29c-3p showed therapeutic potential by targeting MLF1 in iCCA. CONCLUSIONS Our results demonstrated that hypermethylation-mediated miR-29c-3p downregulation contributes to MLF1 upregulation in iCCA, which resulted in tumor cells' proliferation and metastasis through comodulating EGFR/AKT and Wnt/β-catenin signalings.
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Affiliation(s)
- Zengwei Tang
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, Zhejiang, China
- Zhejiang University Cancer Center, Hangzhou, Zhejiang, China
| | - Yuan Yang
- Department of Hematology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wen Chen
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, Zhejiang, China
- Zhejiang University Cancer Center, Hangzhou, Zhejiang, China
| | - Tingbo Liang
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, Zhejiang, China
- Zhejiang University Cancer Center, Hangzhou, Zhejiang, China
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Wang H, Wang X, Xu L, Zhang J. RARRES2 is Downregulated in Isocitrate Dehydrogenase 1 Mutant Glioma Patients and Served as an Unfavorable Prognostic Factor of Glioma. World Neurosurg 2023; 176:e610-e622. [PMID: 37271257 DOI: 10.1016/j.wneu.2023.05.109] [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: 05/25/2023] [Accepted: 05/29/2023] [Indexed: 06/06/2023]
Abstract
BACKGROUND Mutations in isocitrate dehydrogenase 1 (IDH1) induce extensive transcriptional alterations to promote glioma development. However, IDH1 mutation contributes the better clinical outcomes of glioma. Further understanding the transcriptional and DNA methylation changes mediated by IDH1 mutation will provide new therapeutic targets for glioma. METHODS Public glioma cohorts were collected and processed using R software. The transcriptional changes mediated by IDH1 mutation were determined and presented using heatmap. The differentially expressed genes in IDH1 mutant glioma were overlapped using TBtools. The prognostic effects of IDH1 regulated genes were determined by Kaplan-Meier survival analysis. RESULTS Retinoic acid receptor responder 2 (RARRES2) was upregulated in IDH1 wild type lower-grade glioma (LGG) patients, and higher expression levels of RARRES2 were associated with worse clinical outcomes of LGG. Moreover, IDH1 wild type LGG patients with higher expression levels of RARRES2 had even worse overall survival. Compared with LGG, RARRES2 was upregulated in grade IV glioma (glioblastoma multiforme, GBM). Also, RARRES2 represented an unfavorable prognostic factor of glioma. In GBM, RARRES2 was also associated with IDH1 mutation. In both LGG and GBM, IDH1 mutation induced extensive DNA hypermethylation, and more than half genes that were downregulated in IDH1 mutant glioma were contributed by DNA hypermethylation. RARRES2 was also hypermethylated in IDH1 mutant LGG or GBM patients. Furthermore, RARRES2 hypomethylation was an unfavorable prognostic factor in patients with LGG. CONCLUSIONS RARRES2 was downregulated by IDH1 mutation and served as an unfavorable prognostic factor in glioma.
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Affiliation(s)
- Haiwei Wang
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China.
| | - Xinrui Wang
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Liangpu Xu
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Ji Zhang
- State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital Affiliated to School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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Zeng X, Ou H, Zeng C, Liu Q, Wang W, Yao J. Multi-omics integrated analyzed the origin of intrahepatic mucinous cholangiocarcinoma: a case report. Front Oncol 2023; 13:1175707. [PMID: 37546424 PMCID: PMC10401833 DOI: 10.3389/fonc.2023.1175707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 07/03/2023] [Indexed: 08/08/2023] Open
Abstract
Intrahepatic mucinous cholangiocarcinoma (IMCC) is a rare subtype of intrahepatic cholangiocarcinoma (IHCC). Limited data describe the genetic characteristics of IMCC and insights on its pathogenesis are lacking. Here, we employed a multi-omics approach to analyze somatic mutations, transcriptome, proteome and metabolome of tumor tissue obtained from a case of IMCC in order to clarify the pathogenesis of IMCC. A total of 54 somatic mutations were detected, including a G12D mutation in KRAS that is likely to be involved in the onset of IMCC. The genes consistently up-regulated at the transcription level and in the proteome were enriched for mucin and mucopolysaccharide biosynthesis, for cell cycle functions and for inflammatory signaling pathways. The consistently down-regulated genes were enriched in bile synthesis and fatty acid metabolism pathways. Further multi-omics analysis found that mucin synthesis by MUC4 and MUC16 was elevated by up-regulated expression of mesothelin (MSLN). Moreover, transcription factor ONECUT3 was identified that possibly activates the transcription of mucin and mucopolysaccharide biosynthesis in IMCC.
