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Schupp PG, Shelton SJ, Brody DJ, Eliscu R, Johnson BE, Mazor T, Kelley KW, Potts MB, McDermott MW, Huang EJ, Lim DA, Pieper RO, Berger MS, Costello JF, Phillips JJ, Oldham MC. Deconstructing Intratumoral Heterogeneity through Multiomic and Multiscale Analysis of Serial Sections. Cancers (Basel) 2024; 16:2429. [PMID: 39001492 PMCID: PMC11240479 DOI: 10.3390/cancers16132429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Revised: 06/27/2024] [Accepted: 06/28/2024] [Indexed: 07/16/2024] Open
Abstract
Tumors may contain billions of cells, including distinct malignant clones and nonmalignant cell types. Clarifying the evolutionary histories, prevalence, and defining molecular features of these cells is essential for improving clinical outcomes, since intratumoral heterogeneity provides fuel for acquired resistance to targeted therapies. Here we present a statistically motivated strategy for deconstructing intratumoral heterogeneity through multiomic and multiscale analysis of serial tumor sections (MOMA). By combining deep sampling of IDH-mutant astrocytomas with integrative analysis of single-nucleotide variants, copy-number variants, and gene expression, we reconstruct and validate the phylogenies, spatial distributions, and transcriptional profiles of distinct malignant clones. By genotyping nuclei analyzed by single-nucleus RNA-seq for truncal mutations, we further show that commonly used algorithms for identifying cancer cells from single-cell transcriptomes may be inaccurate. We also demonstrate that correlating gene expression with tumor purity in bulk samples can reveal optimal markers of malignant cells and use this approach to identify a core set of genes that are consistently expressed by astrocytoma truncal clones, including AKR1C3, whose expression is associated with poor outcomes in several types of cancer. In summary, MOMA provides a robust and flexible strategy for precisely deconstructing intratumoral heterogeneity and clarifying the core molecular properties of distinct cellular populations in solid tumors.
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Affiliation(s)
- Patrick G. Schupp
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Samuel J. Shelton
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
| | - Daniel J. Brody
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
| | - Rebecca Eliscu
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
| | - Brett E. Johnson
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
| | - Tali Mazor
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kevin W. Kelley
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94143, USA
- Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Matthew B. Potts
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
| | - Michael W. McDermott
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
| | - Eric J. Huang
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA;
| | - Daniel A. Lim
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
| | - Russell O. Pieper
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
| | - Mitchel S. Berger
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
| | - Joseph F. Costello
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
| | - Joanna J. Phillips
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA;
| | - Michael C. Oldham
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; (P.G.S.); (S.J.S.); (D.J.B.); (R.E.); (B.E.J.); (T.M.); (K.W.K.); (M.B.P.); (M.W.M.); (D.A.L.); (R.O.P.); (M.S.B.); (J.F.C.); (J.J.P.)
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Plekhanov AA, Kozlov DS, Shepeleva AA, Kiseleva EB, Shimolina LE, Druzhkova IN, Plekhanova MA, Karabut MM, Gubarkova EV, Gavrina AI, Krylov DP, Sovetsky AA, Gamayunov SV, Kuznetsova DS, Zaitsev VY, Sirotkina MA, Gladkova ND. Tissue Elasticity as a Diagnostic Marker of Molecular Mutations in Morphologically Heterogeneous Colorectal Cancer. Int J Mol Sci 2024; 25:5337. [PMID: 38791375 PMCID: PMC11120711 DOI: 10.3390/ijms25105337] [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: 03/20/2024] [Revised: 04/25/2024] [Accepted: 05/04/2024] [Indexed: 05/26/2024] Open
Abstract
The presence of molecular mutations in colorectal cancer (CRC) is a decisive factor in selecting the most effective first-line therapy. However, molecular analysis is routinely performed only in a limited number of patients with remote metastases. We propose to use tissue stiffness as a marker of the presence of molecular mutations in CRC samples. For this purpose, we applied compression optical coherence elastography (C-OCE) to calculate stiffness values in regions corresponding to specific CRC morphological patterns (n = 54). In parallel to estimating stiffness, molecular analysis from the same zones was performed to establish their relationships. As a result, a high correlation between the presence of KRAS/NRAS/BRAF driver mutations and high stiffness values was revealed regardless of CRC morphological pattern type. Further, we proposed threshold stiffness values for label-free targeted detection of molecular alterations in CRC tissues: for KRAS, NRAS, or BRAF driver mutation-above 803 kPa (sensitivity-91%; specificity-80%; diagnostic accuracy-85%), and only for KRAS driver mutation-above 850 kPa (sensitivity-90%; specificity-88%; diagnostic accuracy-89%). To conclude, C-OCE estimation of tissue stiffness can be used as a clinical diagnostic tool for preliminary screening of genetic burden in CRC tissues.
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Affiliation(s)
- Anton A. Plekhanov
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Sq., 603950 Nizhny Novgorod, Russia
| | - Dmitry S. Kozlov
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Sq., 603950 Nizhny Novgorod, Russia
| | - Anastasia A. Shepeleva
- Nizhny Novgorod Regional Oncologic Hospital, 11/1 Delovaya St., 603126 Nizhny Novgorod, Russia
| | - Elena B. Kiseleva
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Sq., 603950 Nizhny Novgorod, Russia
| | - Liubov E. Shimolina
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Sq., 603950 Nizhny Novgorod, Russia
| | - Irina N. Druzhkova
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Sq., 603950 Nizhny Novgorod, Russia
| | - Maria A. Plekhanova
- Nizhny Novgorod Regional Oncologic Hospital, 11/1 Delovaya St., 603126 Nizhny Novgorod, Russia
- Nizhny Novgorod City Polyclinic #1, 5 Marshala Zhukova Sq., 603107 Nizhny Novgorod, Russia
| | - Maria M. Karabut
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Sq., 603950 Nizhny Novgorod, Russia
| | - Ekaterina V. Gubarkova
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Sq., 603950 Nizhny Novgorod, Russia
| | - Alena I. Gavrina
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Sq., 603950 Nizhny Novgorod, Russia
| | - Dmitry P. Krylov
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Sq., 603950 Nizhny Novgorod, Russia
| | - Alexander A. Sovetsky
- Institute of Applied Physics of the Russian Academy of Sciences, 46 Ulyanova St., 603950 Nizhny Novgorod, Russia
| | - Sergey V. Gamayunov
- Nizhny Novgorod Regional Oncologic Hospital, 11/1 Delovaya St., 603126 Nizhny Novgorod, Russia
| | - Daria S. Kuznetsova
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Sq., 603950 Nizhny Novgorod, Russia
| | - Vladimir Y. Zaitsev
- Institute of Applied Physics of the Russian Academy of Sciences, 46 Ulyanova St., 603950 Nizhny Novgorod, Russia
| | - Marina A. Sirotkina
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Sq., 603950 Nizhny Novgorod, Russia
| | - Natalia D. Gladkova
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Sq., 603950 Nizhny Novgorod, Russia
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Schupp PG, Shelton SJ, Brody DJ, Eliscu R, Johnson BE, Mazor T, Kelley KW, Potts MB, McDermott MW, Huang EJ, Lim DA, Pieper RO, Berger MS, Costello JF, Phillips JJ, Oldham MC. Deconstructing intratumoral heterogeneity through multiomic and multiscale analysis of serial sections. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.21.545365. [PMID: 37645893 PMCID: PMC10461981 DOI: 10.1101/2023.06.21.545365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Tumors may contain billions of cells including distinct malignant clones and nonmalignant cell types. Clarifying the evolutionary histories, prevalence, and defining molecular features of these cells is essential for improving clinical outcomes, since intratumoral heterogeneity provides fuel for acquired resistance to targeted therapies. Here we present a statistically motivated strategy for deconstructing intratumoral heterogeneity through multiomic and multiscale analysis of serial tumor sections (MOMA). By combining deep sampling of IDH-mutant astrocytomas with integrative analysis of single-nucleotide variants, copy-number variants, and gene expression, we reconstruct and validate the phylogenies, spatial distributions, and transcriptional profiles of distinct malignant clones. By genotyping nuclei analyzed by single-nucleus RNA-seq for truncal mutations, we further show that commonly used algorithms for identifying cancer cells from single-cell transcriptomes may be inaccurate. We also demonstrate that correlating gene expression with tumor purity in bulk samples can reveal optimal markers of malignant cells and use this approach to identify a core set of genes that is consistently expressed by astrocytoma truncal clones, including AKR1C3, whose expression is associated with poor outcomes in several types of cancer. In summary, MOMA provides a robust and flexible strategy for precisely deconstructing intratumoral heterogeneity and clarifying the core molecular properties of distinct cellular populations in solid tumors.
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Affiliation(s)
- Patrick G. Schupp
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, California, USA
| | - Samuel J. Shelton
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Daniel J. Brody
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Rebecca Eliscu
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Brett E. Johnson
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Tali Mazor
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, California, USA
- Medical Scientist Training Program and Neuroscience Graduate Program, University of California San Francisco, San Francisco, California, USA
| | - Kevin W. Kelley
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
- Medical Scientist Training Program and Neuroscience Graduate Program, University of California San Francisco, San Francisco, California, USA
- Neuroscience Graduate Program, University of California San Francisco, San Francisco, California, USA
| | - Matthew B. Potts
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Michael W. McDermott
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Eric J. Huang
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Daniel A. Lim
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Russell O. Pieper
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Mitchel S. Berger
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Joseph F. Costello
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Joanna J. Phillips
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Michael C. Oldham
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
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Kothalawala WJ, Barták BK, Nagy ZB, Zsigrai S, Szigeti KA, Valcz G, Takács I, Kalmár A, Molnár B. A Detailed Overview About the Single-Cell Analyses of Solid Tumors Focusing on Colorectal Cancer. PATHOLOGY AND ONCOLOGY RESEARCH 2022; 28:1610342. [PMID: 35928965 PMCID: PMC9344373 DOI: 10.3389/pore.2022.1610342] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 06/15/2022] [Indexed: 11/21/2022]
Abstract
In recent years, the evolution of the molecular biological technical background led to the widespread application of single-cell sequencing, a versatile tool particularly useful in the investigation of tumor heterogeneity. Even 10 years ago the comprehensive characterization of colorectal cancers by The Cancer Genome Atlas was based on measurements of bulk samples. Nowadays, with single-cell approaches, tumor heterogeneity, the tumor microenvironment, and the interplay between tumor cells and their surroundings can be described in unprecedented detail. In this review article we aimed to emphasize the importance of single-cell analyses by presenting tumor heterogeneity and the limitations of conventional investigational approaches, followed by an overview of the whole single-cell analytic workflow from sample isolation to amplification, sequencing and bioinformatic analysis and a review of recent literature regarding the single-cell analysis of colorectal cancers.
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Affiliation(s)
- William J. Kothalawala
- Department of Internal Medicine and Oncology, Semmelweis University, Budapest, Hungary
- *Correspondence: William J. Kothalawala,
| | - Barbara K. Barták
- Department of Internal Medicine and Oncology, Semmelweis University, Budapest, Hungary
| | - Zsófia B. Nagy
- Department of Internal Medicine and Oncology, Semmelweis University, Budapest, Hungary
| | - Sára Zsigrai
- Department of Internal Medicine and Oncology, Semmelweis University, Budapest, Hungary
| | - Krisztina A. Szigeti
- Department of Internal Medicine and Oncology, Semmelweis University, Budapest, Hungary
| | - Gábor Valcz
- Department of Internal Medicine and Oncology, Semmelweis University, Budapest, Hungary
- Molecular Medicine Research Group, Eötvös Loránd Research Network, Budapest, Hungary
| | - István Takács
- Department of Internal Medicine and Oncology, Semmelweis University, Budapest, Hungary
| | - Alexandra Kalmár
- Department of Internal Medicine and Oncology, Semmelweis University, Budapest, Hungary
- Molecular Medicine Research Group, Eötvös Loránd Research Network, Budapest, Hungary
| | - Béla Molnár
- Department of Internal Medicine and Oncology, Semmelweis University, Budapest, Hungary
- Molecular Medicine Research Group, Eötvös Loránd Research Network, Budapest, Hungary
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Hálková T, Ptáčková R, Semyakina A, Suchánek Š, Traboulsi E, Ngo O, Hejcmanová K, Májek O, Bureš J, Zavoral M, Minárik M, Benešová L. Somatic Mutations in Exon 7 of the TP53 Gene in Index Colorectal Lesions Are Associated with the Early Occurrence of Metachronous Adenoma. Cancers (Basel) 2022; 14:cancers14122823. [PMID: 35740488 PMCID: PMC9221022 DOI: 10.3390/cancers14122823] [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: 04/19/2022] [Revised: 06/02/2022] [Accepted: 06/05/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Identifying patients with an increased risk of early recurrence of colorectal lesions is still a problem. In our study, we focused on improving this identification by determining the mutation profile of index lesions. We found a statistically significant association between the mutation in exon 7 of the TP53 gene in the index lesion and the risk of early metachronous adenoma. Abstract (1) Background: this prospective study was focused on detailed analysis of the mutation heterogeneity in colorectal lesions removed during baseline (index) colonoscopy to identify patients at high risk of early occurrence of metachronous adenomas. (2) Methods: a total of 120 patients after endoscopic therapy of advanced colorectal neoplasia size ≥10 mm (index lesion) with subsequent surveillance colonoscopy after 10–18 months were included. In total, 143 index lesions and 84 synchronous lesions in paraffin blocks were divided into up to 30 samples. In each of them, the detection of somatic mutations in 11 hot spot gene loci was performed. Statistical analysis to correlate the mutation profiles and the degree of heterogeneity of the lesions with the risk of metachronous adenoma occurrence was undertaken. (3) Results: mutation in exon 7 of the TP53 gene found in the index lesion significantly correlated with the early occurrence of metachronous adenoma (log-rank test p = 0.003, hazard ratio 2.73, 95% confidence interval 1.14–6.56). We did not find an association between the risk of metachronous adenomas and other markers monitored. (4) Conclusions: the findings of this study could lead to an adjustment of existing recommendations for surveillance colonoscopies in a specific group of patients with mutations in exon 7 of the TP53 gene in an index lesion, where a shortening of surveillance interval may be warranted.
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Affiliation(s)
- Tereza Hálková
- Centre for Applied Genomics of Solid Tumors (CEGES), Genomac Research Institute, Drnovská 1112/60, 161 00 Prague, Czech Republic; (T.H.); (R.P.); (A.S.); (M.M.); (L.B.)
| | - Renata Ptáčková
- Centre for Applied Genomics of Solid Tumors (CEGES), Genomac Research Institute, Drnovská 1112/60, 161 00 Prague, Czech Republic; (T.H.); (R.P.); (A.S.); (M.M.); (L.B.)
| | - Anastasiya Semyakina
- Centre for Applied Genomics of Solid Tumors (CEGES), Genomac Research Institute, Drnovská 1112/60, 161 00 Prague, Czech Republic; (T.H.); (R.P.); (A.S.); (M.M.); (L.B.)
| | - Štěpán Suchánek
- Department of Medicine, 1st Faculty of Medicine, Charles University and Military University Hospital Prague, U Vojenské Nemocnice 1200, 169 02 Prague, Czech Republic;
- Department of Gastrointestinal Oncology, Military University Hospital Prague, U Vojenské Nemocnice 1200, 169 02 Prague, Czech Republic;
- Correspondence:
| | - Eva Traboulsi
- Department of Pathology, Military University Hospital Prague, U Vojenské Nemocnice 1200, 169 02 Prague, Czech Republic;
| | - Ondřej Ngo
- Faculty of Medicine, Institute of Biostatistics and Analyses, Masaryk University, Kamenice 126/3, 625 00 Brno, Czech Republic; (O.N.); (K.H.); (O.M.)
| | - Kateřina Hejcmanová
- Faculty of Medicine, Institute of Biostatistics and Analyses, Masaryk University, Kamenice 126/3, 625 00 Brno, Czech Republic; (O.N.); (K.H.); (O.M.)
| | - Ondřej Májek
- Faculty of Medicine, Institute of Biostatistics and Analyses, Masaryk University, Kamenice 126/3, 625 00 Brno, Czech Republic; (O.N.); (K.H.); (O.M.)
| | - Jan Bureš
- Department of Gastrointestinal Oncology, Military University Hospital Prague, U Vojenské Nemocnice 1200, 169 02 Prague, Czech Republic;
| | - Miroslav Zavoral
- Department of Medicine, 1st Faculty of Medicine, Charles University and Military University Hospital Prague, U Vojenské Nemocnice 1200, 169 02 Prague, Czech Republic;
- Department of Gastrointestinal Oncology, Military University Hospital Prague, U Vojenské Nemocnice 1200, 169 02 Prague, Czech Republic;
| | - Marek Minárik
- Centre for Applied Genomics of Solid Tumors (CEGES), Genomac Research Institute, Drnovská 1112/60, 161 00 Prague, Czech Republic; (T.H.); (R.P.); (A.S.); (M.M.); (L.B.)
