Literature DB >> 31130341

Genomic and Transcriptomic Profiling of Combined Hepatocellular and Intrahepatic Cholangiocarcinoma Reveals Distinct Molecular Subtypes.

Ruidong Xue1, Lu Chen2, Chong Zhang1, Masashi Fujita3, Ruoyan Li1, Shu-Mei Yan4, Choon Kiat Ong5, Xiwen Liao6, Qiang Gao7, Shota Sasagawa3, Yanmeng Li1, Jincheng Wang1, Hua Guo8, Qi-Tao Huang4, Qian Zhong4, Jing Tan4, Lisha Qi9, Wenchen Gong9, Zhixian Hong10, Meng Li11, Jingmin Zhao12, Tao Peng6, Yinying Lu13, Kiat Hon Tony Lim14, Arnoud Boot15, Atushi Ono16, Kazuaki Chayama16, Zemin Zhang1, Steve George Rozen15, Bin Tean Teh17, Xin Wei Wang18, Hidewaki Nakagawa19, Mu-Sheng Zeng20, Fan Bai21, Ning Zhang22.   

Abstract

We performed genomic and transcriptomic sequencing of 133 combined hepatocellular and intrahepatic cholangiocarcinoma (cHCC-ICC) cases, including separate, combined, and mixed subtypes. Integrative comparison of cHCC-ICC with hepatocellular carcinoma and intrahepatic cholangiocarcinoma revealed that combined and mixed type cHCC-ICCs are distinct subtypes with different clinical and molecular features. Integrating laser microdissection, cancer cell fraction analysis, and single nucleus sequencing, we revealed both mono- and multiclonal origins in the separate type cHCC-ICCs, whereas combined and mixed type cHCC-ICCs were all monoclonal origin. Notably, cHCC-ICCs showed significantly higher expression of Nestin, suggesting Nestin may serve as a biomarker for diagnosing cHCC-ICC. Our results provide important biological and clinical insights into cHCC-ICC.
Copyright © 2019 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  Allen and Lisa; Nestin; bilinear differentiation; clonal origin; intratumor heterogeneity; liver cancer; metastatic route; molecular subtype; phenotypic transition; single nucleus sequencing

Mesh:

Substances:

Year:  2019        PMID: 31130341      PMCID: PMC8317046          DOI: 10.1016/j.ccell.2019.04.007

Source DB:  PubMed          Journal:  Cancer Cell        ISSN: 1535-6108            Impact factor:   31.743


  67 in total

1.  Expression of nestin-green fluorescent protein transgene marks oval cells in the adult liver.

Authors:  Anatoli S Gleiberman; Juan M Encinas; John L Mignone; Tatyana Michurina; Michael G Rosenfeld; Grigori Enikolopov
Journal:  Dev Dyn       Date:  2005-10       Impact factor: 3.780

2.  A comparison study: applying segmentation to array CGH data for downstream analyses.

Authors:  Hanni Willenbrock; Jane Fridlyand
Journal:  Bioinformatics       Date:  2005-09-13       Impact factor: 6.937

3.  Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma.

Authors:  Apinya Jusakul; Ioana Cutcutache; Chern Han Yong; Jing Quan Lim; Mi Ni Huang; Nisha Padmanabhan; Vishwa Nellore; Sarinya Kongpetch; Alvin Wei Tian Ng; Ley Moy Ng; Su Pin Choo; Swe Swe Myint; Raynoo Thanan; Sanjanaa Nagarajan; Weng Khong Lim; Cedric Chuan Young Ng; Arnoud Boot; Mo Liu; Choon Kiat Ong; Vikneswari Rajasegaran; Stefanus Lie; Alvin Soon Tiong Lim; Tse Hui Lim; Jing Tan; Jia Liang Loh; John R McPherson; Narong Khuntikeo; Vajaraphongsa Bhudhisawasdi; Puangrat Yongvanit; Sopit Wongkham; Yasushi Totoki; Hiromi Nakamura; Yasuhito Arai; Satoshi Yamasaki; Pierce Kah-Hoe Chow; Alexander Yaw Fui Chung; London Lucien Peng Jin Ooi; Kiat Hon Lim; Simona Dima; Dan G Duda; Irinel Popescu; Philippe Broet; Sen-Yung Hsieh; Ming-Chin Yu; Aldo Scarpa; Jiaming Lai; Di-Xian Luo; André Lopes Carvalho; André Luiz Vettore; Hyungjin Rhee; Young Nyun Park; Ludmil B Alexandrov; Raluca Gordân; Steven G Rozen; Tatsuhiro Shibata; Chawalit Pairojkul; Bin Tean Teh; Patrick Tan
Journal:  Cancer Discov       Date:  2017-06-30       Impact factor: 39.397

