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Llovet JM, Kelley RK, Villanueva A, Singal AG, Pikarsky E, Roayaie S, Lencioni R, Koike K, Zucman-Rossi J, Finn RS. Hepatocellular carcinoma. Nat Rev Dis Primers 2021; 7:6. [PMID: 33479224 DOI: 10.1038/s41572-020-00240-3] [Citation(s) in RCA: 2854] [Impact Index Per Article: 951.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/08/2020] [Indexed: 02/07/2023]
Abstract
Liver cancer remains a global health challenge, with an estimated incidence of >1 million cases by 2025. Hepatocellular carcinoma (HCC) is the most common form of liver cancer and accounts for ~90% of cases. Infection by hepatitis B virus and hepatitis C virus are the main risk factors for HCC development, although non-alcoholic steatohepatitis associated with metabolic syndrome or diabetes mellitus is becoming a more frequent risk factor in the West. Moreover, non-alcoholic steatohepatitis-associated HCC has a unique molecular pathogenesis. Approximately 25% of all HCCs present with potentially actionable mutations, which are yet to be translated into the clinical practice. Diagnosis based upon non-invasive criteria is currently challenged by the need for molecular information that requires tissue or liquid biopsies. The current major advancements have impacted the management of patients with advanced HCC. Six systemic therapies have been approved based on phase III trials (atezolizumab plus bevacizumab, sorafenib, lenvatinib, regorafenib, cabozantinib and ramucirumab) and three additional therapies have obtained accelerated FDA approval owing to evidence of efficacy. New trials are exploring combination therapies, including checkpoint inhibitors and tyrosine kinase inhibitors or anti-VEGF therapies, or even combinations of two immunotherapy regimens. The outcomes of these trials are expected to change the landscape of HCC management at all evolutionary stages.
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Affiliation(s)
- Josep M Llovet
- Mount Sinai Liver Cancer Program, Division of Liver Diseases, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Translational Research in Hepatic Oncology, Liver Unit, IDIBAPS, Hospital Clinic, University of Barcelona, Catalonia, Spain. .,Institució Catalana d'Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.
| | - Robin Kate Kelley
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Augusto Villanueva
- Mount Sinai Liver Cancer Program, Division of Liver Diseases, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Amit G Singal
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Eli Pikarsky
- The Lautenberg Center for Immunology and Cancer Research, IMRIC, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sasan Roayaie
- White Plains Hospital Center for Cancer Care, Montefiore Health, White Plains, NY, USA
| | - Riccardo Lencioni
- Department of Radiology, Pisa University School of Medicine, Pisa, Italy.,Department of Radiology, Miami Cancer Insitute, Miami, FL, USA
| | - Kazuhiko Koike
- The University of Tokyo, Department of Gastroenterology, Tokyo, Japan
| | - Jessica Zucman-Rossi
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, USPC, Université Paris Descartes, Université Paris Diderot, Paris, France.,Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Richard S Finn
- Department of Oncology, Geffen School of Medicine at UCLA, Los Angeles, CA, USA
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Das S, Roymondal U, Sahoo S. Analyzing gene expression from relative codon usage bias in Yeast genome: a statistical significance and biological relevance. Gene 2009; 443:121-31. [PMID: 19410638 DOI: 10.1016/j.gene.2009.04.022] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2008] [Revised: 03/08/2009] [Accepted: 04/20/2009] [Indexed: 11/17/2022]
Abstract
Based on the hypothesis that highly expressed genes are often characterized by strong compositional bias in terms of codon usage, there are a number of measures currently in use that quantify codon usage bias in genes, and hence provide numerical indices to predict the expression levels of genes. With the recent advent of expression measure from the score of the relative codon usage bias (RCBS), we have explicitly tested the performance of this numerical measure to predict the gene expression level and illustrate this with an analysis of Yeast genomes. In contradiction with previous other studies, we observe a weak correlations between GC content and RCBS, but a selective pressure on the codon preferences in highly expressed genes. The assertion that the expression of a given gene depends on the score of relative codon usage bias (RCBS) is supported by the data. We further observe a strong correlation between RCBS and protein length indicating natural selection in favour of shorter genes to be expressed at higher level. We also attempt a statistical analysis to assess the strength of relative codon bias in genes as a guide to their likely expression level, suggesting a decrease of the informational entropy in the highly expressed genes.