- Elphogene, Drnovská 1112/60, 161 00 Prague, Czech Republic
- Department of Analytical Chemistry, Faculty of Science, Charles University, Hlavova 2030/8, 128 00 Prague, Czech Republic
| | - Lucie Benešová
- Centre for Applied Genomics of Solid Tumors (CEGES), Genomac Research Institute, Drnovská 1112/60, 161 00 Prague, Czech Republic; (T.H.); (R.P.); (A.S.); (M.M.); (L.B.)
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6
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Petricevic B, Kabiljo J, Zirnbauer R, Walczak H, Laengle J, Bergmann M. Neoadjuvant Immunotherapy in Gastrointestinal Cancers - The New Standard of Care? Semin Cancer Biol 2022; 86:834-850. [PMID: 35671877 DOI: 10.1016/j.semcancer.2022.05.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 05/31/2022] [Accepted: 05/31/2022] [Indexed: 11/25/2022]
Abstract
The development of immune checkpoint inhibitors (ICI) offers novel treatment possibilities for solid cancers, with the crucial benefit of providing higher cure rates. These agents have become part of standard treatments in the metastatic and adjuvant setting for select cancers, such as melanoma, non-small cell lung cancer (NSCLC) or urological malignancies. Currently, there is ample clinical interest in employing ICI in a neoadjuvant setting with a curative intent. This approach is especially supported by the scientific rationale that ICI primarily stimulate the host immune system to eradicate tumor cells, rather than being inherently cytotoxic. Aside from tumor downstaging, neoadjuvant immunotherapy offers the potential of an in situ cancer vaccination, leading to a systemic adjuvant immunological effect after tumor resection. Moreover, preclinical data clearly demonstrate a synergistic effect of ICI with radiotherapy (RT), chemoradiotherapy (CRT) or chemotherapy (ChT). This review harmonizes preclinical concepts with real world data (RWD) in the field of neoadjuvant ICI in gastrointestinal (GI) cancers and discusses their limitations. We believe this is a crucial approach, since up to now, neoadjuvant strategies have been primarily developed by clinicians, whereas the advances in immunotherapy primarily originate from preclinical research. Currently there is limited published data on neoadjuvant ICI in GI cancers, even though neoadjuvant treatments including RT, CRT or ChT are frequently employed in locally advanced/oligometastatic GI cancers (i.e. rectal, pancreatic, esophagus, stomach, etc.). Utilizing established therapies in combination with ICI provides an abundance of opportunities for innovative treatment regimens to further improve survival rates.
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Affiliation(s)
- Branka Petricevic
- Division of Visceral Surgery, Department of General Surgery, Comprehensive Cancer Center Vienna, Medical University of Vienna, Waehringer Guertel 18-20, A-1090 Vienna, Austria
| | - Julijan Kabiljo
- Division of Visceral Surgery, Department of General Surgery, Comprehensive Cancer Center Vienna, Medical University of Vienna, Waehringer Guertel 18-20, A-1090 Vienna, Austria; Ludwig Boltzmann Institute Applied Diagnostics, Medical University of Vienna, Waehringer Guertel 18-20, A-1090 Vienna, Austria
| | - Rebecca Zirnbauer
- Division of Visceral Surgery, Department of General Surgery, Comprehensive Cancer Center Vienna, Medical University of Vienna, Waehringer Guertel 18-20, A-1090 Vienna, Austria
| | - Henning Walczak
- Institute for Biochemistry I, Medical Faculty, University of Cologne, Cologne, Germany; Centre for Cell Death, Cancer, and Inflammation (CCCI), UCL Cancer Institute, University College, London, WC1E 6BT UK
| | - Johannes Laengle
- Division of Visceral Surgery, Department of General Surgery, Comprehensive Cancer Center Vienna, Medical University of Vienna, Waehringer Guertel 18-20, A-1090 Vienna, Austria; Ludwig Boltzmann Institute Applied Diagnostics, Medical University of Vienna, Waehringer Guertel 18-20, A-1090 Vienna, Austria.
| | - Michael Bergmann
- Division of Visceral Surgery, Department of General Surgery, Comprehensive Cancer Center Vienna, Medical University of Vienna, Waehringer Guertel 18-20, A-1090 Vienna, Austria; Ludwig Boltzmann Institute Applied Diagnostics, Medical University of Vienna, Waehringer Guertel 18-20, A-1090 Vienna, Austria
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7
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Hamed RA, Marks S, Mcelligott H, Kalachand R, Ibrahim H, Atyani S, Korpanty G, Osman N. Inoperable de novo metastatic colorectal cancer with primary tumour in situ: Evaluating discordant responses to upfront systemic therapy of the primary tumours and metastatic sites and complications arising from primary tumours (experiences from an Irish Cancer Centre). Mol Clin Oncol 2022; 16:40. [PMID: 35003738 PMCID: PMC8739439 DOI: 10.3892/mco.2021.2472] [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: 03/25/2021] [Accepted: 11/22/2021] [Indexed: 12/24/2022] Open
Abstract
Systemic therapy is the mainstay of treatment for de novo metastatic colorectal cancer (mCRC). Heterogeneity between primary tumours and metastases may lead to discordant responses to systemic therapy at these sites. The aim of the present study was to examine these discrepancies and to evaluate the rates of complications arising from the primary tumour and the strategies employed to manage these complications. Electronic medical records were screened for patients eligible for data analysis between January 1st, 2014 and December 31st, 2019. All patients diagnosed with de novo mCRC with primary tumour in situ at the time of initial systemic therapy were included in data analysis. Responses in primary tumour and metastatic sites (according to the Response Evaluation Criteria In Solid Tumours v1.1), discrepancies in these responses and rates of complications arising from primary tumours were assessed along with patient, pathological or molecular factors that may be associated with these discrepant responses or primary tumour complications. A total of 50 patients were identified (median age, 62 years). Right-colon, left-colon and rectal primary tumours comprised 34, 44 and 22% of CRC cases, respectively. All patients received 5-fluorouracil-based chemotherapy (either alone or in combination with oxaliplatin or irinotecan). Disease response (DR), stable disease (SD) and progressive disease (PD) were observed as the first response to systemic therapy in 24, 62 and 12% of primary tumours and in 36, 18 and 44% of metastatic sites, respectively. Only 36% of patients demonstrated concordant responses between the primary tumours and metastases, while the remaining 62% demonstrated discordant responses between the primary tumour and distant metastases (22% had DR with SD; 36% had DR or SD with PD; and 4% had PD with SD in the primary tumour and metastases, respectively). Restaging images were not available for 2% of the patients. Approximately 30% of patients developed complications from primary tumours, including bowel obstruction (6.12%), perforation (6%), rectal pain (6%) and rectal bleeding (10%). Approximately 10% of patients underwent palliative stoma creation. Additionally, 12% required palliative radiotherapy to the primary tumour (due to localized complications arising from the tumour). Discordant responses to systemic therapy between primary tumours and metastases occurred in 60% of patients with de novo mCRC (with primary tumour in situ at the time of first systemic therapy). The observations of the present study have potential implications for molecular tissue analysis to help guide systemic therapy. Tissue from metastatic sites may be preferable to confirm biomarker status in mCRC based on this study.
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Affiliation(s)
- Ruba A Hamed
- Department of Oncology, Mid-Western Cancer Centre, University Hospital Limerick, Limerick V94 F858, Ireland
| | - Sam Marks
- Department of Oncology, Mid-Western Cancer Centre, University Hospital Limerick, Limerick V94 F858, Ireland
| | - Helen Mcelligott
- Department of Oncology, Mid-Western Cancer Centre, University Hospital Limerick, Limerick V94 F858, Ireland
| | - Roshni Kalachand
- Department of Oncology, Mid-Western Cancer Centre, University Hospital Limerick, Limerick V94 F858, Ireland
| | - Hawa Ibrahim
- Palliative Department, St. Francis Hospice, Dublin 5 D05 T9K8, Ireland
| | - Said Atyani
- Radiology Department, University Hospital Limerick, Limerick V94 F858, Ireland
| | - Greg Korpanty
- Department of Oncology, Mid-Western Cancer Centre, University Hospital Limerick, Limerick V94 F858, Ireland
| | - Nemer Osman
- Department of Oncology, Mid-Western Cancer Centre, University Hospital Limerick, Limerick V94 F858, Ireland
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8
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Non-contrast-enhanced CT texture analysis of primary and metastatic pancreatic ductal adenocarcinomas: value in assessment of histopathological grade and differences between primary and metastatic lesions. Abdom Radiol (NY) 2022; 47:4151-4159. [PMID: 36104481 PMCID: PMC9626421 DOI: 10.1007/s00261-022-03646-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 08/02/2022] [Accepted: 08/03/2022] [Indexed: 01/18/2023]
Abstract
PURPOSE To evaluate the utility of non-contrast-enhanced CT texture analysis (CTTA) for predicting the histopathological differentiation of pancreatic ductal adenocarcinomas (PDAC) and to compare non-contrast-enhanced CTTA texture features between primary PDAC and hepatic metastases of PDAC. METHODS This retrospective study included 120 patients with histopathologically confirmed PDAC. Sixty-five patients underwent CT-guided biopsy of primary PDAC, while 55 patients underwent CT-guided biopsy of hepatic PDAC metastasis. All lesions were segmented in non-contrast-enhanced CT scans for CTTA based on histogram analysis, co-occurrence matrix, and run-length matrix. Statistical analysis was conducted for 372 texture features using Mann-Whitney U test, Bonferroni-Holm correction, and receiver operating characteristic (ROC) analysis. A p value < 0.05 was considered statistically significant. RESULTS Three features were identified that differed significantly between histopathological G2 and G3 primary tumors. Of these, "low gray-level zone emphasis" yielded the largest AUC (0.87 ± 0.04), reaching a sensitivity and specificity of 0.76 and 0.83, respectively, when a cut-off value of 0.482 was applied. Fifty-four features differed significantly between primary and hepatic metastatic PDAC. CONCLUSION Non-contrast-enhanced CTTA of PDAC identified differences in texture features between primary G2 and G3 tumors that could be used for non-invasive tumor assessment. Extensive differences between the features of primary and metastatic PDAC on CTTA suggest differences in tumor microenvironment.
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9
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Suphavilai C, Chia S, Sharma A, Tu L, Da Silva RP, Mongia A, DasGupta R, Nagarajan N. Predicting heterogeneity in clone-specific therapeutic vulnerabilities using single-cell transcriptomic signatures. Genome Med 2021; 13:189. [PMID: 34915921 PMCID: PMC8680165 DOI: 10.1186/s13073-021-01000-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 11/02/2021] [Indexed: 12/22/2022] Open
Abstract
While understanding molecular heterogeneity across patients underpins precision oncology, there is increasing appreciation for taking intra-tumor heterogeneity into account. Based on large-scale analysis of cancer omics datasets, we highlight the importance of intra-tumor transcriptomic heterogeneity (ITTH) for predicting clinical outcomes. Leveraging single-cell RNA-seq (scRNA-seq) with a recommender system (CaDRReS-Sc), we show that heterogeneous gene-expression signatures can predict drug response with high accuracy (80%). Using patient-proximal cell lines, we established the validity of CaDRReS-Sc's monotherapy (Pearson r>0.6) and combinatorial predictions targeting clone-specific vulnerabilities (>10% improvement). Applying CaDRReS-Sc to rapidly expanding scRNA-seq compendiums can serve as in silico screen to accelerate drug-repurposing studies. Availability: https://github.com/CSB5/CaDRReS-Sc .
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Affiliation(s)
| | - Shumei Chia
- Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Ankur Sharma
- Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Lorna Tu
- Genome Institute of Singapore, A*STAR, Singapore, Singapore
- Department of Physics and Astronomy, University of British Columbia, Vancouver, British Columbia, Canada
| | - Rafael Peres Da Silva
- Genome Institute of Singapore, A*STAR, Singapore, Singapore
- School of Computing, National University of Singapore, Singapore, Singapore
| | - Aanchal Mongia
- Genome Institute of Singapore, A*STAR, Singapore, Singapore
- Department of Computer Science and Engineering, Indraprastha Institute of Information Technology, Delhi, India
| | | | - Niranjan Nagarajan
- Genome Institute of Singapore, A*STAR, Singapore, Singapore.
- Department of Physics and Astronomy, University of British Columbia, Vancouver, British Columbia, Canada.
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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10
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Hu LF, Lan HR, Huang D, Li XM, Jin KT. Personalized Immunotherapy in Colorectal Cancers: Where Do We Stand? Front Oncol 2021; 11:769305. [PMID: 34888246 PMCID: PMC8649954 DOI: 10.3389/fonc.2021.769305] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 10/26/2021] [Indexed: 12/17/2022] Open
Abstract
Colorectal cancer (CRC) is the second leading cause of cancer death in the world. Immunotherapy using monoclonal antibodies, immune-checkpoint inhibitors, adoptive cell therapy, and cancer vaccines has raised great hopes for treating poor prognosis metastatic CRCs that are resistant to the conventional therapies. However, high inter-tumor and intra-tumor heterogeneity hinder the success of immunotherapy in CRC. Patients with a similar tumor phenotype respond differently to the same immunotherapy regimen. Mutation-based classification, molecular subtyping, and immunoscoring of CRCs facilitated the multi-aspect grouping of CRC patients and improved immunotherapy. Personalized immunotherapy using tumor-specific neoantigens provides the opportunity to consider each patient as an independent group deserving of individualized immunotherapy. In the recent decade, the development of sequencing and multi-omics techniques has helped us classify patients more precisely. The expansion of such advanced techniques along with the neoantigen-based immunotherapy could herald a new era in treating heterogeneous tumors such as CRC. In this review article, we provided the latest findings in immunotherapy of CRC. We elaborated on the heterogeneity of CRC patients as a bottleneck of CRC immunotherapy and reviewed the latest advances in personalized immunotherapy to overcome CRC heterogeneity.
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Affiliation(s)
- Li-Feng Hu
- Department of Colorectal Surgery, Shaoxing People’s Hospital (Shaoxing Hospital, Zhejiang University School of Medicine), Shaoxing, China
| | - Huan-Rong Lan
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Dong Huang
- Department of Colorectal Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Xue-Min Li
- Department of Hepatobiliary Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Ke-Tao Jin
- Department of Colorectal Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
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11
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Lakatos G, Köhne CH, Bodoky G. Current therapy of advanced colorectal cancer according to RAS/RAF mutational status. Cancer Metastasis Rev 2021; 39:1143-1157. [PMID: 32648137 DOI: 10.1007/s10555-020-09913-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Colorectal cancer is a clinically and molecularly heterogeneous disease. Currently, extended RAS and BRAF mutation testing is obligatory in routine clinical practice before starting any treatment in the metastatic setting. Treatment decision making also includes assessment of the clinical condition of the patient, definition of the treatment goal, and consideration of the primary tumor site. Biological treatment is part of the first-line drug combination unless contraindicated. Mutational status is significantly associated with the outcome of patients and is strongly predictive for anti-EGFR-targeted therapy. The prognosis of RAS mutant CRC is clearly inferior to wild-type cases. RAS remains an elusive target, and specific treatment options are not yet available. Recently, promising results of a direct KRAS G12C inhibitor have been reported; however, further confirmation is needed. The biomarker landscape in mCRC is evolving; new promising markers are awaited with the chance of more precise targeted treatment.
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Affiliation(s)
- Gábor Lakatos
- Department of Oncology, South-Pest Hospital Centre - National Institute for Infectology and Haematology, Budapest, Hungary.
| | - Claus-Henning Köhne
- Klinikum Oldenburg, University Clinic of Oncology and Haematology, Oldenburg, Germany
| | - György Bodoky
- Department of Oncology, South-Pest Hospital Centre - National Institute for Infectology and Haematology, Budapest, Hungary
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12
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Chan DKH, Buczacki SJA. Tumour heterogeneity and evolutionary dynamics in colorectal cancer. Oncogenesis 2021; 10:53. [PMID: 34272358 PMCID: PMC8285471 DOI: 10.1038/s41389-021-00342-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/21/2021] [Accepted: 06/28/2021] [Indexed: 12/25/2022] Open
Abstract
Colorectal cancer (CRC) has a global burden of disease. Our current understanding of CRC has progressed from initial discoveries which focused on the stepwise accumulation of key driver mutations, as encapsulated in the Vogelstein model, to one in which marked heterogeneity leads to a complex interplay between clonal populations. Current evidence suggests that an initial explosion, or “Big Bang”, of genetic diversity is followed by a period of neutral dynamics. A thorough understanding of this interplay between clonal populations during neutral evolution gives insights into the roles in which driver genes may participate in the progress from normal colonic epithelium to adenoma and carcinoma. Recent advances have focused not only on genetics, transcriptomics, and proteomics but have also investigated the ecological and evolutionary processes which transform normal cells into cancer. This review first describes the role which driver mutations play in the Vogelstein model and subsequently demonstrates the evidence which supports a more complex model. This article also aims to underscore the significance of tumour heterogeneity and diverse clonal populations in cancer progression.