4.  Aristolochic acids and their derivatives are widely implicated in liver cancers in Taiwan and throughout Asia.

Authors:  Alvin W T Ng; Song Ling Poon; Mi Ni Huang; Jing Quan Lim; Arnoud Boot; Willie Yu; Yuka Suzuki; Saranya Thangaraju; Cedric C Y Ng; Patrick Tan; See-Tong Pang; Hao-Yi Huang; Ming-Chin Yu; Po-Huang Lee; Sen-Yung Hsieh; Alex Y Chang; Bin T Teh; Steven G Rozen
Journal:  Sci Transl Med       Date:  2017-10-18       Impact factor: 17.956

5.  Combined hepatocellular and cholangiocarcinoma: a clinicopathologic study of 26 resected cases.

Authors:  Yoshiko Yano; Junji Yamamoto; Tomoo Kosuge; Yoshihiro Sakamoto; Susumu Yamasaki; Kazuaki Shimada; Hidenori Ojima; Michiie Sakamoto; Tadatoshi Takayama; Masatoshi Makuuchi
Journal:  Jpn J Clin Oncol       Date:  2003-06       Impact factor: 3.019

6.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.

Authors:  Michael I Love; Wolfgang Huber; Simon Anders
Journal:  Genome Biol       Date:  2014       Impact factor: 13.583

7.  Universal Patterns of Selection in Cancer and Somatic Tissues.

Authors:  Iñigo Martincorena; Keiran M Raine; Moritz Gerstung; Kevin J Dawson; Kerstin Haase; Peter Van Loo; Helen Davies; Michael R Stratton; Peter J Campbell
Journal:  Cell       Date:  2017-10-19       Impact factor: 41.582

8.  Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples.

Authors:  Kristian Cibulskis; Michael S Lawrence; Scott L Carter; Andrey Sivachenko; David Jaffe; Carrie Sougnez; Stacey Gabriel; Matthew Meyerson; Eric S Lander; Gad Getz
Journal:  Nat Biotechnol       Date:  2013-02-10       Impact factor: 54.908

9.  Punctuated copy number evolution and clonal stasis in triple-negative breast cancer.

Authors:  Ruli Gao; Alexander Davis; Thomas O McDonald; Emi Sei; Xiuqing Shi; Yong Wang; Pei-Ching Tsai; Anna Casasent; Jill Waters; Hong Zhang; Funda Meric-Bernstam; Franziska Michor; Nicholas E Navin
Journal:  Nat Genet       Date:  2016-08-15       Impact factor: 38.330

10.  Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles.

Authors:  Farshad Farshidfar; Siyuan Zheng; Marie-Claude Gingras; Yulia Newton; Juliann Shih; A Gordon Robertson; Toshinori Hinoue; Katherine A Hoadley; Ewan A Gibb; Jason Roszik; Kyle R Covington; Chia-Chin Wu; Eve Shinbrot; Nicolas Stransky; Apurva Hegde; Ju Dong Yang; Ed Reznik; Sara Sadeghi; Chandra Sekhar Pedamallu; Akinyemi I Ojesina; Julian M Hess; J Todd Auman; Suhn K Rhie; Reanne Bowlby; Mitesh J Borad; Andrew X Zhu; Josh M Stuart; Chris Sander; Rehan Akbani; Andrew D Cherniack; Vikram Deshpande; Taofic Mounajjed; Wai Chin Foo; Michael S Torbenson; David E Kleiner; Peter W Laird; David A Wheeler; Autumn J McRee; Oliver F Bathe; Jesper B Andersen; Nabeel Bardeesy; Lewis R Roberts; Lawrence N Kwong
Journal:  Cell Rep       Date:  2017-03-14       Impact factor: 9.995

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  53 in total

Review 1.  Cholangiocarcinoma 2020: the next horizon in mechanisms and management.

