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Lakbir S, Buranelli C, Meijer GA, Heringa J, Fijneman RJA, Abeln S. CIBRA identifies genomic alterations with a system-wide impact on tumor biology. Bioinformatics 2024; 40:ii37-ii44. [PMID: 39230704 PMCID: PMC11373315 DOI: 10.1093/bioinformatics/btae384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2024] Open
Abstract
MOTIVATION Genomic instability is a hallmark of cancer, leading to many somatic alterations. Identifying which alterations have a system-wide impact is a challenging task. Nevertheless, this is an essential first step for prioritizing potential biomarkers. We developed CIBRA (Computational Identification of Biologically Relevant Alterations), a method that determines the system-wide impact of genomic alterations on tumor biology by integrating two distinct omics data types: one indicating genomic alterations (e.g. genomics), and another defining a system-wide expression response (e.g. transcriptomics). CIBRA was evaluated with genome-wide screens in 33 cancer types using primary and metastatic cancer data from the Cancer Genome Atlas and Hartwig Medical Foundation. RESULTS We demonstrate the capability of CIBRA by successfully confirming the impact of point mutations in experimentally validated oncogenes and tumor suppressor genes (0.79 AUC). Surprisingly, many genes affected by structural variants were identified to have a strong system-wide impact (30.3%), suggesting that their role in cancer development has thus far been largely under-reported. Additionally, CIBRA can identify impact with only 10 cases and controls, providing a novel way to prioritize genomic alterations with a prominent role in cancer biology. Our findings demonstrate that CIBRA can identify cancer drivers by combining genomics and transcriptomics data. Moreover, our work shows an unexpected substantial system-wide impact of structural variants in cancer. Hence, CIBRA has the potential to preselect and refine current definitions of genomic alterations to derive more nuanced biomarkers for diagnostics, disease progression, and treatment response. AVAILABILITY AND IMPLEMENTATION The R package CIBRA is available at https://github.com/AIT4LIFE-UU/CIBRA.
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Affiliation(s)
- Soufyan Lakbir
- Bioinformatics Section, Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Translational Gastrointestinal Oncology Group, Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- AI Technology for Life group, Department of Information and Computing Sciences and Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Caterina Buranelli
- Bioinformatics Section, Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Translational Gastrointestinal Oncology Group, Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Gerrit A Meijer
- Translational Gastrointestinal Oncology Group, Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jaap Heringa
- Bioinformatics Section, Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Remond J A Fijneman
- Translational Gastrointestinal Oncology Group, Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Sanne Abeln
- Bioinformatics Section, Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- AI Technology for Life group, Department of Information and Computing Sciences and Department of Biology, Utrecht University, Utrecht, The Netherlands
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Uil SH, Coupé VMH, Bril H, Meijer GA, Fijneman RJA, Stockmann HBAC. KCNQ1 and lymphovascular invasion are key features in a prognostic classifier for stage II and III colon cancer. BMC Cancer 2022; 22:372. [PMID: 35395779 PMCID: PMC8991490 DOI: 10.1186/s12885-022-09473-9] [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: 06/21/2021] [Accepted: 03/24/2022] [Indexed: 12/15/2022] Open
Abstract
Background The risk of recurrence after resection of a stage II or III colon cancer, and therefore qualification for adjuvant chemotherapy (ACT), is traditionally based on clinicopathological parameters. However, the parameters used in clinical practice are not able to accurately identify all patients with or without minimal residual disease. Some patients considered ‘low-risk’ do develop recurrence (undertreatment), whilst other patients receiving ACT might not have developed recurrence at all (overtreatment). We previously analysed tumour tissue expression of 28 protein biomarkers that might improve identification of patients at risk of recurrence. In the present study we aimed to build a prognostic classifier based on these 28 biomarkers and clinicopathological parameters. Methods Classification and regression tree (CART) analysis was used to build a prognostic classifier based on a well described cohort of 386 patients with stage II and III colon cancer. Separate classifiers were built for patients who were or were not treated with ACT. Routine clinicopathological parameters and tumour tissue immunohistochemistry data were included, available for 28 proteins previously published. Classification trees were pruned until lowest misclassification error was obtained. Survival of the identified subgroups was analysed, and robustness of the selected CART variables was assessed by random forest analysis (1000 trees). Results In patients not treated with ACT, prognosis was estimated best based on expression of KCNQ1. Poor disease-free survival (DFS) was observed in those with loss of expression of KCNQ1 (HR = 3.38 (95% CI 2.12 – 5.40); p < 0.001). In patients treated with ACT, key prognostic factors were lymphovascular invasion (LVI) and expression of KCNQ1. Patients with LVI showed poorest DFS, whilst patients without LVI and high expression of KCNQ1 showed most favourable survival (HR = 7.50 (95% CI 3.57—15.74); p < 0.001). Patients without LVI and loss of expression of KCNQ1 had intermediate survival (HR = 3.91 (95% CI 1.76 – 8.72); p = 0.001). Conclusion KCNQ1 and LVI were identified as key features in prognostic classifiers for disease-free survival in stage II and III colon cancer patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09473-9.