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Affiliation(s)
- Dedrick Kok Hong Chan
- Nuffield Department of Surgical Sciences, Medical Sciences Division, University of Oxford, Oxford, UK
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13
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Prediction of recurrence after surgery in colorectal cancer patients using radiomics from diagnostic contrast-enhanced computed tomography: a two-center study. Eur Radiol 2021; 32:405-414. [PMID: 34170367 DOI: 10.1007/s00330-021-08104-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/11/2021] [Accepted: 05/27/2021] [Indexed: 12/24/2022]
Abstract
OBJECTIVES To assess the value of contrast-enhanced (CE) diagnostic CT scans characterized through radiomics as predictors of recurrence for patients with stage II and III colorectal cancer in a two-center context. MATERIALS AND METHODS This study included 193 patients diagnosed with stage II and III colorectal adenocarcinoma from 1 July 2008 to 15 March 2017 in two different French University Hospitals. To compensate for the variability in two-center data, a statistical harmonization method Bootstrapped ComBat (B-ComBat) was used. Models predicting disease-free survival (DFS) were built using 3 different machine learning (ML): (1) multivariate regression (MR) with 10-fold cross-validation after feature selection based on least absolute shrinkage and selection operator (LASSO), (2) random forest (RF), and (3) support vector machine (SVM), both with embedded feature selection. RESULTS The performance for both balanced and 95% sensitivity models was systematically higher after our proposed B-ComBat harmonization compared to the use of the original untransformed data. The most clinically relevant performance was achieved by the multivariate regression model combining a clinical variable (postoperative chemotherapy) with two radiomics shape descriptors (compactness and least axis length) with a BAcc of 0.78 and an MCC of 0.6 associated with a required sensitivity of 95%. The resulting stratification in terms of DFS was significant (p = 0.00021), especially compared to the use of unharmonized original data (p = 0.17). CONCLUSIONS Radiomics models derived from contrast-enhanced CT could be trained and validated in a two-center cohort with a good predictive performance of recurrence in stage II et III colorectal cancer patients. KEY POINTS • Adjuvant therapy decision in colorectal cancer can be a challenge in medical oncology. • Radiomics models, derived from diagnostic CT, trained and validated in a two-center cohort, could predict recurrence in stage II and III colorectal cancer patients. • Identifying patients with a low risk of recurrence, these models could facilitate treatment optimization and avoid unnecessary treatment.
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14
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Vuijk FA, van de Water C, Lent-van Vliet S, van der Valk MJM, Simmer F, van de Velde CJH, Vahrmeijer AL, Nagtegaal ID, Hilling DE. Intra-Tumoral Genomic Heterogeneity in Rectal Cancer: Mutational Status Is Dependent on Preoperative Biopsy Depth and Location. Cancers (Basel) 2021; 13:cancers13092271. [PMID: 34065112 PMCID: PMC8125993 DOI: 10.3390/cancers13092271] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 04/18/2021] [Accepted: 04/28/2021] [Indexed: 01/09/2023] Open
Abstract
Neoadjuvant therapy before surgical resection is indicated for patients with locally advanced rectal cancer. However, a significant number of patients show minimal or no response to neoadjuvant therapy. Unfortunately, we are currently unable to predict response and identify non-responding patients before neoadjuvant treatment is given. Genomic mutational status might provide valuable prognostic information. However, it is unclear whether predictions based on genomic mutational status in single preoperative biopsies are reliable due to intra-tumoral heterogeneity. In this study we aim to investigate the reliability of genomic mutations found in single pre-operative biopsies by comparing genomic mutations to four other locations within the same tumor using next generation sequencing. Rectal cancer patients undergoing primary resection without neoadjuvant therapy were included. From each patient, one biopsy, two deep and two superficial samples were obtained and sequenced using a targeted next generation sequencing gene panel. Concordance between these five samples was assessed. In this feasibility study we included 11 patients. In 7 out of 11 (64%) patients, all 5 samples showed concordant mutations. In 4 out of 11 patients (36%) discordant mutations were observed. In conclusion, assessment of mutational status on a single pre-operative biopsy shows discordance with tumor tissue from other locations in 36% of cases. These results warrant careful interpretation of biopsy material analysis, as these might be influenced by tumor heterogeneity.
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Affiliation(s)
- Floris A. Vuijk
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (F.A.V.); (M.J.M.v.d.V.); (C.J.H.v.d.V.); (A.L.V.)
| | - Carlijn van de Water
- Department of Pathology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (C.v.d.W.); (S.L.-v.V.); (F.S.); (I.D.N.)
| | - Shannon Lent-van Vliet
- Department of Pathology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (C.v.d.W.); (S.L.-v.V.); (F.S.); (I.D.N.)
| | - Maxime J. M. van der Valk
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (F.A.V.); (M.J.M.v.d.V.); (C.J.H.v.d.V.); (A.L.V.)
| | - Femke Simmer
- Department of Pathology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (C.v.d.W.); (S.L.-v.V.); (F.S.); (I.D.N.)
| | - Cornelis J. H. van de Velde
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (F.A.V.); (M.J.M.v.d.V.); (C.J.H.v.d.V.); (A.L.V.)
| | - Alexander L. Vahrmeijer
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (F.A.V.); (M.J.M.v.d.V.); (C.J.H.v.d.V.); (A.L.V.)
| | - Iris D. Nagtegaal
- Department of Pathology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (C.v.d.W.); (S.L.-v.V.); (F.S.); (I.D.N.)
| | - Denise E. Hilling
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (F.A.V.); (M.J.M.v.d.V.); (C.J.H.v.d.V.); (A.L.V.)
- Department of Surgical Oncology and Gastrointestinal Surgery, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands
- Correspondence:
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15
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Salomao N, Karakostis K, Hupp T, Vollrath F, Vojtesek B, Fahraeus R. What do we need to know and understand about p53 to improve its clinical value? J Pathol 2021; 254:443-453. [DOI: 10.1002/path.5677] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/25/2021] [Accepted: 04/01/2021] [Indexed: 12/19/2022]
Affiliation(s)
- Norman Salomao
- Inserm UMRS1131, Institut de Génétique Moléculaire, Université Paris 7, Hôpital St Louis Paris France
| | - Konstantinos Karakostis
- Inserm UMRS1131, Institut de Génétique Moléculaire, Université Paris 7, Hôpital St Louis Paris France
| | - Ted Hupp
- University of Gdansk, International Centre for Cancer Vaccine Science Gdansk Poland
- University of Edinburgh, Institute of Genetics and Molecular Medicine Edinburgh UK
| | - Friz Vollrath
- Department of Zoology, Zoology Research and Administration Building University of Oxford Oxford UK
| | | | - Robin Fahraeus
- Inserm UMRS1131, Institut de Génétique Moléculaire, Université Paris 7, Hôpital St Louis Paris France
- University of Gdansk, International Centre for Cancer Vaccine Science Gdansk Poland
- RECAMO, Masaryk Memorial Cancer Institute Brno Czech Republic
- Department of Medical Biosciences Building 6M, Umeå University Umeå Sweden
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16
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Capp JP, DeGregori J, Nedelcu AM, Dujon AM, Boutry J, Pujol P, Alix-Panabières C, Hamede R, Roche B, Ujvari B, Marusyk A, Gatenby R, Thomas F. Group phenotypic composition in cancer. eLife 2021; 10:63518. [PMID: 33784238 PMCID: PMC8009660 DOI: 10.7554/elife.63518] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 03/09/2021] [Indexed: 12/13/2022] Open
Abstract
Although individual cancer cells are generally considered the Darwinian units of selection in malignant populations, they frequently act as members of groups where fitness of the group cannot be reduced to the average fitness of individual group members. A growing body of studies reveals limitations of reductionist approaches to explaining biological and clinical observations. For example, induction of angiogenesis, inhibition of the immune system, and niche engineering through environmental acidification and/or remodeling of extracellular matrix cannot be achieved by single tumor cells and require collective actions of groups of cells. Success or failure of such group activities depends on the phenotypic makeup of the individual group members. Conversely, these group activities affect the fitness of individual members of the group, ultimately affecting the composition of the group. This phenomenon, where phenotypic makeup of individual group members impacts the fitness of both members and groups, has been captured in the term 'group phenotypic composition' (GPC). We provide examples where considerations of GPC could help in understanding the evolution and clinical progression of cancers and argue that use of the GPC framework can facilitate new insights into cancer biology and assist with the development of new therapeutic strategies.
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Affiliation(s)
- Jean-Pascal Capp
- Toulouse Biotechnology Institute, University of Toulouse, INSA, CNRS, INRAE, Toulouse, France
| | - James DeGregori
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, United States
| | - Aurora M Nedelcu
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Antoine M Dujon
- CREEC/CANECEV, MIVEGEC (CREES), University of Montpellier, CNRS, IRD, Montpellier, France.,Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Australia
| | - Justine Boutry
- CREEC/CANECEV, MIVEGEC (CREES), University of Montpellier, CNRS, IRD, Montpellier, France
| | - Pascal Pujol
- CREEC/CANECEV, MIVEGEC (CREES), University of Montpellier, CNRS, IRD, Montpellier, France
| | - Catherine Alix-Panabières
- CREEC/CANECEV, MIVEGEC (CREES), University of Montpellier, CNRS, IRD, Montpellier, France.,Laboratory of Rare Human Circulating Cells (LCCRH), University Medical Centre of Montpellier, Montpellier, France
| | - Rodrigo Hamede
- School of Natural Sciences, University of Tasmania, Hobart, Australia
| | - Benjamin Roche
- CREEC/CANECEV, MIVEGEC (CREES), University of Montpellier, CNRS, IRD, Montpellier, France
| | - Beata Ujvari
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Australia.,School of Natural Sciences, University of Tasmania, Hobart, Australia
| | - Andriy Marusyk
- Department of Cancer Physiology, H Lee Moffitt Cancer Center and Research Institute, Tampa, United States
| | - Robert Gatenby
- Department of Cancer Physiology, H Lee Moffitt Cancer Center and Research Institute, Tampa, United States
| | - Frédéric Thomas
- CREEC/CANECEV, MIVEGEC (CREES), University of Montpellier, CNRS, IRD, Montpellier, France
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17
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Bungsy M, Palmer MCL, Jeusset LM, Neudorf NM, Lichtensztejn Z, Nachtigal MW, McManus KJ. Reduced RBX1 expression induces chromosome instability and promotes cellular transformation in high-grade serous ovarian cancer precursor cells. Cancer Lett 2020; 500:194-207. [PMID: 33290867 DOI: 10.1016/j.canlet.2020.11.051] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/26/2020] [Accepted: 11/30/2020] [Indexed: 12/14/2022]
Abstract
Despite high-grade serous ovarian cancer (HGSOC) being the most common and lethal gynecological cancer in women, the early etiological events driving disease development remain largely unknown. Emerging evidence now suggests that chromosome instability (CIN; ongoing changes in chromosome numbers) may play a central role in the development and progression of HGSOC. Importantly, genomic amplification of the Cyclin E1 gene (CCNE1) contributes to HGSOC pathogenesis in ~20% of patients, while Cyclin E1 overexpression induces CIN in model systems. Cyclin E1 levels are normally regulated by the SCF (SKP1-CUL1-FBOX) complex, an E3 ubiquitin ligase that includes RBX1 as a core component. Interestingly, RBX1 is heterozygously lost in ~80% of HGSOC cases and reduced expression corresponds with worse outcomes, suggesting it may be a pathogenic event. Using both short (siRNA) and long (CRISPR/Cas9) term approaches, we show that reduced RBX1 expression corresponds with significant increases in CIN phenotypes in fallopian tube secretory epithelial cells, a cellular precursor of HGSOC. Moreover, reduced RBX1 expression corresponds with increased Cyclin E1 levels and anchorage-independent growth. Collectively, these data identify RBX1 as a novel CIN gene with pathogenic implications for HGSOC.
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Affiliation(s)
- Manisha Bungsy
- Research Institute in Oncology & Hematology, Winnipeg, Manitoba, R3E 0V9, Canada; Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, R3E 0V9, Canada
| | - Michaela C L Palmer
- Research Institute in Oncology & Hematology, Winnipeg, Manitoba, R3E 0V9, Canada; Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, R3E 0V9, Canada
| | - Lucile M Jeusset
- Research Institute in Oncology & Hematology, Winnipeg, Manitoba, R3E 0V9, Canada; Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, R3E 0V9, Canada
| | - Nicole M Neudorf
- Research Institute in Oncology & Hematology, Winnipeg, Manitoba, R3E 0V9, Canada; Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, R3E 0V9, Canada
| | - Zelda Lichtensztejn
- Research Institute in Oncology & Hematology, Winnipeg, Manitoba, R3E 0V9, Canada; Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, R3E 0V9, Canada
| | - Mark W Nachtigal
- Research Institute in Oncology & Hematology, Winnipeg, Manitoba, R3E 0V9, Canada; Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, R3E 0V9, Canada; Department of Obstetrics, Gynecology & Reproductive Sciences, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Kirk J McManus
- Research Institute in Oncology & Hematology, Winnipeg, Manitoba, R3E 0V9, Canada; Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, R3E 0V9, Canada.
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18
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Freitas MO, Gartner J, Rangel-Pozzo A, Mai S. Genomic Instability in Circulating Tumor Cells. Cancers (Basel) 2020; 12:cancers12103001. [PMID: 33081135 PMCID: PMC7602879 DOI: 10.3390/cancers12103001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/09/2020] [Accepted: 10/13/2020] [Indexed: 12/21/2022] Open
Abstract
Simple Summary In this review, we focus on recent advances in the detection and quantification of tumor cell heterogeneity and genomic instability of CTCs and the contribution of chromosome instability studies to genetic heterogeneity in CTCs at the single-CTC level. Abstract Circulating tumor cells (CTCs) can promote distant metastases and can be obtained through minimally invasive liquid biopsy for clinical assessment in cancer patients. Having both genomic heterogeneity and instability as common features, the genetic characterization of CTCs can serve as a powerful tool for a better understanding of the molecular changes occurring at tumor initiation and during tumor progression/metastasis. In this review, we will highlight recent advances in the detection and quantification of tumor cell heterogeneity and genomic instability in CTCs. We will focus on the contribution of chromosome instability studies to genetic heterogeneity in CTCs at the single-CTC level by discussing data from different cancer subtypes and their impact on diagnosis and precision medicine.
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Affiliation(s)
- Monique Oliveira Freitas
- Cell Biology, Research Institute of Oncology and Hematology, University of Manitoba, Cancer Care Manitoba, Winnipeg, MB R3C 2B7, Canada;
- Genetic Service, Institute of Paediatrics and Puericulture Martagão Gesteira (IPPMG), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-912, Brazil
- Clinical Medicine Postgraduate Programme, College of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-913, Brazil
| | - John Gartner
- Departments of Pathology and Immunology, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 3P5, Canada;
| | - Aline Rangel-Pozzo
- Cell Biology, Research Institute of Oncology and Hematology, University of Manitoba, Cancer Care Manitoba, Winnipeg, MB R3C 2B7, Canada;
- Correspondence: (A.R.-P.); (S.M.); Tel.: +1-204-787-4125 (S.M.)
| | - Sabine Mai
- Cell Biology, Research Institute of Oncology and Hematology, University of Manitoba, Cancer Care Manitoba, Winnipeg, MB R3C 2B7, Canada;
- Correspondence: (A.R.-P.); (S.M.); Tel.: +1-204-787-4125 (S.M.)
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19
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Palazzolo G, Mollica H, Lusi V, Rutigliani M, Di Francesco M, Pereira RC, Filauro M, Paleari L, DeCensi A, Decuzzi P. Modulating the Distant Spreading of Patient-Derived Colorectal Cancer Cells via Aspirin and Metformin. Transl Oncol 2020; 13:100760. [PMID: 32247264 PMCID: PMC7118176 DOI: 10.1016/j.tranon.2020.100760] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/09/2020] [Accepted: 03/11/2020] [Indexed: 12/16/2022] Open
Abstract
Although screening has reduced mortality rates for colorectal cancer (CRC), about 20% of patients still carry metastases at diagnosis. Postsurgery chemotherapy is toxic and induces drug resistance. Promising alternative strategies rely on repurposing drugs such as aspirin (ASA) and metformin (MET). Here, tumor spheroids were generated in suspension by primary CRCs and metastatic lymph nodes from 11 patients. These spheroids presented a heterogeneous cell population including a small core of CD133+/ESA+ cancer stem cells surrounded by a thick corona of CDX2+/CK20+ CRC cells, thus maintaining the molecular hallmarks of the tumor source. Spheroids were exposed to ASA and/or MET at different doses for up to 7 days to assess cell growth, migration, and adhesion in three-dimensional assays. While ASA at 5 mM was always sufficient to mitigate cell migration, the response to MET was patient specific. Only in MET-sensitive spheroids, the 5 mM ASA/MET combination showed an effect. Interestingly, CRCs from diabetic patients daily pretreated with MET gave a very low spheroid yield due to reduced cancer cell survival. This study highlights the potential of ASA/MET treatments to modulate CRC spreading.