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Affiliation(s)
- Shibsankar Das
- Department of Mathematics, Uluberia College, Uluberia, Howrah, W.B., India
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The capabilities of chaos and complexity. Int J Mol Sci 2009; 10:247-291. [PMID: 19333445 PMCID: PMC2662469 DOI: 10.3390/ijms10010247] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2008] [Revised: 12/27/2008] [Accepted: 01/04/2009] [Indexed: 11/17/2022] Open
Abstract
To what degree could chaos and complexity have organized a Peptide or RNA World of crude yet necessarily integrated protometabolism? How far could such protolife evolve in the absence of a heritable linear digital symbol system that could mutate, instruct, regulate, optimize and maintain metabolic homeostasis? To address these questions, chaos, complexity, self-ordered states, and organization must all be carefully defined and distinguished. In addition their cause-and-effect relationships and mechanisms of action must be delineated. Are there any formal (non physical, abstract, conceptual, algorithmic) components to chaos, complexity, self-ordering and organization, or are they entirely physicodynamic (physical, mass/energy interaction alone)? Chaos and complexity can produce some fascinating self-ordered phenomena. But can spontaneous chaos and complexity steer events and processes toward pragmatic benefit, select function over non function, optimize algorithms, integrate circuits, produce computational halting, organize processes into formal systems, control and regulate existing systems toward greater efficiency? The question is pursued of whether there might be some yet-to-be discovered new law of biology that will elucidate the derivation of prescriptive information and control. “System” will be rigorously defined. Can a low-informational rapid succession of Prigogine’s dissipative structures self-order into bona fide organization?
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Gatherer D. Evolution of the G+C Content Frontier in the Rat Cytomegalovirus Genome. Virology (Auckl) 2008. [DOI: 10.4137/vrt.s1023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Within the 230138 bp of the rat cytomegalovirus (RCMV) genome, the G+C content changes abruptly at position 142644, constituting a G+C content frontier. To the left of this point, overall G+C content is 69.2%, and to the right it is only 47.6%. A region of extremely low G+C content (33.8%) is found in the 5 kb immediately to the right of the frontier, in which there are no predicted coding sequences. To the right of position 147501, the G+C content rises and predicted coding sequences reappear. However, these genes are much shorter (average 848 bp, 50% G+C) than those in the left two-thirds of the genome (average 1462 bp, 70% G+C). Whole genome alignment of several viruses indicates that the initial ultra-low G+C region appeared in the common ancestor of the genera Cytomegalovirus and Muromegalovirus, and that the lowering of G+C in the right third has been a subsequent process in the lineage leading to RCMV. The left two-thirds of RCMV has stop codon occurrences at 67.5% of their expected level, based on a modified Markov chain model of stop codon distribution, and the corresponding figure for the right third is 78%. Therefore, despite heavy mutation pressure, selective constraint has operated in the right third of the RCMV genome to maintain a degree of gene length unusual for such low G+C sequences.
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Affiliation(s)
- Derek Gatherer
- MRC Virology Unit, Institute of Virology, University of Glasgow, Church Street, Glasgow, G11 5JR, U.K
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Arakawa K, Suzuki H, Fujishima K, Fujimoto K, Ueda S, Matsui M, Tomita M. A Comprehensive Software Suite for the Analysis of cDNAs. GENOMICS, PROTEOMICS & BIOINFORMATICS 2005; 3:179-88. [PMID: 16487083 PMCID: PMC5172547 DOI: 10.1016/s1672-0229(05)03023-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We have developed a comprehensive software suite for bioinformatics research of cDNAs; it is aimed at rapid characterization of the features of genes and the proteins they code. Methods implemented include the detection of translation initiation and termination signals, statistical analysis of codon usage, comparative study of amino acid composition, comparative modeling of the structures of product proteins, prediction of alternative splice forms, and metabolic pathway reconstruction. The software package is freely available under the GNU General Public License at http://www.g-language.org/data/cdna/.
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Affiliation(s)
- Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Fujisawa 252-8520, Japan.