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Affiliation(s)
- Xiaokang Zeng
- Medical Research Center, Shunde Hospital, Southern Medical University, Foshan, China
| | - Huohui Ou
- Department of Hepatobiliary Surgery, Shunde Hospital, Southern Medical University, Foshan, China
| | - Chong Zeng
- Medical Research Center, Shunde Hospital, Southern Medical University, Foshan, China
| | - Qingbo Liu
- Department of Hepatobiliary Surgery, Shunde Hospital, Southern Medical University, Foshan, China
| | - Weidong Wang
- Department of Hepatobiliary Surgery, Shunde Hospital, Southern Medical University, Foshan, China
| | - Jie Yao
- Medical Research Center, Shunde Hospital, Southern Medical University, Foshan, China
- Department of Laboratory Medicine, Shunde Hospital, Southern Medical University, Foshan, China
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Rimini M, Burgio V, Antonuzzo L, Rimassa L, Oneda E, Soldà C, Cito P, Nasti G, Lavacchi D, Zanuso V, Rizzato MD, Zaniboni A, Ottaiano A, Persano M, Cornara N, Scartozzi M, Cascinu S, Casadei-Gardini A. Updated survival outcomes with ivosidenib in patients with previously treated IDH1-mutated intrahepatic-cholangiocarcinoma: an Italian real-world experience. Ther Adv Med Oncol 2023; 15:17588359231171574. [PMID: 37457302 PMCID: PMC10345913 DOI: 10.1177/17588359231171574] [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: 01/17/2023] [Accepted: 04/05/2023] [Indexed: 07/18/2023] Open
Abstract
Background The results of the phase III ClarIDHy trial led to the FDA approval of ivosidenib as a therapeutic option for patients with locally advanced or metastatic cholangiocarcinoma (CCA) harboring isocitrate dehydrogenase 1 (IDH1) mutations. We recently published the first data on the use of ivosidenib in a real-world setting. Objective Here we report the updated survival results of 11 patients with locally advanced or metastatic IDH1-mutated CCA who received ivosidenib in clinical practice. Patients and methods Patients treated with ivosidenib as second- and third-line treatments for advanced CCA have been collected with the aim to evaluate the survival outcomes. A molecular study has been performed by next generation sequencing essay. Results Overall, 11 patients were included. After a median follow-up of 13.7 months, median progression-free survival from the start of treatment with ivosidenib was 4.4 months (95% CI: 2.0-5.8), whereas median overall survival was 15 months (95% CI: 6.6-15.0) regardless of treatment line. Disease control rate was 63%, with two patients achieving a partial response (18%). Eighteen percent of patients experienced at least one treatment-related adverse events (AEs), but no grade ⩾3 was reported. The most frequently observed grade 2 AEs were prolonged QT interval and hypomagnesemia. A molecular profiling was performed on 8 out of 11 patients, highlighting TP53, BAP1, CDKN2A, and CDKN2B as the most common co-altered genes in these patients. Conclusion The present update confirms the results of our previous real-world experience on the use of ivosidenib in IDH1-mutated CCA. Real-world evidence on larger numbers of patients is needed to confirm our findings.