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Affiliation(s)
- Gemma Palazzolo
- Laboratory of Nanotechnology for Precision Medicine, Fondazione Istituto Italiano di Tecnologia, 16163 Genoa, Italy.
| | - Hilaria Mollica
- Laboratory of Nanotechnology for Precision Medicine, Fondazione Istituto Italiano di Tecnologia, 16163 Genoa, Italy
| | - Valeria Lusi
- Laboratory of Nanotechnology for Precision Medicine, Fondazione Istituto Italiano di Tecnologia, 16163 Genoa, Italy
| | - Mariangela Rutigliani
- Department of Laboratory and Service, Histological and Anatomical Pathology Unit, E.O. Ospedali Galliera, Genoa, Italy
| | - Martina Di Francesco
- Laboratory of Nanotechnology for Precision Medicine, Fondazione Istituto Italiano di Tecnologia, 16163 Genoa, Italy
| | - Rui Cruz Pereira
- Laboratory of Nanotechnology for Precision Medicine, Fondazione Istituto Italiano di Tecnologia, 16163 Genoa, Italy
| | - Marco Filauro
- Department of Surgery, E.O. Ospedali Galliera, Genoa, Italy
| | | | - Andrea DeCensi
- Department of Medicine Area, Medical Oncology Unit, E.O. Ospedali Galliera, Genoa, Italy
| | - Paolo Decuzzi
- Laboratory of Nanotechnology for Precision Medicine, Fondazione Istituto Italiano di Tecnologia, 16163 Genoa, Italy
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20
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Mizuno Y, Hattori K, Taniguchi K, Tanaka K, Uchiyama K, Hirose Y. Intratumoral heterogeneity of glutaminase and lactate dehydrogenase A protein expression in colorectal cancer. Oncol Lett 2020; 19:2934-2942. [PMID: 32218849 PMCID: PMC7068422 DOI: 10.3892/ol.2020.11390] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 01/21/2020] [Indexed: 12/17/2022] Open
Abstract
The high expression of metabolic enzymes, including glutaminase (GA) and lactate dehydrogenase A (LDHA), which contribute to bioenergetics and biosynthesis of mammalian cells, has been identified in a variety of cancer types. The current study indicated intratumoral heterogeneity with respect to protein expression of the metabolic enzymes in colorectal cancer (CRC). GA protein expression was determined using immunohistochemistry in 98 cases of surgically resected T3 CRC. A total of 75 cases (74%) exhibited moderate to strong immunopositivity of GA based on whole-section examination. A significant correlation was demonstrated between GA expression and clinicopathological features, including histological type and tumor budding in a patient population. Detailed histological analysis revealed the upregulation of GA protein expression at the invasive margin, including tumor budding of CRC tissues. Semi-quantitative examination revealed a significant difference in immunoexpression level of GA between the invasive margin and central CRC. However, LDHA expression exhibited an opposite pattern, with expression elevated at the center and significantly decreased at the tumors invasive margin. Immunohistochemical expression of another glycolytic enzyme hexokinase II was equivalent in both regions. Furthermore, gene silencing of GLS1, which encodes GA protein, and GA inhibitor treatment significantly inhibited cell growth of CRC cell lines. Therefore, the results of the present study demonstrated that the alteration in GA and LDHA expression is more prominent at the invasive margin, which involves tumor budding in CRC.
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Affiliation(s)
- Yuta Mizuno
- Department of Pathology, Osaka Medical College, Takatsuki, Osaka 569-8686, Japan.,Department of General and Gastroenterological Surgery, Osaka Medical College, Takatsuki, Osaka 569-8686, Japan
| | - Kimiaki Hattori
- Department of Pathology, Osaka Medical College, Takatsuki, Osaka 569-8686, Japan
| | - Kohei Taniguchi
- Department of General and Gastroenterological Surgery, Osaka Medical College, Takatsuki, Osaka 569-8686, Japan.,Department of Translational Research Program, Osaka Medical College, Takatsuki, Osaka 569-8686, Japan
| | - Keitaro Tanaka
- Department of General and Gastroenterological Surgery, Osaka Medical College, Takatsuki, Osaka 569-8686, Japan
| | - Kazuhisa Uchiyama
- Department of General and Gastroenterological Surgery, Osaka Medical College, Takatsuki, Osaka 569-8686, Japan
| | - Yoshinobu Hirose
- Department of Pathology, Osaka Medical College, Takatsuki, Osaka 569-8686, Japan
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21
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Leylek TR, Jeusset LM, Lichtensztejn Z, McManus KJ. Reduced Expression of Genes Regulating Cohesion Induces Chromosome Instability that May Promote Cancer and Impact Patient Outcomes. Sci Rep 2020; 10:592. [PMID: 31953484 PMCID: PMC6969069 DOI: 10.1038/s41598-020-57530-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 01/03/2020] [Indexed: 12/15/2022] Open
Abstract
Chromosome instability (CIN), or continual changes in chromosome complements, is an enabling feature of cancer; however, the molecular determinants of CIN remain largely unknown. Emerging data now suggest that aberrant sister chromatid cohesion may induce CIN and contribute to cancer. To explore this possibility, we employed clinical and fundamental approaches to systematically assess the impact reduced cohesion gene expression has on CIN and cancer. Ten genes encoding critical functions in cohesion were evaluated and remarkably, each exhibits copy number losses in 12 common cancer types, and reduced expression is associated with worse patient survival. To gain mechanistic insight, we combined siRNA-based silencing with single cell quantitative imaging microscopy to comprehensively assess the impact reduced expression has on CIN in two karyotypically stable cell lines. We show that reduced expression induces CIN phenotypes, namely increases in micronucleus formation and nuclear areas. Subsequent direct tests involving a subset of prioritized genes also revealed significant changes in chromosome numbers with corresponding increases in moderate and severe cohesion defects within mitotic chromosome spreads. Collectively, our clinical and fundamental findings implicate reduced sister chromatid cohesion, resulting from gene copy number losses, as a key pathogenic event in the development and progression of many cancer types.
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Affiliation(s)
- Tarik R Leylek
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, Manitoba, R3E 0J9, Canada
| | - Lucile M Jeusset
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, Manitoba, R3E 0J9, Canada
- Research Institute in Oncology & Hematology, CancerCare Manitoba, Winnipeg, Manitoba, R3E 0V9, Canada
| | - Zelda Lichtensztejn
- Research Institute in Oncology & Hematology, CancerCare Manitoba, Winnipeg, Manitoba, R3E 0V9, Canada
| | - Kirk J McManus
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, Manitoba, R3E 0J9, Canada.
- Research Institute in Oncology & Hematology, CancerCare Manitoba, Winnipeg, Manitoba, R3E 0V9, Canada.
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22
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Harris KL, Myers MB, McKim KL, Elespuru RK, Parsons BL. Rationale and Roadmap for Developing Panels of Hotspot Cancer Driver Gene Mutations as Biomarkers of Cancer Risk. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:152-175. [PMID: 31469467 PMCID: PMC6973253 DOI: 10.1002/em.22326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/23/2019] [Accepted: 08/26/2019] [Indexed: 05/24/2023]
Abstract
Cancer driver mutations (CDMs) are necessary and causal for carcinogenesis and have advantages as reporters of carcinogenic risk. However, little progress has been made toward developing measurements of CDMs as biomarkers for use in cancer risk assessment. Impediments for using a CDM-based metric to inform cancer risk include the complexity and stochastic nature of carcinogenesis, technical difficulty in quantifying low-frequency CDMs, and lack of established relationships between cancer driver mutant fractions and tumor incidence. Through literature review and database analyses, this review identifies the most promising targets to investigate as biomarkers of cancer risk. Mutational hotspots were discerned within the 20 most mutated genes across the 10 deadliest cancers. Forty genes were identified that encompass 108 mutational hotspot codons overrepresented in the COSMIC database; 424 different mutations within these hotspot codons account for approximately 63,000 tumors and their prevalence across tumor types is described. The review summarizes literature on the prevalence of CDMs in normal tissues and suggests such mutations are direct and indirect substrates for chemical carcinogenesis, which occurs in a spatially stochastic manner. Evidence that hotspot CDMs (hCDMs) frequently occur as tumor subpopulations is presented, indicating COSMIC data may underestimate mutation prevalence. Analyses of online databases show that genes containing hCDMs are enriched in functions related to intercellular communication. In its totality, the review provides a roadmap for the development of tissue-specific, CDM-based biomarkers of carcinogenic potential, comprised of batteries of hCDMs and can be measured by error-correct next-generation sequencing. Environ. Mol. Mutagen. 61:152-175, 2020. Published 2019. This article is a U.S. Government work and is in the public domain in the USA. Environmental and Molecular Mutagenesis published by Wiley Periodicals, Inc. on behalf of Environmental Mutagen Society.
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Affiliation(s)
- Kelly L. Harris
- Division of Genetic and Molecular ToxicologyNational Center for Toxicological Research, US Food and Drug AdministrationJeffersonArkansas
| | - Meagan B. Myers
- Division of Genetic and Molecular ToxicologyNational Center for Toxicological Research, US Food and Drug AdministrationJeffersonArkansas
| | - Karen L. McKim
- Division of Genetic and Molecular ToxicologyNational Center for Toxicological Research, US Food and Drug AdministrationJeffersonArkansas
| | - Rosalie K. Elespuru
- Division of Biology, Chemistry and Materials ScienceCDRH/OSEL, US Food and Drug AdministrationSilver SpringMaryland
| | - Barbara L. Parsons
- Division of Genetic and Molecular ToxicologyNational Center for Toxicological Research, US Food and Drug AdministrationJeffersonArkansas
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23
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Bin Y, Wang X, Zhao L, Wen P, Xia J. An analysis of mutational signatures of synonymous mutations across 15 cancer types. BMC MEDICAL GENETICS 2019; 20:190. [PMID: 31815613 PMCID: PMC6900878 DOI: 10.1186/s12881-019-0926-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Background Synonymous mutations have been identified to play important roles in cancer development, although they do not modify the protein sequences. However, relatively little research has specifically delineated the functionality of synonymous mutations in cancer. Results We investigated the nucleotide-based and amino acid-based features of synonymous mutations across 15 cancer types from The Cancer Genome Atlas (TCGA), and revealed novel driver candidates by identifying hotspot mutations. Firstly, synonymous mutations were analyzed between TCGA and 1000 Genomes Project at nucleotide and amino acid levels. We found that C:G → T:A transitions were the most frequent single-base substitutions, and leucine underwent the largest number of synonymous mutations in TCGA due to prevalent C → T transition, which induced the transformation between optimal and non-optimal codons. Next, 97 synonymous hotspot mutations in 86 genes were nominated as candidate drivers with potential cancer risk by considering the mutational rates across different sequence contexts. We observed that non-CpG-island GC transition sequence context was positively selected across most of cancer types, and different sequence contexts under which hotspot mutations occur could be significance for genetic differences and functional features. We also found that the hotspots were more conserved than neutral mutations of hotspot-mutation-containing-genes and frequently happened at leucine. In addition, we mapped hotspots, neutral and non-hotspot mutations of hotspot-mutation-containing-genes to their respective protein domains and found ion transport domain was the most frequent one, which could mediate the cell interaction and had relevant implication for tumor therapy. And the signatures of synonymous hotspots were qualitatively similar with those of harmful missense variants. Conclusions We illustrated the preferences of cancer associated synonymous mutations, especially hotspots, and laid the groundwork for understanding the synonymous mutations act as drivers in cancer.
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Affiliation(s)
- Yannan Bin
- Institutes of Physical Science and Information Technology, School of Computer Science and Technology, Anhui University, Hefei, 230601, Anhui, China
| | - Xiaojuan Wang
- Institutes of Physical Science and Information Technology, School of Computer Science and Technology, Anhui University, Hefei, 230601, Anhui, China
| | - Le Zhao
- Institutes of Physical Science and Information Technology, School of Computer Science and Technology, Anhui University, Hefei, 230601, Anhui, China
| | - Pengbo Wen
- Institutes of Physical Science and Information Technology, School of Computer Science and Technology, Anhui University, Hefei, 230601, Anhui, China
| | - Junfeng Xia
- Institutes of Physical Science and Information Technology, School of Computer Science and Technology, Anhui University, Hefei, 230601, Anhui, China.
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24
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Sena P, Fioresi R, Faglioni F, Losi L, Faglioni G, Roncucci L. Deep learning techniques for detecting preneoplastic and neoplastic lesions in human colorectal histological images. Oncol Lett 2019; 18:6101-6107. [PMID: 31788084 PMCID: PMC6865164 DOI: 10.3892/ol.2019.10928] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 08/30/2019] [Indexed: 12/12/2022] Open
Abstract
Trained pathologists base colorectal cancer identification on the visual interpretation of microscope images. However, image labeling is not always straightforward and this repetitive task is prone to mistakes due to human distraction. Significant efforts are underway to develop informative tools to assist pathologists and decrease the burden and frequency of errors. The present study proposes a deep learning approach to recognize four different stages of cancerous tissue development, including normal mucosa, early preneoplastic lesion, adenoma and cancer. A dataset of human colon tissue images collected and labeled over a 10-year period by a team of pathologists was partitioned into three sets. These were used to train, validate and test the neural network, comprising several convolutional and a few linear layers. The approach used in the present study is 'direct'; it labels raw images and bypasses the segmentation step. An overall accuracy of >95% was achieved, with the majority of mislabeling referring to a near category. Tests on an external dataset with a different resolution yielded accuracies >80%. The present study demonstrated that the neural network, when properly trained, can provide fast, accurate and reproducible labeling for colon cancer images, with the potential to significantly improve the quality and speed of medical diagnoses.
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Affiliation(s)
- Paola Sena
- Department of Biomedical, Metabolic and Neurosciences, University of Modena and Reggio Emilia, I-41125 Modena, Italy
| | - Rita Fioresi
- Department of Mathematics, University of Bologna, I-40126 Bologna, Italy
| | - Francesco Faglioni
- Department of Chemistry and Geology, University of Modena and Reggio Emiliaa, I-41125 Modena, Italy
| | - Lorena Losi
- Department of Life Sciences, University of Modena and Reggio Emiliaa, I-41125 Modena, Italy
| | | | - Luca Roncucci
- Department of Diagnostic and Clinical Medicine, and Public Health, University of Modena and Reggio Emilia, I-41125 Modena, Italy
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25
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Schick U, Lucia F, Dissaux G, Visvikis D, Badic B, Masson I, Pradier O, Bourbonne V, Hatt M. MRI-derived radiomics: methodology and clinical applications in the field of pelvic oncology. Br J Radiol 2019; 92:20190105. [PMID: 31538516 DOI: 10.1259/bjr.20190105] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Personalized medicine aims at offering optimized treatment options and improved survival for cancer patients based on individual variability. The success of precision medicine depends on robust biomarkers. Recently, the requirement for improved non-biologic biomarkers that reflect tumor biology has emerged and there has been a growing interest in the automatic extraction of quantitative features from medical images, denoted as radiomics. Radiomics as a methodological approach can be applied to any image and most studies have focused on PET, CT, ultrasound, and MRI. Here, we aim to present an overview of the radiomics workflow as well as the major challenges with special emphasis on the use of multiparametric MRI datasets. We then reviewed recent studies on radiomics in the field of pelvic oncology including prostate, cervical, and colorectal cancer.