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Suzuki H, Saito R, Tomita M. The 'weighted sum of relative entropy': a new index for synonymous codon usage bias. Gene 2004; 335:19-23. [PMID: 15194186 DOI: 10.1016/j.gene.2004.03.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2003] [Revised: 02/12/2004] [Accepted: 03/05/2004] [Indexed: 11/29/2022]
Abstract
Shannon entropy from information theory has been applied to estimate the degree of deviation from equal usage of synonymous codons; however, previous attempts have failed to take into account all three aspects of amino acid usage, i.e. (i) the number of distinct amino acids, (ii) their relative frequencies, and (iii) their degree of codon degeneracy. A new index taking into account all of these aspects is proposed. The index, designated as the 'weighted sum of relative entropy' (E(w)), is defined as the sum of the relative entropy of each amino acid weighted by its relative frequency in the sequence. In this paper, we demonstrate that E(w) allows us to avoid some amino acid usage biases and can yield results contradictory to those obtained by previous methods.
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Affiliation(s)
- Haruo Suzuki
- Institute for Advanced Biosciences, Keio University, Fujisawa 252-8520, Japan
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Jansen R, Bussemaker HJ, Gerstein M. Revisiting the codon adaptation index from a whole-genome perspective: analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models. Nucleic Acids Res 2003; 31:2242-51. [PMID: 12682375 PMCID: PMC153734 DOI: 10.1093/nar/gkg306] [Citation(s) in RCA: 115] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2002] [Revised: 01/23/2003] [Accepted: 02/18/2003] [Indexed: 02/03/2023] Open
Abstract
Highly expressed genes in many bacteria and small eukaryotes often have a strong compositional bias, in terms of codon usage. Two widely used numerical indices, the codon adaptation index (CAI) and the codon usage, use this bias to predict the expression level of genes. When these indices were first introduced, they were based on fairly simple assumptions about which genes are most highly expressed: the CAI was originally based on the codon composition of a set of only 24 highly expressed genes, and the codon usage on assumptions about which functional classes of genes are highly expressed in fast-growing bacteria. Given the recent advent of genome-wide expression data, we should be able to improve on these assumptions. Here, we measure, in yeast, the degree to which consideration of the current genome-wide expression data sets improves the performance of both numerical indices. Indeed, we find that by changing the parameterization of each model its correlation with actual expression levels can be somewhat improved, although both indices are fairly insensitive to the exact way they are parameterized. This insensitivity indicates a consistent codon bias amongst highly expressed genes. We also attempt direct linear regression of codon composition against genome-wide expression levels (and protein abundance data). This has some similarity with the CAI formalism and yields an alternative model for the prediction of expression levels based on the coding sequences of genes. More information is available at http://bioinfo.mbb.yale.edu/expression/codons.
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Affiliation(s)
- Ronald Jansen
- Department of Molecular Biophysics and Biochemistry, 266 Whitney Avenue, Yale University, PO Box 208114, New Haven, CT 06520, USA
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Cosmi C, Cuomo V, Ragosta M, Macchiato MF. Characterization of nucleotidic sequences using maximum entropy techniques. J Theor Biol 1990; 147:423-32. [PMID: 2292889 DOI: 10.1016/s0022-5193(05)80497-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A statistical method for characterizing nucleotidic sequences based on maximum entropy techniques is presented. The method uses only codon usage tables and takes into account the length of sequences, and preserves the information contained in each codon by a punctual index. We present the methodological aspects of the analysis, showing an application relative to nucleotidic sequences of eukaryotes.
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Affiliation(s)
- C Cosmi
- Istituto di Fisica, Facoltà di Ingegneria, Università della Basilicata, Potenza, Italy
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Tavaré S, Song B. Codon preference and primary sequence structure in protein-coding regions. Bull Math Biol 1989; 51:95-115. [PMID: 2706404 DOI: 10.1007/bf02458838] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The stochastic complexity of a data base of 365 protein-coding regions is analysed. When the primary sequence is modeled as a spatially homogeneous Markov source, the fit to observed codon preference is very poor. The situation improves substantially when a non-homogeneous model is used. Some implications for the estimation of species phylogeny and substitution rates are discussed.
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Abstract
The theory of degenerate coding is presented in a way enabling further application to molecular biology. There are two kinds of redundancy of a degenerate code. The first is due to the excess in codon length and the second to the code degeneracy. If the code is asymmetrically degenerate, the second kind of redundancy can be profitable for control of error rate. This control can be performed just by selective synonymous codon usage. Utilisation of the genetic code is partially influenced by this theoretical possibility. In particular the degree of error protectivity is well correlated with deviation from equiprobability in synonymous codon usage. The biological significance of this fact is discussed.
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