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Affiliation(s)
| | - Valentina Burgio
- Department of Oncology, IRCCS San Raffaele Hospital, Milan, Italy
| | - Lorenzo Antonuzzo
- Clinical Oncology Unit, Careggi University Hospital, Florence, Italy
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Lorenza Rimassa
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele (Milan), Italy
- Medical Oncology and Hematology Unit, Humanitas Cancer Center, IRCCS Humanitas Research Hospital, Rozzano (Milan), Italy
| | - Ester Oneda
- Department of Oncology, Poliambulanza Hospital of Brescia, Brescia, Italy
- Oncology Unit 1, Veneto Institute of Oncology IOV – IRCCS, Padua, Italy
| | - Caterina Soldà
- Medical Oncology 1, Veneto Institute of Oncology IOV – IRCCS, Padua, Italy
| | - Pasqua Cito
- Oncologia Medica, Ospedale San Pio Di Castellaneta, Taranto, Italy
| | - Guglielmo Nasti
- Abdominal Oncology Division, Istituto Nazionale Tumori IRCCS Fondazione Pascale – IRCCS Di Napoli, Naples, Italy
| | - Daniele Lavacchi
- Clinical Oncology Unit, Careggi University Hospital, Florence, Italy
| | - Valentina Zanuso
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele (Milan), Italy
- Medical Oncology and Hematology Unit, Humanitas Cancer Center, IRCCS Humanitas Research Hospital, Rozzano (Milan), Italy
| | - Mario Domenico Rizzato
- Medical Oncology 1, Veneto Institute of Oncology IOV – IRCCS, Padua, Italy
- Department of Surgical, Oncological and Gastroenterological Sciences, University of Padua, Padua, Italy
| | - Alberto Zaniboni
- Department of Oncology, Poliambulanza Hospital of Brescia, Brescia, Italy
- Oncology Unit 1, Veneto Institute of Oncology IOV – IRCCS, Padua, Italy
| | - Alessandro Ottaiano
- Abdominal Oncology Division, Istituto Nazionale Tumori IRCCS Fondazione Pascale – IRCCS Di Napoli, Naples, Italy
| | - Mara Persano
- Department of Oncology, University Hospital of Cagliari, Cagliari, Italy
| | - Noemi Cornara
- Department of Oncology, IRCCS San Raffaele Hospital, Milan, Italy
| | - Mario Scartozzi
- Department of Oncology, University Hospital of Cagliari, Cagliari, Italy
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Liu D, Shi Y, Chen H, Nisar MA, Jabara N, Langwinski N, Mattson S, Nagaoka K, Bai X, Lu S, Huang CK. Molecular profiling reveals potential targets in cholangiocarcinoma. World J Gastroenterol 2023; 29:4053-4071. [PMID: 37476584 PMCID: PMC10354586 DOI: 10.3748/wjg.v29.i25.4053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 02/16/2023] [Accepted: 05/23/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND Cholangiocarcinoma (CCA) is a devastating malignancy and has a very poor prognosis if tumors spread outside the liver. Understanding the molecular mechanisms underlying the CCA progression will likely yield therapeutic approaches toward treating this deadly disease. AIM To determine the molecular pathogenesis in CCA progression. METHODS In silico analysis, in vitro cell culture, CCA transgenic animals, histological, and molecular assays were adopted to determine the molecular pathogenesis. RESULTS The transcriptomic data of human CCA samples were retrieved from The Cancer Genome Atlas (TGCA, CHOL), European Bioinformatics Institute (EBI, GAD00001001076), and Gene Expression Omnibus (GEO, GSE107943) databases. Using Gene set enrichment analysis, the cell cycle and Notch related pathways were demonstrated to be significantly activated in CCA in TCGA and GEO datasets. We, through differentially expressed genes, found several cell cycle and notch associated genes were significantly up-regulated in cancer tissues when compared with the non-cancerous control samples. The associated genes, via quantitative real-time PCR and western blotting assays, were further examined in normal human cholangiocytes, CCA cell lines, mouse normal bile ducts, and mouse CCA tumors established by specifically depleting P53 and expressing KrasG12D mutation in the liver. Consistently, we validated that the cell cycle and Notch pathways are up-regulated in CCA cell lines and mouse CCA tumors. Interestingly, targeting cell cycle and notch pathways using small molecules also exhibited significant beneficial effects in controlling tumor malignancy. More importantly, we demonstrated that several cell cycle and Notch associated genes are significantly associated with poor overall survival and disease-free survival using the Log-Rank test. CONCLUSION In summary, our study comprehensively analyzed the gene expression pattern of CCA samples using publicly available datasets and identified the cell cycle and Notch pathways are potential therapeutic targets in this deadly disease.