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Affiliation(s)
- Ulrike Schick
- Radiation Oncology department, University Hospital, Brest, France.,LaTIM, INSERM, UMR 1101, University of Brest, ISBAM, UBO, UBL, Brest, France.,Faculté de Médecine et des Sciences de la Santé, Université de Bretagne Occidentale, Brest, France
| | - François Lucia
- Radiation Oncology department, University Hospital, Brest, France.,LaTIM, INSERM, UMR 1101, University of Brest, ISBAM, UBO, UBL, Brest, France
| | - Gurvan Dissaux
- Radiation Oncology department, University Hospital, Brest, France.,LaTIM, INSERM, UMR 1101, University of Brest, ISBAM, UBO, UBL, Brest, France.,Faculté de Médecine et des Sciences de la Santé, Université de Bretagne Occidentale, Brest, France
| | - Dimitris Visvikis
- LaTIM, INSERM, UMR 1101, University of Brest, ISBAM, UBO, UBL, Brest, France
| | - Bogdan Badic
- LaTIM, INSERM, UMR 1101, University of Brest, ISBAM, UBO, UBL, Brest, France.,Department of General and Digestive Surgery, University Hospital, Brest, France
| | - Ingrid Masson
- LaTIM, INSERM, UMR 1101, University of Brest, ISBAM, UBO, UBL, Brest, France
| | - Olivier Pradier
- Radiation Oncology department, University Hospital, Brest, France.,LaTIM, INSERM, UMR 1101, University of Brest, ISBAM, UBO, UBL, Brest, France.,Faculté de Médecine et des Sciences de la Santé, Université de Bretagne Occidentale, Brest, France
| | - Vincent Bourbonne
- Radiation Oncology department, University Hospital, Brest, France.,LaTIM, INSERM, UMR 1101, University of Brest, ISBAM, UBO, UBL, Brest, France
| | - Mathieu Hatt
- LaTIM, INSERM, UMR 1101, University of Brest, ISBAM, UBO, UBL, Brest, France
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26
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Diminished Condensin Gene Expression Drives Chromosome Instability That May Contribute to Colorectal Cancer Pathogenesis. Cancers (Basel) 2019; 11:cancers11081066. [PMID: 31357676 PMCID: PMC6721357 DOI: 10.3390/cancers11081066] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/17/2019] [Accepted: 07/25/2019] [Indexed: 12/28/2022] Open
Abstract
Chromosome instability (CIN), or constantly evolving chromosome complements, is a form of genome instability implicated in the development and progression of many cancer types, however, the molecular determinants of CIN remain poorly understood. Condensin is a protein complex involved in chromosome compaction, and recent studies in model organisms show that aberrant compaction adversely impacts mitotic fidelity. To systematically assess the clinical and fundamental impacts that reduced condensin gene expression have in cancer, we first assessed gene copy number alterations of all eight condensin genes. Using patient derived datasets, we show that shallow/deep deletions occur frequently in 12 common cancer types. Furthermore, we show that reduced expression of each gene is associated with worse overall survival in colorectal cancer patients. To determine the overall impact that reduced condensin gene expression has on CIN, a comprehensive siRNA-based screen was performed in two karyotypically stable cell lines. Following gene silencing, quantitative imaging microscopy identified increases in CIN-associated phenotypes, including changes in nuclear areas, micronucleus formation, and chromosome numbers. Although silencing corresponded with increases in CIN phenotypes, the most pronounced phenotypes were observed following SMC2 and SMC4 silencing. Collectively, our clinical and fundamental findings suggest reduced condensin expression and function may be a significant, yet, underappreciated driver of colorectal cancer.
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27
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Radiogenomics-based cancer prognosis in colorectal cancer. Sci Rep 2019; 9:9743. [PMID: 31278324 PMCID: PMC6611779 DOI: 10.1038/s41598-019-46286-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 06/20/2019] [Indexed: 12/21/2022] Open
Abstract
Radiogenomics aims at investigating the relationship between imaging radiomic features and gene expression alterations. This study addressed the potential prognostic complementary value of contrast enhanced computed tomography (CE-CT) radiomic features and gene expression data in primary colorectal cancers (CRC). Sixty-four patients underwent CT scans and radiomic features were extracted from the delineated tumor volume. Gene expression analysis of a small set of genes, previously identified as relevant for CRC, was conducted on surgical samples from the same tumors. The relationships between radiomic and gene expression data was assessed using the Kruskal–Wallis test. Multiple testing was not performed, as this was a pilot study. Cox regression was used to identify variables related to overall survival (OS) and progression free survival (PFS). ABCC2 gene expression was correlated with N (p = 0.016) and M stages (p = 0.022). Expression changes of ABCC2, CD166, CDKNV1 and INHBB genes exhibited significant correlations with some radiomic features. OS was associated with Ratio 3D Surface/volume (p = 0.022) and ALDH1A1 expression (p = 0.042), whereas clinical stage (p = 0.004), ABCC2 expression (p = 0.035), and EntropyGLCM_E (p = 0.0031), were prognostic factors for PFS. Combining CE-CT radiomics with gene expression analysis and histopathological examination of primary CRC could provide higher prognostic stratification power, leading to improved patient management.
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28
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Visioli A, Giani F, Trivieri N, Pracella R, Miccinilli E, Cariglia MG, Palumbo O, Arleo A, Dezi F, Copetti M, Cajola L, Restelli S, Papa V, Sciuto A, Latiano TP, Carella M, Amadori D, Gallerani G, Ricci R, Alfieri S, Pesole G, Vescovi AL, Binda E. Stemness underpinning all steps of human colorectal cancer defines the core of effective therapeutic strategies. EBioMedicine 2019; 44:346-360. [PMID: 31056474 PMCID: PMC6603803 DOI: 10.1016/j.ebiom.2019.04.049] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 04/24/2019] [Accepted: 04/24/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Despite their lethality and ensuing clinical and therapeutic relevance, circulating tumor cells (CTCs) from colorectal carcinoma (CRC) remain elusive, poorly characterized biological entities. METHODS AND FINDINGS We perfected a cell system of stable, primary lines from human CRC showing that they possess the full complement of ex- and in-vivo, in xenogeneic models, characteristics of CRC stem cells (CCSCs). Here we show how tumor-initiating, CCSCs cells can establish faithful orthotopic phenocopies of the original disease, which contain cells that spread into the circulatory system. While in the vascular bed, these cells retain stemness, thus qualifying as circulating CCSCs (cCCSCs). This is followed by the establishment of lesions in distant organs, which also contain resident metastatic CCSCs (mCCSCs). INTERPRETATION Our results support the concept that throughout all the stages of CRC, stemness is retained as a continuous property by some of their tumor cells. Importantly, we describe a useful standardized model that can enable isolation and stable perpetuation of human CRC's CCSCs, cCCSCs and mCCSCs, providing a useful platform for studies of CRC initiation and progression that is suitable for the discovery of reliable stage-specific biomarkers and the refinement of new patient-tailored therapies. FUND: This work was financially supported by grants from "Ministero della Salute Italiano"(GR-2011-02351534, RC1703IC36 and RC1803IC35) to Elena Binda and from "Associazione Italiana Cancro" (IG-14368) Angelo L. Vescovi. None of the above funders have any role in study design, data collection, data analysis, interpretation, writing the project.
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Affiliation(s)
| | | | - Nadia Trivieri
- Fondazione IRCCS Casa Sollievo della Sofferenza, Cancer Stem Cells Unit, ISBReMIT, Foggia, Italy
| | - Riccardo Pracella
- Fondazione IRCCS Casa Sollievo della Sofferenza, Cancer Stem Cells Unit, ISBReMIT, Foggia, Italy
| | - Elide Miccinilli
- Fondazione IRCCS Casa Sollievo della Sofferenza, Cancer Stem Cells Unit, ISBReMIT, Foggia, Italy
| | - Maria Grazia Cariglia
- Fondazione IRCCS Casa Sollievo della Sofferenza, Cancer Stem Cells Unit, ISBReMIT, Foggia, Italy
| | - Orazio Palumbo
- Fondazione IRCCS Casa Sollievo della Sofferenza, Medical Genetics Unit, Foggia, Italy
| | - Andrea Arleo
- Fondazione IRCCS Casa Sollievo della Sofferenza, Cancer Stem Cells Unit, ISBReMIT, Foggia, Italy
| | - Fabio Dezi
- Fondazione IRCCS Casa Sollievo della Sofferenza, Cancer Stem Cells Unit, ISBReMIT, Foggia, Italy
| | - Massimiliano Copetti
- Fondazione IRCCS Casa Sollievo della Sofferenza, Biostatistic Unit, Foggia, Italy
| | | | | | - Valerio Papa
- Digestive Surgery Unit, IRCCS "A. Gemelli", Catholic University of the Sacred Heart, Rome, Italy
| | - Antonio Sciuto
- IRCCS Casa Sollievo della Sofferenza, Abdominal Surgery Unit, Foggia, Italy
| | | | - Massimo Carella
- Fondazione IRCCS Casa Sollievo della Sofferenza, Medical Genetics Unit, Foggia, Italy
| | - Dino Amadori
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS Meldola, Italy
| | - Giulia Gallerani
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS Meldola, Biosciences Laboratory, Italy
| | - Riccardo Ricci
- Department of Pathology, IRCCS "A. Gemelli", Catholic University of the Sacred Heart, Rome, Italy
| | - Sergio Alfieri
- Department of Pathology, IRCCS "A. Gemelli", Catholic University of the Sacred Heart, Rome, Italy
| | - Graziano Pesole
- Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari del Consiglio Nazionale delle Ricerche, Bari, Italy; Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica dell'Università di Bari "A. Moro". Bari, Italy
| | - Angelo L Vescovi
- Fondazione IRCCS Casa Sollievo della Sofferenza, Cancer Stem Cells Unit, ISBReMIT, Foggia, Italy; Hyperstem SA, Lugano, Switzerland.
| | - Elena Binda
- Fondazione IRCCS Casa Sollievo della Sofferenza, Cancer Stem Cells Unit, ISBReMIT, Foggia, Italy.
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Bolhaqueiro ACF, Ponsioen B, Bakker B, Klaasen SJ, Kucukkose E, van Jaarsveld RH, Vivié J, Verlaan-Klink I, Hami N, Spierings DCJ, Sasaki N, Dutta D, Boj SF, Vries RGJ, Lansdorp PM, van de Wetering M, van Oudenaarden A, Clevers H, Kranenburg O, Foijer F, Snippert HJG, Kops GJPL. Ongoing chromosomal instability and karyotype evolution in human colorectal cancer organoids. Nat Genet 2019; 51:824-834. [PMID: 31036964 DOI: 10.1038/s41588-019-0399-6] [Citation(s) in RCA: 140] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 03/19/2019] [Indexed: 11/09/2022]
Abstract
Chromosome segregation errors cause aneuploidy and genomic heterogeneity, which are hallmarks of cancer in humans. A persistent high frequency of these errors (chromosomal instability (CIN)) is predicted to profoundly impact tumor evolution and therapy response. It is unknown, however, how prevalent CIN is in human tumors. Using three-dimensional live-cell imaging of patient-derived tumor organoids (tumor PDOs), we show that CIN is widespread in colorectal carcinomas regardless of background genetic alterations, including microsatellite instability. Cell-fate tracking showed that, although mitotic errors are frequently followed by cell death, some tumor PDOs are largely insensitive to mitotic errors. Single-cell karyotype sequencing confirmed heterogeneity of copy number alterations in tumor PDOs and showed that monoclonal lines evolved novel karyotypes over time in vitro. We conclude that ongoing CIN is common in colorectal cancer organoids, and propose that CIN levels and the tolerance for mitotic errors shape aneuploidy landscapes and karyotype heterogeneity.
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Affiliation(s)
- Ana C F Bolhaqueiro
- Oncode Institute, Hubrecht Institute-KNAW, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Bas Ponsioen
- Oncode Institute, Center for Molecular Medicine, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Bjorn Bakker
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Sjoerd J Klaasen
- Oncode Institute, Hubrecht Institute-KNAW, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Emre Kucukkose
- Department of Surgical Oncology, UMC Utrecht Cancer Centre, University Medical Centre, Utrecht, the Netherlands
| | - Richard H van Jaarsveld
- Oncode Institute, Hubrecht Institute-KNAW, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Judith Vivié
- Oncode Institute, Hubrecht Institute-KNAW, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Ingrid Verlaan-Klink
- Oncode Institute, Center for Molecular Medicine, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Nizar Hami
- Oncode Institute, Center for Molecular Medicine, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Diana C J Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Nobuo Sasaki
- Oncode Institute, Hubrecht Institute-KNAW, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Devanjali Dutta
- Oncode Institute, Hubrecht Institute-KNAW, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Sylvia F Boj
- Foundation Hubrecht Organoid Technology (HUB), Utrecht, the Netherlands
| | - Robert G J Vries
- Foundation Hubrecht Organoid Technology (HUB), Utrecht, the Netherlands
| | - Peter M Lansdorp
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands.,Terry Fox Laboratory, BC Cancer Agency, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marc van de Wetering
- Oncode Institute, Princess Maxima Centre for Paediatric Oncology, Utrecht, the Netherlands
| | - Alexander van Oudenaarden
- Oncode Institute, Hubrecht Institute-KNAW, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Hans Clevers
- Oncode Institute, Hubrecht Institute-KNAW, University Medical Centre Utrecht, Utrecht, the Netherlands.,Oncode Institute, Princess Maxima Centre for Paediatric Oncology, Utrecht, the Netherlands
| | - Onno Kranenburg
- Department of Surgical Oncology, UMC Utrecht Cancer Centre, University Medical Centre, Utrecht, the Netherlands
| | - Floris Foijer
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Hugo J G Snippert
- Oncode Institute, Center for Molecular Medicine, University Medical Centre Utrecht, Utrecht, the Netherlands.
| | - Geert J P L Kops
- Oncode Institute, Hubrecht Institute-KNAW, University Medical Centre Utrecht, Utrecht, the Netherlands.
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30
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Badic B, Desseroit MC, Hatt M, Visvikis D. Potential Complementary Value of Noncontrast and Contrast Enhanced CT Radiomics in Colorectal Cancers. Acad Radiol 2019; 26:469-479. [PMID: 30072293 DOI: 10.1016/j.acra.2018.06.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 05/31/2018] [Accepted: 06/02/2018] [Indexed: 01/08/2023]
Abstract
RATIONALE AND OBJECTIVES The aim of our study was to assess the relationships between textural features extracted from contrast enhanced (CE) and noncontrast enhanced (NCE) computed tomography (CT) images of primary colorectal cancer, in order to identify radiomics features more likely to provide potential complementary information regarding outcome. MATERIALS AND METHODS Sixty-one patients with primary colorectal cancer underwent both CE-CT and NCE-CT scans within the same acquisition. First-order and textural features (with three different methods for grey-level discretization) were extracted from the tumor volume in both modalities and their correlation was assessed with Spearman's rank correlation (rs). Significance was assessed at p < 0.05 with correction for multiple comparisons. Kaplan-Meier estimation and log-rank tests were used to identify features associated with long term patient survival. RESULTS Moderate positive correlations were observed between CE-CT and NCE-CT histogram-derived entropy (EntropyHist) and area under the curve (CHAUC) (rs = 0.49, p < 0.001 and rs= 0.45, p < 0.001, respectively). Some second and third order textural features were found highly correlated between CE-CT and NCE-CT, such as small zone-size emphasis SZSE (rs = 0.729, p < 0.001) and zone-size percentage (rs = 0.770, p < 0.001). Grey-levels discretization methods influenced these correlations. A few of the third order NCE-CT and CE-CT features were significantly associated with survival. CONCLUSION Some radiomics features with moderate correlations between nonenhanced and enhanced CT images were found to be associated with survival, thus suggesting that complementary prognostic value may be extracted from both modalities when available.
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31
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Bhullar DS, Barriuso J, Mullamitha S, Saunders MP, O'Dwyer ST, Aziz O. Biomarker concordance between primary colorectal cancer and its metastases. EBioMedicine 2019; 40:363-374. [PMID: 30733075 PMCID: PMC6413540 DOI: 10.1016/j.ebiom.2019.01.050] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 01/13/2019] [Accepted: 01/24/2019] [Indexed: 12/17/2022] Open
Abstract
Background The use of biomarkers to target anti-EGFR treatments for metastatic colorectal cancer (CRC) is well-established, requiring molecular analysis of primary or metastatic biopsies. We aim to review concordance between primary CRC and its metastatic sites. Methods A systematic review and meta-analysis of all published studies (1991–2018) reporting on biomarker concordance between primary CRC and its metastatic site(s) was undertaken according to PRISMA guidelines using several medical databases. Studies without matched samples or using peripheral blood for biomarker analysis were excluded. Findings 61 studies including 3565 patient samples were included. Median biomarker concordance for KRAS (n = 50) was 93.7% [[67], [68], [69], [70], [71], [72], [73], [74], [75], [76], [77], [78], [79], [80], [81], [82], [83], [84], [85], [86], [87], [88], [89], [90], [91], [92], [93], [94], [95], [96], [97], [98], [99], [100]], NRAS (n = 11) was 100% [[90], [91], [92], [93], [94], [95], [96], [97], [98], [99], [100]], BRAF (n = 22) was 99.4% [[80], [81], [82], [83], [84], [85], [86], [87], [88], [89], [90], [91], [92], [93], [94], [95], [96], [97], [98], [99], [100]], and PIK3CA (n = 17) was 93% [[42], [43], [44], [45], [46], [47], [48], [49], [50], [51], [52], [53], [54], [55], [56], [57], [58], [59], [60], [61], [62], [63], [64], [65], [66], [67], [68], [69], [70], [71], [72], [73], [74], [75], [76], [77], [78], [79], [80], [81], [82], [83], [84], [85], [86], [87], [88], [89], [90], [91], [92], [93], [94], [95], [96], [97], [98], [99], [100]]. Meta-analytic pooled discordance was 8% for KRAS (95% CI = 5–10%), 8% for BRAF (95% CI = 5–10%), 7% for PIK3CA (95% CI = 2–13%), and 28% overall (95% CI = 14–44%). The liver was the most commonly biopsied metastatic site (n = 2276), followed by lung (n = 438), lymph nodes (n = 1123), and peritoneum (n = 132). Median absolute concordance in multiple biomarkers was 81% (5–95%). Interpretation Metastatic CRC demonstrates high concordance across multiple biomarkers, suggesting that molecular testing of either the primary or liver and lung metastasis is adequate. More research on colorectal peritoneal metastases is required.