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Affiliation(s)
- Sjoerd H Uil
- Department of Surgery, Spaarne Gasthuis, Boerhaavelaan 22, 2035 RC, Haarlem, The Netherlands
| | - Veerle M H Coupé
- Department of Epidemiology and Data Science, Amsterdam University Medical Center, de Boelelaan 1089a, 1081 HV, Amsterdam, The Netherlands
| | - Herman Bril
- Department of Pathology, Spaarne Gasthuis, Boerhaavelaan 22, 2035 RC, Haarlem, The Netherlands
| | - Gerrit A Meijer
- Department of Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Remond J A Fijneman
- Department of Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
| | - Hein B A C Stockmann
- Department of Surgery, Spaarne Gasthuis, Boerhaavelaan 22, 2035 RC, Haarlem, The Netherlands
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He Y, Huang C, Cai K, Liu P, Chen X, Xu YI, Ming Z, Liu Q, Xie Q, Xia X, Sun Y, Luo J, Wei R. PRPF19 promotes tongue cancer growth and chemoradiotherapy resistance. Acta Biochim Biophys Sin (Shanghai) 2021; 53:893-902. [PMID: 33954334 DOI: 10.1093/abbs/gmab059] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Indexed: 12/19/2022] Open
Abstract
Pre-mRNA processing factor 19 (PRPF19) is a multifaceted protein and participates in DNA damage response and pre-mRNA processing. The role of PRPF19 in cancer is unclear. Here, we report that the expression of PRPF19 in human tongue cancer is associated with unfavorable prognosis. Overexpression of PRPF19 promotes while knockdown of PRPF19 inhibits tongue cancer cell migration, proliferation, and tumor growth. Overexpression of PRPF19 increases the resistance of tongue cancer cells to radiation and cisplatin treatment. Furthermore, PRPF19 regulates the expression of solute carrier family 40 member 1 (SLC40A1) and mono-ADP ribosylhydrolase 2 (MACROD2), knockdown of SLC40A1 or MACROD2 decreases the sensitivity of tongue cancer cells to radiation and cisplatin treatment. Thus, our results establish a key role of PRPF19 in tongue cancer growth and chemoradiotherapy resistance, targeting PRPF19 would be an effective therapeutic strategy for tongue cancer, especially for those resistant to chemoradiotherapy.