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Affiliation(s)
- Dan Liu
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Yang Shi
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Hongze Chen
- Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA 70112, United States
| | - Muhammad Azhar Nisar
- Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA 70112, United States
| | - Nicholas Jabara
- Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA 70112, United States
| | - Noah Langwinski
- Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA 70112, United States
| | - Sophia Mattson
- Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA 70112, United States
| | - Katsuya Nagaoka
- Department of Medicine, Rhode Island Hospital and the Alpert Medical School of Brown University, Providence, RI 02903, United States
| | - Xuewei Bai
- Department of Medicine, Rhode Island Hospital and the Alpert Medical School of Brown University, Providence, RI 02903, United States
| | - Shaolei Lu
- Department of Pathology, Alpert Medical School of Brown University, Providence, RI 02903, United States
| | - Chiung-Kuei Huang
- Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA 70112, United States
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Amadeo E, Rossari F, Vitiello F, Burgio V, Persano M, Cascinu S, Casadei-Gardini A, Rimini M. Past, present, and future of FGFR inhibitors in cholangiocarcinoma: from biological mechanisms to clinical applications. Expert Rev Clin Pharmacol 2023; 16:631-642. [PMID: 37387533 DOI: 10.1080/17512433.2023.2232302] [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: 05/09/2023] [Accepted: 06/29/2023] [Indexed: 07/01/2023]
Abstract
INTRODUCTION Biliary tract carcinoma (BTC) is a heterogenous group of aggressive hepatic malignancies, second to hepatocellular carcinoma per prevalence. Despite clinical research advancement, the overall 5-year survival rate is just above 2%. With the identification of somatic core mutations in half of cholangiocarcinomas. In the intrahepatic subtype (iCCA), it is possible to target mutational pathways of pharmacological interest. AREAS COVERED Major attention has been drawn to fibroblast growth factor receptor (FGFR), especially the type 2 (FGFR2), found mutated in 10-15% of iCCAs. FGFR2 fusions became the target of novel tyrosine-kinase inhibitors investigated in clinical studies, showing promising results so as to gain regulatory approval by American and European committees in recent years. Such drugs demonstrated a better impact on the quality of life compared to standard chemotherapy; however, side effects including hyperphosphatemia, gastrointestinal, eye, and nail disorders are common although mostly manageable. EXPERT OPINION As FGFR inhibitors may soon become the new alternative to standard chemotherapy in FGFR-mutated cholangiocarcinoma, accurate molecular testing and monitoring of acquired resistance mechanisms will be essential. The possible application of FGFR inhibitors in first-line treatment, as well as in combination with current standard treatments, remains the next step to be taken.
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Affiliation(s)
- Elisabeth Amadeo
- Department of Oncology, Vita-Salute San Raffaele University, IRCCS San Raffaele Scientific Institute Hospital, Milan, Italy
| | - Federico Rossari
- Department of Oncology, Vita-Salute San Raffaele University, IRCCS San Raffaele Scientific Institute Hospital, Milan, Italy
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute Hospital, Milan, Italy
| | - Francesco Vitiello
- Department of Oncology, Vita-Salute San Raffaele University, IRCCS San Raffaele Scientific Institute Hospital, Milan, Italy
| | - Valentina Burgio
- Department of Oncology, Vita-Salute San Raffaele University, IRCCS San Raffaele Scientific Institute Hospital, Milan, Italy
| | - Mara Persano
- Medical Oncology, University and University Hospital of Cagliari, Cagliari, Italy
| | - Stefano Cascinu
- Department of Oncology, Vita-Salute San Raffaele University, IRCCS San Raffaele Scientific Institute Hospital, Milan, Italy
| | - Andrea Casadei-Gardini
- Department of Oncology, Vita-Salute San Raffaele University, IRCCS San Raffaele Scientific Institute Hospital, Milan, Italy
| | - Margherita Rimini
- Department of Oncology, Vita-Salute San Raffaele University, IRCCS San Raffaele Scientific Institute Hospital, Milan, Italy
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Lu X, Green BL, Xie C, Liu C, Chen X. Preclinical and clinical studies of immunotherapy for the treatment of cholangiocarcinoma. JHEP Rep 2023; 5:100723. [PMID: 37229173 PMCID: PMC10205436 DOI: 10.1016/j.jhepr.2023.100723] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 02/10/2023] [Accepted: 02/16/2023] [Indexed: 05/27/2023] Open
Abstract
Cholangiocarcinoma (CCA) is a rare primary liver cancer associated with high mortality and few systemic treatment options. The behaviour of the immune system has come into focus as a potential treatment modality for many cancer types, but immunotherapy has yet to dramatically alter the treatment paradigm for CCA as it has for other diseases. Herein, we review recent studies describing the relevance of the tumour immune microenvironment (TIME) in CCA. Various non-parenchymal cell types are critically important in controlling CCA progression, prognosis, and response to systemic therapy. Knowledge of the behaviour of these leukocytes could help generate hypotheses to guide the development of potential immune-directed therapies. Recently, an immunotherapy-containing combination was approved for the treatment of advanced-stage CCA. However, despite level 1 evidence demonstrating the improved efficacy of this therapy, survival remained suboptimal. In the current manuscript, we provide a comprehensive review of the TIME in CCA, preclinical studies of immunotherapies against CCA, as well as ongoing clinical trials applying immunotherapies for the treatment of CCA. Particular emphasis is placed on microsatellite unstable tumours, a rare CCA subtype that demonstrates heightened sensitivity to approved immune checkpoint inhibitors. We also discuss the challenges involved in applying immunotherapies to the treatment of CCA and the importance of understanding the TIME.