Authors:  Jesus M Banales; Jose J G Marin; Angela Lamarca; Pedro M Rodrigues; Shahid A Khan; Lewis R Roberts; Vincenzo Cardinale; Guido Carpino; Jesper B Andersen; Chiara Braconi; Diego F Calvisi; Maria J Perugorria; Luca Fabris; Luke Boulter; Rocio I R Macias; Eugenio Gaudio; Domenico Alvaro; Sergio A Gradilone; Mario Strazzabosco; Marco Marzioni; Cédric Coulouarn; Laura Fouassier; Chiara Raggi; Pietro Invernizzi; Joachim C Mertens; Anja Moncsek; Sumera Rizvi; Julie Heimbach; Bas Groot Koerkamp; Jordi Bruix; Alejandro Forner; John Bridgewater; Juan W Valle; Gregory J Gores
Journal:  Nat Rev Gastroenterol Hepatol       Date:  2020-06-30       Impact factor: 46.802

2.  Yap-Sox9 signaling determines hepatocyte plasticity and lineage-specific hepatocarcinogenesis.

Authors:  Yuchen Liu; Shu Zhuo; Yaxing Zhou; Lichun Ma; Zhonghe Sun; Xiaolin Wu; Xin Wei Wang; Bin Gao; Yingzi Yang
Journal:  J Hepatol       Date:  2021-11-15       Impact factor: 25.083

3.  Panel of potential lncRNA biomarkers can distinguish various types of liver malignant and benign tumors.

Authors:  Olga Y Burenina; Natalia L Lazarevich; Inna F Kustova; Daria A Shavochkina; Ekaterina A Moroz; Nikolay E Kudashkin; Yuriy I Patyutko; Alexey V Metelin; Eduard F Kim; Dmitry A Skvortsov; Timofei S Zatsepin; Maria P Rubtsova; Olga A Dontsova
Journal:  J Cancer Res Clin Oncol       Date:  2020-09-12       Impact factor: 4.553

Review 4.  Tumour evolution in hepatocellular carcinoma.

Authors:  Amanda J Craig; Johann von Felden; Teresa Garcia-Lezana; Samantha Sarcognato; Augusto Villanueva
Journal:  Nat Rev Gastroenterol Hepatol       Date:  2019-12-02       Impact factor: 46.802

Review 5.  The immunological and metabolic landscape in primary and metastatic liver cancer.

Authors:  Xin Li; Pierluigi Ramadori; Dominik Pfister; Marco Seehawer; Lars Zender; Mathias Heikenwalder
Journal:  Nat Rev Cancer       Date:  2021-07-29       Impact factor: 60.716

6.  Elucidating transcriptomic profiles from single-cell RNA sequencing data using nature-inspired compressed sensing.

Authors:  Zhuohan Yu; Chuang Bian; Genggeng Liu; Shixiong Zhang; Ka-Chun Wong; Xiangtao Li
Journal:  Brief Bioinform       Date:  2021-09-02       Impact factor: 11.622

Review 7.  Intrahepatic cholangiocarcinoma: Morpho-molecular pathology, tumor reactive microenvironment, and malignant progression.

Authors:  Alphonse E Sirica; Mario Strazzabosco; Massimiliano Cadamuro
Journal:  Adv Cancer Res       Date:  2020-12-09       Impact factor: 6.242

8.  Aldolase A Enhances Intrahepatic Cholangiocarcinoma Proliferation and Invasion through Promoting Glycolysis.

Authors:  Xiang Li; Chang Yu; Yichun Luo; Jiacheng Lin; Fang Wang; Xuehua Sun; Yueqiu Gao; Weifeng Tan; Qiang Xia; Xiaoni Kong
Journal:  Int J Biol Sci       Date:  2021-04-23       Impact factor: 6.580

9.  Genomic and transcriptomic profiling of hepatoid adenocarcinoma of the stomach.

Authors:  Ziyang Liu; Anqiang Wang; Yingying Pu; Zhongwu Li; Ruidong Xue; Chong Zhang; Xiao Xiang; Jian-Yu E; Zhaode Bu; Fan Bai; Jiafu Ji
Journal:  Oncogene       Date:  2021-07-30       Impact factor: 9.867

10.  Single-cell RNA sequencing shows the immunosuppressive landscape and tumor heterogeneity of HBV-associated hepatocellular carcinoma.

Authors:  Daniel Wai-Hung Ho; Yu-Man Tsui; Lo-Kong Chan; Karen Man-Fong Sze; Xin Zhang; Jacinth Wing-Sum Cheu; Yung-Tuen Chiu; Joyce Man-Fong Lee; Albert Chi-Yan Chan; Elaine Tin-Yan Cheung; Derek Tsz-Wai Yau; Nam-Hung Chia; Irene Lai-Oi Lo; Pak-Chung Sham; Tan-To Cheung; Carmen Chak-Lui Wong; Irene Oi-Lin Ng
Journal:  Nat Commun       Date:  2021-06-17       Impact factor: 14.919

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