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Affiliation(s)
- Yihong He
- Department of General Surgery and the Hunan Provincial Key Lab of Precision Diagnosis and Treatment for Gastrointestinal Tumor, Xiangya Hospital, Central South University, Changsha 410008, China
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Changhao Huang
- Department of General Surgery and the Hunan Provincial Key Lab of Precision Diagnosis and Treatment for Gastrointestinal Tumor, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Kaimei Cai
- Department of General Surgery and the Hunan Provincial Key Lab of Precision Diagnosis and Treatment for Gastrointestinal Tumor, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Pei Liu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Xueyan Chen
- Department of General Surgery and the Hunan Provincial Key Lab of Precision Diagnosis and Treatment for Gastrointestinal Tumor, Xiangya Hospital, Central South University, Changsha 410008, China
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Y i Xu
- Department of General Surgery and the Hunan Provincial Key Lab of Precision Diagnosis and Treatment for Gastrointestinal Tumor, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Zhengnan Ming
- Department of General Surgery and the Hunan Provincial Key Lab of Precision Diagnosis and Treatment for Gastrointestinal Tumor, Xiangya Hospital, Central South University, Changsha 410008, China
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Central South University, Changsha 410008, China
| | - Qingqing Liu
- Department of General Surgery and the Hunan Provincial Key Lab of Precision Diagnosis and Treatment for Gastrointestinal Tumor, Xiangya Hospital, Central South University, Changsha 410008, China
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Qiongxuan Xie
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Xue Xia
- Department of General Surgery and the Hunan Provincial Key Lab of Precision Diagnosis and Treatment for Gastrointestinal Tumor, Xiangya Hospital, Central South University, Changsha 410008, China
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Central South University, Changsha 410008, China
| | - Yangqing Sun
- Department of General Surgery and the Hunan Provincial Key Lab of Precision Diagnosis and Treatment for Gastrointestinal Tumor, Xiangya Hospital, Central South University, Changsha 410008, China
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Junli Luo
- Department of General Surgery and the Hunan Provincial Key Lab of Precision Diagnosis and Treatment for Gastrointestinal Tumor, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Rui Wei
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
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Wang CL, Tang Y, Li M, Xiao M, Li QS, Yang L, Li X, Yin L, Wang YL. Analysis of Mono-ADP-Ribosylation Levels in Human Colorectal Cancer. Cancer Manag Res 2021; 13:2401-2409. [PMID: 33737837 PMCID: PMC7965690 DOI: 10.2147/cmar.s303064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 02/25/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Colorectal cancer remains a major public health problem with high morbidity and mortality rates. In the search for the mechanisms of colorectal cancer occurrence and development, increasing attention has been focused on epigenetics. The overall level of Mono-ADP-ribosylation, an epigenetic, has not been investigated now. The aim of our study was to analysis of the overall level of mono-ADP-ribosylation in colorectal cancer. METHODS Immunohistochemistry was used to investigate the level of mono-ADP-ribosylation in colorectal cancer and normal colorectal adjacent tissue from 64 CRC patients. The data of patient demographic, clinical and pathological characteristics were acquired and analyzed. RESULTS Mono-ADP-ribosylation was present in both colorectal adenocarcinoma and normal colorectal tissue. The overall level of mono-ADP-ribosylation in colorectal cancer was significantly higher than that in normal colorectal adjacent tissue. In the nucleus, the majority of samples in the high-level group were colorectal adenocarcinoma (55/64), but the opposite was true for normal colorectal tissues (7/32). In particular, increases in the level of mono-ADP-ribosylation in the cytoplasm of colorectal cancer cells was associated with a greater invasion depth of the tumor. CONCLUSION The increased level of mono-ADP-ribosylation in colorectal cancer enhances tumor invasion, which suggests that mono-ADP-ribosylation is involved in the development of colorectal cancer and may become a new direction to solve the problem of colorectal cancer.