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Affiliation(s)
- Xinjun Lu
- Department of Biliary-Pancreatic Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Benjamin L. Green
- Cancer Biology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Changqing Xie
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Chao Liu
- Department of Biliary-Pancreatic Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xin Chen
- Cancer Biology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
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Dragomir MP, Calina TG, Perez E, Schallenberg S, Chen M, Albrecht T, Koch I, Wolkenstein P, Goeppert B, Roessler S, Calin GA, Sers C, Horst D, Roßner F, Capper D. DNA methylation-based classifier differentiates intrahepatic pancreato-biliary tumours. EBioMedicine 2023; 93:104657. [PMID: 37348162 DOI: 10.1016/j.ebiom.2023.104657] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 05/21/2023] [Accepted: 06/02/2023] [Indexed: 06/24/2023] Open
Abstract
BACKGROUND Differentiating intrahepatic cholangiocarcinomas (iCCA) from hepatic metastases of pancreatic ductal adenocarcinoma (PAAD) is challenging. Both tumours have similar morphological and immunohistochemical pattern and share multiple driver mutations. We hypothesised that DNA methylation-based machine-learning algorithms may help perform this task. METHODS We assembled genome-wide DNA methylation data for iCCA (n = 259), PAAD (n = 431), and normal bile duct (n = 70) from publicly available sources. We split this cohort into a reference (n = 399) and a validation set (n = 361). Using the reference cohort, we trained three machine learning models to differentiate between these entities. Furthermore, we validated the classifiers on the technical validation set and used an internal cohort (n = 72) to test our classifier. FINDINGS On the validation cohort, the neural network, support vector machine, and the random forest classifiers reached accuracies of 97.68%, 95.62%, and 96.5%, respectively. Filtering by anomaly detection and thresholds improved the accuracy to 99.07% (37 samples excluded by filtering), 96.22% (17 samples excluded), and 100% (44 samples excluded) for the neural network, support vector machine and random forest, respectively. Because of best balance between accuracy and number of predictable cases we tested the neural network with applied filters on the in-house cohort, obtaining an accuracy of 95.45%. INTERPRETATION We developed a classifier that can differentiate between iCCAs, intrahepatic metastases of a PAAD, and normal bile duct tissue with high accuracy. This tool can be used for improving the diagnosis of pancreato-biliary cancers of the liver. FUNDING This work was supported by Berlin Institute of Health (JCS Program), DKTK Berlin (Young Investigator Grant 2022), German Research Foundation (493697503 and 314905040 - SFB/TRR 209 Liver Cancer B01), and German Cancer Aid (70113922).
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Affiliation(s)
- Mihnea P Dragomir
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany; German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany; Berlin Institute of Health, Berlin, Germany.
| | | | - Eilís Perez
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany; Berlin School of Integrative Oncology (BSIO), Charite - Universitätsmedizin Berlin (CVK), Berlin, Germany
| | - Simon Schallenberg
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Meng Chen
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Thomas Albrecht
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Ines Koch
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Peggy Wolkenstein
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Benjamin Goeppert
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany; Institute of Pathology and Neuropathology, Hospital RKH Kliniken Ludwigsburg, 71640 Ludwigsburg, Germany
| | - Stephanie Roessler
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - George A Calin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christine Sers
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - David Horst
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany; German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Florian Roßner
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - David Capper
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Neuropathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
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Li Z, Zhang H, Li Q, Feng W, Jia X, Zhou R, Huang Y, Li Y, Hu Z, Hu X, Zhu X, Huang S. GepLiver: an integrative liver expression atlas spanning developmental stages and liver disease phases. Sci Data 2023; 10:376. [PMID: 37301898 PMCID: PMC10257690 DOI: 10.1038/s41597-023-02257-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 05/22/2023] [Indexed: 06/12/2023] Open
Abstract
Chronic liver diseases usually developed through stepwise pathological transitions under the persistent risk factors. The molecular changes during liver transitions are pivotal to improve liver diagnostics and therapeutics yet still remain elusive. Cumulative large-scale liver transcriptomic studies have been revealing molecular landscape of various liver conditions at bulk and single-cell resolution, however, neither single experiment nor databases enabled thorough investigations of transcriptomic dynamics along the progression of liver diseases. Here we establish GepLiver, a longitudinal and multidimensional liver expression atlas integrating expression profiles of 2469 human bulk tissues, 492 mouse samples, 409,775 single cells from 347 human samples and 27 liver cell lines spanning 16 liver phenotypes with uniformed processing and annotating methods. Using GepLiver, we have demonstrated dynamic changes of gene expression, cell abundance and crosstalk harboring meaningful biological associations. GepLiver can be applied to explore the evolving expression patterns and transcriptomic features for genes and cell types respectively among liver phenotypes, assisting the investigation of liver transcriptomic dynamics and informing biomarkers and targets for liver diseases.