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Affiliation(s)
- D S Bhullar
- Colorectal & Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, UK; Division of Cancer Sciences, School of Medical Science, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - J Barriuso
- Colorectal & Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, UK; Division of Cancer Sciences, School of Medical Science, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - S Mullamitha
- Colorectal & Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, UK; Division of Cancer Sciences, School of Medical Science, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - M P Saunders
- Colorectal & Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, UK; Division of Cancer Sciences, School of Medical Science, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - S T O'Dwyer
- Colorectal & Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, UK; Division of Cancer Sciences, School of Medical Science, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - O Aziz
- Colorectal & Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, UK; Division of Cancer Sciences, School of Medical Science, Faculty of Biology, Medicine and Health, University of Manchester, UK.
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32
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Droplet digital PCR revealed high concordance between primary tumors and lymph node metastases in multiplex screening of KRAS mutations in colorectal cancer. Clin Exp Med 2019; 19:219-224. [PMID: 30661213 DOI: 10.1007/s10238-019-00545-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 01/11/2019] [Indexed: 10/27/2022]
Abstract
The proto-oncogene KRAS belongs among the most frequently mutated genes in all types of cancer and is also very important oncogene related to colorectal tumors. The detection of mutations in this gene in primary tumor is a predictive biomarker for the anti-EGFR therapy in metastatic CRC (mCRC); however, the patients with wild-type KRAS can also show resistance to the personalized medicine. The droplet-based digital PCR technology has improved the analytical sensitivity of the mutations detection, which led us to the idea about the optimization of this approach for KRAS testing. In this study, we report the application of ddPCR technology in order to analyze the presence of KRAS mutations in primary tumor and matched metastasis in lymph nodes (LNs) from patients with mCRC and address the question, whether the improvement in the detection method can lower the discrepancies of KRAS mutations detection between the primary tumor and regional LNs. Genomic DNA with wtKRAS and commercial DNA with mtKRAS (G12D) were used to set up the ddPCR reaction. Formalin-fixed paraffin-embedded tissues from primary tumor and positive lymph node from 31 patients with mCRC were analyzed using ddPCR and Sanger sequencing. KRAS status of primary tumors was known; however, the mutation status of lymph nodes was not detected previously. From 31 samples of primary tumors, our results corresponded to results from IVD kit in 30 cases. For one patient, ddPCR detected KRAS mutation in comparison with negative result of the IVD kit. In the samples of metastatic infiltrated LNs, ddPCR detected 16 samples as a WT KRAS and 15 lymph nodes showed positivity for KRAS mutation, whereby Sanger sequencing found KRAS mutations in 8 cases only. We also found two cases where genetic conditions of KRAS gene differed between primary tumor and infiltrated lymph node, both "low-grade" adenocarcinoma. Our study approved that ddPCR method is adequate technique with high sensitivity and in the future may be used as a diagnostic tool for evaluation of KRAS mutations, especially in infiltrated LNs of patients with mCRC.
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Fiedler D, Heselmeyer-Haddad K, Hirsch D, Hernandez LS, Torres I, Wangsa D, Hu Y, Zapata L, Rueschoff J, Belle S, Ried T, Gaiser T. Single-cell genetic analysis of clonal dynamics in colorectal adenomas indicates CDX2 gain as a predictor of recurrence. Int J Cancer 2018; 144:1561-1573. [PMID: 30229897 DOI: 10.1002/ijc.31869] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 07/11/2018] [Accepted: 08/13/2018] [Indexed: 12/19/2022]
Abstract
Colorectal adenomas are common precancerous lesions with the potential for malignant transformation to colorectal adenocarcinoma. Endoscopic polypectomy provides an opportunity for cancer prevention; however, recurrence rates are high. We collected formalin-fixed paraffin-embedded tissue of 15 primary adenomas with recurrence, 15 adenomas without recurrence, and 14 matched pair samples (primary adenoma and the corresponding recurrent adenoma). The samples were analysed by array-comparative genomic hybridisation (aCGH) and single-cell multiplex interphase fluorescence in situ hybridisation (miFISH) to understand clonal evolution, to examine the dynamics of copy number alterations (CNAs) and to identify molecular markers for recurrence prediction. The miFISH probe panel consisted of 14 colorectal carcinogenesis-relevant genes (COX2, PIK3CA, APC, CLIC1, EGFR, MYC, CCND1, CDX2, CDH1, TP53, HER2, SMAD7, SMAD4 and ZNF217), and a centromere probe (CEP10). The aCGH analysis confirmed the genetic landscape typical for colorectal tumorigenesis, that is, CNAs of chromosomes 7, 13q, 18 and 20q. Focal aberrations (≤10 Mbp) were mapped to chromosome bands 6p22.1-p21.33 (33.3%), 7q22.1 (31.4%) and 16q21 (29.4%). MiFISH detected gains of EGFR (23.6%), CDX2 (21.8%) and ZNF217 (18.2%). Most adenomas exhibited a major clone population which was accompanied by multiple smaller clone populations. Gains of CDX2 were exclusively seen in primary adenomas with recurrence (25%) compared to primary adenomas without recurrence (0%). Generation of phylogenetic trees for matched pair samples revealed four distinct patterns of clonal dynamics. In conclusion, adenoma development and recurrence are complex genetic processes driven by multiple CNAs whose evaluations by miFISH, with emphasis on CDX2, might serve as a predictor of recurrence.
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Affiliation(s)
- David Fiedler
- Institute of Pathology, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Kerstin Heselmeyer-Haddad
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Daniela Hirsch
- Institute of Pathology, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Leanora S Hernandez
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Irianna Torres
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Darawalee Wangsa
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Yue Hu
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Luis Zapata
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom.,Genomic and Epigenomic Variation in Disease Group, Centre for Genomic Regulation (CGR), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Sebastian Belle
- Department of Internal Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,Central Interdisciplinary Endoscopy Unit, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Thomas Ried
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Timo Gaiser
- Institute of Pathology, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
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Molinari C, Marisi G, Passardi A, Matteucci L, De Maio G, Ulivi P. Heterogeneity in Colorectal Cancer: A Challenge for Personalized Medicine? Int J Mol Sci 2018; 19:E3733. [PMID: 30477151 PMCID: PMC6321493 DOI: 10.3390/ijms19123733] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/19/2018] [Accepted: 11/20/2018] [Indexed: 12/15/2022] Open
Abstract
High inter-patient variability and high spatial heterogeneity are features of colorectal cancer (CRC). This may influence the molecular characterization of tumor tissue, now mandatory for patients with metastatic CRC who are candidates for treatment with an anti-EGFR mAb, as false-negative results can occur, leading to non optimal therapy. Moreover, temporal molecular heterogeneity during treatment is known to influence the response to therapy and prognosis. We present a literature overview of advances made in characterizing molecular heterogeneity in CRC, underlining that the analysis of liquid biopsy could represent an efficient non-invasive tool to overcome the problem. We believe that understanding CRC heterogeneity is fundamental for a more accurate diagnosis, for selecting the best targets to ensure prolonged antitumor response, and for monitoring minimal residual disease and the onset of resistance to therapy, all essential components of successful personalized treatment.
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Affiliation(s)
- Chiara Molinari
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy.
| | - Giorgia Marisi
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy.
| | - Alessandro Passardi
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy.
| | - Laura Matteucci
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy.
| | - Giulia De Maio
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy.
| | - Paola Ulivi
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy.
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35
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Blank A, Roberts DE, Dawson H, Zlobec I, Lugli A. Tumor Heterogeneity in Primary Colorectal Cancer and Corresponding Metastases. Does the Apple Fall Far From the Tree? Front Med (Lausanne) 2018; 5:234. [PMID: 30234115 PMCID: PMC6128217 DOI: 10.3389/fmed.2018.00234] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/01/2018] [Indexed: 01/05/2023] Open
Abstract
Colorectal cancer harbors tremendous heterogeneity, with temporal and spatial differences in genetic mutations, epigenetic regulation, and tumor microenvironment. Analyzing the distribution and frequency of genetic, epigenetic, and microenvironment differences within a given tumor and between different sites of a metastatic tumor has been used as a powerful tool to investigate tumorigenesis, tumor progression, and to yield insight into various models of tumor development. A better understanding of tumor heterogeneity would have tremendous clinical relevance, which may manifest most clearly when genetic analyses to inform treatment decisions are performed on a very limited sample of a large tumor. This review summarizes the current concepts of tumor heterogeneity, with a focus on primary colorectal cancers and their corresponding metastases as well as potential clinical implications.
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Affiliation(s)
- Annika Blank
- Department of Pathology, University of California, San Francisco, San Francisco, CA, United States.,Clinical Pathology Division, Institute of Pathology, University of Bern, Bern, Switzerland
| | - Daniel Edward Roberts
- Department of Pathology, University of California, San Francisco, San Francisco, CA, United States
| | - Heather Dawson
- Clinical Pathology Division, Institute of Pathology, University of Bern, Bern, Switzerland
| | - Inti Zlobec
- Translational Research Unit, Institute of Pathology, University of Bern, Bern, Switzerland
| | - Alessandro Lugli
- Clinical Pathology Division, Institute of Pathology, University of Bern, Bern, Switzerland
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36
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Fogelman D, Cubillo A, García-Alfonso P, Mirón MLL, Nemunaitis J, Flora D, Borg C, Mineur L, Vieitez JM, Cohn A, Saylors G, Assad A, Switzky J, Zhou L, Bendell J. Randomized, double-blind, phase two study of ruxolitinib plus regorafenib in patients with relapsed/refractory metastatic colorectal cancer. Cancer Med 2018; 7:5382-5393. [PMID: 30123970 PMCID: PMC6246927 DOI: 10.1002/cam4.1703] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 07/02/2018] [Accepted: 07/03/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The Janus kinase/signal transducer and activator of transcription (JAK-STAT) signaling pathway plays a key role in the systemic inflammatory response in many cancers, including colorectal cancer (CRC). This study evaluated the addition of ruxolitinib, a potent JAK1/2 inhibitor, to regorafenib in patients with relapsed/refractory metastatic CRC. METHODS In this two-part, multicenter, phase 2 study, eligible adult patients had metastatic adenocarcinoma of the colon or rectum; an Eastern Cooperative Oncology Group performance status of 0-2; received fluoropyrimidine, oxaliplatin, and irinotecan-based chemotherapy, an anti-vascular endothelial growth factor therapy (if no contraindication); and if KRAS wild-type (and no contraindication), an anti-epidermal growth factor receptor therapy; and progressed following the last administration of approved therapy. Patients who received previous treatment with regorafenib, had an established cardiac or gastrointestinal disease, or had an active infection requiring treatment were excluded. The study was conducted in 95 sites in North America, European Union, Asia Pacific, and Israel. After an open-label, safety run-in phase (part 1; ruxolitinib 20 mg twice daily [BID] plus regorafenib 160 mg once daily [QD]), the double-blind, randomized phase (part 2) was conducted wherein patients were randomized 1:1 to receive ruxolitinib 15 mg BID plus regorafenib 160 mg QD [ruxolitinib group] or placebo plus regorafenib 160 mg QD [placebo group]. Part 2 included substudy 1 (patients with high systemic inflammation, ie, C-reactive protein [CRP] >10 mg/L) and substudy 2 (patients with low systemic inflammation, ie, CRP ≤10 mg/L); the primary endpoint was overall survival (OS). RESULTS The study was terminated early; substudy 1 was terminated for futility at interim analysis and substudy 2 was terminated per sponsor decision. Ruxolitinib 20 mg BID was well tolerated in the safety run-in (n = 11). Overall, 396 patients were randomized (substudy 1: n = 175 [ruxolitinib group, n = 87; placebo group, n = 88]; substudy 2: n = 221 [ruxolitinib group, n = 110; placebo group, n = 111]). There was no significant difference in OS or progression-free survival (PFS) between treatments in substudy 1 (OS: hazard ratio [HR] = 1.040 [95% confidence interval: 0.725-1.492]; PFS: HR = 1.004 [0.724-1.391]) and substudy 2 (OS: HR = 0.767 [0.478-1.231]; PFS: HR = 0.787 [0.576-1.074]). The most common hematologic adverse event was anemia. No new safety signals with ruxolitinib were identified. CONCLUSIONS Although addition of ruxolitinib to regorafenib did not show increased safety concerns in patients with relapsed/refractory metastatic CRC, this combination did not improve OS/PFS vs. regorafenib plus placebo.
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Affiliation(s)
- David Fogelman
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | | | - John Nemunaitis
- University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
| | | | | | | | - Jose M Vieitez
- Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Allen Cohn
- Rocky Mountain Cancer Centers, Denver, Colorado
| | - Gene Saylors
- Charleston Hematology Oncology Associates, Charleston, South Carolina
| | | | | | - Li Zhou
- Incyte Corporation, Wilmington, Delaware
| | - Johanna Bendell
- Sarah Cannon Research Institute/Tennessee Oncology, Nashville, Tennessee
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37
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Saito T, Niida A, Uchi R, Hirata H, Komatsu H, Sakimura S, Hayashi S, Nambara S, Kuroda Y, Ito S, Eguchi H, Masuda T, Sugimachi K, Tobo T, Nishida H, Daa T, Chiba K, Shiraishi Y, Yoshizato T, Kodama M, Okimoto T, Mizukami K, Ogawa R, Okamoto K, Shuto M, Fukuda K, Matsui Y, Shimamura T, Hasegawa T, Doki Y, Nagayama S, Yamada K, Kato M, Shibata T, Mori M, Aburatani H, Murakami K, Suzuki Y, Ogawa S, Miyano S, Mimori K. A temporal shift of the evolutionary principle shaping intratumor heterogeneity in colorectal cancer. Nat Commun 2018; 9:2884. [PMID: 30038269 PMCID: PMC6056524 DOI: 10.1038/s41467-018-05226-0] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 06/22/2018] [Indexed: 12/17/2022] Open
Abstract
Advanced colorectal cancer harbors extensive intratumor heterogeneity shaped by neutral evolution; however, intratumor heterogeneity in colorectal precancerous lesions has been poorly studied. We perform multiregion whole-exome sequencing on ten early colorectal tumors, which contained adenoma and carcinoma in situ. By comparing with sequencing data from advanced colorectal tumors, we show that the early tumors accumulate a higher proportion of subclonal driver mutations than the advanced tumors, which is highlighted by subclonal mutations in KRAS and APC. We also demonstrate that variant allele frequencies of subclonal mutations tend to be higher in early tumors, suggesting that the subclonal mutations are subject to selective sweep in early tumorigenesis while neutral evolution is dominant in advanced ones. This study establishes that the evolutionary principle underlying intratumor heterogeneity shifts from Darwinian to neutral evolution during colorectal tumor progression.
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Affiliation(s)
- Tomoko Saito
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
- Department of Gastroenterology, Oita University Hospital, 1-1 Idaigaoka, Yufu, 879-5593, Japan
| | - Atsushi Niida
- Division of Health Medical Computational Science, Health Intelligence Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Ryutaro Uchi
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
| | - Hidenari Hirata
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
| | - Hisateru Komatsu
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
| | - Shotaro Sakimura
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
| | - Shuto Hayashi
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Sho Nambara
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
| | - Yosuke Kuroda
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
| | - Shuhei Ito
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
| | - Hidetoshi Eguchi
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
| | - Takaaki Masuda
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
| | - Keishi Sugimachi
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
| | - Taro Tobo
- Department of Pathology, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
| | - Haruto Nishida
- Department of Diagnostic Pathology, Oita University Hospital, 1-1 Idaigaoka, Yufu, 879-5593, Japan
| | - Tsutomu Daa
- Department of Diagnostic Pathology, Oita University Hospital, 1-1 Idaigaoka, Yufu, 879-5593, Japan
| | - Kenichi Chiba
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Yuichi Shiraishi
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Tetsuichi Yoshizato
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Kyoto-shi Sakyo-ku, Kyoto, 606-8501, Japan
| | - Masaaki Kodama
- Department of Gastroenterology, Oita University Hospital, 1-1 Idaigaoka, Yufu, 879-5593, Japan
| | - Tadayoshi Okimoto
- Department of Gastroenterology, Oita University Hospital, 1-1 Idaigaoka, Yufu, 879-5593, Japan
| | - Kazuhiro Mizukami
- Department of Gastroenterology, Oita University Hospital, 1-1 Idaigaoka, Yufu, 879-5593, Japan
| | - Ryo Ogawa
- Department of Gastroenterology, Oita University Hospital, 1-1 Idaigaoka, Yufu, 879-5593, Japan
| | - Kazuhisa Okamoto
- Department of Gastroenterology, Oita University Hospital, 1-1 Idaigaoka, Yufu, 879-5593, Japan
| | - Mitsutaka Shuto
- Department of Gastroenterology, Oita University Hospital, 1-1 Idaigaoka, Yufu, 879-5593, Japan
| | - Kensuke Fukuda
- Department of Gastroenterology, Oita University Hospital, 1-1 Idaigaoka, Yufu, 879-5593, Japan
| | - Yusuke Matsui
- Division of Systems Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Teppei Shimamura
- Division of Systems Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Takanori Hasegawa
- Division of Health Medical Data Science, Health Intelligence Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Yuichiro Doki
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, 565-0871, Japan
| | - Satoshi Nagayama
- Gastroenterological Center, Department of Gastroenterological Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto, Tokyo, 135-8550, Japan
| | - Kazutaka Yamada
- Department of Surgery, Takano Hospital, 4-2-88 Obiyama, Chuo-ku, Kumamoto, 862-0924, Japan
| | - Mamoru Kato
- Department of Bioinformatics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Tatsuhiro Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Masaki Mori
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, 565-0871, Japan
| | - Hiroyuki Aburatani
- Genome Science Division, Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan
| | - Kazunari Murakami
- Department of Gastroenterology, Oita University Hospital, 1-1 Idaigaoka, Yufu, 879-5593, Japan
| | - Yutaka Suzuki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba, 277-8561, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Kyoto-shi Sakyo-ku, Kyoto, 606-8501, Japan
| | - Satoru Miyano
- Division of Health Medical Computational Science, Health Intelligence Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Koshi Mimori
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan.