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Affiliation(s)
- Chuan-Ling Wang
- Department of Pathology, Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, 400016, People’s Republic of China
| | - Yi Tang
- Department of Pathology, Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, 400016, People’s Republic of China
| | - Ming Li
- Department of Pathology, Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, 400016, People’s Republic of China
| | - Ming Xiao
- Department of Pathology, Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, 400016, People’s Republic of China
| | - Qing-Shu Li
- Department of Pathology, Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, 400016, People’s Republic of China
| | - Lian Yang
- Department of Pathology, Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, 400016, People’s Republic of China
| | - Xian Li
- Department of Pathology, Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, 400016, People’s Republic of China
| | - Ling Yin
- Department of Pathology, Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, 400016, People’s Republic of China
| | - Ya-Lan Wang
- Department of Pathology, Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, 400016, People’s Republic of China
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Žaja R, Aydin G, Lippok BE, Feederle R, Lüscher B, Feijs KLH. Comparative analysis of MACROD1, MACROD2 and TARG1 expression, localisation and interactome. Sci Rep 2020; 10:8286. [PMID: 32427867 PMCID: PMC7237415 DOI: 10.1038/s41598-020-64623-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 04/20/2020] [Indexed: 02/06/2023] Open
Abstract
The posttranslational modification ADP-ribosylation is involved in many cellular processes, with distinct roles for poly- and mono(ADP-ribosyl)ation (PAR- and MARylation, respectively). Reversibility of intracellular MARylation was demonstrated with the discovery of MACROD1, MACROD2 and TARG1, three macrodomain-containing enzymes capable of reversing MARylation of proteins and RNA. While the three enzymes have identical activities in vitro, their roles in cells are unclear and published data are partially contradictory, possibly due to a lack of validated reagents. We developed monoclonal antibodies to study these proteins and analysed their tissue distribution and intracellular localisation. MACROD1 is most prevalent in mitochondria of skeletal muscle, MACROD2 localises to nucleo- and cytoplasm and is found so far only in neuroblastoma cells, whereas the more ubiquitously expressed TARG1 is present in nucleoplasm, nucleolus and stress granules. Loss of MACROD1 or loss of TARG1 leads to disruption of mitochondrial or nucleolar morphology, respectively, hinting at their importance for these organelles. To start elucidating the underlying mechanisms, we have mapped their interactomes using BioID. The cellular localisation of interactors supports the mitochondrial, nucleolar and stress granule localisation of MACROD1 and TARG1, respectively. Gene ontology analysis suggests an involvement of MACROD1 and TARG1 in RNA metabolism in their respective compartments. The detailed description of the hydrolases’ expression, localisation and interactome presented here provides a solid basis for future work addressing their physiological function in more detail.
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Affiliation(s)
- R Žaja
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Pauwelsstrasse 30, 52074, Aachen, Germany.
| | - G Aydin
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Pauwelsstrasse 30, 52074, Aachen, Germany
| | - B E Lippok
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Pauwelsstrasse 30, 52074, Aachen, Germany
| | - R Feederle
- Monoclonal Antibody Core Facility, Institute for Diabetes and Obesity, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - B Lüscher
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Pauwelsstrasse 30, 52074, Aachen, Germany
| | - K L H Feijs
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Pauwelsstrasse 30, 52074, Aachen, Germany.
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Feijs KL, Cooper CD, Žaja R. The Controversial Roles of ADP-Ribosyl Hydrolases MACROD1, MACROD2 and TARG1 in Carcinogenesis. Cancers (Basel) 2020; 12:E604. [PMID: 32151005 PMCID: PMC7139919 DOI: 10.3390/cancers12030604] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/20/2020] [Accepted: 02/27/2020] [Indexed: 01/12/2023] Open
Abstract
Post-translational modifications (PTM) of proteins are crucial for fine-tuning a cell's response to both intracellular and extracellular cues. ADP-ribosylation is a PTM, which occurs in two flavours: modification of a target with multiple ADP-ribose moieties (poly(ADP-ribosyl)ation or PARylation) or with only one unit (MARylation), which are added by the different enzymes of the PARP family (also known as the ARTD family). PARylation has been relatively well-studied, particularly in the DNA damage response. This has resulted in the development of PARP inhibitors such as olaparib, which are increasingly employed in cancer chemotherapeutic approaches. Despite the fact that the majority of PARP enzymes catalyse MARylation, MARylation is not as well understood as PARylation. MARylation is a dynamic process: the enzymes reversing intracellular MARylation of acidic amino acids (MACROD1, MACROD2, and TARG1) were discovered in 2013. Since then, however, little information has been published about their physiological function. MACROD1, MACROD2, and TARG1 have a 'macrodomain' harbouring the catalytic site, but no other domains have been identified. Despite the lack of information regarding their cellular roles, there are a number of studies linking them to cancer. However, some of these publications oppose each other, some rely on poorly-characterised antibodies, or on aberrant localisation of overexpressed rather than native protein. In this review, we critically assess the available literature on a role for the hydrolases in cancer and find that, currently, there is limited evidence for a role for MACROD1, MACROD2, or TARG1 in tumorigenesis.