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Affiliation(s)
- Ziteng Li
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hena Zhang
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Qin Li
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Wanjing Feng
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiya Jia
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Runye Zhou
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yi Huang
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Yan Li
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhixiang Hu
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xichun Hu
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Xiaodong Zhu
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Shenglin Huang
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
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Qi S, Zhong Z, Zhu Y, Wang Y, Ma M, Wang Y, Liu X, Jin R, Jiao Z, Zhu R, Sha Z, Dang K, Liu Y, Lim D, Mao J, Zhang L, Yu F. Two Hippo signaling modules orchestrate liver size and tumorigenesis. EMBO J 2023; 42:e112126. [PMID: 36919851 PMCID: PMC10233384 DOI: 10.15252/embj.2022112126] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 02/12/2023] [Accepted: 02/21/2023] [Indexed: 03/16/2023] Open
Abstract
The Hippo pathway is a central regulator of organ size and tumorigenesis and is commonly depicted as a kinase cascade, with an increasing number of regulatory and adaptor proteins linked to its regulation over recent years. Here, we propose that two Hippo signaling modules, MST1/2-SAV1-WWC1-3 (HPO1) and MAP4K1-7-NF2 (HPO2), together regulate the activity of LATS1/2 kinases and YAP/TAZ transcriptional co-activators. In mouse livers, the genetic inactivation of either HPO1 or HPO2 module results in partial activation of YAP/TAZ, bile duct hyperplasia, and hepatocellular carcinoma (HCC). On the contrary, inactivation of both HPO1 and HPO2 modules results in full activation of YAP/TAZ, rapid development of intrahepatic cholangiocarcinoma (iCCA), and early lethality. Interestingly, HPO1 has a predominant role in regulating organ size. HPO1 inactivation causes a homogenous YAP/TAZ activation and cell proliferation across the whole liver, resulting in a proportional and rapid increase in liver size. Thus, this study has reconstructed the order of the Hippo signaling network and suggests that LATS1/2 and YAP/TAZ activities are finetuned by HPO1 and HPO2 modules to cause different cell fates, organ size changes, and tumorigenesis trajectories.
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Affiliation(s)
- Sixian Qi
- Institute of PediatricsChildren's Hospital of Fudan UniversityShanghaiChina
- The Shanghai Key Laboratory of Medical Epigenetics, The International Co‐laboratory of Medical Epigenetics and Metabolism, The State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Shanghai Medical CollegeFudan UniversityShanghaiChina
| | - Zhenxing Zhong
- Institute of PediatricsChildren's Hospital of Fudan UniversityShanghaiChina
- The Shanghai Key Laboratory of Medical Epigenetics, The International Co‐laboratory of Medical Epigenetics and Metabolism, The State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Shanghai Medical CollegeFudan UniversityShanghaiChina
| | - Yuwen Zhu
- Institute of PediatricsChildren's Hospital of Fudan UniversityShanghaiChina
- The Shanghai Key Laboratory of Medical Epigenetics, The International Co‐laboratory of Medical Epigenetics and Metabolism, The State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Shanghai Medical CollegeFudan UniversityShanghaiChina
| | - Yebin Wang
- Institute of PediatricsChildren's Hospital of Fudan UniversityShanghaiChina
- The Shanghai Key Laboratory of Medical Epigenetics, The International Co‐laboratory of Medical Epigenetics and Metabolism, The State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Shanghai Medical CollegeFudan UniversityShanghaiChina
| | - Mingyue Ma
- Institute of PediatricsChildren's Hospital of Fudan UniversityShanghaiChina
- The Shanghai Key Laboratory of Medical Epigenetics, The International Co‐laboratory of Medical Epigenetics and Metabolism, The State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Shanghai Medical CollegeFudan UniversityShanghaiChina
| | - Yu Wang
- Institute of PediatricsChildren's Hospital of Fudan UniversityShanghaiChina
- The Shanghai Key Laboratory of Medical Epigenetics, The International Co‐laboratory of Medical Epigenetics and Metabolism, The State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Shanghai Medical CollegeFudan UniversityShanghaiChina
| | - Xincheng Liu
- Institute of PediatricsChildren's Hospital of Fudan UniversityShanghaiChina