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Sebagh M, Bosselut N, Santos AD, Allard MA, Ruiz A, Saffroy R, Cherqui D, Vibert E, Castaing D, Adam R, Cunha AS, Lemoine A. Rare genetic heterogeneity within single tumor discovered for the first time in colorectal liver metastases after liver resection. Oncotarget 2018; 9:21921-21929. [PMID: 29774112 PMCID: PMC5955166 DOI: 10.18632/oncotarget.25119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 03/21/2018] [Indexed: 02/07/2023] Open
Abstract
Effective individualized treatment of patients with colorectal liver metastases (CLM) requires tumor genotyping, usually based on the analysis of one single sample per patient. Therapy failure may partially be explained by sampling errors and/or intratumoral genetic heterogeneity. We aimed to demonstrate intratumoral genetic heterogeneity in CLM and enable pathologists to select tumor tissue for genotyping. All the tumors of 86 patients who underwent liver resection for a single CLM were reviewed. Of the 86 patients, 66 patients received chemotherapy and 20 patients did not receive chemotherapy before liver resection. All the tumor areas sampled were analyzed for KRAS, BRAF, PIK3CA, and NRAS mutations. The mutational status was tested in 74 cases, 7 cases had no tumoral cells due to complete responses and 5 blocks were unavailable. Of the 59/74 CLM with > 1 sample, 56 showed the same mutational status between the samples. The remaining 3 cases (5% of all cases) showed genetic heterogeneity for KRAS in 2 and BRAF in 1 patient. Genetic heterogeneity correlated with lower rate of viable tumor cells (p=0.009) and higher rate of mucin pools (p=0.013). We demonstrate for the first time the existence of genetic intratumoral heterogeneity in 5% of CLM. In routine practice, this low incidence does not require the genotyping of additional tumor samples. The correlation between the genetic heterogeneity and some histological components of the CLM should be verified by further in situ mutation assay.
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Affiliation(s)
- Mylène Sebagh
- AP-HP Hôpital Paul Brousse, Laboratoire d'Anatomie Pathologique, Villejuif, France.,Inserm, Unité 1193, Université Paris-Saclay, Villejuif, France.,Univ Paris-Sud, UMR-S 1193, Université Paris-Saclay, Villejuif, France.,DHU Hepatinov, Villejuif, France
| | - Nelly Bosselut
- Inserm, Unité 1193, Université Paris-Saclay, Villejuif, France.,Univ Paris-Sud, UMR-S 1193, Université Paris-Saclay, Villejuif, France.,DHU Hepatinov, Villejuif, France.,AP-HP Hôpital Paul Brousse, Département d'Oncogénétique, Villejuif, France
| | - Alexandre Dos Santos
- Inserm, Unité 1193, Université Paris-Saclay, Villejuif, France.,Univ Paris-Sud, UMR-S 1193, Université Paris-Saclay, Villejuif, France.,DHU Hepatinov, Villejuif, France
| | - Marc-Antoine Allard
- Inserm, Unité 1193, Université Paris-Saclay, Villejuif, France.,Univ Paris-Sud, UMR-S 1193, Université Paris-Saclay, Villejuif, France.,DHU Hepatinov, Villejuif, France.,AP-HP Hôpital Paul-Brousse, Centre Hépato-Biliaire, Villejuif, France.,Inserm, Unité 935, Université Paris-Saclay, Villejuif, France
| | - Aldrick Ruiz
- AP-HP Hôpital Paul-Brousse, Centre Hépato-Biliaire, Villejuif, France.,University Medical Center Utrecht, Department of Surgery, Utrecht, The Netherlands
| | - Raphaël Saffroy
- Inserm, Unité 1193, Université Paris-Saclay, Villejuif, France.,Univ Paris-Sud, UMR-S 1193, Université Paris-Saclay, Villejuif, France.,DHU Hepatinov, Villejuif, France.,AP-HP Hôpital Paul Brousse, Département d'Oncogénétique, Villejuif, France
| | - Daniel Cherqui
- Inserm, Unité 1193, Université Paris-Saclay, Villejuif, France.,Univ Paris-Sud, UMR-S 1193, Université Paris-Saclay, Villejuif, France.,DHU Hepatinov, Villejuif, France.,AP-HP Hôpital Paul-Brousse, Centre Hépato-Biliaire, Villejuif, France
| | - Eric Vibert
- Inserm, Unité 1193, Université Paris-Saclay, Villejuif, France.,Univ Paris-Sud, UMR-S 1193, Université Paris-Saclay, Villejuif, France.,DHU Hepatinov, Villejuif, France.,AP-HP Hôpital Paul-Brousse, Centre Hépato-Biliaire, Villejuif, France
| | - Denis Castaing
- Inserm, Unité 1193, Université Paris-Saclay, Villejuif, France.,Univ Paris-Sud, UMR-S 1193, Université Paris-Saclay, Villejuif, France.,DHU Hepatinov, Villejuif, France.,AP-HP Hôpital Paul-Brousse, Centre Hépato-Biliaire, Villejuif, France
| | - René Adam
- Univ Paris-Sud, UMR-S 1193, Université Paris-Saclay, Villejuif, France.,DHU Hepatinov, Villejuif, France.,AP-HP Hôpital Paul-Brousse, Centre Hépato-Biliaire, Villejuif, France.,Inserm, Unité 935, Université Paris-Saclay, Villejuif, France
| | - Antonio Sa Cunha
- Inserm, Unité 1193, Université Paris-Saclay, Villejuif, France.,Univ Paris-Sud, UMR-S 1193, Université Paris-Saclay, Villejuif, France.,DHU Hepatinov, Villejuif, France.,AP-HP Hôpital Paul-Brousse, Centre Hépato-Biliaire, Villejuif, France
| | - Antoinette Lemoine
- Inserm, Unité 1193, Université Paris-Saclay, Villejuif, France.,Univ Paris-Sud, UMR-S 1193, Université Paris-Saclay, Villejuif, France.,DHU Hepatinov, Villejuif, France.,AP-HP Hôpital Paul Brousse, Département d'Oncogénétique, Villejuif, France
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39
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Parasido EM, Silvestri A, Canzonieri V, Belluco C, Diodoro MG, Milione M, Melotti F, De Maria R, Liotta L, Petricoin EF, Pierobon M. Protein drug target activation homogeneity in the face of intra-tumor heterogeneity: implications for precision medicine. Oncotarget 2018; 8:48534-48544. [PMID: 28159918 PMCID: PMC5564706 DOI: 10.18632/oncotarget.14019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 12/09/2016] [Indexed: 12/17/2022] Open
Abstract
Introduction: Recent studies indicated tumors may be comprised of heterogeneous molecular subtypes and incongruent molecular portraits may emerge if different areas of the tumor are sampled. This study explored the impact of intra-tumoral heterogeneity in terms of activation/phosphorylation of FDA approved drug targets and downstream kinase substrates. Material and methods: Two independent sets of liver metastases from colorectal cancer were used to evaluate protein kinase-driven signaling networks within different areas using laser capture microdissection and reverse phase protein array. Results: Unsupervised hierarchical clustering analysis indicated that the signaling architecture and activation of the MAPK and AKT-mTOR pathways were consistently maintained within different regions of the same biopsy. Intra-patient variability of the MAPK and AKT-mTOR pathway were <1.06 fold change, while inter-patients variability reached fold change values of 5.01. Conclusions: Protein pathway activation mapping of enriched tumor cells obtained from different regions of the same tumor indicated consistency and robustness independent of the region sampled. This suggests a dominant protein pathway network may be activated in a high percentage of the tumor cell population. Given the genomic intra-tumoral variability, our data suggest that protein/phosphoprotein signaling measurements should be integrated with genomic analysis for precision medicine based analysis.
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Affiliation(s)
- Erika Maria Parasido
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA.,Department of Experimental Oncology, CRO-National Cancer Institute, Aviano, Italy
| | - Alessandra Silvestri
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | | | - Claudio Belluco
- Department of Surgical Oncology, CRO-National Cancer Institute, Aviano, Italy
| | | | - Massimo Milione
- Department of Pathology, Fondazione IRCCS Istituto Nazionale Tumori, Milano, Italy
| | - Flavia Melotti
- Department of Pathology, Fondazione IRCCS Istituto Nazionale Tumori, Milano, Italy
| | - Ruggero De Maria
- Department of Pathology, Sacred Heart Catholic University of Rome, Roma, Italy
| | - Lance Liotta
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Emanuel F Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
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40
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Abstract
Our understanding of the genetics of colorectal cancer has changed dramatically over recent years. Colorectal cancer can be classified in multiple different ways. Along with the advent of whole-exome sequencing, we have gained an understanding of the scale of the genetic changes found in sporadic colorectal cancer. We now know that there are multiple pathways that are commonly involved in the evolution of colorectal cancer including Wnt/β-catenin, RAS, EGFR, and PIK3 kinase. Another recent leap in our understanding of colorectal cancer genetics is the recognition that many, if not all tumors, are actually genetically heterogeneous within individual tumors and also between tumors. Recent research has revealed the prognostic and possibly therapeutic implications of various specific mutations, including specific mutations in BRAF and KRAS . There is increasing interest in the use of mutation testing for screening and surveillance through stool and circulating DNA testing. Recent advances in translational research in colorectal cancer genetics are dramatically changing our understanding of colorectal cancer and will likely change therapy and surveillance in the near future.
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Affiliation(s)
- Karin M Hardiman
- Division of Colon and Rectal Surgery, Department of Surgery, University of Michigan, Ann Arbor, Michigan
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41
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Sagaert X, Vanstapel A, Verbeek S. Tumor Heterogeneity in Colorectal Cancer: What Do We Know So Far? Pathobiology 2018; 85:72-84. [PMID: 29414818 DOI: 10.1159/000486721] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 01/10/2018] [Indexed: 12/17/2022] Open
Abstract
Colorectal cancer is not one disease but rather a collection of neoplastic diseases. Due to heterogeneity in the disease biology, therapy response, and prognosis, extensive disease stratification is required. Therefore, TNM stage, microsatellite status, tumor grade, lymphovascular invasion, and other parameters are assessed in the pathology report to indicate the extent and prognosis of the disease. The mutation status of KRAS, BRAF, and NRAS is also investigated in a metastatic context to predict the response to anti-EGFR therapy. Recently, 4 distinct molecular subtypes of colorectal cancer have been described that have both prognostic and therapeutic relevance. In addition, characterization of the inflammatory infiltrate revealed major differences in the amount and location of inflammatory cells in distinct colorectal tumor types. Together, all of these parameters help to stratify patients into different therapeutic and prognostic subgroups. However, this stratification is not unambiguous since tumors often display intratumoral heterogeneity, whereby several subpopulations within one tumor show differences in morphology, inflammatory infiltrate, mutational status, or gene expression profile. This article gives an overview of all of the current known data with regard to tumor heterogeneity at both inter- and intratumoral levels.
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42
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Büttner J, Jöhrens K, Klauschen F, Hummel M, Lenze D, Saeger W, Lehmann A. Intratumoral morphological heterogeneity can be an indicator of genetic heterogeneity in colorectal cancer. Exp Mol Pathol 2018; 104:76-81. [DOI: 10.1016/j.yexmp.2018.01.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 01/10/2018] [Indexed: 12/24/2022]
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43
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Nelson AC, Boone J, Cartwright D, Thyagarajan B, Kincaid R, Lambert AP, Karnuth K, Henzler C, Yohe S. Optimal detection of clinically relevant mutations in colorectal carcinoma: sample pooling overcomes intra-tumoral heterogeneity. Mod Pathol 2018; 31:343-349. [PMID: 29027537 DOI: 10.1038/modpathol.2017.120] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 08/04/2017] [Accepted: 08/05/2017] [Indexed: 11/09/2022]
Abstract
Intra-tumoral genomic heterogeneity is a well-established biologic property of human malignancies with emerging roles in cancer progression and therapy resistance. However, its impact on the clinical utility of genomic testing in patient management remains unclear. Furthermore, best practices to account for heterogeneity in the provision of highly accurate, clinically valid molecular testing have yet to be firmly established. Genomic biomarkers for the management of colorectal carcinoma are both well-established (ie, KRAS, NRAS) and emerging (BRAF, PIK3CA, and others) in respect to therapy selection and clinical trial eligibility. Critically, standard colorectal carcinoma management requires the exclusion of KRAS and NRAS mutations; thus optimal procedures to control for potential intra-tumoral heterogeneity are clinically important. Here, we assessed heterogeneity among three intra-tumoral sites within 99 colorectal carcinomas cases on a CLIA-validated oncology next generation sequencing assay and examined whether a pooling strategy overcame any discordant results. Overall, 11% of cases demonstrated discordant mutation results between sites; 2% of cases were discrepant for mutations within RAS genes while the remainder was discrepant in PIK3CA. Half of the discrepant cases were associated with borderline tumor cellularity assessment. Further, a sample pooling strategy across all three sites successfully detected the relevant mutation in all but one case. Our results indicate that intra-tumoral genomic heterogeneity of clinically relevant genes within colorectal carcinoma is a relatively infrequent occurrence and that a simple strategy to pool DNA from several tumor sites with adequate cellularity minimizes the risk of false negative results even further to ensure optimal patient management.
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Affiliation(s)
- Andrew C Nelson
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Jamie Boone
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - David Cartwright
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Bharat Thyagarajan
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Robyn Kincaid
- Molecular Diagnostics Laboratory, M Health, Minneapolis, MN, USA
| | - Aaron P Lambert
- Molecular Diagnostics Laboratory, M Health, Minneapolis, MN, USA
| | - Kylene Karnuth
- Molecular Diagnostics Laboratory, M Health, Minneapolis, MN, USA
| | - Christine Henzler
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Sophia Yohe
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
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44
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Sebagh M, Allard MA, Bosselut N, Dao M, Vibert E, Lewin M, Lemoine A, Cherqui D, Adam R, Sa Cunha A. Evidence of intermetastatic heterogeneity for pathological response and genetic mutations within colorectal liver metastases following preoperative chemotherapy. Oncotarget 2017; 7:21591-600. [PMID: 26943031 PMCID: PMC5008308 DOI: 10.18632/oncotarget.7809] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 01/29/2016] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND In patients receiving preoperative chemotherapy, colorectal liver metastases (CLM) are expected to demonstrate a similar behaviour because of similar organ microenvironment and tumour cell chemosensitivity. We focused on the occurrence of pathological and genetic heterogeneity within CLM. METHODS Patients resected for multiple CLM between 2004 and 2011 after > three cycles of chemotherapy were included. Pathological heterogeneity was arbitrarily defined as a > 50% difference in the percentage of remaining tumour cells between individual CLM. In patients with pathological heterogeneity, the mutational genotyping (KRAS, NRAS, BRAF and PIK3CA) was determined from the most heterogeneous CLM. RESULTS Pathological heterogeneity was observed in 31 of 157 patients with multiple CLM (median = 4, range, 2-32) (19.7%). In 72.4% of them, we found a concordance of the mutation status between the paired CLM: both wild-type in 55%, and both mutated in 17.2%. We observed a discordance of the mutation status of 27.6% between CLM: one mutated and the other wild-type. The mutated CLM was the less florid one in 75% of patients with genetic heterogeneity. CONCLUSIONS Pathological heterogeneity is present in 19.7% of patients with multiple CLM. Genetic heterogeneity is present in 27.6% of patients with pathological heterogeneity. Heterogeneity could refine guide management for tissue sampling.