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Affiliation(s)
- Karla L.H. Feijs
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Pauwelsstrasse 30, 52074 Aachen, Germany;
| | - Christopher D.O. Cooper
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield West Yorkshire HD3 4AP, UK;
| | - Roko Žaja
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Pauwelsstrasse 30, 52074 Aachen, Germany;
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Ried T, Meijer GA, Harrison DJ, Grech G, Franch-Expósito S, Briffa R, Carvalho B, Camps J. The landscape of genomic copy number alterations in colorectal cancer and their consequences on gene expression levels and disease outcome. Mol Aspects Med 2019; 69:48-61. [PMID: 31365882 DOI: 10.1016/j.mam.2019.07.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 07/23/2019] [Accepted: 07/26/2019] [Indexed: 12/18/2022]
Abstract
Aneuploidy, the unbalanced state of the chromosome content, represents a hallmark of most solid tumors, including colorectal cancer. Such aneuploidies result in tumor specific genomic imbalances, which emerge in premalignant precursor lesions. Moreover, increasing levels of chromosomal instability have been observed in adenocarcinomas and are maintained in distant metastases. A number of studies have systematically integrated copy number alterations with gene expression changes in primary carcinomas, cell lines, and experimental models of aneuploidy. In fact, chromosomal aneuploidies target a number of genes conferring a selective advantage for the metabolism of the cancer cell. Copy number alterations not only have a positive correlation with expression changes of the majority of genes on the altered genomic segment, but also have effects on the transcriptional levels of genes genome-wide. Finally, copy number alterations have been associated with disease outcome; nevertheless, the translational applicability in clinical practice requires further studies. Here, we (i) review the spectrum of genetic alterations that lead to colorectal cancer, (ii) describe the most frequent copy number alterations at different stages of colorectal carcinogenesis, (iii) exemplify their positive correlation with gene expression levels, and (iv) discuss copy number alterations that are potentially involved in disease outcome of individual patients.
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Affiliation(s)
- Thomas Ried
- Genetics Branch, Center for Cancer Research, National Cancer Institute/National Institutes of Health, Bethesda, MD, USA.
| | - Gerrit A Meijer
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - David J Harrison
- School of Medicine, University of St Andrews, St Andrews, Scotland, UK
| | - Godfrey Grech
- Laboratory of Molecular Pathology, Department of Pathology, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
| | - Sebastià Franch-Expósito
- Gastrointestinal and Pancreatic Oncology Group, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), CIBEREHD, Barcelona, Spain
| | - Romina Briffa
- School of Medicine, University of St Andrews, St Andrews, Scotland, UK; Laboratory of Molecular Pathology, Department of Pathology, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
| | - Beatriz Carvalho
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Jordi Camps
- Gastrointestinal and Pancreatic Oncology Group, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), CIBEREHD, Barcelona, Spain; Unitat de Biologia Cel·lular i Genètica Mèdica, Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain.
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Sexton T, Kucera GL, Levine EA, Watabe K, O'Neill SS. Optimization of Tissue Microarrays from Banked Human Formalin-Fixed Paraffin Embedded Tissues in the Cancer Research Setting. Biopreserv Biobank 2019; 17:452-457. [PMID: 31194582 DOI: 10.1089/bio.2019.0011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The tissue microarray (TMA) is a powerful tool for cancer biomarker discovery and validation. Tens to hundreds of samples can be evaluated simultaneously for molecular marker status at the protein or nucleic acid level. Although fully automated or semiautomated technologies for TMA creation provide excellent precision with respect to core transfer, they do not obviate the need for technical expertise to successfully generate high-quality TMA blocks and derivative sections. We have leveraged our expanding bank of formalin-fixed paraffin embedded paired tumor and normal tissues in our academic cancer center to provide a rich source of input material for cancer research TMAs. In this study, we report a stepwise optimization of TMA generation parameters, including paraffin wax selection, tempering protocol, and sectioning conditions, to achieve the best ribbon sectioning.