- The Shanghai Key Laboratory of Medical Epigenetics, The International Co‐laboratory of Medical Epigenetics and Metabolism, The State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Shanghai Medical CollegeFudan UniversityShanghaiChina
| | - Ruxin Jin
- Institute of PediatricsChildren's Hospital of Fudan UniversityShanghaiChina
- The Shanghai Key Laboratory of Medical Epigenetics, The International Co‐laboratory of Medical Epigenetics and Metabolism, The State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Shanghai Medical CollegeFudan UniversityShanghaiChina
| | - Zhihan Jiao
- Institute of PediatricsChildren's Hospital of Fudan UniversityShanghaiChina
- The Shanghai Key Laboratory of Medical Epigenetics, The International Co‐laboratory of Medical Epigenetics and Metabolism, The State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Shanghai Medical CollegeFudan UniversityShanghaiChina
| | - Rui Zhu
- Institute of PediatricsChildren's Hospital of Fudan UniversityShanghaiChina
- The Shanghai Key Laboratory of Medical Epigenetics, The International Co‐laboratory of Medical Epigenetics and Metabolism, The State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Shanghai Medical CollegeFudan UniversityShanghaiChina
| | - Zhao Sha
- Institute of PediatricsChildren's Hospital of Fudan UniversityShanghaiChina
- The Shanghai Key Laboratory of Medical Epigenetics, The International Co‐laboratory of Medical Epigenetics and Metabolism, The State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Shanghai Medical CollegeFudan UniversityShanghaiChina
| | - Kyvan Dang
- Department of Molecular, Cell and Cancer BiologyUniversity of Massachusetts Medical SchoolWorcesterMAUSA
| | - Ying Liu
- Department of Pathology, School of Basic Medical Sciences, Shanghai Medical CollegeFudan UniversityShanghaiChina
| | - Dae‐Sik Lim
- Department of Biological Sciences, National Creative Research Initiatives CenterKorea Advanced Institute of Science and TechnologyDaejeonRepublic of Korea
| | - Junhao Mao
- Department of Molecular, Cell and Cancer BiologyUniversity of Massachusetts Medical SchoolWorcesterMAUSA
| | - Lei Zhang
- State Key Laboratory of Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghaiChina
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Fa‐Xing Yu
- Institute of PediatricsChildren's Hospital of Fudan UniversityShanghaiChina
- The Shanghai Key Laboratory of Medical Epigenetics, The International Co‐laboratory of Medical Epigenetics and Metabolism, The State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Shanghai Medical CollegeFudan UniversityShanghaiChina
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Khoury R, Chahine C, Ibrahim R, Khalife N, Saleh M, Saleh K. Futibatinib: paving the way to personalized medicine in intrahepatic cholangiocarcinoma. Future Oncol 2023; 19:1161-1163. [PMID: 37293779 DOI: 10.2217/fon-2023-0318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023] Open
Affiliation(s)
- Rita Khoury
- International Department, Gustave Roussy Cancer Campus, Villejuif, 94800, France
| | - Claude Chahine
- International Department, Gustave Roussy Cancer Campus, Villejuif, 94800, France
| | - Rebecca Ibrahim
- International Department, Gustave Roussy Cancer Campus, Villejuif, 94800, France
| | - Nadine Khalife
- Department of Head & Neck Oncology, Gustave Roussy Cancer Campus, Villejuif, 94800, France
| | - Mohammad Saleh
- Department of Hematology & Oncology, Lebanese American University Medical Center-Rizk Hopsital, Beirut, 11-3288, Lebanon
| | - Khalil Saleh
- International Department, Gustave Roussy Cancer Campus, Villejuif, 94800, France
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49
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Solomou G, Finch A, Asghar A, Bardella C. Mutant IDH in Gliomas: Role in Cancer and Treatment Options. Cancers (Basel) 2023; 15:cancers15112883. [PMID: 37296846 DOI: 10.3390/cancers15112883] [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: 04/17/2023] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023] Open
Abstract
Altered metabolism is a common feature of many cancers and, in some cases, is a consequence of mutation in metabolic genes, such as the ones involved in the TCA cycle. Isocitrate dehydrogenase (IDH) is mutated in many gliomas and other cancers. Physiologically, IDH converts isocitrate to α-ketoglutarate (α-KG), but when mutated, IDH reduces α-KG to D2-hydroxyglutarate (D2-HG). D2-HG accumulates at elevated levels in IDH mutant tumours, and in the last decade, a massive effort has been made to develop small inhibitors targeting mutant IDH. In this review, we summarise the current knowledge about the cellular and molecular consequences of IDH mutations and the therapeutic approaches developed to target IDH mutant tumours, focusing on gliomas.