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Affiliation(s)
- Mylène Sebagh
- AP-HP Hôpital Paul Brousse, Department of Pathology, Villejuif, France.,Inserm U1193, Paris-Sud University, Villejuif, France
| | - Marc-Antoine Allard
- AP-HP Hôpital Paul Brousse, Hepatobiliary Centre, Villejuif, France.,Inserm U935, Paris-Sud University, Villejuif, France
| | - Nelly Bosselut
- Inserm U1193, Paris-Sud University, Villejuif, France.,AP-HP Hôpital Paul Brousse, Department of Oncogenetics, Villejuif, France
| | - Myriam Dao
- AP-HP Hôpital Paul Brousse, Department of Pathology, Villejuif, France
| | - Eric Vibert
- Inserm U1193, Paris-Sud University, Villejuif, France.,AP-HP Hôpital Paul Brousse, Hepatobiliary Centre, Villejuif, France
| | - Maïté Lewin
- AP-HP Hôpital Paul Brousse, Radiology, Villejuif, France
| | - Antoinette Lemoine
- Inserm U1193, Paris-Sud University, Villejuif, France.,AP-HP Hôpital Paul Brousse, Department of Oncogenetics, Villejuif, France
| | - Daniel Cherqui
- Inserm U1193, Paris-Sud University, Villejuif, France.,AP-HP Hôpital Paul Brousse, Hepatobiliary Centre, Villejuif, France
| | - René Adam
- AP-HP Hôpital Paul Brousse, Hepatobiliary Centre, Villejuif, France.,Inserm U935, Paris-Sud University, Villejuif, France
| | - Antonio Sa Cunha
- AP-HP Hôpital Paul Brousse, Hepatobiliary Centre, Villejuif, France.,Inserm U935, Paris-Sud University, Villejuif, France
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45
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Sugai T, Eizuka M, Takahashi Y, Fukagawa T, Habano W, Yamamoto E, Akasaka R, Otuska K, Matsumoto T, Suzuki H. Molecular subtypes of colorectal cancers determined by PCR-based analysis. Cancer Sci 2017; 108:427-434. [PMID: 28083970 PMCID: PMC5378279 DOI: 10.1111/cas.13164] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 12/05/2016] [Accepted: 01/02/2017] [Indexed: 12/15/2022] Open
Abstract
Tumor tissue consists of a heterogeneous cell population. The allelic imbalance (AI) ratio, determined in isolated tumor glands, is a good index of tumor heterogeneity. However, associations of the patterns of AI and microsatellite instability (MSI) development, observed in most cases of colorectal cancer (CRC), with tumor progression have not been reported previously. In this study, we examined whether CRC genetic profiles stratified by a combination of the AI ratio and MSI facilitate categorization of CRC, and whether these genetic profiles are associated with specific molecular alterations in CRC. A crypt isolation method was used to isolate DNA from tumors and normal glands obtained from 147 sporadic CRCs. AI and MSI statuses were determined using PCR‐based microsatellite analysis and stratified based on AI ratio and MSI status. DNA methylation status (high methylation, intermediate methylation and low methylation status and mutations in KRAS,BRAF, and TP53 were examined. In addition, mucin markers were immunostained. Based on this analysis, four subgroups were categorized. Subgroup 1 was characterized by a high MSI status and BRAF mutation; subgroup 2 was closely associated with a high AI ratio, which accumulated during the early phases of colorectal carcinogenesis, and TP53 mutation; subgroup 3 was associated with a low AI ratio, seen during the later phases of colorectal carcinogenesis, and KRAS mutation; and subgroup 4 was defined as a minor subgroup. These results confirmed that classification of distinct molecular profiles provides important insights into colorectal carcinogenesis.
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Affiliation(s)
- Tamotsu Sugai
- Department of Molecular Diagnostic Pathology, School of Pharmacy, Iwate Medical University, Morioka, Japan
| | - Makoto Eizuka
- Department of Molecular Diagnostic Pathology, School of Pharmacy, Iwate Medical University, Morioka, Japan
| | - Yayoi Takahashi
- Department of Molecular Diagnostic Pathology, School of Pharmacy, Iwate Medical University, Morioka, Japan
| | - Tomoyuki Fukagawa
- Department of Molecular Diagnostic Pathology, School of Pharmacy, Iwate Medical University, Morioka, Japan
| | - Wataru Habano
- Pharmacodynamics and Molecular Genetics, School of Pharmacy, Iwate Medical University, Morioka, Japan
| | - Eiichiro Yamamoto
- Department of Molecular Biology, Sapporo Medical University, Sapporo, Japan
| | - Risaburo Akasaka
- Division of Gastroenterology, Department of Internal Medicine, School of Pharmacy, Iwate Medical University, Morioka, Japan
| | - Kouki Otuska
- Department of Surgery, School of Medicine, School of Pharmacy, Iwate Medical University, Morioka, Japan
| | - Takayuki Matsumoto
- Division of Gastroenterology, Department of Internal Medicine, School of Pharmacy, Iwate Medical University, Morioka, Japan
| | - Hiromu Suzuki
- Department of Molecular Biology, Sapporo Medical University, Sapporo, Japan
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46
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Resistance to mTORC1 Inhibitors in Cancer Therapy: From Kinase Mutations to Intratumoral Heterogeneity of Kinase Activity. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2017; 2017:1726078. [PMID: 28280521 PMCID: PMC5322438 DOI: 10.1155/2017/1726078] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 01/22/2017] [Indexed: 01/19/2023]
Abstract
Targeting mTORC1 has been thoroughly explored in cancer therapy. Following encouraging preclinical studies, mTORC1 inhibitors however failed to provide substantial benefits in cancer patients. Several resistance mechanisms have been identified including mutations of mTOR and activation of alternate proliferation pathways. Moreover, emerging evidence discloses intratumoral heterogeneity of mTORC1 activity that further contributes to a reduced anticancer efficacy of mTORC1 inhibitors. Genetic heterogeneity as well as heterogeneous conditions of the tumor environment such as hypoxia profoundly modifies mTORC1 activity in tumors and hence influences the response of tumors to mTORC1 inhibitors. Intriguingly, the heterogeneity of mTORC1 activity also occurs towards its substrates at the single cell level, as mutually exclusive pattern of activation of mTORC1 downstream effectors has been reported in tumors. After briefly describing mTORC1 biology and the use of mTORC1 inhibitors in patients, this review will give an overview on concepts of resistance to mTORC1 inhibition in cancer with a particular focus on intratumoral heterogeneity of mTORC1 activity.
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47
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Fujiyoshi K, Yamamoto G, Takahashi A, Arai Y, Yamada M, Kakuta M, Yamaguchi K, Akagi Y, Nishimura Y, Sakamoto H, Akagi K. High concordance rate of KRAS/BRAF mutations and MSI-H between primary colorectal cancer and corresponding metastases. Oncol Rep 2016; 37:785-792. [PMID: 28000889 DOI: 10.3892/or.2016.5323] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 11/28/2016] [Indexed: 12/15/2022] Open
Abstract
Genetic testing is needed for the treatment of colorectal cancer (CRC), especially molecular-targeted therapy. The effects of anti-EGFR therapy and prognosis are affected by the presence of KRAS mutations. However, whether primary CRC or metastatic tissues are appropriate in the analysis is still unclear. In the present study, we assessed the concordance of KRAS/BRAF mutation status and microsatellite instability (MSI) in primary CRC and corresponding metastases. This study enrolled 457 patients with surgically resected primary and corresponding metastatic CRC (499 synchronous metastases and 57 metachronous metastases) and seven local recurrences, and KRAS/BRAF mutation and MSI status were analysed for these tumours. The concordance rates of KRAS mutation, BRAF mutation, wild-type, MSI-H and MSS between primary CRC and corresponding metastases were 93.9% (214/228), 100% (30/30), 99.3% (304/306), 87.5% (21/24) and 100% (137/137), respectively. These high concordance rates were not different between synchronous and metachronous metastases. In conclusion, a high concordance of KRAS/BRAF mutation status and MSI status was observed between primary CRC and corresponding metastases in this study. Either primary CRC or metastatic tissues can be used for testing KRAS/BRAF mutation status and MSI status.
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Affiliation(s)
- Kenji Fujiyoshi
- Division of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama 362-0806, Japan
| | - Gou Yamamoto
- Division of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama 362-0806, Japan
| | - Akemi Takahashi
- Division of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama 362-0806, Japan
| | - Yoshiko Arai
- Division of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama 362-0806, Japan
| | - Mina Yamada
- Division of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama 362-0806, Japan
| | - Miho Kakuta
- Division of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama 362-0806, Japan
| | - Kensei Yamaguchi
- Department of Gastrointestinal Oncology, Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan
| | - Yoshito Akagi
- Department of Surgery, Kurume University, Fukuoka 830-0011, Japan
| | - Yoji Nishimura
- Divisions of Gastroenterological Surgery, Saitama Cancer Center, Saitama 362-0806, Japan
| | - Hirohiko Sakamoto
- Divisions of Gastroenterological Surgery, Saitama Cancer Center, Saitama 362-0806, Japan
| | - Kiwamu Akagi
- Division of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama 362-0806, Japan
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48
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Suzuki Y, Ng SB, Chua C, Leow WQ, Chng J, Liu SY, Ramnarayanan K, Gan A, Ho DL, Ten R, Su Y, Lezhava A, Lai JH, Koh D, Lim KH, Tan P, Rozen SG, Tan IB. Multiregion ultra-deep sequencing reveals early intermixing and variable levels of intratumoral heterogeneity in colorectal cancer. Mol Oncol 2016; 11:124-139. [PMID: 28145097 PMCID: PMC5527459 DOI: 10.1002/1878-0261.12012] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 09/07/2016] [Indexed: 12/11/2022] Open
Abstract
Intratumor heterogeneity (ITH) contributes to cancer progression and chemoresistance. We sought to comprehensively describe ITH of somatic mutations, copy number, and transcriptomic alterations involving clinically and biologically relevant gene pathways in colorectal cancer (CRC). We performed multiregion, high‐depth (384× on average) sequencing of 799 cancer‐associated genes in 24 spatially separated primary tumor and nonmalignant tissues from four treatment‐naïve CRC patients. We then used ultra‐deep sequencing (17 075× on average) to accurately verify the presence or absence of identified somatic mutations in each sector. We also digitally measured gene expression and copy number alterations using NanoString assays. We identified the subclonal point mutations and determined the mutational timing and phylogenetic relationships among spatially separated sectors of each tumor. Truncal mutations, those shared by all sectors in the tumor, affected the well‐described driver genes such as APC, TP53, and KRAS. With sequencing at 17 075×, we found that mutations first detected at a sequencing depth of 384× were in fact more widely shared among sectors than originally assessed. Interestingly, ultra‐deep sequencing also revealed some mutations that were present in all spatially dispersed sectors, but at subclonal levels. Ultra‐high‐depth validation sequencing, copy number analysis, and gene expression profiling provided a comprehensive and accurate genomic landscape of spatial heterogeneity in CRC. Ultra‐deep sequencing allowed more sensitive detection of somatic mutations and a more accurate assessment of ITH. By detecting the subclonal mutations with ultra‐deep sequencing, we traced the genomic histories of each tumor and the relative timing of mutational events. We found evidence of early mixing, in which the subclonal ancestral mutations intermixed across the sectors before the acquisition of subsequent nontruncal mutations. Our findings also indicate that different CRC patients display markedly variable ITH, suggesting that each patient's tumor possesses a unique genomic history and spatial organization.
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Affiliation(s)
- Yuka Suzuki
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Sarah Boonhsi Ng
- Institute of Cellular and Molecular Biology, Singapore, Singapore
| | - Clarinda Chua
- Department of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Wei Qiang Leow
- Department of Pathology, Singapore General Hospital, Singapore
| | - Jermain Chng
- Genome Institute of Singapore, A*STAR, Singapore
| | - Shi Yang Liu
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Kalpana Ramnarayanan
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Anna Gan
- Genome Institute of Singapore, A*STAR, Singapore
| | - Dan Liang Ho
- Department of Medical Oncology, National Cancer Centre Singapore, Singapore.,Genome Institute of Singapore, A*STAR, Singapore
| | - Rachel Ten
- Department of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Yan Su
- Genome Institute of Singapore, A*STAR, Singapore
| | | | - Jiunn Herng Lai
- Department of Colorectal Surgery, Singapore General Hospital, Singapore
| | - Dennis Koh
- Colorectal Practice, Mount Elizabeth Medical Centre, Singapore, Singapore
| | - Kiat Hon Lim
- Department of Pathology, Singapore General Hospital, Singapore
| | - Patrick Tan
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore.,Genome Institute of Singapore, A*STAR, Singapore.,Cancer Science Institute, National University of Singapore, Singapore
| | - Steven G Rozen
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Iain Beehuat Tan
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore.,Department of Medical Oncology, National Cancer Centre Singapore, Singapore.,Genome Institute of Singapore, A*STAR, Singapore
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49
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Gozzi G, Chelbi ST, Manni P, Alberti L, Fonda S, Saponaro S, Fabbiani L, Rivasi F, Benhattar J, Losi L. Promoter methylation and downregulated expression of the TBX15 gene in ovarian carcinoma. Oncol Lett 2016; 12:2811-2819. [PMID: 27698863 DOI: 10.3892/ol.2016.5019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 06/29/2016] [Indexed: 12/12/2022] Open
Abstract
TBX15 is a gene involved in the development of mesodermal derivatives. As the ovaries and the female reproductive system are of mesodermal origin, the aim of the present study was to determine the methylation status of the TBX15 gene promoter and the expression levels of TBX15 in ovarian carcinoma, which is the most lethal and aggressive type of gynecological tumor, in order to determine the role of TBX15 in the pathogenesis of ovarian carcinoma. This alteration could be used to predict tumor development, progression, recurrence and therapeutic effects. The study was conducted on 80 epithelial ovarian carcinoma and 17 control cases (normal ovarian and tubal tissues). TBX15 promoter methylation was first determined by pyrosequencing following bisulfite modification, then by cloning and sequencing, in order to obtain information about the epigenetic haplotype. Immunohistochemical analysis was performed to evaluate the correlation between the methylation and protein expression levels. Data revealed a statistically significant increase of the TBX15 promoter region methylation in 82% of the tumor samples and in various histological subtypes. Immunohistochemistry showed an inverse correlation between methylation levels and the expression of the TBX15 protein. Furthermore, numerous tumor samples displayed varying degrees of intratumor heterogeneity. Thus, the present study determined that ovarian carcinoma typically expresses low levels of TBX15 protein, predominantly due to an epigenetic mechanism. This may have a role in the pathogenesis of ovarian carcinoma independent of the histological subtype.
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Affiliation(s)
- Gaia Gozzi
- Pathological Anatomy Unit, Department of Life Sciences, University of Modena and Reggio Emilia, I-41124 Modena, Italy; University Institute of Pathology, Lausanne University Hospital, 1011 Lausanne, Switzerland
| | - Sonia T Chelbi
- University Institute of Pathology, Lausanne University Hospital, 1011 Lausanne, Switzerland; Department of Biochemistry, University of Lausanne, 1066 Epalinges, Switzerland
| | - Paola Manni
- Pathological Anatomy Unit, Department of Life Sciences, University of Modena and Reggio Emilia, I-41124 Modena, Italy
| | - Loredana Alberti
- University Institute of Pathology, Lausanne University Hospital, 1011 Lausanne, Switzerland
| | - Sergio Fonda
- Pathological Anatomy Unit, Department of Life Sciences, University of Modena and Reggio Emilia, I-41124 Modena, Italy
| | - Sara Saponaro
- Pathological Anatomy Unit, Department of Life Sciences, University of Modena and Reggio Emilia, I-41124 Modena, Italy; University Institute of Pathology, Lausanne University Hospital, 1011 Lausanne, Switzerland
| | - Luca Fabbiani
- Department of Diagnostic Medicine, Clinic and Public Health, University of Modena and Reggio Emilia, I-41124 Modena, Italy
| | - Francesco Rivasi
- Department of Diagnostic Medicine, Clinic and Public Health, University of Modena and Reggio Emilia, I-41124 Modena, Italy
| | - Jean Benhattar
- University Institute of Pathology, Lausanne University Hospital, 1011 Lausanne, Switzerland; Biopath Lab, Medical Biology and Pathology, 1006 Lausanne, Switzerland
| | - Lorena Losi
- Pathological Anatomy Unit, Department of Life Sciences, University of Modena and Reggio Emilia, I-41124 Modena, Italy
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50
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Abstract
Fighting Cancer with Immunotherapy. 21st Century Cancer Warfare: A Glimpse into the Operations of a Modern Radiotherapy Unit. Is Colorectal Carcinomas due to ‘Bad Luck’ or Is It Preventable? Asian Point of View on Cancer. Improving Overall Survival in Hepatocellular Carcinoma through a Multi-Disciplinary Approach: Intra-Tumoral Heterogeneity, Immunology and the Promise of Better Outcomes. Cancer of the Cervix – Can It be Prevented?
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