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Affiliation(s)
- Tammy Sexton
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Gregory L Kucera
- Department of Internal Medicine, Section on Hematology and Oncology, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Edward A Levine
- Surgical Oncology Service, Department of General Surgery, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Kounosuke Watabe
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Stacey S O'Neill
- Department of Pathology, Wake Forest School of Medicine, Winston-Salem, North Carolina
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Lehrer S, Rheinstein PH. Three Poliovirus Sequences in the Human Genome Associated With Colorectal Cancer. Cancer Genomics Proteomics 2018; 16:65-70. [PMID: 30587500 DOI: 10.21873/cgp.20112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 11/19/2018] [Accepted: 11/21/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND/AIM In a previous study we analyzed poliomyelitis incidence in US states, before the introduction of the polio vaccine. We noted an inverse correlation between polio incidence in US states, between 1937 and 1951, and colorectal cancer incidence (2005-2009). To further elucidate the role that poliovirus could play in colorectal cancer, the full human genome for poliovirus sequences was analyzed using the UCSC Genome Browser. MATERIALS AND METHODS BLAT, the Blast-Like Alignment Tool of the UCSC Genome Browser, was used to compare the poliovirus genome to the human genome. RESULTS BLAT revealed three poliovirus sequences in three chromosomes: Chromosome 20p12.1 (MACROD2 gene), chromosome 1p13.3 (SLC25A24 gene), and chromosome 2p25.1. CONCLUSION Poliovirus sequences in the human genome may contribute to programmed cell death and lysis of colorectal cancer cells. A recombinant poliovirus, incapable of reverting to neurovirulence, might be given orally at intervals as a colorectal cancer vaccine to prevent colorectal cancer.
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Affiliation(s)
- Steven Lehrer
- Radiation Oncology, Mount Sinai Medical Center, New York, NY, U.S.A.
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Lo Re O, Mazza T, Vinciguerra M. Mono-ADP-Ribosylhydrolase MACROD2 Is Dispensable for Murine Responses to Metabolic and Genotoxic Insults. Front Genet 2018; 9:654. [PMID: 30619475 PMCID: PMC6305994 DOI: 10.3389/fgene.2018.00654] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 12/03/2018] [Indexed: 11/13/2022] Open
Abstract
ADP-ribosylation is an important post-translational protein modification that regulates diverse biological processes, controlled by dedicated transferases, and hydrolases. Disruption in the gene encoding for MACROD2, a mono-ADP-ribosylhydrolase, has been associated to the Kabuki syndrome, a pediatric congenital disorder characterized by facial anomalies, and mental retardation. Non-coding and structural mutations/variations in MACROD2 have been associated to psychiatric disorders, to obesity, and to cancer. Mechanistically, it has been recently shown that frequent deletions of the MACROD2 alter DNA repair and sensitivity to DNA damage, resulting in chromosome instability, and colorectal tumorigenesis. Whether MACROD2 deletion sensitizes the organism to metabolic and tumorigenic stressors, in absence of other genetic drivers, is unclear. As MACROD2 is ubiquitously expressed in mice, here we generated constitutively whole-body knock-out mice for MACROD2, starting from mouse embryonic stem (ES) cells deleted for the gene using the VelociGene® technology, belonging to the Knockout Mouse Project (KOMP) repository, a NIH initiative. MACROD2 knock-out mice were viable and healthy, indistinguishable from wild type littermates. High-fat diet administration induced obesity, and glucose/insulin intolerance in mice independent of MACROD2 gene deletion. Moreover, sub-lethal irradiation did not indicate a survival or lethality bias in MACROD2 knock-out mice compared to wild type littermates. Altogether, our data point against a sufficient role of MACROD2 deletion in aggravating high-fat induced obesity and DNA damage-associated lethality, in absence of other genetic drivers.
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Affiliation(s)
- Oriana Lo Re
- International Clinical Research Center, St Anne's University Hospital, Brno, Czechia.,Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czechia
| | - Tommaso Mazza
- Bioinformatics Unit, Casa Sollievo della Sofferenza (IRCCS), San Giovanni Rotondo, Italy
| | - Manlio Vinciguerra
- International Clinical Research Center, St Anne's University Hospital, Brno, Czechia.,Institute for Liver and Digestive Health, Division of Medicine, University College London, London, United Kingdom
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