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Affiliation(s)
- Georgios Solomou
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- Division of Academic Neurosurgery, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Alina Finch
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Asim Asghar
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Chiara Bardella
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
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50
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Budhu A, Pehrsson EC, He A, Goyal L, Kelley RK, Dang H, Xie C, Monge C, Tandon M, Ma L, Revsine M, Kuhlman L, Zhang K, Baiev I, Lamm R, Patel K, Kleiner DE, Hewitt SM, Tran B, Shetty J, Wu X, Zhao Y, Shen TW, Choudhari S, Kriga Y, Ylaya K, Warner AC, Edmondson EF, Forgues M, Greten TF, Wang XW. Tumor biology and immune infiltration define primary liver cancer subsets linked to overall survival after immunotherapy. Cell Rep Med 2023:101052. [PMID: 37224815 DOI: 10.1016/j.xcrm.2023.101052] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 12/22/2022] [Accepted: 04/27/2023] [Indexed: 05/26/2023]
Abstract
Primary liver cancer is a rising cause of cancer deaths in the US. Although immunotherapy with immune checkpoint inhibitors induces a potent response in a subset of patients, response rates vary among individuals. Predicting which patients will respond to immune checkpoint inhibitors is of great interest in the field. In a retrospective arm of the National Cancer Institute Cancers of the Liver: Accelerating Research of Immunotherapy by a Transdisciplinary Network (NCI-CLARITY) study, we use archived formalin-fixed, paraffin-embedded samples to profile the transcriptome and genomic alterations among 86 hepatocellular carcinoma and cholangiocarcinoma patients prior to and following immune checkpoint inhibitor treatment. Using supervised and unsupervised approaches, we identify stable molecular subtypes linked to overall survival and distinguished by two axes of aggressive tumor biology and microenvironmental features. Moreover, molecular responses to immune checkpoint inhibitor treatment differ between subtypes. Thus, patients with heterogeneous liver cancer may be stratified by molecular status indicative of treatment response to immune checkpoint inhibitors.
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Affiliation(s)
- Anuradha Budhu
- Liver Cancer Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Erica C Pehrsson
- Liver Cancer Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; CCR Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Aiwu He
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Lipika Goyal
- Department of Medical Oncology, Mass General Cancer Center, Harvard Medical School, Boston, MA 02114, USA
| | - Robin Kate Kelley
- Department of Medicine (Hematology/Oncology), UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA 94143, USA
| | - Hien Dang
- Department of Surgery, Thomas Jefferson University, Philadelphia, PA, USA; Sidney Kimmel Cancer Center, Philadelphia, PA 19107, USA
| | - Changqing Xie
- Gastrointestinal Malignancies Section, Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cecilia Monge
- Gastrointestinal Malignancies Section, Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mayank Tandon
- CCR Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Lichun Ma
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mahler Revsine
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Laura Kuhlman
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Karen Zhang
- Department of Medicine (Hematology/Oncology), UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA 94143, USA
| | - Islam Baiev
- Department of Medical Oncology, Mass General Cancer Center, Harvard Medical School, Boston, MA 02114, USA
| | - Ryan Lamm
- Department of Surgery, Thomas Jefferson University, Philadelphia, PA, USA; Sidney Kimmel Cancer Center, Philadelphia, PA 19107, USA
| | - Keyur Patel
- Department of Surgery, Thomas Jefferson University, Philadelphia, PA, USA; Sidney Kimmel Cancer Center, Philadelphia, PA 19107, USA
| | - David E Kleiner
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD 21701, USA
| | - Stephen M Hewitt
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD 21701, USA
| | - Bao Tran
- Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Jyoti Shetty
- Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Xiaolin Wu
- Genomics Technology Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Yongmei Zhao
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Tsai-Wei Shen
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Sulbha Choudhari
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Yuliya Kriga
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Kris Ylaya
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD 21701, USA
| | - Andrew C Warner
- Molecular Histopathology Laboratory, Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Elijah F Edmondson
- Molecular Histopathology Laboratory, Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Marshonna Forgues
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tim F Greten
- Liver Cancer Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; Gastrointestinal Malignancies Section, Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Xin Wei Wang
- Liver Cancer Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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